diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 000000000..c2f9bb75b --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,11 @@ +version: 2 +updates: + - package-ecosystem: maven + directory: "/" + schedule: + interval: weekly + open-pull-requests-limit: 5 + - package-ecosystem: github-actions + directory: "/" + schedule: + interval: weekly diff --git a/.github/workflows/github-actions-test.yml b/.github/workflows/github-actions-test.yml index 2d656e7b0..c7df9b58e 100644 --- a/.github/workflows/github-actions-test.yml +++ b/.github/workflows/github-actions-test.yml @@ -13,7 +13,8 @@ jobs: with: java-version: '25' distribution: 'temurin' + cache: maven - name: Test with Maven - run: mvn --update-snapshots test + run: ./mvnw --update-snapshots test env: GITHUB_TOKEN: ${{ github.token }} diff --git a/.github/workflows/pic-sure-auth-microapp-test.yml b/.github/workflows/pic-sure-auth-microapp-test.yml new file mode 100644 index 000000000..4a949002f --- /dev/null +++ b/.github/workflows/pic-sure-auth-microapp-test.yml @@ -0,0 +1,22 @@ +name: pic-sure-auth-microapp tests +on: + pull_request: + paths: ['services/pic-sure-auth-microapp/**'] + push: + branches: [main] + paths: ['services/pic-sure-auth-microapp/**'] +jobs: + test: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd #v6.0.2 + - name: Set up JDK 25 + uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 #v5.2.0 + with: + java-version: '25' + distribution: 'temurin' + cache: maven + - name: Test with Maven + run: ./mvnw -B -pl services/pic-sure-auth-microapp/pic-sure-auth-services -am verify + env: + GITHUB_TOKEN: ${{ github.token }} diff --git a/.github/workflows/pic-sure-hpds-test.yml b/.github/workflows/pic-sure-hpds-test.yml new file mode 100644 index 000000000..6380b72c2 --- /dev/null +++ b/.github/workflows/pic-sure-hpds-test.yml @@ -0,0 +1,22 @@ +name: pic-sure-hpds tests +on: + pull_request: + paths: ['services/pic-sure-hpds/**'] + push: + branches: [main] + paths: ['services/pic-sure-hpds/**'] +jobs: + test: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd #v6.0.2 + - name: Set up JDK 25 + uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 #v5.2.0 + with: + java-version: '25' + distribution: 'temurin' + cache: maven + - name: Test with Maven + run: ./mvnw -B -pl services/pic-sure-hpds/common,services/pic-sure-hpds/data,services/pic-sure-hpds/etl,services/pic-sure-hpds/processing,services/pic-sure-hpds/service,services/pic-sure-hpds/genomic-processor,services/pic-sure-hpds/war,services/pic-sure-hpds/docker -am verify + env: + GITHUB_TOKEN: ${{ github.token }} diff --git a/.github/workflows/pic-sure-logging-test.yml b/.github/workflows/pic-sure-logging-test.yml new file mode 100644 index 000000000..9b79a39bf --- /dev/null +++ b/.github/workflows/pic-sure-logging-test.yml @@ -0,0 +1,22 @@ +name: pic-sure-logging tests +on: + pull_request: + paths: ['services/pic-sure-logging/**'] + push: + branches: [main] + paths: ['services/pic-sure-logging/**'] +jobs: + test: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd #v6.0.2 + - name: Set up JDK 25 + uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 #v5.2.0 + with: + java-version: '25' + distribution: 'temurin' + cache: maven + - name: Test with Maven + run: ./mvnw -B -pl services/pic-sure-logging -am verify + env: + GITHUB_TOKEN: ${{ github.token }} diff --git a/.github/workflows/pic-sure-services-test.yml b/.github/workflows/pic-sure-services-test.yml new file mode 100644 index 000000000..e2cb2652a --- /dev/null +++ b/.github/workflows/pic-sure-services-test.yml @@ -0,0 +1,22 @@ +name: pic-sure-services tests +on: + pull_request: + paths: ['services/pic-sure-services/**'] + push: + branches: [main] + paths: ['services/pic-sure-services/**'] +jobs: + test: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd #v6.0.2 + - name: Set up JDK 25 + uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 #v5.2.0 + with: + java-version: '25' + distribution: 'temurin' + cache: maven + - name: Test with Maven + run: ./mvnw -B -pl services/pic-sure-services/info-service,services/pic-sure-services/uploader -am verify + env: + GITHUB_TOKEN: ${{ github.token }} diff --git a/.github/workflows/picsure-dictionary-test.yml b/.github/workflows/picsure-dictionary-test.yml new file mode 100644 index 000000000..af822d448 --- /dev/null +++ b/.github/workflows/picsure-dictionary-test.yml @@ -0,0 +1,22 @@ +name: picsure-dictionary tests +on: + pull_request: + paths: ['services/picsure-dictionary/**'] + push: + branches: [main] + paths: ['services/picsure-dictionary/**'] +jobs: + test: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd #v6.0.2 + - name: Set up JDK 25 + uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 #v5.2.0 + with: + java-version: '25' + distribution: 'temurin' + cache: maven + - name: Test with Maven + run: ./mvnw -B -pl services/picsure-dictionary,services/picsure-dictionary/aggregate,services/picsure-dictionary/dictionaryweights -am verify + env: + GITHUB_TOKEN: ${{ github.token }} diff --git a/.github/workflows/secrets-scan.yml b/.github/workflows/secrets-scan.yml new file mode 100644 index 000000000..08e369f47 --- /dev/null +++ b/.github/workflows/secrets-scan.yml @@ -0,0 +1,19 @@ +name: secrets scan +on: + pull_request: +jobs: + gitleaks: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd #v6.0.2 + with: + fetch-depth: 0 + - name: Install gitleaks 8.30.1 (checksum-verified) + run: | + curl -sSfL -o /tmp/gitleaks.tar.gz https://github.com/gitleaks/gitleaks/releases/download/v8.30.1/gitleaks_8.30.1_linux_x64.tar.gz + echo "551f6fc83ea457d62a0d98237cbad105af8d557003051f41f3e7ca7b3f2470eb /tmp/gitleaks.tar.gz" | sha256sum -c - + tar -xzf /tmp/gitleaks.tar.gz -C /tmp gitleaks + - name: Scan PR commits + run: > + /tmp/gitleaks git --redact --no-banner + --log-opts="${{ github.event.pull_request.base.sha }}..${{ github.event.pull_request.head.sha }}" . diff --git a/.github/workflows/visualization-service-test.yml b/.github/workflows/visualization-service-test.yml new file mode 100644 index 000000000..4ed68f568 --- /dev/null +++ b/.github/workflows/visualization-service-test.yml @@ -0,0 +1,22 @@ +name: visualization-service tests +on: + pull_request: + paths: ['services/pic-sure-visualization-service/**'] + push: + branches: [main] + paths: ['services/pic-sure-visualization-service/**'] +jobs: + test: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd #v6.0.2 + - name: Set up JDK 25 + uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 #v5.2.0 + with: + java-version: '25' + distribution: 'temurin' + cache: maven + - name: Test with Maven + run: ./mvnw -B -pl services/pic-sure-visualization-service -am verify + env: + GITHUB_TOKEN: ${{ github.token }} diff --git a/.gitignore b/.gitignore index 6d02fe6ae..153242893 100644 --- a/.gitignore +++ b/.gitignore @@ -5,6 +5,7 @@ pom.xml.versionsBackup pom.xml.next release.properties dependency-reduced-pom.xml +.flattened-pom.xml buildNumber.properties .mvn/timing.properties log/ @@ -32,3 +33,6 @@ log/ docs/superpowers/ *.http +# TODO: Remove once development is complete +george_development_notes.md +fable-master-handoff.md diff --git a/.gitleaksignore b/.gitleaksignore new file mode 100644 index 000000000..0c42eae91 --- /dev/null +++ b/.gitleaksignore @@ -0,0 +1,4 @@ +# gitleaks false-positive fingerprints — one per line: +# ::: +# Put a comment above each entry explaining why the finding is safe. +# Honored by the pre-commit hook, the pre-push hook, and the secrets-scan workflow. diff --git a/.mvn/wrapper/maven-wrapper.properties b/.mvn/wrapper/maven-wrapper.properties new file mode 100644 index 000000000..ffcab66aa --- /dev/null +++ b/.mvn/wrapper/maven-wrapper.properties @@ -0,0 +1,3 @@ +wrapperVersion=3.3.4 +distributionType=only-script +distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.9.9/apache-maven-3.9.9-bin.zip diff --git a/.sdkmanrc b/.sdkmanrc index aee00bc87..d2344323e 100644 --- a/.sdkmanrc +++ b/.sdkmanrc @@ -1 +1 @@ -java=11.0.30-tem +java=25.0.3-tem diff --git a/README.md b/README.md index 99068a94f..816e6d289 100644 --- a/README.md +++ b/README.md @@ -1,55 +1,73 @@ -[![Swagger Validator](https://img.shields.io/swagger/valid/3.0?specUrl=https://nhanes-dev.hms.harvard.edu/picsure/openapi.json)](https://app.gitbook.com/o/HwwUMljKAspjFDq5CK7G/s/meNaViOuPB9U832fUSEa/pic-sure-api) -[![GitBook](https://img.shields.io/badge/GitBook-PIC‑SURE-brightgreen)](https://pic-sure.gitbook.io/pic-sure/) -[![GitHub Wiki](https://img.shields.io/badge/GitHub%20Wiki-PIC‑SURE%20Home-blueviolet)](https://github.com/hms-dbmi/pic-sure/wiki) +# pic-sure (monorepo) -# PIC-SURE API +Maven monorepo for the PIC-SURE API platform — the gateway rewrite lands here as modules, replacing the WildFly-deployed `pic-sure-api-war` incrementally (strangler-fig). The legacy WAR remains in-repo but quarantined until decommission. -This is the git repository for version 2+ of the PIC-SURE API. +## Layout -## Pre-requisites +``` +pic-sure/ root pom — PARENT + aggregator +│ edu.harvard.hms.dbmi.avillach:pic-sure-api:${revision} +├── platform/ pic-sure-bom — the single version catalog (STANDALONE; no parent) +├── libs/ +│ ├── pic-sure-commons/ pic-sure-common aggregator (subtree of hms-dbmi/pic-sure-common) +│ │ ├── pic-sure-api-model/ domain DTOs (pkg edu.harvard.dbmi.avillach.{domain,util}) +│ │ └── pic-sure-hpds-model/ HPDS query model (groupId …avillach.hpds — frozen) +│ └── pic-sure-logging-client/ audit/logging client (groupId edu.harvard.dbmi.avillach — frozen) +├── services/ +│ └── pic-sure-gateway/ Spring Cloud Gateway MVC front door (Phase 1: transparent) +└── pic-sure-legacy/ QUARANTINED — WildFly WAR, Java 11/javax, own parent pom, + NOT aggregated; builds independently +``` -* Java 11 -* Before contributing code, please set up our git hook: - `cp code-formatting/pre-commit.sh .git/hooks/pre-commit` - * To skip formatting on a block of code, wrap in `spotless:off`, `spotless:on` comments +## Version strategy -## Build -The build consists of the following top level maven modules: -* pic-sure-api-data - for anything database related -* pic-sure-api-war - the actual packaged web application -* pic-sure-api-wildfly - a fully configured wildfly environment which serves as an example configuration as well as an integration testing environment. -* pic-sure-resources - the API that resources must implement to become PIC-SURE compatible as well as any resources we choose to develop(HAIL, i2b2, gNOME, etc) +| Line | Meaning | +|---|---| +| `3.0.0` (`${revision}`) | The monorepo line — Java 25, everything in the new reactor. Never publish it from the sibling repos. | +| `2.x` | The legacy WAR family (`pic-sure-legacy` parent is `pic-sure-api:2.2.0-SNAPSHOT`). | +| `1.x` | Frozen Java 11 releases the legacy WAR pins (e.g. `pic-sure-api-model:1.0.0`, `pic-sure-logging-client:1.0.0`). Immutable — the frozen and `3.0.0` lines must never share a coordinate+version. | -To build the entire project, change directory to the projects top level, and execute: +Versions are CI-friendly (`${revision}` + `flatten-maven-plugin`). Dependency versions come from the `platform` BOM (`pic-sure-bom`), which imports the Spring Boot 3.5.x and Spring Cloud 2025.0.x BOMs. Internal modules inherit everything through the root parent; **external consumers import the published `pic-sure-bom` directly** instead of inheriting the parent (see `platform/README.md`). -```shell - mvn clean install -``` +> The BOM is standalone (no ``) by design — the root parent imports it, so a back-reference would create a model-resolution cycle. Its `spring-boot.version` / `spring-cloud.version` properties are duplicated from the root pom; bump both files in lockstep. -This command will run all tests, with the included WildFly server. +## Toolchain -## Deployment +**Java 25 is the standard and is enforced** (maven-enforcer requires JDK 25 at build time, compiler `--release 25`). `.sdkmanrc` pins `25.0.3-tem` (`sdk env` to activate). The quarantined legacy tree pins its own `pic-sure-legacy/.sdkmanrc` (`11.0.30-tem`). -In order to run the app for development you need to set the following environment variables: +## Build -PIC_SURE_CLIENT_SECRET - This can be anything you want for testing, foo, bar, just set it to something. -PIC_SURE_USER_ID_CLAIM - This should be "email" +```bash +# whole new reactor (platform + libs + services); legacy is NOT included +mvn verify -To run the app for development, go into the pic-sure-api-wildfly folder and use this: +# just the gateway (and what it needs) +mvn -pl services/pic-sure-gateway -am verify -```shell - mvn wildfly:run && mvn wildfly:shutdown +# legacy WAR (independent build, JDK 11) +cd pic-sure-legacy && mvn package ``` -This will start the app with the console output in your terminal session and CTRL-C will kill it correctly. +Formatting: Spotless (Eclipse formatter, config inherited from the root) — `mvn spotless:apply`. + +## Gateway migration + +Design docs live in `docs/superpowers/` (local-only, gitignored). The migration is tracked under Jira epic ALS-10463; work happens on the long-lived `pic_sure_api_rewrite` branch, merged when complete. + +## Git hooks + +Two optional-but-recommended local hooks live in `code-formatting/`: -If you wish to debug your tests from Eclipse, use `mvnDebug clean install` and connect your debugger. +- `pre-commit.sh` — formats staged Java files with Spotless and blocks commits containing secrets (gitleaks). +- `pre-push.sh` — blocks pushes whose outgoing commits contain secrets (gitleaks). -If you wish to debug your services while the tests run, set the `suspend=n` to `suspend=y` in -the wildfly-maven-plugin configuration in the pom file for pic-sure-api-wildfly on the line that looks like: +Install both: -```pom --agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=5005 +```sh +cp code-formatting/pre-commit.sh .git/hooks/pre-commit && chmod +x .git/hooks/pre-commit +cp code-formatting/pre-push.sh .git/hooks/pre-push && chmod +x .git/hooks/pre-push ``` -Both of these will pause the build allowing you to connect your debuggers. +Secret-scan false positives: add a `gitleaks:allow` trailing comment on the flagged line, or record +the finding's fingerprint in `.gitleaksignore` with a comment explaining why it is safe. CI runs the +same scan on every pull request (`.github/workflows/secrets-scan.yml`). diff --git a/code-formatting/pre-commit.sh b/code-formatting/pre-commit.sh index ed051d182..a17c18d52 100755 --- a/code-formatting/pre-commit.sh +++ b/code-formatting/pre-commit.sh @@ -5,10 +5,72 @@ format_cmd="" # skip if NO_VERIFY env var set if [ "$NO_VERIFY" ]; then - echo 'code formatting skipped' 1>&2 + echo 'pre-commit checks skipped' 1>&2 exit 0 fi +# --- Secret scanning (gitleaks) ------------------------------------------- +# Abort the commit if a secret is detected in the staged changes. +if command -v gitleaks >/dev/null 2>&1; then + if ! gitleaks git --staged --redact --no-banner; then + echo '✖ gitleaks detected a secret in staged changes. Commit aborted.' 1>&2 + echo ' Remove the secret, or if it is a false positive add a "gitleaks:allow" trailing comment' 1>&2 + echo ' on the line, or record its fingerprint in .gitleaksignore.' 1>&2 + cd "$CWD" + exit 1 + fi +else + echo '⚠ gitleaks not installed — skipping secret scan. Install: brew install gitleaks' 1>&2 +fi + +# --- Block binary blobs and oversized files ------------------------------- +STAGED=$(git diff --staged --name-only --diff-filter=ACMR) +JAVABIN=$(printf '%s\n' "$STAGED" | grep -i '\.javabin$' || true) +if [ -n "$JAVABIN" ]; then + echo '✖ Refusing to commit .javabin data file(s):' 1>&2 + printf ' %s\n' $JAVABIN 1>&2 + echo ' HPDS .javabin blobs are build/data artifacts and must not be committed.' 1>&2 + echo ' Unstage them: git reset HEAD ' 1>&2 + cd "$CWD"; exit 1 +fi + +MAX_BYTES=$((5 * 1024 * 1024)) # 5 MB +LARGE="" +for f in $STAGED; do + sz=$(git cat-file -s ":$f" 2>/dev/null || echo 0) + if [ "$sz" -gt "$MAX_BYTES" ]; then + LARGE="$LARGE $f ($sz bytes)\n" + fi +done +if [ -n "$LARGE" ]; then + echo '✖ Refusing to commit file(s) larger than 5 MB:' 1>&2 + printf '%b' "$LARGE" 1>&2 + echo ' Use Git LFS, or bypass intentionally with: NO_VERIFY=1 git commit ...' 1>&2 + cd "$CWD"; exit 1 +fi + +# --- Flyway migration immutability ---------------------------------------- +# Applied migrations are immutable; changing one breaks Flyway checksum validation. +CHANGED_MIGRATIONS=$(git diff --staged --name-only --diff-filter=MRD | grep -E '(^|/)V[0-9][^/]*__[^/]*\.sql$' || true) +if [ -n "$CHANGED_MIGRATIONS" ]; then + echo '✖ Refusing to modify/delete existing Flyway migration(s):' 1>&2 + printf ' %s\n' $CHANGED_MIGRATIONS 1>&2 + echo ' Create a NEW V__.sql migration instead of editing an applied one.' 1>&2 + cd "$CWD"; exit 1 +fi + +# --- Focused tests / debug leftovers -------------------------------------- +# Only inspects lines ADDED in this commit, so pre-existing code is unaffected. +ADDED=$(git diff --staged --diff-filter=ACMR -U0 | grep -E '^\+[^+]' || true) +DEBUG_HITS=$(printf '%s\n' "$ADDED" | grep -E 'System\.(out|err)\.println|\.printStackTrace\(|(describe|context|it|test)\.only\(|fdescribe\(|fit\(' || true) +if [ -n "$DEBUG_HITS" ]; then + echo '✖ Debug / focused-test markers introduced in staged changes:' 1>&2 + printf '%s\n' "$DEBUG_HITS" | sed 's/^/ /' 1>&2 + echo ' Remove stray println/printStackTrace or .only-focused tests,' 1>&2 + echo ' or bypass intentionally with: NO_VERIFY=1 git commit ...' 1>&2 + cd "$CWD"; exit 1 +fi + # I'm not great at bash, so this is a bit ugly, but I'll explain each pipe # 1. Get all staged files # 2. Reduce to just .java files @@ -21,8 +83,22 @@ STAGED_JAVA_FILES_AS_REGEX=$(git diff --staged --name-only --diff-filter=ACMR | FILES_TO_RESTAGE=$(git diff --staged --name-only --diff-filter=ACMR) if [ -n "$STAGED_JAVA_FILES_AS_REGEX" ]; then echo "Found the following staged java files to format: $STAGED_JAVA_FILES_AS_REGEX" - mvn spotless:apply -DspotlessFiles=^.*$STAGED_JAVA_FILES_AS_REGEX - git add $FILES_TO_RESTAGE + # Spotless must run in the Maven modules that own the staged files. Running `spotless:apply` at + # the aggregator root fails ("No plugin found for prefix 'spotless'" — the root only manages the + # plugin), and the fully-qualified goal errors on modules that don't configure Spotless (e.g. the + # BOM). So derive each staged file's owning module (nearest ancestor with a pom.xml) and pass them + # via -pl. -DspotlessFiles still restricts formatting to exactly the staged files within them. + SPOTLESS_MODULES=$(git diff --staged --name-only --diff-filter=ACMR | grep '.java$' | while read -r f; do + d=$(dirname "$f") + while [ "$d" != "." ] && [ ! -f "$d/pom.xml" ]; do d=$(dirname "$d"); done + [ -f "$d/pom.xml" ] && printf '%s\n' "$d" + done | sort -u | paste -sd',' -) + if [ -n "$SPOTLESS_MODULES" ]; then + mvn -pl "$SPOTLESS_MODULES" spotless:apply -DspotlessFiles=^.*$STAGED_JAVA_FILES_AS_REGEX + git add $FILES_TO_RESTAGE + else + echo '⚠ could not determine owning Maven module(s) for staged Java files — skipping Spotless.' 1>&2 + fi fi cd $CWD \ No newline at end of file diff --git a/code-formatting/pre-push.sh b/code-formatting/pre-push.sh new file mode 100755 index 000000000..af3101cec --- /dev/null +++ b/code-formatting/pre-push.sh @@ -0,0 +1,32 @@ +#!/bin/sh -e +# Git pre-push hook: block pushing commits that contain secrets. +# Install: cp code-formatting/pre-push.sh .git/hooks/pre-push && chmod +x .git/hooks/pre-push +# Skip once: NO_VERIFY=1 git push ... (or git push --no-verify) + +if [ "$NO_VERIFY" ]; then + echo 'pre-push checks skipped' 1>&2 + exit 0 +fi + +if ! command -v gitleaks >/dev/null 2>&1; then + echo 'warning: gitleaks not installed - skipping pre-push secret scan. Install: brew install gitleaks' 1>&2 + exit 0 +fi + +# stdin lines: +while read -r _local_ref local_sha _remote_ref remote_sha; do + # branch deletion: nothing outgoing + [ "$local_sha" = "0000000000000000000000000000000000000000" ] && continue + if [ "$remote_sha" = "0000000000000000000000000000000000000000" ]; then + # new branch: scan commits not yet on any remote + range="$local_sha --not --remotes" + else + range="$remote_sha..$local_sha" + fi + if ! gitleaks git --redact --no-banner --log-opts="$range" &2 + echo 'Fix the commit, or for a false positive record its fingerprint in .gitleaksignore.' 1>&2 + exit 1 + fi +done +exit 0 diff --git a/docker/README.md b/docker/README.md deleted file mode 100644 index ae1d0b38d..000000000 --- a/docker/README.md +++ /dev/null @@ -1,22 +0,0 @@ -## Overview -This directory contains dockerfiles and supporting scripts for building and running the PIC-SURE WildFly container. - -### Build Dockerfile -This `build.Dockerfile` builds the PIC-SURE-API project using maven and the appropriate Java version. This Dockerfile -should always be built using the project root as context. This means you will need to use `-f docker/build.Dockerfile` -with your `docker build` command. - -### BDC -This directory contains dockerfiles and supporting scripts for building the Biodatacatalyst PIC-SURE WildFly container. -This Dockerfile uses the `build.Dockerfile` as a base to copy the built WAR files into the WildFly container. - -#### Generate-module-xml.sh -- `generate-module-xml.sh`: Generates a module.xml which is copied into the WildFly container's module directory. This - is necessary for the WildFly container to recognize and use the dependencies in the bdc/pom.xml file. - -#### pom.xml (In the bdc directory) -- `pom.xml`: Contains dependencies that are specific to the Biodatacatalyst PIC-SURE WildFly container. - -## all-in-one -This directory contains a dockerfile named `all-in-one.Dockerfile`. This dockerfile uses the `build.Dockerfile` as a -base to copy the built WAR files into the WildFly container. diff --git a/docker/all-in-one/all-in-one.Dockerfile b/docker/all-in-one/all-in-one.Dockerfile deleted file mode 100644 index 4b89de3c0..000000000 --- a/docker/all-in-one/all-in-one.Dockerfile +++ /dev/null @@ -1,9 +0,0 @@ -FROM --platform=linux/amd64 jboss/wildfly:23.0.0.Final - -COPY /pic-sure-api-war/target/pic-sure-api-war.war /tmp/pic-sure-api-2.war - -USER root - -RUN mv /tmp/*.war /opt/jboss/wildfly/standalone/deployments/ - -USER jboss \ No newline at end of file diff --git a/docker/bdc/bdc.Dockerfile b/docker/bdc/bdc.Dockerfile deleted file mode 100644 index c9393dad8..000000000 --- a/docker/bdc/bdc.Dockerfile +++ /dev/null @@ -1,32 +0,0 @@ -# This image layer is used to cache dependencies specifically used for BDC. The dependencies can be found in the -# pom.xml in this directory. -FROM maven:3.6.3-jdk-11 as dependencies -COPY docker/bdc/pom.xml /tmp/ -# Resolve and download dependencies, potentially using the dependency:copy-dependencies goal to place them into a target directory -RUN mvn -f /tmp/pom.xml dependency:copy-dependencies -DoutputDirectory=/tmp/dependencies - -FROM jboss/wildfly:17.0.0.Final - -USER root - -# Now, copy the resolved dependencies from the 'dependencies' stage into the WildFly deployments directory -COPY --from=dependencies /tmp/dependencies/*.jar /opt/jboss/wildfly/modules/system/layers/base/com/sql/mysql/main/ - -# Copy the script that generates module.xml -COPY docker/bdc/generate-module-xml.sh /tmp/generate-module-xml.sh -RUN chmod +x /tmp/generate-module-xml.sh && /tmp/generate-module-xml.sh - -# cat the generated module.xml file to see if it was generated correctly -RUN cat /opt/jboss/wildfly/modules/system/layers/base/com/sql/mysql/main/module.xml - -USER jboss - -# Copy pre-built WAR files from workspace -COPY pic-sure-api-war/target/pic-sure-api-war.war /tmp/pic-sure-api-2.war -COPY pic-sure-resources/pic-sure-aggregate-data-sharing-resource/target/pic-sure-aggregate-data-sharing-resource.war /tmp/pic-sure-aggregate-resource.war - -USER root - -RUN mv /tmp/*.war /opt/jboss/wildfly/standalone/deployments/ - -USER jboss diff --git a/docker/bdc/generate-module-xml.sh b/docker/bdc/generate-module-xml.sh deleted file mode 100644 index 88a2f41e1..000000000 --- a/docker/bdc/generate-module-xml.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/sh - -# Directory where JAR files are located -JAR_DIR="/opt/jboss/wildfly/modules/system/layers/base/com/sql/mysql/main" - -# Start of the module.xml file -cat < ${JAR_DIR}/module.xml - - -EOF - -# Loop through all JAR files and add them as resource-root entries -for jar in ${JAR_DIR}/*.jar; do - echo " " >> ${JAR_DIR}/module.xml -done - -# End of the module.xml file -cat <> ${JAR_DIR}/module.xml - - - - - -EOF \ No newline at end of file diff --git a/docker/bdc/pom.xml b/docker/bdc/pom.xml deleted file mode 100644 index 46c92e30a..000000000 --- a/docker/bdc/pom.xml +++ /dev/null @@ -1,36 +0,0 @@ - - 4.0.0 - - - com.hms.dbmi - dependency_jar - 1.0-SNAPSHOT - - dbmi_wildfly_dependencies - This project was created, so we can use maven for dependency management. - - - UTF-8 - 11 - 11 - - - - - - com.amazonaws.secretsmanager - aws-secretsmanager-jdbc - 2.0.2 - - - - mysql - mysql-connector-java - 8.0.33 - - - - - diff --git a/libs/pic-sure-commons/.github/release.yml b/libs/pic-sure-commons/.github/release.yml new file mode 100644 index 000000000..0db6cd02d --- /dev/null +++ b/libs/pic-sure-commons/.github/release.yml @@ -0,0 +1,20 @@ +changelog: + exclude: + labels: + - ignore-for-release + categories: + - title: Breaking Changes + labels: + - breaking-change + - title: Features + labels: + - feature + - title: Enhancements + labels: + - enhancement + - title: Bug Fixes + labels: + - bug + - title: Other Changes + labels: + - "*" diff --git a/libs/pic-sure-commons/.github/workflows/github-actions-deploy-snapshots.yml b/libs/pic-sure-commons/.github/workflows/github-actions-deploy-snapshots.yml new file mode 100644 index 000000000..e235aabb2 --- /dev/null +++ b/libs/pic-sure-commons/.github/workflows/github-actions-deploy-snapshots.yml @@ -0,0 +1,21 @@ +name: Maven Deploy Snapshots + +on: + push: + branches: [ main, ALS-11850 ] + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd #v6.0.2 + - name: Set up JDK 25 + uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 #v5.2.0 + with: + java-version: '25' + distribution: 'temurin' + - name: Build with Maven + run: mvn --update-snapshots deploy + env: + GITHUB_TOKEN: ${{ github.token }} diff --git a/libs/pic-sure-commons/.github/workflows/github-actions-test.yml b/libs/pic-sure-commons/.github/workflows/github-actions-test.yml new file mode 100644 index 000000000..2d656e7b0 --- /dev/null +++ b/libs/pic-sure-commons/.github/workflows/github-actions-test.yml @@ -0,0 +1,19 @@ +name: Maven Run Tests + +on: [ push ] + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd #v6.0.2 + - name: Set up JDK 25 + uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 #v5.2.0 + with: + java-version: '25' + distribution: 'temurin' + - name: Test with Maven + run: mvn --update-snapshots test + env: + GITHUB_TOKEN: ${{ github.token }} diff --git a/libs/pic-sure-commons/.github/workflows/label-checker.yml b/libs/pic-sure-commons/.github/workflows/label-checker.yml new file mode 100644 index 000000000..4806967a4 --- /dev/null +++ b/libs/pic-sure-commons/.github/workflows/label-checker.yml @@ -0,0 +1,21 @@ +name: Label Checker +on: + pull_request: + types: + - opened + - synchronize + - reopened + - labeled + - unlabeled + +jobs: + + check_labels: + name: Check labels + runs-on: ubuntu-latest + steps: + - uses: agilepathway/label-checker@c3d16ad512e7cea5961df85ff2486bb774caf3c5 # v1.6.65 + with: + one_of: breaking-change,enhancement,bug,documentation,ignore-for-release,dependencies + repo_token: ${{ secrets.GITHUB_TOKEN }} + diff --git a/libs/pic-sure-commons/.gitignore b/libs/pic-sure-commons/.gitignore new file mode 100644 index 000000000..c6ee66478 --- /dev/null +++ b/libs/pic-sure-commons/.gitignore @@ -0,0 +1,60 @@ +# Compiled class file +*.class + +# Log file +*.log + +# BlueJ files +*.ctxt + +# Mobile Tools for Java (J2ME) +.mtj.tmp/ + +# Package Files # +*.jar +*.war +*.nar +*.ear +*.zip +*.tar.gz +*.rar + +# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml +hs_err_pid* +replay_pid* + +target/ +!.mvn/wrapper/maven-wrapper.jar +!**/src/main/**/target/ +!**/src/test/**/target/ + +### STS ### +.apt_generated +.classpath +.factorypath +.project +.settings +.springBeans +.sts4-cache + +### IntelliJ IDEA ### +.idea +*.iws +*.iml +*.ipr + +### NetBeans ### +/nbproject/private/ +/nbbuild/ +/dist/ +/nbdist/ +/.nb-gradle/ +build/ +!**/src/main/**/build/ +!**/src/test/**/build/ + +### VS Code ### +.vscode/ + +.env +db/flyway/flyway.conf \ No newline at end of file diff --git a/libs/pic-sure-commons/README.md b/libs/pic-sure-commons/README.md new file mode 100644 index 000000000..5afad8dfc --- /dev/null +++ b/libs/pic-sure-commons/README.md @@ -0,0 +1,9 @@ +# pic-sure-common +Common Java code shared by PIC-SURE applications + +## Pre-requisites + +* Java 25 +* Before contributing code, please set up our git hook: + `cp code-formatting/pre-commit.sh .git/hooks/pre-commit` + * To skip formatting on a block of code, wrap in `spotless:off`, `spotless:on` comments \ No newline at end of file diff --git a/libs/pic-sure-commons/code-formatting/eclipse-formatter.xml b/libs/pic-sure-commons/code-formatting/eclipse-formatter.xml new file mode 100644 index 000000000..e7cfababf --- /dev/null +++ b/libs/pic-sure-commons/code-formatting/eclipse-formatter.xml @@ -0,0 +1,402 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/libs/pic-sure-commons/code-formatting/pre-commit.sh b/libs/pic-sure-commons/code-formatting/pre-commit.sh new file mode 100755 index 000000000..ed051d182 --- /dev/null +++ b/libs/pic-sure-commons/code-formatting/pre-commit.sh @@ -0,0 +1,28 @@ +#!/bin/sh -e +CWD=$(pwd) +cd $(git rev-parse --show-toplevel) +format_cmd="" + +# skip if NO_VERIFY env var set +if [ "$NO_VERIFY" ]; then + echo 'code formatting skipped' 1>&2 + exit 0 +fi + +# I'm not great at bash, so this is a bit ugly, but I'll explain each pipe +# 1. Get all staged files +# 2. Reduce to just .java files +# 3. Replace newlines with commas (this was really hard to do in sed) +# 4. Replace commas with $,^.* +# 5. Crop off the last 4 chars +# This results in foo.java$,^.*bar.java$,^.*baz.java$ +# I then append ^.* to the beginning of that. +STAGED_JAVA_FILES_AS_REGEX=$(git diff --staged --name-only --diff-filter=ACMR | grep '.java$' | tr '\n' ',' | sed -e 's/,/$,^.*/g' | sed 's/.\{4\}$//') +FILES_TO_RESTAGE=$(git diff --staged --name-only --diff-filter=ACMR) +if [ -n "$STAGED_JAVA_FILES_AS_REGEX" ]; then + echo "Found the following staged java files to format: $STAGED_JAVA_FILES_AS_REGEX" + mvn spotless:apply -DspotlessFiles=^.*$STAGED_JAVA_FILES_AS_REGEX + git add $FILES_TO_RESTAGE +fi + +cd $CWD \ No newline at end of file diff --git a/libs/pic-sure-commons/docker/README.md b/libs/pic-sure-commons/docker/README.md new file mode 100644 index 000000000..e69de29bb diff --git a/libs/pic-sure-commons/docker/build.Dockerfile b/libs/pic-sure-commons/docker/build.Dockerfile new file mode 100644 index 000000000..f3bb5ad47 --- /dev/null +++ b/libs/pic-sure-commons/docker/build.Dockerfile @@ -0,0 +1,3 @@ +FROM maven:3.9.11-amazoncorretto-25 + +RUN yum update -y && yum install -y git && yum clean all \ No newline at end of file diff --git a/libs/pic-sure-commons/pic-sure-api-model/pom.xml b/libs/pic-sure-commons/pic-sure-api-model/pom.xml new file mode 100755 index 000000000..b56d7f24a --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-api-model/pom.xml @@ -0,0 +1,38 @@ + + + 4.0.0 + + edu.harvard.hms.dbmi.avillach + pic-sure-common + ${revision} + + pic-sure-api-model + pic-sure-api-common + http://maven.apache.org + jar + + + com.fasterxml.jackson.core + jackson-databind + 2.16.0 + + + commons-io + commons-io + 2.15.1 + + + io.swagger.core.v3 + swagger-annotations + + + org.junit.vintage + junit-vintage-engine + + test + + + + + diff --git a/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/QueryFormatDeserializer.java b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/QueryFormatDeserializer.java new file mode 100644 index 000000000..33d677125 --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/QueryFormatDeserializer.java @@ -0,0 +1,47 @@ +package edu.harvard.dbmi.avillach; + +import com.fasterxml.jackson.core.JsonParser; +import com.fasterxml.jackson.databind.*; +import edu.harvard.dbmi.avillach.domain.QueryFormat; + +import java.io.IOException; +import java.util.*; + +public class QueryFormatDeserializer extends JsonDeserializer { + + private final static ObjectMapper mapper = new ObjectMapper(); + + // All extra fields are just shoved into specification + // TODO Not sure this is the format we want this in actually but for now it's readable at least + @Override + public QueryFormat deserialize(JsonParser jp, DeserializationContext context) throws IOException { + JsonNode node = jp.getCodec().readTree(jp); + QueryFormat qf = new QueryFormat(); + + Iterator> fields = node.fields(); + HashMap extraFields = new HashMap<>(); + List> examples = new ArrayList<>(); + while (fields.hasNext()) { + Map.Entry field = fields.next(); + if (field.getKey().equalsIgnoreCase("name")) { + qf.setName(field.getValue().asText()); + } else if (field.getKey().equalsIgnoreCase("description")) { + qf.setDescription(field.getValue().asText()); + } else if (field.getKey().equalsIgnoreCase("examples")) { + List> test = mapper.convertValue(field.getValue(), ArrayList.class); + examples = test; + } else { + extraFields.put(field.getKey(), mapper.convertValue(field.getValue(), Object.class)); + } + } + if (!extraFields.isEmpty()) { + qf.setSpecification(extraFields); + } + if (!examples.isEmpty()) { + qf.setExamples(examples); + } + return qf; + } + + +} diff --git a/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/GeneralQueryRequest.java b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/GeneralQueryRequest.java new file mode 100644 index 000000000..fd2ba645d --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/GeneralQueryRequest.java @@ -0,0 +1,81 @@ +package edu.harvard.dbmi.avillach.domain; + +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; +import io.swagger.v3.oas.annotations.media.Schema; + +import java.util.HashMap; +import java.util.Map; +import java.util.UUID; + +@Schema( + name = "QueryRequest", + description = "Object containing credentials map under 'resourceCredentials' and query" + + " object under 'query'. The query object expectedResultType can be on of the following " + + "\"COUNT\", \"CROSS_COUNT\", \"INFO_COLUMN_LISTING\", \"OBSERVATION_COUNT\", \"OBSERVATION_CROSS_COUNT\", \"DATAFRAME\". ", + example = "{\n" + " \"resourceUUID\": \"\",\n" + " \"query\": {\n" + " \"categoryFilters\": {\n" + + " \"\\\\demographics\\\\SEX\\\\\": [\n" + " \"female\",\n" + " \"male\"\n" + + " ]\n" + " },\n" + " \"numericFilters\": {\n" + " \"\\\\demographics\\\\AGE\\\\\": {\n" + + " \"min\": \"0\",\n" + " \"max\": \"85\"\n" + " }\n" + " },\n" + + " \"requiredFields\": [],\n" + " \"anyRecordOf\": [\n" + " \"\\\\demographics\\\\RACE\\\\\"\n" + + " ],\n" + " \"variantInfoFilters\": [\n" + " {\n" + + " \"categoryVariantInfoFilters\": {},\n" + " \"numericVariantInfoFilters\": {}\n" + + " }\n" + " ],\n" + " \"expectedResultType\": \"DATAFRAME\",\n" + " \"fields\": []\n" + " }\n" + + "}" +) + +/* + * QueryRequests for vanilla PIC-SURE + */ +public class GeneralQueryRequest implements QueryRequest { + + @Schema(hidden = true) + private Map resourceCredentials = new HashMap<>(); + + @Schema(hidden = true) + private Object query; + + @Schema(hidden = true) + private UUID resourceUUID; + + @Override + public Map getResourceCredentials() { + return resourceCredentials; + } + + @Override + public GeneralQueryRequest setResourceCredentials(Map resourceCredentials) { + this.resourceCredentials = resourceCredentials; + return this; + } + + @Override + public Object getQuery() { + return query; + } + + @Override + public GeneralQueryRequest setQuery(Object query) { + this.query = query; + return this; + } + + @Override + public UUID getResourceUUID() { + return resourceUUID; + } + + @Override + public void setResourceUUID(UUID resourceUUID) { + this.resourceUUID = resourceUUID; + } + + @Override + public GeneralQueryRequest copy() { + GeneralQueryRequest request = new GeneralQueryRequest(); + request.setQuery(getQuery()); + request.setResourceCredentials(getResourceCredentials()); + request.setResourceUUID(getResourceUUID()); + + return request; + } +} diff --git a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/PaginatedSearchResult.java b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/PaginatedSearchResult.java similarity index 87% rename from pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/PaginatedSearchResult.java rename to libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/PaginatedSearchResult.java index 6a9a72b3d..b76aa8c06 100644 --- a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/PaginatedSearchResult.java +++ b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/PaginatedSearchResult.java @@ -12,7 +12,9 @@ public class PaginatedSearchResult { private final int total; @JsonCreator - public PaginatedSearchResult(@JsonProperty("results") List results, @JsonProperty("page") int page, @JsonProperty("total") int total) { + public PaginatedSearchResult( + @JsonProperty("results") List results, @JsonProperty("page") int page, @JsonProperty("total") int total + ) { this.results = results; this.page = page; this.total = total; diff --git a/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/PicSureStatus.java b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/PicSureStatus.java new file mode 100644 index 000000000..bdf189f0e --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/PicSureStatus.java @@ -0,0 +1,5 @@ +package edu.harvard.dbmi.avillach.domain; + +public enum PicSureStatus { + QUEUED, PENDING, ERROR, AVAILABLE +} diff --git a/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/QueryFormat.java b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/QueryFormat.java new file mode 100644 index 000000000..93f534667 --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/QueryFormat.java @@ -0,0 +1,64 @@ +package edu.harvard.dbmi.avillach.domain; + +import com.fasterxml.jackson.annotation.JsonInclude; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; +import edu.harvard.dbmi.avillach.QueryFormatDeserializer; +import io.swagger.v3.oas.annotations.media.Schema; + +import java.util.List; +import java.util.Map; + +@Schema(description = "Information about the query format supported by a resource.") +@JsonDeserialize(using = QueryFormatDeserializer.class) +@JsonInclude(JsonInclude.Include.NON_NULL) +public class QueryFormat { + + @Schema(description = "The name of the query format.") + private String name; + + @Schema(description = "A description of the query format.") + private String description; + + @Schema(description = "A specification of the query format.") + private Map specification; + + @Schema(description = "A list of examples of the query format.") + private List> examples; + + public String getName() { + return name; + } + + public QueryFormat setName(String name) { + this.name = name; + return this; + } + + public String getDescription() { + return description; + } + + public QueryFormat setDescription(String description) { + this.description = description; + return this; + } + + public Map getSpecification() { + return specification; + } + + public QueryFormat setSpecification(Map specification) { + this.specification = specification; + return this; + } + + public List> getExamples() { + return examples; + } + + public QueryFormat setExamples(List> examples) { + this.examples = examples; + return this; + } + +} diff --git a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/QueryRequest.java b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/QueryRequest.java similarity index 87% rename from pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/QueryRequest.java rename to libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/QueryRequest.java index a54a486f8..25f914602 100644 --- a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/QueryRequest.java +++ b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/QueryRequest.java @@ -9,16 +9,19 @@ import java.util.UUID; @JsonTypeInfo(use = JsonTypeInfo.Id.NAME, defaultImpl = GeneralQueryRequest.class) -@JsonSubTypes({ @JsonSubTypes.Type(GeneralQueryRequest.class), @JsonSubTypes.Type(FederatedQueryRequest.class) }) +@JsonSubTypes({@JsonSubTypes.Type(GeneralQueryRequest.class)}) @JsonIgnoreProperties(ignoreUnknown = true) public interface QueryRequest { public Map getResourceCredentials(); + public QueryRequest setResourceCredentials(Map resourceCredentials); public Object getQuery(); + public QueryRequest setQuery(Object query); public UUID getResourceUUID(); + public void setResourceUUID(UUID resourceUUID); public QueryRequest copy(); diff --git a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/QueryStatus.java b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/QueryStatus.java similarity index 100% rename from pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/QueryStatus.java rename to libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/QueryStatus.java diff --git a/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/ResourceInfo.java b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/ResourceInfo.java new file mode 100644 index 000000000..e85373222 --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/ResourceInfo.java @@ -0,0 +1,57 @@ +package edu.harvard.dbmi.avillach.domain; + +import com.fasterxml.jackson.annotation.JsonInclude; +import io.swagger.v3.oas.annotations.media.Schema; + +import java.util.ArrayList; +import java.util.List; +import java.util.UUID; + +/** + * Information about interacting with a specific resource. + * + */ +@Schema(description = "Information about interacting with a specific resource.") +@JsonInclude(JsonInclude.Include.NON_NULL) +public class ResourceInfo { + + @Schema(description = "The UUID of the resource.") + private UUID id; + + @Schema(description = "The name of the resource.") + private String name; + + @Schema(description = "The query formats supported by the resource.") + private List queryFormats; + + public UUID getId() { + return id; + } + + public ResourceInfo setId(UUID id) { + this.id = id; + return this; + } + + public String getName() { + return name; + } + + public ResourceInfo setName(String name) { + this.name = name; + return this; + } + + public List getQueryFormats() { + if (queryFormats == null) { + queryFormats = new ArrayList<>(); + } + return queryFormats; + } + + public ResourceInfo setQueryFormats(List queryFormats) { + this.queryFormats = queryFormats; + return this; + } + +} diff --git a/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/SearchResults.java b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/SearchResults.java new file mode 100644 index 000000000..2397ea3bf --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/SearchResults.java @@ -0,0 +1,31 @@ +package edu.harvard.dbmi.avillach.domain; + +import io.swagger.v3.oas.annotations.media.Schema; + +@Schema(description = "A search results object") +public class SearchResults { + + @Schema(description = "The results of the search.") + Object results; + + @Schema(description = "The query that was used to generate the results.") + String searchQuery; + + public Object getResults() { + return results; + } + + public SearchResults setResults(Object results) { + this.results = results; + return this; + } + + public String getSearchQuery() { + return searchQuery; + } + + public SearchResults setSearchQuery(String searchQuery) { + this.searchQuery = searchQuery; + return this; + } +} diff --git a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/SignedUrlResponse.java b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/SignedUrlResponse.java similarity index 100% rename from pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/SignedUrlResponse.java rename to libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/domain/SignedUrlResponse.java diff --git a/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/util/UUIDv5.java b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/util/UUIDv5.java new file mode 100644 index 000000000..853542e2b --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/util/UUIDv5.java @@ -0,0 +1,67 @@ +package edu.harvard.dbmi.avillach.util; + +import java.nio.charset.Charset; +import java.security.MessageDigest; +import java.security.NoSuchAlgorithmException; +import java.util.Objects; +import java.util.UUID; + +public class UUIDv5 { + private static final Charset UTF8 = Charset.forName("UTF-8"); + + /// random UUID for namespace; do NOT change this! + public static final UUID NAMESPACE_AVL = UUID.fromString("a4f66130-cb71-4d7f-a58c-9f1831ebfb8e"); + + /** + * Generate a Type 5 UUID based on a single sting input and a default namespace. + * @param namespace + * @param source + * @return + */ + public static UUID UUIDFromString(String source) { + return UUIDFromNamespaceAndBytes(NAMESPACE_AVL, Objects.requireNonNull(source, "source == null").getBytes(UTF8)); + } + + /** + * Generates a Type 5 UUID based on the provided namespace ID and a byte array. + * @param namespace + * @param source + * @return + */ + public static UUID UUIDFromNamespaceAndBytes(UUID namespace, byte[] source) { + MessageDigest md; + try { + md = MessageDigest.getInstance("SHA-1"); + } catch (NoSuchAlgorithmException nsae) { + throw new InternalError("SHA-1 not supported"); + } + md.update(toBytes(Objects.requireNonNull(namespace, "namespace is null"))); + md.update(Objects.requireNonNull(source, "name is null")); + byte[] sha1Bytes = md.digest(); + sha1Bytes[6] &= 0x0f; /* clear version */ + sha1Bytes[6] |= 0x50; /* set to version 5 */ + sha1Bytes[8] &= 0x3f; /* clear variant */ + sha1Bytes[8] |= 0x80; /* set to IETF variant */ + return fromBytes(sha1Bytes); + } + + private static UUID fromBytes(byte[] data) { + // Based on the private UUID(bytes[]) constructor + long msb = 0; + long lsb = 0; + assert data.length >= 16; + for (int i = 0; i < 8; i++) msb = (msb << 8) | (data[i] & 0xff); + for (int i = 8; i < 16; i++) lsb = (lsb << 8) | (data[i] & 0xff); + return new UUID(msb, lsb); + } + + private static byte[] toBytes(UUID uuid) { + // inverted logic of fromBytes() + byte[] out = new byte[16]; + long msb = uuid.getMostSignificantBits(); + long lsb = uuid.getLeastSignificantBits(); + for (int i = 0; i < 8; i++) out[i] = (byte) ((msb >> ((7 - i) * 8)) & 0xff); + for (int i = 8; i < 16; i++) out[i] = (byte) ((lsb >> ((15 - i) * 8)) & 0xff); + return out; + } +} diff --git a/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/util/exception/ResourceCommunicationException.java b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/util/exception/ResourceCommunicationException.java new file mode 100644 index 000000000..34acb7326 --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-api-model/src/main/java/edu/harvard/dbmi/avillach/util/exception/ResourceCommunicationException.java @@ -0,0 +1,15 @@ +package edu.harvard.dbmi.avillach.util.exception; + +public class ResourceCommunicationException extends RuntimeException { + + private static final long serialVersionUID = -3039213913753996987L; + + public ResourceCommunicationException(String targetIrctUrl, Exception e) { + super("An error has occurred attempting to process a request for " + targetIrctUrl, e); + } + + public ResourceCommunicationException(String targetIrctUrl, String message) { + super("An error has occurred attempting to process a request for " + targetIrctUrl + ": " + message); + } + +} diff --git a/pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/domain/PaginatedSearchResultTest.java b/libs/pic-sure-commons/pic-sure-api-model/src/test/java/edu/harvard/dbmi/avillach/domain/PaginatedSearchResultTest.java similarity index 100% rename from pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/domain/PaginatedSearchResultTest.java rename to libs/pic-sure-commons/pic-sure-api-model/src/test/java/edu/harvard/dbmi/avillach/domain/PaginatedSearchResultTest.java diff --git a/libs/pic-sure-commons/pic-sure-api-model/src/test/java/edu/harvard/dbmi/avillach/domain/QueryRequestTest.java b/libs/pic-sure-commons/pic-sure-api-model/src/test/java/edu/harvard/dbmi/avillach/domain/QueryRequestTest.java new file mode 100644 index 000000000..cfdde629c --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-api-model/src/test/java/edu/harvard/dbmi/avillach/domain/QueryRequestTest.java @@ -0,0 +1,55 @@ +package edu.harvard.dbmi.avillach.domain; + + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import org.junit.Assert; +import org.junit.Test; + +import java.util.HashMap; +import java.util.UUID; + +public class QueryRequestTest { + private static final ObjectMapper mapper = new ObjectMapper(); + + @Test + public void shouldSerializeGeneralQueryRequest() throws JsonProcessingException { + GeneralQueryRequest expected = new GeneralQueryRequest(); + expected.setQuery(null); + expected.setResourceCredentials(new HashMap<>()); + expected.setResourceUUID(UUID.randomUUID()); + String json = mapper.writeValueAsString(expected); + + QueryRequest actual = mapper.readValue(json, QueryRequest.class); + + Assert.assertEquals(GeneralQueryRequest.class, actual.getClass()); + Assert.assertEquals(expected.getResourceUUID(), actual.getResourceUUID()); + } + + @Test + public void shouldSerializeRequestWithNoType() throws JsonProcessingException { + // Make sure json without the @Type annotation doesn't break this + String json = "{\"resourceCredentials\":{},\"query\":null,\"resourceUUID\":\"e4513cca-12c0-4fe2-b2fd-5d05b821056c\"}"; + QueryRequest actual = mapper.readValue(json, QueryRequest.class); + + Assert.assertEquals(GeneralQueryRequest.class, actual.getClass()); + } + + /** + * Pins the fallback that makes HpdsQueryV3Controller#rejectInstitutionalQuery necessary. FederatedQueryRequest was removed, but + * @JsonTypeInfo(defaultImpl = GeneralQueryRequest.class) resolves an UNKNOWN type id to the default impl before FAIL_ON_INVALID_SUBTYPE + * is consulted, and @JsonIgnoreProperties(ignoreUnknown = true) swallows the surplus GIC fields. So a + * federated body does not 400 -- it is silently reinterpreted. If this test ever fails, the 410 guard's + * rationale has changed; read it before touching either. + */ + @Test + public void shouldDeserializeRemovedFederatedTypeAsGeneralQueryRequest() throws JsonProcessingException { + String json = "{\"@type\":\"FederatedQueryRequest\",\"query\":\"q\"," + "\"commonAreaUUID\":\"" + UUID.randomUUID() + "\"," + + "\"institutionOfOrigin\":\"BCH\",\"requesterEmail\":\"alice@harvard.edu\"}"; + + QueryRequest parsed = new ObjectMapper().readValue(json, QueryRequest.class); + + Assert.assertTrue("unknown @type must fall back to the defaultImpl", parsed instanceof GeneralQueryRequest); + Assert.assertEquals("q", parsed.getQuery()); + } +} diff --git a/pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/domain/SignedUrlResponseTest.java b/libs/pic-sure-commons/pic-sure-api-model/src/test/java/edu/harvard/dbmi/avillach/domain/SignedUrlResponseTest.java similarity index 100% rename from pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/domain/SignedUrlResponseTest.java rename to libs/pic-sure-commons/pic-sure-api-model/src/test/java/edu/harvard/dbmi/avillach/domain/SignedUrlResponseTest.java diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/pom.xml b/libs/pic-sure-commons/pic-sure-hpds-model/pom.xml new file mode 100644 index 000000000..862da330a --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/pom.xml @@ -0,0 +1,47 @@ + + + 4.0.0 + + edu.harvard.hms.dbmi.avillach.hpds + pic-sure-hpds-model + + + edu.harvard.hms.dbmi.avillach + pic-sure-common + ${revision} + + + pic-sure-hpds-model + https://avillach-lab.hms.harvard.edu/pic-sure + + + edu.harvard.hms.dbmi.avillach + pic-sure-api-model + ${project.version} + + + io.swagger.core.v3 + swagger-annotations + + + com.fasterxml.jackson.core + jackson-databind + + + org.slf4j + slf4j-api + + + org.junit.jupiter + junit-jupiter + test + + + + org.assertj + assertj-core + 3.27.6 + test + + + diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genomic/VariantUtils.java b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genomic/VariantUtils.java new file mode 100644 index 000000000..3fa3dc91d --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genomic/VariantUtils.java @@ -0,0 +1,8 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genomic; + +public class VariantUtils { + public static boolean pathIsVariantSpec(String key) { + return key.matches("rs[0-9]+.*") || key.matches(".*,[0-9\\\\.]+,[CATGcatg]*,[CATGcatg]*") + || key.matches(".*,[0-9\\\\.]+,[CATGcatg]*,[CATGcatg]*,[\\w\\d_]*,[\\w\\d_]*"); + } +} diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/Filter.java b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/Filter.java new file mode 100644 index 000000000..08aef1343 --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/Filter.java @@ -0,0 +1,101 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.query; + +public interface Filter { + public boolean apply(T value); + + public static class DoubleFilter implements Filter { + + Double min, max; + + public Double getMin() { + return min; + } + + public void setMin(Double min) { + this.min = min; + } + + public Double getMax() { + return max; + } + + public void setMax(Double max) { + this.max = max; + } + + public DoubleFilter() { + + } + + public DoubleFilter(Double min, Double max) { + this.min = min; + this.max = max; + } + + public boolean apply(Double value) { + return value >= min && value <= max; + } + + public String toString() { + String strVal = ""; + if (min != null) { + strVal = "Greater than " + min; + if (max != null) { + strVal += " and "; + } + } + if (max != null) { + strVal += "Less than " + max; + } + return strVal; + } + } + public static class FloatFilter implements Filter { + + Float min, max; + + public Float getMin() { + return min; + } + + public void setMin(Float min) { + this.min = min; + } + + public Float getMax() { + return max; + } + + public void setMax(Float max) { + this.max = max; + } + + public FloatFilter() { + + } + + public FloatFilter(Float min, Float max) { + this.min = min; + this.max = max; + } + + public boolean apply(Float value) { + return value >= min && value <= max; + } + + public String toString() { + String strVal = ""; + if (min != null) { + strVal = "Greater than " + min; + if (max != null) { + strVal += " and "; + } + } + if (max != null) { + strVal += "Less than " + max; + } + return strVal; + } + } + +} diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/Query.java b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/Query.java new file mode 100644 index 000000000..bb0186057 --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/Query.java @@ -0,0 +1,311 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.query; + +import java.util.*; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Filter.DoubleFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Filter.FloatFilter; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +public class Query { + + private static final Logger log = LoggerFactory.getLogger(Query.class); + + public Query() { + + } + + public Query(Query query) { + this.expectedResultType = query.expectedResultType; + this.crossCountFields = new ArrayList(query.crossCountFields); + this.fields = new ArrayList(query.fields); + this.requiredFields = new ArrayList(query.requiredFields); + this.anyRecordOf = new ArrayList(query.anyRecordOf); + this.numericFilters = new TreeMap(query.numericFilters); + this.categoryFilters = new TreeMap(query.categoryFilters); + this.variantInfoFilters = new ArrayList(); + if (query.variantInfoFilters != null) { + query.variantInfoFilters.forEach((filter) -> { + this.variantInfoFilters.add(new VariantInfoFilter(filter)); + }); + } + this.id = query.id; + this.picSureId = query.picSureId; + } + + private ResultType expectedResultType = ResultType.COUNT; + private List crossCountFields = new ArrayList<>(); + private List fields = new ArrayList<>(); + private List requiredFields = new ArrayList<>(); + private List anyRecordOf = new ArrayList<>(); + private List> anyRecordOfMulti = new ArrayList<>(); + private Map numericFilters = new HashMap<>(); + private Map categoryFilters = new HashMap<>(); + private List variantInfoFilters = new ArrayList<>(); + private String id; + + private String picSureId; + + public ResultType getExpectedResultType() { + return expectedResultType; + } + + public List getCrossCountFields() { + return crossCountFields; + } + + public List getFields() { + return fields; + } + + public List getRequiredFields() { + return requiredFields; + } + + @Deprecated + public List getAnyRecordOf() { + return anyRecordOf; + } + + public List> getAnyRecordOfMulti() { + return anyRecordOfMulti; + } + + public List> getAllAnyRecordOf() { + List> anyRecordOfMultiCopy = new ArrayList<>(anyRecordOfMulti); + anyRecordOfMultiCopy.add(anyRecordOf); + return anyRecordOfMultiCopy; + } + + public Map getNumericFilters() { + return numericFilters; + } + + public Map getCategoryFilters() { + return categoryFilters; + } + + public List getVariantInfoFilters() { + return variantInfoFilters; + } + + public String getId() { + return id; + } + + public void setExpectedResultType(ResultType expectedResultType) { + this.expectedResultType = expectedResultType; + } + + public void setCrossCountFields(Collection crossCountFields) { + this.crossCountFields = crossCountFields != null ? new ArrayList<>(crossCountFields) : new ArrayList<>(); + } + + public void setFields(Collection fields) { + this.fields = fields != null ? new ArrayList<>(fields) : new ArrayList<>(); + } + + public void setRequiredFields(Collection requiredFields) { + this.requiredFields = requiredFields != null ? new ArrayList<>(requiredFields) : new ArrayList<>(); + } + + public void setAnyRecordOf(Collection anyRecordOf) { + this.anyRecordOf = anyRecordOf != null ? new ArrayList<>(anyRecordOf) : new ArrayList<>(); + } + + public void setAnyRecordOfMulti(Collection> anyRecordOfMulti) { + this.anyRecordOfMulti = anyRecordOfMulti != null ? new ArrayList<>(anyRecordOfMulti) : new ArrayList<>(); + } + + public void setNumericFilters(Map numericFilters) { + this.numericFilters = numericFilters != null ? new HashMap<>(numericFilters) : new HashMap<>(); + } + + public void setCategoryFilters(Map categoryFilters) { + this.categoryFilters = categoryFilters != null ? new HashMap<>(categoryFilters) : new HashMap<>(); + } + + public void setVariantInfoFilters(Collection variantInfoFilters) { + this.variantInfoFilters = variantInfoFilters != null ? new ArrayList<>(variantInfoFilters) : new ArrayList<>(); + } + + public void setId(String id) { + this.id = id; + } + + public String getPicSureId() { + return picSureId; + } + + public void setPicSureId(String picSureId) { + this.picSureId = picSureId; + } + + public static class VariantInfoFilter { + public VariantInfoFilter() { + + } + + public VariantInfoFilter(VariantInfoFilter filter) { + this.numericVariantInfoFilters = new TreeMap(filter.numericVariantInfoFilters); + this.categoryVariantInfoFilters = new TreeMap(filter.categoryVariantInfoFilters); + } + + public Map numericVariantInfoFilters; + public Map categoryVariantInfoFilters; + + public String toString() { + StringBuilder builder = new StringBuilder(); + writePartFormat("Numeric Variant Info Filters", numericVariantInfoFilters, builder); + writePartFormat("Category Variant Info Filters", categoryVariantInfoFilters, builder); + return builder.toString(); + } + } + + /** + * Some of these query objects can be enormous. We want to condense them to a readable form. + */ + @Override + public String toString() { + StringBuilder builder = new StringBuilder(); + builder.append("Query of type " + expectedResultType); + if (id != null) { + builder.append(" with ID " + id + "\n"); + } else { + builder.append(" (no ID assigned)\n"); + } + // We want to show different data based on the query type + switch (expectedResultType) { + case INFO_COLUMN_LISTING: + // info column listing has no query body + return builder.toString(); + + case CROSS_COUNT: + writePartFormat("Cross Count Fields", crossCountFields, builder, true); + break; + case CATEGORICAL_CROSS_COUNT: + writePartFormat("Categorical Cross Count Fields", categoryFilters.entrySet(), builder, true); + break; + case CONTINUOUS_CROSS_COUNT: + writePartFormat("Continuous Cross Count Fields", numericFilters.entrySet(), builder, true); + break; + case DATAFRAME: + case SECRET_ADMIN_DATAFRAME: + case PATIENTS: + writePartFormat("Data Export Fields", fields, builder, true); + break; + case DATAFRAME_TIMESERIES: + writePartFormat("Data Export Fields", fields, builder, true); + writePartFormat("Data Export Fields", requiredFields, builder, true); + writePartFormat("Data Export Fields", anyRecordOf, builder, true); + writePartFormat("Data Export Fields", numericFilters.keySet(), builder, true); + writePartFormat("Data Export Fields", categoryFilters.keySet(), builder, true); + case COUNT: + case VARIANT_COUNT_FOR_QUERY: + case AGGREGATE_VCF_EXCERPT: + case VCF_EXCERPT: + break; + default: + // no logic here; all enum values should be present above + log.warn("Formatting not supported for type {}", expectedResultType); + } + + writePartFormat("Required Fields", requiredFields, builder, false); + writePartFormat("Numeric filters", numericFilters, builder); + writePartFormat("Category filters", categoryFilters, builder); + writePartFormat("Variant Info filters", variantInfoFilters, builder, false); + writePartFormat("Any-Record-Of filters", getAllAnyRecordOf(), builder, true); + + return builder.toString(); + } + + /** + * For some elements of the query, we will iterate over the list of items and send them each to the string builder + * @param queryPart + * @param items + * @param builder + */ + @SuppressWarnings("rawtypes") + private static void writePartFormat(String queryPart, Collection items, StringBuilder builder, boolean allowRollup) { + final Collection collectionToWrite = Optional.ofNullable(items).orElseGet(Collections::emptyList); + // same beginning + builder.append(queryPart + ": ["); + // if there are many elements, we want to truncate the display + if (allowRollup && collectionToWrite.size() > 5) { + builder.append("\n"); + showTopLevelValues(collectionToWrite, builder); + } else { + String sep1 = ""; + for (Object val : collectionToWrite) { + builder.append(sep1 + val); + sep1 = ", "; + } + } + // same ending + builder.append("]\n"); + } + + @SuppressWarnings("rawtypes") + private static void showTopLevelValues(Collection varList, StringBuilder builder) { + + Map countMap = new HashMap(); + + for (Object var : varList) { + if (var instanceof String) { + int index = ((String) var).startsWith("\\") ? 1 : 0; + String firstLevel = ((String) var).split("\\\\")[index]; + + Integer count = countMap.get(firstLevel); + if (count == null) { + count = 1; + } else { + count = count + 1; + } + countMap.put(firstLevel, count); + } else { + System.out.println("Object is not string! " + var); + } + } + + for (String key : countMap.keySet()) { + builder.append("\t" + countMap.get(key) + " values under " + key + "\n"); + } + } + + /** + * For other items that are mapped (e.g., 'variable -> range') we want to show both the name and the values requested (unless + * truncating) We can't combine this with the List/Collection method, as the two classes are not compatible (even though the method + * names are the same) + * @param queryPart + * @param varMap + * @param builder + */ + @SuppressWarnings("rawtypes") + private static void writePartFormat(String queryPart, Map varMap, StringBuilder builder) { + if (varMap == null || varMap.isEmpty()) { + return; + } + + // for the mapped elements, we never want to roll up the values; always show + builder.append(queryPart + ": ["); + String sep1 = ""; + for (Object key : varMap.keySet()) { + builder.append(sep1 + key + ": "); + Object value = varMap.get(key); + + if (value instanceof Object[]) { + builder.append("{"); + String sep2 = ""; + for (Object val : (Object[]) value) { + builder.append(sep2 + val); + sep2 = ", "; + } + builder.append("}"); + } else { + builder.append(value); + } + sep1 = ", "; + } + builder.append("]\n"); + } +} diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/QueryDecorator.java b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/QueryDecorator.java new file mode 100644 index 000000000..778b0f5d2 --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/QueryDecorator.java @@ -0,0 +1,55 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.query; + +import edu.harvard.dbmi.avillach.util.UUIDv5; +import edu.harvard.hms.dbmi.avillach.hpds.data.genomic.VariantUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.*; + +public class QueryDecorator { + private static final Logger LOG = LoggerFactory.getLogger(QueryDecorator.class); + + public void setId(Query query) { + query.setId(""); // the id is included in the toString + // I clear it here to keep the ID setting stable for any query + // of identical structure and content + + // Some places where we call toString, we call mergeFilterFieldsIntoSelectedFields + // first. This can mutate the query, resulting in shifting UUIDs + // To stabilize things, we're always going to call that, and shift the logic here + mergeFilterFieldsIntoSelectedFields(query); + + // we also sort things sometimes + List fields = query.getFields(); + Collections.sort(fields); + query.setFields(fields); + + String id = UUIDv5.UUIDFromString(query.toString()).toString(); + query.setId(id); + } + + public void mergeFilterFieldsIntoSelectedFields(Query query) { + LinkedHashSet fields = new LinkedHashSet<>(query.getFields()); + + if (!query.getCategoryFilters().isEmpty()) { + Set categoryFilters = new TreeSet<>(query.getCategoryFilters().keySet()); + Set toBeRemoved = new TreeSet<>(); + for (String categoryFilter : categoryFilters) { + LOG.debug("In : {}", categoryFilter); + if (VariantUtils.pathIsVariantSpec(categoryFilter)) { + toBeRemoved.add(categoryFilter); + } + } + categoryFilters.removeAll(toBeRemoved); + for (String categoryFilter : categoryFilters) { + LOG.debug("Out : {}", categoryFilter); + } + fields.addAll(categoryFilters); + } + fields.addAll(query.getAnyRecordOf()); + fields.addAll(query.getRequiredFields()); + fields.addAll(query.getNumericFilters().keySet()); + query.setFields(fields); + } +} diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/ResultType.java b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/ResultType.java new file mode 100644 index 000000000..e2a17c0b3 --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/ResultType.java @@ -0,0 +1,69 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.query; + +import io.swagger.v3.oas.annotations.media.Schema; + +@Schema(description = "Specifies the return type of this query") +public enum ResultType { + + @Schema(description = "Return a count of patients matching this query") + COUNT, + + @Schema( + description = "Return a CSV with an observation for each concept for each patient included in the query. If there are multiple facts for a specific patient, they will be tab separated" + ) + DATAFRAME, + + @Schema( + description = "Create a `DATAFRAME`, but do not allow conventional access to it. Instead, the dataframe can be sent to a S3 bucket by an admin" + ) + SECRET_ADMIN_DATAFRAME, + + @Schema(description = "Return one patient count for each concept path included in the `select` field of the Query") + CROSS_COUNT, + + @Schema( + description = "Return multiple patient count for each categorical concept and its given variables included in any filters of the Query" + ) + CATEGORICAL_CROSS_COUNT, + + @Schema(description = "Return one patient count for each continuous concept path included in any filters of the query") + CONTINUOUS_CROSS_COUNT, + + @Schema(description = "Return all variant info column metadata") + INFO_COLUMN_LISTING, + + @Schema( + description = "Return the number of observations for included patients and included fields, broken up across the included cross count fields." + ) + OBSERVATION_CROSS_COUNT, + + @Schema( + description = "Return the count of unique `VariantSpec` that are the result of applying all genomic and phenotypic filters in the query. This is used by clients to limit queries to reasonable numbers of variants." + ) + VARIANT_COUNT_FOR_QUERY, + + @Schema( + description = "Return unique `VariantSpec` as strings that are the result of applying all genomic and phenotypic filters in the query." + ) + VARIANT_LIST_FOR_QUERY, + + @Schema(description = "Return quasi-VCF lines for the variants expressed in the query.") + VCF_EXCERPT, + + @Schema(description = "Return quasi-VCF lines for the variants expressed in the query without patient data.") + AGGREGATE_VCF_EXCERPT, + + @Schema( + description = "Export data in the same format as the HPDS csv loader, which is suitable to time series analysis and/or loading into another instance of HPDS." + ) + DATAFRAME_TIMESERIES, + + /** + * Exports data as PFB, using avro https://uc-cdis.github.io/pypfb/ + */ + @Schema(description = "Export data as PFB, using avro [https://uc-cdis.github.io/pypfb/](https://uc-cdis.github.io/pypfb/)") + DATAFRAME_PFB, + + @Schema(description = "Return patients associated with this query") + PATIENTS +} diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/translation/QueryTranslator.java b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/translation/QueryTranslator.java new file mode 100644 index 000000000..2febd839f --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/translation/QueryTranslator.java @@ -0,0 +1,168 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.query.translation; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.LinkedHashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.TreeMap; +import java.util.UUID; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Filter.DoubleFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Filter.FloatFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query.VariantInfoFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.GenomicFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Operator; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicClause; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicFilterType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicSubquery; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; + +/** + * Translates a legacy (v1) {@link edu.harvard.hms.dbmi.avillach.hpds.data.query.Query} into the v3 {@link Query} shape. Pure function, no + * I/O. Faithful to v1 semantics: each any-record-of list is an OR of its paths, and the whole query is an AND of every filter family. + * Multiple non-empty {@code variantInfoFilters} groups (an OR the flat v3 genomic list cannot express) raise + * {@link UntranslatableQueryException} rather than being silently merged. + */ +public class QueryTranslator { + + private QueryTranslator() {} + + public static Query translate(edu.harvard.hms.dbmi.avillach.hpds.data.query.Query v1) throws UntranslatableQueryException { + return new Query( + buildSelect(v1), List.of(), buildPhenotypicClause(v1), buildGenomicFilters(v1), v1.getExpectedResultType(), + parseUuid(v1.getPicSureId()), parseUuid(v1.getId()) + ); + } + + private static List buildSelect(edu.harvard.hms.dbmi.avillach.hpds.data.query.Query v1) { + LinkedHashSet select = new LinkedHashSet<>(); + if (v1.getFields() != null) { + select.addAll(v1.getFields()); + } + if (v1.getCrossCountFields() != null) { + select.addAll(v1.getCrossCountFields()); + } + return new ArrayList<>(select); + } + + private static PhenotypicClause buildPhenotypicClause(edu.harvard.hms.dbmi.avillach.hpds.data.query.Query v1) { + List clauses = new ArrayList<>(); + + // Category filters, sorted by concept path (v1 map is unordered). + new TreeMap<>(nullSafe(v1.getCategoryFilters())).forEach( + (path, values) -> clauses.add(new PhenotypicFilter(PhenotypicFilterType.FILTER, path, toSet(values), null, null, false)) + ); + + // Numeric filters, sorted by concept path. + new TreeMap<>(nullSafe(v1.getNumericFilters())).forEach( + (path, f) -> clauses.add(new PhenotypicFilter(PhenotypicFilterType.FILTER, path, null, f.getMin(), f.getMax(), false)) + ); + + // Required fields, in list order. + for (String path : nullSafeList(v1.getRequiredFields())) { + clauses.add(new PhenotypicFilter(PhenotypicFilterType.REQUIRED, path, null, null, null, false)); + } + + // Any-record-of groups: the anyRecordOf list first, then anyRecordOfMulti lists in order. + for (List group : anyRecordOfGroups(v1)) { + clauses.add(anyRecordOfClause(group)); + } + + if (clauses.isEmpty()) { + return null; + } + if (clauses.size() == 1) { + return clauses.get(0); + } + return new PhenotypicSubquery(false, clauses, Operator.AND); + } + + private static List> anyRecordOfGroups(edu.harvard.hms.dbmi.avillach.hpds.data.query.Query v1) { + List> groups = new ArrayList<>(); + List single = nullSafeList(v1.getAnyRecordOf()); + if (!single.isEmpty()) { + groups.add(single); + } + for (List group : nullSafeList(v1.getAnyRecordOfMulti())) { + if (group != null && !group.isEmpty()) { + groups.add(group); + } + } + return groups; + } + + private static PhenotypicClause anyRecordOfClause(List paths) { + List filters = new ArrayList<>(); + for (String path : paths) { + filters.add(new PhenotypicFilter(PhenotypicFilterType.ANY_RECORD_OF, path, null, null, null, false)); + } + if (filters.size() == 1) { + return filters.get(0); + } + return new PhenotypicSubquery(false, filters, Operator.OR); + } + + private static List buildGenomicFilters(edu.harvard.hms.dbmi.avillach.hpds.data.query.Query v1) + throws UntranslatableQueryException { + List nonEmpty = new ArrayList<>(); + for (VariantInfoFilter group : nullSafeList(v1.getVariantInfoFilters())) { + if (isNonEmpty(group)) { + nonEmpty.add(group); + } + } + if (nonEmpty.isEmpty()) { + return List.of(); + } + if (nonEmpty.size() > 1) { + throw new UntranslatableQueryException( + "multiple variantInfoFilter groups (OR semantics) cannot be represented in a v3 flat genomic filter list" + ); + } + VariantInfoFilter group = nonEmpty.get(0); + List result = new ArrayList<>(); + if (group.categoryVariantInfoFilters != null) { + new TreeMap<>(group.categoryVariantInfoFilters) + .forEach((key, values) -> result.add(new GenomicFilter(key, values == null ? null : Arrays.asList(values), null, null))); + } + if (group.numericVariantInfoFilters != null) { + new TreeMap<>(group.numericVariantInfoFilters) + .forEach((key, f) -> result.add(new GenomicFilter(key, null, f.getMin(), f.getMax()))); + } + return result; + } + + private static boolean isNonEmpty(VariantInfoFilter group) { + if (group == null) { + return false; + } + boolean hasCategory = group.categoryVariantInfoFilters != null && !group.categoryVariantInfoFilters.isEmpty(); + boolean hasNumeric = group.numericVariantInfoFilters != null && !group.numericVariantInfoFilters.isEmpty(); + return hasCategory || hasNumeric; + } + + private static Set toSet(String[] values) { + return values == null ? null : new LinkedHashSet<>(Arrays.asList(values)); + } + + private static UUID parseUuid(String value) { + if (value == null) { + return null; + } + try { + return UUID.fromString(value); + } catch (IllegalArgumentException e) { + return null; + } + } + + private static Map nullSafe(Map map) { + return map == null ? Map.of() : map; + } + + private static List nullSafeList(List list) { + return list == null ? List.of() : list; + } +} diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/translation/UntranslatableQueryException.java b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/translation/UntranslatableQueryException.java new file mode 100644 index 000000000..a59e58756 --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/translation/UntranslatableQueryException.java @@ -0,0 +1,12 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.query.translation; + +/** + * Thrown when a legacy (v1) query expresses semantics the v3 model cannot represent -- currently only the case of multiple non-empty + * {@code variantInfoFilters} groups, which HPDS OR's together but v3's flat {@code List} cannot express. + */ +public class UntranslatableQueryException extends Exception { + + public UntranslatableQueryException(String message) { + super(message); + } +} diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/AuthorizationFilter.java b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/AuthorizationFilter.java new file mode 100644 index 000000000..595f884eb --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/AuthorizationFilter.java @@ -0,0 +1,13 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.query.v3; + +import io.swagger.v3.oas.annotations.media.Schema; + +import java.util.Set; + +public record AuthorizationFilter( + @Schema(description = "A concept path this filter must match") String conceptPath, + @Schema( + description = "Values for this concept path. Patients returned by this query must match at least one value for this concept path" + ) Set values +) { +} diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/GenomicFilter.java b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/GenomicFilter.java new file mode 100644 index 000000000..662fc931f --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/GenomicFilter.java @@ -0,0 +1,24 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.query.v3; + +import io.swagger.v3.oas.annotations.media.Schema; + +import java.util.List; + +public record GenomicFilter( + @Schema( + description = "The genomic filter to query", example = "Gene_with_variant", requiredMode = Schema.RequiredMode.REQUIRED + ) String key, + @Schema( + description = "Values that must match for a given key. Cannot be combined with `min` or `max`", example = "APOE", + requiredMode = Schema.RequiredMode.NOT_REQUIRED + ) List values, + @Schema( + description = "Minimum value for a given key. Cannot be combined with `values`", example = "0.5", + requiredMode = Schema.RequiredMode.NOT_REQUIRED + ) Float min, + @Schema( + description = "Maximum value for a given key. Cannot be combined with `values`", example = "100", + requiredMode = Schema.RequiredMode.NOT_REQUIRED + ) Float max +) { +} diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/Operator.java b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/Operator.java new file mode 100644 index 000000000..cf40b66f6 --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/Operator.java @@ -0,0 +1,9 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.query.v3; + +import io.swagger.v3.oas.annotations.media.Schema; + +public enum Operator { + @Schema(description = "Filters combined with AND will return patients who match all filters") + AND, @Schema(description = "Filters combined with OR will return patients who match any filters") + OR +} diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/PhenotypicClause.java b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/PhenotypicClause.java new file mode 100644 index 000000000..aa1e98b9b --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/PhenotypicClause.java @@ -0,0 +1,10 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.query.v3; + +import com.fasterxml.jackson.annotation.JsonSubTypes; +import com.fasterxml.jackson.annotation.JsonTypeInfo; + +@JsonTypeInfo(use = JsonTypeInfo.Id.DEDUCTION) +@JsonSubTypes({@JsonSubTypes.Type(PhenotypicSubquery.class), @JsonSubTypes.Type(PhenotypicFilter.class)}) +public sealed interface PhenotypicClause permits PhenotypicSubquery, PhenotypicFilter { + +} diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/PhenotypicFilter.java b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/PhenotypicFilter.java new file mode 100644 index 000000000..70bd5324b --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/PhenotypicFilter.java @@ -0,0 +1,34 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.query.v3; + +import com.fasterxml.jackson.annotation.JsonIgnore; +import io.swagger.v3.oas.annotations.media.Schema; + +import java.util.Set; + +public record PhenotypicFilter( + @Schema(requiredMode = Schema.RequiredMode.REQUIRED) PhenotypicFilterType phenotypicFilterType, + @Schema(description = "A concept path this filter must match") String conceptPath, + @Schema( + description = "Values to match on for a given `conceptPath`. Cannot be combined with `min` or `max`", + requiredMode = Schema.RequiredMode.NOT_REQUIRED + ) Set values, + @Schema( + description = "Minimum value to filter for a given `conceptPath`. Cannot be combined with `values`", + requiredMode = Schema.RequiredMode.NOT_REQUIRED + ) Double min, + @Schema( + description = "Maximum value to filter for a given `conceptPath`. Cannot be combined with `values`", + requiredMode = Schema.RequiredMode.NOT_REQUIRED + ) Double max, Boolean not +) implements PhenotypicClause { + + @JsonIgnore + public boolean isCategoricalFilter() { + return PhenotypicFilterType.FILTER.equals(phenotypicFilterType) && values != null && !values.isEmpty(); + } + + @JsonIgnore + public boolean isNumericFilter() { + return PhenotypicFilterType.FILTER.equals(phenotypicFilterType) && (min != null || max != null); + } +} diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/PhenotypicFilterType.java b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/PhenotypicFilterType.java new file mode 100644 index 000000000..25480a4db --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/PhenotypicFilterType.java @@ -0,0 +1,14 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.query.v3; + +import io.swagger.v3.oas.annotations.media.Schema; + +public enum PhenotypicFilterType { + @Schema(description = "Specifies that a filter will match if a concept path contains any value") + REQUIRED, @Schema( + description = "Specifies that a filter will match if a concept path matches the values specified in the `PhenotypicFilter`" + ) + FILTER, @Schema( + description = "Specifies that a filter will match if the concept path contains any value for itself or any child concept paths" + ) + ANY_RECORD_OF +} diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/PhenotypicSubquery.java b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/PhenotypicSubquery.java new file mode 100644 index 000000000..cf5e0132d --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/PhenotypicSubquery.java @@ -0,0 +1,14 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.query.v3; + +import io.swagger.v3.oas.annotations.media.Schema; + +import java.util.List; + +public record PhenotypicSubquery( + @Schema(description = "Not implemented yet") Boolean not, + @Schema( + description = "A list of phenotypic clauses to be evaluated and combined using the `operator`" + ) List phenotypicClauses, + @Schema(description = "Specifies logic to combine `phenotypicClauses` in this subquery") Operator operator +) implements PhenotypicClause { +} diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/Query.java b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/Query.java new file mode 100644 index 000000000..f9d29a381 --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/Query.java @@ -0,0 +1,78 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.query.v3; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import io.swagger.v3.oas.annotations.media.Schema; + +import java.util.ArrayList; +import java.util.List; +import java.util.UUID; + +public record Query( + @Schema( + description = "A list of concept paths to select. Ignored for expectedResultType that do not return fields, such as COUNT" + ) List select, + @Schema( + description = "A list of filters specifically applied for authorization purposes" + ) List authorizationFilters, + @Schema(description = "An object specifying phenotypic filters") PhenotypicClause phenotypicClause, + @Schema(description = "A list of genomic filters") List genomicFilters, + @Schema(description = "An object specifying the result type") ResultType expectedResultType, + @Schema(description = "An externally passed UUID to assign to this query") UUID picsureId, + @Schema(description = "An internally generated UUID identifying this query") UUID id +) { + + @Override + public List select() { + return select == null ? List.of() : select; + } + + @Override + public List authorizationFilters() { + return authorizationFilters == null ? List.of() : authorizationFilters; + } + + public Query setAuthorizationFilters(List authorizationFilters) { + return new Query( + this.select, authorizationFilters == null ? List.of() : authorizationFilters, this.phenotypicClause, this.genomicFilters, + this.expectedResultType, this.picsureId, this.id + ); + } + + + @Override + public List genomicFilters() { + return genomicFilters == null ? List.of() : genomicFilters; + } + + public List allFilters() { + return flatten(phenotypicClause); + } + + private List flatten(PhenotypicClause phenotypicClause) { + if (phenotypicClause == null) { + return List.of(); + } + return switch (phenotypicClause) { + case PhenotypicSubquery phenotypicSubquery -> phenotypicSubquery.phenotypicClauses().parallelStream().map(this::flatten) + .reduce((list1, list2) -> { + List copy = new ArrayList<>(list1); + copy.addAll(list2); + return copy; + }).orElseGet(List::of); + case PhenotypicFilter phenotypicFilter -> List.of(phenotypicFilter); + }; + } + + /** + * Creates a UUID for this query if it does not already exist. Note: this behavior is different than previously, I do not believe there + * is ever a valid reason to change the id once it is set, we should verify this with full regression testing in all environments. + * + * @return this query or a copy of this query with the UUID set + */ + public Query generateId() { + if (id != null) { + return this; + } + return new Query(select, authorizationFilters, phenotypicClause, genomicFilters, expectedResultType, picsureId, UUID.randomUUID()); + } +} diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genomic/VariantUtilsTest.java b/libs/pic-sure-commons/pic-sure-hpds-model/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genomic/VariantUtilsTest.java new file mode 100644 index 000000000..cd7f08f0f --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genomic/VariantUtilsTest.java @@ -0,0 +1,28 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genomic; + +import org.junit.jupiter.api.Test; + +import static org.junit.jupiter.api.Assertions.*; + +class VariantUtilsTest { + + @Test + public void pathIsVariantSpec_oldFormat() { + assertTrue(VariantUtils.pathIsVariantSpec("chr21,5032061,A,G")); + } + + @Test + public void pathIsVariantSpec_newFormat() { + assertTrue(VariantUtils.pathIsVariantSpec("chr21,5032061,A,G,LOC102723996,missense_variant")); + } + + @Test + public void pathIsVariantSpec_notMatching() { + assertFalse(VariantUtils.pathIsVariantSpec("chr21,5032061,A,Z,LOC102723996,missense_variant")); + assertFalse(VariantUtils.pathIsVariantSpec("chr21,5032061,Q,G,LOC102723996,missense_variant")); + assertFalse(VariantUtils.pathIsVariantSpec("chr21,5032061,A,G,LOC102723996")); + assertFalse(VariantUtils.pathIsVariantSpec("chr21,5032061,A,G,^&*,missense_variant")); + assertFalse(VariantUtils.pathIsVariantSpec("chr21,5032061,A,G,LOC102723996,&*(")); + assertFalse(VariantUtils.pathIsVariantSpec("chr21,ABC,A,G,LOC102723996,missense_variant")); + } +} diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/translation/QueryTranslatorTest.java b/libs/pic-sure-commons/pic-sure-hpds-model/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/translation/QueryTranslatorTest.java new file mode 100644 index 000000000..b51904772 --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/translation/QueryTranslatorTest.java @@ -0,0 +1,470 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.query.translation; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.assertj.core.api.Assertions.assertThatThrownBy; +import static org.junit.jupiter.api.Assertions.assertDoesNotThrow; + +import java.util.ArrayList; +import java.util.LinkedHashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.TreeMap; +import java.util.UUID; + +import org.junit.jupiter.api.Test; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Filter.DoubleFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Filter.FloatFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query.VariantInfoFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.GenomicFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Operator; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicClause; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicFilterType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicSubquery; + +class QueryTranslatorTest { + + private static Query v1() { + return new Query(); + } + + private static VariantInfoFilter group(Map cat, Map num) { + VariantInfoFilter g = new VariantInfoFilter(); + g.categoryVariantInfoFilters = cat; + g.numericVariantInfoFilters = num; + return g; + } + + private static PhenotypicFilter asFilter(PhenotypicClause c) { + return (PhenotypicFilter) c; + } + + private static PhenotypicSubquery asSub(PhenotypicClause c) { + return (PhenotypicSubquery) c; + } + + // ---------- select assembly ---------- + + @Test + void selectFromFieldsOnly() throws Exception { + Query q = v1(); + q.setFields(List.of("\\a\\", "\\b\\")); + assertThat(QueryTranslator.translate(q).select()).containsExactly("\\a\\", "\\b\\"); + } + + @Test + void selectFromCrossCountFieldsOnly() throws Exception { + Query q = v1(); + q.setCrossCountFields(List.of("\\c\\")); + assertThat(QueryTranslator.translate(q).select()).containsExactly("\\c\\"); + } + + @Test + void selectDedupesFieldsFirstThenCrossCount() throws Exception { + Query q = v1(); + q.setFields(List.of("\\a\\", "\\b\\")); + q.setCrossCountFields(List.of("\\b\\", "\\d\\")); + assertThat(QueryTranslator.translate(q).select()).containsExactly("\\a\\", "\\b\\", "\\d\\"); + } + + @Test + void selectEmptyWhenNoFields() throws Exception { + assertThat(QueryTranslator.translate(v1()).select()).isEmpty(); + } + + // ---------- empty / trivial ---------- + + @Test + void emptyQueryProducesEmptyV3() throws Exception { + edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query out = QueryTranslator.translate(v1()); + assertThat(out.phenotypicClause()).isNull(); + assertThat(out.genomicFilters()).isEmpty(); + assertThat(out.select()).isEmpty(); + assertThat(out.authorizationFilters()).isEmpty(); + assertThat(out.expectedResultType()).isEqualTo(ResultType.COUNT); // v1 default + assertThat(out.id()).isNull(); + assertThat(out.picsureId()).isNull(); + } + + @Test + void expectedResultTypeCarriedThrough() throws Exception { + Query q = v1(); + q.setExpectedResultType(ResultType.DATAFRAME); + assertThat(QueryTranslator.translate(q).expectedResultType()).isEqualTo(ResultType.DATAFRAME); + } + + @Test + void expectedResultTypeNullStaysNull() throws Exception { + Query q = v1(); + q.setExpectedResultType(null); + assertThat(QueryTranslator.translate(q).expectedResultType()).isNull(); + } + + // ---------- single-clause collapse ---------- + + @Test + void singleCategoryFilterCollapsesToBareFilter() throws Exception { + Query q = v1(); + q.setCategoryFilters(Map.of("\\sex\\", new String[] {"M", "F"})); + PhenotypicFilter f = asFilter(QueryTranslator.translate(q).phenotypicClause()); + assertThat(f.phenotypicFilterType()).isEqualTo(PhenotypicFilterType.FILTER); + assertThat(f.conceptPath()).isEqualTo("\\sex\\"); + assertThat(f.values()).containsExactly("M", "F"); + assertThat(f.min()).isNull(); + assertThat(f.max()).isNull(); + assertThat(f.not()).isFalse(); + } + + @Test + void singleNumericFilterMinAndMax() throws Exception { + Query q = v1(); + q.setNumericFilters(Map.of("\\age\\", new DoubleFilter(1.0, 9.0))); + PhenotypicFilter f = asFilter(QueryTranslator.translate(q).phenotypicClause()); + assertThat(f.phenotypicFilterType()).isEqualTo(PhenotypicFilterType.FILTER); + assertThat(f.values()).isNull(); + assertThat(f.min()).isEqualTo(1.0); + assertThat(f.max()).isEqualTo(9.0); + } + + @Test + void singleNumericFilterMinOnly() throws Exception { + Query q = v1(); + q.setNumericFilters(Map.of("\\age\\", new DoubleFilter(5.0, null))); + PhenotypicFilter f = asFilter(QueryTranslator.translate(q).phenotypicClause()); + assertThat(f.min()).isEqualTo(5.0); + assertThat(f.max()).isNull(); + } + + @Test + void singleNumericFilterMaxOnly() throws Exception { + Query q = v1(); + q.setNumericFilters(Map.of("\\age\\", new DoubleFilter(null, 5.0))); + PhenotypicFilter f = asFilter(QueryTranslator.translate(q).phenotypicClause()); + assertThat(f.min()).isNull(); + assertThat(f.max()).isEqualTo(5.0); + } + + @Test + void singleRequiredField() throws Exception { + Query q = v1(); + q.setRequiredFields(List.of("\\req\\")); + PhenotypicFilter f = asFilter(QueryTranslator.translate(q).phenotypicClause()); + assertThat(f.phenotypicFilterType()).isEqualTo(PhenotypicFilterType.REQUIRED); + assertThat(f.conceptPath()).isEqualTo("\\req\\"); + assertThat(f.values()).isNull(); + assertThat(f.min()).isNull(); + assertThat(f.max()).isNull(); + } + + @Test + void singlePathAnyRecordOfCollapsesToBareFilter() throws Exception { + Query q = v1(); + q.setAnyRecordOf(List.of("\\only\\")); + PhenotypicFilter f = asFilter(QueryTranslator.translate(q).phenotypicClause()); + assertThat(f.phenotypicFilterType()).isEqualTo(PhenotypicFilterType.ANY_RECORD_OF); + assertThat(f.conceptPath()).isEqualTo("\\only\\"); + } + + // ---------- multi-clause AND ---------- + + @Test + void twoCategoryFiltersFormAndSubquerySortedByPath() throws Exception { + Query q = v1(); + Map cats = new TreeMap<>(); + cats.put("\\zeta\\", new String[] {"1"}); + cats.put("\\alpha\\", new String[] {"2"}); + q.setCategoryFilters(cats); + PhenotypicSubquery sub = asSub(QueryTranslator.translate(q).phenotypicClause()); + assertThat(sub.operator()).isEqualTo(Operator.AND); + assertThat(sub.not()).isFalse(); + assertThat(sub.phenotypicClauses()).hasSize(2); + assertThat(asFilter(sub.phenotypicClauses().get(0)).conceptPath()).isEqualTo("\\alpha\\"); + assertThat(asFilter(sub.phenotypicClauses().get(1)).conceptPath()).isEqualTo("\\zeta\\"); + } + + @Test + void oneOfEachFamilyFormsAndSubqueryInFamilyOrder() throws Exception { + Query q = v1(); + q.setCategoryFilters(Map.of("\\cat\\", new String[] {"x"})); + q.setNumericFilters(Map.of("\\num\\", new DoubleFilter(1.0, 2.0))); + q.setRequiredFields(List.of("\\req\\")); + q.setAnyRecordOf(List.of("\\aro\\")); + PhenotypicSubquery sub = asSub(QueryTranslator.translate(q).phenotypicClause()); + assertThat(sub.operator()).isEqualTo(Operator.AND); + List cs = sub.phenotypicClauses(); + assertThat(cs).hasSize(4); + assertThat(asFilter(cs.get(0)).phenotypicFilterType()).isEqualTo(PhenotypicFilterType.FILTER); + assertThat(asFilter(cs.get(0)).conceptPath()).isEqualTo("\\cat\\"); + assertThat(asFilter(cs.get(1)).phenotypicFilterType()).isEqualTo(PhenotypicFilterType.FILTER); + assertThat(asFilter(cs.get(1)).conceptPath()).isEqualTo("\\num\\"); + assertThat(asFilter(cs.get(2)).phenotypicFilterType()).isEqualTo(PhenotypicFilterType.REQUIRED); + assertThat(asFilter(cs.get(3)).phenotypicFilterType()).isEqualTo(PhenotypicFilterType.ANY_RECORD_OF); + } + + @Test + void categoryFilterWithEmptyValuesIsStillEmitted() throws Exception { + Query q = v1(); + q.setCategoryFilters(Map.of("\\empty\\", new String[] {})); + PhenotypicFilter f = asFilter(QueryTranslator.translate(q).phenotypicClause()); + assertThat(f.phenotypicFilterType()).isEqualTo(PhenotypicFilterType.FILTER); + assertThat(f.values()).isEmpty(); + } + + // ---------- any-record-of OR/AND ---------- + + @Test + void anyRecordOfMultiPathBecomesOrSubqueryAsTopLevel() throws Exception { + Query q = v1(); + q.setAnyRecordOf(List.of("\\a\\", "\\b\\")); + PhenotypicSubquery sub = asSub(QueryTranslator.translate(q).phenotypicClause()); + assertThat(sub.operator()).isEqualTo(Operator.OR); + assertThat(sub.phenotypicClauses()).hasSize(2); + assertThat(asFilter(sub.phenotypicClauses().get(0)).phenotypicFilterType()).isEqualTo(PhenotypicFilterType.ANY_RECORD_OF); + assertThat(asFilter(sub.phenotypicClauses().get(0)).conceptPath()).isEqualTo("\\a\\"); + assertThat(asFilter(sub.phenotypicClauses().get(1)).conceptPath()).isEqualTo("\\b\\"); + } + + @Test + void anyRecordOfMultiOnlyBecomesOrSubquery() throws Exception { + Query q = v1(); + q.setAnyRecordOfMulti(List.of(List.of("\\c\\", "\\d\\"))); + PhenotypicSubquery sub = asSub(QueryTranslator.translate(q).phenotypicClause()); + assertThat(sub.operator()).isEqualTo(Operator.OR); + assertThat(sub.phenotypicClauses()).hasSize(2); + } + + @Test + void anyRecordOfPlusMultiFormsAndOfOrs() throws Exception { + Query q = v1(); + q.setAnyRecordOf(List.of("\\a\\", "\\b\\")); + q.setAnyRecordOfMulti(List.of(List.of("\\c\\", "\\d\\"))); + PhenotypicSubquery top = asSub(QueryTranslator.translate(q).phenotypicClause()); + assertThat(top.operator()).isEqualTo(Operator.AND); + assertThat(top.phenotypicClauses()).hasSize(2); + // anyRecordOf group first + PhenotypicSubquery first = asSub(top.phenotypicClauses().get(0)); + PhenotypicSubquery second = asSub(top.phenotypicClauses().get(1)); + assertThat(first.operator()).isEqualTo(Operator.OR); + assertThat(asFilter(first.phenotypicClauses().get(0)).conceptPath()).isEqualTo("\\a\\"); + assertThat(second.operator()).isEqualTo(Operator.OR); + assertThat(asFilter(second.phenotypicClauses().get(0)).conceptPath()).isEqualTo("\\c\\"); + } + + @Test + void anyRecordOfMultiEmptyInnerListIsSkipped() throws Exception { + Query q = v1(); + q.setAnyRecordOf(List.of("\\a\\")); + q.setAnyRecordOfMulti(List.of(new ArrayList<>())); + // only the single-path anyRecordOf survives -> bare filter, no AND wrapper + PhenotypicFilter f = asFilter(QueryTranslator.translate(q).phenotypicClause()); + assertThat(f.conceptPath()).isEqualTo("\\a\\"); + } + + @Test + void anyRecordOfMultiSinglePathInnerListIsBareFilterInsideAnd() throws Exception { + Query q = v1(); + q.setCategoryFilters(Map.of("\\cat\\", new String[] {"x"})); + q.setAnyRecordOfMulti(List.of(List.of("\\x\\"))); + PhenotypicSubquery top = asSub(QueryTranslator.translate(q).phenotypicClause()); + assertThat(top.operator()).isEqualTo(Operator.AND); + assertThat(top.phenotypicClauses()).hasSize(2); + assertThat(asFilter(top.phenotypicClauses().get(1)).phenotypicFilterType()).isEqualTo(PhenotypicFilterType.ANY_RECORD_OF); + assertThat(asFilter(top.phenotypicClauses().get(1)).conceptPath()).isEqualTo("\\x\\"); + } + + @Test + void anyRecordOfGroupCombinesWithCategoryUnderAnd() throws Exception { + Query q = v1(); + q.setCategoryFilters(Map.of("\\cat\\", new String[] {"x"})); + q.setAnyRecordOf(List.of("\\a\\", "\\b\\")); + PhenotypicSubquery top = asSub(QueryTranslator.translate(q).phenotypicClause()); + assertThat(top.operator()).isEqualTo(Operator.AND); + assertThat(asFilter(top.phenotypicClauses().get(0)).phenotypicFilterType()).isEqualTo(PhenotypicFilterType.FILTER); + assertThat(asSub(top.phenotypicClauses().get(1)).operator()).isEqualTo(Operator.OR); + } + + // ---------- genomic ---------- + + @Test + void oneGroupOneCategoryKey() throws Exception { + Query q = v1(); + q.setVariantInfoFilters(List.of(group(Map.of("Gene_with_variant", new String[] {"APOE"}), null))); + List gfs = QueryTranslator.translate(q).genomicFilters(); + assertThat(gfs).hasSize(1); + assertThat(gfs.get(0).key()).isEqualTo("Gene_with_variant"); + assertThat(gfs.get(0).values()).containsExactly("APOE"); + assertThat(gfs.get(0).min()).isNull(); + assertThat(gfs.get(0).max()).isNull(); + } + + @Test + void oneGroupOneNumericKey() throws Exception { + Query q = v1(); + q.setVariantInfoFilters(List.of(group(null, Map.of("freq", new FloatFilter(0.1f, 0.9f))))); + List gfs = QueryTranslator.translate(q).genomicFilters(); + assertThat(gfs).hasSize(1); + assertThat(gfs.get(0).key()).isEqualTo("freq"); + assertThat(gfs.get(0).values()).isNull(); + assertThat(gfs.get(0).min()).isEqualTo(0.1f); + assertThat(gfs.get(0).max()).isEqualTo(0.9f); + } + + @Test + void oneGroupMixedKeysCategoryBeforeNumericEachSorted() throws Exception { + Query q = v1(); + Map cat = new TreeMap<>(); + cat.put("Zebra", new String[] {"z"}); + cat.put("Alpha", new String[] {"a"}); + Map num = new TreeMap<>(); + num.put("nZeta", new FloatFilter(1f, 2f)); + num.put("nAlpha", new FloatFilter(3f, 4f)); + q.setVariantInfoFilters(List.of(group(cat, num))); + List gfs = QueryTranslator.translate(q).genomicFilters(); + assertThat(gfs).extracting(GenomicFilter::key).containsExactly("Alpha", "Zebra", "nAlpha", "nZeta"); + } + + @Test + void arbitraryGenomicKeyTranslatesGenerically() throws Exception { + Query q = v1(); + q.setVariantInfoFilters(List.of(group(Map.of("Variant_severity", new String[] {"HIGH"}), null))); + List gfs = QueryTranslator.translate(q).genomicFilters(); + assertThat(gfs).hasSize(1); + assertThat(gfs.get(0).key()).isEqualTo("Variant_severity"); + } + + @Test + void numericGenomicMinOnly() throws Exception { + Query q = v1(); + q.setVariantInfoFilters(List.of(group(null, Map.of("freq", new FloatFilter(0.2f, null))))); + GenomicFilter gf = QueryTranslator.translate(q).genomicFilters().get(0); + assertThat(gf.min()).isEqualTo(0.2f); + assertThat(gf.max()).isNull(); + } + + @Test + void nullVariantInfoFiltersYieldsEmptyGenomic() throws Exception { + Query q = v1(); + q.setVariantInfoFilters(null); + assertThat(QueryTranslator.translate(q).genomicFilters()).isEmpty(); + } + + @Test + void emptyGroupListYieldsEmptyGenomic() throws Exception { + Query q = v1(); + q.setVariantInfoFilters(List.of()); + assertThat(QueryTranslator.translate(q).genomicFilters()).isEmpty(); + } + + @Test + void groupWithBothMapsNullCountsAsEmpty() throws Exception { + Query q = v1(); + q.setVariantInfoFilters(List.of(group(null, null))); + assertThat(QueryTranslator.translate(q).genomicFilters()).isEmpty(); + } + + @Test + void oneEmptyOneNonEmptyGroupTranslates() throws Exception { + Query q = v1(); + q.setVariantInfoFilters(List.of(group(Map.of(), Map.of()), group(Map.of("Gene_with_variant", new String[] {"APOE"}), null))); + List gfs = QueryTranslator.translate(q).genomicFilters(); + assertThat(gfs).hasSize(1); + assertThat(gfs.get(0).key()).isEqualTo("Gene_with_variant"); + } + + @Test + void twoNonEmptyGroupsThrow() { + Query q = v1(); + q.setVariantInfoFilters( + List.of( + group(Map.of("Gene_with_variant", new String[] {"A"}), null), group(Map.of("Gene_with_variant", new String[] {"B"}), null) + ) + ); + assertThatThrownBy(() -> QueryTranslator.translate(q)).isInstanceOf(UntranslatableQueryException.class) + .hasMessageContaining("multiple"); + } + + @Test + void twoNonEmptyDuplicateGroupsStillThrow() { + Query q = v1(); + String[] same = {"A"}; + q.setVariantInfoFilters(List.of(group(Map.of("Gene_with_variant", same), null), group(Map.of("Gene_with_variant", same), null))); + assertThatThrownBy(() -> QueryTranslator.translate(q)).isInstanceOf(UntranslatableQueryException.class); + } + + // ---------- ids ---------- + + @Test + void validUuidsAreParsed() throws Exception { + Query q = v1(); + UUID id = UUID.randomUUID(); + UUID pid = UUID.randomUUID(); + q.setId(id.toString()); + q.setPicSureId(pid.toString()); + edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query out = QueryTranslator.translate(q); + assertThat(out.id()).isEqualTo(id); + assertThat(out.picsureId()).isEqualTo(pid); + } + + @Test + void nonUuidIdsBecomeNull() throws Exception { + Query q = v1(); + q.setId("12345"); + q.setPicSureId("not-a-uuid"); + edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query out = QueryTranslator.translate(q); + assertThat(out.id()).isNull(); + assertThat(out.picsureId()).isNull(); + } + + @Test + void nullIdsStayNull() throws Exception { + edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query out = QueryTranslator.translate(v1()); + assertThat(out.id()).isNull(); + assertThat(out.picsureId()).isNull(); + } + + // ---------- kitchen sink ---------- + + @Test + void kitchenSinkStructuralEquality() throws Exception { + Query q = v1(); + q.setFields(List.of("\\exp1\\")); + q.setCrossCountFields(List.of("\\cc1\\")); + q.setCategoryFilters(Map.of("\\sex\\", new String[] {"M"})); + q.setNumericFilters(Map.of("\\age\\", new DoubleFilter(0.0, 100.0))); + q.setRequiredFields(List.of("\\req\\")); + q.setAnyRecordOfMulti(List.of(List.of("\\aro1\\", "\\aro2\\"))); + q.setVariantInfoFilters(List.of(group(Map.of("Gene_with_variant", new String[] {"APOE"}), null))); + q.setExpectedResultType(ResultType.DATAFRAME); + + edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query out = QueryTranslator.translate(q); + + assertThat(out.select()).containsExactly("\\exp1\\", "\\cc1\\"); + assertThat(out.expectedResultType()).isEqualTo(ResultType.DATAFRAME); + assertThat(out.genomicFilters()).hasSize(1); + PhenotypicSubquery top = asSub(out.phenotypicClause()); + assertThat(top.operator()).isEqualTo(Operator.AND); + // 3 leaf filters (cat, num, req) + 1 OR subquery = 4 children + assertThat(top.phenotypicClauses()).hasSize(4); + assertThat(asSub(top.phenotypicClauses().get(3)).operator()).isEqualTo(Operator.OR); + } + + @Test + void jacksonRoundTripFromRawJson() throws Exception { + ObjectMapper mapper = new ObjectMapper(); + String rawV1 = "{\"expectedResultType\":\"COUNT\",\"categoryFilters\":{\"\\\\sex\\\\\":[\"M\"]}," + + "\"numericFilters\":{\"\\\\age\\\\\":{\"min\":1.0,\"max\":2.0}},\"fields\":[\"\\\\f\\\\\"]}"; + Query q = mapper.readValue(rawV1, Query.class); + edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query out = QueryTranslator.translate(q); + assertThat(out.select()).containsExactly("\\f\\"); + PhenotypicSubquery top = asSub(out.phenotypicClause()); + assertThat(top.phenotypicClauses()).hasSize(2); + // round-trips through Jackson without throwing + assertDoesNotThrow(() -> mapper.writeValueAsString(out)); + } +} diff --git a/libs/pic-sure-commons/pic-sure-hpds-model/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/QueryTest.java b/libs/pic-sure-commons/pic-sure-hpds-model/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/QueryTest.java new file mode 100644 index 000000000..cdc61cb0a --- /dev/null +++ b/libs/pic-sure-commons/pic-sure-hpds-model/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/v3/QueryTest.java @@ -0,0 +1,101 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.query.v3; + + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import org.junit.jupiter.api.Test; + +import java.util.List; +import java.util.Set; +import java.util.UUID; + +import static org.junit.jupiter.api.Assertions.*; + +public class QueryTest { + + + @Test + public void jacksonSerialization_validValues() throws JsonProcessingException { + ObjectMapper objectMapper = new ObjectMapper(); + + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "//abc//123///", Set.of("turtle"), 10.0, 20.0, true); + + List authorizationFilters = List.of(new AuthorizationFilter("\\_consents\\", Set.of("phs123", "phs456"))); + + PhenotypicSubquery phenotypicSubquery = new PhenotypicSubquery(true, List.of(phenotypicFilter), Operator.AND); + PhenotypicSubquery phenotypicSubquery2 = new PhenotypicSubquery(true, List.of(phenotypicFilter), Operator.AND); + + PhenotypicSubquery phenotypicQuery = + new PhenotypicSubquery(null, List.of(phenotypicSubquery, phenotypicSubquery2, phenotypicFilter), Operator.OR); + Query query = new Query(List.of("PATIENT_ID"), authorizationFilters, phenotypicQuery, List.of(), ResultType.COUNT, null, null); + + String serialized = objectMapper.writeValueAsString(query); + System.out.println(serialized); + + Query deserialized = objectMapper.readValue(serialized, Query.class); + + assertEquals(query, deserialized); + } + + @Test + public void jacksonSerialization_validNullValues() throws JsonProcessingException { + ObjectMapper objectMapper = new ObjectMapper(); + + Query query = new Query(null, null, null, null, null, null, null); + + String serialized = objectMapper.writeValueAsString(query); + System.out.println(serialized); + + Query deserialized = objectMapper.readValue(serialized, Query.class); + + assertEquals(List.of(), deserialized.select()); + assertEquals(List.of(), deserialized.authorizationFilters()); + assertNull(deserialized.phenotypicClause()); + assertEquals(List.of(), deserialized.genomicFilters()); + assertNull(deserialized.expectedResultType()); + assertNull(deserialized.picsureId()); + assertNull(deserialized.id()); + } + + @Test + public void jacksonSerialization_validNullSecondLevelValues() throws JsonProcessingException { + ObjectMapper objectMapper = new ObjectMapper(); + + PhenotypicFilter phenotypicFilter = new PhenotypicFilter(PhenotypicFilterType.FILTER, "//abc//123///", null, null, null, null); + + List authorizationFilters = List.of(new AuthorizationFilter(null, null)); + + PhenotypicSubquery phenotypicSubquery = new PhenotypicSubquery(null, List.of(phenotypicFilter), null); + PhenotypicSubquery phenotypicSubquery2 = new PhenotypicSubquery(null, List.of(phenotypicFilter), null); + + PhenotypicSubquery phenotypicQuery = + new PhenotypicSubquery(null, List.of(phenotypicSubquery, phenotypicSubquery2, phenotypicFilter), null); + Query query = new Query(List.of("PATIENT_ID"), authorizationFilters, phenotypicQuery, List.of(), ResultType.COUNT, null, null); + + String serialized = objectMapper.writeValueAsString(query); + System.out.println(serialized); + + Query deserialized = objectMapper.readValue(serialized, Query.class); + + assertEquals(query, deserialized); + } + + @Test + public void generateId_nullId_createNewId() { + Query query = new Query(List.of("PATIENT_ID"), List.of(), null, List.of(), ResultType.COUNT, null, null); + + query = query.generateId(); + assertNotNull(query.id()); + } + + @Test + public void generateId_idExists_doNotReplaceId() { + UUID uuid = UUID.randomUUID(); + Query query = new Query(List.of("PATIENT_ID"), List.of(), null, List.of(), ResultType.COUNT, null, uuid); + + query = query.generateId(); + assertEquals(uuid, query.id()); + } +} diff --git a/libs/pic-sure-commons/pom.xml b/libs/pic-sure-commons/pom.xml new file mode 100644 index 000000000..065abd198 --- /dev/null +++ b/libs/pic-sure-commons/pom.xml @@ -0,0 +1,51 @@ + + + 4.0.0 + + edu.harvard.hms.dbmi.avillach + pic-sure-api + ${revision} + ../../pom.xml + + pic-sure-common + pom + pic-sure-common + + pic-sure-api-model + pic-sure-hpds-model + + + + + io.swagger.core.v3 + swagger-annotations + 2.2.40 + + + com.fasterxml.jackson.core + jackson-databind + 2.19.4 + + + org.slf4j + slf4j-api + 2.0.17 + + + org.junit.jupiter + junit-jupiter + 5.12.2 + test + + + + + + github + GitHub HMS-DBMI Apache Maven Packages + https://maven.pkg.github.com/hms-dbmi/pic-sure-common + + + diff --git a/libs/pic-sure-logging-client/.gitattributes b/libs/pic-sure-logging-client/.gitattributes new file mode 100644 index 000000000..dfe077042 --- /dev/null +++ b/libs/pic-sure-logging-client/.gitattributes @@ -0,0 +1,2 @@ +# Auto detect text files and perform LF normalization +* text=auto diff --git a/libs/pic-sure-logging-client/.github/workflows/ci.yml b/libs/pic-sure-logging-client/.github/workflows/ci.yml new file mode 100644 index 000000000..061723db5 --- /dev/null +++ b/libs/pic-sure-logging-client/.github/workflows/ci.yml @@ -0,0 +1,22 @@ +name: CI + +on: + push: + branches: [main] + pull_request: + branches: [main] + +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - name: Set up JDK 11 + uses: actions/setup-java@v3 + with: + java-version: '11' + distribution: 'temurin' + - name: Check formatting + run: mvn --batch-mode spotless:check + - name: Build and test + run: mvn --batch-mode clean verify diff --git a/libs/pic-sure-logging-client/.github/workflows/label-checker.yml b/libs/pic-sure-logging-client/.github/workflows/label-checker.yml new file mode 100644 index 000000000..ebc834573 --- /dev/null +++ b/libs/pic-sure-logging-client/.github/workflows/label-checker.yml @@ -0,0 +1,19 @@ +name: Label Checker +on: + pull_request: + types: + - opened + - synchronize + - reopened + - labeled + - unlabeled + +jobs: + check_labels: + name: Check labels + runs-on: ubuntu-latest + steps: + - uses: docker://agilepathway/pull-request-label-checker:latest + with: + any_of: breaking-change,enhancement,bug,documentation,ignore-for-release,dependencies + repo_token: ${{ secrets.GITHUB_TOKEN }} diff --git a/libs/pic-sure-logging-client/.github/workflows/publish.yml b/libs/pic-sure-logging-client/.github/workflows/publish.yml new file mode 100644 index 000000000..8ecedd314 --- /dev/null +++ b/libs/pic-sure-logging-client/.github/workflows/publish.yml @@ -0,0 +1,25 @@ +name: Publish to GitHub Packages + +on: + release: + types: [created] + +jobs: + publish: + runs-on: ubuntu-latest + permissions: + contents: read + packages: write + steps: + - uses: actions/checkout@v3 + - name: Set up JDK 11 + uses: actions/setup-java@v3 + with: + java-version: '11' + distribution: 'temurin' + - name: Set version from release tag + run: mvn --batch-mode versions:set -DnewVersion=${{ github.event.release.tag_name }} -DgenerateBackupPoms=false + - name: Publish package + run: mvn --batch-mode deploy + env: + GITHUB_TOKEN: ${{ github.token }} diff --git a/libs/pic-sure-logging-client/.gitignore b/libs/pic-sure-logging-client/.gitignore new file mode 100644 index 000000000..ba80ced84 --- /dev/null +++ b/libs/pic-sure-logging-client/.gitignore @@ -0,0 +1,5 @@ +.DS_Store + +# Maven build output +target/ +!target/*.jar diff --git a/libs/pic-sure-logging-client/README.md b/libs/pic-sure-logging-client/README.md new file mode 100644 index 000000000..864011c91 --- /dev/null +++ b/libs/pic-sure-logging-client/README.md @@ -0,0 +1,345 @@ +# PIC-SURE Logging Client + +Lightweight Java client library for sending structured audit events to the [PIC-SURE Logging](https://github.com/hms-dbmi/PIC-SURE-Logging) service. Used by PIC-SURE platform components (API, Auth, HPDS, UI, etc.) to emit query, login, access, and error events to a centralized logging service. + +- **Java 11+** compatible (works with WildFly 17 through Spring Boot 3.x) +- **Minimal dependencies** — uses `java.net.http.HttpClient` (built into JDK 11+), Jackson, and SLF4J +- **Fire-and-forget** — async sends that never throw or block the caller +- **Thread-safe** — create one instance and share it across your application +- **No-op mode** — gracefully degrades when the logging service isn't configured +- **Environment-based factory** — auto-configures from `LOGGING_SERVICE_URL` and `LOGGING_API_KEY` +- **Secret-safe logging** — exception messages are sanitized to avoid leaking API keys in logs + +## Installation + +Add the GitHub Packages repository and dependency to your `pom.xml`: + +```xml + + + github + GitHub HMS-DBMI Apache Maven Packages + https://maven.pkg.github.com/hms-dbmi/pic-sure-logging-client + + + + + edu.harvard.dbmi.avillach + pic-sure-logging-client + 1.0.0 + +``` + +## Quick Start + +### Using the factory (recommended) + +Set environment variables and let `LoggingClientFactory` handle configuration: + +```bash +export LOGGING_SERVICE_URL=http://pic-sure-logging:80 +export LOGGING_API_KEY=your-api-key +``` + +```java +// Returns a configured client, or no-op if env vars are missing +LoggingClient client = LoggingClientFactory.create("api"); + +client.send(LoggingEvent.builder("QUERY").action("execute").build()); +``` + +### Manual configuration + +```java +import edu.harvard.dbmi.avillach.logging.*; + +// 1. Configure (once at startup) +LoggingClientConfig config = LoggingClientConfig.builder("http://pic-sure-logging:80", apiKey) + .clientType("api") // default client_type for all events + .build(); + +// 2. Create client (thread-safe, share everywhere) +LoggingClient client = new LoggingClient(config); + +// 3. Send events +client.send(LoggingEvent.builder("QUERY").action("execute").build()); +``` + +## Usage Examples + +### Simple event + +```java +client.send(LoggingEvent.builder("LOGIN").action("success").build()); +``` + +### With request context + +```java +client.send(LoggingEvent.builder("QUERY") + .action("execute") + .request(RequestInfo.builder() + .method("POST") + .url("/query/sync") + .srcIp(httpRequest.getRemoteAddr()) + .status(200) + .duration(elapsed) + .build()) + .metadata(Map.of("resourceId", resourceUUID.toString())) + .build()); +``` + +### With JWT passthrough and request correlation + +The logging service can extract user claims from a JWT. Pass the Authorization header through so it can attribute events to users: + +```java +client.send( + LoggingEvent.builder("QUERY") + .action("execute") + .request(RequestInfo.builder() + .method("POST") + .url("/query/sync") + .srcIp(httpRequest.getRemoteAddr()) + .status(200) + .duration(elapsed) + .build()) + .build(), + httpRequest.getHeader("Authorization"), // JWT passthrough + httpRequest.getHeader("X-Request-Id") // request correlation +); +``` + +### Error events + +```java +client.send(LoggingEvent.builder("QUERY") + .action("execute") + .request(RequestInfo.builder() + .method("POST") + .url("/query/sync") + .status(500) + .duration(elapsed) + .build()) + .error(Map.of( + "type", e.getClass().getSimpleName(), + "message", e.getMessage() + )) + .build()); +``` + +### No-op mode + +When the logging service isn't available, use the no-op client. It silently discards all events so calling code doesn't need null checks or conditionals: + +```java +LoggingClient client = LoggingClient.noOp(); +client.isEnabled(); // false +client.send(...); // does nothing +``` + +## Event Model + +### LoggingEvent fields + +| Field | Type | Required | Description | +|---|---|---|---| +| `event_type` | String | Yes | Event category (e.g. `QUERY`, `LOGIN`, `ACCESS`, `ERROR`) | +| `action` | String | No | Specific action (e.g. `execute`, `attempt`, `success`, `failure`, `read`) | +| `client_type` | String | No | Source component (e.g. `api`, `auth`, `hpds`, `ui`). Falls back to config default. | +| `request` | RequestInfo | No | HTTP request details (see below) | +| `metadata` | Map | No | Arbitrary key-value pairs (max 50 keys) | +| `error` | Map | No | Error details (max 20 keys) | + +### RequestInfo fields + +| Field | Type | Description | +|---|---|---| +| `request_id` | String | Correlation ID | +| `method` | String | HTTP method | +| `url` | String | Request URL/path | +| `query_string` | String | Query parameters | +| `src_ip` | String | Client IP address | +| `dest_ip` | String | Destination IP | +| `dest_port` | Integer | Destination port | +| `http_user_agent` | String | User-Agent header | +| `http_content_type` | String | Content-Type header | +| `status` | Integer | HTTP response status | +| `bytes` | Long | Response size in bytes | +| `duration` | Long | Request duration in ms | +| `referrer` | String | Referrer URL | + +### JSON format + +Events are serialized with snake_case field names. Null fields are omitted. + +```json +{ + "event_type": "QUERY", + "action": "execute", + "client_type": "api", + "request": { + "method": "POST", + "url": "/query/sync", + "src_ip": "192.168.1.1", + "status": 200, + "duration": 150 + }, + "metadata": { + "resourceId": "uuid-123" + } +} +``` + +### Graceful degradation + +For consumers where the logging-client JAR may not be on the classpath: + +```java +LoggingClient client; +try { + client = LoggingClientFactory.create("api"); +} catch (NoClassDefFoundError e) { + client = null; +} +``` + +## Integration + +### pic-sure (Java 11, CDI / WildFly) + +```java +@ApplicationScoped +public class LoggingClientProducer { + + @Produces + @ApplicationScoped + public LoggingClient loggingClient() { + return LoggingClientFactory.create("api"); + } +} +``` + +Then inject it anywhere: + +```java +@ApplicationScoped +public class PicsureQueryService { + + @Inject + LoggingClient loggingClient; + + public Response query(QueryRequest queryRequest, HttpServletRequest httpRequest) { + long start = System.currentTimeMillis(); + // ... execute query ... + long duration = System.currentTimeMillis() - start; + + loggingClient.send( + LoggingEvent.builder("QUERY") + .action("execute") + .request(RequestInfo.builder() + .method("POST") + .url(httpRequest.getRequestURI()) + .srcIp(httpRequest.getRemoteAddr()) + .status(200) + .duration(duration) + .build()) + .build(), + httpRequest.getHeader("Authorization"), + httpRequest.getHeader("X-Request-Id") + ); + + return response; + } +} +``` + +### Spring Boot (PSAMA, HPDS, dictionary) + +```java +@Configuration +public class LoggingConfig { + + @Bean + public LoggingClient loggingClient( + @Value("${logging.service.url:}") String url, + @Value("${logging.service.api-key:}") String key) { + if (url.isEmpty() || key.isEmpty()) { + return LoggingClient.noOp(); + } + return new LoggingClient( + LoggingClientConfig.builder(url, key).clientType("auth").build() + ); + } +} +``` + +`application.properties`: + +```properties +logging.service.url=http://pic-sure-logging:80 +logging.service.api-key=${LOGGING_API_KEY:} +``` + +Then autowire it: + +```java +@Service +public class AuthService { + + @Autowired + LoggingClient loggingClient; + + public Token login(Credentials creds, HttpServletRequest httpRequest) { + boolean success = authenticate(creds); + + loggingClient.send(LoggingEvent.builder("LOGIN") + .action(success ? "success" : "failure") + .request(RequestInfo.builder() + .method("POST") + .url("/login") + .srcIp(httpRequest.getRemoteAddr()) + .build()) + .metadata(Map.of("email", creds.getEmail())) + .build()); + + return token; + } +} +``` + +## Configuration Options + +```java +LoggingClientConfig.builder(baseUrl, apiKey) + .clientType("api") // default client_type for all events + .connectTimeout(Duration.ofSeconds(5)) // TCP connect timeout (default: 5s) + .requestTimeout(Duration.ofSeconds(10)) // HTTP request timeout (default: 10s) + .build(); +``` + +## Validation + +The client enforces the same limits as the server: + +- `event_type` is required (enforced at builder time) +- `metadata` map must not exceed 50 keys +- `error` map must not exceed 20 keys + +## Resilience + +- **Async fire-and-forget** — `send()` returns void immediately; the HTTP call runs on the JDK's internal executor +- **Never throws** — serialization errors are caught, connection failures are handled via `CompletableFuture.exceptionally()`, all failures logged at WARN +- **No retries, no circuit breaker** — lost events during outages are acceptable; failing user requests is not +- **No-op fallback** — when env vars are missing, producers return `LoggingClient.noOp()` so existing deployments without the logging service aren't affected + +## Building + +```bash +mvn clean install # build + test +mvn clean install -DskipTests # build only +mvn spotless:apply # auto-format code +mvn spotless:check # check formatting (CI uses this) +``` + +Requires Java 11+. diff --git a/libs/pic-sure-logging-client/code-formatting/eclipse-formatter.xml b/libs/pic-sure-logging-client/code-formatting/eclipse-formatter.xml new file mode 100644 index 000000000..e7cfababf --- /dev/null +++ b/libs/pic-sure-logging-client/code-formatting/eclipse-formatter.xml @@ -0,0 +1,402 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/libs/pic-sure-logging-client/pom.xml b/libs/pic-sure-logging-client/pom.xml new file mode 100644 index 000000000..acdad357f --- /dev/null +++ b/libs/pic-sure-logging-client/pom.xml @@ -0,0 +1,61 @@ + + + 4.0.0 + + + edu.harvard.hms.dbmi.avillach + pic-sure-api + ${revision} + ../../pom.xml + + + + edu.harvard.dbmi.avillach + pic-sure-logging-client + jar + + PIC-SURE Logging Client + Lightweight client library for sending logging events to the PIC-SURE Logging service + + + 2.16.0 + 1.7.36 + + + + + com.fasterxml.jackson.core + jackson-databind + ${jackson.version} + + + org.slf4j + slf4j-api + ${slf4j.version} + + + + + org.junit.jupiter + junit-jupiter + 5.10.1 + test + + + org.slf4j + slf4j-simple + ${slf4j.version} + test + + + + + + github + GitHub HMS-DBMI Apache Maven Packages + https://maven.pkg.github.com/hms-dbmi/pic-sure-logging-client + + + diff --git a/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/AuditEvent.java b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/AuditEvent.java new file mode 100644 index 000000000..8fd7961bf --- /dev/null +++ b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/AuditEvent.java @@ -0,0 +1,14 @@ +package edu.harvard.dbmi.avillach.logging; + +import java.lang.annotation.ElementType; +import java.lang.annotation.Retention; +import java.lang.annotation.RetentionPolicy; +import java.lang.annotation.Target; + +@Target(ElementType.METHOD) +@Retention(RetentionPolicy.RUNTIME) +public @interface AuditEvent { + String type(); + + String action(); +} diff --git a/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/JdkHttpSender.java b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/JdkHttpSender.java new file mode 100644 index 000000000..8d7e47f16 --- /dev/null +++ b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/JdkHttpSender.java @@ -0,0 +1,46 @@ +package edu.harvard.dbmi.avillach.logging; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.net.URI; + +final class JdkHttpSender implements Sender { + + private static final Logger LOG = LoggerFactory.getLogger(LoggingClient.class); + + private final java.net.http.HttpClient httpClient; + + JdkHttpSender(LoggingClientConfig config) { + this.httpClient = java.net.http.HttpClient.newBuilder().connectTimeout(config.getConnectTimeout()).build(); + } + + @Override + public void send( + byte[] body, URI auditEndpoint, LoggingClientConfig config, LoggingEvent resolved, String bearerToken, String requestId + ) { + + java.net.http.HttpRequest.Builder requestBuilder = java.net.http.HttpRequest.newBuilder().uri(auditEndpoint) + .timeout(config.getRequestTimeout()).header("Content-Type", "application/json").header("X-API-Key", config.getApiKey()) + .POST(java.net.http.HttpRequest.BodyPublishers.ofByteArray(body)); + + if (bearerToken != null && !bearerToken.isEmpty()) { + requestBuilder.header("Authorization", bearerToken); + } + if (requestId != null && !requestId.isEmpty()) { + requestBuilder.header("X-Request-Id", requestId); + } + + httpClient.sendAsync(requestBuilder.build(), java.net.http.HttpResponse.BodyHandlers.discarding()).thenAccept(response -> { + if (response.statusCode() >= 300) { + LOG.warn("logging-client: server returned {} for event_type={}", response.statusCode(), resolved.getEventType()); + } + }).exceptionally(throwable -> { + LOG.warn( + "logging-client: failed to send event_type={}: {} - {}", resolved.getEventType(), throwable.getClass().getSimpleName(), + LoggingClient.sanitizeExceptionMessageForSender(throwable) + ); + return null; + }); + } +} diff --git a/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/LoggingClient.java b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/LoggingClient.java new file mode 100644 index 000000000..333825f67 --- /dev/null +++ b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/LoggingClient.java @@ -0,0 +1,144 @@ +package edu.harvard.dbmi.avillach.logging; + +import com.fasterxml.jackson.databind.ObjectMapper; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.net.URI; + +/** + * Thread-safe, fire-and-forget client for the PIC-SURE Logging service.

Create a single instance via the constructor and share it + * across the application. All {@link #send} calls are async and never throw exceptions — failures are logged at WARN level.

Use + * {@link #noOp()} for testing or when the logging service is not configured.

Implements {@link AutoCloseable} so container-managed + * producers (CDI {@code @PreDestroy}, Spring destroy methods) can clean up the internal HTTP client thread pool on redeployment. + */ +public class LoggingClient implements AutoCloseable { + + private static final Logger LOG = LoggerFactory.getLogger(LoggingClient.class); + private static final LoggingClient NO_OP = new NoOpLoggingClient(); + + private final LoggingClientConfig config; + private final Sender sender; + private final ObjectMapper objectMapper; + private final URI auditEndpoint; + + /** + * Create a new LoggingClient with the given configuration. + * + * @param config the client configuration + */ + public LoggingClient(LoggingClientConfig config) { + this.config = config; + this.sender = new JdkHttpSender(config); + // NON_NULL inclusion is declared on the model classes via @JsonInclude. + // The ObjectMapper itself uses default settings so behaviour is consistent + // whether events are serialized here or elsewhere. + this.objectMapper = new ObjectMapper(); + this.auditEndpoint = URI.create(config.getBaseUrl() + "/audit"); + } + + // For NoOp subclass + LoggingClient() { + this.config = null; + this.sender = new NoOpSender(); + this.objectMapper = null; + this.auditEndpoint = null; + } + + /** + * Returns a no-op client that silently discards all events. Use when the logging service is not configured or in tests. + */ + public static LoggingClient noOp() { + return NO_OP; + } + + /** + * Send a logging event asynchronously. Returns immediately. If the config has a default clientType and the event doesn't specify one, + * it will be applied. + * + * @param event the logging event to send + */ + public void send(LoggingEvent event) { + send(event, null, null); + } + + /** + * Send a logging event asynchronously with optional authorization and request ID headers. + * + * @param event the logging event to send + * @param bearerToken optional Authorization header value (e.g. "Bearer xxx") — passed through so the server can extract JWT claims + * @param requestId optional X-Request-Id header for correlation + */ + public void send(LoggingEvent event, String bearerToken, String requestId) { + if (event == null) { + LOG.warn("logging-client: ignoring null event"); + return; + } + + LoggingEvent resolved = resolveClientType(event); + + byte[] body; + try { + body = objectMapper.writeValueAsBytes(resolved); + } catch (Exception e) { + LOG.warn("logging-client: failed to serialize event {}: {}", resolved.getEventType(), e.getMessage()); + return; + } + + sender.send(body, auditEndpoint, config, resolved, bearerToken, requestId); + } + + static String sanitizeExceptionMessageForSender(Throwable t) { + String message = t.getMessage(); + if (message == null) { + return "(no message)"; + } + // Strip anything after a header-like pattern to avoid leaking secrets + int headerIdx = message.indexOf("X-API-Key"); + if (headerIdx >= 0) { + return message.substring(0, headerIdx) + "[headers redacted]"; + } + return message; + } + + private LoggingEvent resolveClientType(LoggingEvent event) { + if (event.getClientType() != null || config.getClientType() == null) { + return event; + } + return event.withClientType(config.getClientType()); + } + + /** + * Returns true if this is a live client (not the no-op instance). + */ + public boolean isEnabled() { + return true; + } + + /** + * Shuts down the internal HTTP client, releasing its thread pool and connections. Safe to call multiple times. After closing, + * subsequent {@link #send} calls will fail asynchronously (errors logged at WARN level).

Call this from CDI {@code @PreDestroy} or + * Spring destroy methods to prevent thread leaks during application redeployment. + */ + @Override + public void close() { + // No-op on JDK 11. On newer JDKs, sender lifecycle can be enhanced if needed. + } + + private static final class NoOpLoggingClient extends LoggingClient { + @Override + public void send(LoggingEvent event) { + // silently discard + } + + @Override + public void send(LoggingEvent event, String bearerToken, String requestId) { + // silently discard + } + + @Override + public boolean isEnabled() { + return false; + } + } +} diff --git a/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/LoggingClientConfig.java b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/LoggingClientConfig.java new file mode 100644 index 000000000..fe69ed011 --- /dev/null +++ b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/LoggingClientConfig.java @@ -0,0 +1,96 @@ +package edu.harvard.dbmi.avillach.logging; + +import java.time.Duration; + +/** + * Configuration for {@link LoggingClient}. Use {@link #builder(String, String)} to construct instances. + */ +public final class LoggingClientConfig { + + private final String baseUrl; + private final String apiKey; + private final String clientType; + private final Duration connectTimeout; + private final Duration requestTimeout; + + private LoggingClientConfig(Builder builder) { + this.baseUrl = normalizeUrl(builder.baseUrl); + this.apiKey = builder.apiKey; + this.clientType = builder.clientType; + this.connectTimeout = builder.connectTimeout; + this.requestTimeout = builder.requestTimeout; + } + + private static String normalizeUrl(String url) { + return url.endsWith("/") ? url.substring(0, url.length() - 1) : url; + } + + public String getBaseUrl() { + return baseUrl; + } + + public String getApiKey() { + return apiKey; + } + + public String getClientType() { + return clientType; + } + + public Duration getConnectTimeout() { + return connectTimeout; + } + + public Duration getRequestTimeout() { + return requestTimeout; + } + + /** + * Create a builder with required parameters. + * + * @param baseUrl the base URL of the PIC-SURE Logging service (e.g. "http://pic-sure-logging:80") + * @param apiKey the API key for authentication + * @return a new builder + */ + public static Builder builder(String baseUrl, String apiKey) { + if (baseUrl == null || baseUrl.trim().isEmpty()) { + throw new IllegalArgumentException("baseUrl is required"); + } + if (apiKey == null || apiKey.trim().isEmpty()) { + throw new IllegalArgumentException("apiKey is required"); + } + return new Builder(baseUrl, apiKey); + } + + public static final class Builder { + private final String baseUrl; + private final String apiKey; + private String clientType; + private Duration connectTimeout = Duration.ofSeconds(5); + private Duration requestTimeout = Duration.ofSeconds(10); + + private Builder(String baseUrl, String apiKey) { + this.baseUrl = baseUrl; + this.apiKey = apiKey; + } + + public Builder clientType(String clientType) { + this.clientType = clientType; + return this; + } + + public Builder connectTimeout(Duration connectTimeout) { + this.connectTimeout = connectTimeout; + return this; + } + + public Builder requestTimeout(Duration requestTimeout) { + this.requestTimeout = requestTimeout; + return this; + } + + public LoggingClientConfig build() { + return new LoggingClientConfig(this); + } + } +} diff --git a/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/LoggingClientFactory.java b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/LoggingClientFactory.java new file mode 100644 index 000000000..c80feb155 --- /dev/null +++ b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/LoggingClientFactory.java @@ -0,0 +1,41 @@ +package edu.harvard.dbmi.avillach.logging; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * Factory that creates a {@link LoggingClient} from environment variables, returning {@link LoggingClient#noOp()} when the service is not + * configured.

Expected environment variables:

  • {@code LOGGING_SERVICE_URL} — base URL of the logging service
    • + *
  • {@code LOGGING_API_KEY} — API key for authentication

Used by Spring Boot apps (HPDS, PSAMA, dictionary). For JAX-RS + * apps on WildFly, use JNDI injection with {@link LoggingClientConfig#builder(String, String)} directly. + */ +public final class LoggingClientFactory { + + private static final Logger LOG = LoggerFactory.getLogger(LoggingClientFactory.class); + + private LoggingClientFactory() {} + + /** + * Create a LoggingClient from environment variables. Returns {@link LoggingClient#noOp()} if the URL or API key is missing. + * + * @param clientType the default client_type for events (e.g. "api", "auth", "hpds") + * @return a configured LoggingClient, or no-op if not configured + */ + public static LoggingClient create(String clientType) { + String url = System.getenv("LOGGING_SERVICE_URL"); + String key = System.getenv("LOGGING_API_KEY"); + + if (url == null || url.trim().isEmpty() || key == null || key.trim().isEmpty()) { + LOG.info("logging-client: LOGGING_SERVICE_URL or LOGGING_API_KEY not set; audit logging disabled"); + return LoggingClient.noOp(); + } + + LoggingClientConfig.Builder builder = LoggingClientConfig.builder(url, key); + if (clientType != null && !clientType.trim().isEmpty()) { + builder.clientType(clientType); + } + + LOG.info("logging-client: configured for {} (clientType={})", url, clientType); + return new LoggingClient(builder.build()); + } +} diff --git a/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/LoggingEvent.java b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/LoggingEvent.java new file mode 100644 index 000000000..2dd3dd8d8 --- /dev/null +++ b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/LoggingEvent.java @@ -0,0 +1,188 @@ +package edu.harvard.dbmi.avillach.logging; + +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; +import com.fasterxml.jackson.annotation.JsonInclude; +import com.fasterxml.jackson.annotation.JsonProperty; + +import java.util.Collections; +import java.util.LinkedHashMap; +import java.util.Map; + +/** + * Mirrors the server-side AuditEvent model. Use {@link #builder(String)} to construct instances. + */ +@JsonIgnoreProperties(ignoreUnknown = true) +@JsonInclude(JsonInclude.Include.NON_NULL) +public final class LoggingEvent { + + private static final int MAX_METADATA_KEYS = 50; + private static final int MAX_ERROR_KEYS = 20; + + @JsonProperty("event_type") + private final String eventType; + + @JsonProperty("action") + private final String action; + + @JsonProperty("client_type") + private final String clientType; + + @JsonProperty("caller") + private final String caller; + + @JsonProperty("session_id") + private final String sessionId; + + @JsonProperty("request") + private final RequestInfo request; + + @JsonProperty("metadata") + private final Map metadata; + + @JsonProperty("error") + private final Map error; + + private LoggingEvent(Builder builder) { + this.eventType = builder.eventType; + this.action = builder.action; + this.clientType = builder.clientType; + this.caller = builder.caller; + this.sessionId = builder.sessionId; + this.request = builder.request; + this.metadata = builder.metadata != null ? Collections.unmodifiableMap(new LinkedHashMap<>(builder.metadata)) : null; + this.error = builder.error != null ? Collections.unmodifiableMap(new LinkedHashMap<>(builder.error)) : null; + } + + // Jackson deserialization constructor + @SuppressWarnings("unused") + private LoggingEvent() { + this.eventType = null; + this.action = null; + this.clientType = null; + this.caller = null; + this.sessionId = null; + this.request = null; + this.metadata = null; + this.error = null; + } + + public String getEventType() { + return eventType; + } + + public String getAction() { + return action; + } + + public String getClientType() { + return clientType; + } + + public String getCaller() { + return caller; + } + + public String getSessionId() { + return sessionId; + } + + public RequestInfo getRequest() { + return request; + } + + public Map getMetadata() { + return metadata; + } + + public Map getError() { + return error; + } + + /** + * Create a builder with the required event type. + * + * @param eventType the event type (e.g. "QUERY", "LOGIN", "ACCESS") + * @return a new builder + */ + public static Builder builder(String eventType) { + if (eventType == null || eventType.trim().isEmpty()) { + throw new IllegalArgumentException("eventType is required"); + } + return new Builder(eventType); + } + + public static final class Builder { + private final String eventType; + private String action; + private String clientType; + private String caller; + private String sessionId; + private RequestInfo request; + private Map metadata; + private Map error; + + private Builder(String eventType) { + this.eventType = eventType; + } + + public Builder action(String action) { + this.action = action; + return this; + } + + public Builder clientType(String clientType) { + this.clientType = clientType; + return this; + } + + public Builder caller(String caller) { + this.caller = caller; + return this; + } + + public Builder sessionId(String sessionId) { + this.sessionId = sessionId; + return this; + } + + public Builder request(RequestInfo request) { + this.request = request; + return this; + } + + public Builder metadata(Map metadata) { + this.metadata = metadata; + return this; + } + + public Builder error(Map error) { + this.error = error; + return this; + } + + public LoggingEvent build() { + if (metadata != null && metadata.size() > MAX_METADATA_KEYS) { + throw new IllegalArgumentException("metadata must not exceed " + MAX_METADATA_KEYS + " keys, got " + metadata.size()); + } + if (error != null && error.size() > MAX_ERROR_KEYS) { + throw new IllegalArgumentException("error must not exceed " + MAX_ERROR_KEYS + " keys, got " + error.size()); + } + return new LoggingEvent(this); + } + } + + /** + * Returns a copy of this event with the given clientType applied. All other fields are preserved. Used by {@link LoggingClient} to + * apply config defaults. + */ + LoggingEvent withClientType(String clientType) { + return LoggingEvent.builder(this.eventType).action(this.action).clientType(clientType).caller(this.caller).sessionId(this.sessionId) + .request(this.request).metadata(this.metadata).error(this.error).build(); + } + + @Override + public String toString() { + return "LoggingEvent{eventType='" + eventType + "', action='" + action + "', clientType='" + clientType + "', caller='" + caller + + "', sessionId='" + sessionId + "'}"; + } +} diff --git a/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/NoOpSender.java b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/NoOpSender.java new file mode 100644 index 000000000..dd3cda82d --- /dev/null +++ b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/NoOpSender.java @@ -0,0 +1,12 @@ +package edu.harvard.dbmi.avillach.logging; + +import java.net.URI; + +final class NoOpSender implements Sender { + @Override + public void send( + byte[] body, URI auditEndpoint, LoggingClientConfig config, LoggingEvent resolved, String bearerToken, String requestId + ) { + // no-op + } +} diff --git a/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/RequestInfo.java b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/RequestInfo.java new file mode 100644 index 000000000..eb76f93b1 --- /dev/null +++ b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/RequestInfo.java @@ -0,0 +1,222 @@ +package edu.harvard.dbmi.avillach.logging; + +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; +import com.fasterxml.jackson.annotation.JsonInclude; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** + * Mirrors the server-side RequestInfo model. Use {@link #builder()} to construct instances. + */ +@JsonIgnoreProperties(ignoreUnknown = true) +@JsonInclude(JsonInclude.Include.NON_NULL) +public final class RequestInfo { + + @JsonProperty("request_id") + private final String requestId; + + @JsonProperty("method") + private final String method; + + @JsonProperty("url") + private final String url; + + @JsonProperty("query_string") + private final String queryString; + + @JsonProperty("src_ip") + private final String srcIp; + + @JsonProperty("dest_ip") + private final String destIp; + + @JsonProperty("dest_port") + private final Integer destPort; + + @JsonProperty("http_user_agent") + private final String httpUserAgent; + + @JsonProperty("http_content_type") + private final String httpContentType; + + @JsonProperty("status") + private final Integer status; + + @JsonProperty("bytes") + private final Long bytes; + + @JsonProperty("duration") + private final Long duration; + + @JsonProperty("referrer") + private final String referrer; + + private RequestInfo(Builder builder) { + this.requestId = builder.requestId; + this.method = builder.method; + this.url = builder.url; + this.queryString = builder.queryString; + this.srcIp = builder.srcIp; + this.destIp = builder.destIp; + this.destPort = builder.destPort; + this.httpUserAgent = builder.httpUserAgent; + this.httpContentType = builder.httpContentType; + this.status = builder.status; + this.bytes = builder.bytes; + this.duration = builder.duration; + this.referrer = builder.referrer; + } + + // Jackson deserialization constructor + @SuppressWarnings("unused") + private RequestInfo() { + this(new Builder()); + } + + public String getRequestId() { + return requestId; + } + + public String getMethod() { + return method; + } + + public String getUrl() { + return url; + } + + public String getQueryString() { + return queryString; + } + + public String getSrcIp() { + return srcIp; + } + + public String getDestIp() { + return destIp; + } + + public Integer getDestPort() { + return destPort; + } + + public String getHttpUserAgent() { + return httpUserAgent; + } + + public String getHttpContentType() { + return httpContentType; + } + + public Integer getStatus() { + return status; + } + + public Long getBytes() { + return bytes; + } + + public Long getDuration() { + return duration; + } + + public String getReferrer() { + return referrer; + } + + public static Builder builder() { + return new Builder(); + } + + public static final class Builder { + private String requestId; + private String method; + private String url; + private String queryString; + private String srcIp; + private String destIp; + private Integer destPort; + private String httpUserAgent; + private String httpContentType; + private Integer status; + private Long bytes; + private Long duration; + private String referrer; + + private Builder() {} + + public Builder requestId(String requestId) { + this.requestId = requestId; + return this; + } + + public Builder method(String method) { + this.method = method; + return this; + } + + public Builder url(String url) { + this.url = url; + return this; + } + + public Builder queryString(String queryString) { + this.queryString = queryString; + return this; + } + + public Builder srcIp(String srcIp) { + this.srcIp = srcIp; + return this; + } + + public Builder destIp(String destIp) { + this.destIp = destIp; + return this; + } + + public Builder destPort(Integer destPort) { + this.destPort = destPort; + return this; + } + + public Builder httpUserAgent(String httpUserAgent) { + this.httpUserAgent = httpUserAgent; + return this; + } + + public Builder httpContentType(String httpContentType) { + this.httpContentType = httpContentType; + return this; + } + + public Builder status(Integer status) { + this.status = status; + return this; + } + + public Builder bytes(Long bytes) { + this.bytes = bytes; + return this; + } + + public Builder duration(Long duration) { + this.duration = duration; + return this; + } + + public Builder referrer(String referrer) { + this.referrer = referrer; + return this; + } + + public RequestInfo build() { + return new RequestInfo(this); + } + } + + @Override + public String toString() { + return "RequestInfo{method='" + method + "', url='" + url + "', status=" + status + "}"; + } +} diff --git a/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/Sender.java b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/Sender.java new file mode 100644 index 000000000..eae5cb451 --- /dev/null +++ b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/Sender.java @@ -0,0 +1,7 @@ +package edu.harvard.dbmi.avillach.logging; + +import java.net.URI; + +interface Sender { + void send(byte[] body, URI auditEndpoint, LoggingClientConfig config, LoggingEvent resolved, String bearerToken, String requestId); +} diff --git a/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/SessionIdResolver.java b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/SessionIdResolver.java new file mode 100644 index 000000000..bf68d4330 --- /dev/null +++ b/libs/pic-sure-logging-client/src/main/java/edu/harvard/dbmi/avillach/logging/SessionIdResolver.java @@ -0,0 +1,54 @@ +package edu.harvard.dbmi.avillach.logging; + +import java.nio.charset.StandardCharsets; +import java.security.MessageDigest; +import java.security.NoSuchAlgorithmException; + +/** + * Resolves a session identifier from an explicit header value, falling back to a deterministic hash of source IP and User-Agent. This + * centralizes session ID logic that was previously duplicated across multiple PIC-SURE services.

The fallback hash uses SHA-256 + * truncated to 16 hex characters (64 bits), providing strong collision resistance even when many users share the same IP (e.g. behind a VPN + * or institutional NAT).

No servlet dependency — accepts raw string values so it works in both javax.servlet (WildFly) and + * jakarta.servlet (Spring Boot) environments. + */ +public final class SessionIdResolver { + + private static final int HASH_HEX_LENGTH = 16; + private static final char[] HEX = "0123456789abcdef".toCharArray(); + + private SessionIdResolver() {} + + /** + * Resolve a session identifier. + * + * @param sessionIdHeader the value of the {@code X-Session-Id} header (may be null or empty) + * @param srcIp the client IP address (may be null) + * @param userAgent the {@code User-Agent} header value (may be null) + * @return a non-null session identifier — either the header value or a 16-char hex SHA-256 hash of IP + User-Agent + */ + public static String resolve(String sessionIdHeader, String srcIp, String userAgent) { + if (sessionIdHeader != null && !sessionIdHeader.isEmpty()) { + return sessionIdHeader; + } + String raw = (srcIp != null ? srcIp : "") + "|" + (userAgent != null ? userAgent : ""); + return sha256Hex(raw, HASH_HEX_LENGTH); + } + + static String sha256Hex(String input, int hexLength) { + try { + MessageDigest digest = MessageDigest.getInstance("SHA-256"); + byte[] hash = digest.digest(input.getBytes(StandardCharsets.UTF_8)); + // Convert first (hexLength / 2) bytes to hex + int bytesNeeded = (hexLength + 1) / 2; + StringBuilder sb = new StringBuilder(hexLength); + for (int i = 0; i < bytesNeeded && i < hash.length; i++) { + sb.append(HEX[(hash[i] >> 4) & 0x0f]); + sb.append(HEX[hash[i] & 0x0f]); + } + return sb.substring(0, hexLength); + } catch (NoSuchAlgorithmException e) { + // SHA-256 is required by the Java spec; this should never happen + throw new RuntimeException("SHA-256 not available", e); + } + } +} diff --git a/libs/pic-sure-logging-client/src/test/java/edu/harvard/dbmi/avillach/logging/AuditEventTest.java b/libs/pic-sure-logging-client/src/test/java/edu/harvard/dbmi/avillach/logging/AuditEventTest.java new file mode 100644 index 000000000..1a9131ba7 --- /dev/null +++ b/libs/pic-sure-logging-client/src/test/java/edu/harvard/dbmi/avillach/logging/AuditEventTest.java @@ -0,0 +1,30 @@ +package edu.harvard.dbmi.avillach.logging; + +import static org.junit.jupiter.api.Assertions.*; +import java.lang.reflect.Method; +import org.junit.jupiter.api.Test; + +class AuditEventTest { + + static class TestController { + @AuditEvent(type = "QUERY", action = "query.submitted") + public void annotatedMethod() {} + + public void unannotatedMethod() {} + } + + @Test + void annotationRetainedAtRuntime() throws Exception { + Method m = TestController.class.getMethod("annotatedMethod"); + AuditEvent event = m.getAnnotation(AuditEvent.class); + assertNotNull(event); + assertEquals("QUERY", event.type()); + assertEquals("query.submitted", event.action()); + } + + @Test + void unannotatedMethodReturnsNull() throws Exception { + Method m = TestController.class.getMethod("unannotatedMethod"); + assertNull(m.getAnnotation(AuditEvent.class)); + } +} diff --git a/libs/pic-sure-logging-client/src/test/java/edu/harvard/dbmi/avillach/logging/LoggingClientFactoryTest.java b/libs/pic-sure-logging-client/src/test/java/edu/harvard/dbmi/avillach/logging/LoggingClientFactoryTest.java new file mode 100644 index 000000000..ee438c815 --- /dev/null +++ b/libs/pic-sure-logging-client/src/test/java/edu/harvard/dbmi/avillach/logging/LoggingClientFactoryTest.java @@ -0,0 +1,34 @@ +package edu.harvard.dbmi.avillach.logging; + +import org.junit.jupiter.api.Test; + +import static org.junit.jupiter.api.Assertions.*; + +class LoggingClientFactoryTest { + + @Test + void returnsNoOpWhenEnvVarsNotSet() { + // In the test environment, LOGGING_SERVICE_URL and LOGGING_API_KEY are not set, + // so create() should return a no-op client. + LoggingClient client = LoggingClientFactory.create("api"); + + assertNotNull(client); + assertFalse(client.isEnabled()); + } + + @Test + void createHandlesNullClientType() { + LoggingClient client = LoggingClientFactory.create(null); + + assertNotNull(client); + assertFalse(client.isEnabled()); + } + + @Test + void createHandlesEmptyClientType() { + LoggingClient client = LoggingClientFactory.create(" "); + + assertNotNull(client); + assertFalse(client.isEnabled()); + } +} diff --git a/libs/pic-sure-logging-client/src/test/java/edu/harvard/dbmi/avillach/logging/LoggingClientTest.java b/libs/pic-sure-logging-client/src/test/java/edu/harvard/dbmi/avillach/logging/LoggingClientTest.java new file mode 100644 index 000000000..586947cb8 --- /dev/null +++ b/libs/pic-sure-logging-client/src/test/java/edu/harvard/dbmi/avillach/logging/LoggingClientTest.java @@ -0,0 +1,193 @@ +package edu.harvard.dbmi.avillach.logging; + +import com.sun.net.httpserver.HttpServer; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +import java.io.IOException; +import java.net.InetSocketAddress; +import java.nio.charset.StandardCharsets; +import java.time.Duration; +import java.util.Map; +import java.util.concurrent.CopyOnWriteArrayList; +import java.util.concurrent.CountDownLatch; +import java.util.concurrent.TimeUnit; + +import static org.junit.jupiter.api.Assertions.*; + +class LoggingClientTest { + + private HttpServer server; + private int port; + private final CopyOnWriteArrayList received = new CopyOnWriteArrayList<>(); + private CountDownLatch latch; + + static class ReceivedRequest { + final String body; + final String contentType; + final String apiKey; + final String authorization; + final String requestId; + final int responseCode; + + ReceivedRequest(String body, String contentType, String apiKey, String authorization, String requestId, int responseCode) { + this.body = body; + this.contentType = contentType; + this.apiKey = apiKey; + this.authorization = authorization; + this.requestId = requestId; + this.responseCode = responseCode; + } + } + + @BeforeEach + void setUp() throws IOException { + received.clear(); + latch = new CountDownLatch(1); + + server = HttpServer.create(new InetSocketAddress(0), 0); + port = server.getAddress().getPort(); + + server.createContext("/audit", exchange -> { + byte[] bodyBytes = exchange.getRequestBody().readAllBytes(); + String body = new String(bodyBytes, StandardCharsets.UTF_8); + String contentType = exchange.getRequestHeaders().getFirst("Content-Type"); + String apiKey = exchange.getRequestHeaders().getFirst("X-API-Key"); + String authorization = exchange.getRequestHeaders().getFirst("Authorization"); + String requestId = exchange.getRequestHeaders().getFirst("X-Request-Id"); + + received.add(new ReceivedRequest(body, contentType, apiKey, authorization, requestId, 202)); + exchange.sendResponseHeaders(202, -1); + exchange.close(); + latch.countDown(); + }); + + server.start(); + } + + @AfterEach + void tearDown() { + if (server != null) { + server.stop(0); + } + } + + private LoggingClient createClient() { + return new LoggingClient( + LoggingClientConfig.builder("http://localhost:" + port, "test-api-key").clientType("api").connectTimeout(Duration.ofSeconds(2)) + .requestTimeout(Duration.ofSeconds(5)).build() + ); + } + + @Test + void sendsEventToServer() throws Exception { + LoggingClient client = createClient(); + + client.send(LoggingEvent.builder("QUERY").action("execute").build()); + + assertTrue(latch.await(5, TimeUnit.SECONDS), "Server should receive request"); + assertEquals(1, received.size()); + + ReceivedRequest req = received.get(0); + assertEquals("application/json", req.contentType); + assertEquals("test-api-key", req.apiKey); + assertTrue(req.body.contains("\"event_type\":\"QUERY\"")); + assertTrue(req.body.contains("\"action\":\"execute\"")); + // Default clientType from config should be applied + assertTrue(req.body.contains("\"client_type\":\"api\"")); + } + + @Test + void sendsAuthorizationAndRequestIdHeaders() throws Exception { + LoggingClient client = createClient(); + + client.send(LoggingEvent.builder("ACCESS").action("read").build(), "Bearer jwt-token-123", "req-abc-456"); + + assertTrue(latch.await(5, TimeUnit.SECONDS), "Server should receive request"); + ReceivedRequest req = received.get(0); + assertEquals("Bearer jwt-token-123", req.authorization); + assertEquals("req-abc-456", req.requestId); + } + + @Test + void eventClientTypeOverridesConfigDefault() throws Exception { + LoggingClient client = createClient(); + + client.send(LoggingEvent.builder("LOGIN").clientType("auth").build()); + + assertTrue(latch.await(5, TimeUnit.SECONDS), "Server should receive request"); + ReceivedRequest req = received.get(0); + assertTrue(req.body.contains("\"client_type\":\"auth\"")); + assertFalse(req.body.contains("\"client_type\":\"api\"")); + } + + @Test + void noOpClientDiscardsSilently() { + LoggingClient client = LoggingClient.noOp(); + + assertDoesNotThrow(() -> client.send(LoggingEvent.builder("TEST").build())); + assertDoesNotThrow(() -> client.send(LoggingEvent.builder("TEST").build(), "Bearer token", "req-id")); + assertDoesNotThrow(() -> client.send(null)); + assertFalse(client.isEnabled()); + } + + @Test + void liveClientIsEnabled() { + LoggingClient client = createClient(); + assertTrue(client.isEnabled()); + } + + @Test + void handleNullEventGracefully() { + LoggingClient client = createClient(); + assertDoesNotThrow(() -> client.send(null)); + } + + @Test + void handlesConnectionFailureGracefully() throws Exception { + LoggingClient client = new LoggingClient( + LoggingClientConfig.builder("http://192.0.2.1:1", "key").connectTimeout(Duration.ofMillis(200)) + .requestTimeout(Duration.ofMillis(500)).build() + ); + + assertDoesNotThrow(() -> client.send(LoggingEvent.builder("TEST").action("fail").build())); + + CountDownLatch errorLatch = new CountDownLatch(1); + errorLatch.await(1, TimeUnit.SECONDS); + } + + @Test + void sendsRequestInfoInBody() throws Exception { + LoggingClient client = createClient(); + + RequestInfo request = + RequestInfo.builder().method("POST").url("/query/sync").srcIp("192.168.1.1").status(200).duration(150L).build(); + + client.send(LoggingEvent.builder("QUERY").action("execute").request(request).metadata(Map.of("resourceId", "uuid-123")).build()); + + assertTrue(latch.await(5, TimeUnit.SECONDS), "Server should receive request"); + ReceivedRequest req = received.get(0); + assertTrue(req.body.contains("\"method\":\"POST\"")); + assertTrue(req.body.contains("\"url\":\"/query/sync\"")); + assertTrue(req.body.contains("\"src_ip\":\"192.168.1.1\"")); + assertTrue(req.body.contains("\"status\":200")); + assertTrue(req.body.contains("\"duration\":150")); + assertTrue(req.body.contains("\"resourceId\":\"uuid-123\"")); + } + + @Test + void handlesServerErrorGracefully() throws Exception { + server.removeContext("/audit"); + server.createContext("/audit", exchange -> { + exchange.sendResponseHeaders(500, -1); + exchange.close(); + latch.countDown(); + }); + + LoggingClient client = createClient(); + + assertDoesNotThrow(() -> client.send(LoggingEvent.builder("TEST").build())); + assertTrue(latch.await(5, TimeUnit.SECONDS), "Server should receive request"); + } +} diff --git a/libs/pic-sure-logging-client/src/test/java/edu/harvard/dbmi/avillach/logging/LoggingEventTest.java b/libs/pic-sure-logging-client/src/test/java/edu/harvard/dbmi/avillach/logging/LoggingEventTest.java new file mode 100644 index 000000000..90fef27c3 --- /dev/null +++ b/libs/pic-sure-logging-client/src/test/java/edu/harvard/dbmi/avillach/logging/LoggingEventTest.java @@ -0,0 +1,247 @@ +package edu.harvard.dbmi.avillach.logging; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import org.junit.jupiter.api.Test; + +import java.util.HashMap; +import java.util.Map; + +import static org.junit.jupiter.api.Assertions.*; + +class LoggingEventTest { + + private final ObjectMapper mapper = new ObjectMapper(); + + @Test + void serializesWithSnakeCaseFieldNames() { + LoggingEvent event = LoggingEvent.builder("QUERY").action("execute").clientType("api").build(); + + JsonNode json = mapper.valueToTree(event); + assertEquals("QUERY", json.get("event_type").asText()); + assertEquals("execute", json.get("action").asText()); + assertEquals("api", json.get("client_type").asText()); + } + + @Test + void serializesCaller() { + LoggingEvent event = LoggingEvent.builder("QUERY").action("execute").caller("PYTHON_ADAPTER").build(); + + JsonNode json = mapper.valueToTree(event); + assertEquals("PYTHON_ADAPTER", json.get("caller").asText()); + } + + @Test + void omitsNullFields() { + LoggingEvent event = LoggingEvent.builder("LOGIN").action("attempt").build(); + + JsonNode json = mapper.valueToTree(event); + assertTrue(json.has("event_type")); + assertTrue(json.has("action")); + assertFalse(json.has("client_type")); + assertFalse(json.has("caller")); + assertFalse(json.has("request")); + assertFalse(json.has("metadata")); + assertFalse(json.has("error")); + } + + @Test + void serializesRequestInfo() { + RequestInfo request = RequestInfo.builder().method("POST").url("/query/sync").srcIp("10.0.0.1").status(200).duration(150L) + .httpContentType("application/json").build(); + + LoggingEvent event = LoggingEvent.builder("QUERY").action("execute").request(request).build(); + + JsonNode json = mapper.valueToTree(event); + JsonNode reqJson = json.get("request"); + + assertNotNull(reqJson); + assertEquals("POST", reqJson.get("method").asText()); + assertEquals("/query/sync", reqJson.get("url").asText()); + assertEquals("10.0.0.1", reqJson.get("src_ip").asText()); + assertEquals(200, reqJson.get("status").asInt()); + assertEquals(150, reqJson.get("duration").asLong()); + assertEquals("application/json", reqJson.get("http_content_type").asText()); + + // null fields should be absent + assertFalse(reqJson.has("query_string")); + assertFalse(reqJson.has("dest_ip")); + assertFalse(reqJson.has("referrer")); + } + + @Test + void serializesMetadata() { + Map metadata = new HashMap<>(); + metadata.put("resourceId", "abc-123"); + metadata.put("queryCount", 5); + + LoggingEvent event = LoggingEvent.builder("QUERY").metadata(metadata).build(); + + JsonNode json = mapper.valueToTree(event); + JsonNode metaJson = json.get("metadata"); + + assertNotNull(metaJson); + assertEquals("abc-123", metaJson.get("resourceId").asText()); + assertEquals(5, metaJson.get("queryCount").asInt()); + } + + @Test + void serializesError() { + Map error = new HashMap<>(); + error.put("message", "Not found"); + error.put("code", 404); + + LoggingEvent event = LoggingEvent.builder("ERROR").error(error).build(); + + JsonNode json = mapper.valueToTree(event); + JsonNode errorJson = json.get("error"); + + assertNotNull(errorJson); + assertEquals("Not found", errorJson.get("message").asText()); + assertEquals(404, errorJson.get("code").asInt()); + } + + @Test + void requiresEventType() { + assertThrows(IllegalArgumentException.class, () -> LoggingEvent.builder(null)); + assertThrows(IllegalArgumentException.class, () -> LoggingEvent.builder("")); + assertThrows(IllegalArgumentException.class, () -> LoggingEvent.builder(" ")); + } + + @Test + void rejectsMetadataExceeding50Keys() { + Map metadata = new HashMap<>(); + for (int i = 0; i < 51; i++) { + metadata.put("key" + i, "value"); + } + + assertThrows(IllegalArgumentException.class, () -> LoggingEvent.builder("TEST").metadata(metadata).build()); + } + + @Test + void rejectsErrorExceeding20Keys() { + Map error = new HashMap<>(); + for (int i = 0; i < 21; i++) { + error.put("key" + i, "value"); + } + + assertThrows(IllegalArgumentException.class, () -> LoggingEvent.builder("TEST").error(error).build()); + } + + @Test + void metadataIsImmutableAfterBuild() { + Map metadata = new HashMap<>(); + metadata.put("key", "value"); + + LoggingEvent event = LoggingEvent.builder("TEST").metadata(metadata).build(); + + assertThrows(UnsupportedOperationException.class, () -> event.getMetadata().put("newKey", "newValue")); + } + + @Test + void deserializesFromServerFormat() throws Exception { + String json = "{\"event_type\":\"QUERY\",\"action\":\"execute\",\"client_type\":\"api\",\"caller\":\"PYTHON_ADAPTER\"," + + "\"request\":{\"method\":\"POST\",\"url\":\"/query\",\"src_ip\":\"127.0.0.1\",\"status\":200}}"; + + LoggingEvent event = mapper.readValue(json, LoggingEvent.class); + + assertEquals("QUERY", event.getEventType()); + assertEquals("execute", event.getAction()); + assertEquals("api", event.getClientType()); + assertEquals("PYTHON_ADAPTER", event.getCaller()); + assertNotNull(event.getRequest()); + assertEquals("POST", event.getRequest().getMethod()); + assertEquals("/query", event.getRequest().getUrl()); + assertEquals("127.0.0.1", event.getRequest().getSrcIp()); + assertEquals(200, event.getRequest().getStatus()); + } + + @Test + void roundTripSerialization() throws Exception { + RequestInfo request = RequestInfo.builder().method("GET").url("/info").status(200).duration(42L).build(); + + Map metadata = new HashMap<>(); + metadata.put("key", "value"); + + LoggingEvent original = LoggingEvent.builder("ACCESS").action("read").clientType("ui").request(request).metadata(metadata).build(); + + String json = mapper.writeValueAsString(original); + LoggingEvent deserialized = mapper.readValue(json, LoggingEvent.class); + + assertEquals(original.getEventType(), deserialized.getEventType()); + assertEquals(original.getAction(), deserialized.getAction()); + assertEquals(original.getClientType(), deserialized.getClientType()); + assertEquals(original.getRequest().getMethod(), deserialized.getRequest().getMethod()); + assertEquals(original.getRequest().getUrl(), deserialized.getRequest().getUrl()); + assertEquals(original.getRequest().getStatus(), deserialized.getRequest().getStatus()); + assertEquals(original.getRequest().getDuration(), deserialized.getRequest().getDuration()); + assertEquals("value", deserialized.getMetadata().get("key")); + } + + @Test + void serializesSessionId() { + LoggingEvent event = LoggingEvent.builder("QUERY").action("execute").sessionId("sess-abc").build(); + + JsonNode json = mapper.valueToTree(event); + assertEquals("sess-abc", json.get("session_id").asText()); + } + + @Test + void omitsNullSessionId() { + LoggingEvent event = LoggingEvent.builder("QUERY").action("execute").build(); + + JsonNode json = mapper.valueToTree(event); + assertFalse(json.has("session_id")); + } + + @Test + void roundTripPreservesSessionId() throws Exception { + LoggingEvent original = LoggingEvent.builder("ACCESS").action("read").sessionId("sess-xyz").build(); + + String json = mapper.writeValueAsString(original); + LoggingEvent deserialized = mapper.readValue(json, LoggingEvent.class); + + assertEquals("sess-xyz", deserialized.getSessionId()); + } + + @Test + void withClientTypePreservesSessionId() { + LoggingEvent original = LoggingEvent.builder("QUERY").action("execute").sessionId("sess-123").build(); + LoggingEvent copy = original.withClientType("api"); + + assertEquals("sess-123", copy.getSessionId()); + assertEquals("api", copy.getClientType()); + } + + @Test + void withClientTypePreservesCaller() { + LoggingEvent original = LoggingEvent.builder("QUERY").action("execute").caller("PYTHON_ADAPTER").build(); + LoggingEvent copy = original.withClientType("api"); + + assertEquals("PYTHON_ADAPTER", copy.getCaller()); + assertEquals("api", copy.getClientType()); + } + + @Test + void requestInfoAllFields() { + RequestInfo request = RequestInfo.builder().requestId("req-123").method("POST").url("/query/sync").queryString("limit=100") + .srcIp("10.0.0.1").destIp("10.0.0.2").destPort(8080).httpUserAgent("PIC-SURE/2.0").httpContentType("application/json") + .status(200).bytes(4096L).duration(250L).referrer("https://picsure.example.com").build(); + + JsonNode json = mapper.valueToTree(request); + + assertEquals("req-123", json.get("request_id").asText()); + assertEquals("POST", json.get("method").asText()); + assertEquals("/query/sync", json.get("url").asText()); + assertEquals("limit=100", json.get("query_string").asText()); + assertEquals("10.0.0.1", json.get("src_ip").asText()); + assertEquals("10.0.0.2", json.get("dest_ip").asText()); + assertEquals(8080, json.get("dest_port").asInt()); + assertEquals("PIC-SURE/2.0", json.get("http_user_agent").asText()); + assertEquals("application/json", json.get("http_content_type").asText()); + assertEquals(200, json.get("status").asInt()); + assertEquals(4096, json.get("bytes").asLong()); + assertEquals(250, json.get("duration").asLong()); + assertEquals("https://picsure.example.com", json.get("referrer").asText()); + } +} diff --git a/libs/pic-sure-logging-client/src/test/java/edu/harvard/dbmi/avillach/logging/SessionIdResolverTest.java b/libs/pic-sure-logging-client/src/test/java/edu/harvard/dbmi/avillach/logging/SessionIdResolverTest.java new file mode 100644 index 000000000..27f3867ff --- /dev/null +++ b/libs/pic-sure-logging-client/src/test/java/edu/harvard/dbmi/avillach/logging/SessionIdResolverTest.java @@ -0,0 +1,66 @@ +package edu.harvard.dbmi.avillach.logging; + +import org.junit.jupiter.api.Test; + +import static org.junit.jupiter.api.Assertions.*; + +class SessionIdResolverTest { + + @Test + void returnsHeaderValueWhenPresent() { + assertEquals("my-session", SessionIdResolver.resolve("my-session", "10.0.0.1", "Mozilla/5.0")); + } + + @Test + void fallsBackToHashWhenHeaderIsNull() { + String result = SessionIdResolver.resolve(null, "10.0.0.1", "Mozilla/5.0"); + assertNotNull(result); + assertEquals(16, result.length(), "SHA-256 truncated hash should be 16 hex chars"); + // Should be valid hex + assertDoesNotThrow(() -> Long.parseUnsignedLong(result, 16)); + } + + @Test + void fallsBackToHashWhenHeaderIsEmpty() { + String result = SessionIdResolver.resolve("", "10.0.0.1", "Mozilla/5.0"); + assertNotNull(result); + assertEquals(16, result.length()); + } + + @Test + void hashIsDeterministic() { + String first = SessionIdResolver.resolve(null, "10.0.0.1", "Mozilla/5.0"); + String second = SessionIdResolver.resolve(null, "10.0.0.1", "Mozilla/5.0"); + assertEquals(first, second); + } + + @Test + void differentInputsProduceDifferentHashes() { + String hash1 = SessionIdResolver.resolve(null, "10.0.0.1", "Mozilla/5.0"); + String hash2 = SessionIdResolver.resolve(null, "10.0.0.2", "Mozilla/5.0"); + assertNotEquals(hash1, hash2); + } + + @Test + void handlesNullIpAndUserAgent() { + String result = SessionIdResolver.resolve(null, null, null); + assertNotNull(result); + assertEquals(16, result.length()); + // Should be the SHA-256 of "|" + assertEquals(SessionIdResolver.sha256Hex("|", 16), result); + } + + @Test + void hashIsLowercaseHex() { + String result = SessionIdResolver.resolve(null, "10.0.0.1", "Mozilla/5.0"); + assertTrue(result.matches("[0-9a-f]{16}"), "Hash should be 16 lowercase hex characters, got: " + result); + } + + @Test + void sameIpDifferentUserAgentProducesDifferentHash() { + // Important for VPN scenarios where many users share an IP + String hash1 = SessionIdResolver.resolve(null, "10.0.0.1", "Mozilla/5.0 (Windows NT 10.0)"); + String hash2 = SessionIdResolver.resolve(null, "10.0.0.1", "Mozilla/5.0 (Macintosh; Intel Mac OS X)"); + assertNotEquals(hash1, hash2); + } +} diff --git a/libs/pic-sure-spring-commons/pom.xml b/libs/pic-sure-spring-commons/pom.xml new file mode 100644 index 000000000..435c980f2 --- /dev/null +++ b/libs/pic-sure-spring-commons/pom.xml @@ -0,0 +1,75 @@ + + + 4.0.0 + + + edu.harvard.hms.dbmi.avillach + pic-sure-api + ${revision} + ../../pom.xml + + + pic-sure-spring-commons + jar + + PIC-SURE Spring Commons + DB-free shared library for gateway/WAR auth and audit: PicsureException, audit filter base, GatewayUser identity, RequestIdFilter + + + + org.springframework.boot + spring-boot-starter-web + provided + + + edu.harvard.dbmi.avillach + pic-sure-logging-client + + + com.fasterxml.jackson.core + jackson-databind + provided + + + org.slf4j + slf4j-api + provided + + + org.springframework.boot + spring-boot-starter-security + + true + + + org.springframework.boot + spring-boot-starter-actuator + + true + + + + + org.springframework.boot + spring-boot-starter-test + test + + + io.micrometer + micrometer-registry-prometheus + test + + + + + + github + GitHub HMS-DBMI Apache Maven Packages + https://maven.pkg.github.com/hms-dbmi/pic-sure + + + diff --git a/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditContext.java b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditContext.java new file mode 100644 index 000000000..3329d4168 --- /dev/null +++ b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditContext.java @@ -0,0 +1,25 @@ +package edu.harvard.hms.dbmi.avillach.commons.audit; + +import java.util.HashMap; +import java.util.Map; + +/** + * Per-request holder for audit metadata (username, resource id, etc.), modeled on the legacy + * {@code edu.harvard.dbmi.avillach.service.AuditContext}. Services populate this with domain-specific context; {@link AuditLoggingFilter} + * merges it into the emitted logging event's metadata. No-arg-constructable so callers can scope one instance per request without a DI + * container (e.g. a request-scoped Spring bean, or plain {@code new} in a filter chain). + */ +public class AuditContext { + + private final Map metadata = new HashMap<>(); + + public void put(String key, Object value) { + if (key != null && value != null) { + metadata.put(key, value); + } + } + + public Map getMetadata() { + return metadata; + } +} diff --git a/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditLoggingFilter.java b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditLoggingFilter.java new file mode 100644 index 000000000..0ceaa29e5 --- /dev/null +++ b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditLoggingFilter.java @@ -0,0 +1,141 @@ +package edu.harvard.hms.dbmi.avillach.commons.audit; + +import java.io.IOException; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.slf4j.MDC; +import org.springframework.web.filter.OncePerRequestFilter; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.dbmi.avillach.logging.RequestInfo; +import edu.harvard.dbmi.avillach.logging.SessionIdResolver; +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +/** + * Base {@link OncePerRequestFilter} that maps each non-skipped request to an {@link AuditRoute} and emits an audit event via the + * {@link LoggingClient}, mirroring the legacy {@code edu.harvard.dbmi.avillach.security.AuditLoggingFilter}'s route table and skip-list + * semantics (DB-free, no JAX-RS). {@code shouldNotFilter} is deliberately {@code protected} and non-final so gateway subclasses can widen + * the skip set (e.g. interim/pass-through paths). + */ +public class AuditLoggingFilter extends OncePerRequestFilter { + + private static final Logger logger = LoggerFactory.getLogger(AuditLoggingFilter.class); + + private final LoggingClient client; + private final AuditRouteTable routes; + private final AuditContext audit; + private final List skipContains; + + public AuditLoggingFilter(LoggingClient client, AuditRouteTable routes, AuditContext audit, List skipContains) { + this.client = client; + this.routes = routes; + this.audit = audit; + this.skipContains = skipContains != null ? List.copyOf(skipContains) : List.of(); + } + + @Override + protected boolean shouldNotFilter(HttpServletRequest request) { + if (client == null || !client.isEnabled()) { + return true; + } + if ("OPTIONS".equalsIgnoreCase(request.getMethod())) { + return true; + } + + String path = request.getRequestURI(); + if (path == null) { + return false; + } + if (path.endsWith("/system/status") || path.endsWith("/openapi.json")) { + return true; + } + for (String skip : skipContains) { + if (skip != null && path.contains(skip)) { + return true; + } + } + return false; + } + + @Override + protected void doFilterInternal(HttpServletRequest request, HttpServletResponse response, FilterChain filterChain) + throws ServletException, IOException { + long startTime = System.currentTimeMillis(); + try { + filterChain.doFilter(request, response); + } finally { + try { + emit(request, response, System.currentTimeMillis() - startTime); + } catch (Exception e) { + logger.warn("AuditLoggingFilter failed to log request", e); + } + } + } + + private void emit(HttpServletRequest request, HttpServletResponse response, long duration) { + String path = request.getRequestURI(); + String method = request.getMethod(); + + AuditRoute route = routes != null ? routes.match(path, method).orElse(null) : null; + String eventType = route != null ? route.getEventType() : "OTHER"; + String action = route != null ? route.getAction() : method; + + String requestId = request.getHeader("X-Request-Id"); + if (requestId == null || requestId.isBlank()) { + requestId = MDC.get("requestId"); + } + + String srcIp = resolveSourceIp(request); + String userAgent = request.getHeader("User-Agent"); + String sessionId = SessionIdResolver.resolve(request.getHeader("X-Session-Id"), srcIp, userAgent); + + RequestInfo requestInfo = RequestInfo.builder().requestId(requestId).method(method).url(path).queryString(request.getQueryString()) + .srcIp(srcIp).status(response.getStatus()).duration(duration).httpUserAgent(userAgent) + .httpContentType(response.getContentType()).referrer(request.getHeader("Referer")).build(); + + Map metadata = new LinkedHashMap<>(); + if (audit != null) { + audit.getMetadata().forEach(metadata::putIfAbsent); + } + + LoggingEvent.Builder eventBuilder = LoggingEvent.builder(eventType).action(action).sessionId(sessionId).request(requestInfo) + .metadata(metadata.isEmpty() ? null : metadata); + + String clientType = request.getHeader("X-Client-Type"); + if (clientType != null && !clientType.isBlank()) { + eventBuilder.caller(clientType); + } + + if (response.getStatus() >= 400) { + Map error = new LinkedHashMap<>(); + error.put("status", response.getStatus()); + error.put("error_type", response.getStatus() >= 500 ? "server_error" : "client_error"); + eventBuilder.error(error); + } + + LoggingEvent event = eventBuilder.build(); + + String authHeader = request.getHeader("Authorization"); + if (authHeader != null || requestId != null) { + client.send(event, authHeader, requestId); + } else { + client.send(event); + } + } + + private String resolveSourceIp(HttpServletRequest request) { + String forwardedFor = request.getHeader("X-Forwarded-For"); + if (forwardedFor != null && !forwardedFor.isBlank()) { + return forwardedFor.split(",")[0].trim(); + } + return request.getRemoteAddr(); + } +} diff --git a/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditRoute.java b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditRoute.java new file mode 100644 index 000000000..718565d6d --- /dev/null +++ b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditRoute.java @@ -0,0 +1,54 @@ +package edu.harvard.hms.dbmi.avillach.commons.audit; + +import java.util.regex.Pattern; + +/** + * A single audit route rule, re-expressing the shape of the legacy AuditLoggingFilter's route table (a {@code Pattern} plus an optional + * HTTP method, mapped to an {@code eventType}/{@code action} pair). {@code method == null} means "any method". {@code useFind} selects + * {@code matcher.find()} (pattern may match anywhere in the path) vs {@code matcher.matches()} (pattern must match the whole path). + */ +public final class AuditRoute { + + private final Pattern pattern; + private final String method; + private final String eventType; + private final String action; + private final boolean useFind; + + public AuditRoute(Pattern pattern, String method, String eventType, String action) { + this(pattern, method, eventType, action, false); + } + + public AuditRoute(Pattern pattern, String method, String eventType, String action, boolean useFind) { + this.pattern = pattern; + this.method = method; + this.eventType = eventType; + this.action = action; + this.useFind = useFind; + } + + public boolean matches(String path, String httpMethod) { + boolean patternMatch = useFind ? pattern.matcher(path).find() : pattern.matcher(path).matches(); + return patternMatch && (method == null || method.equals(httpMethod)); + } + + public Pattern getPattern() { + return pattern; + } + + public String getMethod() { + return method; + } + + public String getEventType() { + return eventType; + } + + public String getAction() { + return action; + } + + public boolean isUseFind() { + return useFind; + } +} diff --git a/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditRouteTable.java b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditRouteTable.java new file mode 100644 index 000000000..2d73f0c2d --- /dev/null +++ b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditRouteTable.java @@ -0,0 +1,21 @@ +package edu.harvard.hms.dbmi.avillach.commons.audit; + +import java.util.List; +import java.util.Optional; + +/** + * First-match-wins lookup over an ordered list of {@link AuditRoute}s. Order matters for overlapping patterns (e.g. {@code /query/sync} + * must be listed before the more general {@code /query}). + */ +public final class AuditRouteTable { + + private final List routes; + + public AuditRouteTable(List routes) { + this.routes = List.copyOf(routes); + } + + public Optional match(String path, String method) { + return routes.stream().filter(route -> route.matches(path, method)).findFirst(); + } +} diff --git a/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/error/GatewayExceptionAdvice.java b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/error/GatewayExceptionAdvice.java new file mode 100644 index 000000000..5f6a797d5 --- /dev/null +++ b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/error/GatewayExceptionAdvice.java @@ -0,0 +1,28 @@ +package edu.harvard.hms.dbmi.avillach.commons.error; + +import java.util.LinkedHashMap; +import java.util.Map; + +import org.slf4j.MDC; +import org.springframework.http.ResponseEntity; +import org.springframework.web.bind.annotation.ExceptionHandler; +import org.springframework.web.bind.annotation.RestControllerAdvice; + +/** + * Base {@code @RestControllerAdvice} mapping {@link PicsureException} to its carried status with an additive JSON body of + * {@code {errorType, message, requestId}}, where {@code requestId} comes from {@code MDC[requestId]} (set by + * {@code edu.harvard.hms.dbmi.avillach.commons.request.RequestIdFilter}). Kept minimal and non-final so gateway/WAR call sites can extend + * it with additional {@code @ExceptionHandler}s. + */ +@RestControllerAdvice +public class GatewayExceptionAdvice { + + @ExceptionHandler(PicsureException.class) + public ResponseEntity> handlePicsureException(PicsureException exception) { + Map body = new LinkedHashMap<>(); + body.put("errorType", exception.getErrorType()); + body.put("message", exception.getMessage()); + body.put("requestId", MDC.get("requestId")); + return ResponseEntity.status(exception.getStatus()).body(body); + } +} diff --git a/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/error/PicsureException.java b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/error/PicsureException.java new file mode 100644 index 000000000..ea520f5e1 --- /dev/null +++ b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/error/PicsureException.java @@ -0,0 +1,27 @@ +package edu.harvard.hms.dbmi.avillach.commons.error; + +import org.springframework.http.HttpStatus; + +/** + * Fail-closed exception used by the gateway's auth filters. Carries an HTTP status and a machine-readable error type so callers (e.g. + * {@link GatewayExceptionAdvice}) can render a consistent error body without inspecting the exception message. + */ +public class PicsureException extends RuntimeException { + + private final HttpStatus status; + private final String errorType; + + public PicsureException(HttpStatus status, String errorType, String message) { + super(message); + this.status = status; + this.errorType = errorType; + } + + public HttpStatus getStatus() { + return status; + } + + public String getErrorType() { + return errorType; + } +} diff --git a/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/identity/GatewayUser.java b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/identity/GatewayUser.java new file mode 100644 index 000000000..c664e1821 --- /dev/null +++ b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/identity/GatewayUser.java @@ -0,0 +1,45 @@ +package edu.harvard.hms.dbmi.avillach.commons.identity; + +import java.util.Set; + +/** + * Immutable holder for the identity the gateway has already resolved (via header injection or introspection) and forwards downstream. + * {@code privileges} are the real {@code @RolesAllowed} signal; {@code roles} is carried through as an opaque, comma-joined string for + * logging/back-compat. + */ +public final class GatewayUser { + + private final String userId; + private final String subject; + private final String email; + private final String roles; + private final Set privileges; + + public GatewayUser(String userId, String subject, String email, String roles, Set privileges) { + this.userId = userId; + this.subject = subject; + this.email = email; + this.roles = roles; + this.privileges = privileges == null ? Set.of() : Set.copyOf(privileges); + } + + public String getUserId() { + return userId; + } + + public String getSubject() { + return subject; + } + + public String getEmail() { + return email; + } + + public String getRoles() { + return roles; + } + + public Set getPrivileges() { + return privileges; + } +} diff --git a/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/identity/GatewayUserResolver.java b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/identity/GatewayUserResolver.java new file mode 100644 index 000000000..2058f4409 --- /dev/null +++ b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/identity/GatewayUserResolver.java @@ -0,0 +1,50 @@ +package edu.harvard.hms.dbmi.avillach.commons.identity; + +import java.util.Arrays; +import java.util.LinkedHashSet; +import java.util.Optional; +import java.util.Set; +import java.util.stream.Collectors; + +import jakarta.servlet.http.HttpServletRequest; + +/** + * Header-name contract between the gateway's identity/introspection filters (which set these headers on the way in) and the WAR's + * GatewayHeaderFilter (which rebuilds the SecurityContext from them). + */ +public final class GatewayUserResolver { + + public static final String HEADER_USER_ID = "X-User-Id"; + public static final String HEADER_USER_SUBJECT = "X-User-Subject"; + public static final String HEADER_USER_EMAIL = "X-User-Email"; + public static final String HEADER_USER_ROLES = "X-User-Roles"; + public static final String HEADER_USER_PRIVILEGES = "X-User-Privileges"; + + private GatewayUserResolver() {} + + /** + * Builds a {@link GatewayUser} from the identity headers on the given request. Empty when {@link #HEADER_USER_ID} is missing or blank, + * since a request without a resolved user id carries no identity to rebuild. + */ + public static Optional resolve(HttpServletRequest request) { + String userId = request.getHeader(HEADER_USER_ID); + if (userId == null || userId.isBlank()) { + return Optional.empty(); + } + + String subject = request.getHeader(HEADER_USER_SUBJECT); + String email = request.getHeader(HEADER_USER_EMAIL); + String roles = request.getHeader(HEADER_USER_ROLES); + Set privileges = splitPrivileges(request.getHeader(HEADER_USER_PRIVILEGES)); + + return Optional.of(new GatewayUser(userId, subject, email, roles, privileges)); + } + + private static Set splitPrivileges(String header) { + if (header == null || header.isBlank()) { + return Set.of(); + } + return Arrays.stream(header.split(",")).map(String::trim).filter(value -> !value.isEmpty()) + .collect(Collectors.toCollection(LinkedHashSet::new)); + } +} diff --git a/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/request/RequestIdFilter.java b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/request/RequestIdFilter.java new file mode 100644 index 000000000..211644013 --- /dev/null +++ b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/request/RequestIdFilter.java @@ -0,0 +1,38 @@ +package edu.harvard.hms.dbmi.avillach.commons.request; + +import java.io.IOException; +import java.util.UUID; + +import org.slf4j.MDC; +import org.springframework.web.filter.OncePerRequestFilter; + +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +/** + * Assigns or propagates {@code X-Request-Id}: echoed on the response and bound to {@code MDC[requestId]} so every log line of the request + * carries it, and so {@link edu.harvard.hms.dbmi.avillach.commons.error.GatewayExceptionAdvice} can surface it in error bodies. + */ +public class RequestIdFilter extends OncePerRequestFilter { + + public static final String HEADER = "X-Request-Id"; + public static final String MDC_KEY = "requestId"; + + @Override + protected void doFilterInternal(HttpServletRequest request, HttpServletResponse response, FilterChain filterChain) + throws ServletException, IOException { + String requestId = request.getHeader(HEADER); + if (requestId == null || requestId.isBlank()) { + requestId = UUID.randomUUID().toString(); + } + MDC.put(MDC_KEY, requestId); + response.setHeader(HEADER, requestId); + try { + filterChain.doFilter(request, response); + } finally { + MDC.remove(MDC_KEY); + } + } +} diff --git a/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/security/ActuatorSecurityHelper.java b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/security/ActuatorSecurityHelper.java new file mode 100644 index 000000000..b54b659ad --- /dev/null +++ b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/security/ActuatorSecurityHelper.java @@ -0,0 +1,134 @@ +package edu.harvard.hms.dbmi.avillach.commons.security; + +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; +import org.springframework.boot.actuate.autoconfigure.security.servlet.EndpointRequest; +import org.springframework.security.authentication.UsernamePasswordAuthenticationToken; +import org.springframework.security.config.annotation.web.builders.HttpSecurity; +import org.springframework.security.core.authority.AuthorityUtils; +import org.springframework.security.core.context.SecurityContext; +import org.springframework.security.core.context.SecurityContextHolder; +import org.springframework.security.web.SecurityFilterChain; +import org.springframework.security.web.access.intercept.AuthorizationFilter; +import org.springframework.web.filter.OncePerRequestFilter; + +import java.io.IOException; +import java.nio.charset.StandardCharsets; + +/** + * Shared actuator access control for PIC-SURE Spring Boot services behind the gateway. + * + *

The returned chain matches EVERY actuator endpoint (health included) and is gated by {@link TokenAuthenticationFilter}:

  • Valid + * X-Application-Token -> install a synthetic authenticated principal (ROLE_ACTUATOR), continue. Because a principal is now present, + * {@code show-details: when_authorized} reveals component detail on {@code /actuator/health}, and protected endpoints + * (prometheus/metrics/info) are reachable.
  • Shallow health / liveness / readiness without a token -> continue UNauthenticated -> + * the load balancer gets shallow {@code {"status":"UP"}} only.
  • Any other actuator path without a valid token -> 401 + * (short-circuit; guarantees 401, not 403).
  • require-token=false -> authenticate unconditionally and permit all (AIO dev / + * rollback).
  • Token unconfigured (blank) while require-token=true -> fail closed: the token can never match (a blank configured + * token is never treated as a valid credential, even against a blank header), so every protected endpoint 401s; shallow + * health/liveness/readiness remain open regardless.
+ * + *

Register the chain at {@code @Order(0)}; the service's main chain must be {@code @Order(>=1)}. + */ +public final class ActuatorSecurityHelper { + + /** + * Authority granted to a valid-token caller. With {@code show-details: when_authorized} and no {@code management.endpoint.health.roles} + * configured, an authenticated principal suffices to reveal detail; the authority documents intent and lets operators tighten via that + * property if desired. + */ + public static final String ACTUATOR_AUTHORITY = "ROLE_ACTUATOR"; + + /** Synthetic principal name for the token-authenticated monitoring caller. */ + public static final String ACTUATOR_PRINCIPAL = "actuator-monitor"; + + private ActuatorSecurityHelper() {} + + public static SecurityFilterChain actuatorChain(HttpSecurity http, ActuatorTokenProperties props) throws Exception { + return http.securityMatcher(EndpointRequest.toAnyEndpoint()) // ALL actuator endpoints, health included + .csrf(csrf -> csrf.disable()) + // The TokenAuthenticationFilter is the real gate (it 401s directly and installs the principal); + // the authorization layer permits and lets the filter decide. Spring Security's default + // SecurityContextHolderAwareRequestFilter wraps the request so HealthEndpoint's when_authorized + // check sees the principal the filter set into the SecurityContext. + .authorizeHttpRequests(auth -> auth.anyRequest().permitAll()) + .addFilterBefore(new TokenAuthenticationFilter(props), AuthorizationFilter.class).build(); + } + + static final class TokenAuthenticationFilter extends OncePerRequestFilter { + + private final ActuatorTokenProperties props; + + TokenAuthenticationFilter(ActuatorTokenProperties props) { + this.props = props; + } + + @Override + protected void doFilterInternal(HttpServletRequest req, HttpServletResponse resp, FilterChain chain) + throws ServletException, IOException { + + // Rollback / AIO dev: no enforcement. Authenticate so detail is visible locally, permit all. + if (!props.isRequireToken()) { + authenticate(); + chain.doFilter(req, resp); + return; + } + + String header = req.getHeader(props.getHeaderName()); + if (hasConfiguredToken() && header != null && constantTimeEquals(header, props.getToken())) { + authenticate(); // valid token -> reveal detail + reach protected endpoints + chain.doFilter(req, resp); + return; + } + + if (isOpenHealthPath(req)) { // shallow health + LB probe groups stay open + chain.doFilter(req, resp); // no principal -> shallow status only + return; + } + + resp.sendError(HttpServletResponse.SC_UNAUTHORIZED); // prometheus/metrics/info/links/etc. + } + + /** + * A blank/unset configured token is never a valid credential — fail closed rather than let a blank header match a blank token. + */ + private boolean hasConfiguredToken() { + String token = props.getToken(); + return token != null && !token.isBlank(); + } + + /** + * Install a synthetic authenticated principal so HealthEndpoint's when_authorized check (principal != null) reveals component + * detail and protected endpoints are reachable. + */ + private static void authenticate() { + UsernamePasswordAuthenticationToken authn = + new UsernamePasswordAuthenticationToken(ACTUATOR_PRINCIPAL, "N/A", AuthorityUtils.createAuthorityList(ACTUATOR_AUTHORITY)); + SecurityContext ctx = SecurityContextHolder.createEmptyContext(); + ctx.setAuthentication(authn); + SecurityContextHolder.setContext(ctx); + } + + /** + * True only for paths that must stay open to the load balancer without a token: the shallow health aggregate and the + * liveness/readiness probe groups. Component-detail paths (e.g. /actuator/health/db) are NOT open — they require the token. + */ + private boolean isOpenHealthPath(HttpServletRequest req) { + String uri = req.getRequestURI(); + return uri.endsWith("/health") || uri.endsWith("/health/liveness") || uri.endsWith("/health/readiness"); + } + + /** Constant-time comparison to avoid leaking the token via timing. */ + private static boolean constantTimeEquals(String a, String b) { + if (a == null || b == null) return false; + byte[] aa = a.getBytes(StandardCharsets.UTF_8); + byte[] bb = b.getBytes(StandardCharsets.UTF_8); + if (aa.length != bb.length) return false; + int diff = 0; + for (int i = 0; i < aa.length; i++) diff |= aa[i] ^ bb[i]; + return diff == 0; + } + } +} diff --git a/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/security/ActuatorTokenProperties.java b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/security/ActuatorTokenProperties.java new file mode 100644 index 000000000..535a4007f --- /dev/null +++ b/libs/pic-sure-spring-commons/src/main/java/edu/harvard/hms/dbmi/avillach/commons/security/ActuatorTokenProperties.java @@ -0,0 +1,44 @@ +package edu.harvard.hms.dbmi.avillach.commons.security; + +import org.springframework.boot.context.properties.ConfigurationProperties; + +/** + * Binds picsure.actuator.* — the inter-service application/monitoring token config. This is NOT a user token; it gates machine-to-machine + * access to /actuator/**. + */ +@ConfigurationProperties(prefix = "picsure.actuator") +public class ActuatorTokenProperties { + + /** When false, no token check is enforced (AIO dev convenience / production rollback). */ + private boolean requireToken = true; + + /** The value the X-Application-Token header must equal (env: PICSURE_APPLICATION_TOKEN). */ + private String token = ""; + + /** Header name. Default X-Application-Token; overridable for testing. */ + private String headerName = "X-Application-Token"; + + public boolean isRequireToken() { + return requireToken; + } + + public void setRequireToken(boolean requireToken) { + this.requireToken = requireToken; + } + + public String getToken() { + return token; + } + + public void setToken(String token) { + this.token = token; + } + + public String getHeaderName() { + return headerName; + } + + public void setHeaderName(String headerName) { + this.headerName = headerName; + } +} diff --git a/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditContextTest.java b/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditContextTest.java new file mode 100644 index 000000000..04de0311d --- /dev/null +++ b/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditContextTest.java @@ -0,0 +1,35 @@ +package edu.harvard.hms.dbmi.avillach.commons.audit; + +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.Test; + +class AuditContextTest { + + @Test + void isNoArgConstructableWithEmptyMetadataByDefault() { + AuditContext context = new AuditContext(); + + assertThat(context.getMetadata()).isEmpty(); + } + + @Test + void putAddsKeyValuePairsToMetadata() { + AuditContext context = new AuditContext(); + + context.put("resource_id", "abc-123"); + context.put("username", "researcher1"); + + assertThat(context.getMetadata()).containsEntry("resource_id", "abc-123").containsEntry("username", "researcher1"); + } + + @Test + void putIgnoresNullKeysAndValues() { + AuditContext context = new AuditContext(); + + context.put(null, "value"); + context.put("key", null); + + assertThat(context.getMetadata()).isEmpty(); + } +} diff --git a/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditLoggingFilterTest.java b/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditLoggingFilterTest.java new file mode 100644 index 000000000..441a4a9bb --- /dev/null +++ b/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditLoggingFilterTest.java @@ -0,0 +1,166 @@ +package edu.harvard.hms.dbmi.avillach.commons.audit; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.never; +import static org.mockito.Mockito.times; +import static org.mockito.Mockito.verify; +import static org.mockito.Mockito.when; + +import java.util.List; +import java.util.regex.Pattern; + +import org.junit.jupiter.api.Test; +import org.mockito.ArgumentCaptor; +import org.springframework.mock.web.MockFilterChain; +import org.springframework.mock.web.MockHttpServletRequest; +import org.springframework.mock.web.MockHttpServletResponse; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; + +class AuditLoggingFilterTest { + + private final AuditRouteTable routes = + new AuditRouteTable(List.of(new AuditRoute(Pattern.compile("^/query/sync/?$"), "POST", "QUERY", "query.sync"))); + + @Test + void shouldNotFilterIsTrueWhenClientIsDisabled() { + LoggingClient client = mock(LoggingClient.class); + when(client.isEnabled()).thenReturn(false); + AuditLoggingFilter filter = new AuditLoggingFilter(client, routes, new AuditContext(), List.of()); + + assertThat(filter.shouldNotFilter(new MockHttpServletRequest("POST", "/query/sync"))).isTrue(); + } + + @Test + void shouldNotFilterIsTrueForOptionsRequests() { + LoggingClient client = mock(LoggingClient.class); + when(client.isEnabled()).thenReturn(true); + AuditLoggingFilter filter = new AuditLoggingFilter(client, routes, new AuditContext(), List.of()); + + assertThat(filter.shouldNotFilter(new MockHttpServletRequest("OPTIONS", "/query/sync"))).isTrue(); + } + + @Test + void shouldNotFilterIsTrueForSystemStatusAndOpenapiPaths() { + LoggingClient client = mock(LoggingClient.class); + when(client.isEnabled()).thenReturn(true); + AuditLoggingFilter filter = new AuditLoggingFilter(client, routes, new AuditContext(), List.of()); + + assertThat(filter.shouldNotFilter(new MockHttpServletRequest("GET", "/system/status"))).isTrue(); + assertThat(filter.shouldNotFilter(new MockHttpServletRequest("GET", "/openapi.json"))).isTrue(); + } + + @Test + void shouldNotFilterIsTrueWhenPathContainsASkipContainsEntry() { + LoggingClient client = mock(LoggingClient.class); + when(client.isEnabled()).thenReturn(true); + AuditLoggingFilter filter = new AuditLoggingFilter(client, routes, new AuditContext(), List.of("/proxy/pic-sure-logging/")); + + assertThat(filter.shouldNotFilter(new MockHttpServletRequest("GET", "/proxy/pic-sure-logging/audit"))).isTrue(); + } + + @Test + void shouldNotFilterIsFalseForAnOrdinaryRequest() { + LoggingClient client = mock(LoggingClient.class); + when(client.isEnabled()).thenReturn(true); + AuditLoggingFilter filter = new AuditLoggingFilter(client, routes, new AuditContext(), List.of()); + + assertThat(filter.shouldNotFilter(new MockHttpServletRequest("POST", "/query/sync"))).isFalse(); + } + + @Test + void shouldNotFilterIsOverridableBySubclasses() { + LoggingClient client = mock(LoggingClient.class); + when(client.isEnabled()).thenReturn(true); + AuditLoggingFilter filter = new AuditLoggingFilter(client, routes, new AuditContext(), List.of()) { + @Override + protected boolean shouldNotFilter(jakarta.servlet.http.HttpServletRequest request) { + return true; + } + }; + + assertThat(filter.shouldNotFilter(new MockHttpServletRequest("POST", "/query/sync"))).isTrue(); + } + + @Test + void emitsAnAuditEventForAMatchedRouteOnANonSkippedRequest() throws Exception { + LoggingClient client = mock(LoggingClient.class); + when(client.isEnabled()).thenReturn(true); + AuditLoggingFilter filter = new AuditLoggingFilter(client, routes, new AuditContext(), List.of()); + + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/query/sync"); + request.addHeader("X-Session-Id", "session-123"); + request.addHeader("Referer", "https://picsure.example.org/explore"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor eventCaptor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(client, times(1)).send(eventCaptor.capture()); + + LoggingEvent event = eventCaptor.getValue(); + assertThat(event.getEventType()).isEqualTo("QUERY"); + assertThat(event.getAction()).isEqualTo("query.sync"); + assertThat(event.getSessionId()).isEqualTo("session-123"); + assertThat(event.getRequest().getReferrer()).isEqualTo("https://picsure.example.org/explore"); + } + + @Test + void emitsAnAuditEventWithCallerWhenXClientTypeHeaderIsPresent() throws Exception { + LoggingClient client = mock(LoggingClient.class); + when(client.isEnabled()).thenReturn(true); + AuditLoggingFilter filter = new AuditLoggingFilter(client, routes, new AuditContext(), List.of()); + + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/query/sync"); + request.addHeader("X-Client-Type", "PYTHON_ADAPTER"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor eventCaptor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(client, times(1)).send(eventCaptor.capture()); + + LoggingEvent event = eventCaptor.getValue(); + assertThat(event.getCaller()).isEqualTo("PYTHON_ADAPTER"); + } + + @Test + void doesNotSetCallerWhenXClientTypeHeaderIsAbsentOrBlank() throws Exception { + LoggingClient client = mock(LoggingClient.class); + when(client.isEnabled()).thenReturn(true); + AuditLoggingFilter filter = new AuditLoggingFilter(client, routes, new AuditContext(), List.of()); + + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/query/sync"); + request.addHeader("X-Client-Type", " "); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor eventCaptor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(client, times(1)).send(eventCaptor.capture()); + + LoggingEvent event = eventCaptor.getValue(); + assertThat(event.getCaller()).isNull(); + } + + @Test + void doesNotEmitWhenTheRequestIsSkipped() throws Exception { + LoggingClient client = mock(LoggingClient.class); + when(client.isEnabled()).thenReturn(true); + AuditLoggingFilter filter = new AuditLoggingFilter(client, routes, new AuditContext(), List.of()); + + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/system/status"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, new MockFilterChain()); + + verify(client, never()).send(any(LoggingEvent.class)); + verify(client, never()).send(any(LoggingEvent.class), any(), any()); + } +} diff --git a/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditRouteTableTest.java b/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditRouteTableTest.java new file mode 100644 index 000000000..683f70f78 --- /dev/null +++ b/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditRouteTableTest.java @@ -0,0 +1,40 @@ +package edu.harvard.hms.dbmi.avillach.commons.audit; + +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.List; +import java.util.Optional; +import java.util.regex.Pattern; + +import org.junit.jupiter.api.Test; + +class AuditRouteTableTest { + + @Test + void firstMatchWinsForOverlappingPatterns() { + AuditRoute syncRoute = new AuditRoute(Pattern.compile("^/query/sync/?$"), "POST", "QUERY", "query.sync"); + AuditRoute queryRoute = new AuditRoute(Pattern.compile("^/query/?$"), "POST", "QUERY", "query.submitted"); + AuditRouteTable table = new AuditRouteTable(List.of(syncRoute, queryRoute)); + + Optional match = table.match("/query/sync", "POST"); + + assertThat(match).contains(syncRoute); + } + + @Test + void returnsEmptyWhenNoRouteMatches() { + AuditRouteTable table = + new AuditRouteTable(List.of(new AuditRoute(Pattern.compile("^/query/?$"), "POST", "QUERY", "query.submitted"))); + + assertThat(table.match("/unrelated", "GET")).isEmpty(); + } + + @Test + void matchRespectsMethodFiltering() { + AuditRouteTable table = + new AuditRouteTable(List.of(new AuditRoute(Pattern.compile("^/query/?$"), "POST", "QUERY", "query.submitted"))); + + assertThat(table.match("/query", "GET")).isEmpty(); + assertThat(table.match("/query", "POST")).isPresent(); + } +} diff --git a/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditRouteTest.java b/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditRouteTest.java new file mode 100644 index 000000000..4be2d2d2e --- /dev/null +++ b/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/audit/AuditRouteTest.java @@ -0,0 +1,49 @@ +package edu.harvard.hms.dbmi.avillach.commons.audit; + +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.regex.Pattern; + +import org.junit.jupiter.api.Test; + +class AuditRouteTest { + + @Test + void matchesOnlyGivenMethodWhenMethodIsSpecified() { + AuditRoute route = new AuditRoute(Pattern.compile("^/query/sync/?$"), "POST", "QUERY", "query.sync"); + + assertThat(route.matches("/query/sync", "POST")).isTrue(); + assertThat(route.matches("/query/sync", "GET")).isFalse(); + } + + @Test + void nullMethodMeansAnyMethod() { + AuditRoute route = new AuditRoute(Pattern.compile("^/query/[^/]+/status/?$"), null, "QUERY", "query.status"); + + assertThat(route.matches("/query/abc/status", "GET")).isTrue(); + assertThat(route.matches("/query/abc/status", "POST")).isTrue(); + } + + @Test + void defaultConstructorUsesMatchesNotFind() { + AuditRoute route = new AuditRoute(Pattern.compile("^/search/[^/]+/?$"), "POST", "SEARCH", "search.execute"); + + // "matches" requires the whole string to match; a trailing segment should not match. + assertThat(route.matches("/search/abc/values", "POST")).isFalse(); + } + + @Test + void useFindTrueMatchesAnywhereInThePath() { + AuditRoute route = new AuditRoute(Pattern.compile("^/search/[^/]+/values/"), null, "SEARCH", "search.values", true); + + assertThat(route.matches("/search/abc/values/1", "GET")).isTrue(); + } + + @Test + void useFindFalseRequiresFullMatch() { + AuditRoute route = new AuditRoute(Pattern.compile("^/search/[^/]+/values/"), null, "SEARCH", "search.values", false); + + // The pattern has no trailing anchor, so a full-string match against extra characters fails. + assertThat(route.matches("/search/abc/values/1", "GET")).isFalse(); + } +} diff --git a/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/error/GatewayExceptionAdviceTest.java b/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/error/GatewayExceptionAdviceTest.java new file mode 100644 index 000000000..ababa866e --- /dev/null +++ b/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/error/GatewayExceptionAdviceTest.java @@ -0,0 +1,41 @@ +package edu.harvard.hms.dbmi.avillach.commons.error; + +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.Map; + +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.Test; +import org.slf4j.MDC; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; + +class GatewayExceptionAdviceTest { + + private final GatewayExceptionAdvice advice = new GatewayExceptionAdvice(); + + @AfterEach + void clearMdc() { + MDC.clear(); + } + + @Test + void mapsExceptionToItsStatusWithAdditiveJsonBody() { + MDC.put("requestId", "req-123"); + + PicsureException exception = new PicsureException(HttpStatus.UNAUTHORIZED, "auth.missing_token", "No authorization header found."); + ResponseEntity> response = advice.handlePicsureException(exception); + + assertThat(response.getStatusCode()).isEqualTo(HttpStatus.UNAUTHORIZED); + assertThat(response.getBody()).containsEntry("errorType", "auth.missing_token") + .containsEntry("message", "No authorization header found.").containsEntry("requestId", "req-123"); + } + + @Test + void requestIdIsNullWhenMdcIsEmpty() { + PicsureException exception = new PicsureException(HttpStatus.FORBIDDEN, "auth.forbidden", "nope"); + ResponseEntity> response = advice.handlePicsureException(exception); + + assertThat(response.getBody()).containsEntry("requestId", null); + } +} diff --git a/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/error/PicsureExceptionTest.java b/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/error/PicsureExceptionTest.java new file mode 100644 index 000000000..75c7d5964 --- /dev/null +++ b/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/error/PicsureExceptionTest.java @@ -0,0 +1,23 @@ +package edu.harvard.hms.dbmi.avillach.commons.error; + +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.Test; +import org.springframework.http.HttpStatus; + +class PicsureExceptionTest { + + @Test + void exposesStatusErrorTypeAndMessage() { + PicsureException exception = new PicsureException(HttpStatus.UNAUTHORIZED, "auth.missing_token", "No authorization header found."); + + assertThat(exception.getStatus()).isEqualTo(HttpStatus.UNAUTHORIZED); + assertThat(exception.getErrorType()).isEqualTo("auth.missing_token"); + assertThat(exception.getMessage()).isEqualTo("No authorization header found."); + } + + @Test + void isARuntimeException() { + assertThat(new PicsureException(HttpStatus.FORBIDDEN, "auth.forbidden", "nope")).isInstanceOf(RuntimeException.class); + } +} diff --git a/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/identity/GatewayUserResolverTest.java b/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/identity/GatewayUserResolverTest.java new file mode 100644 index 000000000..e39a1f24c --- /dev/null +++ b/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/identity/GatewayUserResolverTest.java @@ -0,0 +1,57 @@ +package edu.harvard.hms.dbmi.avillach.commons.identity; + +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.Optional; + +import org.junit.jupiter.api.Test; +import org.springframework.mock.web.MockHttpServletRequest; + +class GatewayUserResolverTest { + + @Test + void resolvesGatewayUserFromHeaders() { + MockHttpServletRequest request = new MockHttpServletRequest(); + request.addHeader(GatewayUserResolver.HEADER_USER_ID, "user-1"); + request.addHeader(GatewayUserResolver.HEADER_USER_SUBJECT, "subject-1"); + request.addHeader(GatewayUserResolver.HEADER_USER_EMAIL, "user@example.com"); + request.addHeader(GatewayUserResolver.HEADER_USER_ROLES, "ADMIN,USER"); + request.addHeader(GatewayUserResolver.HEADER_USER_PRIVILEGES, "query.read, query.write ,,admin.all"); + + Optional resolved = GatewayUserResolver.resolve(request); + + assertThat(resolved).isPresent(); + GatewayUser user = resolved.get(); + assertThat(user.getUserId()).isEqualTo("user-1"); + assertThat(user.getSubject()).isEqualTo("subject-1"); + assertThat(user.getEmail()).isEqualTo("user@example.com"); + assertThat(user.getRoles()).isEqualTo("ADMIN,USER"); + assertThat(user.getPrivileges()).containsExactlyInAnyOrder("query.read", "query.write", "admin.all"); + } + + @Test + void returnsEmptyWhenUserIdHeaderIsMissing() { + MockHttpServletRequest request = new MockHttpServletRequest(); + + assertThat(GatewayUserResolver.resolve(request)).isEmpty(); + } + + @Test + void privilegesAreEmptySetWhenHeaderIsAbsent() { + MockHttpServletRequest request = new MockHttpServletRequest(); + request.addHeader(GatewayUserResolver.HEADER_USER_ID, "user-1"); + + GatewayUser user = GatewayUserResolver.resolve(request).orElseThrow(); + + assertThat(user.getPrivileges()).isEmpty(); + } + + @Test + void headerConstantsMatchTheAgreedContract() { + assertThat(GatewayUserResolver.HEADER_USER_ID).isEqualTo("X-User-Id"); + assertThat(GatewayUserResolver.HEADER_USER_SUBJECT).isEqualTo("X-User-Subject"); + assertThat(GatewayUserResolver.HEADER_USER_EMAIL).isEqualTo("X-User-Email"); + assertThat(GatewayUserResolver.HEADER_USER_ROLES).isEqualTo("X-User-Roles"); + assertThat(GatewayUserResolver.HEADER_USER_PRIVILEGES).isEqualTo("X-User-Privileges"); + } +} diff --git a/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/request/RequestIdFilterTest.java b/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/request/RequestIdFilterTest.java new file mode 100644 index 000000000..50cc5227e --- /dev/null +++ b/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/request/RequestIdFilterTest.java @@ -0,0 +1,45 @@ +package edu.harvard.hms.dbmi.avillach.commons.request; + +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.Test; +import org.slf4j.MDC; +import org.springframework.mock.web.MockFilterChain; +import org.springframework.mock.web.MockHttpServletRequest; +import org.springframework.mock.web.MockHttpServletResponse; + +class RequestIdFilterTest { + + private final RequestIdFilter filter = new RequestIdFilter(); + + @Test + void generatesAndEchoesARequestIdWhenNoneIsSupplied() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/query"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, new MockFilterChain()); + + assertThat(response.getHeader(RequestIdFilter.HEADER)).isNotBlank(); + assertThat(MDC.get(RequestIdFilter.MDC_KEY)).isNull(); + } + + @Test + void propagatesAnExistingRequestId() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/query"); + request.addHeader(RequestIdFilter.HEADER, "given-request-id"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, new MockFilterChain()); + + assertThat(response.getHeader(RequestIdFilter.HEADER)).isEqualTo("given-request-id"); + } + + @Test + void mdcCarriesTheRequestIdWhileTheChainExecutes() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/query"); + request.addHeader(RequestIdFilter.HEADER, "mdc-check-id"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, (req, resp) -> assertThat(MDC.get(RequestIdFilter.MDC_KEY)).isEqualTo("mdc-check-id")); + } +} diff --git a/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/security/ActuatorSecurityHelperTest.java b/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/security/ActuatorSecurityHelperTest.java new file mode 100644 index 000000000..e951bf00a --- /dev/null +++ b/libs/pic-sure-spring-commons/src/test/java/edu/harvard/hms/dbmi/avillach/commons/security/ActuatorSecurityHelperTest.java @@ -0,0 +1,82 @@ +package edu.harvard.hms.dbmi.avillach.commons.security; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.autoconfigure.SpringBootApplication; +import org.springframework.boot.context.properties.EnableConfigurationProperties; +import org.springframework.boot.test.autoconfigure.actuate.observability.AutoConfigureObservability; +import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.context.annotation.Bean; +import org.springframework.core.annotation.Order; +import org.springframework.security.config.annotation.web.builders.HttpSecurity; +import org.springframework.security.web.SecurityFilterChain; +import org.springframework.test.context.TestPropertySource; +import org.springframework.test.web.servlet.MockMvc; +import org.springframework.test.web.servlet.MvcResult; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status; + +@SpringBootTest(classes = ActuatorSecurityHelperTest.TestApp.class) +@AutoConfigureMockMvc +@AutoConfigureObservability // Spring Boot disables metrics export in tests by default; the /actuator/prometheus + // endpoint this test exercises needs it enabled to be registered. +@TestPropertySource( + properties = {"picsure.actuator.require-token=true", "picsure.actuator.token=secret-123", + "management.endpoints.web.exposure.include=health,info,prometheus,metrics", + "management.endpoint.health.show-details=when_authorized"} +) +class ActuatorSecurityHelperTest { + + @SpringBootApplication + @EnableConfigurationProperties(ActuatorTokenProperties.class) + static class TestApp { + @Bean + @Order(0) + SecurityFilterChain actuator(HttpSecurity http, ActuatorTokenProperties props) throws Exception { + return ActuatorSecurityHelper.actuatorChain(http, props); + } + + @Bean + @Order(10) + SecurityFilterChain main(HttpSecurity http) throws Exception { + return http.csrf(c -> c.disable()).authorizeHttpRequests(a -> a.anyRequest().permitAll()).build(); + } + } + + @Autowired + MockMvc mvc; + private final ObjectMapper json = new ObjectMapper(); + + @Test + void healthIsOpenAndShallowWithoutToken() throws Exception { + MvcResult res = mvc.perform(get("/actuator/health")).andExpect(status().isOk()).andReturn(); + JsonNode body = json.readTree(res.getResponse().getContentAsString()); + assertThat(body.get("status").asText()).isEqualTo("UP"); + assertThat(body.has("components")).isFalse(); // no detail leaks to anonymous callers + } + + @Test + void healthRevealsComponentDetailWithValidToken() throws Exception { + MvcResult res = + mvc.perform(get("/actuator/health").header("X-Application-Token", "secret-123")).andExpect(status().isOk()).andReturn(); + JsonNode body = json.readTree(res.getResponse().getContentAsString()); + assertThat(body.get("status").asText()).isEqualTo("UP"); + assertThat(body.has("components")).isTrue(); // DETAIL revealed + assertThat(body.get("components").has("diskSpace")).isTrue(); // an always-present component + } + + @Test + void prometheusRequiresToken() throws Exception { + mvc.perform(get("/actuator/prometheus")).andExpect(status().isUnauthorized()); + } + + @Test + void prometheusOkWithToken() throws Exception { + mvc.perform(get("/actuator/prometheus").header("X-Application-Token", "secret-123")).andExpect(status().isOk()); + } +} diff --git a/mvnw b/mvnw new file mode 100755 index 000000000..bd8896bf2 --- /dev/null +++ b/mvnw @@ -0,0 +1,295 @@ +#!/bin/sh +# ---------------------------------------------------------------------------- +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. +# ---------------------------------------------------------------------------- + +# ---------------------------------------------------------------------------- +# Apache Maven Wrapper startup batch script, version 3.3.4 +# +# Optional ENV vars +# ----------------- +# JAVA_HOME - location of a JDK home dir, required when download maven via java source +# MVNW_REPOURL - repo url base for downloading maven distribution +# MVNW_USERNAME/MVNW_PASSWORD - user and password for downloading maven +# MVNW_VERBOSE - true: enable verbose log; debug: trace the mvnw script; others: silence the output +# ---------------------------------------------------------------------------- + +set -euf +[ "${MVNW_VERBOSE-}" != debug ] || set -x + +# OS specific support. +native_path() { printf %s\\n "$1"; } +case "$(uname)" in +CYGWIN* | MINGW*) + [ -z "${JAVA_HOME-}" ] || JAVA_HOME="$(cygpath --unix "$JAVA_HOME")" + native_path() { cygpath --path --windows "$1"; } + ;; +esac + +# set JAVACMD and JAVACCMD +set_java_home() { + # For Cygwin and MinGW, ensure paths are in Unix format before anything is touched + if [ -n "${JAVA_HOME-}" ]; then + if [ -x "$JAVA_HOME/jre/sh/java" ]; then + # IBM's JDK on AIX uses strange locations for the executables + JAVACMD="$JAVA_HOME/jre/sh/java" + JAVACCMD="$JAVA_HOME/jre/sh/javac" + else + JAVACMD="$JAVA_HOME/bin/java" + JAVACCMD="$JAVA_HOME/bin/javac" + + if [ ! -x "$JAVACMD" ] || [ ! -x "$JAVACCMD" ]; then + echo "The JAVA_HOME environment variable is not defined correctly, so mvnw cannot run." >&2 + echo "JAVA_HOME is set to \"$JAVA_HOME\", but \"\$JAVA_HOME/bin/java\" or \"\$JAVA_HOME/bin/javac\" does not exist." >&2 + return 1 + fi + fi + else + JAVACMD="$( + 'set' +e + 'unset' -f command 2>/dev/null + 'command' -v java + )" || : + JAVACCMD="$( + 'set' +e + 'unset' -f command 2>/dev/null + 'command' -v javac + )" || : + + if [ ! -x "${JAVACMD-}" ] || [ ! -x "${JAVACCMD-}" ]; then + echo "The java/javac command does not exist in PATH nor is JAVA_HOME set, so mvnw cannot run." >&2 + return 1 + fi + fi +} + +# hash string like Java String::hashCode +hash_string() { + str="${1:-}" h=0 + while [ -n "$str" ]; do + char="${str%"${str#?}"}" + h=$(((h * 31 + $(LC_CTYPE=C printf %d "'$char")) % 4294967296)) + str="${str#?}" + done + printf %x\\n $h +} + +verbose() { :; } +[ "${MVNW_VERBOSE-}" != true ] || verbose() { printf %s\\n "${1-}"; } + +die() { + printf %s\\n "$1" >&2 + exit 1 +} + +trim() { + # MWRAPPER-139: + # Trims trailing and leading whitespace, carriage returns, tabs, and linefeeds. + # Needed for removing poorly interpreted newline sequences when running in more + # exotic environments such as mingw bash on Windows. + printf "%s" "${1}" | tr -d '[:space:]' +} + +scriptDir="$(dirname "$0")" +scriptName="$(basename "$0")" + +# parse distributionUrl and optional distributionSha256Sum, requires .mvn/wrapper/maven-wrapper.properties +while IFS="=" read -r key value; do + case "${key-}" in + distributionUrl) distributionUrl=$(trim "${value-}") ;; + distributionSha256Sum) distributionSha256Sum=$(trim "${value-}") ;; + esac +done <"$scriptDir/.mvn/wrapper/maven-wrapper.properties" +[ -n "${distributionUrl-}" ] || die "cannot read distributionUrl property in $scriptDir/.mvn/wrapper/maven-wrapper.properties" + +case "${distributionUrl##*/}" in +maven-mvnd-*bin.*) + MVN_CMD=mvnd.sh _MVNW_REPO_PATTERN=/maven/mvnd/ + case "${PROCESSOR_ARCHITECTURE-}${PROCESSOR_ARCHITEW6432-}:$(uname -a)" in + *AMD64:CYGWIN* | *AMD64:MINGW*) distributionPlatform=windows-amd64 ;; + :Darwin*x86_64) distributionPlatform=darwin-amd64 ;; + :Darwin*arm64) distributionPlatform=darwin-aarch64 ;; + :Linux*x86_64*) distributionPlatform=linux-amd64 ;; + *) + echo "Cannot detect native platform for mvnd on $(uname)-$(uname -m), use pure java version" >&2 + distributionPlatform=linux-amd64 + ;; + esac + distributionUrl="${distributionUrl%-bin.*}-$distributionPlatform.zip" + ;; +maven-mvnd-*) MVN_CMD=mvnd.sh _MVNW_REPO_PATTERN=/maven/mvnd/ ;; +*) MVN_CMD="mvn${scriptName#mvnw}" _MVNW_REPO_PATTERN=/org/apache/maven/ ;; +esac + +# apply MVNW_REPOURL and calculate MAVEN_HOME +# maven home pattern: ~/.m2/wrapper/dists/{apache-maven-,maven-mvnd--}/ +[ -z "${MVNW_REPOURL-}" ] || distributionUrl="$MVNW_REPOURL$_MVNW_REPO_PATTERN${distributionUrl#*"$_MVNW_REPO_PATTERN"}" +distributionUrlName="${distributionUrl##*/}" +distributionUrlNameMain="${distributionUrlName%.*}" +distributionUrlNameMain="${distributionUrlNameMain%-bin}" +MAVEN_USER_HOME="${MAVEN_USER_HOME:-${HOME}/.m2}" +MAVEN_HOME="${MAVEN_USER_HOME}/wrapper/dists/${distributionUrlNameMain-}/$(hash_string "$distributionUrl")" + +exec_maven() { + unset MVNW_VERBOSE MVNW_USERNAME MVNW_PASSWORD MVNW_REPOURL || : + exec "$MAVEN_HOME/bin/$MVN_CMD" "$@" || die "cannot exec $MAVEN_HOME/bin/$MVN_CMD" +} + +if [ -d "$MAVEN_HOME" ]; then + verbose "found existing MAVEN_HOME at $MAVEN_HOME" + exec_maven "$@" +fi + +case "${distributionUrl-}" in +*?-bin.zip | *?maven-mvnd-?*-?*.zip) ;; +*) die "distributionUrl is not valid, must match *-bin.zip or maven-mvnd-*.zip, but found '${distributionUrl-}'" ;; +esac + +# prepare tmp dir +if TMP_DOWNLOAD_DIR="$(mktemp -d)" && [ -d "$TMP_DOWNLOAD_DIR" ]; then + clean() { rm -rf -- "$TMP_DOWNLOAD_DIR"; } + trap clean HUP INT TERM EXIT +else + die "cannot create temp dir" +fi + +mkdir -p -- "${MAVEN_HOME%/*}" + +# Download and Install Apache Maven +verbose "Couldn't find MAVEN_HOME, downloading and installing it ..." +verbose "Downloading from: $distributionUrl" +verbose "Downloading to: $TMP_DOWNLOAD_DIR/$distributionUrlName" + +# select .zip or .tar.gz +if ! command -v unzip >/dev/null; then + distributionUrl="${distributionUrl%.zip}.tar.gz" + distributionUrlName="${distributionUrl##*/}" +fi + +# verbose opt +__MVNW_QUIET_WGET=--quiet __MVNW_QUIET_CURL=--silent __MVNW_QUIET_UNZIP=-q __MVNW_QUIET_TAR='' +[ "${MVNW_VERBOSE-}" != true ] || __MVNW_QUIET_WGET='' __MVNW_QUIET_CURL='' __MVNW_QUIET_UNZIP='' __MVNW_QUIET_TAR=v + +# normalize http auth +case "${MVNW_PASSWORD:+has-password}" in +'') MVNW_USERNAME='' MVNW_PASSWORD='' ;; +has-password) [ -n "${MVNW_USERNAME-}" ] || MVNW_USERNAME='' MVNW_PASSWORD='' ;; +esac + +if [ -z "${MVNW_USERNAME-}" ] && command -v wget >/dev/null; then + verbose "Found wget ... using wget" + wget ${__MVNW_QUIET_WGET:+"$__MVNW_QUIET_WGET"} "$distributionUrl" -O "$TMP_DOWNLOAD_DIR/$distributionUrlName" || die "wget: Failed to fetch $distributionUrl" +elif [ -z "${MVNW_USERNAME-}" ] && command -v curl >/dev/null; then + verbose "Found curl ... using curl" + curl ${__MVNW_QUIET_CURL:+"$__MVNW_QUIET_CURL"} -f -L -o "$TMP_DOWNLOAD_DIR/$distributionUrlName" "$distributionUrl" || die "curl: Failed to fetch $distributionUrl" +elif set_java_home; then + verbose "Falling back to use Java to download" + javaSource="$TMP_DOWNLOAD_DIR/Downloader.java" + targetZip="$TMP_DOWNLOAD_DIR/$distributionUrlName" + cat >"$javaSource" <<-END + public class Downloader extends java.net.Authenticator + { + protected java.net.PasswordAuthentication getPasswordAuthentication() + { + return new java.net.PasswordAuthentication( System.getenv( "MVNW_USERNAME" ), System.getenv( "MVNW_PASSWORD" ).toCharArray() ); + } + public static void main( String[] args ) throws Exception + { + setDefault( new Downloader() ); + java.nio.file.Files.copy( java.net.URI.create( args[0] ).toURL().openStream(), java.nio.file.Paths.get( args[1] ).toAbsolutePath().normalize() ); + } + } + END + # For Cygwin/MinGW, switch paths to Windows format before running javac and java + verbose " - Compiling Downloader.java ..." + "$(native_path "$JAVACCMD")" "$(native_path "$javaSource")" || die "Failed to compile Downloader.java" + verbose " - Running Downloader.java ..." + "$(native_path "$JAVACMD")" -cp "$(native_path "$TMP_DOWNLOAD_DIR")" Downloader "$distributionUrl" "$(native_path "$targetZip")" +fi + +# If specified, validate the SHA-256 sum of the Maven distribution zip file +if [ -n "${distributionSha256Sum-}" ]; then + distributionSha256Result=false + if [ "$MVN_CMD" = mvnd.sh ]; then + echo "Checksum validation is not supported for maven-mvnd." >&2 + echo "Please disable validation by removing 'distributionSha256Sum' from your maven-wrapper.properties." >&2 + exit 1 + elif command -v sha256sum >/dev/null; then + if echo "$distributionSha256Sum $TMP_DOWNLOAD_DIR/$distributionUrlName" | sha256sum -c - >/dev/null 2>&1; then + distributionSha256Result=true + fi + elif command -v shasum >/dev/null; then + if echo "$distributionSha256Sum $TMP_DOWNLOAD_DIR/$distributionUrlName" | shasum -a 256 -c >/dev/null 2>&1; then + distributionSha256Result=true + fi + else + echo "Checksum validation was requested but neither 'sha256sum' or 'shasum' are available." >&2 + echo "Please install either command, or disable validation by removing 'distributionSha256Sum' from your maven-wrapper.properties." >&2 + exit 1 + fi + if [ $distributionSha256Result = false ]; then + echo "Error: Failed to validate Maven distribution SHA-256, your Maven distribution might be compromised." >&2 + echo "If you updated your Maven version, you need to update the specified distributionSha256Sum property." >&2 + exit 1 + fi +fi + +# unzip and move +if command -v unzip >/dev/null; then + unzip ${__MVNW_QUIET_UNZIP:+"$__MVNW_QUIET_UNZIP"} "$TMP_DOWNLOAD_DIR/$distributionUrlName" -d "$TMP_DOWNLOAD_DIR" || die "failed to unzip" +else + tar xzf${__MVNW_QUIET_TAR:+"$__MVNW_QUIET_TAR"} "$TMP_DOWNLOAD_DIR/$distributionUrlName" -C "$TMP_DOWNLOAD_DIR" || die "failed to untar" +fi + +# Find the actual extracted directory name (handles snapshots where filename != directory name) +actualDistributionDir="" + +# First try the expected directory name (for regular distributions) +if [ -d "$TMP_DOWNLOAD_DIR/$distributionUrlNameMain" ]; then + if [ -f "$TMP_DOWNLOAD_DIR/$distributionUrlNameMain/bin/$MVN_CMD" ]; then + actualDistributionDir="$distributionUrlNameMain" + fi +fi + +# If not found, search for any directory with the Maven executable (for snapshots) +if [ -z "$actualDistributionDir" ]; then + # enable globbing to iterate over items + set +f + for dir in "$TMP_DOWNLOAD_DIR"/*; do + if [ -d "$dir" ]; then + if [ -f "$dir/bin/$MVN_CMD" ]; then + actualDistributionDir="$(basename "$dir")" + break + fi + fi + done + set -f +fi + +if [ -z "$actualDistributionDir" ]; then + verbose "Contents of $TMP_DOWNLOAD_DIR:" + verbose "$(ls -la "$TMP_DOWNLOAD_DIR")" + die "Could not find Maven distribution directory in extracted archive" +fi + +verbose "Found extracted Maven distribution directory: $actualDistributionDir" +printf %s\\n "$distributionUrl" >"$TMP_DOWNLOAD_DIR/$actualDistributionDir/mvnw.url" +mv -- "$TMP_DOWNLOAD_DIR/$actualDistributionDir" "$MAVEN_HOME" || [ -d "$MAVEN_HOME" ] || die "fail to move MAVEN_HOME" + +clean || : +exec_maven "$@" diff --git a/mvnw.cmd b/mvnw.cmd new file mode 100644 index 000000000..92450f932 --- /dev/null +++ b/mvnw.cmd @@ -0,0 +1,189 @@ +<# : batch portion +@REM ---------------------------------------------------------------------------- +@REM Licensed to the Apache Software Foundation (ASF) under one +@REM or more contributor license agreements. See the NOTICE file +@REM distributed with this work for additional information +@REM regarding copyright ownership. The ASF licenses this file +@REM to you under the Apache License, Version 2.0 (the +@REM "License"); you may not use this file except in compliance +@REM with the License. You may obtain a copy of the License at +@REM +@REM http://www.apache.org/licenses/LICENSE-2.0 +@REM +@REM Unless required by applicable law or agreed to in writing, +@REM software distributed under the License is distributed on an +@REM "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +@REM KIND, either express or implied. See the License for the +@REM specific language governing permissions and limitations +@REM under the License. +@REM ---------------------------------------------------------------------------- + +@REM ---------------------------------------------------------------------------- +@REM Apache Maven Wrapper startup batch script, version 3.3.4 +@REM +@REM Optional ENV vars +@REM MVNW_REPOURL - repo url base for downloading maven distribution +@REM MVNW_USERNAME/MVNW_PASSWORD - user and password for downloading maven +@REM MVNW_VERBOSE - true: enable verbose log; others: silence the output +@REM ---------------------------------------------------------------------------- + +@IF "%__MVNW_ARG0_NAME__%"=="" (SET __MVNW_ARG0_NAME__=%~nx0) +@SET __MVNW_CMD__= +@SET __MVNW_ERROR__= +@SET __MVNW_PSMODULEP_SAVE=%PSModulePath% +@SET PSModulePath= +@FOR /F "usebackq tokens=1* delims==" %%A IN (`powershell -noprofile "& {$scriptDir='%~dp0'; $script='%__MVNW_ARG0_NAME__%'; icm -ScriptBlock ([Scriptblock]::Create((Get-Content -Raw '%~f0'))) -NoNewScope}"`) DO @( + IF "%%A"=="MVN_CMD" (set __MVNW_CMD__=%%B) ELSE IF "%%B"=="" (echo %%A) ELSE (echo %%A=%%B) +) +@SET PSModulePath=%__MVNW_PSMODULEP_SAVE% +@SET __MVNW_PSMODULEP_SAVE= +@SET __MVNW_ARG0_NAME__= +@SET MVNW_USERNAME= +@SET MVNW_PASSWORD= +@IF NOT "%__MVNW_CMD__%"=="" ("%__MVNW_CMD__%" %*) +@echo Cannot start maven from wrapper >&2 && exit /b 1 +@GOTO :EOF +: end batch / begin powershell #> + +$ErrorActionPreference = "Stop" +if ($env:MVNW_VERBOSE -eq "true") { + $VerbosePreference = "Continue" +} + +# calculate distributionUrl, requires .mvn/wrapper/maven-wrapper.properties +$distributionUrl = (Get-Content -Raw "$scriptDir/.mvn/wrapper/maven-wrapper.properties" | ConvertFrom-StringData).distributionUrl +if (!$distributionUrl) { + Write-Error "cannot read distributionUrl property in $scriptDir/.mvn/wrapper/maven-wrapper.properties" +} + +switch -wildcard -casesensitive ( $($distributionUrl -replace '^.*/','') ) { + "maven-mvnd-*" { + $USE_MVND = $true + $distributionUrl = $distributionUrl -replace '-bin\.[^.]*$',"-windows-amd64.zip" + $MVN_CMD = "mvnd.cmd" + break + } + default { + $USE_MVND = $false + $MVN_CMD = $script -replace '^mvnw','mvn' + break + } +} + +# apply MVNW_REPOURL and calculate MAVEN_HOME +# maven home pattern: ~/.m2/wrapper/dists/{apache-maven-,maven-mvnd--}/ +if ($env:MVNW_REPOURL) { + $MVNW_REPO_PATTERN = if ($USE_MVND -eq $False) { "/org/apache/maven/" } else { "/maven/mvnd/" } + $distributionUrl = "$env:MVNW_REPOURL$MVNW_REPO_PATTERN$($distributionUrl -replace "^.*$MVNW_REPO_PATTERN",'')" +} +$distributionUrlName = $distributionUrl -replace '^.*/','' +$distributionUrlNameMain = $distributionUrlName -replace '\.[^.]*$','' -replace '-bin$','' + +$MAVEN_M2_PATH = "$HOME/.m2" +if ($env:MAVEN_USER_HOME) { + $MAVEN_M2_PATH = "$env:MAVEN_USER_HOME" +} + +if (-not (Test-Path -Path $MAVEN_M2_PATH)) { + New-Item -Path $MAVEN_M2_PATH -ItemType Directory | Out-Null +} + +$MAVEN_WRAPPER_DISTS = $null +if ((Get-Item $MAVEN_M2_PATH).Target[0] -eq $null) { + $MAVEN_WRAPPER_DISTS = "$MAVEN_M2_PATH/wrapper/dists" +} else { + $MAVEN_WRAPPER_DISTS = (Get-Item $MAVEN_M2_PATH).Target[0] + "/wrapper/dists" +} + +$MAVEN_HOME_PARENT = "$MAVEN_WRAPPER_DISTS/$distributionUrlNameMain" +$MAVEN_HOME_NAME = ([System.Security.Cryptography.SHA256]::Create().ComputeHash([byte[]][char[]]$distributionUrl) | ForEach-Object {$_.ToString("x2")}) -join '' +$MAVEN_HOME = "$MAVEN_HOME_PARENT/$MAVEN_HOME_NAME" + +if (Test-Path -Path "$MAVEN_HOME" -PathType Container) { + Write-Verbose "found existing MAVEN_HOME at $MAVEN_HOME" + Write-Output "MVN_CMD=$MAVEN_HOME/bin/$MVN_CMD" + exit $? +} + +if (! $distributionUrlNameMain -or ($distributionUrlName -eq $distributionUrlNameMain)) { + Write-Error "distributionUrl is not valid, must end with *-bin.zip, but found $distributionUrl" +} + +# prepare tmp dir +$TMP_DOWNLOAD_DIR_HOLDER = New-TemporaryFile +$TMP_DOWNLOAD_DIR = New-Item -Itemtype Directory -Path "$TMP_DOWNLOAD_DIR_HOLDER.dir" +$TMP_DOWNLOAD_DIR_HOLDER.Delete() | Out-Null +trap { + if ($TMP_DOWNLOAD_DIR.Exists) { + try { Remove-Item $TMP_DOWNLOAD_DIR -Recurse -Force | Out-Null } + catch { Write-Warning "Cannot remove $TMP_DOWNLOAD_DIR" } + } +} + +New-Item -Itemtype Directory -Path "$MAVEN_HOME_PARENT" -Force | Out-Null + +# Download and Install Apache Maven +Write-Verbose "Couldn't find MAVEN_HOME, downloading and installing it ..." +Write-Verbose "Downloading from: $distributionUrl" +Write-Verbose "Downloading to: $TMP_DOWNLOAD_DIR/$distributionUrlName" + +$webclient = New-Object System.Net.WebClient +if ($env:MVNW_USERNAME -and $env:MVNW_PASSWORD) { + $webclient.Credentials = New-Object System.Net.NetworkCredential($env:MVNW_USERNAME, $env:MVNW_PASSWORD) +} +[Net.ServicePointManager]::SecurityProtocol = [Net.SecurityProtocolType]::Tls12 +$webclient.DownloadFile($distributionUrl, "$TMP_DOWNLOAD_DIR/$distributionUrlName") | Out-Null + +# If specified, validate the SHA-256 sum of the Maven distribution zip file +$distributionSha256Sum = (Get-Content -Raw "$scriptDir/.mvn/wrapper/maven-wrapper.properties" | ConvertFrom-StringData).distributionSha256Sum +if ($distributionSha256Sum) { + if ($USE_MVND) { + Write-Error "Checksum validation is not supported for maven-mvnd. `nPlease disable validation by removing 'distributionSha256Sum' from your maven-wrapper.properties." + } + Import-Module $PSHOME\Modules\Microsoft.PowerShell.Utility -Function Get-FileHash + if ((Get-FileHash "$TMP_DOWNLOAD_DIR/$distributionUrlName" -Algorithm SHA256).Hash.ToLower() -ne $distributionSha256Sum) { + Write-Error "Error: Failed to validate Maven distribution SHA-256, your Maven distribution might be compromised. If you updated your Maven version, you need to update the specified distributionSha256Sum property." + } +} + +# unzip and move +Expand-Archive "$TMP_DOWNLOAD_DIR/$distributionUrlName" -DestinationPath "$TMP_DOWNLOAD_DIR" | Out-Null + +# Find the actual extracted directory name (handles snapshots where filename != directory name) +$actualDistributionDir = "" + +# First try the expected directory name (for regular distributions) +$expectedPath = Join-Path "$TMP_DOWNLOAD_DIR" "$distributionUrlNameMain" +$expectedMvnPath = Join-Path "$expectedPath" "bin/$MVN_CMD" +if ((Test-Path -Path $expectedPath -PathType Container) -and (Test-Path -Path $expectedMvnPath -PathType Leaf)) { + $actualDistributionDir = $distributionUrlNameMain +} + +# If not found, search for any directory with the Maven executable (for snapshots) +if (!$actualDistributionDir) { + Get-ChildItem -Path "$TMP_DOWNLOAD_DIR" -Directory | ForEach-Object { + $testPath = Join-Path $_.FullName "bin/$MVN_CMD" + if (Test-Path -Path $testPath -PathType Leaf) { + $actualDistributionDir = $_.Name + } + } +} + +if (!$actualDistributionDir) { + Write-Error "Could not find Maven distribution directory in extracted archive" +} + +Write-Verbose "Found extracted Maven distribution directory: $actualDistributionDir" +Rename-Item -Path "$TMP_DOWNLOAD_DIR/$actualDistributionDir" -NewName $MAVEN_HOME_NAME | Out-Null +try { + Move-Item -Path "$TMP_DOWNLOAD_DIR/$MAVEN_HOME_NAME" -Destination $MAVEN_HOME_PARENT | Out-Null +} catch { + if (! (Test-Path -Path "$MAVEN_HOME" -PathType Container)) { + Write-Error "fail to move MAVEN_HOME" + } +} finally { + try { Remove-Item $TMP_DOWNLOAD_DIR -Recurse -Force | Out-Null } + catch { Write-Warning "Cannot remove $TMP_DOWNLOAD_DIR" } +} + +Write-Output "MVN_CMD=$MAVEN_HOME/bin/$MVN_CMD" diff --git a/pic-sure-api-data/pom.xml b/pic-sure-api-data/pom.xml deleted file mode 100755 index c696b0fc9..000000000 --- a/pic-sure-api-data/pom.xml +++ /dev/null @@ -1,49 +0,0 @@ - - - 4.0.0 - - edu.harvard.hms.dbmi.avillach - pic-sure-api - 2.2.0-SNAPSHOT - - pic-sure-api-data - pic-sure-api-data - http://maven.apache.org - - UTF-8 - - - - edu.harvard.hms.dbmi.avillach - pic-sure-util - ${project.version} - - - edu.harvard.hms.dbmi.avillach - pic-sure-api-model - - - javax - javaee-api - provided - - - org.hibernate.javax.persistence - hibernate-jpa-2.1-api - - - org.hibernate - hibernate-annotations - - - org.hibernate - hibernate-core - - - io.swagger.core.v3 - swagger-annotations - - - diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/AuthUser.java b/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/AuthUser.java deleted file mode 100755 index 32333a424..000000000 --- a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/AuthUser.java +++ /dev/null @@ -1,80 +0,0 @@ -package edu.harvard.dbmi.avillach.data.entity; - -import java.security.Principal; -import java.util.Set; - -import javax.json.Json; - -/* - * This class is used to mirror the User object from the auth DB to maintain schema separation. - nc - */ -public class AuthUser extends BaseEntity implements Principal { - private String userId; - - private String subject; - - private String roles; - - private String email; - private Set privileges; - - public String getUserId() { - return userId; - } - - public AuthUser setUserId(String userId) { - this.userId = userId; - return this; - } - - public String getSubject() { - return subject; - } - - public AuthUser setSubject(String subject) { - this.subject = subject; - return this; - } - - public String getRoles() { - return roles; - } - - public AuthUser setRoles(String roles) { - this.roles = roles; - return this; - } - - public String getEmail(){ - return email; - } - - public AuthUser setEmail(String email){ - this.email = email; - return this; - } - - public Set getPrivileges() { - return privileges; - } - - public AuthUser setPrivileges(Set privileges) { - this.privileges = privileges; - return this; - } - - @Override // Principal method - public String getName() { - return getEmail(); - } - - @Override - public String toString() { - return Json.createObjectBuilder() - .add("userId", userId) - .add("subject", subject) - .add("email", email) - .add("roles", roles) - .build().toString(); - } -} diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/BaseEntity.java b/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/BaseEntity.java deleted file mode 100644 index 93cdafe26..000000000 --- a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/BaseEntity.java +++ /dev/null @@ -1,50 +0,0 @@ -package edu.harvard.dbmi.avillach.data.entity; - -import java.util.Objects; -import java.util.UUID; - -import javax.persistence.*; - -import org.hibernate.annotations.GenericGenerator; - -@MappedSuperclass -public abstract class BaseEntity { - @Id - @GeneratedValue(generator = "UUID") - @GenericGenerator( - name = "UUID", - strategy = "org.hibernate.id.UUIDGenerator") - @Column(columnDefinition = "BINARY(16)") - protected UUID uuid; - - public UUID getUuid() { - return uuid; - } - - public void setUuid(UUID uuid) { - this.uuid = uuid; - } - - @Override - public int hashCode() { - return Objects.hash(uuid); - } - - @Override - public boolean equals(Object obj) { - if (obj == this) return true; - if (!(obj instanceof BaseEntity)) { - return false; - } - if (this.uuid == null){ - return false; - } - BaseEntity entity = (BaseEntity) obj; - return this.uuid.equals(entity.uuid); - } - - @Override - public String toString() { - return this.uuid.toString(); - } -} diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Configuration.java b/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Configuration.java deleted file mode 100644 index e5375dd79..000000000 --- a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Configuration.java +++ /dev/null @@ -1,103 +0,0 @@ -package edu.harvard.dbmi.avillach.data.entity; - -import javax.json.Json; -import javax.persistence.*; - -import edu.harvard.dbmi.avillach.data.request.ConfigurationRequest; -import io.swagger.v3.oas.annotations.media.Schema; - -@Schema(description = "A Configuration object containing name, kind, enabled status, and description.") -@Entity(name = "configuration") -@Table( - name = "configuration", - uniqueConstraints = {@UniqueConstraint(name = "unique_uuid", columnNames = {"uuid"}), - @UniqueConstraint(name = "unique_name_kind", columnNames = {"name", "kind"})} -) -public class Configuration extends BaseEntity { - @Schema(description = "The configuration name") - @Column(length = 255) - private String name; - - @Schema(description = "The configuration kind/type") - @Column(length = 255) - private String kind; - - @Schema(description = "The configuration value") - @Lob - @Column(columnDefinition = "TEXT") - private String value; - - @Schema(description = "The configuration description") - @Column(length = 255) - private String description; - - @Schema(description = "This configuration is flagged for deletion") - private Boolean markForDelete = false; - - public Configuration setName(String name) { - this.name = name; - return this; - } - - public String getName() { - return name; - } - - public Configuration setKind(String kind) { - this.kind = kind; - return this; - } - - public String getKind() { - return kind; - } - - public Configuration setValue(String value) { - this.value = value; - return this; - } - - public String getValue() { - return value; - } - - public Configuration setDescription(String description) { - this.description = description; - return this; - } - - public String getDescription() { - return description; - } - - public Configuration setMarkForDelete(Boolean markForDelete) { - this.markForDelete = markForDelete; - return this; - } - - public Boolean getMarkForDelete() { - return markForDelete; - } - - @Override - public String toString() { - return Json.createObjectBuilder().add("uuid", uuid != null ? uuid.toString() : "").add("name", name != null ? name : "") - .add("kind", kind != null ? kind : "").add("description", description != null ? description : "") - .add("markForDelete", markForDelete != null ? markForDelete : false).build().toString(); - } - - public Configuration patch(ConfigurationRequest request) { - if (request.getName() != null) this.setName(request.getName()); - if (request.getKind() != null) this.setKind(request.getKind()); - if (request.getValue() != null) this.setValue(request.getValue()); - if (request.getDescription() != null) this.setDescription(request.getDescription()); - if (request.getMarkForDelete() != null) this.setMarkForDelete(request.getMarkForDelete()); - - return this; - } - - public static Configuration fromRequest(ConfigurationRequest request) { - Configuration config = new Configuration(); - return config.patch(request); - } -} diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/DataSharingStatus.java b/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/DataSharingStatus.java deleted file mode 100644 index 97d08e27f..000000000 --- a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/DataSharingStatus.java +++ /dev/null @@ -1,5 +0,0 @@ -package edu.harvard.dbmi.avillach.data.entity; - -public enum DataSharingStatus { - Unknown, Pending, Error, Complete, NotShared -} diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/NamedDataset.java b/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/NamedDataset.java deleted file mode 100644 index 23c9f7621..000000000 --- a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/NamedDataset.java +++ /dev/null @@ -1,101 +0,0 @@ -package edu.harvard.dbmi.avillach.data.entity; - -import java.util.Map; - -import javax.json.Json; -import javax.persistence.Column; -import javax.persistence.Convert; -import javax.persistence.Entity; -import javax.persistence.JoinColumn; -import javax.persistence.OneToOne; -import javax.persistence.Table; -import javax.persistence.UniqueConstraint; - -import io.swagger.v3.oas.annotations.media.Schema; - -import edu.harvard.dbmi.avillach.data.entity.convert.JsonConverter; - -@Schema(description = "A NamedDataset object containing query, name, user, and archived status.") -@Entity(name = "named_dataset") -@Table(uniqueConstraints = { - @UniqueConstraint(name = "unique_queryId_user", columnNames = { "queryId", "user" }) -}) -public class NamedDataset extends BaseEntity { - @Schema(description = "The associated Query") - @OneToOne - @JoinColumn(name = "queryId") - private Query query; - - @Schema(description = "The user identifier") - @Column(length = 255) - private String user; - - @Schema(description = "The name user has assigned to this dataset") - @Column(length = 255) - private String name; - - @Schema(description = "The archived state") - private Boolean archived = false; - - @Schema(description = "A json string object containing override specific values") - @Column(length = 8192) - @Convert(converter = JsonConverter.class) - private Map metadata; - - public NamedDataset setName(String name) { - this.name = name; - return this; - } - - public String getName() { - return name; - } - - public NamedDataset setArchived(Boolean archived) { - this.archived = archived; - return this; - } - - public Boolean getArchived() { - return archived; - } - - public NamedDataset setQuery(Query query) { - this.query = query; - return this; - } - - public Query getQuery(){ - return query; - } - - public NamedDataset setUser(String user) { - this.user = user; - return this; - } - - public String getUser(){ - return user; - } - - public Map getMetadata(){ - return metadata; - } - - public NamedDataset setMetadata(Map metadata){ - this.metadata = metadata; - return this; - } - - @Override - public String toString() { - return Json.createObjectBuilder() - .add("uuid", uuid.toString()) - .add("name", name) - .add("archived", archived) - .add("queryId", query.getUuid().toString()) - .add("user", user) - .add("metadata", metadata.toString()) - .build().toString(); - } -} diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Query.java b/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Query.java deleted file mode 100644 index 56cddf2ef..000000000 --- a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Query.java +++ /dev/null @@ -1,132 +0,0 @@ -package edu.harvard.dbmi.avillach.data.entity; - -import java.io.*; -import java.sql.Date; -import java.util.zip.GZIPInputStream; -import java.util.zip.GZIPOutputStream; - -import javax.persistence.*; - -import edu.harvard.dbmi.avillach.domain.PicSureStatus; - -@Entity(name = "query") -public class Query extends BaseEntity { - - // TODO may not need these two things - private Date startTime; - - private Date readyTime; - - // Resource is responsible for mapping internal status to picsurestatus - private PicSureStatus status; - - private String resourceResultId; - - // Original query request - @Lob - @Column(columnDefinition = "BLOB") - private byte[] query; - - @ManyToOne - @JoinColumn(name = "resourceId") - private Resource resource; - - @Column(length = 8192) - private byte[] metadata; - - private String version; - - public Resource getResource() { - return resource; - } - - public void setResource(Resource resource) { - this.resource = resource; - } - - public String getResourceResultId() { - return resourceResultId; - } - - public void setResourceResultId(String resourceResultId) { - this.resourceResultId = resourceResultId; - } - - public void setStartTime(Date startTime) { - this.startTime = startTime; - } - - public Date getStartTime() { - return startTime; - } - - public Date getReadyTime() { - return readyTime; - } - - public PicSureStatus getStatus() { - return status; - } - - public void setReadyTime(Date readyTime) { - this.readyTime = readyTime; - } - - public void setStatus(PicSureStatus status) { - this.status = status; - } - - public String getVersion() { - return version; - } - - public Query setVersion(String version) { - this.version = version; - return this; - } - - public String getQuery() { - - if (this.query == null || this.query.length == 0) { - return ""; - } - - String outStr = ""; - try ( - GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream(this.query)); BufferedReader bf = - new BufferedReader(new InputStreamReader(gis, "UTF-8")); - ) { - - String line; - while ((line = bf.readLine()) != null) { - outStr += line; - } - } catch (IOException e) { - throw new UncheckedIOException(e); - } - return outStr; - } - - public void setQuery(String queryStr) { - if (queryStr == null || queryStr.length() == 0) { - this.query = new byte[0]; - return; - } - - try (ByteArrayOutputStream obj = new ByteArrayOutputStream(); GZIPOutputStream gzip = new GZIPOutputStream(obj);) { - gzip.write(queryStr.getBytes("UTF-8")); - gzip.close(); - this.query = obj.toByteArray(); - } catch (IOException e) { - throw new UncheckedIOException(e); - } - } - - public byte[] getMetadata() { - return metadata; - } - - public void setMetadata(byte[] metadata) { - this.metadata = metadata; - } -} diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Resource.java b/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Resource.java deleted file mode 100644 index b2cb4367a..000000000 --- a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Resource.java +++ /dev/null @@ -1,135 +0,0 @@ -package edu.harvard.dbmi.avillach.data.entity; - -import java.io.StringReader; -import java.util.Optional; - -import javax.json.Json; -import javax.json.JsonObject; -import javax.json.JsonReader; -import javax.persistence.*; - -import com.fasterxml.jackson.annotation.JsonIgnore; -import com.fasterxml.jackson.annotation.JsonProperty; - -@Entity(name = "resource") -public class Resource extends BaseEntity{ - - private String name; - @Column(length = 8192) - private String description; - private String targetURL; - - - @Convert(converter = ResourcePathConverter.class) - private String resourceRSPath; - - @Column(length = 8192) - private String token; - - private Boolean hidden; - - private String metadata; - - public String getName() { - return name; - } - public Resource setName(String name) { - this.name = name; - return this; - } - - public String getDescription() { - return description; - } - public Resource setDescription(String description) { - this.description = description; - return this; - } - - public String getTargetURL() { - return targetURL; - } - public Resource setTargetURL(String targetURL) { - this.targetURL = targetURL; - return this; - } - - public String getResourceRSPath() { - return resourceRSPath; - } - - public Resource setResourceRSPath(String resourceRSPath) { - this.resourceRSPath = resourceRSPath; - return this; - } - - @JsonIgnore - public String getToken() { - return token; - } - - @JsonProperty - public Resource setToken(String token) { - this.token = token; - return this; - } - - //visible (not hidden) by default - public Boolean getHidden() { - return hidden == null ? Boolean.FALSE : hidden; - } - public void setHidden(Boolean hidden) { - this.hidden = hidden; - } - - public String getMetadata() { - return metadata; - } - public void setMetadata(String metadata) { - this.metadata = metadata; - } - - @Override - public String toString() { - JsonObject metadataObj = null; - if(metadata != null) { - JsonReader jsonReader = Json.createReader(new StringReader(metadata)); - metadataObj = jsonReader.readObject(); - jsonReader.close(); - } - return Json.createObjectBuilder() - .add("uuid", uuid.toString()) - .add("name", name) - .add("description", description) - .add("hidden", Boolean.toString(hidden)) - .add("metadata", metadataObj) - .build().toString(); - } - - /** - * This resource path converter allows resource paths to contain a reference to a specific stack that is - * imputed at runtime based an an environment parameter. This allows multiple stacks to share the same database. - * - * The ___target_stack___ token in any resource path value will be replaced with the TARGET_STACK environment variable - */ - @Converter - public static class ResourcePathConverter implements AttributeConverter { - - public ResourcePathConverter() { - } - - private static final Optional targetStack = Optional.ofNullable(System.getProperty("TARGET_STACK", null)); - - @Override - public String convertToDatabaseColumn(String attribute) { - return attribute; - } - - @Override - public String convertToEntityAttribute(String dbData) { - return targetStack - .map(stack -> dbData.replace("___target_stack___", stack)) - .orElse(dbData); - } - } -} diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Site.java b/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Site.java deleted file mode 100644 index 644863cf4..000000000 --- a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Site.java +++ /dev/null @@ -1,53 +0,0 @@ -package edu.harvard.dbmi.avillach.data.entity; - -import io.swagger.v3.oas.annotations.media.Schema; - -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Table; -import javax.persistence.UniqueConstraint; - -@Schema(description = "A site that contains a PIC-SURE installation that we can send data to") -@Table(uniqueConstraints = { - @UniqueConstraint(name = "unique_code", columnNames = { "code" }), - @UniqueConstraint(name = "unique_email", columnNames = { "domain" }) -}) -@Entity(name = "site") -public class Site extends BaseEntity { - - @Schema(description = "The site code. Ex: BCH") - @Column(length = 15) - private String code; - - @Schema(description = "The site name. Ex: Boston Children's") - @Column(length = 255) - private String name; - - @Schema(description = "The email domain of users for this site. Ex: childrens.harvard.edu") - @Column(length = 255) - private String domain; - - public String getCode() { - return code; - } - - public void setCode(String code) { - this.code = code; - } - - public String getName() { - return name; - } - - public void setName(String name) { - this.name = name; - } - - public String getDomain() { - return domain; - } - - public void setDomain(String domain) { - this.domain = domain; - } -} diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/BaseRepository.java b/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/BaseRepository.java deleted file mode 100644 index dec417e17..000000000 --- a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/BaseRepository.java +++ /dev/null @@ -1,249 +0,0 @@ -package edu.harvard.dbmi.avillach.data.repository; - -import edu.harvard.dbmi.avillach.data.entity.BaseEntity; -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.persistence.*; -import javax.persistence.criteria.*; -import java.util.*; - -/** - * - * @param the type of the entity class - * @param the type of the primary key - */ -public abstract class BaseRepository { - - Logger logger = LoggerFactory.getLogger(BaseRepository.class); - - protected final Class type; - - protected BaseRepository(Class type) { - this.type = type; - } - - @PersistenceContext - protected EntityManager em; - - protected EntityManager em() { - return em; - } - - protected CriteriaBuilder cb() { - return em().getCriteriaBuilder(); - } - - /** - * - * @return a criteriaQuery instance created by criteriaBuilder in entityManager - */ - public CriteriaQuery query() { - return cb().createQuery(type); - } - - public Predicate eq(Root root, String columnName, Object value) { - return eq(cb(), root, columnName, value); - } - - public Predicate eq(CriteriaBuilder cb, Root root, String columnName, Object value) { - return cb.equal(root.get(columnName), value); - } - - public Predicate lt(CriteriaBuilder cb, Root root, String columnName, V value) { - return cb.lt(root.get(columnName), value); - } - - public Predicate gt(CriteriaBuilder cb, Root root, String columnName, V value) { - return cb.gt(root.get(columnName), value); - } - - public Predicate between(CriteriaBuilder cb, Root root, String columnName, V value1, V value2) { - Expression exp = root.get(columnName); - return cb.between(exp, value1, value2); - } - - public Predicate like(CriteriaBuilder cb, Root root, String columnName, String value) { - Expression exp = root.get(columnName); - return cb.like(exp, value); - } - - public Predicate or(CriteriaBuilder cb, Predicate... restrictions) { - return cb.or(restrictions); - } - - public T getById(K id) { - return em().find(type, id); - } - - /** - * assume the operator is eq - * @param columnName - * @param value - * @return - */ - public List getByColumn(String columnName, Object value) { - CriteriaQuery query = query(); - Root root = root(query); - return getByColumns(query, root, eq(cb(), root, columnName, value)); - } - - /** - * assume the operator is eq - * @param columnName - * @param value - * @return - */ - public T getUniqueResultByColumn(String columnName, Object value) { - CriteriaQuery query = query(); - Root root = root(query); - return getUniqueResultByColumns(query, root, eq(cb(), root, columnName, value)); - } - - /** - * assume the operator is eq - * @param columnNameValueMap - * @return - */ - public List getByColumns(CriteriaQuery query, Map columnNameValueMap) { - CriteriaBuilder cb = cb(); - List predicates = new ArrayList<>(); - Root root = root(query); - for (Map.Entry entry : columnNameValueMap.entrySet()) { - predicates.add(eq(cb, root, entry.getKey(), entry.getValue())); - } - return getByColumns(query, root, predicates.toArray(new Predicate[0])); - } - - /** - * assume the operator is eq - * @param columnNameValueMap - * @return - */ - public T getUniqueResultByColumns(CriteriaQuery query, Map columnNameValueMap) { - CriteriaBuilder cb = cb(); - List predicates = new ArrayList<>(); - Root root = root(query); - for (Map.Entry entry : columnNameValueMap.entrySet()) { - predicates.add(eq(cb, root, entry.getKey(), entry.getValue())); - } - return getUniqueResultByColumns(query, root, predicates.toArray(new Predicate[0])); - } - - /** - * given the ability to assign your own predicates like lt, eq, like - * @param root - * @param predicates provide your own predicates - * @return - */ - public List getByColumns(CriteriaQuery query, Root root, Predicate... predicates) { - - query.select(root); - if (predicates != null && predicates.length > 0) query.where(predicates); - return em().createQuery(query).getResultList(); - - } - - /** - * given the ability to assign your own predicates like lt, eq, like - * @param root - * @param predicates provide your own predicates - * @return - */ - public T getUniqueResultByColumns(CriteriaQuery query, Root root, Predicate... predicates) { - - query.select(root); - if (predicates != null && predicates.length > 0) query.where(predicates); - try { - return (T) em().createQuery(query).getSingleResult(); - } catch (NoResultException e) { - return null; - } - } - - public List list() { - CriteriaQuery query = query(); - return getByColumns(query, root(query)); - } - - protected Root root(CriteriaQuery query) { - return query.from(type); - } - - public class InParam { - private String parameterName; - private Class parameterValueClass; - private S parameterValue; - - public InParam(Class type) { - this.parameterValueClass = type; - } - - public String getParameterName() { - return parameterName; - } - - public InParam name(String parameterName) { - this.parameterName = parameterName; - return this; - } - - public Class getParameterValueClass() { - return parameterValueClass; - } - - public InParam type(Class parameterValueClass) { - this.parameterValueClass = parameterValueClass; - return this; - } - - public S getParameterValue() { - return parameterValue; - } - - public InParam value(S parameterValue) { - this.parameterValue = parameterValue; - return this; - } - } - - public InParam inParam(Class type) { - return new InParam(type); - } - - public StoredProcedureQuery createQueryFor(String procedureName, Class entityType, InParam... inParams) { - StoredProcedureQuery validationsQuery = em().createStoredProcedureQuery(procedureName, entityType); - for (InParam param : inParams) { - validationsQuery.registerStoredProcedureParameter(param.parameterName, param.parameterValueClass, ParameterMode.IN) - .setParameter(param.parameterName, param.parameterValue); - } - return validationsQuery; - } - - public void persist(T t) { - em().persist(t); - } - - public void remove(T t) { - em().remove(t); - } - - public T merge(T t) { - return em().merge(t); - } - - public void addObjectToSet(Set set, BaseRepository baseRepository, T t) throws ProtocolException { - - if (t.getUuid() == null) return; - - T temp = baseRepository.getById(t.getUuid()); - if (temp == null) { - String className = type.getSimpleName(); - logger.error("Cannot find " + className + " instance by uuid: " + t.getUuid().toString()); - throw new ProtocolException("Cannot find " + className + " instance by uuid: " + t.getUuid().toString()); - } else { - set.add(temp); - } - } -} diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/ConfigurationRepository.java b/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/ConfigurationRepository.java deleted file mode 100644 index aa047a00a..000000000 --- a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/ConfigurationRepository.java +++ /dev/null @@ -1,15 +0,0 @@ -package edu.harvard.dbmi.avillach.data.repository; - -import edu.harvard.dbmi.avillach.data.entity.Configuration; - -import javax.enterprise.context.ApplicationScoped; -import javax.transaction.Transactional; -import java.util.UUID; - -@Transactional -@ApplicationScoped -public class ConfigurationRepository extends BaseRepository { - protected ConfigurationRepository() { - super(Configuration.class); - } -} diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/NamedDatasetRepository.java b/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/NamedDatasetRepository.java deleted file mode 100644 index 5dd6ffa35..000000000 --- a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/NamedDatasetRepository.java +++ /dev/null @@ -1,13 +0,0 @@ -package edu.harvard.dbmi.avillach.data.repository; - -import edu.harvard.dbmi.avillach.data.entity.NamedDataset; - -import javax.enterprise.context.ApplicationScoped; -import javax.transaction.Transactional; -import java.util.UUID; - -@Transactional -@ApplicationScoped -public class NamedDatasetRepository extends BaseRepository{ - protected NamedDatasetRepository() {super(NamedDataset.class);} -} diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/QueryRepository.java b/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/QueryRepository.java deleted file mode 100644 index 0c867ed00..000000000 --- a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/QueryRepository.java +++ /dev/null @@ -1,27 +0,0 @@ -package edu.harvard.dbmi.avillach.data.repository; - -import edu.harvard.dbmi.avillach.data.entity.Query; - -import javax.enterprise.context.ApplicationScoped; -import javax.persistence.PersistenceException; -import javax.transaction.Transactional; -import java.util.UUID; - -@Transactional -@ApplicationScoped -public class QueryRepository extends BaseRepository { - - protected QueryRepository() { - super(Query.class); - } - - public Query getQueryUUIDFromCommonAreaUUID(UUID caID) { - String caIDRegex = "%commonAreaUUID\":\"" + caID + "\"%"; - String query = "SELECT * FROM query WHERE CONVERT(metadata USING utf8) LIKE ?"; - try { - return (Query) em().createNativeQuery(query, Query.class).setParameter(1, caIDRegex).getSingleResult(); - } catch (PersistenceException ignored) { - return null; - } - } -} diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/ResourceRepository.java b/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/ResourceRepository.java deleted file mode 100644 index f377c9d69..000000000 --- a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/ResourceRepository.java +++ /dev/null @@ -1,19 +0,0 @@ -package edu.harvard.dbmi.avillach.data.repository; - -import javax.enterprise.context.ApplicationScoped; -import javax.transaction.Transactional; - -import edu.harvard.dbmi.avillach.data.entity.Resource; - -import java.util.UUID; - -@Transactional -@ApplicationScoped -public class ResourceRepository extends BaseRepository { - - protected ResourceRepository() { - super(Resource.class); - } - - -} diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/SiteRepository.java b/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/SiteRepository.java deleted file mode 100644 index b58e1a0db..000000000 --- a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/SiteRepository.java +++ /dev/null @@ -1,14 +0,0 @@ -package edu.harvard.dbmi.avillach.data.repository; - -import edu.harvard.dbmi.avillach.data.entity.NamedDataset; -import edu.harvard.dbmi.avillach.data.entity.Site; - -import javax.enterprise.context.ApplicationScoped; -import javax.transaction.Transactional; -import java.util.UUID; - -@Transactional -@ApplicationScoped -public class SiteRepository extends BaseRepository{ - protected SiteRepository() {super(Site.class);} -} diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/request/ConfigurationRequest.java b/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/request/ConfigurationRequest.java deleted file mode 100644 index a65d5dcc0..000000000 --- a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/request/ConfigurationRequest.java +++ /dev/null @@ -1,82 +0,0 @@ -package edu.harvard.dbmi.avillach.data.request; - -import javax.validation.constraints.Pattern; -import javax.validation.constraints.Size; - -import io.swagger.v3.oas.annotations.media.Schema; - -import java.util.UUID; - -@Schema( - description = "Request to add or update a configuration.", - example = "{\n" + " \"uuid\": \"076d4f2a-cfe8-486e-a7f9-b938086f3e1e\",\n" + " \"name\": \"FEATURE_FLAG_X\",\n" - + " \"kind\": \"ui\",\n" + " \"value\": \"true\",\n" + " \"markForDelete\": false,\n" - + " \"description\": \"This configuration controls feature X\"\n" + "}" -) -public class ConfigurationRequest { - private UUID uuid; - - // Matches strings containing only alphanumeric characters, underscores, hyphens, - // question marks, brackets, parentheses, colons, and periods from start to end - @Pattern(regexp = "^[\\w\\d\\-?\\[\\].():]+$") - @Size(max = 255) - private String name; - @Pattern(regexp = "^[\\w\\d\\-?\\[\\].():]+$") - @Size(max = 255) - private String kind; - - private String value; - - @Size(max = 255) - private String description; - - private Boolean markForDelete; - - public UUID getUuid() { - return uuid; - } - - public void setUuid(UUID uuid) { - this.uuid = uuid; - } - - public String getName() { - return name; - } - - public void setName(String name) { - this.name = name; - } - - public String getKind() { - return this.kind; - } - - public void setKind(String kind) { - this.kind = kind; - } - - public String getValue() { - return this.value; - } - - public void setValue(String value) { - this.value = value; - } - - public String getDescription() { - return this.description; - } - - public void setDescription(String description) { - this.description = description; - } - - public Boolean getMarkForDelete() { - return this.markForDelete; - } - - public void setMarkForDelete(Boolean markForDelete) { - this.markForDelete = markForDelete; - } -} diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/request/NamedDatasetRequest.java b/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/request/NamedDatasetRequest.java deleted file mode 100644 index 1f35dd3f0..000000000 --- a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/request/NamedDatasetRequest.java +++ /dev/null @@ -1,64 +0,0 @@ -package edu.harvard.dbmi.avillach.data.request; - -import java.util.HashMap; -import java.util.Map; -import java.util.UUID; - -import javax.validation.constraints.NotNull; -import javax.validation.constraints.Pattern; - -import io.swagger.v3.oas.annotations.media.Schema; - -@Schema( - description = "Request to add or update a named dataset.", - example = "{\n" + // - " \"queryId\": \"ec780aeb-d981-432a-b72b-51d4ecb3fd53\",\n" + // - " \"name\": \"My first Query\",\n" + // - " \"archived\": false\n" + // - " \"metadata\": {}\n" + // - "}" -) -public class NamedDatasetRequest { - @NotNull - private UUID queryId; - - @NotNull - @Pattern(regexp = "^[\\w\\d \\-\\\\/?+=\\[\\].():\"']+$") - private String name; - - private Boolean archived = false; - - private Map metadata = new HashMap(); - - public UUID getQueryId() { - return queryId; - } - - public void setQueryId(UUID query) { - this.queryId = query; - } - - public String getName() { - return name; - } - - public void setName(String name) { - this.name = name; - } - - public Boolean getArchived(){ - return archived; - } - - public void setArchived(Boolean archived) { - this.archived = archived; - } - - public Map getMetadata(){ - return metadata; - } - - public void setMetadata(Map metadata){ - this.metadata = metadata; - } -} diff --git a/pic-sure-api-data/src/main/resources/db/create_db_picsure.sql b/pic-sure-api-data/src/main/resources/db/create_db_picsure.sql deleted file mode 100644 index 75a772830..000000000 --- a/pic-sure-api-data/src/main/resources/db/create_db_picsure.sql +++ /dev/null @@ -1,85 +0,0 @@ -DROP DATABASE IF EXISTS `picsure`; -CREATE DATABASE IF NOT EXISTS `picsure` /*!40100 DEFAULT CHARACTER SET utf8 COLLATE utf8_bin */; -USE `picsure`; --- MySQL dump 10.13 Distrib 5.7.17, for macos10.12 (x86_64) --- --- Host: 127.0.0.1 Database: picsure --- ------------------------------------------------------ --- Server version 5.7.20 - -/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; -/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; -/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */; -/*!40101 SET NAMES utf8 */; -/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */; -/*!40103 SET TIME_ZONE='+00:00' */; -/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */; -/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */; -/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */; -/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; - --- --- Table structure for table `query` --- - -/*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; -CREATE TABLE `query` ( - `uuid` binary(16) NOT NULL, - `query` longblob, - `readyTime` date DEFAULT NULL, - `resourceResultId` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `startTime` date DEFAULT NULL, - `status` int(11) DEFAULT NULL, - `resourceId` binary(16), - `metadata` blob, - PRIMARY KEY (`uuid`), - KEY `FKhgiwd8kmi6pjw16txfhyqk2w0` (`resourceId`), - CONSTRAINT `FKhgiwd8kmi6pjw16txfhyqk2w0` FOREIGN KEY (`resourceId`) REFERENCES `resource` (`uuid`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; -/*!40101 SET character_set_client = @saved_cs_client */; - --- --- Table structure for table `resource` --- - -/*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; -CREATE TABLE `resource` ( - `uuid` binary(16) NOT NULL, - `targetURL` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `resourceRSPath` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `description` varchar(8192) COLLATE utf8_bin DEFAULT NULL, - `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `token` varchar(8192) COLLATE utf8_bin DEFAULT NULL, - PRIMARY KEY (`uuid`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; -/*!40101 SET character_set_client = @saved_cs_client */; - --- --- Table structure for table `user` --- - -/*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; -CREATE TABLE `user` ( - `uuid` binary(16) NOT NULL, - `roles` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `subject` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `userId` varchar(255) COLLATE utf8_bin DEFAULT NULL, - PRIMARY KEY (`uuid`), - UNIQUE KEY `subject_UNIQUE` (`subject`), - UNIQUE KEY `userId_UNIQUE` (`userId`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; -/*!40101 SET character_set_client = @saved_cs_client */; -/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; - -/*!40101 SET SQL_MODE=@OLD_SQL_MODE */; -/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */; -/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */; -/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */; -/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */; -/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; -/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; - --- Dump completed on 2018-05-24 16:46:11 diff --git a/pic-sure-api-data/src/main/resources/db/insert_resource_irct-nhanes.sql b/pic-sure-api-data/src/main/resources/db/insert_resource_irct-nhanes.sql deleted file mode 100644 index 3859ed79e..000000000 --- a/pic-sure-api-data/src/main/resources/db/insert_resource_irct-nhanes.sql +++ /dev/null @@ -1,23 +0,0 @@ -START TRANSACTION; - -DELETE FROM `resource` WHERE `name` = 'irct-nhanes'; - -SET @uuidResource = REPLACE(uuid(),'-',''); - -INSERT INTO `resource` ( - `uuid`, - `targetURL`, - `resourceRSPath`, - `description`, - `name`, - `token` -) VALUES ( - unhex(@uuidResource), - NULL, - '/i2b2-nhanes/Demo/Demo', - 'Basic IRCT resource, for NHANES data', - 'irct-nhanes', - NULL -); - -COMMIT; \ No newline at end of file diff --git a/pic-sure-api-data/src/main/resources/db/picsure2-dump-initial.sql b/pic-sure-api-data/src/main/resources/db/picsure2-dump-initial.sql deleted file mode 100644 index 8b61b8a21..000000000 --- a/pic-sure-api-data/src/main/resources/db/picsure2-dump-initial.sql +++ /dev/null @@ -1,86 +0,0 @@ --- // TODO: Delete if this is not being used - -CREATE DATABASE IF NOT EXISTS `picsure` /*!40100 DEFAULT CHARACTER SET utf8 COLLATE utf8_bin */; -USE `picsure`; --- MySQL dump 10.13 Distrib 5.7.17, for macos10.12 (x86_64) --- --- Host: 127.0.0.1 Database: picsure --- ------------------------------------------------------ --- Server version 5.7.20 - -/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; -/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; -/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */; -/*!40101 SET NAMES utf8 */; -/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */; -/*!40103 SET TIME_ZONE='+00:00' */; -/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */; -/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */; -/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */; -/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; - --- --- Table structure for table `query` --- - -/*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; -CREATE TABLE `query` ( - `uuid` binary(16) NOT NULL, - `query` longtext COLLATE utf8_bin, - `readyTime` date DEFAULT NULL, - `resourceResultId` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `startTime` date DEFAULT NULL, - `status` int(11) DEFAULT NULL, - `resourceId` binary(16), - `metadata` blob, - PRIMARY KEY (`uuid`), - KEY `FKhgiwd8kmi6pjw16txfhyqk2w0` (`resourceId`), - CONSTRAINT `FKhgiwd8kmi6pjw16txfhyqk2w0` FOREIGN KEY (`resourceId`) REFERENCES `resource` (`uuid`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; -/*!40101 SET character_set_client = @saved_cs_client */; - --- --- Table structure for table `resource` --- - -/*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; -CREATE TABLE `resource` ( - `uuid` binary(16) NOT NULL, - `targetURL` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `resourceRSPath` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `description` varchar(8192) COLLATE utf8_bin DEFAULT NULL, - `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `token` varchar(8192) COLLATE utf8_bin DEFAULT NULL, - PRIMARY KEY (`uuid`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; -/*!40101 SET character_set_client = @saved_cs_client */; - --- --- Table structure for table `user` --- - -/*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; -CREATE TABLE `user` ( - `uuid` binary(16) NOT NULL, - `roles` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `subject` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `userId` varchar(255) COLLATE utf8_bin DEFAULT NULL, - PRIMARY KEY (`uuid`), - UNIQUE KEY `subject_UNIQUE` (`subject`), - UNIQUE KEY `userId_UNIQUE` (`userId`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; -/*!40101 SET character_set_client = @saved_cs_client */; -/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; - -/*!40101 SET SQL_MODE=@OLD_SQL_MODE */; -/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */; -/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */; -/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */; -/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */; -/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; -/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; - --- Dump completed on 2018-05-24 16:46:11 diff --git a/pic-sure-api-data/src/main/resources/db/sql/V1__CREATE_PICSURE_INITIAL.sql b/pic-sure-api-data/src/main/resources/db/sql/V1__CREATE_PICSURE_INITIAL.sql deleted file mode 100644 index fb1d429d2..000000000 --- a/pic-sure-api-data/src/main/resources/db/sql/V1__CREATE_PICSURE_INITIAL.sql +++ /dev/null @@ -1,83 +0,0 @@ -USE `picsure`; --- MySQL dump 10.13 Distrib 5.7.17, for macos10.12 (x86_64) --- --- Host: 127.0.0.1 Database: picsure --- ------------------------------------------------------ --- Server version 5.7.20 - -/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; -/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; -/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */; -/*!40101 SET NAMES utf8 */; -/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */; -/*!40103 SET TIME_ZONE='+00:00' */; -/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */; -/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */; -/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */; -/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; - --- --- Table structure for table `query` --- - -/*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; -CREATE TABLE `query` ( - `uuid` binary(16) NOT NULL, - `query` longtext COLLATE utf8_bin, - `readyTime` date DEFAULT NULL, - `resourceResultId` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `startTime` date DEFAULT NULL, - `status` int(11) DEFAULT NULL, - `resourceId` binary(16), - `metadata` blob, - PRIMARY KEY (`uuid`), - KEY `FKhgiwd8kmi6pjw16txfhyqk2w0` (`resourceId`), - CONSTRAINT `FKhgiwd8kmi6pjw16txfhyqk2w0` FOREIGN KEY (`resourceId`) REFERENCES `resource` (`uuid`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; -/*!40101 SET character_set_client = @saved_cs_client */; - --- --- Table structure for table `resource` --- - -/*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; -CREATE TABLE `resource` ( - `uuid` binary(16) NOT NULL, - `targetURL` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `resourceRSPath` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `description` varchar(8192) COLLATE utf8_bin DEFAULT NULL, - `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `token` varchar(8192) COLLATE utf8_bin DEFAULT NULL, - PRIMARY KEY (`uuid`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; -/*!40101 SET character_set_client = @saved_cs_client */; - --- --- Table structure for table `user` --- - -/*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; -CREATE TABLE `user` ( - `uuid` binary(16) NOT NULL, - `roles` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `subject` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `userId` varchar(255) COLLATE utf8_bin DEFAULT NULL, - PRIMARY KEY (`uuid`), - UNIQUE KEY `subject_UNIQUE` (`subject`), - UNIQUE KEY `userId_UNIQUE` (`userId`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; -/*!40101 SET character_set_client = @saved_cs_client */; -/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; - -/*!40101 SET SQL_MODE=@OLD_SQL_MODE */; -/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */; -/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */; -/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */; -/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */; -/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; -/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; - --- Dump completed on 2018-05-24 16:46:11 diff --git a/pic-sure-api-data/src/main/resources/db/sql/V2__ALTER_QUERY_TABLE_QUERY_FIELD.sql b/pic-sure-api-data/src/main/resources/db/sql/V2__ALTER_QUERY_TABLE_QUERY_FIELD.sql deleted file mode 100644 index 9e78a8b04..000000000 --- a/pic-sure-api-data/src/main/resources/db/sql/V2__ALTER_QUERY_TABLE_QUERY_FIELD.sql +++ /dev/null @@ -1,3 +0,0 @@ -USE `picsure`; - -alter table `query` modify `query` longblob; \ No newline at end of file diff --git a/pic-sure-api-data/src/main/resources/db/sql/V3__ALTER_RESOURCE_TABLE_ADD_HIDDEN_COLUMN.sql b/pic-sure-api-data/src/main/resources/db/sql/V3__ALTER_RESOURCE_TABLE_ADD_HIDDEN_COLUMN.sql deleted file mode 100644 index 936f3aa8a..000000000 --- a/pic-sure-api-data/src/main/resources/db/sql/V3__ALTER_RESOURCE_TABLE_ADD_HIDDEN_COLUMN.sql +++ /dev/null @@ -1,5 +0,0 @@ -USE `picsure`; - -alter table `resource` add column hidden BOOL; - -update resource set hidden = false; \ No newline at end of file diff --git a/pic-sure-api-data/src/main/resources/db/sql/V4__ALTER_RESOURCE_ADD_METADATA_COLUMN.sql b/pic-sure-api-data/src/main/resources/db/sql/V4__ALTER_RESOURCE_ADD_METADATA_COLUMN.sql deleted file mode 100644 index 0833ae291..000000000 --- a/pic-sure-api-data/src/main/resources/db/sql/V4__ALTER_RESOURCE_ADD_METADATA_COLUMN.sql +++ /dev/null @@ -1,3 +0,0 @@ -USE `picsure`; - -alter table `resource` add column metadata TEXT; \ No newline at end of file diff --git a/pic-sure-api-data/src/main/resources/db/sql/V5__ADD_NAMED_DATASET_TABLE.sql b/pic-sure-api-data/src/main/resources/db/sql/V5__ADD_NAMED_DATASET_TABLE.sql deleted file mode 100644 index 2ae569622..000000000 --- a/pic-sure-api-data/src/main/resources/db/sql/V5__ADD_NAMED_DATASET_TABLE.sql +++ /dev/null @@ -1,13 +0,0 @@ -USE `picsure`; - -CREATE TABLE `named_dataset` ( - `uuid` binary(16) NOT NULL, - `queryId` binary(16) NOT NULL, - `user` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `archived` bit(1) NOT NULL DEFAULT FALSE, - `metadata` TEXT, - PRIMARY KEY (`uuid`), - CONSTRAINT `foreign_queryId` FOREIGN KEY (`queryId`) REFERENCES `query` (`uuid`), - CONSTRAINT `unique_queryId_user` UNIQUE (`queryId`, `user`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; diff --git a/pic-sure-api-data/src/main/resources/db/sql/V6__ADD_SITE_TABLE.sql b/pic-sure-api-data/src/main/resources/db/sql/V6__ADD_SITE_TABLE.sql deleted file mode 100644 index 4eb9f9283..000000000 --- a/pic-sure-api-data/src/main/resources/db/sql/V6__ADD_SITE_TABLE.sql +++ /dev/null @@ -1,11 +0,0 @@ -USE `picsure`; - -CREATE TABLE `site` ( - `uuid` binary(16) NOT NULL, - `code` varchar(15) COLLATE utf8_bin DEFAULT NULL, - `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, - `domain` varchar(255) COLLATE utf8_bin DEFAULT NULL, - PRIMARY KEY (`uuid`), - CONSTRAINT `unique_code` UNIQUE (`code`), - CONSTRAINT `unique_domain` UNIQUE (`domain`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; diff --git a/pic-sure-api-data/src/main/resources/db/sql/V7__ADD_DICTIONARY_RESOURCE.sql b/pic-sure-api-data/src/main/resources/db/sql/V7__ADD_DICTIONARY_RESOURCE.sql deleted file mode 100644 index 1ca2bd558..000000000 --- a/pic-sure-api-data/src/main/resources/db/sql/V7__ADD_DICTIONARY_RESOURCE.sql +++ /dev/null @@ -1,7 +0,0 @@ -USE `picsure`; - -SET @dictUUID = REPLACE(uuid(),'-',''); - - -INSERT INTO `resource` (uuid, resourceRSPath, description, name, hidden) VALUES -(unhex(@dictUUID), 'http://dictionary-api/', 'API for the data dictionary', 'dictionary-api', 1); \ No newline at end of file diff --git a/pic-sure-api-data/src/main/resources/db/sql/V8__ADD_CONFIG_TABLE.sql b/pic-sure-api-data/src/main/resources/db/sql/V8__ADD_CONFIG_TABLE.sql deleted file mode 100644 index 65690ac3d..000000000 --- a/pic-sure-api-data/src/main/resources/db/sql/V8__ADD_CONFIG_TABLE.sql +++ /dev/null @@ -1,12 +0,0 @@ -USE `picsure`; - -CREATE TABLE `configuration` ( - `uuid` binary(16) NOT NULL UNIQUE DEFAULT (UNHEX(REPLACE(UUID(),'-',''))), - `name` varchar(255) COLLATE utf8_bin NOT NULL, - `kind` varchar(255) COLLATE utf8_bin NOT NULL, - `value` TEXT NOT NULL, - `description` varchar(255) COLLATE utf8_bin DEFAULT '', - `markForDelete` bit(1) NOT NULL DEFAULT FALSE, - PRIMARY KEY (`uuid`), - CONSTRAINT `unique_name_kind` UNIQUE (`name`, `kind`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; diff --git a/pic-sure-api-data/src/test/java/edu/harvard/dbmi/avillach/DataTest.java b/pic-sure-api-data/src/test/java/edu/harvard/dbmi/avillach/DataTest.java deleted file mode 100755 index 322791636..000000000 --- a/pic-sure-api-data/src/test/java/edu/harvard/dbmi/avillach/DataTest.java +++ /dev/null @@ -1,26 +0,0 @@ -package edu.harvard.dbmi.avillach; - -import edu.harvard.dbmi.avillach.data.entity.BaseEntity; -import edu.harvard.dbmi.avillach.data.entity.AuthUser; -import org.junit.Test; - -import java.util.UUID; - -import static org.junit.Assert.*; - -/** - * Unit test for simple App. - */ -public class DataTest { - - @Test - public void BaseEntityBasicFunctionsTest() { - BaseEntity user = new AuthUser(); - user.setUuid(UUID.fromString("6ef9387a-4cde-4253-bd47-0bdc74ff76ab")); - - BaseEntity user2 = new AuthUser(); - user2.setUuid(UUID.fromString("6ef9387a-4cde-4253-bd47-0bdc74ff76ab")); - - assertEquals(user, user2); - } -} diff --git a/pic-sure-api-war/pom.xml b/pic-sure-api-war/pom.xml deleted file mode 100755 index 828476a48..000000000 --- a/pic-sure-api-war/pom.xml +++ /dev/null @@ -1,136 +0,0 @@ - - - 4.0.0 - - edu.harvard.hms.dbmi.avillach - pic-sure-api - 2.2.0-SNAPSHOT - - pic-sure-api-war - PIC-SURE API war - war - - - - - - edu.harvard.hms.dbmi.avillach - pic-sure-api-data - ${project.version} - - - edu.harvard.hms.dbmi.avillach - pic-sure-resource-api - ${project.version} - - - edu.harvard.hms.dbmi.avillach - pic-sure-api-model - - - io.jsonwebtoken - jjwt - - - com.github.tomakehurst - wiremock-jre8 - test - - - javax - javaee-api - provided - - - com.fasterxml.jackson.core - jackson-core - - - javax.xml.bind - jaxb-api - - - com.sun.xml.bind - jaxb-core - - - com.sun.xml.bind - jaxb-impl - - - - org.mockito - mockito-core - test - - - org.glassfish.jersey.core - jersey-common - - - org.apache.cxf - cxf-rt-frontend-jaxrs - test - - - org.jboss.resteasy - resteasy-jackson2-provider - - - io.swagger.core.v3 - swagger-jaxrs2 - - - io.swagger.core.v3 - swagger-jaxrs2-servlet-initializer-v2 - - - io.swagger.core.v3 - swagger-annotations - - - edu.harvard.dbmi.avillach - pic-sure-logging-client - - - - ${project.artifactId} - - - org.apache.maven.plugins - maven-dependency-plugin - - - retrieve-mysql-driver - generate-sources - - copy - - false - - - - com.mysql - mysql-connector-j - 8.0.32 - jar - true - ${project.build.directory}/modules/system/layers/base/com/sql/mysql/main/ - - - - - - - - org.apache.maven.plugins - maven-war-plugin - - false - - - - - diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/ConfigurationRS.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/ConfigurationRS.java deleted file mode 100644 index 67f1dd9f9..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/ConfigurationRS.java +++ /dev/null @@ -1,165 +0,0 @@ -package edu.harvard.dbmi.avillach; - -import java.util.UUID; - -import javax.inject.Inject; - -import javax.validation.Valid; - -import javax.ws.rs.*; -import javax.ws.rs.core.Context; -import javax.ws.rs.core.Response; -import javax.ws.rs.core.SecurityContext; -import javax.annotation.security.PermitAll; -import javax.annotation.security.RolesAllowed; - -import edu.harvard.dbmi.avillach.data.entity.Configuration; -import edu.harvard.dbmi.avillach.data.request.ConfigurationRequest; -import edu.harvard.dbmi.avillach.service.ConfigurationService; -import edu.harvard.dbmi.avillach.util.response.PICSUREResponse; - -import io.swagger.v3.oas.annotations.Operation; -import io.swagger.v3.oas.annotations.Parameter; -import io.swagger.v3.oas.annotations.media.ArraySchema; -import io.swagger.v3.oas.annotations.responses.ApiResponse; -import io.swagger.v3.oas.annotations.media.Content; -import io.swagger.v3.oas.annotations.media.ExampleObject; -import io.swagger.v3.oas.annotations.media.Schema; - -@Path("/configuration") -@Produces("application/json") -@Consumes("application/json") -public class ConfigurationRS { - @Inject - ConfigurationService configurationService; - - @GET - @Path("/") - @PermitAll - @Operation( - summary = "Returns a list of all configurations.", tags = {"configuration"}, operationId = "getConfigurations", - responses = { - @ApiResponse( - responseCode = "200", description = "A list of all configurations.", - content = @Content(array = @ArraySchema(schema = @Schema(implementation = Configuration.class))) - ), - @ApiResponse( - responseCode = "500", description = "Error finding configurations.", - content = @Content( - examples = {@ExampleObject( - name = "error", value = "{\"errorType\":\"error\",\"message\":\"Could not retrieve configurations\"}" - )} - ) - )} - ) - public Response getConfigurations(@Context SecurityContext context, @QueryParam("kind") String kind) { - return configurationService.getConfigurations(kind).map(PICSUREResponse::success) - .orElse(PICSUREResponse.error("Could not retrieve configurations")); - } - - @GET - @Path("/{configuration}/") - @PermitAll - @Operation( - summary = "Returns a configuration by ID.", tags = {"configuration"}, operationId = "getConfigurationById", - responses = { - @ApiResponse( - responseCode = "200", description = "The requested configuration.", - content = @Content(schema = @Schema(implementation = Configuration.class)) - ), - @ApiResponse( - responseCode = "500", description = "Error finding the configuration.", - content = @Content( - examples = {@ExampleObject( - name = "error", value = "{\"errorType\":\"error\",\"message\":\"Could not retrieve configuration\"}" - )} - ) - )} - ) - public Response getConfigurationById(@Context SecurityContext context, @PathParam("configuration") String identifier) { - return configurationService.getConfigurationByIdentifier(identifier).map(PICSUREResponse::success) - .orElse(PICSUREResponse.error("Could not retrieve configuration")); - } - - @POST - @Path("/admin/") - @RolesAllowed("SUPER_ADMIN") - @Operation( - summary = "Creates a new configuration.", tags = {"configuration"}, operationId = "addConfiguration", - responses = { - @ApiResponse( - responseCode = "200", description = "The configuration created.", - content = @Content(schema = @Schema(implementation = Configuration.class)) - ), - @ApiResponse( - responseCode = "500", description = "Error adding configuration.", - content = @Content( - examples = { - @ExampleObject(name = "error", value = "{\"errorType\":\"error\",\"message\":\"Could not save configuration\"}")} - ) - )} - ) - public Response addConfiguration(@Context SecurityContext context, @Parameter @Valid ConfigurationRequest request) { - if (request == null) { - return PICSUREResponse.error("Request body is required"); - } - if (request.getName() == null || request.getKind() == null || request.getValue() == null) { - return PICSUREResponse.error("Name, Kind, and Value properties must not be null"); - } - - return configurationService.addConfiguration(request).map(PICSUREResponse::success) - .orElse(PICSUREResponse.error("Could not add configuration")); - } - - @PATCH - @Path("/admin/{configurationId}/") - @RolesAllowed("SUPER_ADMIN") - @Operation( - summary = "Updates an existing configuration.", tags = {"configuration"}, operationId = "updateConfiguration", - responses = { - @ApiResponse( - responseCode = "200", description = "The updated configuration.", - content = @Content(schema = @Schema(implementation = Configuration.class)) - ), - @ApiResponse( - responseCode = "500", description = "Error updating the configuration.", - content = @Content( - examples = { - @ExampleObject(name = "error", value = "{\"errorType\":\"error\",\"message\":\"Could not update configuration\"}")} - ) - )} - ) - public Response updateConfiguration( - @Context SecurityContext context, @PathParam("configurationId") UUID configurationId, @Parameter @Valid ConfigurationRequest request - ) { - if (request == null) { - return PICSUREResponse.error("Request body is required"); - } - if (request.getUuid() != null && !configurationId.equals(request.getUuid())) { - return PICSUREResponse.error("UUID cannot be changed"); - } - - request.setUuid(configurationId); - return configurationService.updateConfiguration(request).map(PICSUREResponse::success) - .orElse(PICSUREResponse.error("Could not update configuration")); - } - - @DELETE - @Path("/admin/{configurationId}/") - @RolesAllowed("SUPER_ADMIN") - @Operation( - summary = "Deletes a configuration.", tags = {"configuration"}, operationId = "deleteConfiguration", - responses = {@ApiResponse(responseCode = "200", description = "Configuration successfully deleted."), - @ApiResponse( - responseCode = "500", description = "Error deleting the configuration.", - content = @Content( - examples = { - @ExampleObject(name = "error", value = "{\"errorType\":\"error\",\"message\":\"Could not delete configuration\"}")} - ) - )} - ) - public Response deleteConfiguration(@Context SecurityContext context, @PathParam("configurationId") UUID configurationId) { - return configurationService.deleteConfiguration(configurationId).map(PICSUREResponse::success) - .orElse(PICSUREResponse.error("Could not delete configuration")); - } -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/ContainerResponseLogger.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/ContainerResponseLogger.java deleted file mode 100644 index 05647be21..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/ContainerResponseLogger.java +++ /dev/null @@ -1,44 +0,0 @@ -package edu.harvard.dbmi.avillach; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.ws.rs.container.ContainerRequestContext; -import javax.ws.rs.container.ContainerResponseContext; -import javax.ws.rs.container.ContainerResponseFilter; -import javax.ws.rs.ext.Provider; - -@Provider -public class ContainerResponseLogger implements ContainerResponseFilter { - - Logger logger = LoggerFactory.getLogger(ContainerResponseLogger.class); - - /** - * Build up a log message to log every request that comes through - */ - @Override - public void filter(ContainerRequestContext requestContext, ContainerResponseContext responseContext) { - - //Capture request method and uri - StringBuilder stringBuilder = new StringBuilder(requestContext.getMethod() + " at " + requestContext.getUriInfo().getRequestUri()); - - //Get the username if it exists - if (requestContext.getProperty("username") != null){ - stringBuilder.insert(0, requestContext.getProperty("username") + " requested "); - } else { - stringBuilder.append(" requested "); - } - - //Get the request body if it exists; don't log token introspection content though - if (requestContext.getProperty("requestContent") != null - && !requestContext.getUriInfo().getRequestUri().getPath().contains("token/inspect")){ - stringBuilder.append("\n" + requestContext.getProperty("requestContent")); - - } - - //What status code was returned - stringBuilder.append("\n returned: " + responseContext.getStatus()); - - logger.info(stringBuilder.toString()); - } -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/EJBAccessExceptionMapper.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/EJBAccessExceptionMapper.java deleted file mode 100644 index 04e0f6025..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/EJBAccessExceptionMapper.java +++ /dev/null @@ -1,22 +0,0 @@ -package edu.harvard.dbmi.avillach; - -import java.util.Map; - -import javax.ejb.EJBAccessException; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; -import javax.ws.rs.ext.ExceptionMapper; -import javax.ws.rs.ext.Provider; - -@Provider -public class EJBAccessExceptionMapper implements ExceptionMapper{ - - @Override - public Response toResponse(EJBAccessException arg0) { - return Response.status(401).type(MediaType.APPLICATION_JSON).entity(Map.of("message", - "User does not have sufficient privileges.")) - .build(); - } - -} - diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/JAXRSConfiguration.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/JAXRSConfiguration.java deleted file mode 100755 index a3f88c788..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/JAXRSConfiguration.java +++ /dev/null @@ -1,45 +0,0 @@ -package edu.harvard.dbmi.avillach; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.annotation.PostConstruct; -import javax.ejb.Startup; -import javax.naming.Context; -import javax.naming.InitialContext; -import javax.naming.NamingException; -import javax.ws.rs.ApplicationPath; -import javax.ws.rs.core.Application; - -@Startup -@ApplicationPath("PICSURE") -public class JAXRSConfiguration extends Application { - - private Logger logger = LoggerFactory.getLogger(JAXRSConfiguration.class); - - public static String rolesClaim; - - @PostConstruct - public void init() { - logger.info("Starting pic-sure core app."); - - logger.info("Initializing roles claim."); - initializeRolesClaim(); - logger.info("Finished initializing roles claim."); - - } - - private void initializeRolesClaim(){ - try{ - Context ctx = new InitialContext(); - rolesClaim = (String) ctx.lookup("global/roles_claim"); - ctx.close(); - } catch (NamingException e) { - rolesClaim = "privileges"; - } - } - - public JAXRSConfiguration(){ - } - -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/LoggerReaderInterceptor.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/LoggerReaderInterceptor.java deleted file mode 100644 index ca0d01d03..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/LoggerReaderInterceptor.java +++ /dev/null @@ -1,57 +0,0 @@ -package edu.harvard.dbmi.avillach; - -import org.apache.commons.io.IOUtils; - -import javax.ws.rs.WebApplicationException; -import javax.ws.rs.ext.Provider; -import javax.ws.rs.ext.ReaderInterceptor; -import javax.ws.rs.ext.ReaderInterceptorContext; -import java.io.ByteArrayInputStream; -import java.io.IOException; -import java.io.InputStream; - -//@Provider -public class LoggerReaderInterceptor implements ReaderInterceptor { - - private final String sentinel = "RESOURCE_CREDENTIALS_REDACTED"; - - @Override - public Object aroundReadFrom(ReaderInterceptorContext interceptorContext) - throws IOException, WebApplicationException { - //Capture the request body to be logged when request completes - try (InputStream inputStream = interceptorContext.getInputStream()) { - - String requestContent = IOUtils.toString(inputStream, "UTF-8"); - - //Totally manually redact resourceCredentials from this string - String requestString = requestContent; - while (requestString.contains("resourceCredentials")){ - int rcBegin = requestString.indexOf("resourceCredentials"); - int startBracket = requestString.indexOf("{", rcBegin); - int bracketCount = 0; - int endBracket = -1; - for (int i = startBracket; i < requestString.length(); i++){ - if (requestString.charAt(i) == '{'){ - bracketCount++; - } if (requestString.charAt(i) == '}'){ - bracketCount--; - } - if (bracketCount < 1){ - endBracket = i; - break; - } - } - requestString = requestString.substring(0, rcBegin-1) +sentinel+ requestString.substring(endBracket+1); - } - - //Put string to context for logging - interceptorContext.setProperty("requestContent", requestString); - - //Return original body to the request - interceptorContext.setInputStream(new ByteArrayInputStream(requestContent.getBytes())); - - return interceptorContext.proceed(); - } - } - -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/NamedDatasetRS.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/NamedDatasetRS.java deleted file mode 100644 index 363ce1291..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/NamedDatasetRS.java +++ /dev/null @@ -1,184 +0,0 @@ -package edu.harvard.dbmi.avillach; - -import java.util.UUID; - -import javax.inject.Inject; - -import javax.validation.Valid; - -import javax.ws.rs.*; -import javax.ws.rs.core.Context; -import javax.ws.rs.core.Response; -import javax.ws.rs.core.SecurityContext; - -import edu.harvard.dbmi.avillach.data.entity.NamedDataset; -import edu.harvard.dbmi.avillach.data.request.NamedDatasetRequest; -import edu.harvard.dbmi.avillach.service.NamedDatasetService; -import edu.harvard.dbmi.avillach.util.response.PICSUREResponse; - -import io.swagger.v3.oas.annotations.Operation; -import io.swagger.v3.oas.annotations.Parameter; -import io.swagger.v3.oas.annotations.responses.ApiResponse; -import io.swagger.v3.oas.annotations.media.Content; -import io.swagger.v3.oas.annotations.media.ExampleObject; -import io.swagger.v3.oas.annotations.media.Schema; - -@Path("/dataset/named") -@Produces("application/json") -@Consumes("application/json") -public class NamedDatasetRS { - @Inject - NamedDatasetService namedDatasetService; - - @GET - @Path("/") - @Operation( - summary = "Returns a list of named datasets saved by the authenticated user.", - tags = { "dataset" }, - operationId = "namedDataset", - responses = { - @ApiResponse( - responseCode = "200", - description = "A list of named datasets saved by the authenticated user.", - content = @Content( - schema = @Schema( - implementation = NamedDataset.class - ) - ) - ), - @ApiResponse( - responseCode = "500", - description = "Error finding any named datasets for user.", - content = @Content( - examples = {@ExampleObject( - name = "namedDatasets", - value = "{\"errorType\":\"error\",\"message\":\"Could not retrieve named datasets\"}" - )} - ) - ) - } - ) - public Response namedDatasets( - @Context SecurityContext context - ) { - String user = context.getUserPrincipal().getName(); - return namedDatasetService.getNamedDatasets(user) - .map(PICSUREResponse::success) - .orElse(PICSUREResponse.error("Could not retrieve named datasets")); - } - - @POST - @Path("/") - @Operation( - summary = "Returns a named dataset saved by the authenticated user.", - tags = { "dataset" }, - operationId = "addNamedDataset", - responses = { - @ApiResponse( - responseCode = "200", - description = "The named dataset saved by the authenticated user.", - content = @Content( - schema = @Schema( - implementation = NamedDataset.class - ) - ) - ), - @ApiResponse( - responseCode = "500", - description = "Error adding any named datasets.", - content = @Content( - examples = {@ExampleObject( - name = "error", - value = "{\"errorType\":\"error\",\"message\":\"Could not save named dataset\"}" - )} - ) - ) - } - ) - public Response addNamedDataset( - @Context SecurityContext context, - @Parameter @Valid NamedDatasetRequest request - ) { - String user = context.getUserPrincipal().getName(); - return namedDatasetService.addNamedDataset(user, request) - .map(PICSUREResponse::success) - .orElse(PICSUREResponse.error("Could not save named dataset")); - } - - @GET - @Path("/{namedDatasetId}/") - @Operation( - summary = "Returns a named dataset requested by the authenticated user.", - tags = { "dataset" }, - operationId = "getNamedDatasetById", - responses = { - @ApiResponse( - responseCode = "200", - description = "The named dataset requested by the authenticated user.", - content = @Content( - schema = @Schema( - implementation = NamedDataset.class - ) - ) - ), - @ApiResponse( - responseCode = "500", - description = "Error finding the named dataset.", - content = @Content( - examples = {@ExampleObject( - name = "error", - value = "{\"errorType\":\"error\",\"message\":\"Could not retrieve named dataset\"}" - )} - ) - ) - } - ) - public Response getNamedDatasetById( - @Context SecurityContext context, - @PathParam("namedDatasetId") UUID datasetId - ){ - String user = context.getUserPrincipal().getName(); - return namedDatasetService.getNamedDatasetById(user, datasetId) - .map(PICSUREResponse::success) - .orElse(PICSUREResponse.error("Could not retrieve named dataset")); - } - - @PUT - @Path("/{namedDatasetId}/") - @Operation( - summary = "Updates a named dataset that the authenticated user perviously saved.", - tags = { "dataset" }, - operationId = "updateNamedDataset", - responses = { - @ApiResponse( - responseCode = "200", - description = "The named dataset updated by the authenticated user.", - content = @Content( - schema = @Schema( - implementation = NamedDataset.class - ) - ) - ), - @ApiResponse( - responseCode = "500", - description = "Error updating the named dataset.", - content = @Content( - examples = {@ExampleObject( - name = "error", - value = "{\"errorType\":\"error\",\"message\":\"Could not update named dataset\"}" - )} - ) - ) - } - ) - public Response updateNamedDataset( - @Context SecurityContext context, - @PathParam("namedDatasetId") UUID datasetId, - @Parameter @Valid NamedDatasetRequest request - ){ - String user = context.getUserPrincipal().getName(); - return namedDatasetService.updateNamedDataset(user, datasetId, request) - .map(PICSUREResponse::success) - .orElse(PICSUREResponse.error("Could not update named dataset")); - } -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/PicSureWarInit.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/PicSureWarInit.java deleted file mode 100644 index bd8626cb9..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/PicSureWarInit.java +++ /dev/null @@ -1,86 +0,0 @@ -package edu.harvard.dbmi.avillach; - -import com.fasterxml.jackson.databind.ObjectMapper; -import org.apache.http.impl.client.CloseableHttpClient; -import org.apache.http.impl.client.HttpClients; -import org.apache.http.impl.conn.PoolingHttpClientConnectionManager; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.annotation.PostConstruct; -import javax.annotation.Resource; -import javax.ejb.Singleton; -import javax.enterprise.context.ApplicationScoped; - -@Singleton -@ApplicationScoped -public class PicSureWarInit { - - Logger logger = LoggerFactory.getLogger(PicSureWarInit.class); - - @Resource(mappedName = "java:global/token_introspection_url") - private String token_introspection_url; - - @Resource(mappedName = "java:global/token_introspection_token") - private String token_introspection_token; - - @Resource(mappedName = "java:global/defaultApplicationUUID") - private String default_application_uuid; - - @Resource(mappedName = "java:global/openAccessEnabled") - private String open_access_enabled_str; - - private boolean open_access_enabled; - - @Resource(mappedName = "java:global/openAccessValidateUrl") - private String open_access_validate_url; - - @PostConstruct - public void init() { - this.open_access_enabled = Boolean.parseBoolean(open_access_enabled_str); - logger.info("Open access enabled: {}", open_access_enabled); - } - - // to be able to pre modified - public static final ObjectMapper objectMapper = new ObjectMapper(); - - // check the example from Apache HttpClient official website: - // http://hc.apache.org/httpcomponents-client-4.5.x/httpclient/examples/org/apache/http/examples/client/ClientMultiThreadedExecution.java - public static final PoolingHttpClientConnectionManager HTTP_CLIENT_CONNECTION_MANAGER; - - // If want to use self sign certificate for https, - // please follow the official httpclient example link: - // https://hc.apache.org/httpcomponents-client-ga/httpclient/examples/org/apache/http/examples/client/ClientCustomSSL.java - public static final CloseableHttpClient CLOSEABLE_HTTP_CLIENT; - static { - HTTP_CLIENT_CONNECTION_MANAGER = new PoolingHttpClientConnectionManager(); - HTTP_CLIENT_CONNECTION_MANAGER.setMaxTotal(100); - CLOSEABLE_HTTP_CLIENT = HttpClients.custom().setConnectionManager(HTTP_CLIENT_CONNECTION_MANAGER).useSystemProperties().build(); - } - - public String getToken_introspection_url() { - return token_introspection_url; - } - - public String getToken_introspection_token() { - return token_introspection_token; - } - - /** - * This method is used to get the default application UUID. This value is either the open or auth hpds resource UUID. - * - * @return the default application UUID - */ - public String getDefaultApplicationUUID() { - return this.default_application_uuid; - } - - public boolean isOpenAccessEnabled() { - return open_access_enabled; - } - - public String getOpenAccessValidateUrl() { - return this.open_access_validate_url; - } - -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/PicsureRS.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/PicsureRS.java deleted file mode 100644 index 49bdb337f..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/PicsureRS.java +++ /dev/null @@ -1,248 +0,0 @@ -package edu.harvard.dbmi.avillach; - -import java.util.Map; -import java.util.UUID; - -import javax.inject.Inject; -import javax.ws.rs.*; -import javax.ws.rs.core.*; - -import edu.harvard.dbmi.avillach.domain.*; -import edu.harvard.dbmi.avillach.service.*; -import io.swagger.v3.oas.annotations.OpenAPIDefinition; -import io.swagger.v3.oas.annotations.Parameter; -import io.swagger.v3.oas.annotations.info.Info; -import io.swagger.v3.oas.annotations.Operation; -import io.swagger.v3.oas.annotations.media.Content; -import io.swagger.v3.oas.annotations.media.Schema; -import io.swagger.v3.oas.annotations.parameters.RequestBody; -import io.swagger.v3.oas.annotations.responses.ApiResponse; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -@OpenAPIDefinition(info = @Info(title = "Pic-sure API", version = "1.0.0", description = "This is the Pic-sure API.")) -@Path("/") -@Produces("application/json") -@Consumes("application/json") -public class PicsureRS { - - private final Logger logger = LoggerFactory.getLogger(PicsureRS.class); - - @Inject - PicsureInfoService infoService; - - @Inject - PicsureSearchService searchService; - - @Inject - PicsureQueryService queryService; - - @Inject - FormatService formatService; - - @Inject - ProxyWebClient proxyWebClient; - - @POST - @Path("/info/{resourceId}") - @Operation( - summary = "Returns information about the provided resource", tags = {"info"}, operationId = "resourceInfo", - responses = {@ApiResponse( - responseCode = "200", description = "Resource information", - content = @Content(schema = @Schema(implementation = ResourceInfo.class)) - )} - ) - public ResourceInfo resourceInfo( - @Parameter(description = "The UUID of the resource to fetch information about") @PathParam("resourceId") String resourceId, - @Parameter QueryRequest credentialsQueryRequest, @Context HttpHeaders headers - ) { - System.out.println("Resource info requested for : " + resourceId); - return infoService.info(UUID.fromString(resourceId), credentialsQueryRequest, headers); - } - - @GET - @Path("/info/resources") - @Operation( - summary = "Returns list of resources available", - responses = {@ApiResponse( - responseCode = "200", description = "Resource information", content = @Content(schema = @Schema(implementation = Map.class)) - )} - ) - public Map resources(@Context HttpHeaders headers) { - return infoService.resources(headers); - } - - @GET - @Path("/search/{resourceId}/values/") - @Consumes("*/*") - public PaginatedSearchResult searchGenomicConceptValues( - @PathParam("resourceId") UUID resourceId, QueryRequest searchQueryRequest, - @QueryParam("genomicConceptPath") String genomicConceptPath, @QueryParam("query") String query, @QueryParam("page") Integer page, - @QueryParam("size") Integer size, @Context HttpHeaders headers - ) { - return searchService.searchGenomicConceptValues(resourceId, searchQueryRequest, genomicConceptPath, query, page, size, headers); - } - - @POST - @Path("/search/{resourceId}") - @Operation( - summary = "Searches for concept paths on the given resource matching the supplied search term", - responses = {@ApiResponse( - responseCode = "200", description = "Search results", content = @Content(schema = @Schema(implementation = SearchResults.class)) - )}, requestBody = @RequestBody(required = true, content = @Content(schema = @Schema(example = "{ \"query\": \"searchTerm\" }"))) - ) - public SearchResults search( - @Parameter(description = "The UUID of the resource to search") @PathParam("resourceId") UUID resourceId, - @Parameter(hidden = true) QueryRequest searchQueryRequest, @Context HttpHeaders headers - ) { - return searchService.search(resourceId, searchQueryRequest, headers); - } - - @POST - @Path("/query") - @Operation( - summary = "Submits a query to the given resource", - responses = {@ApiResponse( - responseCode = "200", description = "Query status", content = @Content(schema = @Schema(implementation = QueryStatus.class)) - )} - ) - public QueryStatus query( - @Parameter QueryRequest dataQueryRequest, - - @Context HttpHeaders headers, - - @Parameter @QueryParam("isInstitute") Boolean isInstitutionQuery, - - @Context SecurityContext context - ) { - if (isInstitutionQuery == null || !isInstitutionQuery) { - return queryService.query(dataQueryRequest, headers); - } else { - String email = context.getUserPrincipal().getName(); - return queryService.institutionalQuery((FederatedQueryRequest) dataQueryRequest, headers, email); - } - } - - @POST - @Path("/query/{queryId}/status") - @Operation( - summary = "Returns the status of the given query", - responses = {@ApiResponse( - responseCode = "200", description = "Query status", content = @Content(schema = @Schema(implementation = QueryStatus.class)) - )} - ) - public QueryStatus queryStatus( - @Parameter( - description = "The UUID of the query to fetch the status of. The UUID is returned by the /query " - + "endpoint as the \"picsureResultId\" in the response object" - ) @PathParam("queryId") UUID queryId, - - @Parameter QueryRequest credentialsQueryRequest, - - @Context HttpHeaders headers, - - @Parameter @QueryParam("isInstitute") Boolean isInstitutionQuery - ) { - if (credentialsQueryRequest instanceof GeneralQueryRequest) { - return queryService.queryStatus(queryId, (GeneralQueryRequest) credentialsQueryRequest, headers); - } else { - return queryService.institutionQueryStatus(queryId, (FederatedQueryRequest) credentialsQueryRequest, headers); - } - } - - @POST - @Path("/query/{queryId}/result") - @Operation( - summary = "Returns result for given query", - responses = {@ApiResponse( - responseCode = "200", description = "Query result", content = @Content(schema = @Schema(implementation = Response.class)) - )} - ) - @Produces(MediaType.APPLICATION_OCTET_STREAM) - public Response queryResult( - @Parameter( - description = "The UUID of the query to fetch the status of. The UUID is " - + "returned by the /query endpoint as the \"picsureResultId\" in the response object" - ) @PathParam("queryId") UUID queryId, @Parameter QueryRequest credentialsQueryRequest, @Context HttpHeaders headers - ) { - return queryService.queryResult(queryId, credentialsQueryRequest, headers); - } - - @POST - @Path("/query/{queryId}/signed-url") - @Operation( - summary = "Returns a signed url for given query", - responses = {@ApiResponse( - responseCode = "200", description = "Query result", content = @Content(schema = @Schema(implementation = Response.class)) - )} - ) - @Produces(MediaType.APPLICATION_JSON) - public Response queryResultSignedUrl( - @Parameter( - description = "The UUID of the query to fetch the status of. The UUID is " - + "returned by the /query endpoint as the \"picsureResultId\" in the response object" - ) @PathParam("queryId") UUID queryId, @Parameter QueryRequest credentialsQueryRequest, @Context HttpHeaders headers - ) { - return queryService.queryResultSignedUrl(queryId, credentialsQueryRequest, headers); - } - - @POST - @Path("/query/sync") - @Operation( - summary = "Returns result for given query", - responses = {@ApiResponse( - responseCode = "200", description = "Query result", content = @Content(schema = @Schema(implementation = Response.class)) - )} - ) - public Response querySync( - @Context HttpHeaders headers, - @Parameter( - description = "Object with field named 'resourceCredentials' which is a key-value map, " - + "key is identifier for resource, value is token for resource" - ) QueryRequest credentialsQueryRequest - ) { - return queryService.querySync(credentialsQueryRequest, headers); - } - - @GET - @Path("/query/{queryId}/metadata") - @Operation( - summary = "Returns metadata for given query", - description = "Generally used to reconstruct a query that was previously submitted. The queryId is " - + "returned by the /query endpoint as the \"picsureResultId\" in the response object", - responses = {@ApiResponse( - responseCode = "200", description = "Query metadata", content = @Content(schema = @Schema(implementation = QueryStatus.class)) - )} - ) - public QueryStatus queryMetadata(@PathParam("queryId") UUID queryId, @Context HttpHeaders headers) { - return queryService.queryMetadata(queryId, headers); - } - - @POST - @Path("/bin/continuous") - public Response generateContinuousBin(QueryRequest continuousData, @Context HttpHeaders headers) { - return formatService.format(continuousData, headers); - } - - - @POST - @Path("/proxy/{container}/{request : .+}") - @Operation(hidden = true) - public Response postProxy( - @PathParam("container") String containerId, @PathParam("request") String request, @Context UriInfo uriInfo, String body, - @Context HttpHeaders headers - ) { - return proxyWebClient.postProxy(containerId, request, body, uriInfo.getQueryParameters(), headers); - } - - @GET - @Path("/proxy/{container}/{request : .+}") - @Operation(hidden = true) - public Response getProxy( - @PathParam("container") String containerId, @PathParam("request") String request, @Context UriInfo uriInfo, - @Context HttpHeaders headers - ) { - return proxyWebClient.getProxy(containerId, request, uriInfo.getQueryParameters(), headers); - } - -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/PicsureRSv3.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/PicsureRSv3.java deleted file mode 100644 index 926486a3b..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/PicsureRSv3.java +++ /dev/null @@ -1,247 +0,0 @@ -package edu.harvard.dbmi.avillach; - -import edu.harvard.dbmi.avillach.domain.*; -import edu.harvard.dbmi.avillach.service.*; -import io.swagger.v3.oas.annotations.OpenAPIDefinition; -import io.swagger.v3.oas.annotations.Operation; -import io.swagger.v3.oas.annotations.Parameter; -import io.swagger.v3.oas.annotations.info.Info; -import io.swagger.v3.oas.annotations.media.Content; -import io.swagger.v3.oas.annotations.media.Schema; -import io.swagger.v3.oas.annotations.parameters.RequestBody; -import io.swagger.v3.oas.annotations.responses.ApiResponse; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.inject.Inject; -import javax.ws.rs.*; -import javax.ws.rs.core.*; -import java.util.Map; -import java.util.UUID; - -@OpenAPIDefinition(info = @Info(title = "Pic-sure API", version = "3.0.0", description = "This is the Pic-sure API.")) -@Path("/v3/") -@Produces("application/json") -@Consumes("application/json") -public class PicsureRSv3 { - - private final Logger logger = LoggerFactory.getLogger(PicsureRSv3.class); - - @Inject - PicsureInfoService infoService; - - @Inject - PicsureSearchService searchService; - - @Inject - PicsureQueryV3Service queryService; - - @Inject - FormatService formatService; - - @Inject - ProxyWebClient proxyWebClient; - - @POST - @Path("/info/{resourceId}") - @Operation( - summary = "Returns information about the provided resource", tags = {"info"}, operationId = "resourceInfo", - responses = {@ApiResponse( - responseCode = "200", description = "Resource information", - content = @Content(schema = @Schema(implementation = ResourceInfo.class)) - )} - ) - public ResourceInfo resourceInfo( - @Parameter(description = "The UUID of the resource to fetch information about") @PathParam("resourceId") String resourceId, - @Parameter QueryRequest credentialsQueryRequest, @Context HttpHeaders headers - ) { - System.out.println("Resource info requested for : " + resourceId); - return infoService.info(UUID.fromString(resourceId), credentialsQueryRequest, headers); - } - - @GET - @Path("/info/resources") - @Operation( - summary = "Returns list of resources available", - responses = {@ApiResponse( - responseCode = "200", description = "Resource information", content = @Content(schema = @Schema(implementation = Map.class)) - )} - ) - public Map resources(@Context HttpHeaders headers) { - return infoService.resources(headers); - } - - @GET - @Path("/search/{resourceId}/values/") - @Consumes("*/*") - public PaginatedSearchResult searchGenomicConceptValues( - @PathParam("resourceId") UUID resourceId, QueryRequest searchQueryRequest, - @QueryParam("genomicConceptPath") String genomicConceptPath, @QueryParam("query") String query, @QueryParam("page") Integer page, - @QueryParam("size") Integer size, @Context HttpHeaders headers - ) { - return searchService.searchGenomicConceptValues(resourceId, searchQueryRequest, genomicConceptPath, query, page, size, headers); - } - - @POST - @Path("/search/{resourceId}") - @Operation( - summary = "Searches for concept paths on the given resource matching the supplied search term", - responses = {@ApiResponse( - responseCode = "200", description = "Search results", content = @Content(schema = @Schema(implementation = SearchResults.class)) - )}, requestBody = @RequestBody(required = true, content = @Content(schema = @Schema(example = "{ \"query\": \"searchTerm\" }"))) - ) - public SearchResults search( - @Parameter(description = "The UUID of the resource to search") @PathParam("resourceId") UUID resourceId, - @Parameter(hidden = true) QueryRequest searchQueryRequest, @Context HttpHeaders headers - ) { - return searchService.search(resourceId, searchQueryRequest, headers); - } - - @POST - @Path("/query") - @Operation( - summary = "Submits a query to the given resource", - responses = {@ApiResponse( - responseCode = "200", description = "Query status", content = @Content(schema = @Schema(implementation = QueryStatus.class)) - )} - ) - public QueryStatus query( - @Parameter QueryRequest dataQueryRequest, - - @Context HttpHeaders headers, - - @Parameter @QueryParam("isInstitute") Boolean isInstitutionQuery, - - @Context SecurityContext context - ) { - if (isInstitutionQuery == null || !isInstitutionQuery) { - return queryService.query(dataQueryRequest, headers); - } else { - String email = context.getUserPrincipal().getName(); - return queryService.institutionalQuery((FederatedQueryRequest) dataQueryRequest, headers, email); - } - } - - @POST - @Path("/query/{queryId}/status") - @Operation( - summary = "Returns the status of the given query", - responses = {@ApiResponse( - responseCode = "200", description = "Query status", content = @Content(schema = @Schema(implementation = QueryStatus.class)) - )} - ) - public QueryStatus queryStatus( - @Parameter( - description = "The UUID of the query to fetch the status of. The UUID is returned by the /query " - + "endpoint as the \"picsureResultId\" in the response object" - ) @PathParam("queryId") UUID queryId, - - @Parameter QueryRequest credentialsQueryRequest, - - @Context HttpHeaders headers, - - @Parameter @QueryParam("isInstitute") Boolean isInstitutionQuery - ) { - if (credentialsQueryRequest instanceof GeneralQueryRequest) { - return queryService.queryStatus(queryId, (GeneralQueryRequest) credentialsQueryRequest, headers); - } else { - return queryService.institutionQueryStatus(queryId, (FederatedQueryRequest) credentialsQueryRequest, headers); - } - } - - @POST - @Path("/query/{queryId}/result") - @Operation( - summary = "Returns result for given query", - responses = {@ApiResponse( - responseCode = "200", description = "Query result", content = @Content(schema = @Schema(implementation = Response.class)) - )} - ) - @Produces(MediaType.APPLICATION_OCTET_STREAM) - public Response queryResult( - @Parameter( - description = "The UUID of the query to fetch the status of. The UUID is " - + "returned by the /query endpoint as the \"picsureResultId\" in the response object" - ) @PathParam("queryId") UUID queryId, @Parameter QueryRequest credentialsQueryRequest, @Context HttpHeaders headers - ) { - return queryService.queryResult(queryId, credentialsQueryRequest, headers); - } - - @POST - @Path("/query/{queryId}/signed-url") - @Operation( - summary = "Returns a signed url for given query", - responses = {@ApiResponse( - responseCode = "200", description = "Query result", content = @Content(schema = @Schema(implementation = Response.class)) - )} - ) - @Produces(MediaType.APPLICATION_JSON) - public Response queryResultSignedUrl( - @Parameter( - description = "The UUID of the query to fetch the status of. The UUID is " - + "returned by the /query endpoint as the \"picsureResultId\" in the response object" - ) @PathParam("queryId") UUID queryId, @Parameter QueryRequest credentialsQueryRequest, @Context HttpHeaders headers - ) { - return queryService.queryResultSignedUrl(queryId, credentialsQueryRequest, headers); - } - - @POST - @Path("/query/sync") - @Operation( - summary = "Returns result for given query", - responses = {@ApiResponse( - responseCode = "200", description = "Query result", content = @Content(schema = @Schema(implementation = Response.class)) - )} - ) - public Response querySync( - @Context HttpHeaders headers, - @Parameter( - description = "Object with field named 'resourceCredentials' which is a key-value map, " - + "key is identifier for resource, value is token for resource" - ) QueryRequest credentialsQueryRequest - ) { - return queryService.querySync(credentialsQueryRequest, headers); - } - - @GET - @Path("/query/{queryId}/metadata") - @Operation( - summary = "Returns metadata for given query", - description = "Generally used to reconstruct a query that was previously submitted. The queryId is " - + "returned by the /query endpoint as the \"picsureResultId\" in the response object", - responses = {@ApiResponse( - responseCode = "200", description = "Query metadata", content = @Content(schema = @Schema(implementation = QueryStatus.class)) - )} - ) - public QueryStatus queryMetadata(@PathParam("queryId") UUID queryId, @Context HttpHeaders headers) { - return queryService.queryMetadata(queryId, headers); - } - - @POST - @Path("/bin/continuous") - public Response generateContinuousBin(QueryRequest continuousData, @Context HttpHeaders headers) { - return formatService.format(continuousData, headers); - } - - - @POST - @Path("/proxy/{container}/{request : .+}") - @Operation(hidden = true) - public Response postProxy( - @PathParam("container") String containerId, @PathParam("request") String request, @Context UriInfo uriInfo, String body, - @Context HttpHeaders headers - ) { - return proxyWebClient.postProxy(containerId, request, body, uriInfo.getQueryParameters(), headers); - } - - @GET - @Path("/proxy/{container}/{request : .+}") - @Operation(hidden = true) - public Response getProxy( - @PathParam("container") String containerId, @PathParam("request") String request, @Context UriInfo uriInfo, - @Context HttpHeaders headers - ) { - return proxyWebClient.getProxy(containerId, request, uriInfo.getQueryParameters(), headers); - } - -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/security/AuditLoggingFilter.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/security/AuditLoggingFilter.java deleted file mode 100644 index f51470c89..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/security/AuditLoggingFilter.java +++ /dev/null @@ -1,262 +0,0 @@ -package edu.harvard.dbmi.avillach.security; - -import java.io.IOException; -import java.security.Principal; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.regex.Pattern; - -import javax.inject.Inject; -import javax.servlet.http.HttpServletRequest; -import javax.ws.rs.container.ContainerRequestContext; -import javax.ws.rs.container.ContainerRequestFilter; -import javax.ws.rs.container.ContainerResponseContext; -import javax.ws.rs.container.ContainerResponseFilter; -import javax.ws.rs.core.Context; -import javax.ws.rs.ext.Provider; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import edu.harvard.dbmi.avillach.data.entity.AuthUser; -import edu.harvard.dbmi.avillach.logging.LoggingClient; -import edu.harvard.dbmi.avillach.logging.LoggingEvent; -import edu.harvard.dbmi.avillach.logging.RequestInfo; -import edu.harvard.dbmi.avillach.logging.SessionIdResolver; -import edu.harvard.dbmi.avillach.service.AuditContext; - -@Provider -public class AuditLoggingFilter implements ContainerRequestFilter, ContainerResponseFilter { - - private static final Logger logger = LoggerFactory.getLogger(AuditLoggingFilter.class); - - private static final String AUDIT_START_TIME = "audit_start_time"; - - private static final String DEST_IP; - private static final Integer DEST_PORT; - - static { - DEST_IP = System.getenv("DEST_IP"); - Integer port = null; - String portStr = System.getenv("DEST_PORT"); - if (portStr != null) { - try { - port = Integer.parseInt(portStr); - } catch (NumberFormatException e) { - // ignore, will fallback to httpServletRequest - } - } - DEST_PORT = port; - } - - // Route table: first match wins. Order matters for overlapping patterns (e.g. /query/sync before /query). - // @formatter:off - private static final List ROUTES = List.of( - new RouteRule(Pattern.compile("^(/v\\d+)?/query/sync/?$"), "POST", "QUERY", "query.sync"), - new RouteRule(Pattern.compile("^(/v\\d+)?/query/?$"), "POST", "QUERY", "query.submitted"), - new RouteRule(Pattern.compile("^(/v\\d+)?/query/[^/]+/status/?$"), null, "QUERY", "query.status"), - new RouteRule(Pattern.compile("^(/v\\d+)?/query/[^/]+/result/?$"), null, "DATA_ACCESS", "query.result"), - new RouteRule(Pattern.compile("^(/v\\d+)?/query/[^/]+/signed-url/?$"), null, "DATA_ACCESS", "query.signed_url"), - new RouteRule(Pattern.compile("^(/v\\d+)?/query/[^/]+/metadata/?$"), null, "QUERY", "query.metadata"), - new RouteRule(Pattern.compile("^(/v\\d+)?/search/[^/]+/?$"), "POST", "SEARCH", "search.execute"), - new RouteRule(Pattern.compile("^(/v\\d+)?/search/[^/]+/values/"), null, "SEARCH", "search.values", true), - new RouteRule(Pattern.compile("/proxy/"), null, "PROXY", "proxy.request", true) - ); - // @formatter:on - - static final class RouteRule { - - final Pattern pattern; - final String method; - final String eventType; - final String action; - final boolean useFind; - - RouteRule(Pattern pattern, String method, String eventType, String action) { - this(pattern, method, eventType, action, false); - } - - RouteRule(Pattern pattern, String method, String eventType, String action, boolean useFind) { - this.pattern = pattern; - this.method = method; - this.eventType = eventType; - this.action = action; - this.useFind = useFind; - } - - boolean matches(String path, String httpMethod) { - boolean patternMatch = useFind ? pattern.matcher(path).find() : pattern.matcher(path).matches(); - return patternMatch && (method == null || method.equals(httpMethod)); - } - } - - @Inject - LoggingClient loggingClient; - - @Context - HttpServletRequest httpServletRequest; - - @Inject - AuditContext auditContext; - - @Override - public void filter(ContainerRequestContext requestContext) throws IOException { - requestContext.setProperty(AUDIT_START_TIME, System.currentTimeMillis()); - } - - @Override - public void filter(ContainerRequestContext requestContext, ContainerResponseContext responseContext) throws IOException { - try { - if (loggingClient == null || !loggingClient.isEnabled()) { - return; - } - - if ("OPTIONS".equals(requestContext.getMethod())) { - return; - } - - String fullPath = requestContext.getUriInfo().getRequestUri().getPath(); - - // Skip paths that should not be logged - if ( - fullPath.endsWith("/system/status") || fullPath.endsWith("/openapi.json") || fullPath.contains("/info/") - || fullPath.contains("/bin/continuous") || fullPath.contains("/proxy/pic-sure-logging/") - ) { - return; - } - - // Strip servlet context path and application path prefix (e.g., /pic-sure-api-2/PICSURE) - String path = fullPath; - // Strip known context prefixes so URL patterns match correctly - int picsureIdx = path.indexOf("/PICSURE"); - if (picsureIdx >= 0) { - path = path.substring(picsureIdx + "/PICSURE".length()); - } - - // Calculate duration - Long startTime = (Long) requestContext.getProperty(AUDIT_START_TIME); - long duration = 0L; - if (startTime != null) { - duration = System.currentTimeMillis() - startTime; - } - - // Categorize event via route table (first match wins) - String method = requestContext.getMethod(); - String eventType = "OTHER"; - String action = method; - - for (RouteRule rule : ROUTES) { - if (rule.matches(path, method)) { - eventType = rule.eventType; - action = rule.action; - break; - } - } - - // Determine source IP - String srcIp = null; - String xForwardedFor = httpServletRequest.getHeader("X-Forwarded-For"); - if (xForwardedFor != null && !xForwardedFor.isEmpty()) { - srcIp = xForwardedFor.split(",")[0].trim(); - } else { - srcIp = httpServletRequest.getRemoteAddr(); - } - - // Determine dest IP and port - String destIp = DEST_IP != null ? DEST_IP : httpServletRequest.getLocalAddr(); - int destPort = DEST_PORT != null ? DEST_PORT : httpServletRequest.getLocalPort(); - - // Response info - int responseStatus = responseContext.getStatus(); - String contentType = responseContext.getHeaderString("Content-Type"); - int lengthRaw = responseContext.getLength(); - Long bytes = lengthRaw >= 0 ? (long) lengthRaw : null; - - // Build RequestInfo - String queryString = requestContext.getUriInfo().getRequestUri().getQuery(); - RequestInfo requestInfo = RequestInfo.builder().method(method).url(fullPath).queryString(queryString).srcIp(srcIp) - .destIp(destIp).destPort(destPort).httpUserAgent(httpServletRequest.getHeader("User-Agent")).status(responseStatus) - .duration(duration).httpContentType(contentType).bytes(bytes).build(); - - // Build metadata map (skip null values) - Map metadata = new HashMap<>(); - String userId = null; - String userEmail = null; - - Principal principal = - requestContext.getSecurityContext() != null ? requestContext.getSecurityContext().getUserPrincipal() : null; - if (principal instanceof AuthUser) { - AuthUser authUser = (AuthUser) principal; - userId = authUser.getUserId(); - userEmail = authUser.getEmail(); - } - if (userId == null) { - Object usernameProp = requestContext.getProperty("username"); - if (usernameProp != null) { - userId = usernameProp.toString(); - } - } - - if (userId != null) { - metadata.put("user_id", userId); - } - if (userEmail != null) { - metadata.put("user_email", userEmail); - } - - // Originating caller (e.g. PYTHON_ADAPTER / R_ADAPTER) - String caller = httpServletRequest.getHeader("X-Client-Type"); - - // Session ID - String sessionId = - SessionIdResolver.resolve(httpServletRequest.getHeader("X-Session-Id"), srcIp, httpServletRequest.getHeader("User-Agent")); - - // API version - if (fullPath.contains("/v3/")) { - metadata.put("api_version", "v3"); - } - - // Merge domain-specific metadata from AuditContext (set by services). - // Filter-managed keys take precedence over AuditContext values. - if (auditContext != null) { - auditContext.getMetadata().forEach(metadata::putIfAbsent); - } - - // Build error map for 4xx/5xx - Map errorMap = null; - if (responseStatus >= 400) { - errorMap = new HashMap<>(); - errorMap.put("status", responseStatus); - errorMap.put("error_type", responseStatus >= 500 ? "server_error" : "client_error"); - } - - // Build the event - LoggingEvent.Builder eventBuilder = - LoggingEvent.builder(eventType).action(action).sessionId(sessionId).request(requestInfo).metadata(metadata); - - if (caller != null && !caller.isEmpty()) { - eventBuilder.caller(caller); - } - - if (errorMap != null) { - eventBuilder.error(errorMap); - } - - LoggingEvent event = eventBuilder.build(); - - // Send the event with bearer token passthrough - String authHeader = requestContext.getHeaderString("Authorization"); - String requestId = httpServletRequest.getHeader("X-Request-Id"); - - if (authHeader != null || requestId != null) { - loggingClient.send(event, authHeader, requestId); - } else { - loggingClient.send(event); - } - - } catch (Exception e) { - logger.warn("AuditLoggingFilter failed to log request", e); - } - } -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/security/AuthSecurityContext.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/security/AuthSecurityContext.java deleted file mode 100644 index f3d862466..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/security/AuthSecurityContext.java +++ /dev/null @@ -1,56 +0,0 @@ -package edu.harvard.dbmi.avillach.security; - -import edu.harvard.dbmi.avillach.data.entity.AuthUser; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.json.Json; -import javax.ws.rs.core.SecurityContext; -import java.security.Principal; -import java.util.Arrays; - -public class AuthSecurityContext implements SecurityContext { - private static final Logger logger = LoggerFactory.getLogger(AuthSecurityContext.class); - private AuthUser user; - private String scheme; - - public AuthSecurityContext(AuthUser user, String scheme) { - this.user = user; - this.scheme = scheme; - } - - @Override - public Principal getUserPrincipal() { - return this.user; - } - - @Override - public boolean isUserInRole(String role) { - boolean result = false; - if (user.getPrivileges() != null) { - result = user.getPrivileges().stream().map(String::trim).anyMatch(r -> r.equals(role)); - } - - logger.info("isUserInRole() check: requestedRole='{}', userRoles='{}', result={}", role, user.getPrivileges(), result); - return result; - } - - @Override - public boolean isSecure() { - return "https".equals(this.scheme); - } - - @Override - public String getAuthenticationScheme() { - return SecurityContext.DIGEST_AUTH; - } - - @Override - public String toString(){ - return Json.createObjectBuilder() - .add("scheme", scheme) - .add("user", user.getName()) - .build().toString(); - } -} \ No newline at end of file diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/security/JWTFilter.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/security/JWTFilter.java deleted file mode 100755 index fa2f9ba59..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/security/JWTFilter.java +++ /dev/null @@ -1,495 +0,0 @@ -package edu.harvard.dbmi.avillach.security; - -import com.fasterxml.jackson.core.JsonParseException; -import com.fasterxml.jackson.core.type.TypeReference; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; -import edu.harvard.dbmi.avillach.PicSureWarInit; -import edu.harvard.dbmi.avillach.data.entity.Query; -import edu.harvard.dbmi.avillach.data.entity.AuthUser; -import edu.harvard.dbmi.avillach.data.repository.QueryRepository; -import edu.harvard.dbmi.avillach.data.repository.ResourceRepository; -import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest; -import edu.harvard.dbmi.avillach.domain.QueryRequest; -import edu.harvard.dbmi.avillach.service.AuditContext; -import edu.harvard.dbmi.avillach.service.ResourceWebClient; -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.response.PICSUREResponse; -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.http.client.methods.CloseableHttpResponse; -import org.apache.http.client.methods.HttpPost; -import org.apache.http.entity.StringEntity; -import org.apache.http.impl.client.CloseableHttpClient; -import org.apache.http.util.EntityUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.annotation.Priority; -import javax.annotation.Resource; -import javax.inject.Inject; -import javax.ws.rs.HttpMethod; -import javax.ws.rs.NotAuthorizedException; -import javax.ws.rs.Priorities; -import javax.ws.rs.container.ContainerRequestContext; -import javax.ws.rs.container.ContainerRequestFilter; -import javax.ws.rs.container.ResourceInfo; -import javax.ws.rs.core.Context; -import javax.ws.rs.core.HttpHeaders; -import javax.ws.rs.core.Response; -import javax.ws.rs.core.UriInfo; -import javax.ws.rs.ext.Provider; -import javax.servlet.http.HttpServletRequest; - -import java.io.*; -import java.util.*; -import java.util.regex.Pattern; - -import static edu.harvard.dbmi.avillach.util.Utilities.buildHttpClientContext; - -class PathRule { - final Pattern pattern; - final Set allowedMethods; // null means all methods - - PathRule(String regex, String... methods) { - this.pattern = Pattern.compile(regex); - this.allowedMethods = methods.length == 0 ? null : Set.of(methods); - } - - boolean matches(String path, String method) { - if (!pattern.matcher(path).find()) { - return false; - } - return allowedMethods == null || allowedMethods.contains(method); - } -} - - -// Runs at AUTHENTICATION priority so the SecurityContext is installed before RESTEasy's -// RolesAllowed enforcement (RoleBasedSecurityFilter, Priorities.AUTHORIZATION); otherwise the -// role check evaluates an anonymous context and @RolesAllowed cannot see the user's roles. -@Provider -@Priority(Priorities.AUTHENTICATION) -public class JWTFilter implements ContainerRequestFilter { - private final Logger logger = LoggerFactory.getLogger(JWTFilter.class); - private static final List EXCLUDED_PATHS = Arrays.asList( - new PathRule("\\/openapi\\.json$"), - // Matches GET /configuration or /configuration/ with optional trailing slash - // Excludes /configuration/admin(/*) routes - new PathRule("^\\/configuration(\\/(?!admin\\/?$)[\\w\\d\\-?\\[\\].():]*)?\\/?$", HttpMethod.GET), - new PathRule("^\\/proxy/pic-sure-logging") - ); - - @Context - UriInfo uriInfo; - - @Context - ResourceInfo resourceInfo; - - @Inject - ResourceRepository resourceRepo; - - @Inject - ResourceWebClient resourceWebClient; - - @Resource(mappedName = "java:global/user_id_claim") - private String userIdClaim; - - ObjectMapper mapper = new ObjectMapper(); - - @Inject - PicSureWarInit picSureWarInit; - - @Inject - QueryRepository queryRepo; - - @Inject - AuditContext auditContext; - - @Context - HttpServletRequest httpServletRequest; - - private String extractClientIp() { - if (httpServletRequest == null) return null; - String xff = httpServletRequest.getHeader("X-Forwarded-For"); - if (xff != null && !xff.isEmpty()) { - return xff.split(",")[0].trim(); - } - return httpServletRequest.getRemoteAddr(); - } - - private String extractSessionId() { - if (httpServletRequest == null) return null; - String sessionHeader = httpServletRequest.getHeader("X-Session-Id"); - if (sessionHeader != null && !sessionHeader.isEmpty()) { - return sessionHeader; - } - String ip = extractClientIp(); - String ua = httpServletRequest.getHeader("User-Agent"); - String raw = (ip != null ? ip : "") + "|" + (ua != null ? ua : ""); - return Integer.toHexString(raw.hashCode()); - } - - @Override - public void filter(ContainerRequestContext requestContext) throws IOException { - logger.debug("Entered jwtfilter.filter()..."); - String rawPath = requestContext.getUriInfo().getPath(); - String path = rawPath.startsWith("/") ? rawPath : "/" + rawPath; - String method = requestContext.getRequest().getMethod(); - - if (EXCLUDED_PATHS.stream().anyMatch(rule -> rule.matches(path, method))) { - logger.info("Accessing excluded path " + path + " method " + method); - return; - } - - if (path.contentEquals("/system/status") && method.contentEquals(HttpMethod.GET)) { - // GET calls to /system/status do not require authentication or authorization - requestContext.setProperty("username", "SYSTEM_MONITOR"); - } else { - // Everything else goes through PSAMA token introspection - String authorizationHeader = requestContext.getHeaderString(HttpHeaders.AUTHORIZATION); - boolean isOpenAccessEnabled = picSureWarInit.isOpenAccessEnabled(); - // get referer header - - if ( - (StringUtils.isBlank(authorizationHeader) && isOpenAccessEnabled) - || (StringUtils.isNotBlank(authorizationHeader) && authorizationHeader.length() <= 7 && isOpenAccessEnabled) - ) { - boolean isAuthorized = callOpenAccessValidationEndpoint(requestContext); - if (!isAuthorized) { - logger.error("User is not authorized."); - auditContext.put("auth_result", "failure"); - auditContext.put("auth_action", "open_access.denied"); - requestContext.abortWith(PICSUREResponse.unauthorizedError("User is not authorized.")); - return; - } - - // There is no user associated with open access request. In order to provide traceability, - // we set the username to OPEN_ACCESS: - requestContext.setProperty("username", "OPEN_ACCESS:" + requestContext.getUriInfo().getRequestUri().getHost()); - auditContext.put("auth_result", "success"); - auditContext.put("auth_action", "open_access.granted"); - } else { - if (authorizationHeader == null || authorizationHeader.isEmpty()) { - auditContext.put("auth_result", "failure"); - auditContext.put("auth_failure_reason", "missing_token"); - throw new NotAuthorizedException("No authorization header found."); - } - - String token = authorizationHeader.substring(6).trim(); - if (token.isEmpty()) { - auditContext.put("auth_result", "failure"); - auditContext.put("auth_failure_reason", "empty_token"); - throw new NotAuthorizedException("No token found in authorization header."); - } - - String userForLogging = null; - try { - AuthUser authenticatedUser = null; - - authenticatedUser = callTokenIntroEndpoint(requestContext, token, userIdClaim); - if (authenticatedUser == null) { - logger.error("Cannot extract a user from token: {}", token); - auditContext.put("auth_result", "failure"); - auditContext.put("auth_failure_reason", "invalid_token"); - auditContext.put("auth_failure_message", "Cannot extract user from token"); - throw new NotAuthorizedException("Cannot find or create a user"); - } - - userForLogging = authenticatedUser.getUserId(); - - // The request context wants to remember who the user is - requestContext.setProperty("username", userForLogging); - // TEMP DIAGNOSTIC (remove after root-causing @RolesAllowed): shows the roles string PSAMA - // introspection returned for this user, which is what @RolesAllowed is matched against. - logger - .info("Installing AuthSecurityContext for user '{}' with roles='{}'", userForLogging, authenticatedUser.getRoles()); - requestContext.setSecurityContext(new AuthSecurityContext(authenticatedUser, uriInfo.getRequestUri().getScheme())); - logger.info("User - {} - has just passed all the authentication and authorization layers.", userForLogging); - auditContext.put("auth_result", "success"); - } catch (NotAuthorizedException e) { - // the detail of this exception should be logged right before the exception thrown out - logger.error("User - {} - is not authorized. {}", userForLogging, e.getChallenges()); - auditContext.put("auth_result", "failure"); - auditContext.put("auth_failure_reason", "not_authorized"); - auditContext.put("auth_failure_message", e.getMessage() != null ? e.getMessage() : "Not authorized"); - requestContext.abortWith(PICSUREResponse.unauthorizedError("User is not authorized. " + e.getChallenges())); - } catch (Exception e) { - logger - .error("User - {} - is not authorized {} and an Inner application error occurred.", userForLogging, e.getMessage()); - auditContext.put("auth_result", "failure"); - auditContext.put("auth_failure_reason", "internal_error"); - auditContext.put("auth_failure_message", e.getMessage() != null ? e.getMessage() : "Internal error"); - requestContext.abortWith(PICSUREResponse.applicationError("Inner application error, please contact system admin")); - } - } - } - } - - /** - * @param token - * @param userIdClaim - * @return - * @throws IOException - */ - - private AuthUser callTokenIntroEndpoint(ContainerRequestContext requestContext, String token, String userIdClaim) { - logger.debug("TokenIntrospection - extractUserFromTokenIntrospection() starting..."); - - String token_introspection_url = picSureWarInit.getToken_introspection_url(); - String token_introspection_token = picSureWarInit.getToken_introspection_token(); - - if (token_introspection_url.isEmpty()) throw new ApplicationException("token_introspection_url is empty"); - - if (token_introspection_token.isEmpty()) { - throw new ApplicationException("token_introspection_token is empty"); - } - - ObjectMapper json = PicSureWarInit.objectMapper; - CloseableHttpClient client = PicSureWarInit.CLOSEABLE_HTTP_CLIENT; - - HttpPost post = new HttpPost(token_introspection_url); - - Map tokenMap = new HashMap<>(); - tokenMap.put("token", token); - - Map requestMap = prepareRequestMap(requestContext); - tokenMap.put("request", requestMap); - - StringEntity entity = null; - try { - entity = new StringEntity(json.writeValueAsString(tokenMap)); - } catch (IOException e) { - logger.error("callTokenIntroEndpoint() - " + e.getClass().getSimpleName() + " when composing post"); - return null; - } - post.setEntity(entity); - post.setHeader("Content-Type", "application/json"); - // Authorize into the token introspection endpoint - post.setHeader("Authorization", "Bearer " + token_introspection_token); - CloseableHttpResponse response = null; - try { - response = client.execute(post, buildHttpClientContext()); - if (response.getStatusLine().getStatusCode() != 200) { - logger.error( - "callTokenIntroEndpoint() error back from token intro host server [" + token_introspection_url + "]: " - + EntityUtils.toString(response.getEntity()) - ); - logger.info( - "This callTokenIntroEndpoint error can happen when your introspection token has expired. " - + "You can fix this by running the Configure PIC-SURE Token Introspection Token job in Jenkins." - ); - throw new ApplicationException( - "Token Introspection host server return " + response.getStatusLine().getStatusCode() + ". Please see the log" - ); - } - JsonNode responseContent = json.readTree(response.getEntity().getContent()); - if (!responseContent.get("active").asBoolean()) { - logger.error("callTokenIntroEndpoint() Token intro endpoint return invalid token, content: " + responseContent); - throw new NotAuthorizedException("Token invalid or expired"); - } - - if (responseContent.has("tokenRefreshed") && responseContent.get("tokenRefreshed").asBoolean()) { - requestContext.setProperty("refreshedToken", responseContent.get("token")); - } - - String userId = responseContent.get(userIdClaim) != null ? responseContent.get(userIdClaim).asText() : null; - String sub = responseContent.get("sub") != null ? responseContent.get("sub").asText() : null; - String email = responseContent.get("email") != null ? responseContent.get("email").asText() : null; - String roles = responseContent.get("roles") != null ? responseContent.get("roles").asText() : null; - Set privileges = - responseContent.get("privileges") != null ? json.convertValue(responseContent.get("privileges"), new TypeReference<>() {}) - : Collections.emptySet(); - AuthUser user = new AuthUser().setUserId(userId).setSubject(sub).setEmail(email).setRoles(roles).setPrivileges(privileges); - - // If there is a query in the response, PSAMA has updated the authorization filters and we must update the query - if (responseContent.get("query") != null) { - QueryRequest queryObject = new ObjectMapper().readValue(requestContext.getEntityStream(), QueryRequest.class); - JsonNode updatedQuery = responseContent.get("query"); - // PSAMA sends the updated query as a JSON string; parse it back into an object instead of - // storing the raw text, otherwise it gets re-escaped as a string when the request is - // re-serialized below, and again when it's persisted, corrupting stored queries with extra slashes. - Object parsedQuery = updatedQuery.isTextual() ? json.readValue(updatedQuery.asText(), Object.class) - : json.convertValue(updatedQuery, Object.class); - queryObject.setQuery(parsedQuery); - requestContext.setEntityStream(new ByteArrayInputStream(new ObjectMapper().writeValueAsBytes(queryObject))); - } - return user; - } catch (IOException ex) { - logger.error("callTokenIntroEndpoint() IOException when hitting url: " + post + " with exception msg: " + ex.getMessage()); - } finally { - try { - if (response != null) response.close(); - } catch (IOException ex) { - logger.error("callTokenIntroEndpoint() IOExcpetion when closing http response: " + ex.getMessage()); - } - } - - return null; - } - - private HashMap prepareRequestMap(ContainerRequestContext requestContext) { - ByteArrayOutputStream buffer = new ByteArrayOutputStream(); - HashMap requestMap = new HashMap(); - try { - String requestPath = requestContext.getUriInfo().getPath(); - requestMap.put("Target Service", requestPath); - - Query initialQuery = null; - // Read the query from the backing store if we are getting the results (full query may not be specified in request) - if ( - (requestPath.startsWith("/query/") || requestPath.startsWith("/v3/query/")) && (requestPath.endsWith("result") - || requestPath.endsWith("result/") || requestPath.endsWith("signed-url") || requestPath.endsWith("signed-url/")) - ) { - // Path: /query/{queryId}/result - String[] pathParts = requestPath.split("/"); - UUID uuid = UUID.fromString(pathParts[requestPath.startsWith("/query/") ? 2 : 3]); - logger.debug("Query ID: " + uuid); - initialQuery = queryRepo.getById(uuid); - } - - if (initialQuery != null) { - logger.debug("Initial Query found:" + initialQuery); - IOUtils.copy(new ByteArrayInputStream(initialQuery.getQuery().getBytes()), buffer); - } else { - logger.debug("Initial Query is null"); - // This stream is only consumable once, so we need to save & reset it. - InputStream entityStream = requestContext.getEntityStream(); - IOUtils.copy(entityStream, buffer); - requestContext.setEntityStream(new ByteArrayInputStream(buffer.toByteArray())); - } - - if (buffer.size() > 0) { - /* - * We remove the resourceCredentials from the token introspection copy of the query to prevent logging them as part of token - * introspection. These credentials are between the backing resource and the user, PIC-SURE should do its best to keep them - * confidential. - */ - // todo: only do this when appropriate. this is expected to fail A LOT, so we can't log errors when it fails for reasons we - // would like to know about - Object queryObject = new ObjectMapper().readValue(new ByteArrayInputStream(buffer.toByteArray()), Object.class); - if (queryObject instanceof Collection) { - for (Object query : (Collection) queryObject) { - if (query instanceof Map) { - ((Map) query).remove("resourceCredentials"); - } - } - } else if (queryObject instanceof Map) { - ((Map) queryObject).remove("resourceCredentials"); - } - requestMap.put("query", queryObject); - - if (requestPath.startsWith("/query/")) { - - UUID resourceUUID = null; - String resourceUUIDStr = (String) ((Map) queryObject).get("resourceUUID"); - if (resourceUUIDStr != null) { - resourceUUID = UUID.fromString(resourceUUIDStr); - } - - if (resourceUUID != null) { - edu.harvard.dbmi.avillach.data.entity.Resource resource = resourceRepo.getById(resourceUUID); - // logger.info("resource obj: " + resource + " path: " + resource.getResourceRSPath()); - if (resource != null && resource.getResourceRSPath() != null) { - GeneralQueryRequest queryRequest = new GeneralQueryRequest(); - queryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken()); - queryRequest.setResourceUUID(resourceUUID); - queryRequest.setQuery(((Map) queryObject).get("query")); - - Response formatResponse = resourceWebClient.queryFormat(resource.getResourceRSPath(), queryRequest); - if (formatResponse.getStatus() == 200) { - // add the formatted query if available - String formattedQuery = (String) formatResponse.getEntity(); - logger.debug("Formatted response: " + formattedQuery); - requestMap.put("formattedQuery", formattedQuery); - } - } - } - } - } - return requestMap; - } catch (JsonParseException ex) { - logger.warn("Error parsing json", ex); - requestMap.put("query", buffer.toString()); - return requestMap; - } catch (IOException e1) { - logger.error("IOException caught trying to build requestMap for auditing.", e1); - throw new NotAuthorizedException( - "The request could not be properly audited. If you receive this error multiple times, please contact an administrator." - ); - } - } - - private boolean callOpenAccessValidationEndpoint(ContainerRequestContext requestContext) { - String openAccessValidateUrl = picSureWarInit.getOpenAccessValidateUrl(); - String token_introspection_token = picSureWarInit.getToken_introspection_token(); - - if (openAccessValidateUrl.isEmpty()) { - throw new ApplicationException("callOpenAccessValidationEndpoint - openAccessValidateUrl is empty in application properties"); - } - - Map requestMap = new HashMap<>(); - Map queryMap = prepareRequestMap(requestContext); - requestMap.put("request", queryMap); - // There is no user associated with open access request. In order to provide traceability, - // we set the username to OPEN_ACCESS: - requestMap.put("ipAddress", "OPEN_ACCESS:" + requestContext.getUriInfo().getRequestUri().getHost()); - ObjectMapper json = PicSureWarInit.objectMapper; - - StringEntity entity = null; - try { - entity = new StringEntity(json.writeValueAsString(requestMap)); - } catch (IOException e) { - logger.error("callOpenAccessValidationEndpoint() - FAILED TO parse requestMap to json", e); - return false; - } - - CloseableHttpClient client = PicSureWarInit.CLOSEABLE_HTTP_CLIENT; - HttpPost post = new HttpPost(openAccessValidateUrl); - post.setEntity(entity); - post.setHeader("Content-Type", "application/json"); - // Authorize into the token introspection endpoint - post.setHeader("Authorization", "Bearer " + token_introspection_token); - CloseableHttpResponse response = null; - boolean isValid = false; - try { - response = client.execute(post, buildHttpClientContext()); - - if (response.getStatusLine().getStatusCode() == 200) { - - // A 200 is return as long as the request is successful, the actual validation result is in the response body - JsonNode responseContent = json.readTree(response.getEntity().getContent()); - if (!responseContent.isBoolean()) { - logger.error( - "callOpenAccessValidateEndpoint() Open access validate endpoint return invalid response, content: {}", - responseContent - ); - throw new ApplicationException("Open access validate endpoint returned an invalid response"); - } - - isValid = responseContent.asBoolean(); - } else { - logger.error( - "callOpenAccessValidateEndpoint() error returned from psama [{}]: {}", openAccessValidateUrl, - EntityUtils.toString(response.getEntity()) - ); - throw new ApplicationException("Not able to validate open access request"); - } - - } catch (IOException ex) { - logger.error("callOpenAccessValidateEndpoint() IOException when hitting url: {} with exception msg: {}", post, ex.getMessage()); - } finally { - try { - if (response != null) response.close(); - } catch (IOException ex) { - logger.error("callOpenAccessValidateEndpoint() IOException when closing http response: {}", ex.getMessage()); - } - } - - return isValid; - } - - void setUserIdClaim(String userIdClaim) { - this.userIdClaim = userIdClaim; - } -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/security/JWTResponseFilter.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/security/JWTResponseFilter.java deleted file mode 100644 index a26e936e7..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/security/JWTResponseFilter.java +++ /dev/null @@ -1,28 +0,0 @@ -package edu.harvard.dbmi.avillach.security; - -import com.fasterxml.jackson.databind.node.TextNode; - -import javax.ws.rs.container.ContainerRequestContext; -import javax.ws.rs.container.ContainerResponseContext; -import javax.ws.rs.container.ContainerResponseFilter; -import javax.ws.rs.core.HttpHeaders; -import javax.ws.rs.ext.Provider; -import java.io.IOException; - -@Provider -public class JWTResponseFilter implements ContainerResponseFilter { - - @Override - public void filter(ContainerRequestContext containerRequestContext, ContainerResponseContext containerResponseContext) - throws IOException { - Object tokenObject = containerRequestContext.getProperty("refreshedToken"); - - if (tokenObject instanceof TextNode) { - String newToken = ((TextNode) tokenObject).asText(); - containerResponseContext.getHeaders().add(HttpHeaders.AUTHORIZATION, "Bearer " + newToken); - } else if (tokenObject instanceof String) { - String newToken = (String) tokenObject; - containerResponseContext.getHeaders().add(HttpHeaders.AUTHORIZATION, "Bearer " + newToken); - } - } -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/AuditContext.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/AuditContext.java deleted file mode 100644 index 87ffd9a5d..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/AuditContext.java +++ /dev/null @@ -1,26 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import java.util.HashMap; -import java.util.Map; - -import javax.enterprise.context.RequestScoped; - -/** - * Request-scoped holder for audit metadata. Services populate this with domain-specific context (resource_id, query_id, etc.) and the - * AuditLoggingFilter merges it into the logging event alongside request-level metadata (IP, duration, status). - */ -@RequestScoped -public class AuditContext { - - private final Map metadata = new HashMap<>(); - - public void put(String key, Object value) { - if (key != null && value != null) { - metadata.put(key, value); - } - } - - public Map getMetadata() { - return metadata; - } -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/ConfigurationService.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/ConfigurationService.java deleted file mode 100644 index 48e316a72..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/ConfigurationService.java +++ /dev/null @@ -1,127 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import edu.harvard.dbmi.avillach.data.entity.Configuration; -import edu.harvard.dbmi.avillach.data.repository.ConfigurationRepository; -import edu.harvard.dbmi.avillach.data.request.ConfigurationRequest; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.inject.Inject; -import javax.transaction.Transactional; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Optional; -import java.util.UUID; - -public class ConfigurationService { - private final Logger logger = LoggerFactory.getLogger(ConfigurationService.class); - - @Inject - ConfigurationRepository configurationRepository; - - // If the request has no uuid it's new so match any uuid with this name &/or kind - // else, match any uuid with this name &/or kind that isn't the one we're updating - private boolean nameKindPairExists(Configuration config) { - Map columns = new HashMap<>(); - columns.put("name", config.getName()); - columns.put("kind", config.getKind()); - return configurationRepository.getByColumns(configurationRepository.query(), columns).stream().map(Configuration::getUuid) - .anyMatch(uuid -> config.getUuid() == null || !uuid.equals(config.getUuid())); - } - - public Optional> getConfigurations(String kind) { - try { - List configs = kind != null ? configurationRepository.getByColumn("kind", kind) : configurationRepository.list(); - return Optional.ofNullable(configs); - } catch (Exception exception) { - logger.error("Error retrieving configurations " + (kind != null ? "with kind " + kind : ""), exception); - return Optional.empty(); - } - } - - public Optional getConfigurationByIdentifier(String identifier) { - try { - // Try to parse as UUID first, but fall back to name lookup if not found - UUID uuid = UUID.fromString(identifier); - Configuration config = configurationRepository.getById(uuid); - if (config != null) { - return Optional.of(config); - } - List byName = configurationRepository.getByColumn("name", identifier); - return byName != null && !byName.isEmpty() ? Optional.of(byName.get(0)) : Optional.empty(); - } catch (IllegalArgumentException e) { - // Not a valid UUID, treat as name - List configs = configurationRepository.getByColumn("name", identifier); - return configs != null && !configs.isEmpty() ? Optional.of(configs.get(0)) : Optional.empty(); - } catch (Exception exception) { - logger.error("Error retrieving configurations with uuid " + identifier, exception); - return Optional.empty(); - } - } - - @Transactional - public Optional addConfiguration(ConfigurationRequest request) { - try { - Configuration config = Configuration.fromRequest(request); - - if (nameKindPairExists(config)) { - logger.error("Error persisting configuration: name already exists " + request.getName()); - return Optional.empty(); - } - - configurationRepository.persist(config); - logger.debug("Added configuration: " + config.getUuid()); - return Optional.of(config); - } catch (Exception exception) { - logger.error("Error persisting configuration " + request.getName(), exception); - return Optional.empty(); - } - } - - @Transactional - public Optional updateConfiguration(ConfigurationRequest request) { - try { - Configuration config = configurationRepository.getById(request.getUuid()); - if (config == null) { - logger.error("Configuration not found with id " + request.getUuid().toString()); - return Optional.empty(); - } - Configuration proposed = new Configuration(); - proposed.setUuid(config.getUuid()); - proposed.setName(request.getName() != null ? request.getName() : config.getName()); - proposed.setKind(request.getKind() != null ? request.getKind() : config.getKind()); - - if (nameKindPairExists(proposed)) { - logger.error("Error updating configuration: new name already exists " + request.getName()); - return Optional.empty(); - } - - config.patch(request); - configurationRepository.merge(config); - logger.debug("Updated configuration " + config.getUuid().toString() + "(" + config.getName() + ")"); - return Optional.of(config); - } catch (Exception exception) { - String requestName = request != null ? request.getName() : ""; - logger.error("Error updating configuration {}", requestName, exception); - return Optional.empty(); - } - } - - @Transactional - public Optional deleteConfiguration(UUID configurationId) { - try { - Configuration config = configurationRepository.getById(configurationId); - if (config == null) { - logger.error("Configuration not found with id " + configurationId.toString()); - return Optional.empty(); - } - configurationRepository.remove(config); - logger.debug("Deleted configuration " + config.getUuid().toString() + "(" + config.getName() + ")"); - return Optional.of(config); - } catch (Exception exception) { - logger.error("Error deleting configuration " + configurationId.toString(), exception); - return Optional.empty(); - } - } -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/FormatService.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/FormatService.java deleted file mode 100644 index abd7c0c4e..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/FormatService.java +++ /dev/null @@ -1,54 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import com.fasterxml.jackson.databind.ObjectMapper; -import edu.harvard.dbmi.avillach.data.entity.Resource; -import edu.harvard.dbmi.avillach.data.repository.ResourceRepository; -import edu.harvard.dbmi.avillach.domain.QueryRequest; -import edu.harvard.dbmi.avillach.util.Utilities; -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.inject.Inject; -import javax.ws.rs.core.HttpHeaders; -import javax.ws.rs.core.Response; -import java.util.HashMap; - -public class FormatService { - - private final Logger logger = LoggerFactory.getLogger(FormatService.class); - - private final static ObjectMapper mapper = new ObjectMapper(); - - @Inject - ResourceRepository resourceRepo; - - @Inject - ResourceWebClient resourceWebClient; - - public Response format(QueryRequest credentialsQueryRequest, HttpHeaders headers) { - Resource resource = resourceRepo.getById(credentialsQueryRequest.getResourceUUID()); - if (resource == null){ - throw new ProtocolException(ProtocolException.RESOURCE_NOT_FOUND + credentialsQueryRequest.getResourceUUID().toString()); - } - - if (resource.getResourceRSPath() == null){ - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - - if (credentialsQueryRequest.getResourceCredentials() == null) { - credentialsQueryRequest.setResourceCredentials(new HashMap()); - } - - String requestSourceFromHeader = Utilities.getRequestSourceFromHeader(headers); - logger.info("path=/bin/continuous, resourceId={}, requestSource={}, credentialsQueryRequest={}", - credentialsQueryRequest.getResourceUUID().toString(), - requestSourceFromHeader, - Utilities.convertQueryRequestToString(mapper, credentialsQueryRequest) - ); - - return resourceWebClient.queryContinuous(resource.getResourceRSPath(), credentialsQueryRequest, requestSourceFromHeader); - } - -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/LoggingClientProducer.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/LoggingClientProducer.java deleted file mode 100644 index d9ce8a0ff..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/LoggingClientProducer.java +++ /dev/null @@ -1,58 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import edu.harvard.dbmi.avillach.logging.LoggingClient; -import edu.harvard.dbmi.avillach.logging.LoggingClientConfig; - -import javax.annotation.PreDestroy; -import javax.enterprise.context.ApplicationScoped; -import javax.enterprise.inject.Produces; -import javax.naming.InitialContext; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -@ApplicationScoped -public class LoggingClientProducer { - - private static final Logger LOG = LoggerFactory.getLogger(LoggingClientProducer.class); - - private LoggingClient loggingClient; - - @Produces - @ApplicationScoped - public LoggingClient loggingClient() { - String url = jndiLookup("java:global/logging_service_url"); - String key = jndiLookup("java:global/logging_api_key"); - - if (!isConfigured(url) || !isConfigured(key)) { - LOG.info("logging-client: JNDI bindings not set; audit logging disabled"); - loggingClient = LoggingClient.noOp(); - } else { - LOG.info("logging-client: configured for {} (clientType=api)", url); - loggingClient = new LoggingClient(LoggingClientConfig.builder(url, key).clientType("api").build()); - } - return loggingClient; - } - - @PreDestroy - public void cleanup() { - try { - if (loggingClient != null) { - loggingClient.close(); - } - } catch (Exception ignored) { - } - } - - private static boolean isConfigured(String value) { - return value != null && !value.trim().isEmpty() && !"disabled".equalsIgnoreCase(value.trim()); - } - - private static String jndiLookup(String name) { - try { - return (String) new InitialContext().lookup(name); - } catch (Exception e) { - return null; - } - } -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/NamedDatasetService.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/NamedDatasetService.java deleted file mode 100644 index 04b916b8b..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/NamedDatasetService.java +++ /dev/null @@ -1,110 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import javax.inject.Inject; - -import java.util.List; -import java.util.Optional; -import java.util.UUID; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import edu.harvard.dbmi.avillach.data.entity.NamedDataset; -import edu.harvard.dbmi.avillach.data.entity.Query; -import edu.harvard.dbmi.avillach.data.repository.NamedDatasetRepository; -import edu.harvard.dbmi.avillach.data.repository.QueryRepository; -import edu.harvard.dbmi.avillach.data.request.NamedDatasetRequest; -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; - -public class NamedDatasetService { - private final Logger logger = LoggerFactory.getLogger(NamedDatasetService.class); - - @Inject - NamedDatasetRepository namedDatasetRepo; - - @Inject - QueryRepository queryRepo; - - public Optional> getNamedDatasets(String user){ - List queries = namedDatasetRepo.getByColumn("user", user); - return Optional.ofNullable(queries); - } - - public Optional getNamedDatasetById(String user, UUID datasetId){ - NamedDataset dataset = namedDatasetRepo.getById(datasetId); - if (dataset == null){ - logger.error("named dataset not found with id " + datasetId.toString()); - return Optional.empty(); - } - - if (!dataset.getUser().toString().equals(user)){ - logger.error("named dataset with id " + datasetId.toString() + " not able to be viewed by user " + user); - return Optional.empty(); - } - - return Optional.of(dataset); - } - - public Optional addNamedDataset(String user, NamedDatasetRequest request){ - UUID queryId = request.getQueryId(); - Query query = queryRepo.getById(queryId); - if (query == null){ - logger.error(ProtocolException.QUERY_NOT_FOUND + queryId.toString()); - return Optional.empty(); - } - - NamedDataset dataset = new NamedDataset() - .setName(request.getName()) - .setQuery(query) - .setUser(user) - .setArchived(request.getArchived()) - .setMetadata(request.getMetadata()); - - try { - namedDatasetRepo.persist(dataset); - logger.debug("persisted named dataset with query id " + queryId.toString()); - } catch (Exception exception){ - logger.error("Error persisting named dataset with query id " + queryId.toString(), exception); - return Optional.empty(); - } - - return Optional.of(dataset); - } - - public Optional updateNamedDataset(String user, UUID datasetId, NamedDatasetRequest request){ - NamedDataset dataset = namedDatasetRepo.getById(datasetId); - if (dataset == null){ - logger.error("named dataset not found with id " + datasetId.toString()); - return Optional.empty(); - } - - if (!dataset.getUser().equals(user)){ - logger.error("named dataset with id " + datasetId.toString() + " not able to be updated by user " + user); - return Optional.empty(); - } - - UUID queryId = request.getQueryId(); - if (!dataset.getQuery().getUuid().equals(queryId)){ - Query query = queryRepo.getById(queryId); - if (query == null){ - logger.error(ProtocolException.QUERY_NOT_FOUND + queryId.toString()); - return Optional.empty(); - } - dataset.setQuery(query); - } - - dataset.setName(request.getName()) - .setArchived(request.getArchived()) - .setMetadata(request.getMetadata()); - - try { - namedDatasetRepo.merge(dataset); - logger.debug("updated named dataset with id " + datasetId.toString() + " and query id " + queryId.toString()); - } catch (Exception exception){ - logger.error("Error updating named dataset with id " + datasetId.toString() + " and query id " + queryId.toString(), exception); - return Optional.empty(); - } - - return Optional.of(dataset); - } -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureBaseEntityService.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureBaseEntityService.java deleted file mode 100644 index b3eaa49d6..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureBaseEntityService.java +++ /dev/null @@ -1,144 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import edu.harvard.dbmi.avillach.data.entity.BaseEntity; -import edu.harvard.dbmi.avillach.data.repository.BaseRepository; -import edu.harvard.dbmi.avillach.util.response.PICSUREResponse; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.validation.constraints.NotNull; -import javax.ws.rs.core.Response; -import java.util.ArrayList; -import java.util.List; -import java.util.UUID; - -public abstract class PicsureBaseEntityService { - - private Logger logger; - - protected final Class type; - - protected PicsureBaseEntityService (Class type){ - this.type = type; - logger = LoggerFactory.getLogger(type); - } - - public Response getEntityById(String id, BaseRepository baseRepository){ - logger.info("Looking for " + type.getSimpleName().toLowerCase() + - " by ID: " + id + "..."); - - T t = (T) baseRepository.getById(UUID.fromString(id)); - - if (t == null) - return PICSUREResponse.protocolError(type.getSimpleName() + " is not found by given " + - type.getSimpleName().toLowerCase() + " ID: " + id); - else - return PICSUREResponse.success(t); - } - - public Response getEntityAll(BaseRepository baseRepository){ - logger.info("Getting all " + type.getSimpleName() + - "s..."); - List ts = null; - - ts = baseRepository.list(); - - if (ts == null) - return PICSUREResponse.applicationError("Error occurs when listing all " - + type.getSimpleName() + - "s."); - - return PICSUREResponse.success(ts); - } - - public Response addEntity(List entities, BaseRepository baseRepository){ - if (entities == null || entities.isEmpty()) - return PICSUREResponse.protocolError("No " + type.getSimpleName().toLowerCase() + - " to be added."); - - List addedEntities = addOrUpdate(entities, true, baseRepository); - - if (addedEntities.isEmpty()) - return PICSUREResponse.protocolError("No " + type.getSimpleName().toLowerCase() + - "(s) has been added."); - - if (addedEntities.size() < entities.size()) - return PICSUREResponse.success(Integer.toString(entities.size()-addedEntities.size()) - + " " + type.getSimpleName().toLowerCase() + - "s are NOT operated." + - " Added " + type.getSimpleName().toLowerCase() + - "s are as follow: ", addedEntities); - - return PICSUREResponse.success("All " + type.getSimpleName().toLowerCase() + - "s are added.", addedEntities); - } - - public Response updateEntity(List entities, BaseRepository baseRepository){ - if (entities == null || entities.isEmpty()) - return PICSUREResponse.protocolError("No " + type.getSimpleName().toLowerCase() + - " to be updated."); - - List addedEntities = addOrUpdate(entities, false, baseRepository); - - if (addedEntities.isEmpty()) - return PICSUREResponse.protocolError("No " + type.getSimpleName().toLowerCase() + - "(s) has been updated."); - - - if (addedEntities.size() < entities.size()) - return PICSUREResponse.success(Integer.toString(entities.size()-addedEntities.size()) - + " " +type.getSimpleName().toLowerCase()+ - "s are NOT operated." + - " Updated " + type.getSimpleName().toLowerCase() + - "(s) are as follow: ", addedEntities); - - return PICSUREResponse.success("All " + type.getSimpleName().toLowerCase() + - "(s) are updated.", addedEntities); - - } - - protected List addOrUpdate(@NotNull List entities, boolean forAdd, BaseRepository baseRepository){ - List operatedEntities = new ArrayList<>(); - for (T t : entities){ - boolean dbContacted = false; - if (forAdd) { - t.setUuid(null); - baseRepository.persist(t); - dbContacted = true; - } - else if (baseRepository.getById(t.getUuid()) != null) { - baseRepository.merge(t); - dbContacted = true; - } - - if (!dbContacted || t.getUuid() == null || baseRepository.getById(t.getUuid()) == null){ - continue; - } - operatedEntities.add(t); - } - return operatedEntities; - } - - public Response removeEntityById(String id, BaseRepository baseRepository) { - UUID uuid = UUID.fromString(id); - T t = (T) baseRepository.getById(uuid); - if (t == null) - return PICSUREResponse.protocolError(type.getSimpleName() + - " is not found by " + type.getSimpleName().toLowerCase() + - " ID"); - - baseRepository.remove(t); - - t = (T) baseRepository.getById(uuid); - if (t != null){ - return PICSUREResponse.applicationError("Cannot delete the " + type.getSimpleName().toLowerCase()+ - " by id: " + id); - } - - return PICSUREResponse.success("Successfully deleted " + type.getSimpleName().toLowerCase() + - " by id: " + id + ", listing rest of the " + type.getSimpleName().toLowerCase() + - "(s) as below" - , baseRepository.list()); - - } -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureInfoService.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureInfoService.java deleted file mode 100644 index a64cf005d..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureInfoService.java +++ /dev/null @@ -1,75 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import com.fasterxml.jackson.databind.ObjectMapper; -import edu.harvard.dbmi.avillach.data.entity.Resource; -import edu.harvard.dbmi.avillach.data.repository.ResourceRepository; -import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest; -import edu.harvard.dbmi.avillach.domain.QueryRequest; -import edu.harvard.dbmi.avillach.domain.ResourceInfo; -import edu.harvard.dbmi.avillach.util.Utilities; -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.inject.Inject; -import javax.ws.rs.core.HttpHeaders; -import java.util.HashMap; -import java.util.Map; -import java.util.UUID; -import java.util.stream.Collectors; - -public class PicsureInfoService { - - private final Logger logger = LoggerFactory.getLogger(PicsureQueryService.class); - - private final static ObjectMapper mapper = new ObjectMapper(); - - @Inject - ResourceRepository resourceRepo; - - @Inject - ResourceWebClient resourceWebClient; - - /** - * Retrieve resource info for a specific resource. - * - * @param resourceId - Resource UUID - * @param credentialsQueryRequest - Contains resource specific credentials map - * @return a {@link edu.harvard.dbmi.avillach.domain.ResourceInfo ResourceInfo} - */ - public ResourceInfo info(UUID resourceId, QueryRequest credentialsQueryRequest, HttpHeaders headers) { - Resource resource = resourceRepo.getById(resourceId); - if (resource == null) { - throw new ProtocolException(ProtocolException.RESOURCE_NOT_FOUND + resourceId.toString()); - } - if (resource.getResourceRSPath() == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - if (credentialsQueryRequest == null) { - credentialsQueryRequest = new GeneralQueryRequest(); - } - if (credentialsQueryRequest.getResourceCredentials() == null) { - credentialsQueryRequest.setResourceCredentials(new HashMap()); - } - - logger.info( - "path=/info/{resourceId}, resourceId={}, requestSource={}, credentialsQueryRequest={}", resourceId, - Utilities.getRequestSourceFromHeader(headers), Utilities.convertQueryRequestToString(mapper, credentialsQueryRequest) - ); - - credentialsQueryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken()); - return resourceWebClient.info(resource.getResourceRSPath(), credentialsQueryRequest); - } - - /** - * Retrieve a list of all available resources. - * - * @return List containing limited metadata about all available resources and ids. - */ - public Map resources(HttpHeaders headers) { - logger.info("path=/info/resources, requestSource={}", Utilities.getRequestSourceFromHeader(headers)); - return resourceRepo.list().stream().filter(resource -> !resource.getHidden()) - .collect(Collectors.toMap(Resource::getUuid, Resource::getName)); - } -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureQueryService.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureQueryService.java deleted file mode 100644 index bc9ad4778..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureQueryService.java +++ /dev/null @@ -1,483 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; -import edu.harvard.dbmi.avillach.data.entity.DataSharingStatus; -import edu.harvard.dbmi.avillach.data.entity.Query; -import edu.harvard.dbmi.avillach.data.entity.Resource; -import edu.harvard.dbmi.avillach.data.repository.QueryRepository; -import edu.harvard.dbmi.avillach.data.repository.ResourceRepository; -import edu.harvard.dbmi.avillach.domain.*; -import edu.harvard.dbmi.avillach.security.JWTFilter; -import edu.harvard.dbmi.avillach.util.Utilities; -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.inject.Inject; -import javax.transaction.Transactional; -import javax.ws.rs.core.HttpHeaders; -import javax.ws.rs.core.Response; -import java.nio.charset.StandardCharsets; -import java.sql.Date; -import java.util.*; - -/** - * Service handling business logic for queries to resources - */ -public class PicsureQueryService { - - public static final String QUERY_RESULT_METADATA_FIELD = "queryResultMetadata"; - private static final String QUERY_JSON_FIELD = "queryJson"; - - private final Logger logger = LoggerFactory.getLogger(PicsureQueryService.class); - - private final static ObjectMapper mapper = new ObjectMapper(); - - @Inject - JWTFilter jwtFilter; - - @Inject - ResourceRepository resourceRepo; - - @Inject - QueryRepository queryRepo; - - @Inject - ResourceWebClient resourceWebClient; - - @Inject - SiteParsingService siteParsingService; - - @Inject - AuditContext auditContext; - - @Inject - PicsureQueryV3Service picsureQueryV3Service; - - /** - * Executes a query on a PIC-SURE resource and creates a Query entity in the database for the query. - * - * @param dataQueryRequest - - {@link QueryRequest} containing resource specific credentials object and resource specific query (could - * be a string or a json object) - * @return {@link QueryStatus} - */ - @Transactional - public QueryStatus query(QueryRequest dataQueryRequest, HttpHeaders headers) { - Resource resource = verifyQueryRequest(dataQueryRequest, headers); - - dataQueryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken()); - - QueryStatus results = resourceWebClient.query(resource.getResourceRSPath(), dataQueryRequest); - - Query queryEntity = copyQuery(dataQueryRequest, resource, results); - queryRepo.persist(queryEntity); - - logger.debug("PicsureQueryService() persisted queryEntity with id: " + queryEntity.getUuid()); - - if (auditContext != null) { - auditContext.put("resource_id", resource.getUuid().toString()); - auditContext.put("resource_name", resource.getName()); - auditContext.put("query_id", queryEntity.getUuid().toString()); - } - - results.setPicsureResultId(queryEntity.getUuid()); - // In cases where there is no resource result id, the picsure result id will stand in - if (queryEntity.getResourceResultId() == null) { - results.setResourceResultId(queryEntity.getUuid().toString()); - queryEntity.setResourceResultId(results.getPicsureResultId().toString()); - queryRepo.persist(queryEntity); - } - results.setResourceID(resource.getUuid()); - return results; - } - - /** - * Retrieves the {@link QueryStatus} for a given queryId by looking up the target resource from the database and calling the target - * resource for an updated status. The Query entities in the database are updated each time this is called. - * - * @param queryId - id of targeted resource - * @param credentialsQueryRequest - contains resource specific credentials object - * @return {@link QueryStatus} - */ - @Transactional - public QueryStatus queryStatus(UUID queryId, GeneralQueryRequest credentialsQueryRequest, HttpHeaders headers) { - if (queryId == null) { - throw new ProtocolException(ProtocolException.MISSING_QUERY_ID); - } - Query query = queryRepo.getById(queryId); - if (query == null) { - throw new ProtocolException(ProtocolException.QUERY_NOT_FOUND + queryId.toString()); - } - if (credentialsQueryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - if (isV3Query(query)) { - return picsureQueryV3Service.queryStatus(queryId, credentialsQueryRequest, headers); - } - Resource resource = query.getResource(); - verifyQueryStatusRequest(resource, credentialsQueryRequest, queryId, headers); - - // Update status on query object - QueryStatus status = - resourceWebClient.queryStatus(resource.getResourceRSPath(), query.getResourceResultId(), credentialsQueryRequest); - status.setPicsureResultId(queryId); - query.setStatus(status.getStatus()); - queryRepo.persist(query); - status.setStartTime(query.getStartTime().getTime()); - status.setResourceID(resource.getUuid()); - return status; - } - - /** - * Streams the result for a given queryId by looking up the target resource from the database and calling the target resource for a - * result. The queryStatus method should be used to verify that the result is available prior to retrieving it. - * - * @param queryId - id of target resource - * @param credentialsQueryRequest - contains resource specific credentials object - * @return Response - */ - @Transactional - public Response queryResult(UUID queryId, QueryRequest credentialsQueryRequest, HttpHeaders headers) { - if (queryId == null) { - throw new ProtocolException(ProtocolException.MISSING_QUERY_ID); - } - Query query = queryRepo.getById(queryId); - if (query == null) { - throw new ProtocolException(ProtocolException.QUERY_NOT_FOUND + queryId.toString()); - } - if (isV3Query(query)) { - return picsureQueryV3Service.queryResult(queryId, credentialsQueryRequest, headers); - } - Resource resource = query.getResource(); - if (resource == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE); - } - if (resource.getResourceRSPath() == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - if (credentialsQueryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - if (credentialsQueryRequest.getResourceCredentials() == null) { - credentialsQueryRequest.setResourceCredentials(new HashMap<>()); - } - - logger.info( - "path=/query/{queryId}/result, resourceId={}, requestSource={}, queryRequest={}", queryId, - Utilities.getRequestSourceFromHeader(headers), Utilities.convertQueryRequestToString(mapper, credentialsQueryRequest) - ); - - if (auditContext != null) { - auditContext.put("resource_id", resource.getUuid().toString()); - auditContext.put("resource_name", resource.getName()); - auditContext.put("query_id", queryId.toString()); - } - - credentialsQueryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken()); - return resourceWebClient.queryResult(resource.getResourceRSPath(), query.getResourceResultId(), credentialsQueryRequest); - } - - private boolean isV3Query(Query query) { - if (query.getVersion() == null) { - return false; - } - return query.getVersion().split("\\.")[0].equals("3"); - } - - /** - * Returns a signed URL from HPDS that is a reference to the query result - * - * @param queryId - id of target resource - * @param credentialsQueryRequest - contains resource specific credentials object - * @return Response containing a signed URL - */ - @Transactional - public Response queryResultSignedUrl(UUID queryId, QueryRequest credentialsQueryRequest, HttpHeaders headers) { - if (queryId == null) { - throw new ProtocolException(ProtocolException.MISSING_QUERY_ID); - } - Query query = queryRepo.getById(queryId); - if (query == null) { - throw new ProtocolException(ProtocolException.QUERY_NOT_FOUND + queryId.toString()); - } - Resource resource = query.getResource(); - if (resource == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE); - } - if (resource.getResourceRSPath() == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - if (credentialsQueryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - if (credentialsQueryRequest.getResourceCredentials() == null) { - credentialsQueryRequest.setResourceCredentials(new HashMap<>()); - } - - logger.info( - "path=/query/{queryId}/signed-url, resourceId={}, requestSource={}, queryRequest={}", queryId, - Utilities.getRequestSourceFromHeader(headers), Utilities.convertQueryRequestToString(mapper, credentialsQueryRequest) - ); - - if (auditContext != null) { - auditContext.put("resource_id", resource.getUuid().toString()); - auditContext.put("resource_name", resource.getName()); - auditContext.put("query_id", queryId.toString()); - } - - credentialsQueryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken()); - return resourceWebClient.queryResultSignedUrl(resource.getResourceRSPath(), query.getResourceResultId(), credentialsQueryRequest); - } - - /** - * Streams the result for a query by looking up the target resource from the database and calling the target resource for a result. - * - * @param queryRequest - contains resource specific credentials object - * @return Response - */ - @Transactional - public Response querySync(QueryRequest queryRequest, HttpHeaders headers) { - if (queryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - UUID resourceId = queryRequest.getResourceUUID(); - if (resourceId == null) { - throw new ProtocolException(ProtocolException.MISSING_RESOURCE_ID); - } - Resource resource = resourceRepo.getById(resourceId); - if (resource == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE); - } - - if (resource.getResourceRSPath() == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - - if (queryRequest.getResourceCredentials() == null) { - queryRequest.setResourceCredentials(new HashMap<>()); - } - - String requestSource = Utilities.getRequestSourceFromHeader(headers); - logger.info( - "path=/query/sync, resourceId={}, requestSource={}, queryRequest={}", queryRequest.getResourceUUID(), requestSource, - Utilities.convertQueryRequestToString(mapper, queryRequest) - ); - - Query queryEntity = new Query(); - queryEntity.setResource(resource); - queryEntity.setStartTime(new Date(Calendar.getInstance().getTime().getTime())); - - - String queryJson = null; - if (queryRequest.getQuery() != null) { - try { - ObjectMapper mapper = new ObjectMapper(); - queryJson = mapper.writeValueAsString(queryRequest); - } catch (JsonProcessingException e) { - throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); - } - } - - queryEntity.setQuery(queryJson); - queryRepo.persist(queryEntity); - - if (auditContext != null) { - auditContext.put("resource_id", resource.getUuid().toString()); - auditContext.put("resource_name", resource.getName()); - auditContext.put("query_id", queryEntity.getUuid().toString()); - } - - queryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken()); - Response syncResponse = resourceWebClient.querySync(resource.getResourceRSPath(), queryRequest, requestSource); - String queryMetadata = queryEntity.getUuid().toString(); // if no response ID, use the queryID (maintain behavior) - - if (syncResponse.getHeaders() != null) { - Object metadataHeader = syncResponse.getHeaders().get(ResourceWebClient.QUERY_METADATA_FIELD); - if (metadataHeader != null) { - try { - if (metadataHeader instanceof List) { - queryMetadata = ((List) metadataHeader).get(0).toString(); - logger.debug("found List metadata " + queryMetadata); - } else { - logger.debug("Header is " + metadataHeader.getClass().getCanonicalName() + " :: " + metadataHeader); - } - } catch (ClassCastException | ArrayIndexOutOfBoundsException e) { - logger.warn("failed to parse Header : ", e); - } - } - } - - queryEntity.setResourceResultId(queryMetadata); - queryRepo.persist(queryEntity); - - return syncResponse; - } - - /** - * @param queryId The UUID of the query to get metadata about - * @return a QueryStatus object containing the metadata stored about the given query - */ - public QueryStatus queryMetadata(UUID queryId, HttpHeaders headers) { - Query query = queryRepo.getById(queryId); - query = query == null ? queryRepo.getQueryUUIDFromCommonAreaUUID(queryId) : query; - if (query == null) { - throw new ProtocolException(ProtocolException.QUERY_NOT_FOUND + queryId.toString()); - } - - logger.info("path=/query/{queryId}/metadata, requestSource={}, queryId={}", Utilities.getRequestSourceFromHeader(headers), queryId); - - - QueryStatus response = new QueryStatus(); - response.setStartTime(query.getStartTime().getTime()); - response.setPicsureResultId(query.getUuid()); - response.setResourceID(query.getResource().getUuid()); - response.setStatus(query.getStatus()); - response.setResourceResultId(query.getResourceResultId()); - - Map metadata = new HashMap(); - try { - metadata.put(QUERY_JSON_FIELD, new ObjectMapper().readValue(query.getQuery(), Object.class)); - metadata.put(QUERY_RESULT_METADATA_FIELD, new String(query.getMetadata(), StandardCharsets.UTF_8)); - } catch (JsonProcessingException | NullPointerException e) { - logger.warn("Unable to use object mapper", e); - } - - response.setResultMetadata(metadata); - - return response; - } - - /** - * Executes a query on a PIC-SURE resource and creates a Query entity in the database for the query. - * - * @param dataQueryRequest - - {@link QueryRequest} containing resource specific credentials object and resource specific query (could - * be a string or a json object) - * @return {@link QueryStatus} - */ - public QueryStatus institutionalQuery(FederatedQueryRequest dataQueryRequest, HttpHeaders headers, String email) { - String siteCode = siteParsingService.parseSiteOfOrigin(email).orElse("Unknown"); - dataQueryRequest.setInstitutionOfOrigin(siteCode); - dataQueryRequest.setRequesterEmail(email); - Resource resource = verifyQueryRequest(dataQueryRequest, headers); - dataQueryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken()); - - QueryStatus response = resourceWebClient.query(resource.getResourceRSPath(), dataQueryRequest); - Query queryEntity = copyQuery(dataQueryRequest, resource, response); - queryRepo.persist(queryEntity); - - if (auditContext != null) { - auditContext.put("resource_id", resource.getUuid().toString()); - auditContext.put("resource_name", resource.getName()); - auditContext.put("query_id", queryEntity.getUuid().toString()); - auditContext.put("institution", siteCode); - } - - return response; - } - - private Query copyQuery(QueryRequest dataQueryRequest, Resource resource, QueryStatus response) { - Query queryEntity = new Query(); - queryEntity.setResourceResultId(response.getResourceResultId()); - queryEntity.setResource(resource); - queryEntity.setStatus(response.getStatus()); - queryEntity.setStartTime(new Date(response.getStartTime())); - - ObjectMapper mapper = new ObjectMapper(); - String queryJson = null; - if (dataQueryRequest.getQuery() != null) { - try { - queryJson = mapper.writeValueAsString(dataQueryRequest); - } catch (JsonProcessingException e) { - throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); - } - } - if (response.getResultMetadata() == null) { - response.setResultMetadata(new HashMap<>()); - } - Map metaData = response.getResultMetadata(); - - if (dataQueryRequest instanceof FederatedQueryRequest) { - FederatedQueryRequest gicRequest = (FederatedQueryRequest) dataQueryRequest; - metaData.put("commonAreaUUID", gicRequest.getCommonAreaUUID()); - metaData.put("site", gicRequest.getInstitutionOfOrigin()); - metaData.put("sharingStatus", DataSharingStatus.Unknown); - metaData.put("requesterEmail", gicRequest.getRequesterEmail()); - } - - queryEntity.setQuery(queryJson); - - if (!metaData.isEmpty()) { - try { - queryEntity.setMetadata(mapper.writeValueAsString(metaData).getBytes()); - } catch (JsonProcessingException e) { - logger.warn("Unable to parse metadata ", e); - } - } - return queryEntity; - } - - public QueryStatus institutionQueryStatus(UUID queryId, FederatedQueryRequest credentialsQueryRequest, HttpHeaders headers) { - if (queryId == null) { - throw new ProtocolException(ProtocolException.MISSING_QUERY_ID); - } - if (credentialsQueryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - Resource resource = resourceRepo.getById(credentialsQueryRequest.getResourceUUID()); - - verifyQueryStatusRequest(resource, credentialsQueryRequest, queryId, headers); - - // Update status on query object - return resourceWebClient.queryStatus(resource.getResourceRSPath(), queryId.toString(), credentialsQueryRequest); - } - - private void verifyQueryStatusRequest(Resource resource, QueryRequest credentialsQueryRequest, UUID queryId, HttpHeaders headers) - throws ProtocolException { - if (resource == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE); - } - if (resource.getResourceRSPath() == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - if (credentialsQueryRequest.getResourceCredentials() == null) { - credentialsQueryRequest.setResourceCredentials(new HashMap<>()); - } - if (resource.getToken() != null) { - credentialsQueryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken()); - } - - logger.info( - "path=/query/{queryId}/status, queryId={}, requestSource={}, queryRequest={}", queryId, - Utilities.getRequestSourceFromHeader(headers), Utilities.convertQueryRequestToString(mapper, credentialsQueryRequest) - ); - } - - private Resource verifyQueryRequest(QueryRequest dataQueryRequest, HttpHeaders headers) throws ProtocolException { - if (dataQueryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - UUID resourceId = dataQueryRequest.getResourceUUID(); - if (resourceId == null) { - throw new ProtocolException(ProtocolException.MISSING_RESOURCE_ID); - } - Resource resource = resourceRepo.getById(resourceId); - if (resource == null) { - throw new ProtocolException(ProtocolException.RESOURCE_NOT_FOUND + resourceId); - } - if (resource.getResourceRSPath() == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - if (dataQueryRequest.getResourceCredentials() == null) { - dataQueryRequest.setResourceCredentials(new HashMap<>()); - } - - logger.info( - "path=/query, requestSource={}, queryRequest={}", Utilities.getRequestSourceFromHeader(headers), - Utilities.convertQueryRequestToString(mapper, dataQueryRequest) - ); - return resource; - } -} - diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureQueryV3Service.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureQueryV3Service.java deleted file mode 100644 index 7508ffcfe..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureQueryV3Service.java +++ /dev/null @@ -1,483 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; -import edu.harvard.dbmi.avillach.data.entity.DataSharingStatus; -import edu.harvard.dbmi.avillach.data.entity.Query; -import edu.harvard.dbmi.avillach.data.entity.Resource; -import edu.harvard.dbmi.avillach.data.repository.QueryRepository; -import edu.harvard.dbmi.avillach.data.repository.ResourceRepository; -import edu.harvard.dbmi.avillach.domain.FederatedQueryRequest; -import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest; -import edu.harvard.dbmi.avillach.domain.QueryRequest; -import edu.harvard.dbmi.avillach.domain.QueryStatus; -import edu.harvard.dbmi.avillach.security.JWTFilter; -import edu.harvard.dbmi.avillach.util.Utilities; -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.inject.Inject; -import javax.transaction.Transactional; -import javax.ws.rs.core.HttpHeaders; -import javax.ws.rs.core.Response; -import java.nio.charset.StandardCharsets; -import java.sql.Date; -import java.util.*; -import java.util.Map; - -/** - * Service handling business logic for queries to resources - */ -public class PicsureQueryV3Service { - - public static final String QUERY_RESULT_METADATA_FIELD = "queryResultMetadata"; - private static final String QUERY_JSON_FIELD = "queryJson"; - - private final Logger logger = LoggerFactory.getLogger(PicsureQueryV3Service.class); - - private final static ObjectMapper mapper = new ObjectMapper(); - - public static final String CURRENT_VERSION = "3"; - - @Inject - JWTFilter jwtFilter; - - @Inject - ResourceRepository resourceRepo; - - @Inject - QueryRepository queryRepo; - - @Inject - ResourceWebClient resourceWebClient; - - @Inject - SiteParsingService siteParsingService; - - @Inject - AuditContext auditContext; - - /** - * Executes a query on a PIC-SURE resource and creates a Query entity in the database for the query. - * - * @param dataQueryRequest - - {@link QueryRequest} containing resource specific credentials object and resource specific query (could - * be a string or a json object) - * @return {@link QueryStatus} - */ - @Transactional - public QueryStatus query(QueryRequest dataQueryRequest, HttpHeaders headers) { - Resource resource = verifyQueryRequest(dataQueryRequest, headers); - - dataQueryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken()); - - QueryStatus results = resourceWebClient.query(resource.getResourceRSPath() + "/v3/", dataQueryRequest); - - Query queryEntity = copyQuery(dataQueryRequest, resource, results); - queryEntity.setVersion(CURRENT_VERSION); - queryRepo.persist(queryEntity); - - if (auditContext != null) { - auditContext.put("resource_id", resource.getUuid().toString()); - auditContext.put("resource_name", resource.getName()); - auditContext.put("query_id", queryEntity.getUuid().toString()); - auditContext.put("api_version", "v3"); - } - - logger.debug("PicsureQueryService() persisted queryEntity with id: " + queryEntity.getUuid()); - results.setPicsureResultId(queryEntity.getUuid()); - // In cases where there is no resource result id, the picsure result id will stand in - if (queryEntity.getResourceResultId() == null) { - results.setResourceResultId(queryEntity.getUuid().toString()); - queryEntity.setResourceResultId(results.getPicsureResultId().toString()); - queryRepo.persist(queryEntity); - } - results.setResourceID(resource.getUuid()); - return results; - } - - /** - * Retrieves the {@link QueryStatus} for a given queryId by looking up the target resource from the database and calling the target - * resource for an updated status. The Query entities in the database are updated each time this is called. - * - * @param queryId - id of targeted resource - * @param credentialsQueryRequest - contains resource specific credentials object - * @return {@link QueryStatus} - */ - @Transactional - public QueryStatus queryStatus(UUID queryId, GeneralQueryRequest credentialsQueryRequest, HttpHeaders headers) { - if (queryId == null) { - throw new ProtocolException(ProtocolException.MISSING_QUERY_ID); - } - Query query = queryRepo.getById(queryId); - if (query == null) { - throw new ProtocolException(ProtocolException.QUERY_NOT_FOUND + queryId.toString()); - } - if (credentialsQueryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - Resource resource = query.getResource(); - verifyQueryStatusRequest(resource, credentialsQueryRequest, queryId, headers); - - // Update status on query object - QueryStatus status = - resourceWebClient.queryStatus(resource.getResourceRSPath() + "/v3/", query.getResourceResultId(), credentialsQueryRequest); - status.setPicsureResultId(queryId); - query.setStatus(status.getStatus()); - queryRepo.persist(query); - status.setStartTime(query.getStartTime().getTime()); - status.setResourceID(resource.getUuid()); - return status; - } - - /** - * Streams the result for a given queryId by looking up the target resource from the database and calling the target resource for a - * result. The queryStatus method should be used to verify that the result is available prior to retrieving it. - * - * @param queryId - id of target resource - * @param credentialsQueryRequest - contains resource specific credentials object - * @return Response - */ - @Transactional - public Response queryResult(UUID queryId, QueryRequest credentialsQueryRequest, HttpHeaders headers) { - if (queryId == null) { - throw new ProtocolException(ProtocolException.MISSING_QUERY_ID); - } - Query query = queryRepo.getById(queryId); - if (query == null) { - throw new ProtocolException(ProtocolException.QUERY_NOT_FOUND + queryId); - } - Resource resource = query.getResource(); - if (resource == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE); - } - if (resource.getResourceRSPath() == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - if (credentialsQueryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - if (credentialsQueryRequest.getResourceCredentials() == null) { - credentialsQueryRequest.setResourceCredentials(new HashMap<>()); - } - - logger.info( - "path=/v3/query/{queryId}/result, resourceId={}, requestSource={}, queryRequest={}", queryId, - Utilities.getRequestSourceFromHeader(headers), Utilities.convertQueryRequestToString(mapper, credentialsQueryRequest) - ); - - if (auditContext != null) { - auditContext.put("resource_id", resource.getUuid().toString()); - auditContext.put("resource_name", resource.getName()); - auditContext.put("query_id", queryId.toString()); - auditContext.put("api_version", "v3"); - } - - credentialsQueryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken()); - return resourceWebClient.queryResult(resource.getResourceRSPath() + "/v3/", query.getResourceResultId(), credentialsQueryRequest); - } - - /** - * Returns a signed URL from HPDS that is a reference to the query result - * - * @param queryId - id of target resource - * @param credentialsQueryRequest - contains resource specific credentials object - * @return Response containing a signed URL - */ - @Transactional - public Response queryResultSignedUrl(UUID queryId, QueryRequest credentialsQueryRequest, HttpHeaders headers) { - if (queryId == null) { - throw new ProtocolException(ProtocolException.MISSING_QUERY_ID); - } - Query query = queryRepo.getById(queryId); - if (query == null) { - throw new ProtocolException(ProtocolException.QUERY_NOT_FOUND + queryId.toString()); - } - Resource resource = query.getResource(); - if (resource == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE); - } - if (resource.getResourceRSPath() == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - if (credentialsQueryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - if (credentialsQueryRequest.getResourceCredentials() == null) { - credentialsQueryRequest.setResourceCredentials(new HashMap<>()); - } - - logger.info( - "path=/v3/query/{queryId}/signed-url, resourceId={}, requestSource={}, queryRequest={}", queryId, - Utilities.getRequestSourceFromHeader(headers), Utilities.convertQueryRequestToString(mapper, credentialsQueryRequest) - ); - - if (auditContext != null) { - auditContext.put("resource_id", resource.getUuid().toString()); - auditContext.put("resource_name", resource.getName()); - auditContext.put("query_id", queryId.toString()); - auditContext.put("api_version", "v3"); - } - - credentialsQueryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken()); - return resourceWebClient - .queryResultSignedUrl(resource.getResourceRSPath() + "/v3/", query.getResourceResultId(), credentialsQueryRequest); - } - - /** - * Streams the result for a query by looking up the target resource from the database and calling the target resource for a result. - * - * @param queryRequest - contains resource specific credentials object - * @return Response - */ - @Transactional - public Response querySync(QueryRequest queryRequest, HttpHeaders headers) { - if (queryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - UUID resourceId = queryRequest.getResourceUUID(); - if (resourceId == null) { - throw new ProtocolException(ProtocolException.MISSING_RESOURCE_ID); - } - Resource resource = resourceRepo.getById(resourceId); - if (resource == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE); - } - - if (resource.getResourceRSPath() == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - - if (queryRequest.getResourceCredentials() == null) { - queryRequest.setResourceCredentials(new HashMap<>()); - } - - String requestSource = Utilities.getRequestSourceFromHeader(headers); - logger.info( - "path=/v3/query/sync, resourceId={}, requestSource={}, queryRequest={}", queryRequest.getResourceUUID(), requestSource, - Utilities.convertQueryRequestToString(mapper, queryRequest) - ); - - Query queryEntity = new Query(); - queryEntity.setResource(resource); - queryEntity.setStartTime(new Date(Calendar.getInstance().getTime().getTime())); - - - String queryJson = null; - if (queryRequest.getQuery() != null) { - try { - ObjectMapper mapper = new ObjectMapper(); - queryJson = mapper.writeValueAsString(queryRequest); - } catch (JsonProcessingException e) { - throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); - } - } - - queryEntity.setQuery(queryJson); - queryEntity.setVersion(CURRENT_VERSION); - queryRepo.persist(queryEntity); - - if (auditContext != null) { - auditContext.put("resource_id", resource.getUuid().toString()); - auditContext.put("resource_name", resource.getName()); - auditContext.put("query_id", queryEntity.getUuid().toString()); - auditContext.put("api_version", "v3"); - } - - queryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken()); - Response syncResponse = resourceWebClient.querySync(resource.getResourceRSPath() + "/v3/", queryRequest, requestSource); - String queryMetadata = queryEntity.getUuid().toString(); // if no response ID, use the queryID (maintain behavior) - - if (syncResponse.getHeaders() != null) { - Object metadataHeader = syncResponse.getHeaders().get(ResourceWebClient.QUERY_METADATA_FIELD); - if (metadataHeader != null) { - try { - if (metadataHeader instanceof List) { - queryMetadata = ((List) metadataHeader).get(0).toString(); - logger.debug("found List metadata " + queryMetadata); - } else { - logger.debug("Header is " + metadataHeader.getClass().getCanonicalName() + " :: " + metadataHeader); - } - } catch (ClassCastException | ArrayIndexOutOfBoundsException e) { - logger.warn("failed to parse Header : ", e); - } - } - } - - queryEntity.setResourceResultId(queryMetadata); - queryRepo.persist(queryEntity); - - return syncResponse; - } - - /** - * @param queryId The UUID of the query to get metadata about - * @return a QueryStatus object containing the metadata stored about the given query - */ - public QueryStatus queryMetadata(UUID queryId, HttpHeaders headers) { - Query query = queryRepo.getById(queryId); - query = query == null ? queryRepo.getQueryUUIDFromCommonAreaUUID(queryId) : query; - if (query == null) { - throw new ProtocolException(ProtocolException.QUERY_NOT_FOUND + queryId.toString()); - } - - logger.info( - "path=/v3/query/{queryId}/metadata, requestSource={}, queryId={}", Utilities.getRequestSourceFromHeader(headers), queryId - ); - - - QueryStatus response = new QueryStatus(); - response.setStartTime(query.getStartTime().getTime()); - response.setPicsureResultId(query.getUuid()); - response.setResourceID(query.getResource().getUuid()); - response.setStatus(query.getStatus()); - response.setResourceResultId(query.getResourceResultId()); - - Map metadata = new HashMap(); - try { - metadata.put(QUERY_JSON_FIELD, new ObjectMapper().readValue(query.getQuery(), Object.class)); - metadata.put(QUERY_RESULT_METADATA_FIELD, new String(query.getMetadata(), StandardCharsets.UTF_8)); - } catch (JsonProcessingException | NullPointerException e) { - logger.warn("Unable to use object mapper", e); - } - - response.setResultMetadata(metadata); - - return response; - } - - /** - * Executes a query on a PIC-SURE resource and creates a Query entity in the database for the query. - * - * @param dataQueryRequest - - {@link QueryRequest} containing resource specific credentials object and resource specific query (could - * be a string or a json object) - * @return {@link QueryStatus} - */ - public QueryStatus institutionalQuery(FederatedQueryRequest dataQueryRequest, HttpHeaders headers, String email) { - String siteCode = siteParsingService.parseSiteOfOrigin(email).orElse("Unknown"); - dataQueryRequest.setInstitutionOfOrigin(siteCode); - dataQueryRequest.setRequesterEmail(email); - Resource resource = verifyQueryRequest(dataQueryRequest, headers); - dataQueryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken()); - - QueryStatus response = resourceWebClient.query(resource.getResourceRSPath() + "/v3/", dataQueryRequest); - Query queryEntity = copyQuery(dataQueryRequest, resource, response); - queryEntity.setVersion(CURRENT_VERSION); - queryRepo.persist(queryEntity); - - if (auditContext != null) { - auditContext.put("resource_id", resource.getUuid().toString()); - auditContext.put("resource_name", resource.getName()); - auditContext.put("query_id", queryEntity.getUuid().toString()); - auditContext.put("institution", siteCode); - auditContext.put("api_version", "v3"); - } - - return response; - } - - private Query copyQuery(QueryRequest dataQueryRequest, Resource resource, QueryStatus response) { - Query queryEntity = new Query(); - queryEntity.setResourceResultId(response.getResourceResultId()); - queryEntity.setResource(resource); - queryEntity.setStatus(response.getStatus()); - queryEntity.setStartTime(new Date(response.getStartTime())); - - ObjectMapper mapper = new ObjectMapper(); - String queryJson = null; - if (dataQueryRequest.getQuery() != null) { - try { - queryJson = mapper.writeValueAsString(dataQueryRequest); - } catch (JsonProcessingException e) { - throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); - } - } - if (response.getResultMetadata() == null) { - response.setResultMetadata(new HashMap<>()); - } - Map metaData = response.getResultMetadata(); - - if (dataQueryRequest instanceof FederatedQueryRequest) { - FederatedQueryRequest gicRequest = (FederatedQueryRequest) dataQueryRequest; - metaData.put("commonAreaUUID", gicRequest.getCommonAreaUUID()); - metaData.put("site", gicRequest.getInstitutionOfOrigin()); - metaData.put("sharingStatus", DataSharingStatus.Unknown); - metaData.put("requesterEmail", gicRequest.getRequesterEmail()); - } - - queryEntity.setQuery(queryJson); - - if (!metaData.isEmpty()) { - try { - queryEntity.setMetadata(mapper.writeValueAsString(metaData).getBytes()); - } catch (JsonProcessingException e) { - logger.warn("Unable to parse metadata ", e); - } - } - return queryEntity; - } - - public QueryStatus institutionQueryStatus(UUID queryId, FederatedQueryRequest credentialsQueryRequest, HttpHeaders headers) { - if (queryId == null) { - throw new ProtocolException(ProtocolException.MISSING_QUERY_ID); - } - if (credentialsQueryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - Resource resource = resourceRepo.getById(credentialsQueryRequest.getResourceUUID()); - - verifyQueryStatusRequest(resource, credentialsQueryRequest, queryId, headers); - - // Update status on query object - return resourceWebClient.queryStatus(resource.getResourceRSPath() + "/v3/", queryId.toString(), credentialsQueryRequest); - } - - private void verifyQueryStatusRequest(Resource resource, QueryRequest credentialsQueryRequest, UUID queryId, HttpHeaders headers) - throws ProtocolException { - if (resource == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE); - } - if (resource.getResourceRSPath() == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - if (credentialsQueryRequest.getResourceCredentials() == null) { - credentialsQueryRequest.setResourceCredentials(new HashMap<>()); - } - if (resource.getToken() != null) { - credentialsQueryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken()); - } - - logger.info( - "path=/v3/query/{queryId}/status, queryId={}, requestSource={}, queryRequest={}", queryId, - Utilities.getRequestSourceFromHeader(headers), Utilities.convertQueryRequestToString(mapper, credentialsQueryRequest) - ); - } - - private Resource verifyQueryRequest(QueryRequest dataQueryRequest, HttpHeaders headers) throws ProtocolException { - if (dataQueryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - UUID resourceId = dataQueryRequest.getResourceUUID(); - if (resourceId == null) { - throw new ProtocolException(ProtocolException.MISSING_RESOURCE_ID); - } - Resource resource = resourceRepo.getById(resourceId); - if (resource == null) { - throw new ProtocolException(ProtocolException.RESOURCE_NOT_FOUND + resourceId); - } - if (resource.getResourceRSPath() == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - if (dataQueryRequest.getResourceCredentials() == null) { - dataQueryRequest.setResourceCredentials(new HashMap<>()); - } - - logger.info( - "path=/v3/query, requestSource={}, queryRequest={}", Utilities.getRequestSourceFromHeader(headers), - Utilities.convertQueryRequestToString(mapper, dataQueryRequest) - ); - return resource; - } -} - diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureResourceService.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureResourceService.java deleted file mode 100644 index e1c6160e3..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureResourceService.java +++ /dev/null @@ -1,51 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import java.util.List; - -import javax.inject.Inject; -import javax.transaction.Transactional; -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import edu.harvard.dbmi.avillach.data.entity.Resource; -import edu.harvard.dbmi.avillach.data.repository.ResourceRepository; -import edu.harvard.dbmi.avillach.util.response.PICSUREResponse; - -/** - * Service handling business logic for CRUD on resources - */ -@Path("/resource") -public class PicsureResourceService extends PicsureBaseEntityService { - - Logger logger = LoggerFactory.getLogger(PicsureResourceService.class); - - @Inject - ResourceRepository resourceRepo; - - public PicsureResourceService() { - super(Resource.class); - } - - @GET - @Path("/{resourceId}") - public Response getEntityById(@PathParam("resourceId") String resourceId) { - return getEntityById(resourceId, resourceRepo); - } - - @GET - @Path("") - public Response getResourceAll() { - logger.info("Getting all resources..."); - List resources = null; - - resources = resourceRepo.list(); - - if (resources == null) return PICSUREResponse.applicationError("Error occurs when listing all resources."); - - return PICSUREResponse.success(resources); - } -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureSearchService.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureSearchService.java deleted file mode 100644 index 21f1a9cc5..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureSearchService.java +++ /dev/null @@ -1,111 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import com.fasterxml.jackson.databind.ObjectMapper; -import edu.harvard.dbmi.avillach.data.entity.Resource; -import edu.harvard.dbmi.avillach.data.repository.ResourceRepository; -import edu.harvard.dbmi.avillach.domain.PaginatedSearchResult; -import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest; -import edu.harvard.dbmi.avillach.domain.QueryRequest; -import edu.harvard.dbmi.avillach.domain.SearchResults; -import edu.harvard.dbmi.avillach.util.Utilities; -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.inject.Inject; -import javax.ws.rs.core.HttpHeaders; -import java.util.HashMap; -import java.util.Map; -import java.util.UUID; - -public class PicsureSearchService { - - private final Logger logger = LoggerFactory.getLogger(PicsureSearchService.class); - - private final static ObjectMapper mapper = new ObjectMapper(); - - @Inject - ResourceRepository resourceRepo; - - @Inject - ResourceWebClient resourceWebClient; - - @Inject - AuditContext auditContext; - - /** - * Executes a concept search against a target resource - * - * @param resourceId - UUID of target resource - * @param searchQueryRequest - {@link QueryRequest} containing resource specific credentials object and resource specific query (could - * be a string or a json object) - * @param headers - * @return {@link SearchResults} - */ - public SearchResults search(UUID resourceId, QueryRequest searchQueryRequest, HttpHeaders headers) { - if (resourceId == null) { - throw new ProtocolException(ProtocolException.MISSING_RESOURCE_ID); - } - Resource resource = resourceRepo.getById(resourceId); - if (resource == null) { - throw new ProtocolException(ProtocolException.RESOURCE_NOT_FOUND + resourceId.toString()); - } - if (resource.getResourceRSPath() == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - if (searchQueryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - - logger.info( - "path=/search/{resourceId}, resourceId={}, requestSource={}, searchQueryRequest={}", resourceId, - Utilities.getRequestSourceFromHeader(headers), Utilities.convertQueryRequestToString(mapper, searchQueryRequest) - ); - - if (auditContext != null) { - auditContext.put("resource_id", resourceId.toString()); - auditContext.put("resource_name", resource.getName()); - if (searchQueryRequest.getQuery() != null) { - auditContext.put("search_term", searchQueryRequest.getQuery().toString()); - } - } - - if (searchQueryRequest.getResourceCredentials() == null) { - searchQueryRequest.setResourceCredentials(new HashMap()); - } - return resourceWebClient.search(resource.getResourceRSPath(), searchQueryRequest); - } - - public PaginatedSearchResult searchGenomicConceptValues( - UUID resourceId, QueryRequest queryRequest, String conceptPath, String query, Integer page, Integer size, HttpHeaders headers - ) { - Resource resource = resourceRepo.getById(resourceId); - if (resource == null) { - throw new ProtocolException(ProtocolException.RESOURCE_NOT_FOUND + resourceId.toString()); - } - if (resource.getResourceRSPath() == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - - logger.info( - "path=/search/{resourceId}/concept/{conceptPath}, resourceId={}, requestSource={}, queryRequest={}, conceptPath={}, query={}", - resourceId, Utilities.getRequestSourceFromHeader(headers), Utilities.convertQueryRequestToString(mapper, queryRequest), - conceptPath, query - ); - - if (auditContext != null) { - auditContext.put("resource_id", resourceId.toString()); - auditContext.put("resource_name", resource.getName()); - if (conceptPath != null) { - auditContext.put("genomic_concept_path", conceptPath); - } - if (query != null) { - auditContext.put("query", query); - } - } - - return resourceWebClient.searchConceptValues(resource.getResourceRSPath(), queryRequest, conceptPath, query, page, size); - } - -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/SiteParsingService.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/SiteParsingService.java deleted file mode 100644 index 41ae2e587..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/SiteParsingService.java +++ /dev/null @@ -1,41 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import edu.harvard.dbmi.avillach.data.entity.Site; -import edu.harvard.dbmi.avillach.data.repository.SiteRepository; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.inject.Inject; -import java.util.List; -import java.util.Optional; -import java.util.regex.Matcher; -import java.util.regex.Pattern; - -public class SiteParsingService { - - private static final Logger LOG = LoggerFactory.getLogger(SiteParsingService.class); - - private static final Pattern emailRegex = Pattern.compile("^([^@]+)(@)(.*)$"); - - @Inject - SiteRepository repository; - - public Optional parseSiteOfOrigin(String email) { - Matcher matcher = emailRegex.matcher(email); - if (!matcher.find()) { - LOG.warn("Unable to parse domain for email: {}", email); - return Optional.empty(); - } - - List matchingDomains = repository.getByColumn("domain", matcher.group(3)); - if (matchingDomains.isEmpty()) { - LOG.warn("Unable to match domain for email: {}, looked for domain: {}", email, matcher.group(3)); - return Optional.empty(); - } - if (matchingDomains.size() > 1) { - LOG.warn("Multiple domains match email. This should never happen! Email: {}", email); - return Optional.empty(); - } - return Optional.of(matchingDomains.get(0).getCode()); - } -} diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/SystemService.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/SystemService.java deleted file mode 100755 index 8a8b0f4be..000000000 --- a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/SystemService.java +++ /dev/null @@ -1,160 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import static edu.harvard.dbmi.avillach.util.Utilities.buildHttpClientContext; - -import java.io.IOException; -import java.util.List; -import java.util.Locale; -import java.util.UUID; - -import javax.annotation.PostConstruct; -import javax.inject.Inject; -import javax.ws.rs.GET; -import javax.ws.rs.Path; -import javax.ws.rs.Produces; - -import org.apache.http.client.methods.CloseableHttpResponse; -import org.apache.http.client.methods.HttpPost; -import org.apache.http.entity.StringEntity; -import org.apache.http.impl.client.CloseableHttpClient; -import org.apache.http.util.EntityUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; - -import edu.harvard.dbmi.avillach.PicSureWarInit; -import edu.harvard.dbmi.avillach.data.entity.Resource; -import edu.harvard.dbmi.avillach.data.repository.ResourceRepository; -import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest; -import edu.harvard.dbmi.avillach.domain.ResourceInfo; -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; - -@Path("/system") -public class SystemService { - static int max_test_frequency = 60000; - - static final String RUNNING = "RUNNING"; - - static final String ONE_OR_MORE_COMPONENTS_DEGRADED = "ONE OR MORE COMPONENTS DEGRADED"; - - Logger logger = LoggerFactory.getLogger(SystemService.class); - - @Inject - PicSureWarInit picSureWarInit; - - String lastStatus = "UNTESTED"; - long lastStatusCheck = 0l; - - @Inject - ResourceRepository resourceRepo; - - String token_introspection_url; - String token_introspection_token; - - String defaultApplicationUUID; - - @PostConstruct - public void init() { - token_introspection_url = picSureWarInit.getToken_introspection_url(); - token_introspection_token = picSureWarInit.getToken_introspection_token(); - defaultApplicationUUID = picSureWarInit.getDefaultApplicationUUID(); - if (token_introspection_url == null || token_introspection_token == null) { - throw new RuntimeException("token_introspection_url and token_introspection_token not configured"); - } - } - - @GET - @Path("/status") - @Produces("text/plain") - public String status() { - // Because there is no auth on this service we limit actually performing the checking to 1 per minute to avoid DOS scenarios. - long timeOfRequest = System.currentTimeMillis(); - if (timeOfRequest - lastStatusCheck < max_test_frequency) { - return lastStatus; - } else { - lastStatusCheck = timeOfRequest; - try { - List resourcesToTest = resourceRepo.list(); - if (resourcesToTest == null || resourcesToTest.isEmpty()) { - lastStatus = ONE_OR_MORE_COMPONENTS_DEGRADED; - return lastStatus; - } - - // convert the default application uuid to an uuid object - UUID defaultApplicationUUID = UUID.fromString(this.defaultApplicationUUID); - - // We need to remove open or auth HPDS from the resource list depending on the environment deployed. - // This because both are included in the database, but only one is actually deployed. - // if the name contains hpds and is not the default application uuid, remove it. - resourcesToTest.removeIf( - resource -> resource.getName().toLowerCase(Locale.ENGLISH).contains("hpds") && !resource.getUuid().equals(defaultApplicationUUID) - ); - - // This proves the MySQL database is serving queries - // This proves at least one resources is configured - // This proves we can perform token introspection - if (testPSAMAResponds() && testResourcesRespond(resourcesToTest)) { // This proves all resources are at least serving info - // requests. - lastStatus = RUNNING; - return lastStatus; - } else { - lastStatus = ONE_OR_MORE_COMPONENTS_DEGRADED; - } - } catch (Exception e) { - logger.error("One or more components degraded", e); - lastStatus = ONE_OR_MORE_COMPONENTS_DEGRADED; - } - return lastStatus; - } - } - - private boolean testPSAMAResponds() throws UnsupportedOperationException, IOException { - CloseableHttpClient client = PicSureWarInit.CLOSEABLE_HTTP_CLIENT; - ObjectMapper json = PicSureWarInit.objectMapper; - - HttpPost post = new HttpPost(token_introspection_url); - post.setEntity(new StringEntity("{}")); - post.setHeader("Content-Type", "application/json"); - // Authorize into the token introspection endpoint - post.setHeader("Authorization", "Bearer " + token_introspection_token); - CloseableHttpResponse response = null; - try { - response = client.execute(post, buildHttpClientContext()); - if (response.getStatusLine().getStatusCode() != 200) { - logger.error( - "callTokenIntroEndpoint() error back from token intro host server [" + token_introspection_url + "]: " - + EntityUtils.toString(response.getEntity()) - ); - throw new ApplicationException( - "Token Introspection host server return " + response.getStatusLine().getStatusCode() + ". Please see the log" - ); - } - JsonNode responseContent = json.readTree(response.getEntity().getContent()); - if (!responseContent.get("active").asBoolean()) { - // This is actually the expected response as we did not send a token in the token_introspection_request. - return true; - } - - return true; - } finally { - try { - if (response != null) response.close(); - } catch (IOException ex) { - logger.error("callTokenIntroEndpoint() IOExcpetion when closing http response: " + ex.getMessage()); - } - } - } - - private boolean testResourcesRespond(List resourcesToTest) { - for (Resource resource : resourcesToTest) { - ResourceInfo info = new ResourceWebClient().info(resource.getResourceRSPath(), new GeneralQueryRequest()); - if (info == null) { - return false; - } - } - return true; - } -} - diff --git a/pic-sure-api-war/src/main/resources/META-INF/persistence.xml b/pic-sure-api-war/src/main/resources/META-INF/persistence.xml deleted file mode 100644 index 68353fc64..000000000 --- a/pic-sure-api-war/src/main/resources/META-INF/persistence.xml +++ /dev/null @@ -1,25 +0,0 @@ - - - - java:jboss/datasources/PicsureDS - edu.harvard.dbmi.avillach.data.entity.Query - edu.harvard.dbmi.avillach.data.entity.Resource - edu.harvard.dbmi.avillach.data.entity.Configuration - edu.harvard.dbmi.avillach.data.entity.NamedDataset - edu.harvard.dbmi.avillach.data.entity.Site - - - - - - - - - - diff --git a/pic-sure-api-war/src/main/resources/wildfly-configuration/standalone.xml b/pic-sure-api-war/src/main/resources/wildfly-configuration/standalone.xml deleted file mode 100644 index 6086001e2..000000000 --- a/pic-sure-api-war/src/main/resources/wildfly-configuration/standalone.xml +++ /dev/null @@ -1,555 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - jdbc:h2:mem:test;DB_CLOSE_DELAY=-1;DB_CLOSE_ON_EXIT=FALSE - h2 - - sa - sa - - - - jdbc:mysql://${env.PICSURE2_MYSQLADDRESS}:${env.PICSURE2_DB_PORT}/picsure?useUnicode=true&characterEncoding=UTF-8&autoReconnect=true&autoReconnectForPools=true - mysql - - 5 - 50 - true - - - ${env.PICSURE2_DB_CONNECTION_USER} - ${env.PICSURE2_MYSQLPASS} - - - - SELECT 1 - true - false - - - - - - com.mysql.jdbc.Driver - - - org.h2.jdbcx.JdbcDataSource - - - - - - - - - - - - - false - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ${jboss.bind.address:127.0.0.1} - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/pic-sure-api-war/src/main/webapp/META-INF/context.xml b/pic-sure-api-war/src/main/webapp/META-INF/context.xml deleted file mode 100755 index 9f4aa7fd7..000000000 --- a/pic-sure-api-war/src/main/webapp/META-INF/context.xml +++ /dev/null @@ -1,3 +0,0 @@ - - - diff --git a/pic-sure-api-war/src/main/webapp/WEB-INF/beans.xml b/pic-sure-api-war/src/main/webapp/WEB-INF/beans.xml deleted file mode 100755 index 9a692dbef..000000000 --- a/pic-sure-api-war/src/main/webapp/WEB-INF/beans.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - \ No newline at end of file diff --git a/pic-sure-api-war/src/main/webapp/WEB-INF/web.xml b/pic-sure-api-war/src/main/webapp/WEB-INF/web.xml deleted file mode 100644 index 6b79a4583..000000000 --- a/pic-sure-api-war/src/main/webapp/WEB-INF/web.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - - resteasy.role.based.security - true - - diff --git a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/BaseServiceTest.java b/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/BaseServiceTest.java deleted file mode 100644 index f89ff5840..000000000 --- a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/BaseServiceTest.java +++ /dev/null @@ -1,24 +0,0 @@ -package edu.harvard.dbmi.avillach; - -import org.glassfish.jersey.internal.RuntimeDelegateImpl; -import org.junit.BeforeClass; - -import org.junit.Ignore; - -import javax.ws.rs.ext.RuntimeDelegate; - -@Ignore -public class BaseServiceTest { - - protected static String endpointUrl; - - @BeforeClass - public static void beforeClass() { - endpointUrl = System.getProperty("service.url"); - - //Need to be able to throw exceptions without container so we can verify correct errors are being thrown - RuntimeDelegate runtimeDelegate = new RuntimeDelegateImpl(); - RuntimeDelegate.setInstance(runtimeDelegate); -} - -} diff --git a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/ConfigurationRSTest.java b/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/ConfigurationRSTest.java deleted file mode 100644 index 7858542dd..000000000 --- a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/ConfigurationRSTest.java +++ /dev/null @@ -1,48 +0,0 @@ -package edu.harvard.dbmi.avillach; - -import edu.harvard.dbmi.avillach.data.request.ConfigurationRequest; -import org.junit.Test; - -import javax.annotation.security.PermitAll; -import javax.annotation.security.RolesAllowed; -import javax.ws.rs.core.SecurityContext; -import java.lang.reflect.Method; -import java.util.Arrays; -import java.util.UUID; - -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertTrue; - -public class ConfigurationRSTest { - private final String SUPER_ADMIN = "SUPER_ADMIN"; - - private void assertRolesAllowed(Method method, String role) { - RolesAllowed annotation = method.getAnnotation(RolesAllowed.class); - assertNotNull("@RolesAllowed missing on " + method.getName(), annotation); - assertTrue(role + " role missing on " + method.getName(), Arrays.asList(annotation.value()).contains(role)); - } - - // These unit tests only guard against accidental removal during refactor & they are not an E2E test of the functionality - @Test - public void adminEndpoints_requireAdminRole() throws NoSuchMethodException { - assertRolesAllowed( - ConfigurationRS.class.getMethod("addConfiguration", SecurityContext.class, ConfigurationRequest.class), SUPER_ADMIN - ); - assertRolesAllowed( - ConfigurationRS.class.getMethod("updateConfiguration", SecurityContext.class, UUID.class, ConfigurationRequest.class), - SUPER_ADMIN - ); - assertRolesAllowed(ConfigurationRS.class.getMethod("deleteConfiguration", SecurityContext.class, UUID.class), SUPER_ADMIN); - } - - private void assertPermitAll(Method method) { - PermitAll permitAll = method.getAnnotation(PermitAll.class); - assertNotNull(method.getName() + " must have @PermitAll annotation", permitAll); - } - - @Test - public void readEndpoints_arePermitAll() throws NoSuchMethodException { - assertPermitAll(ConfigurationRS.class.getMethod("getConfigurations", SecurityContext.class, String.class)); - assertPermitAll(ConfigurationRS.class.getMethod("getConfigurationById", SecurityContext.class, String.class)); - } -} diff --git a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/LoggerReaderInterceptorTest.java b/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/LoggerReaderInterceptorTest.java deleted file mode 100644 index 2da958f44..000000000 --- a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/LoggerReaderInterceptorTest.java +++ /dev/null @@ -1,147 +0,0 @@ -package edu.harvard.dbmi.avillach; - -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.cxf.message.Exchange; -import org.apache.cxf.message.ExchangeImpl; -import org.apache.cxf.message.Message; -import org.apache.cxf.message.MessageImpl; -import org.junit.Test; - -import javax.ws.rs.ext.ReaderInterceptorContext; -import java.io.IOException; -import java.io.InputStream; -import java.util.HashMap; - - -import org.apache.cxf.jaxrs.impl.ReaderInterceptorContextImpl; - -import static org.junit.Assert.*; - -public class LoggerReaderInterceptorTest { - - private LoggerReaderInterceptor cut = new LoggerReaderInterceptor(); - - @Test - public void testCredentialsRedacted() throws IOException{ - - //Different pieces of a query - String resourceCredentials = "resourceCredentials\": " + - "{ \"IRCT_BEARER_TOKEN\": \"eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJzdWIiOiJ0ZXN0fGF2bGJvdEBkYm1pLmhtcy5oYXJ2YXJkLmVkdSIsImVtYWlsIjoiYXZsYm90QGRibWkuaG1zLmhhcnZhcmQuZWR1In0.51TYsm-uw2VtI8aGawdggbGdCSrPJvjtvzafd2Ii9NU\"}"; - - String query = "query\": " + - "{ " + - "\"select\": [" + - " {" + - " \"alias\": \"gender\", \"field\": {\"pui\": \"/nhanes/Demo/demographics/demographics/SEX/male\", \"dataType\":\"STRING\"}" + - " }," + - " {" + - " \"alias\": \"gender\", \"field\": {\"pui\": \"/nhanes/Demo/demographics/demographics/SEX/female\", \"dataType\":\"STRING\"}" + - " }," + - " {" + - " \"alias\": \"age\", \"field\": {\"pui\": \"/nhanes/Demo/demographics/demographics/AGE\", \"dataType\":\"STRING\"}" + - " }" + - " ]," + - " \"where\": [ " + - "{ \"predicate\": \"CONTAINS\", " + - "\"field\": " + - "{ \"pui\": \"/nhanes/Demo/demographics/demographics/SEX/male/\", " + - "\"dataType\": \"STRING\" " + - "}, " + - "\"fields\": " + - "{ \"ENOUNTER\": \"YES\" } " + - "} ]" + - "}"; - - String resourceUUID = "\"resourceUUID\" : \"{{resourceUUID}}\""; - - //Assemble pieces into different test queries - String order1 = "{ " + resourceUUID + "," + query + ", " + resourceCredentials + "}"; - String order2 = "{ " + query + "," + resourceCredentials + ", " + resourceUUID + "}"; - String credentialsOnly = "{" + resourceCredentials + "}"; - String nested1 = "{" + resourceUUID + ", query: " + order1 + ", " + resourceCredentials + "}"; - String nested2 = "{ " + resourceCredentials + "," + "query:" + nested1 + ", " + resourceUUID + "}"; - - - //Mocking turned out to be a mess so let's just do this this dumb way - Message message = new MessageImpl(); - Exchange ex = new ExchangeImpl(); - ex.put("jaxrs.filter.properties", new HashMap()); - message.setExchange(ex); - - //Put the test string into a stream and stuff it in a context to test - InputStream stream = IOUtils.toInputStream(order1, "UTF-8"); - ReaderInterceptorContext context = new ReaderInterceptorContextImpl(null, null, null, stream,message, null); - cut.aroundReadFrom(context); - - //See if it's done what we want - Object result = context.getProperty("requestContent"); - assertNotNull(result); - String resultString = result.toString(); - - assertFalse(resultString.contains("resourceCredentials")); - assertFalse(resultString.contains("IRCT_BEARER_TOKEN")); - assertFalse(resultString.contains("eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9")); - assertTrue(resultString.contains("RESOURCE_CREDENTIALS_REDACTED")); - - //Make sure order isn't an issue - stream = IOUtils.toInputStream(order2, "UTF-8"); - context = new ReaderInterceptorContextImpl(null, null, null, stream,message, null); - cut.aroundReadFrom(context); - - result = context.getProperty("requestContent"); - assertNotNull(result); - resultString = result.toString(); - - assertFalse(resultString.contains("resourceCredentials")); - assertFalse(resultString.contains("IRCT_BEARER_TOKEN")); - assertFalse(resultString.contains("eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9")); - assertTrue(resultString.contains("RESOURCE_CREDENTIALS_REDACTED")); - - //What if there's nothing in there but credentials - stream = IOUtils.toInputStream(credentialsOnly, "UTF-8"); - context = new ReaderInterceptorContextImpl(null, null, null, stream,message, null); - cut.aroundReadFrom(context); - - result = context.getProperty("requestContent"); - assertNotNull(result); - resultString = result.toString(); - - assertFalse(resultString.contains("resourceCredentials")); - assertFalse(resultString.contains("IRCT_BEARER_TOKEN")); - assertFalse(resultString.contains("eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9")); - assertTrue(resultString.contains("RESOURCE_CREDENTIALS_REDACTED")); - - //What if it's nested? - stream = IOUtils.toInputStream(nested1, "UTF-8"); - context = new ReaderInterceptorContextImpl(null, null, null, stream,message, null); - cut.aroundReadFrom(context); - - result = context.getProperty("requestContent"); - assertNotNull(result); - resultString = result.toString(); - - assertFalse(resultString.contains("resourceCredentials")); - assertFalse(resultString.contains("IRCT_BEARER_TOKEN")); - assertFalse(resultString.contains("eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9")); - assertTrue(resultString.contains("RESOURCE_CREDENTIALS_REDACTED")); - assertEquals(2, StringUtils.countMatches(resultString, "RESOURCE_CREDENTIALS_REDACTED")); - - //What if it's nested two layers deep?? - stream = IOUtils.toInputStream(nested2, "UTF-8"); - context = new ReaderInterceptorContextImpl(null, null, null, stream,message, null); - cut.aroundReadFrom(context); - - result = context.getProperty("requestContent"); - assertNotNull(result); - resultString = result.toString(); - - assertFalse(resultString.contains("resourceCredentials")); - assertFalse(resultString.contains("IRCT_BEARER_TOKEN")); - assertFalse(resultString.contains("eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9")); - assertTrue(resultString.contains("RESOURCE_CREDENTIALS_REDACTED")); - assertEquals(3, StringUtils.countMatches(resultString, "RESOURCE_CREDENTIALS_REDACTED")); - - } - -} diff --git a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/PicsureInfoServiceTest.java b/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/PicsureInfoServiceTest.java deleted file mode 100644 index f667c3131..000000000 --- a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/PicsureInfoServiceTest.java +++ /dev/null @@ -1,101 +0,0 @@ -package edu.harvard.dbmi.avillach; - -import edu.harvard.dbmi.avillach.data.entity.Resource; -import edu.harvard.dbmi.avillach.data.repository.ResourceRepository; -import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest; -import edu.harvard.dbmi.avillach.domain.ResourceInfo; -import edu.harvard.dbmi.avillach.service.PicsureInfoService; -import edu.harvard.dbmi.avillach.service.ResourceWebClient; -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; -import org.junit.Before; -import org.junit.Test; -import org.junit.runner.RunWith; -import org.mockito.ArgumentMatchers; -import org.mockito.InjectMocks; -import org.mockito.Mock; -import org.mockito.junit.MockitoJUnitRunner; - -import java.util.*; - -import static junit.framework.TestCase.assertTrue; -import static org.junit.Assert.*; -import static org.mockito.AdditionalMatchers.not; -import static org.mockito.ArgumentMatchers.any; -import static org.mockito.Mockito.mock; -import static org.mockito.Mockito.when; - -@RunWith(MockitoJUnitRunner.class) -public class PicsureInfoServiceTest extends BaseServiceTest { - - private UUID resourceId = UUID.randomUUID(); - - @InjectMocks - private PicsureInfoService infoService = new PicsureInfoService(); - - @Mock - private Resource mockResource = mock(Resource.class); - - @Mock - private ResourceRepository resourceRepo = mock(ResourceRepository.class); - - @Mock - private ResourceWebClient webClient = mock(ResourceWebClient.class); - - @Before - public void setUp() { - ResourceInfo results = new ResourceInfo(); - Resource testResource = new Resource().setName("A Mock Resource"); - testResource.setUuid(resourceId); - List resourceListing = List.of(mockResource); - - when(mockResource.getName()).thenReturn("A Mock Resource"); - when(mockResource.getUuid()).thenReturn(resourceId); - - when(resourceRepo.getById(resourceId)).thenReturn(mockResource); - when(resourceRepo.getById(not(ArgumentMatchers.same(resourceId)))).thenReturn(null); - when(webClient.info(any(), any())).thenReturn(results); - when(resourceRepo.list()).thenReturn(resourceListing); - } - - @Test - public void testInfoEndpoints() { - GeneralQueryRequest infoRequest = new GeneralQueryRequest(); - Map clientCredentials = new HashMap(); - infoRequest.setResourceCredentials(clientCredentials); - - //Should fail with a nonexistent id - try { - ResourceInfo info = infoService.info(UUID.randomUUID(), infoRequest, null); - fail(); - } catch (ProtocolException e){ - assertNotNull(e.getContent()); - assertTrue("Error message should say '" + ProtocolException.RESOURCE_NOT_FOUND + "'", e.getContent().toString().contains(ProtocolException.RESOURCE_NOT_FOUND)); } - - //Should fail without the url in the resource - try { - ResourceInfo info = infoService.info(resourceId, infoRequest, null); - fail(); - } catch (ApplicationException e){ - assertNotNull(e.getContent()); - assertEquals("Error message should say '" + ApplicationException.MISSING_RESOURCE_PATH + "'", ApplicationException.MISSING_RESOURCE_PATH, e.getContent().toString()); - } - when(mockResource.getResourceRSPath()).thenReturn("resourceRsPath"); - - ResourceInfo responseInfo = infoService.info(resourceId, infoRequest, null); - assertNotNull("Resource response should not be null", responseInfo); - - //Should also work without clientCredentials - responseInfo = infoService.info(resourceId, null, null); - assertNotNull("Resource response should not be null", responseInfo); - } - - @Test - public void testResourcesEndpoint() { - //Should give a UUID list of all resources - Map resourceList = infoService.resources(null); - assertNotNull("Resource listing should not be null", resourceList); - assertEquals("Resource listing should only have 1 entry", 1, resourceList.size()); - assertSame("Resource listing should be UUID of our mocked resource", resourceId, resourceList.keySet().iterator().next()); - } -} diff --git a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/PicsureQueryServiceTest.java b/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/PicsureQueryServiceTest.java deleted file mode 100644 index 07f2c2dac..000000000 --- a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/PicsureQueryServiceTest.java +++ /dev/null @@ -1,606 +0,0 @@ -package edu.harvard.dbmi.avillach; - -import static junit.framework.TestCase.assertTrue; -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.fail; -import static org.mockito.ArgumentMatchers.any; -import static org.mockito.ArgumentMatchers.eq; -import static org.mockito.Mockito.doAnswer; -import static org.mockito.Mockito.mock; -import static org.mockito.Mockito.verify; -import static org.mockito.Mockito.when; - -import java.nio.charset.StandardCharsets; -import java.util.*; - -import javax.ws.rs.core.MultivaluedHashMap; -import javax.ws.rs.core.MultivaluedMap; -import javax.ws.rs.core.Response; - -import edu.harvard.dbmi.avillach.domain.PicSureStatus; -import edu.harvard.dbmi.avillach.service.ResourceWebClient; -import org.junit.Assert; -import org.junit.Before; -import org.junit.Test; -import org.junit.runner.RunWith; - -import org.mockito.InjectMocks; -import org.mockito.Mock; -import org.mockito.Mockito; -import org.mockito.invocation.InvocationOnMock; -import org.mockito.junit.MockitoJUnitRunner; -import org.mockito.stubbing.Answer; - -import edu.harvard.dbmi.avillach.data.entity.Query; -import edu.harvard.dbmi.avillach.data.entity.Resource; -import edu.harvard.dbmi.avillach.data.repository.QueryRepository; -import edu.harvard.dbmi.avillach.data.repository.ResourceRepository; -import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest; -import edu.harvard.dbmi.avillach.domain.QueryStatus; -import edu.harvard.dbmi.avillach.service.PicsureQueryService; -import edu.harvard.dbmi.avillach.service.AuditContext; -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; - -@RunWith(MockitoJUnitRunner.class) -public class PicsureQueryServiceTest extends BaseServiceTest { - - private UUID resourceId; - private String queryString; - private UUID queryId; - private Query queryEntity; - private QueryStatus results; - - @InjectMocks - private PicsureQueryService queryService = new PicsureQueryService(); - - @Mock - private Resource mockResource = mock(Resource.class); - - @Mock - private ResourceRepository resourceRepo = mock(ResourceRepository.class); - - @Mock - private QueryRepository queryRepo = mock(QueryRepository.class); - - @Mock - private ResourceWebClient webClient = mock(ResourceWebClient.class); - - @Mock - private AuditContext auditContext = mock(AuditContext.class); - - @Before - public void setUp() { - resourceId = UUID.randomUUID(); - queryString = "queryDoesntMatterForTest"; - queryId = UUID.randomUUID(); - results = new QueryStatus(); - - // Add needed data to results that are returned - results.setResourceID(resourceId); - results.setStatus(PicSureStatus.PENDING); - results.setStartTime(new Date().getTime()); - - // Return mocks when needed - when(webClient.query(any(), any())).thenReturn(results); - when(resourceRepo.getById(resourceId)).thenReturn(mockResource); - when(mockResource.getResourceRSPath()).thenReturn("resourceRsPath"); - when(mockResource.getUuid()).thenReturn(resourceId); - when(mockResource.getName()).thenReturn("test-resource"); - - // Mock persisting the queryentity, so that it has an ID and we can test that - // the correct information is stored in it - doAnswer(new Answer() { - public Void answer(InvocationOnMock invocation) { - Query query = invocation.getArgument(0); - query.setUuid(queryId); - queryEntity = query; - return null; - } - }).when(queryRepo).persist(any(Query.class)); - } - - @Test - public void testQueryEmptyRequest() { - - // Test missing query data - try { - QueryStatus result = queryService.query(null, null); - fail("Missing query request info should throw an error"); - } catch (ProtocolException e) { - assertNotNull(e.getContent()); - assertEquals( - "Error message should say '" + ProtocolException.MISSING_DATA + "'", ProtocolException.MISSING_DATA, - e.getContent().toString() - ); - } - } - - @Test - public void testQueryMissingResourceId() { - - GeneralQueryRequest dataQueryRequest = new GeneralQueryRequest(); - // At this level we don't check the credentials themselves, just that the map - // exists - Map clientCredentials = new HashMap(); - dataQueryRequest.setResourceCredentials(clientCredentials); - - // Test missing resourceId - - dataQueryRequest.setQuery(queryString); - try { - QueryStatus result = queryService.query(dataQueryRequest, null); - fail("Missing resourceId should throw an error"); - } catch (ProtocolException e) { - assertNotNull(e.getContent()); - assertEquals( - "Error message should say '" + ProtocolException.MISSING_RESOURCE_ID + "'", ProtocolException.MISSING_RESOURCE_ID, - e.getContent().toString() - ); - } - - } - - @Test - public void testQueryInvalidResourceId() { - - GeneralQueryRequest dataQueryRequest = new GeneralQueryRequest(); - // At this level we don't check the credentials themselves, just that the map - // exists - Map clientCredentials = new HashMap(); - dataQueryRequest.setResourceCredentials(clientCredentials); - - // Test nonexistent resourceId - dataQueryRequest.setResourceUUID(UUID.randomUUID()); - try { - QueryStatus result = queryService.query(dataQueryRequest, null); - fail("Nonexistent resourceId should throw an error"); - } catch (ProtocolException e) { - assertNotNull(e.getContent()); - assertTrue( - "Error message should say '" + ProtocolException.RESOURCE_NOT_FOUND + "'", - e.getContent().toString().contains(ProtocolException.RESOURCE_NOT_FOUND) - ); - } - - } - - @Test - public void testQueryValidRequest() { - GeneralQueryRequest dataQueryRequest = new GeneralQueryRequest(); - // At this level we don't check the credentials themselves, just that the map exists - Map clientCredentials = new HashMap(); - dataQueryRequest.setResourceCredentials(clientCredentials); - dataQueryRequest.setResourceUUID(resourceId); - dataQueryRequest.setQuery(queryString); - - QueryStatus result = queryService.query(dataQueryRequest, null); - assertNotNull("Status should not be null", result.getStatus()); - assertNotNull("Resource result id should not be null", result.getResourceResultId()); - assertNotNull("Picsure result id should not be null", result.getPicsureResultId()); - // Since there was no resource result id, it should be the same as the picsure - // result id - assertEquals( - "Resource result id and Picsure result id should match in case of no resource result id", result.getResourceResultId(), - result.getPicsureResultId().toString() - ); - - // Make sure the query is persisted - assertNotNull("Query Entity should have been persisted", queryEntity); - assertEquals("QueryEntity should be linked to resource", queryEntity.getResource(), mockResource); - - assertTrue("Query Entity should have query stored", queryEntity.getQuery().contains(queryString)); - assertEquals( - "Resource result id and Picsure result id should match in case of no resource result id", queryEntity.getResourceResultId(), - queryEntity.getUuid().toString() - ); - - } - - @Test - public void testQueryStatusNoId() { - - GeneralQueryRequest statusRequest = new GeneralQueryRequest(); - Map clientCredentials = new HashMap(); - statusRequest.setResourceCredentials(clientCredentials); - try { - QueryStatus result = queryService.queryStatus(null, statusRequest, null); - fail("Missing queryId should throw an error"); - } catch (ProtocolException e) { - assertNotNull(e.getContent()); - assertEquals( - "Error message should say '" + ProtocolException.MISSING_QUERY_ID + "'", ProtocolException.MISSING_QUERY_ID, - e.getContent().toString() - ); - } - - } - - @Test - public void testQueryStatusInvalidId() { - - GeneralQueryRequest statusRequest = new GeneralQueryRequest(); - Map clientCredentials = new HashMap(); - statusRequest.setResourceCredentials(clientCredentials); - - // Nonexistent queryId - try { - QueryStatus result = queryService.queryStatus(UUID.randomUUID(), statusRequest, null); - fail("Nonexistent queryId should throw an error"); - } catch (ProtocolException e) { - assertNotNull(e.getContent()); - assertTrue( - "Error message should say '" + ProtocolException.QUERY_NOT_FOUND + "'", - e.getContent().toString().contains(ProtocolException.QUERY_NOT_FOUND) - ); - } - - } - - @Test - public void testQueryStatusValid() { - - GeneralQueryRequest statusRequest = new GeneralQueryRequest(); - Map clientCredentials = new HashMap(); - statusRequest.setResourceCredentials(clientCredentials); - // Setup a pre-existing query Entity - queryEntity = new Query(); - queryEntity.setUuid(queryId); - queryEntity.setResourceResultId(queryId.toString()); - queryEntity.setResource(mockResource); - queryEntity.setStatus(PicSureStatus.PENDING); - queryEntity.setQuery(queryString); - queryEntity.setStartTime(new java.sql.Date(results.getStartTime())); - when(queryRepo.getById(queryId)).thenReturn(queryEntity); - - results.setStatus(PicSureStatus.AVAILABLE); // this should update the DB entity status - results.setStartTime(new Date().getTime()); - when(webClient.queryStatus(any(), any(), any())).thenReturn(results); - - // This one should work - QueryStatus result = queryService.queryStatus(queryId, statusRequest, null); - // These fields are set by the method - assertNotNull("Result should not be null", result); - assertEquals("Picsure ResultId should match", queryId, result.getPicsureResultId()); - assertEquals("Resource Id should match", resourceId, result.getResourceID()); - assertNotNull("Start time should not be null", result.getStartTime()); - - // Make sure info was saved to the query entity - assertEquals("Query status should have been updated", PicSureStatus.AVAILABLE, queryEntity.getStatus()); - } - - @Test - public void testQueryResultNoId() { - - - GeneralQueryRequest resultRequest = new GeneralQueryRequest(); - Map clientCredentials = new HashMap(); - resultRequest.setResourceCredentials(clientCredentials); - try { - Response result = queryService.queryResult(null, resultRequest, null); - fail("Missing queryId should throw an error"); - } catch (ProtocolException e) { - assertNotNull(e.getContent()); - assertEquals( - "Error message should say '" + ProtocolException.MISSING_QUERY_ID + "'", ProtocolException.MISSING_QUERY_ID, - e.getContent().toString() - ); - } - - } - - @Test - public void testQueryResultInvalidId() { - - - GeneralQueryRequest resultRequest = new GeneralQueryRequest(); - Map clientCredentials = new HashMap(); - resultRequest.setResourceCredentials(clientCredentials); - try { - Response result = queryService.queryResult(UUID.randomUUID(), resultRequest, null); - fail("Nonexistent queryId should throw an error"); - } catch (ProtocolException e) { - assertNotNull(e.getContent()); - assertTrue( - "Error message should say '" + ProtocolException.QUERY_NOT_FOUND + "'", - e.getContent().toString().contains(ProtocolException.QUERY_NOT_FOUND) - ); - } - - - } - - @Test - public void testQueryResultValid() { - - - GeneralQueryRequest resultRequest = new GeneralQueryRequest(); - Map clientCredentials = new HashMap(); - resultRequest.setResourceCredentials(clientCredentials); - - // Setup a pre-existing query Entity - queryEntity = new Query(); - queryEntity.setUuid(queryId); - queryEntity.setResourceResultId(queryId.toString()); - queryEntity.setResource(mockResource); - queryEntity.setStatus(PicSureStatus.AVAILABLE); - queryEntity.setQuery(queryString); - queryEntity.setStartTime(new java.sql.Date(results.getStartTime())); - when(queryRepo.getById(queryId)).thenReturn(queryEntity); - Response resp = mock(Response.class); - when(webClient.queryResult(any(), any(), any())).thenReturn(resp); - - when(mockResource.getResourceRSPath()).thenReturn("resourceRsPath"); - - // This one should work - Response result = queryService.queryResult(queryId, resultRequest, null); - assertNotNull("Result should not be null", result); - } - - @Test - public void testQuerySyncNoQuery() { - - // Test missing query data - try { - Response result = queryService.querySync(null, null); - fail("Missing query request info should throw an error"); - } catch (ProtocolException e) { - assertNotNull(e.getContent()); - assertEquals( - "Error message should say '" + ProtocolException.MISSING_DATA + "'", ProtocolException.MISSING_DATA, - e.getContent().toString() - ); - } - - } - - @Test - public void testQuerySyncNoResourceId() { - - GeneralQueryRequest dataQueryRequest = new GeneralQueryRequest(); - // At this level we don't check the credentials themselves, just that the map - // exists - Map clientCredentials = new HashMap(); - dataQueryRequest.setResourceCredentials(clientCredentials); - - // Test missing resourceId - dataQueryRequest.setQuery(queryString); - try { - Response result = queryService.querySync(dataQueryRequest, null); - fail("Missing resourceId should throw an error"); - } catch (ProtocolException e) { - assertNotNull(e.getContent()); - assertEquals( - "Error message should say '" + ProtocolException.MISSING_RESOURCE_ID + "'", ProtocolException.MISSING_RESOURCE_ID, - e.getContent().toString() - ); - } - - } - - @Test - public void testQuerySyncInvalidResourceId() { - - GeneralQueryRequest dataQueryRequest = new GeneralQueryRequest(); - // At this level we don't check the credentials themselves, just that the map - // exists - Map clientCredentials = new HashMap(); - dataQueryRequest.setResourceCredentials(clientCredentials); - // Test nonexistent resourceId - dataQueryRequest.setResourceUUID(UUID.randomUUID()); - try { - Response result = queryService.querySync(dataQueryRequest, null); - fail("Nonexistent resourceId should throw an error"); - } catch (ApplicationException e) { - assertNotNull(e.getContent()); - assertTrue( - "Error message should say '" + ApplicationException.MISSING_RESOURCE + "'", - e.getContent().toString().contains(ApplicationException.MISSING_RESOURCE) - ); - } - - } - - @Test - public void testQuerySyncValidNoResponseId() { - - GeneralQueryRequest dataQueryRequest = new GeneralQueryRequest(); - // At this level we don't check the credentials themselves, just that the map - // exists - Map clientCredentials = new HashMap(); - dataQueryRequest.setResourceCredentials(clientCredentials); - dataQueryRequest.setQuery(queryString); - - // Add needed data to results that are returned - results.setResourceID(resourceId); - results.setStatus(PicSureStatus.AVAILABLE); - results.setStartTime(new Date().getTime()); - - // Return mocks when needed - Response resp = mock(Response.class); - when(webClient.querySync(any(), any(), any())).thenReturn(resp); - - // Mock persisting the queryentity, so that it has an ID and we can test that - // the correct information is stored in it - doAnswer(new Answer() { - public Void answer(InvocationOnMock invocation) { - Query query = invocation.getArgument(0); - query.setUuid(queryId); - - queryEntity = query; - return null; - } - }).when(queryRepo).persist(any(Query.class)); - - - // Test correct request - dataQueryRequest.setResourceUUID(resourceId); - Response result = queryService.querySync(dataQueryRequest, null); - assertNotNull("Result should not be null", result.getStatus()); - - // Make sure the query is persisted - assertNotNull("Query Entity should have been persisted", queryEntity); - assertEquals("QueryEntity should be linked to resource", queryEntity.getResource(), mockResource); - - assertTrue("Query Entity should have query stored", queryEntity.getQuery().contains(queryString)); - assertEquals( - "Resource result id and Picsure result id should match in case of no resource result id", queryId.toString(), - queryEntity.getResourceResultId() - ); - - } - - @Test - public void testShouldQueryMetadata() { - Resource resource = new Resource(); - resource.setUuid(resourceId); - String resultId = UUID.randomUUID().toString(); - Query query = new Query(); - query.setQuery("{}"); - query.setResource(resource); - query.setStatus(PicSureStatus.AVAILABLE); - query.setStartTime(new java.sql.Date(System.currentTimeMillis())); - query.setResourceResultId(resultId); - - String metaData = "{\\\"picsureQueryId\\\":\\\"b9e6cea7-142e-5859-8e98-1245c959fc0b\\\"," - + "\\\"commonAreaId\\\":\\\"290a9d2e-1a20-4407-b351-499185f5554e\\\"}"; - - query.setMetadata(metaData.getBytes(StandardCharsets.UTF_8)); - - Mockito.when(queryRepo.getById(query.getUuid())).thenReturn(query); - - QueryStatus status = queryService.queryMetadata(query.getUuid(), null); - String actual = (String) status.getResultMetadata().get("queryResultMetadata"); - Assert.assertEquals(metaData, actual); - } - - @Test - public void testQuerySyncValidWithResponseId() { - - GeneralQueryRequest dataQueryRequest = new GeneralQueryRequest(); - // At this level we don't check the credentials themselves, just that the map - // exists - Map clientCredentials = new HashMap(); - dataQueryRequest.setResourceCredentials(clientCredentials); - dataQueryRequest.setQuery(queryString); - - String resultId = UUID.randomUUID().toString(); - - // Add needed data to results that are returned - results.setResourceID(resourceId); - results.setStatus(PicSureStatus.AVAILABLE); - results.setStartTime(new Date().getTime()); - results.setResourceResultId(resultId); - - // Return mocks when needed - Response resp = mock(Response.class); - - MultivaluedMap headerMap = new MultivaluedHashMap(); - headerMap.add(ResourceWebClient.QUERY_METADATA_FIELD, resultId); - when(resp.getHeaders()).thenReturn(headerMap); - when(webClient.querySync(any(), any(), any())).thenReturn(resp); - - // Mock persisting the queryentity, so that it has an ID and we can test that - // the correct information is stored in it - doAnswer(new Answer() { - public Void answer(InvocationOnMock invocation) { - Query query = invocation.getArgument(0); - query.setUuid(queryId); - queryEntity = query; - return null; - } - }).when(queryRepo).persist(any(Query.class)); - - - // Test correct request - dataQueryRequest.setResourceUUID(resourceId); - Response result = queryService.querySync(dataQueryRequest, null); - assertNotNull("Result should not be null", result.getStatus()); - - // Make sure the query is persisted - assertNotNull("Query Entity should have been persisted", queryEntity); - assertEquals("QueryEntity should be linked to resource", queryEntity.getResource(), mockResource); - - assertTrue("Query Entity should have query stored", queryEntity.getQuery().contains(queryString)); - assertEquals("Resource result id should match returned header", resultId, queryEntity.getResourceResultId()); - - } - - @Test - public void testQuerySetsAuditContext() { - GeneralQueryRequest dataQueryRequest = new GeneralQueryRequest(); - dataQueryRequest.setResourceCredentials(new HashMap<>()); - dataQueryRequest.setResourceUUID(resourceId); - dataQueryRequest.setQuery(queryString); - - queryService.query(dataQueryRequest, null); - - verify(auditContext).put("resource_id", resourceId.toString()); - verify(auditContext).put("resource_name", "test-resource"); - verify(auditContext).put(eq("query_id"), any(String.class)); - } - - @Test - public void testQuerySyncSetsAuditContext() { - GeneralQueryRequest dataQueryRequest = new GeneralQueryRequest(); - dataQueryRequest.setResourceCredentials(new HashMap<>()); - dataQueryRequest.setResourceUUID(resourceId); - dataQueryRequest.setQuery(queryString); - - Response resp = mock(Response.class); - when(webClient.querySync(any(), any(), any())).thenReturn(resp); - - queryService.querySync(dataQueryRequest, null); - - verify(auditContext).put("resource_id", resourceId.toString()); - verify(auditContext).put("resource_name", "test-resource"); - verify(auditContext).put(eq("query_id"), any(String.class)); - } - - @Test - public void testQueryResultSetsAuditContext() { - GeneralQueryRequest resultRequest = new GeneralQueryRequest(); - resultRequest.setResourceCredentials(new HashMap<>()); - - queryEntity = new Query(); - queryEntity.setUuid(queryId); - queryEntity.setResourceResultId(queryId.toString()); - queryEntity.setResource(mockResource); - queryEntity.setStatus(PicSureStatus.AVAILABLE); - queryEntity.setQuery(queryString); - queryEntity.setStartTime(new java.sql.Date(results.getStartTime())); - when(queryRepo.getById(queryId)).thenReturn(queryEntity); - Response resp = mock(Response.class); - when(webClient.queryResult(any(), any(), any())).thenReturn(resp); - - queryService.queryResult(queryId, resultRequest, null); - - verify(auditContext).put("resource_id", resourceId.toString()); - verify(auditContext).put("resource_name", "test-resource"); - verify(auditContext).put("query_id", queryId.toString()); - } - - @Test - public void testQuerySignedUrlSetsAuditContext() { - GeneralQueryRequest resultRequest = new GeneralQueryRequest(); - resultRequest.setResourceCredentials(new HashMap<>()); - - queryEntity = new Query(); - queryEntity.setUuid(queryId); - queryEntity.setResourceResultId(queryId.toString()); - queryEntity.setResource(mockResource); - queryEntity.setStatus(PicSureStatus.AVAILABLE); - queryEntity.setQuery(queryString); - queryEntity.setStartTime(new java.sql.Date(results.getStartTime())); - when(queryRepo.getById(queryId)).thenReturn(queryEntity); - Response resp = mock(Response.class); - when(webClient.queryResultSignedUrl(any(), any(), any())).thenReturn(resp); - - queryService.queryResultSignedUrl(queryId, resultRequest, null); - - verify(auditContext).put("resource_id", resourceId.toString()); - verify(auditContext).put("resource_name", "test-resource"); - verify(auditContext).put("query_id", queryId.toString()); - } -} diff --git a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/PicsureSearchServiceTest.java b/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/PicsureSearchServiceTest.java deleted file mode 100644 index 4f82b7c58..000000000 --- a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/PicsureSearchServiceTest.java +++ /dev/null @@ -1,148 +0,0 @@ -package edu.harvard.dbmi.avillach; - -import edu.harvard.dbmi.avillach.data.repository.ResourceRepository; -import edu.harvard.dbmi.avillach.service.AuditContext; -import edu.harvard.dbmi.avillach.domain.SearchResults; -import edu.harvard.dbmi.avillach.service.PicsureSearchService; -import edu.harvard.dbmi.avillach.service.ResourceWebClient; -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; -import org.junit.Before; -import org.junit.Test; - -import java.util.UUID; - -import edu.harvard.dbmi.avillach.data.entity.Resource; -import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest; -import org.junit.runner.RunWith; - -import org.mockito.ArgumentMatchers; -import org.mockito.InjectMocks; -import org.mockito.Mock; -import org.mockito.junit.MockitoJUnitRunner; - -import java.util.HashMap; -import java.util.Map; - -import static junit.framework.TestCase.assertTrue; -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.fail; -import static org.mockito.AdditionalMatchers.not; -import static org.mockito.ArgumentMatchers.any; -import static org.mockito.Mockito.mock; -import static org.mockito.Mockito.verify; -import static org.mockito.Mockito.when; - -@RunWith(MockitoJUnitRunner.class) -public class PicsureSearchServiceTest extends BaseServiceTest { - - private UUID resourceId = UUID.randomUUID(); - - @InjectMocks - private PicsureSearchService searchService = new PicsureSearchService(); - - @Mock - private Resource mockResource = mock(Resource.class); - - @Mock - private ResourceRepository resourceRepo = mock(ResourceRepository.class); - - @Mock - private ResourceWebClient webClient = mock(ResourceWebClient.class); - - @Mock - private AuditContext auditContext = mock(AuditContext.class); - - @Before - public void setUp() { - SearchResults results = new SearchResults(); - when(resourceRepo.getById(resourceId)).thenReturn(mockResource); - when(resourceRepo.getById(not(ArgumentMatchers.same(resourceId)))).thenReturn(null); - when(webClient.search(any(), any())).thenReturn(results); - } - - @Test - public void testSearch() { - GeneralQueryRequest searchQueryRequest = new GeneralQueryRequest(); - Map clientCredentials = new HashMap(); - clientCredentials.put("bearer key", "bearer token"); - searchQueryRequest.setResourceCredentials(clientCredentials); - searchQueryRequest.setQuery("blood"); - - try { - SearchResults results = searchService.search(resourceId, searchQueryRequest, null); - fail("Missing request data should throw an error"); - } catch (ApplicationException e) { - assertNotNull(e.getContent()); - assertEquals( - "Error message should say '" + ApplicationException.MISSING_RESOURCE_PATH + "'", ApplicationException.MISSING_RESOURCE_PATH, - e.getContent().toString() - ); - } - - when(mockResource.getResourceRSPath()).thenReturn("resourceRsPath"); - - // Missing requestdata should throw an error - try { - SearchResults results = searchService.search(resourceId, null, null); - fail("Missing request data should throw an error"); - } catch (ProtocolException e) { - assertNotNull(e.getContent()); - assertEquals( - "Error message should say '" + ProtocolException.MISSING_DATA + "'", ProtocolException.MISSING_DATA, - e.getContent().toString() - ); - } - - // Missing resourceId should error - try { - SearchResults results = searchService.search(null, searchQueryRequest, null); - fail("Missing resourceId should throw an error"); - } catch (ProtocolException e) { - assertNotNull(e.getContent()); - assertEquals( - "Error message should say '" + ProtocolException.MISSING_RESOURCE_ID + "'", ProtocolException.MISSING_RESOURCE_ID, - e.getContent().toString() - ); - - } - - // Nonexistent resourceId should error - try { - SearchResults results = searchService.search(UUID.randomUUID(), searchQueryRequest, null); - fail("Nonexistent resourceId should throw an error"); - } catch (ProtocolException e) { - assertNotNull(e.getContent()); - assertTrue( - "Error message should say '" + ProtocolException.RESOURCE_NOT_FOUND + "'", - e.getContent().toString().contains(ProtocolException.RESOURCE_NOT_FOUND) - ); - } - - // This should work - SearchResults results = searchService.search(resourceId, searchQueryRequest, null); - assertNotNull("SearchResults should not be null", results); - - // There should also be no problem if the resourceCredentials are null - searchQueryRequest.setResourceCredentials(null); - results = searchService.search(resourceId, searchQueryRequest, null); - assertNotNull("SearchResults should not be null", results); - } - - @Test - public void testSearchSetsAuditContext() { - when(mockResource.getResourceRSPath()).thenReturn("resourceRsPath"); - when(mockResource.getName()).thenReturn("test-resource"); - - GeneralQueryRequest searchQueryRequest = new GeneralQueryRequest(); - searchQueryRequest.setResourceCredentials(new HashMap<>()); - searchQueryRequest.setQuery("blood"); - - searchService.search(resourceId, searchQueryRequest, null); - - verify(auditContext).put("resource_id", resourceId.toString()); - verify(auditContext).put("resource_name", "test-resource"); - verify(auditContext).put("search_term", "blood"); - } -} diff --git a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/security/AuditLoggingFilterTest.java b/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/security/AuditLoggingFilterTest.java deleted file mode 100644 index b88fd7c63..000000000 --- a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/security/AuditLoggingFilterTest.java +++ /dev/null @@ -1,579 +0,0 @@ -package edu.harvard.dbmi.avillach.security; - -import static org.junit.Assert.*; -import static org.mockito.Mockito.*; - -import java.io.IOException; -import java.net.URI; -import java.util.Map; - -import javax.servlet.http.HttpServletRequest; -import javax.ws.rs.container.ContainerRequestContext; -import javax.ws.rs.container.ContainerResponseContext; -import javax.ws.rs.core.SecurityContext; -import javax.ws.rs.core.UriInfo; - -import org.junit.Before; -import org.junit.Test; -import org.mockito.ArgumentCaptor; - -import edu.harvard.dbmi.avillach.data.entity.AuthUser; -import edu.harvard.dbmi.avillach.logging.LoggingClient; -import edu.harvard.dbmi.avillach.logging.LoggingEvent; -import edu.harvard.dbmi.avillach.logging.SessionIdResolver; -import edu.harvard.dbmi.avillach.service.AuditContext; - -public class AuditLoggingFilterTest { - - private AuditLoggingFilter filter; - private LoggingClient loggingClient; - private HttpServletRequest httpServletRequest; - private AuditContext auditContext; - - @Before - public void setup() { - filter = new AuditLoggingFilter(); - loggingClient = mock(LoggingClient.class); - when(loggingClient.isEnabled()).thenReturn(true); - httpServletRequest = mock(HttpServletRequest.class); - when(httpServletRequest.getRemoteAddr()).thenReturn("192.168.1.1"); - when(httpServletRequest.getLocalAddr()).thenReturn("10.0.0.1"); - when(httpServletRequest.getLocalPort()).thenReturn(8080); - - auditContext = mock(AuditContext.class); - when(auditContext.getMetadata()).thenReturn(new java.util.HashMap<>()); - - filter.loggingClient = loggingClient; - filter.auditContext = auditContext; - filter.httpServletRequest = httpServletRequest; - } - - private ContainerRequestContext mockRequestContext(String path, String method) { - ContainerRequestContext ctx = mock(ContainerRequestContext.class); - UriInfo uriInfo = mock(UriInfo.class); - when(uriInfo.getRequestUri()).thenReturn(URI.create("http://localhost:8080" + path)); - when(ctx.getUriInfo()).thenReturn(uriInfo); - when(ctx.getMethod()).thenReturn(method); - when(ctx.getProperty("audit_start_time")).thenReturn(System.currentTimeMillis() - 50L); - return ctx; - } - - private ContainerResponseContext mockResponseContext(int status) { - ContainerResponseContext ctx = mock(ContainerResponseContext.class); - when(ctx.getStatus()).thenReturn(status); - when(ctx.getHeaderString("Content-Type")).thenReturn("application/json"); - when(ctx.getLength()).thenReturn(-1); - return ctx; - } - - // ---- Request phase ---- - - @Test - public void testRequestFilterSetsAuditStartTime() throws IOException { - ContainerRequestContext ctx = mock(ContainerRequestContext.class); - filter.filter(ctx); - verify(ctx).setProperty(eq("audit_start_time"), anyLong()); - } - - // ---- URL categorization ---- - - @Test - public void testQueryPostMapsToQuerySubmitted() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/query", "POST"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - LoggingEvent event = captor.getValue(); - assertEquals("QUERY", event.getEventType()); - assertEquals("query.submitted", event.getAction()); - } - - @Test - public void testQuerySyncPostMapsToQuerySync() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/query/sync", "POST"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - LoggingEvent event = captor.getValue(); - assertEquals("QUERY", event.getEventType()); - assertEquals("query.sync", event.getAction()); - } - - @Test - public void testQueryStatusPostMapsToQueryStatus() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/query/abc-123/status", "POST"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - LoggingEvent event = captor.getValue(); - assertEquals("QUERY", event.getEventType()); - assertEquals("query.status", event.getAction()); - } - - @Test - public void testQueryResultPostMapsToDataAccessQueryResult() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/query/abc-123/result", "POST"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - LoggingEvent event = captor.getValue(); - assertEquals("DATA_ACCESS", event.getEventType()); - assertEquals("query.result", event.getAction()); - } - - @Test - public void testQuerySignedUrlPostMapsToDataAccessQuerySignedUrl() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/query/abc-123/signed-url", "POST"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - LoggingEvent event = captor.getValue(); - assertEquals("DATA_ACCESS", event.getEventType()); - assertEquals("query.signed_url", event.getAction()); - } - - @Test - public void testQueryMetadataGetMapsToQueryMetadata() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/query/abc-123/metadata", "GET"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - LoggingEvent event = captor.getValue(); - assertEquals("QUERY", event.getEventType()); - assertEquals("query.metadata", event.getAction()); - } - - @Test - public void testSearchPostMapsToSearch() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/search/abc-123", "POST"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - LoggingEvent event = captor.getValue(); - assertEquals("SEARCH", event.getEventType()); - assertEquals("search.execute", event.getAction()); - } - - @Test - public void testSearchValuesGetMapsToSearchValues() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/search/abc-123/values/", "GET"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - LoggingEvent event = captor.getValue(); - assertEquals("SEARCH", event.getEventType()); - assertEquals("search.values", event.getAction()); - } - - @Test - public void testProxyPostMapsToProxyRequest() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/proxy/container/path", "POST"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - LoggingEvent event = captor.getValue(); - assertEquals("PROXY", event.getEventType()); - assertEquals("proxy.request", event.getAction()); - } - - @Test - public void testV3QueryPostMapsToQuerySubmittedWithApiVersion() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/v3/query", "POST"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - LoggingEvent event = captor.getValue(); - assertEquals("QUERY", event.getEventType()); - assertEquals("query.submitted", event.getAction()); - assertEquals("v3", event.getMetadata().get("api_version")); - } - - @Test - public void testPicsurePrefixIsStrippedForCategorization() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/PICSURE/query", "POST"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - LoggingEvent event = captor.getValue(); - assertEquals("QUERY", event.getEventType()); - assertEquals("query.submitted", event.getAction()); - } - - @Test - public void testUnknownPathMapsToOtherWithHttpMethod() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/something/else", "GET"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - LoggingEvent event = captor.getValue(); - assertEquals("OTHER", event.getEventType()); - assertEquals("GET", event.getAction()); - } - - // ---- Skipped paths ---- - - @Test - public void testSkippedPathsDoNotSendEvents() throws IOException { - String[] skippedPaths = - {"/system/status", "/openapi.json", "/info/resources", "/info/abc-123", "/bin/continuous", "/proxy/pic-sure-logging/audit"}; - - for (String path : skippedPaths) { - reset(loggingClient); - when(loggingClient.isEnabled()).thenReturn(true); - - ContainerRequestContext reqCtx = mockRequestContext(path, "GET"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - verify(loggingClient, never()).send(any(LoggingEvent.class)); - verify(loggingClient, never()).send(any(LoggingEvent.class), anyString(), anyString()); - } - } - - // ---- IP extraction ---- - - @Test - public void testXForwardedForSingleIpUsedAsSrcIp() throws IOException { - when(httpServletRequest.getHeader("X-Forwarded-For")).thenReturn("203.0.113.50"); - - ContainerRequestContext reqCtx = mockRequestContext("/something", "GET"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - assertEquals("203.0.113.50", captor.getValue().getRequest().getSrcIp()); - } - - @Test - public void testXForwardedForMultipleIpsUsesFirst() throws IOException { - when(httpServletRequest.getHeader("X-Forwarded-For")).thenReturn("203.0.113.50, 70.41.3.18, 150.172.238.178"); - - ContainerRequestContext reqCtx = mockRequestContext("/something", "GET"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - assertEquals("203.0.113.50", captor.getValue().getRequest().getSrcIp()); - } - - @Test - public void testNoXForwardedForFallsBackToRemoteAddr() throws IOException { - when(httpServletRequest.getHeader("X-Forwarded-For")).thenReturn(null); - - ContainerRequestContext reqCtx = mockRequestContext("/something", "GET"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - assertEquals("192.168.1.1", captor.getValue().getRequest().getSrcIp()); - } - - // ---- Session ID ---- - - @Test - public void testXSessionIdHeaderUsedWhenPresent() throws IOException { - when(httpServletRequest.getHeader("X-Session-Id")).thenReturn("my-session-123"); - - ContainerRequestContext reqCtx = mockRequestContext("/something", "GET"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - assertEquals("my-session-123", captor.getValue().getSessionId()); - } - - @Test - public void testNoXSessionIdGeneratesHashFromIpAndUserAgent() throws IOException { - when(httpServletRequest.getHeader("X-Session-Id")).thenReturn(null); - when(httpServletRequest.getHeader("X-Forwarded-For")).thenReturn(null); - when(httpServletRequest.getHeader("User-Agent")).thenReturn("TestBrowser/1.0"); - - ContainerRequestContext reqCtx = mockRequestContext("/something", "GET"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - - String expectedHash = SessionIdResolver.resolve(null, "192.168.1.1", "TestBrowser/1.0"); - assertEquals(expectedHash, captor.getValue().getSessionId()); - } - - // ---- Error detection ---- - - @Test - public void testStatus200HasNoErrorMap() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/something", "GET"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - assertNull(captor.getValue().getError()); - } - - @Test - public void testStatus404HasClientErrorMap() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/something", "GET"); - ContainerResponseContext respCtx = mockResponseContext(404); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - Map error = captor.getValue().getError(); - assertNotNull(error); - assertEquals(404, error.get("status")); - assertEquals("client_error", error.get("error_type")); - } - - @Test - public void testStatus500HasServerErrorMap() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/something", "GET"); - ContainerResponseContext respCtx = mockResponseContext(500); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - Map error = captor.getValue().getError(); - assertNotNull(error); - assertEquals(500, error.get("status")); - assertEquals("server_error", error.get("error_type")); - } - - // ---- User extraction ---- - - @Test - public void testAuthUserInSecurityContextExtractsUserIdAndEmail() throws IOException { - AuthUser authUser = new AuthUser(); - authUser.setUserId("user-42"); - authUser.setEmail("user@example.com"); - - SecurityContext secCtx = mock(SecurityContext.class); - when(secCtx.getUserPrincipal()).thenReturn(authUser); - - ContainerRequestContext reqCtx = mockRequestContext("/something", "GET"); - when(reqCtx.getSecurityContext()).thenReturn(secCtx); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - Map metadata = captor.getValue().getMetadata(); - assertEquals("user-42", metadata.get("user_id")); - assertEquals("user@example.com", metadata.get("user_email")); - } - - @Test - public void testNoAuthUserButUsernamePropertyUsesUsernameAsUserId() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/something", "GET"); - when(reqCtx.getProperty("username")).thenReturn("prop-user"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - Map metadata = captor.getValue().getMetadata(); - assertEquals("prop-user", metadata.get("user_id")); - } - - @Test - public void testNoUserInfoDoesNotIncludeUserIdInMetadata() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/something", "GET"); - when(reqCtx.getProperty("username")).thenReturn(null); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - Map metadata = captor.getValue().getMetadata(); - assertFalse(metadata.containsKey("user_id")); - } - - // ---- Bearer token passthrough ---- - - @Test - public void testAuthorizationHeaderPresentCallsSendWithAuthAndRequestId() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/something", "GET"); - when(reqCtx.getHeaderString("Authorization")).thenReturn("Bearer token123"); - when(httpServletRequest.getHeader("X-Request-Id")).thenReturn("req-456"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture(), eq("Bearer token123"), eq("req-456")); - verify(loggingClient, never()).send(any(LoggingEvent.class)); - } - - @Test - public void testNoAuthHeaderAndNoRequestIdCallsSendWithoutExtra() throws IOException { - ContainerRequestContext reqCtx = mockRequestContext("/something", "GET"); - when(reqCtx.getHeaderString("Authorization")).thenReturn(null); - when(httpServletRequest.getHeader("X-Request-Id")).thenReturn(null); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - verify(loggingClient, never()).send(any(LoggingEvent.class), anyString(), anyString()); - } - - // ---- Disabled / null logging client ---- - - @Test - public void testNullLoggingClientDoesNotSendOrThrow() throws IOException { - filter.loggingClient = null; - - ContainerRequestContext reqCtx = mockRequestContext("/query", "POST"); - ContainerResponseContext respCtx = mockResponseContext(200); - - // Should not throw - filter.filter(reqCtx, respCtx); - } - - @Test - public void testDisabledLoggingClientDoesNotSend() throws IOException { - when(loggingClient.isEnabled()).thenReturn(false); - - ContainerRequestContext reqCtx = mockRequestContext("/query", "POST"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - verify(loggingClient, never()).send(any(LoggingEvent.class)); - verify(loggingClient, never()).send(any(LoggingEvent.class), anyString(), anyString()); - } - - // ---- RequestInfo fields ---- - - @Test - public void testRequestInfoPopulatedCorrectly() throws IOException { - when(httpServletRequest.getHeader("X-Forwarded-For")).thenReturn(null); - when(httpServletRequest.getHeader("User-Agent")).thenReturn("TestAgent/2.0"); - - ContainerRequestContext reqCtx = mockRequestContext("/query", "POST"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - LoggingEvent event = captor.getValue(); - - assertEquals("POST", event.getRequest().getMethod()); - assertEquals("/query", event.getRequest().getUrl()); - assertEquals("192.168.1.1", event.getRequest().getSrcIp()); - assertEquals("10.0.0.1", event.getRequest().getDestIp()); - assertEquals(Integer.valueOf(8080), event.getRequest().getDestPort()); - assertEquals("TestAgent/2.0", event.getRequest().getHttpUserAgent()); - assertEquals(Integer.valueOf(200), event.getRequest().getStatus()); - assertEquals("application/json", event.getRequest().getHttpContentType()); - assertNull(event.getRequest().getBytes()); - assertNotNull(event.getRequest().getDuration()); - } - - @Test - public void testMergesAuditContextMetadata() throws IOException { - java.util.Map serviceMetadata = new java.util.HashMap<>(); - serviceMetadata.put("resource_id", "abc-123"); - serviceMetadata.put("resource_name", "test-resource"); - serviceMetadata.put("query_id", "def-456"); - when(auditContext.getMetadata()).thenReturn(serviceMetadata); - - ContainerRequestContext reqCtx = mockRequestContext("/PICSURE/query", "POST"); - ContainerResponseContext respCtx = mockResponseContext(200); - filter.filter(reqCtx, respCtx); - - ArgumentCaptor eventCaptor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(eventCaptor.capture()); - LoggingEvent event = eventCaptor.getValue(); - assertEquals("abc-123", event.getMetadata().get("resource_id")); - assertEquals("test-resource", event.getMetadata().get("resource_name")); - assertEquals("def-456", event.getMetadata().get("query_id")); - // Also has filter-level session_id - assertNotNull(event.getSessionId()); - } - - // ---- Client type (X-Client-Type header) ---- - - @Test - public void testXClientTypeHeaderRecordedAsCaller() throws IOException { - when(httpServletRequest.getHeader("X-Client-Type")).thenReturn("PYTHON_ADAPTER"); - - ContainerRequestContext reqCtx = mockRequestContext("/query", "POST"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - assertEquals("PYTHON_ADAPTER", captor.getValue().getCaller()); - } - - @Test - public void testNoXClientTypeHeaderOmitsCaller() throws IOException { - when(httpServletRequest.getHeader("X-Client-Type")).thenReturn(null); - - ContainerRequestContext reqCtx = mockRequestContext("/query", "POST"); - ContainerResponseContext respCtx = mockResponseContext(200); - - filter.filter(reqCtx, respCtx); - - ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); - verify(loggingClient).send(captor.capture()); - assertNull(captor.getValue().getCaller()); - } -} diff --git a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/security/JWTFilterTest.java b/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/security/JWTFilterTest.java deleted file mode 100644 index 0fdc4ff77..000000000 --- a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/security/JWTFilterTest.java +++ /dev/null @@ -1,407 +0,0 @@ -package edu.harvard.dbmi.avillach.security; - -import static com.github.tomakehurst.wiremock.client.WireMock.*; -import static org.junit.Assert.*; -import static org.mockito.Mockito.*; - -import java.io.ByteArrayInputStream; -import java.io.IOException; -import java.io.InputStream; -import java.util.ArrayList; -import java.util.List; -import java.util.HashMap; -import java.util.Map; -import java.util.UUID; - -import javax.ws.rs.HttpMethod; -import javax.ws.rs.NotAuthorizedException; -import javax.ws.rs.container.ContainerRequestContext; -import javax.ws.rs.core.HttpHeaders; -import javax.ws.rs.core.Request; -import javax.ws.rs.core.Response; -import javax.ws.rs.core.UriInfo; - -import org.junit.Before; -import org.junit.Rule; -import org.junit.Test; -import org.mockito.ArgumentCaptor; - -import com.fasterxml.jackson.databind.ObjectMapper; -import com.github.tomakehurst.wiremock.junit.WireMockRule; - -import edu.harvard.dbmi.avillach.PicSureWarInit; -import edu.harvard.dbmi.avillach.data.entity.Query; -import edu.harvard.dbmi.avillach.data.entity.Resource; -import edu.harvard.dbmi.avillach.data.repository.QueryRepository; -import edu.harvard.dbmi.avillach.data.repository.ResourceRepository; -import edu.harvard.dbmi.avillach.service.AuditContext; -import edu.harvard.dbmi.avillach.service.ResourceWebClient; -import edu.harvard.dbmi.avillach.util.response.PICSUREResponseError; - -public class JWTFilterTest { - private static final UUID QUERY_UUID = UUID.fromString("e830138f-2943-4661-90ae-da053bd94a18"); - - private static final UUID RESOURCE_UUID = UUID.fromString("30ef4941-9656-4b47-af80-528f2b98cf17"); - - @Rule - public WireMockRule wireMockRule = new WireMockRule(0); - - private int port; - - private PicSureWarInit picSureWarInit; - - private JWTFilter filter; - - @Before - public void setup() { - port = wireMockRule.port(); - picSureWarInit = mock(PicSureWarInit.class); - when(picSureWarInit.getToken_introspection_token()).thenReturn("INTROSPECTION_TOKEN"); - when(picSureWarInit.getToken_introspection_url()).thenReturn("http://localhost:" + port + "/introspection_endpoint"); - filter = new JWTFilter(); - filter.setUserIdClaim("sub"); - filter.picSureWarInit = picSureWarInit; - filter.resourceWebClient = new ResourceWebClient(); - filter.queryRepo = mock(QueryRepository.class); - filter.resourceRepo = mock(ResourceRepository.class); - filter.auditContext = new AuditContext(); - filter.uriInfo = mock(UriInfo.class); - when(filter.uriInfo.getPath()).thenReturn("/test"); - } - - private ContainerRequestContext createRequestContext() { - ContainerRequestContext ctx = mock(ContainerRequestContext.class); - UriInfo uriInfo = mock(UriInfo.class); - Request request = mock(Request.class); - when(ctx.getUriInfo()).thenReturn(uriInfo); - when(ctx.getRequest()).thenReturn(request); - return ctx; - } - - - private Query persistedQuery() { - Resource resource = basicResource(); - Query query = new Query(); - query.setUuid(UUID.randomUUID()); - query.setQuery("{\"resourceUUID\":\"" + RESOURCE_UUID + "\"}"); - query.setResource(resource); - when(filter.queryRepo.getById(QUERY_UUID)).thenReturn(query); - return query; - } - - private Resource basicResource() { - Resource resource = mock(Resource.class); - when(resource.getResourceRSPath()).thenReturn("http://localhost:" + wireMockRule.port() + "/resource"); - when(resource.getToken()).thenReturn("RESOURCE_TOKEN"); - when(resource.getUuid()).thenReturn(RESOURCE_UUID); - - when(filter.resourceRepo.getById(RESOURCE_UUID)).thenReturn(resource); - return resource; - } - - private void tokenIntrospectionStub() { - tokenIntrospectionStub(true); - } - - private void tokenIntrospectionStub(Boolean active) { - stubFor( - post(urlEqualTo("/introspection_endpoint")).willReturn( - aResponse().withStatus(200).withHeader("Content-Type", "application/json").withBody( - "{" + "\"active\":" + Boolean.toString(active) + "," + "\"sub\":\"TEST_USER\"," + "\"email\":\"some@email.com\"," - + "\"roles\":\"PIC_SURE_ANY_QUERY\"," + "\"tokenRefreshed\":" + Boolean.FALSE + "}" - ) - ) - ); - } - - @Test - public void testSystemPathDoesNotRequireAuthenticationHeader() throws IOException { - ContainerRequestContext ctx = createRequestContext(); - when(ctx.getUriInfo().getPath()).thenReturn("/system/status"); - when(ctx.getRequest().getMethod()).thenReturn(HttpMethod.GET); - filter.filter(ctx); - verify(ctx).setProperty("username", "SYSTEM_MONITOR"); - } - - @Test - public void testLoggingProxyPathSkipsAuthentication() throws IOException { - ContainerRequestContext ctx = createRequestContext(); - when(ctx.getUriInfo().getPath()).thenReturn("/proxy/pic-sure-logging/audit"); - filter.filter(ctx); - verify(ctx, never()).getHeaderString(HttpHeaders.AUTHORIZATION); - verify(ctx, never()).abortWith(any(Response.class)); - } - - @Test - public void testExcludedFilterPaths_openapi() throws IOException { - ContainerRequestContext ctx = createRequestContext(); - when(ctx.getUriInfo().getPath()).thenReturn("/openapi.json"); - when(ctx.getRequest().getMethod()).thenReturn(HttpMethod.GET); - filter.filter(ctx); - verify(ctx, never()).setProperty(eq("username"), anyString()); - verify(ctx, never()).abortWith(any(Response.class)); - verify(ctx, never()).getHeaderString(HttpHeaders.AUTHORIZATION); - } - - @Test - public void testExcludedFilterPaths_config_validPathsWithNoAuthRequired() throws RuntimeException { - List letters = List.of( - "", "/ui:(feature.flag3)?-wear[e12]", "/address", "/postadmin", "/data", "/meta", "/init", "/names", "/administrators", - "/00000000-0000-0000-0000-000000000000" - ); - - List exceptions = new ArrayList<>(); - for (String letter : letters) { - ContainerRequestContext ctx = createRequestContext(); - when(ctx.getUriInfo().getPath()).thenReturn("/configuration" + letter); - when(ctx.getRequest().getMethod()).thenReturn(HttpMethod.GET); - - try { - filter.filter(ctx); - verify(ctx, never()).setProperty(eq("username"), anyString()); - verify(ctx, never()).abortWith(any(Response.class)); - } catch (Exception e) { - exceptions.add(letter); - } - } - assertEquals(0, exceptions.size()); - } - - @Test(expected = NotAuthorizedException.class) - public void testExcludedFilterPaths_config_invalidPathsHitNoAuthException() throws IOException { - ContainerRequestContext ctx = createRequestContext(); - when(ctx.getUriInfo().getPath()).thenReturn("/configuration/SOME_FLA%G"); - when(ctx.getRequest().getMethod()).thenReturn(HttpMethod.GET); - - filter.filter(ctx); - // Test passes if NotAuthorizedException is thrown - } - - @Test(expected = NotAuthorizedException.class) - public void testExcludedFilterPaths_config_blockedAdminPathHitsNoAuthException() throws IOException { - ContainerRequestContext ctx = createRequestContext(); - when(ctx.getUriInfo().getPath()).thenReturn("/configuration/admin"); - when(ctx.getRequest().getMethod()).thenReturn(HttpMethod.GET); - - filter.filter(ctx); - // Test passes if NotAuthorizedException is thrown - } - - @Test - public void testFilterCallsTokenIntrospectionAppropriatelyForQuerySync() throws IOException { - - tokenIntrospectionStub(); - - ContainerRequestContext ctx = createRequestContext(); - when(ctx.getUriInfo().getPath()).thenReturn("/query/sync"); - when(ctx.getRequest().getMethod()).thenReturn(HttpMethod.POST); - InputStream entityStream = new ByteArrayInputStream("{\"query\":\"test\"}".getBytes()); - when(ctx.getEntityStream()).thenReturn(entityStream); - when(ctx.getHeaderString(HttpHeaders.AUTHORIZATION)).thenReturn("Bearer USER_TOKEN"); - filter.filter(ctx); - - verify( - postRequestedFor(urlEqualTo("/introspection_endpoint")) - .withRequestBody(matchingJsonPath("$.request.['Target Service']", matching("/query/sync"))) - .withRequestBody(matchingJsonPath("$.request.['query']", matchingJsonPath("query", matching("test")))) - .withRequestBody(matchingJsonPath("$.token", matching("USER_TOKEN"))) - ); - } - - @Test - public void testFilterCallsTokenIntrospectionAppropriatelyForQuery() throws IOException { - - tokenIntrospectionStub(); - - ContainerRequestContext ctx = createRequestContext(); - when(ctx.getUriInfo().getPath()).thenReturn("/query"); - when(ctx.getRequest().getMethod()).thenReturn(HttpMethod.POST); - InputStream entityStream = new ByteArrayInputStream("{\"query\":\"test\"}".getBytes()); - when(ctx.getEntityStream()).thenReturn(entityStream); - when(ctx.getHeaderString(HttpHeaders.AUTHORIZATION)).thenReturn("Bearer USER_TOKEN"); - filter.filter(ctx); - - verify( - postRequestedFor(urlEqualTo("/introspection_endpoint")) - .withRequestBody(matchingJsonPath("$.request.['Target Service']", matching("/query"))) - .withRequestBody(matchingJsonPath("$.request.['query']", matchingJsonPath("query", matching("test")))) - .withRequestBody(matchingJsonPath("$.token", matching("USER_TOKEN"))) - ); - } - - @Test - public void testFilterCallsTokenIntrospectionAppropriatelyForResultWithoutTrailingSlash() throws IOException { - - tokenIntrospectionStub(); - - queryFormatStub(); - - Query query = persistedQuery(); - - ContainerRequestContext ctx = createRequestContext(); - when(ctx.getUriInfo().getPath()).thenReturn("/query/e830138f-2943-4661-90ae-da053bd94a18/result"); - when(ctx.getRequest().getMethod()).thenReturn(HttpMethod.POST); - when(ctx.getHeaderString(HttpHeaders.AUTHORIZATION)).thenReturn("Bearer USER_TOKEN"); - filter.filter(ctx); - - verify(postRequestedFor(urlEqualTo("/resource/query/format"))); - verify( - postRequestedFor(urlEqualTo("/introspection_endpoint")) - .withRequestBody( - matchingJsonPath("$.request.['Target Service']", matching("/query/e830138f-2943-4661-90ae-da053bd94a18/result")) - ).withRequestBody(matchingJsonPath("$.request.query", equalToJson(query.getQuery()))) - .withRequestBody(matchingJsonPath("$.request.formattedQuery", equalToJson("{\"formatted\":\"query\"}"))) - .withRequestBody(matchingJsonPath("$.token", matching("USER_TOKEN"))) - ); - } - - @Test - public void testFilterCallsTokenIntrospectionAppropriatelyForResultWithTrailingSlash() throws IOException { - - tokenIntrospectionStub(); - - queryFormatStub(); - - filter.queryRepo = mock(QueryRepository.class); - - Query query = persistedQuery(); - - ContainerRequestContext ctx = createRequestContext(); - when(ctx.getUriInfo().getPath()).thenReturn("/query/e830138f-2943-4661-90ae-da053bd94a18/result/"); - when(ctx.getRequest().getMethod()).thenReturn(HttpMethod.POST); - when(ctx.getHeaderString(HttpHeaders.AUTHORIZATION)).thenReturn("Bearer USER_TOKEN"); - filter.filter(ctx); - verify( - postRequestedFor(urlEqualTo("/introspection_endpoint")) - .withRequestBody( - matchingJsonPath("$.request.['Target Service']", matching("/query/e830138f-2943-4661-90ae-da053bd94a18/result/")) - ).withRequestBody(matchingJsonPath("$.request.query", equalToJson(query.getQuery()))) - .withRequestBody(matchingJsonPath("$.request.formattedQuery", equalToJson("{\"formatted\":\"query\"}"))) - .withRequestBody(matchingJsonPath("$.token", matching("USER_TOKEN"))) - ); - } - - /** - * Regression test for the double-JSON-encoding bug: when PSAMA's token introspection response carries an updated "query" (it rewrote - * authorizationFilters for the caller's consents), the filter must parse that value back into an object before re-attaching it to the - * request, not store PSAMA's raw JSON-string text. Storing it as text causes it to be JSON-escaped an extra time on every subsequent - * serialization - including when the query is ultimately persisted - corrupting stored queries with doubled backslashes. - */ - @Test - public void testFilterParsesPsamaUpdatedQueryIntoObjectInsteadOfRawText() throws IOException { - ObjectMapper mapper = new ObjectMapper(); - - Map updatedQuery = new HashMap<>(); - updatedQuery.put("select", java.util.List.of("\\_consents\\")); - updatedQuery.put("authorizationFilters", java.util.List.of()); - String updatedQueryAsJsonString = mapper.writeValueAsString(updatedQuery); - - // PSAMA's introspection contract carries the rewritten query as a JSON string value, not a nested object - Map introspectionResponse = new HashMap<>(); - introspectionResponse.put("active", true); - introspectionResponse.put("sub", "TEST_USER"); - introspectionResponse.put("email", "some@email.com"); - introspectionResponse.put("roles", "PIC_SURE_ANY_QUERY"); - introspectionResponse.put("tokenRefreshed", false); - introspectionResponse.put("query", updatedQueryAsJsonString); - - stubFor( - post(urlEqualTo("/introspection_endpoint")).willReturn( - aResponse().withStatus(200).withHeader("Content-Type", "application/json") - .withBody(mapper.writeValueAsString(introspectionResponse)) - ) - ); - - String originalRequestBody = "{\"query\":{\"select\":[\"\\\\_consents\\\\\"]},\"resourceUUID\":\"" + RESOURCE_UUID + "\"}"; - - // A mock ContainerRequestContext has no real backing field for its entity stream, so getEntityStream() - // has to be wired to reflect whatever setEntityStream() last stored - mirroring how the filter reads, - // buffers, resets, and re-reads the stream within a single filter() call. - byte[][] currentBody = {originalRequestBody.getBytes()}; - ContainerRequestContext ctx = createRequestContext(); - when(ctx.getUriInfo().getPath()).thenReturn("/query/sync"); - when(ctx.getRequest().getMethod()).thenReturn(HttpMethod.POST); - when(ctx.getEntityStream()).thenAnswer(inv -> new ByteArrayInputStream(currentBody[0])); - doAnswer(inv -> { - currentBody[0] = ((InputStream) inv.getArgument(0)).readAllBytes(); - return null; - }).when(ctx).setEntityStream(any()); - when(ctx.getHeaderString(HttpHeaders.AUTHORIZATION)).thenReturn("Bearer USER_TOKEN"); - - filter.filter(ctx); - - Map finalRequestBody = mapper.readValue(currentBody[0], Map.class); - Object query = finalRequestBody.get("query"); - assertTrue("PSAMA's updated query must be stored as a nested object, not a re-escaped JSON string", query instanceof Map); - assertEquals(updatedQuery, query); - } - - private void queryFormatStub() { - stubFor( - post(urlEqualTo("/resource/query/format")).willReturn( - aResponse().withStatus(200).withHeader("Content-Type", "application/json").withBody("{\"formatted\":\"query\"}") - ) - ); - } - - @Test - public void testFilterAbortsRequestIfTokenIntrospectionReturnsFalse() throws IOException { - tokenIntrospectionStub(false); - - ContainerRequestContext ctx = createRequestContext(); - when(ctx.getUriInfo().getPath()).thenReturn("/query/sync"); - when(ctx.getRequest().getMethod()).thenReturn(HttpMethod.POST); - InputStream entityStream = new ByteArrayInputStream("{}".getBytes()); - when(ctx.getEntityStream()).thenReturn(entityStream); - when(ctx.getHeaderString(HttpHeaders.AUTHORIZATION)).thenReturn("Bearer USER_TOKEN"); - filter.filter(ctx); - verify(postRequestedFor(urlEqualTo("/introspection_endpoint"))); - ArgumentCaptor abortedRequestContext = ArgumentCaptor.forClass(Response.class); - verify(ctx).abortWith(abortedRequestContext.capture()); - assertEquals(abortedRequestContext.getValue().getStatus(), 401); - assertEquals( - ((PICSUREResponseError) abortedRequestContext.getValue().getEntity()).getMessage(), - "User is not authorized. [Token invalid or expired]" - ); - } - - @Test - public void testFilterSetsUsernameIfTokenIntrospectionReturnsTrue() throws IOException { - tokenIntrospectionStub(); - - ContainerRequestContext ctx = createRequestContext(); - when(ctx.getUriInfo().getPath()).thenReturn("/query/sync"); - when(ctx.getRequest().getMethod()).thenReturn(HttpMethod.POST); - InputStream entityStream = new ByteArrayInputStream("{}".getBytes()); - when(ctx.getEntityStream()).thenReturn(entityStream); - when(ctx.getHeaderString(HttpHeaders.AUTHORIZATION)).thenReturn("Bearer USER_TOKEN"); - filter.filter(ctx); - verify(postRequestedFor(urlEqualTo("/introspection_endpoint"))); - verify(ctx).setProperty("username", "TEST_USER"); - } - - @Test - public void testFilterRemovesResourceCredentialsBeforeSendingToTokenIntrospectionOrFormatter() throws IOException { - - tokenIntrospectionStub(); - - ContainerRequestContext ctx = createRequestContext(); - when(ctx.getUriInfo().getPath()).thenReturn("/query"); - when(ctx.getRequest().getMethod()).thenReturn(HttpMethod.POST); - InputStream entityStream = new ByteArrayInputStream( - ("{\"query\":\"test\", \"resourceUUID\":\"" + RESOURCE_UUID + "\", \"resourceCredentials\":\"foobar\"}").getBytes() - ); - when(ctx.getEntityStream()).thenReturn(entityStream); - when(ctx.getHeaderString(HttpHeaders.AUTHORIZATION)).thenReturn("Bearer USER_TOKEN"); - filter.filter(ctx); - - verify( - postRequestedFor(urlEqualTo("/introspection_endpoint")) - .withRequestBody(matchingJsonPath("$.request.['Target Service']", matching("/query"))) - .withRequestBody(matchingJsonPath("$.request.['query']", matchingJsonPath("query", matching("test")))) - .withRequestBody(matchingJsonPath("$.request.['query']", notMatching("resourceCredentials"))) - .withRequestBody(matchingJsonPath("$.token", matching("USER_TOKEN"))) - ); - } - -} diff --git a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/service/ConfigurationServiceTest.java b/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/service/ConfigurationServiceTest.java deleted file mode 100644 index 38bec8790..000000000 --- a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/service/ConfigurationServiceTest.java +++ /dev/null @@ -1,432 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import org.mockito.InjectMocks; -import org.mockito.Mock; -import org.mockito.junit.MockitoJUnitRunner; - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertTrue; -import static org.mockito.ArgumentMatchers.any; -import static org.mockito.Mockito.mock; -import static org.mockito.Mockito.when; -import static org.mockito.Mockito.doThrow; - -import java.util.*; - -import org.junit.Test; -import org.junit.runner.RunWith; - -import edu.harvard.dbmi.avillach.data.entity.Configuration; -import edu.harvard.dbmi.avillach.data.repository.ConfigurationRepository; -import edu.harvard.dbmi.avillach.data.request.ConfigurationRequest; - -@RunWith(MockitoJUnitRunner.class) -public class ConfigurationServiceTest { - private final String testName = "FEATURE_FLAG_X"; - private final String testKind = "ui"; - private final String testValue = "true"; - private final String testDescription = "This configuration controls feature X"; - - @InjectMocks - private ConfigurationService configurationService = new ConfigurationService(); - - @Mock - private ConfigurationRepository configurationRepository = mock(ConfigurationRepository.class); - - private Configuration makeConfiguration(UUID id) { - Configuration config = new Configuration(); - config.setUuid(id); - config.setName(testName); - config.setKind(testKind); - config.setValue(testValue); - config.setDescription(testDescription); - return config; - } - - private ConfigurationRequest makeConfigurationRequest() { - ConfigurationRequest request = new ConfigurationRequest(); - request.setName(testName); - request.setKind(testKind); - request.setValue(testValue); - request.setDescription(testDescription); - return request; - } - - @Test - public void getConfigurations_withKind_success() { - // Given there are saved configurations in the database with a specific kind - Configuration config1 = makeConfiguration(UUID.randomUUID()); - Configuration config2 = makeConfiguration(UUID.randomUUID()); - ArrayList configs = new ArrayList(); - configs.add(config1); - configs.add(config2); - when(configurationRepository.getByColumn("kind", testKind)).thenReturn(configs); - - // When the request is received - Optional> response = configurationService.getConfigurations(testKind); - - // Then return a non-empty optional with the configurations - assertTrue(response.isPresent()); - assertEquals("correct number of configurations returned", 2, response.get().size()); - } - - @Test - public void getConfigurations_withoutKind_success() { - // Given there are saved configurations in the database - Configuration config1 = makeConfiguration(UUID.randomUUID()); - Configuration config2 = makeConfiguration(UUID.randomUUID()); - ArrayList configs = new ArrayList(); - configs.add(config1); - configs.add(config2); - when(configurationRepository.list()).thenReturn(configs); - - // When the request is received without specifying a kind - Optional> response = configurationService.getConfigurations(null); - - // Then return a non-empty optional with all configurations - assertTrue(response.isPresent()); - assertEquals("correct number of configurations returned", 2, response.get().size()); - } - - @Test - public void getConfigurations_noValues() { - // Given there are no saved configurations in the database - ArrayList configs = new ArrayList(); - when(configurationRepository.list()).thenReturn(configs); - - // When the request is received - Optional> response = configurationService.getConfigurations(null); - - // Then return a non-empty optional with an empty list - assertTrue(response.isPresent()); - assertEquals(0, response.get().size()); - } - - @Test - public void getConfigurationByIdentifier_withUUID_success() { - // Given there is a saved configuration in the database with this UUID - UUID configId = UUID.randomUUID(); - Configuration config = makeConfiguration(configId); - when(configurationRepository.getById(configId)).thenReturn(config); - - // When the request is received with a UUID - Optional response = configurationService.getConfigurationByIdentifier(configId.toString()); - - // Then return a non-empty optional - assertTrue(response.isPresent()); - assertEquals("correct configuration returned", configId, response.get().getUuid()); - } - - @Test - public void getConfigurationByIdentifier_withName_success() { - // Given there is a saved configuration in the database with this name - Configuration config = makeConfiguration(UUID.randomUUID()); - ArrayList configs = new ArrayList(); - configs.add(config); - when(configurationRepository.getByColumn("name", testName)).thenReturn(configs); - - // When the request is received with a name - Optional response = configurationService.getConfigurationByIdentifier(testName); - - // Then return a non-empty optional - assertTrue(response.isPresent()); - assertEquals("correct configuration returned", testName, response.get().getName()); - } - - @Test - public void getConfigurationByIdentifier_withUUID_notFound() { - // Given there is no configuration with this UUID - UUID configId = UUID.randomUUID(); - when(configurationRepository.getById(configId)).thenReturn(null); - - // When the request is received - Optional response = configurationService.getConfigurationByIdentifier(configId.toString()); - - // Then return an empty optional - assertTrue(response.isEmpty()); - } - - @Test - public void getConfigurationByIdentifier_withUUIDShapedName_success() { - // Given a config whose name happens to look like a UUID, and no record exists for that UUID - UUID configId = UUID.randomUUID(); - Configuration config = makeConfiguration(UUID.randomUUID()); - config.setName(configId.toString()); - when(configurationRepository.getById(configId)).thenReturn(null); - when(configurationRepository.getByColumn("name", configId.toString())).thenReturn(List.of(config)); - - // When the identifier is that UUID string - Optional response = configurationService.getConfigurationByIdentifier(configId.toString()); - - // Then the config is found via name lookup - assertTrue(response.isPresent()); - assertEquals(configId.toString(), response.get().getName()); - } - - @Test - public void getConfigurationByIdentifier_withName_notFound() { - // Given there is no configuration with this name - ArrayList configs = new ArrayList(); - when(configurationRepository.getByColumn("name", testName)).thenReturn(configs); - - // When the request is received with a name - Optional response = configurationService.getConfigurationByIdentifier(testName); - - // Then return an empty optional - assertTrue(response.isEmpty()); - } - - @Test - public void getConfigurationByIdentifier_withName_nullResult() { - // Given the repository returns null for this name - when(configurationRepository.getByColumn("name", testName)).thenReturn(null); - - // When the request is received with a name - Optional response = configurationService.getConfigurationByIdentifier(testName); - - // Then return an empty optional - assertTrue(response.isEmpty()); - } - - @Test - public void addConfiguration_success() { - // Given a valid configuration request - ConfigurationRequest request = makeConfigurationRequest(); - - // When the request is received - Optional response = configurationService.addConfiguration(request); - - // Then return a non-empty optional - assertTrue(response.isPresent()); - assertEquals("name is saved", testName, response.get().getName()); - assertEquals("kind is saved", testKind, response.get().getKind()); - assertEquals("value is saved", testValue, response.get().getValue()); - assertEquals("description is saved", testDescription, response.get().getDescription()); - } - - @Test - public void addConfiguration_nameKindCollision() { - // Given a valid configuration request - ConfigurationRequest request = makeConfigurationRequest(); - - // And there is a second configuration in the database with desired name - List duplicateNames = new ArrayList<>(List.of(makeConfiguration(UUID.randomUUID()))); - when(configurationRepository.getByColumns(any(), any())).thenReturn(duplicateNames); - - // When the request is received - Optional response = configurationService.addConfiguration(request); - - // Then return an empty optional - assertTrue(response.isEmpty()); - } - - @Test - public void addConfiguration_cannotPersist() { - // Given there is an error saving to the configuration table - doThrow(new RuntimeException("Persistence error")).when(configurationRepository).persist(any(Configuration.class)); - - // When the request is received - ConfigurationRequest request = makeConfigurationRequest(); - Optional response = configurationService.addConfiguration(request); - - // Then return an empty optional - assertTrue(response.isEmpty()); - } - - @Test - public void updateConfiguration_changeValue_success() { - // Given there is a saved configuration in the database with this id - UUID configId = UUID.randomUUID(); - Configuration config = makeConfiguration(configId); - when(configurationRepository.getById(configId)).thenReturn(config); - - // When the request is received with updated values - String newValue = "false"; - ConfigurationRequest request = makeConfigurationRequest(); - request.setUuid(configId); - request.setValue(newValue); - Optional response = configurationService.updateConfiguration(request); - - // Then return a non-empty optional - assertTrue(response.isPresent()); - assertEquals("new value is saved", newValue, response.get().getValue()); - } - - @Test - public void updateConfiguration_changeName_success() { - // Given there is a saved configuration in the database with this id - UUID configId = UUID.randomUUID(); - Configuration config = makeConfiguration(configId); - when(configurationRepository.getById(configId)).thenReturn(config); - - // When the request is received with a new name - String newName = "FEATURE_FLAG_Y"; - ConfigurationRequest request = makeConfigurationRequest(); - request.setUuid(configId); - request.setName(newName); - Optional response = configurationService.updateConfiguration(request); - - // Then return a non-empty optional - assertTrue(response.isPresent()); - assertEquals("new name is saved", newName, response.get().getName()); - } - - - @Test - public void updateConfiguration_changeDeleteRequestedDate() { - // Given there is a saved configuration in the database with this id - UUID configId = UUID.randomUUID(); - Configuration config = makeConfiguration(configId); - when(configurationRepository.getById(configId)).thenReturn(config); - - // When the request is received with updated delete request date - ConfigurationRequest request = makeConfigurationRequest(); - request.setUuid(configId); - request.setMarkForDelete(true); - Optional response = configurationService.updateConfiguration(request); - - // Then return a non-empty optional - assertTrue(response.isPresent()); - assertEquals("new delete requested date is saved", true, response.get().getMarkForDelete()); - } - - @Test - public void updateConfiguration_changeName_nameKindCollision() { - // Given there is a saved configuration in the database with this id - String newName = "FEATURE_FLAG_Y"; - String newKind = "some kind"; - UUID configId = UUID.randomUUID(); - Configuration config = makeConfiguration(UUID.randomUUID()); - when(configurationRepository.getById(configId)).thenReturn(config); - - // And there is a second configuration in the database with desired name and kind - Configuration config2 = makeConfiguration(UUID.randomUUID()); - config2.setName(newName); - config2.setKind("some kind"); - List duplicateNames = new ArrayList<>(List.of(config, config2)); - when(configurationRepository.getByColumns(any(), any())).thenReturn(duplicateNames); - - // When the request is received with a new name - ConfigurationRequest request = makeConfigurationRequest(); - request.setUuid(configId); - request.setName(newName); - request.setKind(newKind); - Optional response = configurationService.updateConfiguration(request); - - // Then return an empty optional - assertTrue(response.isEmpty()); - } - - @Test - public void updateConfiguration_changeKind_success() { - // Given there is a saved configuration in the database with this id - UUID configId = UUID.randomUUID(); - Configuration config = makeConfiguration(configId); - when(configurationRepository.getById(configId)).thenReturn(config); - - // When the request is received with a new kind - String newKind = "backend"; - ConfigurationRequest request = makeConfigurationRequest(); - request.setUuid(configId); - request.setKind(newKind); - Optional response = configurationService.updateConfiguration(request); - - // Then return a non-empty optional - assertTrue(response.isPresent()); - assertEquals("new kind is saved", newKind, response.get().getKind()); - } - - @Test - public void updateConfiguration_changeDescription_success() { - // Given there is a saved configuration in the database with this id - UUID configId = UUID.randomUUID(); - Configuration config = makeConfiguration(configId); - when(configurationRepository.getById(configId)).thenReturn(config); - - // When the request is received with a new description - String newDescription = "Updated description"; - ConfigurationRequest request = makeConfigurationRequest(); - request.setUuid(configId); - request.setDescription(newDescription); - Optional response = configurationService.updateConfiguration(request); - - // Then return a non-empty optional - assertTrue(response.isPresent()); - assertEquals("new description is saved", newDescription, response.get().getDescription()); - } - - @Test - public void updateConfiguration_noConfigurationWithId() { - // Given there is no configuration in the database with this id - UUID configId = UUID.randomUUID(); - when(configurationRepository.getById(configId)).thenReturn(null); - - // When the request is received - ConfigurationRequest request = makeConfigurationRequest(); - request.setUuid(configId); - Optional response = configurationService.updateConfiguration(request); - - // Then return an empty optional - assertTrue(response.isEmpty()); - } - - @Test - public void updateConfiguration_cannotPersistChanges() { - // Given there is an error saving to the configuration table - UUID configId = UUID.randomUUID(); - Configuration config = makeConfiguration(configId); - when(configurationRepository.getById(configId)).thenReturn(config); - doThrow(new RuntimeException()).when(configurationRepository).merge(any(Configuration.class)); - - // When the request is received - ConfigurationRequest request = makeConfigurationRequest(); - request.setUuid(configId); - Optional response = configurationService.updateConfiguration(request); - - // Then return an empty optional - assertTrue(response.isEmpty()); - } - - @Test - public void deleteConfiguration_success() { - // Given there is a saved configuration in the database with this id - UUID configId = UUID.randomUUID(); - Configuration config = makeConfiguration(configId); - when(configurationRepository.getById(configId)).thenReturn(config); - - // When the request is received - Optional response = configurationService.deleteConfiguration(configId); - - // Then return a non-empty optional with the deleted configuration - assertTrue(response.isPresent()); - assertEquals("correct configuration returned", configId, response.get().getUuid()); - } - - @Test - public void deleteConfiguration_noConfigurationWithId() { - // Given there is no configuration in the database with this id - UUID configId = UUID.randomUUID(); - when(configurationRepository.getById(configId)).thenReturn(null); - - // When the request is received - Optional response = configurationService.deleteConfiguration(configId); - - // Then return an empty optional - assertTrue(response.isEmpty()); - } - - @Test - public void deleteConfiguration_cannotDelete() { - // Given there is an error deleting from the configuration table - UUID configId = UUID.randomUUID(); - Configuration config = makeConfiguration(configId); - when(configurationRepository.getById(configId)).thenReturn(config); - doThrow(new RuntimeException()).when(configurationRepository).remove(any(Configuration.class)); - - // When the request is received - Optional response = configurationService.deleteConfiguration(configId); - - // Then return an empty optional - assertTrue(response.isEmpty()); - } -} diff --git a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/service/LoggingClientProducerTest.java b/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/service/LoggingClientProducerTest.java deleted file mode 100644 index a3f8f6814..000000000 --- a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/service/LoggingClientProducerTest.java +++ /dev/null @@ -1,36 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import static org.junit.Assert.*; - -import edu.harvard.dbmi.avillach.logging.LoggingClient; -import org.junit.Test; - -public class LoggingClientProducerTest { - - @Test - public void producesNoOpWhenJndiBindingsAreMissing() { - // JNDI lookups will fail in a plain JUnit context (no container), - // so the producer should gracefully return a no-op client - LoggingClientProducer producer = new LoggingClientProducer(); - LoggingClient client = producer.loggingClient(); - - assertNotNull(client); - assertFalse("Should be no-op when JNDI bindings are missing", client.isEnabled()); - } - - @Test - public void cleanupDoesNotThrowWhenNoOp() { - LoggingClientProducer producer = new LoggingClientProducer(); - producer.loggingClient(); // initialize - // Should not throw - producer.cleanup(); - } - - @Test - public void cleanupDoesNotThrowBeforeInit() { - LoggingClientProducer producer = new LoggingClientProducer(); - // loggingClient() not called — client is null - // Should not throw - producer.cleanup(); - } -} diff --git a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/service/NamedDatasetServiceTest.java b/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/service/NamedDatasetServiceTest.java deleted file mode 100644 index 87466e3c8..000000000 --- a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/service/NamedDatasetServiceTest.java +++ /dev/null @@ -1,367 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import org.mockito.InjectMocks; -import org.mockito.Mock; -import org.mockito.junit.MockitoJUnitRunner; - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertTrue; -import static org.mockito.ArgumentMatchers.any; -import static org.mockito.Mockito.mock; -import static org.mockito.Mockito.when; -import static org.mockito.Mockito.doThrow; - -import java.util.ArrayList; -import java.util.List; -import java.util.UUID; -import java.util.HashMap; -import java.util.Optional; - -import org.junit.Test; -import org.junit.runner.RunWith; - -import edu.harvard.dbmi.avillach.data.entity.NamedDataset; -import edu.harvard.dbmi.avillach.data.entity.Query; -import edu.harvard.dbmi.avillach.data.repository.NamedDatasetRepository; -import edu.harvard.dbmi.avillach.data.repository.QueryRepository; -import edu.harvard.dbmi.avillach.data.request.NamedDatasetRequest; - -@RunWith(MockitoJUnitRunner.class) -public class NamedDatasetServiceTest { - private String user = "test.user@email.com"; - private String testName = "test name"; - - @InjectMocks - private NamedDatasetService namedDatasetService = new NamedDatasetService(); - - @Mock - private NamedDatasetRepository datasetRepo = mock(NamedDatasetRepository.class); - - @Mock - private QueryRepository queryRepo = mock(QueryRepository.class); - - private Query makeQuery(UUID id){ - Query query = new Query(); - query.setUuid(id); - query.setQuery("{}"); - return query; - } - - private NamedDataset makeNamedDataset(UUID id, Query query){ - NamedDataset dataset = new NamedDataset(); - dataset.setUuid(id); - dataset.setUser(user); - dataset.setName(testName); - dataset.setQuery(query); - dataset.setArchived(false); - return dataset; - } - - private NamedDatasetRequest makeNamedDatasetRequest(UUID queryId){ - NamedDatasetRequest request = new NamedDatasetRequest(); - request.setName(testName); - request.setQueryId(queryId); - request.setArchived(false); - return request; - } - - @Test - public void getNamedDataset_success() { - // Given there is a saved dataset in the database for this user - Query query = makeQuery(UUID.randomUUID()); - NamedDataset dataset = makeNamedDataset(UUID.randomUUID(), query); - ArrayList datasets = new ArrayList(); - datasets.add(dataset); - when(datasetRepo.getByColumn("user", user)).thenReturn(datasets); - - // When the request is recieved - Optional> response = namedDatasetService.getNamedDatasets(user); - - // Then return a non-empty optional - assertTrue(response.isPresent()); - } - - @Test - public void getNamedDataset_novalues() { - // Given there is no saved dataset in the database for this user - ArrayList datasets = new ArrayList(); - when(datasetRepo.getByColumn("user", user)).thenReturn(datasets); - - // When the request is recieved - Optional> response = namedDatasetService.getNamedDatasets(user); - - // Then return a non-empty optional with an empy list - assertTrue(response.isPresent()); - assertTrue(response.get().size() == 0); - } - - @Test - public void getNamedDatasetById_success() { - // Given there is a saved dataset in the database for this user - UUID namedDatasetId = UUID.randomUUID(); - Query query = makeQuery(UUID.randomUUID()); - NamedDataset dataset = makeNamedDataset(namedDatasetId, query); - when(datasetRepo.getById(namedDatasetId)).thenReturn(dataset); - - // When the request is recieved - Optional response = namedDatasetService.getNamedDatasetById(user, namedDatasetId); - - // Then return a non-empty optional - assertTrue(response.isPresent()); - } - - @Test - public void getNamedDatasetById_datasetNotFromUser() { - // Given there is a saved dataset in the database with this id but a different user - UUID namedDatasetId = UUID.randomUUID(); - Query query = makeQuery(UUID.randomUUID()); - NamedDataset dataset = makeNamedDataset(namedDatasetId, query); - dataset.setUser("other.user@email.com"); - when(datasetRepo.getById(namedDatasetId)).thenReturn(dataset); - - // When the request is recieved - Optional response = namedDatasetService.getNamedDatasetById(user, namedDatasetId); - - // Then return an empty optional - assertTrue(response.isEmpty()); - } - - @Test - public void getNamedDatasetById_noNamedDatasetWithId() { - // Given there is no saved dataset in the database with this id - UUID namedDatasetId = UUID.randomUUID(); - when(datasetRepo.getById(namedDatasetId)).thenReturn(null); - - // When the request is recieved - Optional response = namedDatasetService.getNamedDatasetById(user, namedDatasetId); - - // Then return an empty optional - assertTrue(response.isEmpty()); - } - - @Test - public void addNamedDataset_success() { - // Given there is a query in the database - UUID queryId = UUID.randomUUID(); - Query query = makeQuery(queryId); - when(queryRepo.getById(queryId)).thenReturn(query); - - // When the request is recieved - NamedDatasetRequest request = makeNamedDatasetRequest(queryId); - Optional response = namedDatasetService.addNamedDataset(user, request); - - // Then return a non-empty optional - assertTrue(response.isPresent()); - assertEquals("related user is saved", user, response.get().getUser()); - assertEquals("related name is saved", testName, response.get().getName()); - assertEquals("related query is saved", queryId, response.get().getQuery().getUuid()); - } - - @Test - public void addNamedDataset_metadataSet_success() { - // Given there is a query in the database - UUID queryId = UUID.randomUUID(); - Query query = makeQuery(queryId); - when(queryRepo.getById(queryId)).thenReturn(query); - String testKey = "test"; - String testValue = "value"; - - // When the request is recieved - NamedDatasetRequest request = makeNamedDatasetRequest(queryId); - HashMap metadata = new HashMap(); - metadata.put(testKey, testValue); - request.setMetadata(metadata); - Optional response = namedDatasetService.addNamedDataset(user, request); - - // Then return a non-empty optional - assertTrue(response.isPresent()); - assertEquals("related metadata is saved", testValue, response.get().getMetadata().get(testKey)); - } - - @Test - public void addNamedDataset_noQueryWithID() { - // Given there is no query in the database with this id - UUID queryId = UUID.randomUUID(); - when(queryRepo.getById(queryId)).thenReturn(null); - - // When the request is recieved - NamedDatasetRequest request = makeNamedDatasetRequest(queryId); - Optional response = namedDatasetService.addNamedDataset(user, request); - - // Then return an empty optional - assertTrue(response.isEmpty()); - } - - @Test - public void addNamedDataset_cannotPersist() { - // Given there is an error saving to the named dataset table - UUID queryId = UUID.randomUUID(); - Query query = makeQuery(queryId); - when(queryRepo.getById(queryId)).thenReturn(query); - doThrow(new RuntimeException()).when(datasetRepo).persist(any(NamedDataset.class)); - - // When the request is recieved - NamedDatasetRequest request = makeNamedDatasetRequest(queryId); - Optional response = namedDatasetService.addNamedDataset(user, request); - - // Then return an empty optional - assertTrue(response.isEmpty()); - } - - @Test - public void updateNamedDataset_changeName_success() { - // Given there is a named dataset saved in the database with this id - UUID queryId = UUID.randomUUID(); - UUID namedDatasetId = UUID.randomUUID(); - Query query = makeQuery(queryId); - NamedDataset dataset = makeNamedDataset(namedDatasetId, query); - when(datasetRepo.getById(namedDatasetId)).thenReturn(dataset); - - // When the request is recieved - String newName = "new name"; - NamedDatasetRequest request = makeNamedDatasetRequest(queryId); - request.setName(newName); - Optional response = namedDatasetService.updateNamedDataset(user, namedDatasetId, request); - - // Then return a non-empty optional - assertTrue(response.isPresent()); - assertEquals("new name id is saved", newName, response.get().getName()); - } - - @Test - public void updateNamedDataset_changeArchiveState_success() { - // Given there is a named dataset saved in the database with this id - UUID queryId = UUID.randomUUID(); - UUID namedDatasetId = UUID.randomUUID(); - Query query = makeQuery(queryId); - NamedDataset dataset = makeNamedDataset(namedDatasetId, query); - when(datasetRepo.getById(namedDatasetId)).thenReturn(dataset); - - // When the request is recieved - NamedDatasetRequest request = makeNamedDatasetRequest(queryId); - request.setArchived(true); - Optional response = namedDatasetService.updateNamedDataset(user, namedDatasetId, request); - - // Then return a non-empty optional - assertTrue(response.isPresent()); - assertEquals("new archive state is retained", true, response.get().getArchived()); - } - - @Test - public void updateNamedDataset_changeMetadata_success() { - // Given there is a named dataset saved in the database with this id - UUID queryId = UUID.randomUUID(); - UUID namedDatasetId = UUID.randomUUID(); - Query query = makeQuery(queryId); - NamedDataset dataset = makeNamedDataset(namedDatasetId, query); - HashMap oldMetadata = new HashMap(); - oldMetadata.put("whatever", "something"); - dataset.setMetadata(oldMetadata); - when(datasetRepo.getById(namedDatasetId)).thenReturn(dataset); - String testKey = "test"; - String testValue = "value"; - - // When the request is recieved - NamedDatasetRequest request = makeNamedDatasetRequest(queryId); - HashMap newMetadata = new HashMap(); - newMetadata.put(testKey, testValue); - request.setMetadata(newMetadata); - Optional response = namedDatasetService.updateNamedDataset(user, namedDatasetId, request); - - // Then return a non-empty optional - assertTrue(response.isPresent()); - assertEquals("new metadata is retained", testValue, response.get().getMetadata().get(testKey)); - } - - @Test - public void updateNamedDataset_changeQueryId_success() { - // Given there is a named dataset saved in the database with this id and the new query id is in the database - UUID queryId = UUID.randomUUID(); - UUID namedDatasetId = UUID.randomUUID(); - Query query = makeQuery(queryId); - NamedDataset dataset = makeNamedDataset(namedDatasetId, query); - when(datasetRepo.getById(namedDatasetId)).thenReturn(dataset); - - UUID newQueryId = UUID.randomUUID(); - Query newQuery = makeQuery(newQueryId); - when(queryRepo.getById(newQueryId)).thenReturn(newQuery); - - // When the request is recieved - NamedDatasetRequest request = makeNamedDatasetRequest(newQueryId); - Optional response = namedDatasetService.updateNamedDataset(user, namedDatasetId, request); - - // Then return a non-empty optional - assertTrue(response.isPresent()); - assertEquals("new query id is saved", newQueryId, response.get().getQuery().getUuid()); - } - - @Test - public void updateNamedDataset_noNamedDatasetWithId() { - // Given there is no named dataset in the database with this id - UUID namedDatasetId = UUID.randomUUID(); - when(datasetRepo.getById(namedDatasetId)).thenReturn(null); - - // When the request is recieved - NamedDatasetRequest request = makeNamedDatasetRequest(UUID.randomUUID()); - Optional response = namedDatasetService.updateNamedDataset(user, namedDatasetId, request); - - // Then return an empty optional - assertTrue(response.isEmpty()); - } - - @Test - public void updateNamedDataset_datasetNotFromUser() { - // Given there is a saved dataset in the database with this id but a different user - UUID queryId = UUID.randomUUID(); - UUID namedDatasetId = UUID.randomUUID(); - Query query = makeQuery(queryId); - NamedDataset dataset = makeNamedDataset(namedDatasetId, query); - dataset.setUser("other.user@email.com"); - when(datasetRepo.getById(namedDatasetId)).thenReturn(dataset); - - // When the request is recieved - NamedDatasetRequest request = makeNamedDatasetRequest(queryId); - Optional response = namedDatasetService.updateNamedDataset(user, namedDatasetId, request); - - // Then return an empty optional - assertTrue(response.isEmpty()); - } - - @Test - public void updateNamedDataset_changeQueryId_noQueryWithID() { - // Given there is a named dataset saved in the database with this id but no query id as passed in - UUID queryId = UUID.randomUUID(); - UUID namedDatasetId = UUID.randomUUID(); - Query query = makeQuery(queryId); - NamedDataset dataset = makeNamedDataset(namedDatasetId, query); - when(datasetRepo.getById(namedDatasetId)).thenReturn(dataset); - - UUID newQueryId = UUID.randomUUID(); - when(queryRepo.getById(newQueryId)).thenReturn(null); - - // When the request is recieved - NamedDatasetRequest request = makeNamedDatasetRequest(newQueryId); - Optional response = namedDatasetService.updateNamedDataset(user, namedDatasetId, request); - - // Then return an empty optional - assertTrue(response.isEmpty()); - } - - @Test - public void updateNamedDataset_cannotPersistChanges() { - // Given there is an error saving to the named dataset table - UUID queryId = UUID.randomUUID(); - UUID namedDatasetId = UUID.randomUUID(); - Query query = makeQuery(queryId); - NamedDataset dataset = makeNamedDataset(namedDatasetId, query); - when(datasetRepo.getById(namedDatasetId)).thenReturn(dataset); - doThrow(new RuntimeException()).when(datasetRepo).merge(any(NamedDataset.class)); - - // When the request is recieved - NamedDatasetRequest request = makeNamedDatasetRequest(queryId); - Optional response = namedDatasetService.updateNamedDataset(user, namedDatasetId, request); - - // Then return an empty optional - assertTrue(response.isEmpty()); - } -} diff --git a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/service/SiteParsingServiceTest.java b/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/service/SiteParsingServiceTest.java deleted file mode 100644 index 22c63dda2..000000000 --- a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/service/SiteParsingServiceTest.java +++ /dev/null @@ -1,74 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import edu.harvard.dbmi.avillach.data.entity.Site; -import edu.harvard.dbmi.avillach.data.repository.SiteRepository; -import org.junit.Assert; -import org.junit.Test; -import org.junit.runner.RunWith; -import org.mockito.InjectMocks; -import org.mockito.Mock; -import org.mockito.Mockito; -import org.mockito.junit.MockitoJUnitRunner; - -import java.util.List; -import java.util.Optional; - -import static org.junit.Assert.assertEquals; - -@RunWith(MockitoJUnitRunner.class) -public class SiteParsingServiceTest { - - @InjectMocks - private SiteParsingService subject; - - @Mock - private SiteRepository repository; - - @Test - public void shouldParse() { - Site site = new Site(); - site.setCode("BCH"); - site.setName("Bowston Children's Hospital"); - site.setDomain("childrens.harvard.edu"); - Mockito - .when(repository.getByColumn("domain", "childrens.harvard.edu")) - .thenReturn(List.of(site)); - - Optional actual = subject.parseSiteOfOrigin("aaaaaaah@childrens.harvard.edu"); - Optional expected = Optional.of("BCH"); - - Assert.assertEquals(expected, actual); - } - - @Test - public void shouldFailWhenNoSite() { - Mockito - .when(repository.getByColumn("domain", "childrens.harvard.edu")) - .thenReturn(List.of()); - - Optional actual = subject.parseSiteOfOrigin("aaaaaaah@childrens.harvard.edu"); - Optional expected = Optional.empty(); - - Assert.assertEquals(expected, actual); - } - - @Test - public void shouldFailWhenManySites() { - Site siteA = new Site(); - siteA.setCode("BCH"); - siteA.setName("Bowston Children's Hospital"); - siteA.setDomain("edu"); - Site siteB = new Site(); - siteB.setCode("CHOP"); - siteB.setName("Children's Hospital of Philly"); - siteB.setDomain("edu"); - Mockito - .when(repository.getByColumn("domain", "edu")) - .thenReturn(List.of(siteA, siteB)); - - Optional actual = subject.parseSiteOfOrigin("aaaaaaah@edu"); - Optional expected = Optional.empty(); - - Assert.assertEquals(expected, actual); - } -} \ No newline at end of file diff --git a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/service/SystemServiceTest.java b/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/service/SystemServiceTest.java deleted file mode 100644 index 354ca31ec..000000000 --- a/pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/service/SystemServiceTest.java +++ /dev/null @@ -1,188 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import static com.github.tomakehurst.wiremock.client.WireMock.*; -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertTrue; -import static org.mockito.Mockito.*; - -import java.util.ArrayList; -import java.util.List; - -import org.junit.Rule; -import org.junit.Test; - -import com.github.tomakehurst.wiremock.junit.WireMockRule; - -import edu.harvard.dbmi.avillach.PicSureWarInit; -import edu.harvard.dbmi.avillach.data.entity.Resource; -import edu.harvard.dbmi.avillach.data.repository.ResourceRepository; - -public class SystemServiceTest { - - @Rule - public WireMockRule wireMockRule = new WireMockRule(0); - - private int port; - - private void tokenIntrospectionStub(int status, String tokenIntrospectionResult) { - stubFor(post(urlEqualTo("/introspection_endpoint")) - .willReturn(aResponse() - .withStatus(status) - .withHeader("Content-Type", "application/json") - .withBody("{\"active\":" + tokenIntrospectionResult + ",\"sub\":\"TEST_USER\"}"))); - } - - private void resourceStub(int status) { - stubFor(post(urlEqualTo("/resource")) - .willReturn(aResponse() - .withStatus(status) - .withHeader("Content-Type", "application/json") - .withBody("{\"info\":\"foobar\"}"))); - } - - - private SystemService basicService() { - SystemService service = new SystemService(); - service.picSureWarInit = mock(PicSureWarInit.class); - when(service.picSureWarInit.getToken_introspection_token()).thenReturn("TOKEN"); - when(service.picSureWarInit.getToken_introspection_url()).thenReturn( - "http://localhost:" + port + "/introspection_endpoint"); - service.init(); - return service; - } - - @Test - public void testStatusDegradedIfResourceRepositoryReturnsNull() { - SystemService service = basicService(); - service.resourceRepo = mock(ResourceRepository.class); - when(service.resourceRepo.list()).thenReturn(null); - String status = service.status(); - assertEquals(status, SystemService.ONE_OR_MORE_COMPONENTS_DEGRADED); - } - - @Test - public void testStatusDegradedIfResourcesNotDefined() { - SystemService service = basicService(); - service.resourceRepo = mock(ResourceRepository.class); - when(service.resourceRepo.list()).thenReturn(new ArrayList()); - String status = service.status(); - assertEquals(status, SystemService.ONE_OR_MORE_COMPONENTS_DEGRADED); - } - - @Test - public void testStatusDegradedIfResourceRepoThrowsException() { - SystemService service = basicService(); - service.resourceRepo = mock(ResourceRepository.class); - when(service.resourceRepo.list()).thenThrow(RuntimeException.class); - String status = service.status(); - assertEquals(status, SystemService.ONE_OR_MORE_COMPONENTS_DEGRADED); - } - - @Test - public void testThrowsExceptionOnStartupIfTokenIntrospectionTokenNotConfigured() { - SystemService service = basicService(); - when(service.picSureWarInit.getToken_introspection_token()).thenReturn(null); - try{ - service.token_introspection_token = null; - service.init(); - }catch(Exception e) { - return; - } - assertTrue("Expected an exception to be thrown.", false); - } - - @Test - public void testThrowsExceptionOnStartupIfTokenIntrospectionUrlNotConfigured() { - SystemService service = basicService(); - when(service.picSureWarInit.getToken_introspection_url()).thenReturn(null); - try{ - service.token_introspection_url = null; - service.init(); - }catch(Exception e) { - return; - } - assertTrue("Expected an exception to be thrown.", false); - } - - @Test - public void testStatusDegradedIfTokenIntrospectionFails() { - tokenIntrospectionStub(500, "false"); - SystemService service = basicService(); - service.resourceRepo = mock(ResourceRepository.class); - when(service.resourceRepo.list()).thenReturn(List.of(mock(Resource.class))); - String status = service.status(); - assertEquals(status, SystemService.ONE_OR_MORE_COMPONENTS_DEGRADED); - } - - @Test - public void testStatusDegradedIfTokenIntrospectionFailsDueToBadToken() { - tokenIntrospectionStub(401, "false"); - SystemService service = basicService(); - service.resourceRepo = mock(ResourceRepository.class); - when(service.resourceRepo.list()).thenReturn(List.of(mock(Resource.class))); - String status = service.status(); - assertEquals(status, SystemService.ONE_OR_MORE_COMPONENTS_DEGRADED); - } - - @Test - public void testStatusDegradedIfResourceUnreachable() { - tokenIntrospectionStub(200, "true"); - resourceStub(500); - SystemService service = basicService(); - service.resourceRepo = mock(ResourceRepository.class); - Resource resource = mock(Resource.class); - when(resource.getResourceRSPath()).thenReturn("http://localhost:"+port+"/resource"); - when(service.resourceRepo.list()).thenReturn(List.of(resource)); - String status = service.status(); - assertEquals(status, SystemService.ONE_OR_MORE_COMPONENTS_DEGRADED); - } - - @Test - public void testStatusRunningIfNothingIsWrong() { - tokenIntrospectionStub(200, "true"); - resourceStub(200); - SystemService service = basicService(); - service.resourceRepo = mock(ResourceRepository.class); - Resource resource = mock(Resource.class); - when(resource.getResourceRSPath()).thenReturn("http://localhost:"+port+"/resource"); - when(service.resourceRepo.list()).thenReturn(List.of(resource)); - String status = service.status(); - assertEquals(status, SystemService.ONE_OR_MORE_COMPONENTS_DEGRADED); - } - - @Test - public void testServiceOnlyChecksStatusOncePerMaxTestFrequency() throws Exception { - tokenIntrospectionStub(200, "true"); - resourceStub(200); - SystemService service = basicService(); - service.resourceRepo = mock(ResourceRepository.class); - Resource resource = mock(Resource.class); - when(resource.getResourceRSPath()).thenReturn("http://localhost:"+port+"/resource"); - when(service.resourceRepo.list()).thenReturn(List.of(resource)); - String status = service.status(); - assertEquals(status, SystemService.ONE_OR_MORE_COMPONENTS_DEGRADED); - SystemService.max_test_frequency = 200; - Thread.sleep(100); - status = service.status(); - assertEquals(status, SystemService.ONE_OR_MORE_COMPONENTS_DEGRADED); - verify(service.resourceRepo, atMost(1)).list(); - } - - @Test - public void testServiceRechecksStatusAfterMaxTestFrequency() throws Exception { - tokenIntrospectionStub(200, "true"); - resourceStub(200); - SystemService service = basicService(); - service.resourceRepo = mock(ResourceRepository.class); - Resource resource = mock(Resource.class); - when(resource.getResourceRSPath()).thenReturn("http://localhost:"+port+"/resource"); - when(service.resourceRepo.list()).thenReturn(List.of(resource)); - String status = service.status(); - assertEquals(status, SystemService.ONE_OR_MORE_COMPONENTS_DEGRADED); - SystemService.max_test_frequency = 100; - Thread.sleep(200); - status = service.status(); - assertEquals(status, SystemService.ONE_OR_MORE_COMPONENTS_DEGRADED); - verify(service.resourceRepo, atLeast(2)).list(); - } -} diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/README.md b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/README.md deleted file mode 100644 index c41c91bb7..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/README.md +++ /dev/null @@ -1,11 +0,0 @@ -### Aggregate Data Sharing Resource - -TBA -```json -{ - "query": { - "expectedResultType": "COUNT" - }, - "resourceUUID": "" -} -``` \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/pom.xml b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/pom.xml deleted file mode 100644 index e057643c9..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/pom.xml +++ /dev/null @@ -1,97 +0,0 @@ - - - 4.0.0 - - edu.harvard.hms.dbmi.avillach - pic-sure-resources - 2.2.0-SNAPSHOT - - pic-sure-aggregate-data-sharing-resource - pic-sure-aggregate-data-sharing-resource - war - http://maven.apache.org - - 13.0.0.Final - ${project.build.directory}/wildfly-${wildfly.version} - UTF-8 - - - pic-sure-aggregate-data-sharing-resource - - - - edu.harvard.hms.dbmi.avillach - pic-sure-resource-api - ${project.version} - - - edu.harvard.hms.dbmi.avillach - pic-sure-api-data - ${project.version} - - - javax - javaee-api - provided - - - - org.apache.httpcomponents - httpclient - - - org.apache.httpcomponents - httpclient - - - com.fasterxml.jackson.core - jackson-databind - - - commons-io - commons-io - - - org.jboss.resteasy - resteasy-jaxb-provider - - - edu.harvard.hms.dbmi.avillach - pic-sure-util - ${project.version} - - - org.apache.commons - commons-lang3 - - - org.hibernate.javax.persistence - hibernate-jpa-2.1-api - - - org.hibernate - hibernate-annotations - - - org.mockito - mockito-core - test - - - com.github.tomakehurst - wiremock-standalone - test - - - org.glassfish.jersey.core - jersey-common - test - - - edu.harvard.dbmi.avillach - pic-sure-logging-client - - - diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/AggregateDataSharingResourceRS.java b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/AggregateDataSharingResourceRS.java deleted file mode 100644 index 9d7bde3ff..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/AggregateDataSharingResourceRS.java +++ /dev/null @@ -1,802 +0,0 @@ -package edu.harvard.hms.dbmi.avillach; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.core.type.TypeReference; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.node.ArrayNode; -import com.fasterxml.jackson.databind.node.ObjectNode; -import edu.harvard.dbmi.avillach.data.entity.Resource; -import edu.harvard.dbmi.avillach.data.repository.ResourceRepository; -import edu.harvard.dbmi.avillach.domain.*; -import edu.harvard.dbmi.avillach.logging.LoggingClient; -import edu.harvard.dbmi.avillach.logging.LoggingEvent; -import edu.harvard.dbmi.avillach.logging.RequestInfo; -import edu.harvard.dbmi.avillach.service.IResourceRS; -import edu.harvard.dbmi.avillach.util.HttpClientUtil; -import edu.harvard.dbmi.avillach.util.VisualizationUtil; -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; -import edu.harvard.hms.dbmi.avillach.service.RequestScopedHeader; -import org.apache.http.Header; -import org.apache.http.HttpEntity; -import org.apache.http.HttpResponse; -import org.apache.http.impl.conn.PoolingHttpClientConnectionManager; -import org.apache.http.message.BasicHeader; -import org.apache.http.util.EntityUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.inject.Inject; -import javax.inject.Singleton; -import javax.servlet.http.HttpServletRequest; -import javax.ws.rs.*; -import javax.ws.rs.core.Context; -import javax.ws.rs.core.HttpHeaders; -import javax.ws.rs.core.Response; -import java.io.IOException; -import java.nio.charset.StandardCharsets; -import java.util.*; -import java.util.stream.Collectors; - -import static edu.harvard.dbmi.avillach.service.ResourceWebClient.QUERY_METADATA_FIELD; -import static edu.harvard.dbmi.avillach.util.HttpClientUtil.*; - -@Path("/aggregate-data-sharing") -@Produces("application/json") -@Consumes("application/json") -@Singleton -public class AggregateDataSharingResourceRS implements IResourceRS { - - - @Inject - private ApplicationProperties properties; - - @Inject - private ResourceRepository resourceRepository; - - @Inject - RequestScopedHeader requestScopedHeader; - - @Inject - LoggingClient loggingClient; - - @Context - HttpServletRequest httpServletRequest; - - private static final ObjectMapper objectMapper = new ObjectMapper(); - - private final Header[] headers; - - private static final String BEARER_STRING = "Bearer "; - - private final Logger logger = LoggerFactory.getLogger(this.getClass()); - - private final int threshold; - private final int variance; - - private final String randomSalt; - - private final HttpClientUtil httpClientUtil; - - public AggregateDataSharingResourceRS() { - this(null); - } - - @Inject - public AggregateDataSharingResourceRS(ApplicationProperties applicationProperties) { - this.properties = applicationProperties; - if (applicationProperties == null) { - logger.info("initialize Aggregate Resource NO INJECTION"); - } else { - logger.info("initialize Aggregate Resource Injected " + applicationProperties); - } - - if (properties == null) { - properties = new ApplicationProperties(); - properties.init("pic-sure-aggregate-resource"); - } - - threshold = properties.getTargetPicsureObfuscationThreshold(); - variance = properties.getTargetPicsureObfuscationVariance(); - randomSalt = properties.getTargetPicsureObfuscationSalt(); - - headers = new Header[] {new BasicHeader(HttpHeaders.AUTHORIZATION, BEARER_STRING + properties.getTargetPicsureToken())}; - - PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(); - connectionManager.setMaxTotal(100); // Maximum total connections - connectionManager.setDefaultMaxPerRoute(20); // Maximum connections per route - httpClientUtil = HttpClientUtil.getInstance(connectionManager); - } - - - @GET - @Path("/status") - public Response status() { - logger.debug("Calling Aggregate Data Sharing Resource status()"); - return Response.ok().build(); - } - - @POST - @Path("/info") - @Override - public ResourceInfo info(QueryRequest infoRequest) { - logger.debug("Calling Aggregate Data Sharing Resource info()"); - String pathName = "/info"; - - HttpResponse response = null; - try { - QueryRequest chainRequest = new GeneralQueryRequest(); - if (infoRequest != null) { - chainRequest.setQuery(infoRequest.getQuery()); - chainRequest.setResourceCredentials(infoRequest.getResourceCredentials()); - // set a default value of the existing uuid here (can override in properties file) - chainRequest.setResourceUUID(infoRequest.getResourceUUID()); - } - if (properties.getTargetResourceId() != null && !properties.getTargetResourceId().isEmpty()) { - chainRequest.setResourceUUID(UUID.fromString(properties.getTargetResourceId())); - } - - String payload = objectMapper.writeValueAsString(chainRequest); - String composedURL = HttpClientUtil.composeURL(properties.getTargetPicsureUrl(), pathName); - response = httpClientUtil.retrievePostResponse(composedURL, headers, payload); - if (!HttpClientUtil.is2xx(response)) { - logger.error( - "{}{} did not return a 200: {} {} ", properties.getTargetPicsureUrl(), pathName, - response.getStatusLine().getStatusCode(), response.getStatusLine().getReasonPhrase() - ); - HttpClientUtil.throwResponseError(response, properties.getTargetPicsureUrl()); - } - - // if we are proxying an info request, we need to return our own resource ID - ResourceInfo resourceInfo = readObjectFromResponse(response, ResourceInfo.class); - if (infoRequest != null && infoRequest.getResourceUUID() != null) { - resourceInfo.setId(infoRequest.getResourceUUID()); - } - return resourceInfo; - } catch (IOException e) { - throw new ApplicationException("Error encoding query for resource with id " + infoRequest.getResourceUUID()); - } catch (ClassCastException | IllegalArgumentException e) { - logger.error(e.getMessage()); - throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); - } finally { - HttpClientUtil.closeHttpResponse(response); - } - } - - @POST - @Path("/search") - @Override - public SearchResults search(QueryRequest searchRequest) { - logger.debug("Calling Aggregate Data Sharing Search"); - checkQuery(searchRequest); - HttpResponse response = null; - try { - response = postRequest(searchRequest, "/search"); - return readObjectFromResponse(response, SearchResults.class); - } finally { - HttpClientUtil.closeHttpResponse(response); - } - } - - @POST - @Path("/query") - @Override - public QueryStatus query(QueryRequest queryRequest) { - logger.debug("Calling Aggregate Data Sharing Resource query()"); - checkQuery(queryRequest); - HttpResponse response = null; - try { - JsonNode jsonNode = objectMapper.valueToTree(queryRequest.getQuery()); - queryRequest.setQuery(jsonNode); - if (!jsonNode.has("expectedResultType")) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - String expectedResultType = jsonNode.get("expectedResultType").asText(); - if ("CROSS_COUNT".equalsIgnoreCase(expectedResultType)) { - changeQueryToOpenCrossCount(queryRequest); - } - response = postRequest(queryRequest, "/query"); - return readObjectFromResponse(response, QueryStatus.class); - } finally { - HttpClientUtil.closeHttpResponse(response); - } - } - - @POST - @Path("/query/{resourceQueryId}/status") - @Override - public QueryStatus queryStatus(@PathParam("resourceQueryId") UUID queryId, QueryRequest statusRequest) { - logger.debug("Calling Aggregate Data Sharing Resource queryStatus() for query {}", queryId); - checkQuery(statusRequest); - HttpResponse response = null; - try { - response = postRequest(statusRequest, "/query/" + queryId + "/status"); - return readObjectFromResponse(response, QueryStatus.class); - } finally { - HttpClientUtil.closeHttpResponse(response); - } - } - - @POST - @Path("/query/{resourceQueryId}/result") - @Override - public Response queryResult(@PathParam("resourceQueryId") UUID queryId, QueryRequest resultRequest) { - logger.debug("Calling Aggregate Data Sharing Resource queryResult() for query {}", queryId); - checkQuery(resultRequest); - HttpResponse response = postRequest(resultRequest, "/query/" + queryId + "/result"); - try { - String responseBody = httpClientUtil.readObjectFromResponse(response, StandardCharsets.UTF_8); - return Response.ok(responseBody).build(); - } finally { - HttpClientUtil.closeHttpResponse(response); - } - } - - private HttpResponse postRequest(QueryRequest statusRequest, String pathName) { - try { - QueryRequest chainRequest = createChainRequest(statusRequest); - String payload = objectMapper.writeValueAsString(chainRequest); - String composedURL = HttpClientUtil.composeURL(properties.getTargetPicsureUrl(), pathName); - HttpResponse response = httpClientUtil.retrievePostResponse(composedURL, headers, payload); - if (!HttpClientUtil.is2xx(response)) { - logger.error( - "{}{} did not return a 200: {} {} ", properties.getTargetPicsureUrl(), pathName, - response.getStatusLine().getStatusCode(), response.getStatusLine().getReasonPhrase() - ); - HttpClientUtil.throwResponseError(response, properties.getTargetPicsureUrl()); - } - return response; - } catch (IOException e) { - // Note: this shouldn't ever happen - logger.error("Error encoding search payload", e); - throw new ApplicationException("Error encoding search for resource with id " + statusRequest.getResourceUUID()); - } - } - - @POST - @Path("/query/sync") - @Override - public Response querySync(QueryRequest queryRequest) { - logger.debug("Calling Aggregate Data Sharing Resource querySync()"); - checkQuery(queryRequest); - - if (loggingClient != null && loggingClient.isEnabled()) { - RequestInfo.Builder reqInfo = RequestInfo.builder().method("POST").url("/aggregate-data-sharing/query/sync"); - if (httpServletRequest != null) { - String xff = httpServletRequest.getHeader("X-Forwarded-For"); - reqInfo.srcIp(xff != null && !xff.isEmpty() ? xff.split(",")[0].trim() : httpServletRequest.getRemoteAddr()) - .destIp(httpServletRequest.getLocalAddr()).destPort(httpServletRequest.getLocalPort()) - .httpUserAgent(httpServletRequest.getHeader("User-Agent")); - } - loggingClient.send( - LoggingEvent.builder("QUERY").action("aggregate.query_sync").request(reqInfo.build()) - .metadata(Map.of("resource_id", String.valueOf(queryRequest.getResourceUUID()))).build() - ); - } - - HttpResponse response = null; - try { - Object query = queryRequest.getQuery(); - UUID resourceUUID = queryRequest.getResourceUUID(); - - JsonNode jsonNode = objectMapper.valueToTree(query); - queryRequest.setQuery(jsonNode); - - if (!jsonNode.has("expectedResultType")) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - String expectedResultType = jsonNode.get("expectedResultType").asText(); - - Set allowedResultTypes = Set.of( - "COUNT", "CROSS_COUNT", "INFO_COLUMN_LISTING", "OBSERVATION_COUNT", "OBSERVATION_CROSS_COUNT", "CATEGORICAL_CROSS_COUNT", - "CONTINUOUS_CROSS_COUNT", "VARIANT_COUNT_FOR_QUERY", "AGGREGATE_VCF_EXCERPT", "VCF_EXCERPT" - ); - - if (!allowedResultTypes.contains(expectedResultType)) { - logger.warn("Incorrect Result Type: " + expectedResultType); - return Response.status(Response.Status.BAD_REQUEST).build(); - } - - if ("CROSS_COUNT".equalsIgnoreCase(expectedResultType)) { - changeQueryToOpenCrossCount(queryRequest); - } - - response = getHttpResponse(queryRequest, resourceUUID, "/query/sync", properties.getTargetPicsureUrl()); - - HttpEntity entity = response.getEntity(); - String entityString = EntityUtils.toString(entity, "UTF-8"); - String responseString = entityString; - - responseString = getExpectedResponse(expectedResultType, entityString, responseString, queryRequest); - - // propagate any metadata from the back end (e.g., resultId) - if (response.containsHeader(QUERY_METADATA_FIELD)) { - Header metadataHeader = ((Header[]) response.getHeaders(QUERY_METADATA_FIELD))[0]; - return Response.ok(responseString).header(QUERY_METADATA_FIELD, metadataHeader.getValue()).build(); - } - - return Response.ok(responseString).build(); - } catch (IOException e) { - logger.error(e.getMessage(), e); - throw new ApplicationException("Error encoding query for resource with id " + queryRequest.getResourceUUID()); - } catch (ClassCastException | IllegalArgumentException e) { - logger.error(e.getMessage()); - throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); - } finally { - closeHttpResponse(response); - } - } - - private HttpResponse getHttpResponse(QueryRequest queryRequest, UUID resourceUUID, String pathName, String targetPicsureUrl) - throws JsonProcessingException { - String queryString = objectMapper.writeValueAsString(queryRequest); - String composedURL = HttpClientUtil.composeURL(targetPicsureUrl, pathName); - - logger.debug("Aggregate Data Sharing Resource, sending query: " + queryString + ", to: " + composedURL); - HttpResponse response = httpClientUtil.retrievePostResponse(composedURL, headers, queryString); - if (!HttpClientUtil.is2xx(response)) { - logger.error("Not 200 status!"); - logger.error( - composedURL + " calling resource with id " + resourceUUID + " did not return a 200: {} {} ", - response.getStatusLine().getStatusCode(), response.getStatusLine().getReasonPhrase() - ); - HttpClientUtil.throwResponseError(response, targetPicsureUrl); - } - return response; - } - - /** - * This method will process the response from the backend and return the expected response based on the expected result type. Currently, - * the only types that are handled are: COUNT, CROSS_COUNT, CATEGORICAL_CROSS_COUNT, CONTINUOUS_CROSS_COUNT - * - * @param expectedResultType The expected result type - * @param entityString The response from the backend that will be processed - * @param responseString The response that will be returned. Will return the passed entityString if no cases are matched. - * @return String The response that will be returned - * @throws JsonProcessingException If there is an error processing the response - */ - private String getExpectedResponse(String expectedResultType, String entityString, String responseString, QueryRequest queryRequest) - throws IOException, JsonProcessingException { - String crossCountResponse; - switch (expectedResultType) { - case "COUNT": - try { - int count = Integer.parseInt(entityString); - int requestVariance = generateRequestVariance(entityString); - responseString = applyThresholdFloor(count) - .map(ObfuscatedCount::display) - .orElseGet(() -> randomize(count, requestVariance).display()); - } catch (NumberFormatException nfe) { - logger.warn("COUNT response was not a number! " + entityString); - responseString = entityString; - } - - break; - case "CROSS_COUNT": - Map crossCounts = processCrossCounts(entityString); - responseString = objectMapper.writeValueAsString(crossCounts); - - break; - case "CATEGORICAL_CROSS_COUNT": - crossCountResponse = getCrossCountForQuery(queryRequest); - responseString = processCategoricalCrossCounts(entityString, crossCountResponse); - - break; - case "CONTINUOUS_CROSS_COUNT": - crossCountResponse = getCrossCountForQuery(queryRequest); - responseString = processContinuousCrossCounts(entityString, crossCountResponse, queryRequest); - - break; - } - return responseString; - } - - /** - * No matter what the expected result type is we will get the cross count instead. Additionally, it will include ALL study consents in - * the query. - * - * @param queryRequest The query request - * @return String The cross count for the query - */ - private String getCrossCountForQuery(QueryRequest queryRequest) throws IOException { - logger.debug("Calling Aggregate Data Sharing Resource getCrossCountForQuery()"); - - HttpResponse response = getHttpResponse( - changeQueryToOpenCrossCount(queryRequest), queryRequest.getResourceUUID(), "/query/sync", properties.getTargetPicsureUrl() - ); - HttpEntity entity = response.getEntity(); - return EntityUtils.toString(entity, "UTF-8"); - } - - /** - * This method will add the study consents to the query. It will also set the expected result type to cross count. - * - * @param queryRequest The query request - * @return QueryRequest The query request with the study consents added and the expected result type set to cross count - */ - private QueryRequest changeQueryToOpenCrossCount(QueryRequest queryRequest) { - logger.debug("Calling Aggregate Data Sharing Resource handleAlterQueryToOpenCrossCount()"); - - Object query = queryRequest.getQuery(); - JsonNode jsonNode = objectMapper.valueToTree(query); - - JsonNode updatedExpectedResulType = setExpectedResultTypeToCrossCount(jsonNode); - JsonNode includesStudyConsents = addStudyConsentsToQuery(updatedExpectedResulType); - - queryRequest.setQuery(includesStudyConsents); - return queryRequest; - } - - private JsonNode setExpectedResultTypeToCrossCount(JsonNode jsonNode) { - logger.debug("Calling Aggregate Data Sharing Resource setExpectedResultTypeToCrossCount()"); - - List expectedResultTypeParents = jsonNode.findParents("expectedResultType"); - - // The reason we need to do this is that expected result type is a TextNode that is immutable. - // This is a jackson work around to replace the expectedResultType field with a new value. - for (JsonNode node : expectedResultTypeParents) { - ((ObjectNode) node).put("expectedResultType", "CROSS_COUNT"); - } - - return jsonNode; - } - - private JsonNode addStudyConsentsToQuery(JsonNode jsonNode) { - logger.debug("Calling Aggregate Data Sharing Resource addStudyConsentsToQuery()"); - - SearchResults consentResults = getAllStudyConsents(); - LinkedHashMap linkedHashMap = objectMapper.convertValue(consentResults.getResults(), new TypeReference<>() {}); - Object phenotypes = linkedHashMap.get("phenotypes"); - LinkedHashMap phenotypesLinkedHashMap = objectMapper.convertValue(phenotypes, new TypeReference<>() {}); - - // get all the keys from phenotypes - Set keys = phenotypesLinkedHashMap.keySet(); - - // create an ArrayNode to hold the keys - ArrayNode arrayNode = objectMapper.createArrayNode(); - - // add the keys to the ArrayNode - for (String key : keys) { - arrayNode.add(key); - } - - // add the ArrayNode to the query - ((ObjectNode) jsonNode).set("crossCountFields", arrayNode); - - return jsonNode; - } - - private SearchResults getAllStudyConsents() { - logger.debug("Calling Aggregate Data Sharing Resource getAllStudyConsents()"); - - QueryRequest studiesConsents = new GeneralQueryRequest(); - studiesConsents.setQuery("\\_studies_consents\\"); - return this.search(studiesConsents); - } - - @Override - @POST - @Path("/query/format") - public Response queryFormat(QueryRequest queryRequest) { - checkQuery(queryRequest); - - UUID resourceUUID = queryRequest.getResourceUUID(); - String pathName = "/query/format"; - - HttpResponse response = null; - try { - String queryString = objectMapper.writeValueAsString(queryRequest); - String composedURL = HttpClientUtil.composeURL(properties.getTargetPicsureUrl(), pathName); - response = httpClientUtil.retrievePostResponse(composedURL, headers, queryString); - if (!HttpClientUtil.is2xx(response)) { - logger.error( - composedURL + " calling resource with id " + resourceUUID + " did not return a 200: {} {} ", - response.getStatusLine().getStatusCode(), response.getStatusLine().getReasonPhrase() - ); - HttpClientUtil.throwResponseError(response, properties.getTargetPicsureUrl()); - } - - return Response.ok(response.getEntity().getContent()).build(); - } catch (IOException e) { - throw new ApplicationException("Error encoding query for resource with id " + queryRequest.getResourceUUID()); - } catch (ClassCastException | IllegalArgumentException e) { - logger.error(e.getMessage()); - throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); - } finally { - HttpClientUtil.closeHttpResponse(response); - } - } - - private Map processCrossCounts(String entityString) throws com.fasterxml.jackson.core.JsonProcessingException { - Map crossCounts = objectMapper.readValue(entityString, new TypeReference<>() {}); - - int requestVariance = generateVarianceWithCrossCounts(crossCounts); - crossCounts = obfuscateCrossCounts(crossCounts, requestVariance); - - return crossCounts; - } - - /** - * This method will appropriately process the obfuscation of the cross counts. - * - * @param crossCounts The cross counts - * @param requestVariance The variance for the request - * @return Map The obfuscated cross counts - */ - private Map obfuscateCrossCounts(Map crossCounts, int requestVariance) { - Set obfuscatedKeys = new HashSet<>(); - if (crossCounts != null) { - crossCounts.keySet().forEach(key -> { - String crossCount = crossCounts.get(key); - Optional floored = applyThresholdFloor(crossCount); - floored.ifPresent((x) -> obfuscatedKeys.add(key)); - crossCounts.put(key, floored.map(ObfuscatedCount::display).orElse(crossCount)); - }); - - crossCounts.keySet().forEach(key -> { - String crossCount = crossCounts.get(key); - if (!obfuscatedKeys.contains(key)) { - crossCounts.put(key, randomize(Integer.parseInt(crossCount), requestVariance).display()); - } - }); - } - - return crossCounts; - } - - /** - * This method is used to generate a variance for Cross Count queries. The variance is generated by taking the cross counts and sorting - * them by key. Then we generate a string with lines like consent:1\n consent:2\ consent:3\n etc. Then we generate a variance using the - * string. This is to give us a random variance that is deterministic for each query. - * - * @param crossCounts A map of cross counts - * @return int The variance - */ - private int generateVarianceWithCrossCounts(Map crossCounts) { - final List> entryList = new ArrayList<>(crossCounts.entrySet()); - - // sort the entry set. By sorting the entry set first we can ensure that the variance is the same for each run. - // This is to give us a random variance that is deterministic. - entryList.sort(Map.Entry.comparingByKey()); - - final StringBuffer crossCountsString = new StringBuffer(); - - // build a string with lines like consent:1\n consent:2\n consent:3\n etc. - entryList.forEach(entry -> crossCountsString.append(entry.getKey()).append(":").append(entry.getValue()).append("\n")); - - return generateRequestVariance(crossCountsString.toString()); - } - - /** - * Returns the obfuscated continuous cross-count JSON. Continuous values can't be obfuscated directly in their - * raw form (one entry per distinct numeric value gives too many cells with small counts), so we first bin them - * via the visualization resource — when a visualization service is configured — and obfuscate the binned counts. - * Without a configured visualization service we obfuscate the raw per-value counts as a fallback. - * - * Either way, every value in the returned map is obfuscated through {@link #obfuscateCrossCount}: counts below - * the threshold collapse to {@code "< threshold"}, larger counts get variance-randomized. Returns null only when - * the upstream produced no data or when {@link #canShowContinuousCrossCounts} signals the cohort is too small - * to safely render. - * - * @param continuousCrossCountResponse The continuous cross count response - * @param crossCountResponse The cross count response - * @param queryRequest The original query request - * @return String The obfuscated continuous cross count JSON, or null if not safe / nothing to return - * @throws IOException If there is an error processing the JSON - */ - protected String processContinuousCrossCounts(String continuousCrossCountResponse, String crossCountResponse, QueryRequest queryRequest) - throws IOException { - logger.info("Processing continuous cross counts"); - - if (continuousCrossCountResponse == null || crossCountResponse == null) { - return null; - } - - Map crossCounts = objectMapper.readValue(crossCountResponse, new TypeReference<>() {}); - int generatedVariance = this.generateVarianceWithCrossCounts(crossCounts); - - if (canShowContinuousCrossCounts(crossCounts)) { - return null; - } - - // Handle the case where there is no visualization service UUID - if (properties.getVisualizationResourceId() != null) { - Map> continuousCrossCounts = - objectMapper.readValue(continuousCrossCountResponse, new TypeReference<>() {}); - Map> binnedContinuousCrossCounts = - getBinnedContinuousCrossCount(queryRequest, continuousCrossCounts); - - // Log the binned continuous cross counts - logger.info("Binned continuous cross counts: {}", binnedContinuousCrossCounts); - - return objectMapper.writeValueAsString(obfuscateCrossCount(generatedVariance, binnedContinuousCrossCounts)); - } else { - Map> continuousCrossCounts = - objectMapper.readValue(continuousCrossCountResponse, new TypeReference<>() {}); - - return objectMapper.writeValueAsString(obfuscateCrossCount(generatedVariance, continuousCrossCounts)); - } - } - - private Map> getBinnedContinuousCrossCount( - QueryRequest queryRequest, Map> continuousCrossCounts - ) throws IOException { - // Create Query for Visualization /bin/continuous - QueryRequest visualizationBinRequest = new GeneralQueryRequest(); - visualizationBinRequest.setResourceUUID(properties.getVisualizationResourceId()); - visualizationBinRequest.setQuery(continuousCrossCounts); - visualizationBinRequest.setResourceCredentials(queryRequest.getResourceCredentials()); - - Resource visResource = resourceRepository.getById(visualizationBinRequest.getResourceUUID()); - if (visResource == null) { - throw new ApplicationException("Visualization resource could not be found"); - } - - // call the binning endpoint - HttpResponse httpResponse = getHttpResponse( - visualizationBinRequest, visualizationBinRequest.getResourceUUID(), "/bin/continuous", visResource.getResourceRSPath() - ); - HttpEntity entity = httpResponse.getEntity(); - String binResponse = EntityUtils.toString(entity, "UTF-8"); - - return objectMapper.readValue(binResponse, new TypeReference>>() {}); - } - - /** - * This method handles the processing of categorical cross counts. It begins by determining whether the cross counts require - * obfuscation. This is accomplished by checking if any of the CROSS_COUNTS must be obfuscated. If obfuscation is required, the - * categorical cross counts will be obfuscated accordingly. Otherwise, if no obfuscation is needed, the method can simply return the - * categorical entity string. - * - * @param categoricalEntityString The categorical entity string - * @param crossCountEntityString The cross count entity string - * @return String The processed categorical entity string - * @throws JsonProcessingException If there is an error processing the JSON - */ - protected String processCategoricalCrossCounts(String categoricalEntityString, String crossCountEntityString) - throws JsonProcessingException { - logger.info("Processing categorical cross counts"); - - if (categoricalEntityString == null || crossCountEntityString == null) { - return null; - } - - Map crossCounts = objectMapper.readValue(crossCountEntityString, new TypeReference<>() {}); - int generatedVariance = this.generateVarianceWithCrossCounts(crossCounts); - - Map> categoricalCrossCount = objectMapper.readValue(categoricalEntityString, new TypeReference<>() {}); - - if (categoricalCrossCount == null) { - logger.info("Categorical cross count is null. Returning categoricalEntityString: {}", categoricalEntityString); - return categoricalEntityString; - } - - // We have not obfuscated yet. We first process the data. - processResults(categoricalCrossCount); - - // Now we need to obfuscate our return data. The only consideration is do we apply < threshold or variance - return objectMapper.writeValueAsString(obfuscateCrossCount(generatedVariance, categoricalCrossCount)); - } - - private static void processResults(Map> categoricalCrossCount) { - for (Map.Entry> entry : categoricalCrossCount.entrySet()) { - // skipKey is expecting an entrySet, so we need to convert the axisMap to an entrySet - if (VisualizationUtil.skipKey(entry.getKey())) continue; - Map axisMap = VisualizationUtil.processResults(entry.getValue()); - categoricalCrossCount.put(entry.getKey(), axisMap); - } - } - - /** - * Obfuscates every value in a cross-count map. Returns a freshly constructed map keyed identically to the - * input but with values replaced by either a threshold-floor obfuscation (for counts below the threshold) - * or a variance-randomized one. - * - * @param generatedVariance The variance for the request - * @param crossCount The cross count to obfuscate; values are JSON-deserialized so may be Integer or String - */ - private Map> obfuscateCrossCount( - int generatedVariance, Map> crossCount - ) { - Map> result = new LinkedHashMap<>(); - crossCount.forEach((key, value) -> { - Map obfuscated = new LinkedHashMap<>(); - value.forEach((innerKey, innerValue) -> { - int count = toInt(innerValue); - obfuscated.put( - innerKey, - applyThresholdFloor(count).orElseGet(() -> randomize(count, generatedVariance)) - ); - }); - result.put(key, obfuscated); - }); - return result; - } - - /** - * Jackson hands us {@code Object}-typed values from JSON; the runtime type depends on the number's magnitude - * (Integer, Long, Double, BigInteger, ...) and on whether the upstream stringified it. Accept anything that - * represents an integral count and narrow to int. The previous shape ({@code innerValue.toString()} into - * {@link Integer#parseInt}) silently accepted Long/Double for free; preserve that breadth via {@link Number}. - */ - static int toInt(Object value) { - if (value instanceof Number) return ((Number) value).intValue(); - if (value instanceof String) return Integer.parseInt((String) value); - throw new IllegalArgumentException("Cross-count value was neither Number nor numeric String: " + value); - } - - - private boolean canShowContinuousCrossCounts(Map crossCounts) { - String lessThanThresholdStr = "< " + this.threshold; - - String v = crossCounts.get("\\_studies_consents\\"); - if (v.contains(lessThanThresholdStr) || v.equals("0")) { - return true; - } - return false; - } - - /** - * This method will generate a random variance for the request based on the passed entityString. The variance will be between -variance - * and +variance. The variance will be generated by adding a random salt to the entityString and then taking the hashcode of the result. - * The variance will be the hashcode mod the variance * 2 + 1 - variance. - * - * @return int The variance for the request - */ - private QueryRequest createChainRequest(QueryRequest queryRequest) { - QueryRequest chainRequest = new GeneralQueryRequest(); - chainRequest.setQuery(queryRequest.getQuery()); - chainRequest.setResourceCredentials(queryRequest.getResourceCredentials()); - - if (properties.getTargetResourceId() != null && !properties.getTargetResourceId().isEmpty()) { - chainRequest.setResourceUUID(UUID.fromString(properties.getTargetResourceId())); - } else { - chainRequest.setResourceUUID(queryRequest.getResourceUUID()); - } - return chainRequest; - } - - private static void checkQuery(QueryRequest searchRequest) { - if (searchRequest == null || searchRequest.getQuery() == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - } - - private int generateRequestVariance(String entityString) { - return Math.abs((entityString + randomSalt).hashCode()) % (variance * 2 + 1) - variance; - } - - ObfuscatedCount randomize(int crossCount, int requestVariance) { - int randomized = Math.max(crossCount + requestVariance, threshold); - return new ObfuscatedCount(randomized, randomized + " \u00B1" + variance, variance); - } - - /** - * Core privacy floor: small (potentially identifiable) cohorts get hidden behind a "< threshold" display. - * The value is encoded as count 0 with variance threshold-1, so consumers rendering the uncertainty band - * [max(0, count - variance), count + variance] draw 0..threshold-1 — the true count lies somewhere in that - * band but we don't disclose where. - * - * Returns empty when the value is at or above the threshold (caller should then call {@link #randomize}). - */ - Optional applyThresholdFloor(int actualCount) { - if (actualCount < threshold) { - return Optional.of(new ObfuscatedCount(0, "< " + threshold, threshold - 1)); - } - return Optional.empty(); - } - - /** - * String overload for callers (COUNT / CROSS_COUNT) that hold the value as a JSON string. Logs and returns - * empty on parse failure so the caller can fall through to its untouched-value path. - */ - Optional applyThresholdFloor(String actualCount) { - try { - return applyThresholdFloor(Integer.parseInt(actualCount)); - } catch (NumberFormatException nfe) { - logger.warn("Count was not a number! " + actualCount); - return Optional.empty(); - } - } -} diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/AggregateDataSharingResourceRSV3.java b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/AggregateDataSharingResourceRSV3.java deleted file mode 100644 index 27bb33dd4..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/AggregateDataSharingResourceRSV3.java +++ /dev/null @@ -1,778 +0,0 @@ -package edu.harvard.hms.dbmi.avillach; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.core.type.TypeReference; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.node.ArrayNode; -import com.fasterxml.jackson.databind.node.ObjectNode; -import edu.harvard.dbmi.avillach.data.entity.Resource; -import edu.harvard.dbmi.avillach.data.repository.ResourceRepository; -import edu.harvard.dbmi.avillach.domain.*; -import edu.harvard.dbmi.avillach.service.IResourceRS; -import edu.harvard.dbmi.avillach.util.HttpClientUtil; -import edu.harvard.dbmi.avillach.util.VisualizationUtil; -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; -import edu.harvard.hms.dbmi.avillach.service.RequestScopedHeader; -import org.apache.http.Header; -import org.apache.http.HttpEntity; -import org.apache.http.HttpResponse; -import org.apache.http.impl.conn.PoolingHttpClientConnectionManager; -import org.apache.http.message.BasicHeader; -import org.apache.http.util.EntityUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.inject.Inject; -import javax.inject.Singleton; -import javax.ws.rs.*; -import javax.ws.rs.core.HttpHeaders; -import javax.ws.rs.core.Response; -import java.io.IOException; -import java.nio.charset.StandardCharsets; -import java.util.*; -import java.util.stream.Collectors; - -import static edu.harvard.dbmi.avillach.service.ResourceWebClient.QUERY_METADATA_FIELD; -import static edu.harvard.dbmi.avillach.util.HttpClientUtil.closeHttpResponse; -import static edu.harvard.dbmi.avillach.util.HttpClientUtil.readObjectFromResponse; - -@Path("/v3/aggregate-data-sharing") -@Produces("application/json") -@Consumes("application/json") -@Singleton -public class AggregateDataSharingResourceRSV3 implements IResourceRS { - - - @Inject - private ApplicationProperties properties; - - @Inject - private ResourceRepository resourceRepository; - - @Inject - RequestScopedHeader requestScopedHeader; - - private static final ObjectMapper objectMapper = new ObjectMapper(); - - private final Header[] headers; - - private static final String BEARER_STRING = "Bearer "; - - private final Logger logger = LoggerFactory.getLogger(this.getClass()); - - private final int threshold; - private final int variance; - - private final String randomSalt; - - private final HttpClientUtil httpClientUtil; - - public AggregateDataSharingResourceRSV3() { - this(null); - } - - @Inject - public AggregateDataSharingResourceRSV3(ApplicationProperties applicationProperties) { - this.properties = applicationProperties; - if (applicationProperties == null) { - logger.info("initialize Aggregate Resource NO INJECTION"); - } else { - logger.info("initialize Aggregate Resource Injected " + applicationProperties); - } - - if (properties == null) { - properties = new ApplicationProperties(); - properties.init("pic-sure-aggregate-resource"); - } - - threshold = properties.getTargetPicsureObfuscationThreshold(); - variance = properties.getTargetPicsureObfuscationVariance(); - randomSalt = properties.getTargetPicsureObfuscationSalt(); - - headers = new Header[] {new BasicHeader(HttpHeaders.AUTHORIZATION, BEARER_STRING + properties.getTargetPicsureToken())}; - - PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(); - connectionManager.setMaxTotal(100); // Maximum total connections - connectionManager.setDefaultMaxPerRoute(20); // Maximum connections per route - httpClientUtil = HttpClientUtil.getInstance(connectionManager); - } - - - @GET - @Path("/status") - public Response status() { - logger.debug("Calling Aggregate Data Sharing Resource status()"); - return Response.ok().build(); - } - - @POST - @Path("/info") - @Override - public ResourceInfo info(QueryRequest infoRequest) { - logger.debug("Calling Aggregate Data Sharing Resource info()"); - String pathName = "/info"; - - HttpResponse response = null; - try { - QueryRequest chainRequest = new GeneralQueryRequest(); - if (infoRequest != null) { - chainRequest.setQuery(infoRequest.getQuery()); - chainRequest.setResourceCredentials(infoRequest.getResourceCredentials()); - // set a default value of the existing uuid here (can override in properties file) - chainRequest.setResourceUUID(infoRequest.getResourceUUID()); - } - if (properties.getTargetResourceId() != null && !properties.getTargetResourceId().isEmpty()) { - chainRequest.setResourceUUID(UUID.fromString(properties.getTargetResourceId())); - } - - String payload = objectMapper.writeValueAsString(chainRequest); - String composedURL = HttpClientUtil.composeURL(properties.getTargetPicsureUrl(), pathName); - response = httpClientUtil.retrievePostResponse(composedURL, headers, payload); - if (!HttpClientUtil.is2xx(response)) { - logger.error( - "{}{} did not return a 200: {} {} ", properties.getTargetPicsureUrl(), pathName, - response.getStatusLine().getStatusCode(), response.getStatusLine().getReasonPhrase() - ); - HttpClientUtil.throwResponseError(response, properties.getTargetPicsureUrl()); - } - - // if we are proxying an info request, we need to return our own resource ID - ResourceInfo resourceInfo = readObjectFromResponse(response, ResourceInfo.class); - if (infoRequest != null && infoRequest.getResourceUUID() != null) { - resourceInfo.setId(infoRequest.getResourceUUID()); - } - return resourceInfo; - } catch (IOException e) { - throw new ApplicationException("Error encoding query for resource with id " + infoRequest.getResourceUUID()); - } catch (ClassCastException | IllegalArgumentException e) { - logger.error(e.getMessage()); - throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); - } finally { - HttpClientUtil.closeHttpResponse(response); - } - } - - @POST - @Path("/search") - @Override - public SearchResults search(QueryRequest searchRequest) { - logger.debug("Calling Aggregate Data Sharing Search"); - checkQuery(searchRequest); - HttpResponse response = null; - try { - response = postRequest(searchRequest, "/search"); - return readObjectFromResponse(response, SearchResults.class); - } finally { - HttpClientUtil.closeHttpResponse(response); - } - } - - @POST - @Path("/query") - @Override - public QueryStatus query(QueryRequest queryRequest) { - logger.debug("Calling Aggregate Data Sharing Resource query()"); - checkQuery(queryRequest); - HttpResponse response = null; - try { - JsonNode jsonNode = objectMapper.valueToTree(queryRequest.getQuery()); - queryRequest.setQuery(jsonNode); - if (!jsonNode.has("expectedResultType")) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - String expectedResultType = jsonNode.get("expectedResultType").asText(); - if ("CROSS_COUNT".equalsIgnoreCase(expectedResultType)) { - changeQueryToOpenCrossCount(queryRequest); - } - response = postRequest(queryRequest, "/query"); - return readObjectFromResponse(response, QueryStatus.class); - } finally { - HttpClientUtil.closeHttpResponse(response); - } - } - - @POST - @Path("/query/{resourceQueryId}/status") - @Override - public QueryStatus queryStatus(@PathParam("resourceQueryId") UUID queryId, QueryRequest statusRequest) { - logger.debug("Calling Aggregate Data Sharing Resource queryStatus() for query {}", queryId); - checkQuery(statusRequest); - HttpResponse response = null; - try { - response = postRequest(statusRequest, "/query/" + queryId + "/status"); - return readObjectFromResponse(response, QueryStatus.class); - } finally { - HttpClientUtil.closeHttpResponse(response); - } - } - - @POST - @Path("/query/{resourceQueryId}/result") - @Override - public Response queryResult(@PathParam("resourceQueryId") UUID queryId, QueryRequest resultRequest) { - logger.debug("Calling Aggregate Data Sharing Resource queryResult() for query {}", queryId); - checkQuery(resultRequest); - HttpResponse response = postRequest(resultRequest, "/query/" + queryId + "/result"); - try { - String responseBody = httpClientUtil.readObjectFromResponse(response, StandardCharsets.UTF_8); - return Response.ok(responseBody).build(); - } finally { - HttpClientUtil.closeHttpResponse(response); - } - } - - private HttpResponse postRequest(QueryRequest statusRequest, String pathName) { - try { - QueryRequest chainRequest = createChainRequest(statusRequest); - String payload = objectMapper.writeValueAsString(chainRequest); - String composedURL = HttpClientUtil.composeURL(properties.getTargetPicsureUrl(), pathName); - HttpResponse response = httpClientUtil.retrievePostResponse(composedURL, headers, payload); - if (!HttpClientUtil.is2xx(response)) { - logger.error( - "{}{} did not return a 200: {} {} ", properties.getTargetPicsureUrl(), pathName, - response.getStatusLine().getStatusCode(), response.getStatusLine().getReasonPhrase() - ); - HttpClientUtil.throwResponseError(response, properties.getTargetPicsureUrl()); - } - return response; - } catch (IOException e) { - // Note: this shouldn't ever happen - logger.error("Error encoding search payload", e); - throw new ApplicationException("Error encoding search for resource with id " + statusRequest.getResourceUUID()); - } - } - - @POST - @Path("/query/sync") - @Override - public Response querySync(QueryRequest queryRequest) { - logger.debug("Calling Aggregate Data Sharing Resource querySync()"); - checkQuery(queryRequest); - - HttpResponse response = null; - try { - Object query = queryRequest.getQuery(); - UUID resourceUUID = queryRequest.getResourceUUID(); - - JsonNode jsonNode = objectMapper.valueToTree(query); - queryRequest.setQuery(jsonNode); - - if (!jsonNode.has("expectedResultType")) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - String expectedResultType = jsonNode.get("expectedResultType").asText(); - - Set allowedResultTypes = Set.of( - "COUNT", "CROSS_COUNT", "INFO_COLUMN_LISTING", "OBSERVATION_COUNT", "OBSERVATION_CROSS_COUNT", "CATEGORICAL_CROSS_COUNT", - "CONTINUOUS_CROSS_COUNT", "VARIANT_COUNT_FOR_QUERY", "AGGREGATE_VCF_EXCERPT", "VCF_EXCERPT" - ); - - if (!allowedResultTypes.contains(expectedResultType)) { - logger.warn("Incorrect Result Type: " + expectedResultType); - return Response.status(Response.Status.BAD_REQUEST).build(); - } - - if ("CROSS_COUNT".equalsIgnoreCase(expectedResultType)) { - changeQueryToOpenCrossCount(queryRequest); - } - - response = getHttpResponse(queryRequest, resourceUUID, "/query/sync", properties.getTargetPicsureUrl()); - - HttpEntity entity = response.getEntity(); - String entityString = EntityUtils.toString(entity, "UTF-8"); - String responseString = entityString; - - responseString = getExpectedResponse(expectedResultType, entityString, responseString, queryRequest); - - // propagate any metadata from the back end (e.g., resultId) - if (response.containsHeader(QUERY_METADATA_FIELD)) { - Header metadataHeader = ((Header[]) response.getHeaders(QUERY_METADATA_FIELD))[0]; - return Response.ok(responseString).header(QUERY_METADATA_FIELD, metadataHeader.getValue()).build(); - } - - return Response.ok(responseString).build(); - } catch (IOException e) { - logger.error(e.getMessage(), e); - throw new ApplicationException("Error encoding query for resource with id " + queryRequest.getResourceUUID()); - } catch (ClassCastException | IllegalArgumentException e) { - logger.error(e.getMessage()); - throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); - } finally { - closeHttpResponse(response); - } - } - - private HttpResponse getHttpResponse(QueryRequest queryRequest, UUID resourceUUID, String pathName, String targetPicsureUrl) - throws JsonProcessingException { - String queryString = objectMapper.writeValueAsString(queryRequest); - String composedURL = HttpClientUtil.composeURL(targetPicsureUrl, "/v3" + pathName); - - logger.debug("Aggregate Data Sharing Resource, sending query: " + queryString + ", to: " + composedURL); - HttpResponse response = httpClientUtil.retrievePostResponse(composedURL, headers, queryString); - if (!HttpClientUtil.is2xx(response)) { - logger.error("Not 200 status!"); - logger.error( - composedURL + " calling resource with id " + resourceUUID + " did not return a 200: {} {} ", - response.getStatusLine().getStatusCode(), response.getStatusLine().getReasonPhrase() - ); - HttpClientUtil.throwResponseError(response, targetPicsureUrl); - } - return response; - } - - /** - * This method will process the response from the backend and return the expected response based on the expected result type. Currently, - * the only types that are handled are: COUNT, CROSS_COUNT, CATEGORICAL_CROSS_COUNT, CONTINUOUS_CROSS_COUNT - * - * @param expectedResultType The expected result type - * @param entityString The response from the backend that will be processed - * @param responseString The response that will be returned. Will return the passed entityString if no cases are matched. - * @return String The response that will be returned - * @throws JsonProcessingException If there is an error processing the response - */ - private String getExpectedResponse(String expectedResultType, String entityString, String responseString, QueryRequest queryRequest) - throws IOException, JsonProcessingException { - String crossCountResponse; - switch (expectedResultType) { - case "COUNT": - try { - int count = Integer.parseInt(entityString); - int requestVariance = generateRequestVariance(entityString); - responseString = applyThresholdFloor(count) - .map(ObfuscatedCount::display) - .orElseGet(() -> randomize(count, requestVariance).display()); - } catch (NumberFormatException nfe) { - logger.warn("COUNT response was not a number! " + entityString); - responseString = entityString; - } - - break; - case "CROSS_COUNT": - Map crossCounts = processCrossCounts(entityString); - responseString = objectMapper.writeValueAsString(crossCounts); - - break; - case "CATEGORICAL_CROSS_COUNT": - crossCountResponse = getCrossCountForQuery(queryRequest); - responseString = processCategoricalCrossCounts(entityString, crossCountResponse); - - break; - case "CONTINUOUS_CROSS_COUNT": - crossCountResponse = getCrossCountForQuery(queryRequest); - responseString = processContinuousCrossCounts(entityString, crossCountResponse, queryRequest); - - break; - } - return responseString; - } - - /** - * No matter what the expected result type is we will get the cross count instead. Additionally, it will include ALL study consents in - * the query. - * - * @param queryRequest The query request - * @return String The cross count for the query - */ - private String getCrossCountForQuery(QueryRequest queryRequest) throws IOException { - logger.debug("Calling Aggregate Data Sharing Resource getCrossCountForQuery()"); - - HttpResponse response = getHttpResponse( - changeQueryToOpenCrossCount(queryRequest), queryRequest.getResourceUUID(), "/query/sync", properties.getTargetPicsureUrl() - ); - HttpEntity entity = response.getEntity(); - return EntityUtils.toString(entity, "UTF-8"); - } - - /** - * This method will add the study consents to the query. It will also set the expected result type to cross count. - * - * @param queryRequest The query request - * @return QueryRequest The query request with the study consents added and the expected result type set to cross count - */ - private QueryRequest changeQueryToOpenCrossCount(QueryRequest queryRequest) { - logger.debug("Calling Aggregate Data Sharing Resource handleAlterQueryToOpenCrossCount()"); - - Object query = queryRequest.getQuery(); - JsonNode jsonNode = objectMapper.valueToTree(query); - - JsonNode updatedExpectedResulType = setExpectedResultTypeToCrossCount(jsonNode); - JsonNode includesStudyConsents = addStudyConsentsToQuery(updatedExpectedResulType); - - queryRequest.setQuery(includesStudyConsents); - return queryRequest; - } - - private JsonNode setExpectedResultTypeToCrossCount(JsonNode jsonNode) { - logger.debug("Calling Aggregate Data Sharing Resource setExpectedResultTypeToCrossCount()"); - - List expectedResultTypeParents = jsonNode.findParents("expectedResultType"); - - // The reason we need to do this is that expected result type is a TextNode that is immutable. - // This is a jackson work around to replace the expectedResultType field with a new value. - for (JsonNode node : expectedResultTypeParents) { - ((ObjectNode) node).put("expectedResultType", "CROSS_COUNT"); - } - - return jsonNode; - } - - private JsonNode addStudyConsentsToQuery(JsonNode jsonNode) { - logger.debug("Calling Aggregate Data Sharing Resource addStudyConsentsToQuery()"); - - SearchResults consentResults = getAllStudyConsents(); - LinkedHashMap linkedHashMap = objectMapper.convertValue(consentResults.getResults(), new TypeReference<>() {}); - Object phenotypes = linkedHashMap.get("phenotypes"); - LinkedHashMap phenotypesLinkedHashMap = objectMapper.convertValue(phenotypes, new TypeReference<>() {}); - - // get all the keys from phenotypes - Set keys = phenotypesLinkedHashMap.keySet(); - - // create an ArrayNode to hold the keys - ArrayNode arrayNode = objectMapper.createArrayNode(); - - // add the keys to the ArrayNode - for (String key : keys) { - arrayNode.add(key); - } - - // add the ArrayNode to the query - ((ObjectNode) jsonNode).set("select", arrayNode); - - return jsonNode; - } - - private SearchResults getAllStudyConsents() { - logger.debug("Calling Aggregate Data Sharing Resource getAllStudyConsents()"); - - QueryRequest studiesConsents = new GeneralQueryRequest(); - studiesConsents.setQuery("\\_studies_consents\\"); - return this.search(studiesConsents); - } - - @Override - @POST - @Path("/query/format") - public Response queryFormat(QueryRequest queryRequest) { - checkQuery(queryRequest); - - UUID resourceUUID = queryRequest.getResourceUUID(); - String pathName = "/query/format"; - - HttpResponse response = null; - try { - String queryString = objectMapper.writeValueAsString(queryRequest); - String composedURL = HttpClientUtil.composeURL(properties.getTargetPicsureUrl(), pathName); - response = httpClientUtil.retrievePostResponse(composedURL, headers, queryString); - if (!HttpClientUtil.is2xx(response)) { - logger.error( - composedURL + " calling resource with id " + resourceUUID + " did not return a 200: {} {} ", - response.getStatusLine().getStatusCode(), response.getStatusLine().getReasonPhrase() - ); - HttpClientUtil.throwResponseError(response, properties.getTargetPicsureUrl()); - } - - return Response.ok(response.getEntity().getContent()).build(); - } catch (IOException e) { - throw new ApplicationException("Error encoding query for resource with id " + queryRequest.getResourceUUID()); - } catch (ClassCastException | IllegalArgumentException e) { - logger.error(e.getMessage()); - throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); - } finally { - HttpClientUtil.closeHttpResponse(response); - } - } - - private Map processCrossCounts(String entityString) throws JsonProcessingException { - Map crossCounts = objectMapper.readValue(entityString, new TypeReference<>() {}); - - int requestVariance = generateVarianceWithCrossCounts(crossCounts); - crossCounts = obfuscateCrossCounts(crossCounts, requestVariance); - - return crossCounts; - } - - /** - * This method will appropriately process the obfuscation of the cross counts. - * - * @param crossCounts The cross counts - * @param requestVariance The variance for the request - * @return Map The obfuscated cross counts - */ - private Map obfuscateCrossCounts(Map crossCounts, int requestVariance) { - Set obfuscatedKeys = new HashSet<>(); - if (crossCounts != null) { - crossCounts.keySet().forEach(key -> { - String crossCount = crossCounts.get(key); - Optional floored = applyThresholdFloor(crossCount); - floored.ifPresent((x) -> obfuscatedKeys.add(key)); - crossCounts.put(key, floored.map(ObfuscatedCount::display).orElse(crossCount)); - }); - - crossCounts.keySet().forEach(key -> { - String crossCount = crossCounts.get(key); - if (!obfuscatedKeys.contains(key)) { - crossCounts.put(key, randomize(Integer.parseInt(crossCount), requestVariance).display()); - } - }); - } - - return crossCounts; - } - - /** - * This method is used to generate a variance for Cross Count queries. The variance is generated by taking the cross counts and sorting - * them by key. Then we generate a string with lines like consent:1\n consent:2\ consent:3\n etc. Then we generate a variance using the - * string. This is to give us a random variance that is deterministic for each query. - * - * @param crossCounts A map of cross counts - * @return int The variance - */ - private int generateVarianceWithCrossCounts(Map crossCounts) { - final List> entryList = new ArrayList<>(crossCounts.entrySet()); - - // sort the entry set. By sorting the entry set first we can ensure that the variance is the same for each run. - // This is to give us a random variance that is deterministic. - entryList.sort(Map.Entry.comparingByKey()); - - final StringBuffer crossCountsString = new StringBuffer(); - - // build a string with lines like consent:1\n consent:2\n consent:3\n etc. - entryList.forEach(entry -> crossCountsString.append(entry.getKey()).append(":").append(entry.getValue()).append("\n")); - - return generateRequestVariance(crossCountsString.toString()); - } - - /** - * Returns the obfuscated continuous cross-count JSON. Continuous values can't be obfuscated directly in their - * raw form (one entry per distinct numeric value gives too many cells with small counts), so we first bin them - * via the visualization resource — when a visualization service is configured — and obfuscate the binned counts. - * Without a configured visualization service we obfuscate the raw per-value counts as a fallback. - * - * Either way, every value in the returned map is obfuscated through {@link #obfuscateCrossCount}: counts below - * the threshold collapse to {@code "< threshold"}, larger counts get variance-randomized. Returns null only when - * the upstream produced no data or when {@link #canShowContinuousCrossCounts} signals the cohort is too small - * to safely render. - * - * @param continuousCrossCountResponse The continuous cross count response - * @param crossCountResponse The cross count response - * @param queryRequest The original query request - * @return String The obfuscated continuous cross count JSON, or null if not safe / nothing to return - * @throws IOException If there is an error processing the JSON - */ - protected String processContinuousCrossCounts(String continuousCrossCountResponse, String crossCountResponse, QueryRequest queryRequest) - throws IOException { - logger.info("Processing continuous cross counts"); - - if (continuousCrossCountResponse == null || crossCountResponse == null) { - return null; - } - - Map crossCounts = objectMapper.readValue(crossCountResponse, new TypeReference<>() {}); - int generatedVariance = this.generateVarianceWithCrossCounts(crossCounts); - - if (canShowContinuousCrossCounts(crossCounts)) { - return null; - } - - // Handle the case where there is no visualization service UUID - if (properties.getVisualizationResourceId() != null) { - Map> continuousCrossCounts = - objectMapper.readValue(continuousCrossCountResponse, new TypeReference<>() {}); - Map> binnedContinuousCrossCounts = - getBinnedContinuousCrossCount(queryRequest, continuousCrossCounts); - - // Log the binned continuous cross counts - logger.info("Binned continuous cross counts: {}", binnedContinuousCrossCounts); - - return objectMapper.writeValueAsString(obfuscateCrossCount(generatedVariance, binnedContinuousCrossCounts)); - } else { - Map> continuousCrossCounts = - objectMapper.readValue(continuousCrossCountResponse, new TypeReference<>() {}); - - return objectMapper.writeValueAsString(obfuscateCrossCount(generatedVariance, continuousCrossCounts)); - } - } - - private Map> getBinnedContinuousCrossCount( - QueryRequest queryRequest, Map> continuousCrossCounts - ) throws IOException { - // Create Query for Visualization /bin/continuous - QueryRequest visualizationBinRequest = new GeneralQueryRequest(); - visualizationBinRequest.setResourceUUID(properties.getVisualizationResourceId()); - visualizationBinRequest.setQuery(continuousCrossCounts); - visualizationBinRequest.setResourceCredentials(queryRequest.getResourceCredentials()); - - Resource visResource = resourceRepository.getById(visualizationBinRequest.getResourceUUID()); - if (visResource == null) { - throw new ApplicationException("Visualization resource could not be found"); - } - - // call the binning endpoint - HttpResponse httpResponse = getHttpResponse( - visualizationBinRequest, visualizationBinRequest.getResourceUUID(), "/bin/continuous", visResource.getResourceRSPath() - ); - HttpEntity entity = httpResponse.getEntity(); - String binResponse = EntityUtils.toString(entity, "UTF-8"); - - return objectMapper.readValue(binResponse, new TypeReference>>() {}); - } - - /** - * This method handles the processing of categorical cross counts. It begins by determining whether the cross counts require - * obfuscation. This is accomplished by checking if any of the CROSS_COUNTS must be obfuscated. If obfuscation is required, the - * categorical cross counts will be obfuscated accordingly. Otherwise, if no obfuscation is needed, the method can simply return the - * categorical entity string. - * - * @param categoricalEntityString The categorical entity string - * @param crossCountEntityString The cross count entity string - * @return String The processed categorical entity string - * @throws JsonProcessingException If there is an error processing the JSON - */ - protected String processCategoricalCrossCounts(String categoricalEntityString, String crossCountEntityString) - throws JsonProcessingException { - logger.info("Processing categorical cross counts"); - - if (categoricalEntityString == null || crossCountEntityString == null) { - return null; - } - - Map crossCounts = objectMapper.readValue(crossCountEntityString, new TypeReference<>() {}); - int generatedVariance = this.generateVarianceWithCrossCounts(crossCounts); - - Map> categoricalCrossCount = objectMapper.readValue(categoricalEntityString, new TypeReference<>() {}); - - if (categoricalCrossCount == null) { - logger.info("Categorical cross count is null. Returning categoricalEntityString: {}", categoricalEntityString); - return categoricalEntityString; - } - - // We have not obfuscated yet. We first process the data. - processResults(categoricalCrossCount); - - // Now we need to obfuscate our return data. The only consideration is do we apply < threshold or variance - return objectMapper.writeValueAsString(obfuscateCrossCount(generatedVariance, categoricalCrossCount)); - } - - private static void processResults(Map> categoricalCrossCount) { - for (Map.Entry> entry : categoricalCrossCount.entrySet()) { - // skipKey is expecting an entrySet, so we need to convert the axisMap to an entrySet - if (VisualizationUtil.skipKey(entry.getKey())) continue; - Map axisMap = VisualizationUtil.processResults(entry.getValue()); - categoricalCrossCount.put(entry.getKey(), axisMap); - } - } - - /** - * Obfuscates every value in a cross-count map. Returns a freshly constructed map keyed identically to the - * input but with values replaced by either a threshold-floor obfuscation (for counts below the threshold) - * or a variance-randomized one. - * - * @param generatedVariance The variance for the request - * @param crossCount The cross count to obfuscate; values are JSON-deserialized so may be Integer or String - */ - private Map> obfuscateCrossCount( - int generatedVariance, Map> crossCount - ) { - Map> result = new LinkedHashMap<>(); - crossCount.forEach((key, value) -> { - Map obfuscated = new LinkedHashMap<>(); - value.forEach((innerKey, innerValue) -> { - int count = toInt(innerValue); - obfuscated.put( - innerKey, - applyThresholdFloor(count).orElseGet(() -> randomize(count, generatedVariance)) - ); - }); - result.put(key, obfuscated); - }); - return result; - } - - /** - * Jackson hands us {@code Object}-typed values from JSON; the runtime type depends on the number's magnitude - * (Integer, Long, Double, BigInteger, ...) and on whether the upstream stringified it. Accept anything that - * represents an integral count and narrow to int. The previous shape ({@code innerValue.toString()} into - * {@link Integer#parseInt}) silently accepted Long/Double for free; preserve that breadth via {@link Number}. - */ - static int toInt(Object value) { - if (value instanceof Number) return ((Number) value).intValue(); - if (value instanceof String) return Integer.parseInt((String) value); - throw new IllegalArgumentException("Cross-count value was neither Number nor numeric String: " + value); - } - - - private boolean canShowContinuousCrossCounts(Map crossCounts) { - String lessThanThresholdStr = "< " + this.threshold; - - String v = crossCounts.get("\\_studies_consents\\"); - if (v.contains(lessThanThresholdStr) || v.equals("0")) { - return true; - } - return false; - } - - /** - * This method will generate a random variance for the request based on the passed entityString. The variance will be between -variance - * and +variance. The variance will be generated by adding a random salt to the entityString and then taking the hashcode of the result. - * The variance will be the hashcode mod the variance * 2 + 1 - variance. - * - * @return int The variance for the request - */ - private QueryRequest createChainRequest(QueryRequest queryRequest) { - QueryRequest chainRequest = new GeneralQueryRequest(); - chainRequest.setQuery(queryRequest.getQuery()); - chainRequest.setResourceCredentials(queryRequest.getResourceCredentials()); - - if (properties.getTargetResourceId() != null && !properties.getTargetResourceId().isEmpty()) { - chainRequest.setResourceUUID(UUID.fromString(properties.getTargetResourceId())); - } else { - chainRequest.setResourceUUID(queryRequest.getResourceUUID()); - } - return chainRequest; - } - - private static void checkQuery(QueryRequest searchRequest) { - if (searchRequest == null || searchRequest.getQuery() == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - } - - private int generateRequestVariance(String entityString) { - return Math.abs((entityString + randomSalt).hashCode()) % (variance * 2 + 1) - variance; - } - - ObfuscatedCount randomize(int crossCount, int requestVariance) { - int randomized = Math.max(crossCount + requestVariance, threshold); - return new ObfuscatedCount(randomized, randomized + " \u00B1" + variance, variance); - } - - /** - * Core privacy floor: small (potentially identifiable) cohorts get hidden behind a "< threshold" display. - * The value is encoded as count 0 with variance threshold-1, so consumers rendering the uncertainty band - * [max(0, count - variance), count + variance] draw 0..threshold-1 — the true count lies somewhere in that - * band but we don't disclose where. - * - * Returns empty when the value is at or above the threshold (caller should then call {@link #randomize}). - */ - Optional applyThresholdFloor(int actualCount) { - if (actualCount < threshold) { - return Optional.of(new ObfuscatedCount(0, "< " + threshold, threshold - 1)); - } - return Optional.empty(); - } - - /** - * String overload for callers (COUNT / CROSS_COUNT) that hold the value as a JSON string. Logs and returns - * empty on parse failure so the caller can fall through to its untouched-value path. - */ - Optional applyThresholdFloor(String actualCount) { - try { - return applyThresholdFloor(Integer.parseInt(actualCount)); - } catch (NumberFormatException nfe) { - logger.warn("Count was not a number! " + actualCount); - return Optional.empty(); - } - } -} diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/ApplicationProperties.java b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/ApplicationProperties.java deleted file mode 100644 index 62a44e63d..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/ApplicationProperties.java +++ /dev/null @@ -1,116 +0,0 @@ -package edu.harvard.hms.dbmi.avillach; - -import java.io.IOException; -import java.io.Serializable; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.Optional; -import java.util.Properties; -import java.util.UUID; - -import javax.enterprise.context.ApplicationScoped; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.exception.PicsureQueryException; - -@ApplicationScoped -public class ApplicationProperties implements Serializable { - - private String contextPath; - private String targetPicsureUrl; - private String targetResourceId; - private String targetPicsureToken; - private int targetPicsureObfuscationThreshold; - private int targetPicsureObfuscationVariance; - private String targetPicsureObfuscationSalt; - private UUID visualizationResourceId; - - public static final int DEFAULT_OBFUSCATION_THRESHOLD = 10; - public static final int DEFAULT_OBFUSCATION_VARIANCE = 3; - - private Logger logger = LoggerFactory.getLogger(this.getClass()); - - public String getContextPath() { - return contextPath; - } - - public String getTargetPicsureUrl() { - return targetPicsureUrl; - } - - public String getTargetResourceId() { - return targetResourceId; - } - - public String getTargetPicsureToken() { - return targetPicsureToken; - } - - public int getTargetPicsureObfuscationThreshold() { - return targetPicsureObfuscationThreshold; - } - - public int getTargetPicsureObfuscationVariance() { - return targetPicsureObfuscationVariance; - } - - public String getTargetPicsureObfuscationSalt() { - return targetPicsureObfuscationSalt; - } - - public UUID getVisualizationResourceId() { - return visualizationResourceId; - } - - public void init(String contextPath) { - logger.info("initializing aggregate Resource properties"); - - this.contextPath = contextPath; - - Path configFile = Path.of(System.getProperty("jboss.server.config.dir"), "aggregate-data-sharing", contextPath, "resource.properties"); - Properties properties = null; - try { - properties = new Properties(); - properties.load(Files.newInputStream(configFile)); - } catch (IOException e) { - throw new ApplicationException("Error while reading resource properties file: " + configFile, e); - } - - targetPicsureUrl = properties.getProperty("target.picsure.url"); - if (targetPicsureUrl == null) { - throw new PicsureQueryException("target.picsure.url property must be set."); - } - - //target resource ID can be empty - targetResourceId = properties.getProperty("target.resource.id"); - if (targetResourceId == null) - targetResourceId = ""; - - targetPicsureToken = properties.getProperty("target.picsure.token"); - if (targetPicsureToken == null) { - throw new PicsureQueryException("target.picsure.token property must be set."); - } - - String visualizationResourceUUIDAsString = properties.getProperty("visualization.resource.id"); - if (visualizationResourceUUIDAsString != null && !visualizationResourceUUIDAsString.trim().isEmpty()) { - visualizationResourceId = UUID.fromString(visualizationResourceUUIDAsString); - logger.debug("visualizationResourceId: " + visualizationResourceId); - if (visualizationResourceId == null) - throw new PicsureQueryException("visualization.resource.id property must be set."); - } - - targetPicsureObfuscationThreshold = Optional.ofNullable(properties.getProperty("target.picsure.obfuscation_threshold")) - .map(Integer::parseInt) - .orElse(DEFAULT_OBFUSCATION_THRESHOLD); - - targetPicsureObfuscationVariance = Optional.ofNullable(properties.getProperty("target.picsure.obfuscation_variance")) - .map(Integer::parseInt) - .orElse(DEFAULT_OBFUSCATION_VARIANCE); - - targetPicsureObfuscationSalt = Optional.ofNullable(properties.getProperty("target.picsure.obfuscation_salt")) - .orElseGet(() -> UUID.randomUUID().toString()); - } -} diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/JAXRSConfiguration.java b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/JAXRSConfiguration.java deleted file mode 100755 index 0ca5c290c..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/JAXRSConfiguration.java +++ /dev/null @@ -1,29 +0,0 @@ -package edu.harvard.hms.dbmi.avillach; - -import javax.inject.Inject; -import javax.servlet.ServletContext; -import javax.servlet.ServletContextEvent; -import javax.servlet.ServletContextListener; -import javax.servlet.annotation.WebListener; -import javax.ws.rs.ApplicationPath; -import javax.ws.rs.core.Application; - -@ApplicationPath("pic-sure") -@WebListener -public class JAXRSConfiguration extends Application implements ServletContextListener { - - @Inject - private ApplicationProperties applicationProperties; - - @Override - public void contextInitialized(ServletContextEvent event) { - ServletContext servletContext = event.getServletContext(); - applicationProperties.init(servletContext.getContextPath()); - servletContext.setInitParameter("resteasy.resources", "org.jboss.resteasy.plugins.stats.RegistryStatsResource"); - } - - @Override - public void contextDestroyed(ServletContextEvent event) { - // NOOP. - } -} diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/LoggingClientProducer.java b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/LoggingClientProducer.java deleted file mode 100644 index ba207b20f..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/LoggingClientProducer.java +++ /dev/null @@ -1,58 +0,0 @@ -package edu.harvard.hms.dbmi.avillach; - -import edu.harvard.dbmi.avillach.logging.LoggingClient; -import edu.harvard.dbmi.avillach.logging.LoggingClientConfig; - -import javax.annotation.PreDestroy; -import javax.enterprise.context.ApplicationScoped; -import javax.enterprise.inject.Produces; -import javax.naming.InitialContext; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -@ApplicationScoped -public class LoggingClientProducer { - - private static final Logger LOG = LoggerFactory.getLogger(LoggingClientProducer.class); - - private LoggingClient loggingClient; - - @Produces - @ApplicationScoped - public LoggingClient loggingClient() { - String url = jndiLookup("java:global/logging_service_url"); - String key = jndiLookup("java:global/logging_api_key"); - - if (!isConfigured(url) || !isConfigured(key)) { - LOG.info("logging-client: JNDI bindings not set; audit logging disabled"); - loggingClient = LoggingClient.noOp(); - } else { - LOG.info("logging-client: configured for {} (clientType=aggregate-data-sharing)", url); - loggingClient = new LoggingClient(LoggingClientConfig.builder(url, key).clientType("aggregate-data-sharing").build()); - } - return loggingClient; - } - - @PreDestroy - public void cleanup() { - try { - if (loggingClient != null) { - loggingClient.close(); - } - } catch (Exception ignored) { - } - } - - private static boolean isConfigured(String value) { - return value != null && !value.trim().isEmpty() && !"disabled".equalsIgnoreCase(value.trim()); - } - - private static String jndiLookup(String name) { - try { - return (String) new InitialContext().lookup(name); - } catch (Exception e) { - return null; - } - } -} diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/ObfuscatedCount.java b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/ObfuscatedCount.java deleted file mode 100644 index 57492be1e..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/ObfuscatedCount.java +++ /dev/null @@ -1,72 +0,0 @@ -package edu.harvard.hms.dbmi.avillach; - -import java.util.Objects; - -import com.fasterxml.jackson.annotation.JsonCreator; -import com.fasterxml.jackson.annotation.JsonProperty; - -public final class ObfuscatedCount { - - @JsonProperty("count") - private final int count; - - @JsonProperty("display") - private final String display; - - /** - * Half-width of the uncertainty band around {@link #count}, or null when the value is exact - * (authorized path). Consumers render the band as [max(0, count - variance), count + variance]. - */ - @JsonProperty("variance") - private final Integer variance; - - @JsonCreator - public ObfuscatedCount( - @JsonProperty("count") int count, - @JsonProperty("display") String display, - @JsonProperty("variance") Integer variance - ) { - this.count = count; - this.display = display; - this.variance = variance; - } - - /** - * Wraps a plain (non-obfuscated) integer count. The display is just the - * stringified number; this is the right factory for the authorized path - * where no threshold floor or variance applies. - */ - public static ObfuscatedCount ofInt(int count) { - return new ObfuscatedCount(count, Integer.toString(count), null); - } - - public int count() { - return count; - } - - public String display() { - return display; - } - - public Integer variance() { - return variance; - } - - @Override - public boolean equals(Object other) { - if (this == other) return true; - if (!(other instanceof ObfuscatedCount)) return false; - ObfuscatedCount that = (ObfuscatedCount) other; - return count == that.count && Objects.equals(display, that.display) && Objects.equals(variance, that.variance); - } - - @Override - public int hashCode() { - return Objects.hash(count, display, variance); - } - - @Override - public String toString() { - return "ObfuscatedCount{count=" + count + ", display='" + display + "', variance=" + variance + "}"; - } -} diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/service/HeaderFilter.java b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/service/HeaderFilter.java deleted file mode 100644 index f3f328e96..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/service/HeaderFilter.java +++ /dev/null @@ -1,30 +0,0 @@ -package edu.harvard.hms.dbmi.avillach.service; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.annotation.Priority; -import javax.inject.Inject; -import javax.ws.rs.container.ContainerRequestContext; -import javax.ws.rs.container.ContainerRequestFilter; -import javax.ws.rs.core.MultivaluedMap; -import javax.ws.rs.ext.Provider; - -@Provider -@Priority(1) -public class HeaderFilter implements ContainerRequestFilter { - - @Inject - private RequestScopedHeader headers; - - private final Logger logger = LoggerFactory.getLogger(HeaderFilter.class); - - @Override - public void filter(ContainerRequestContext containerRequestContext) { - if (containerRequestContext.getUriInfo().getPath().startsWith("/aggregate-data-sharing")) { - logger.info("HeaderFilter called for path: /aggregate-data-sharing with headers: " + containerRequestContext.getHeaders().toString()); - MultivaluedMap httpHeaders = containerRequestContext.getHeaders(); - headers.setHeaders(httpHeaders); - } - } -} diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/service/RequestScopedHeader.java b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/service/RequestScopedHeader.java deleted file mode 100644 index 4ffdc2412..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/service/RequestScopedHeader.java +++ /dev/null @@ -1,19 +0,0 @@ -package edu.harvard.hms.dbmi.avillach.service; - -import javax.enterprise.context.RequestScoped; -import javax.ws.rs.core.MultivaluedMap; - -@RequestScoped -public class RequestScopedHeader { - - private MultivaluedMap headers; - - public void setHeaders(MultivaluedMap headers) { - this.headers = headers; - } - - public MultivaluedMap getHeaders() { - return headers; - } - -} diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/resources/META-INF/persistence.xml b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/resources/META-INF/persistence.xml deleted file mode 100644 index 12c75db55..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/resources/META-INF/persistence.xml +++ /dev/null @@ -1,23 +0,0 @@ - - - - java:jboss/datasources/PicsureDS - edu.harvard.dbmi.avillach.data.entity.User - edu.harvard.dbmi.avillach.data.entity.Query - edu.harvard.dbmi.avillach.data.entity.Resource - - - - - - - - - - diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/resources/webapp/META-INF/context.xml b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/resources/webapp/META-INF/context.xml deleted file mode 100755 index 9f4aa7fd7..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/resources/webapp/META-INF/context.xml +++ /dev/null @@ -1,3 +0,0 @@ - - - diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/resources/webapp/WEB-INF/beans.xml b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/resources/webapp/WEB-INF/beans.xml deleted file mode 100755 index bbd93e527..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/resources/webapp/WEB-INF/beans.xml +++ /dev/null @@ -1,2 +0,0 @@ - - diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/java/edu/harvard/hms/dbmi/avillach/AggregateDataSharingResourceRSAcceptanceTests.java b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/java/edu/harvard/hms/dbmi/avillach/AggregateDataSharingResourceRSAcceptanceTests.java deleted file mode 100644 index 3114d6826..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/java/edu/harvard/hms/dbmi/avillach/AggregateDataSharingResourceRSAcceptanceTests.java +++ /dev/null @@ -1,422 +0,0 @@ -package edu.harvard.hms.dbmi.avillach; - -import edu.harvard.dbmi.avillach.domain.QueryStatus; -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; -import edu.harvard.dbmi.avillach.util.exception.ResourceInterfaceException; -import org.glassfish.jersey.message.internal.OutboundJaxrsResponse; -import org.glassfish.jersey.message.internal.OutboundMessageContext; -import org.junit.Before; -import org.junit.Rule; -import org.junit.Test; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.JsonMappingException; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.github.tomakehurst.wiremock.junit.WireMockClassRule; - -import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest; - -import static com.github.tomakehurst.wiremock.client.WireMock.*; -import static org.junit.Assert.*; -import static org.mockito.Mockito.*; - -import java.io.IOException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.Map; -import java.util.UUID; -import java.util.regex.Matcher; -import java.util.regex.Pattern; - -import javax.ws.rs.core.Response; - -import org.apache.commons.codec.Charsets; -import org.apache.commons.io.IOUtils; - -/* - * Note: All json is in /src/main/resources, see the convenience methods at the bottom of the class. - * - * - */ -public class AggregateDataSharingResourceRSAcceptanceTests { - - private ObjectMapper mapper = new ObjectMapper(); - - private Pattern obfuscatedResultPattern = Pattern.compile("(\\d+) \\u00B13"); - - private ApplicationProperties mockProperties; - - private AggregateDataSharingResourceRS subject; - private AggregateDataSharingResourceRSV3 subjectV3; - - // Pick a random port between 20k and 52k - private final static int port = 40000; - private final static String testURL = "http://localhost:40000/"; - - @Rule - public WireMockClassRule wireMockRule = new WireMockClassRule(port); - - @Before - public void setup() throws IOException { - mockProperties = mock(ApplicationProperties.class); - when(mockProperties.getTargetResourceId()).thenReturn("f0317fa9-0945-4390-993a-840416e97d13"); - when(mockProperties.getTargetPicsureObfuscationThreshold()).thenReturn(10); - when(mockProperties.getTargetPicsureObfuscationVariance()).thenReturn(3); - when(mockProperties.getTargetPicsureObfuscationSalt()).thenReturn("abc123"); - when(mockProperties.getTargetPicsureUrl()).thenReturn(testURL); - when(mockProperties.getTargetPicsureToken()).thenReturn("This actually is not needed here, only for the proxy resource."); - subject = new AggregateDataSharingResourceRS(mockProperties); - subjectV3 = new AggregateDataSharingResourceRSV3(mockProperties); - - // Whenever the ADSRRS submits a search for "any" we return the contents of open_access_search_result.json - wireMockRule.stubFor( - post(urlEqualTo("/search")).withRequestBody(equalToJson("{\"query\":\"any\"}")) - .willReturn(aResponse().withStatus(200).withBody(getTestJson("open_access_search_result"))) - ); - - // Stub for study consents which is now called for every CROSS_COUNT query - wireMockRule.stubFor( - post(urlEqualTo("/search")) - .withRequestBody(matchingJsonPath("$.query", containing("_studies_consents"))) - .willReturn(aResponse().withStatus(200).withBody("{\"results\": {\"phenotypes\": {}}}")) - ); - - - } - - /** - * This is just a test to make sure equalToJson(...).match(...).isExactMatch() handles reordered JSON - * @throws IOException - * @throws JsonProcessingException - * @throws JsonMappingException - */ - @Test - public void testTest() throws JsonMappingException, JsonProcessingException, IOException { - assertTrue(equalToJson("{\"a\":100,\"b\":\"foo\"}").match("{\"b\":\"foo\",\"a\":100}").isExactMatch()); - } - - @Test - public void testNoObfuscationOnLargeCounts() throws IOException { - expect_original_result_to_become_obfuscated_result( - "large_open_access_cross_count_result", "large_open_access_cross_count_obfuscated_result" - ); - } - - @Test - public void testZeroNotObfuscated() throws IOException { - expect_original_result_to_become_obfuscated_result( - "all_zero_open_access_cross_count_result", "obfuscated_all_less_ten_open_access_cross_count_result" - ); - } - - @Test - public void testTenNotObfuscated() throws IOException { - expect_original_result_to_become_obfuscated_result( - "all_ten_open_access_cross_count_result", "all_ten_open_access_cross_count_obfuscated_result" - ); - } - - @Test - public void testOneThroughNineObfuscated() throws IOException { - expect_original_result_to_become_obfuscated_result( - "all_less_ten_open_access_cross_count_result", "obfuscated_all_less_ten_open_access_cross_count_result" - ); - } - - @Test - public void testSingleObfuscationPropagated() throws IOException { - expect_original_result_to_become_obfuscated_result( - "one_obfuscated_open_access_cross_count_result", "one_obfuscated_open_access_cross_count_obfuscated_result" - ); - } - - @Test - public void testMultipleObfuscationPropagated() throws IOException { - expect_original_result_to_become_obfuscated_result( - "two_obfuscated_open_access_cross_count_result", "two_obfuscated_open_access_cross_count_obfuscated_result" - ); - } - - @Test - public void testMiddleLessTenObfuscationPropagated() throws IOException { - expect_original_result_to_become_obfuscated_result( - "middle_less_ten_obfuscated_open_access_cross_count_result", - "middle_less_ten_obfuscated_open_access_cross_count_obfuscated_result" - ); - } - - @Test - public void testObfuscationDoesntChangeWithoutChangeInQuery() throws IOException { - String obfuscated_1 = getObfuscatedResponseForResult("one_obfuscated_open_access_cross_count_result"); - String obfuscated_2 = getObfuscatedResponseForResult("one_obfuscated_open_access_cross_count_result"); - assertTrue(equalToJson(obfuscated_1).match(obfuscated_2).isExactMatch()); - } - - - @Test - public void testSingleObfuscationPropagatedUnsortedResponse() throws IOException { - expect_original_result_to_become_obfuscated_result( - "one_obfuscated_open_access_cross_count_unsorted_result", "one_obfuscated_open_access_cross_count_unsorted_obfuscated_result" - ); - } - - @Test - public void testMinimumThreshold() throws IOException { - String obfuscated = getObfuscatedResponseForResult("test_minimum_threshold"); - Map result = mapper.readValue(obfuscated, Map.class); - - String allDResult = (String) result.remove("\\all\\d\\"); - int numericResult = getObfuscatedNumericResult(allDResult); - assertTrue(numericResult >= 10); - } - - private GeneralQueryRequest getTestQuery() throws JsonProcessingException, JsonMappingException, IOException { - return mapper.readValue(getTestJson("test_cross_count_query"), GeneralQueryRequest.class); - } - - private String getTestJson(String json_file_name) throws IOException { - return IOUtils.toString(this.getClass().getClassLoader().getResourceAsStream(json_file_name + ".json"), Charsets.UTF_8); - } - - private int getObfuscatedNumericResult(String allC2Result) { - Matcher matcher = obfuscatedResultPattern.matcher(allC2Result); - matcher.find(); - return Integer.parseInt(matcher.group(1)); - } - - private void expect_original_result_to_become_obfuscated_result(String originalResult, String obfuscatedResult) throws IOException { - String responseJson = getObfuscatedResponseForResult(originalResult); - String expectedJson = getTestJson(obfuscatedResult); - assertTrue(equalToJson(responseJson).match(expectedJson).isExactMatch()); - } - - private String getObfuscatedResponseForResult(String originalResult) throws JsonProcessingException, JsonMappingException, IOException { - GeneralQueryRequest requestMatcher = getTestQuery(); - // Since we stub /search to return empty consents in setup(), the query sent to /query/sync will have empty crossCountFields - Map queryMap = (Map) requestMatcher.getQuery(); - queryMap.put("crossCountFields", new ArrayList<>()); - requestMatcher.setQuery(queryMap); - - wireMockRule.stubFor( - post(urlEqualTo("/query/sync")).withRequestBody(equalToJson(mapper.writeValueAsString(requestMatcher))) - .withHeader("Authorization", equalTo("Bearer This actually is not needed here, only for the proxy resource.")) - .willReturn(aResponse().withStatus(200).withBody(getTestJson(originalResult))) - ); - - Response response = subject.querySync(getTestQuery()); - Response response2 = subject.querySync(getTestQuery()); - // TODO: This is what should be sent - // Response response = objectUnderTest.querySync(mapper.readValue(getObfuscatedTestQueryJson(), QueryRequest.class)); - - String responseJson = (String) response.getEntity(); - String responseJson2 = (String) response.getEntity(); - assertEquals(responseJson, responseJson2); - return responseJson; - } - - @Test - public void shouldPostQuery() { - UUID targetResourceId = UUID.fromString(mockProperties.getTargetResourceId()); - Map query = new HashMap<>(); - query.put("q", "I seek the holy grail."); - query.put("expectedResultType", "COUNT"); - GeneralQueryRequest originalRequest = createRequest(query, Map.of("name", "Sir Lancelot"), UUID.randomUUID()); - GeneralQueryRequest postedRequest = createRequest(query, Map.of("name", "Sir Lancelot"), targetResourceId); - - QueryStatus expectedResponse = new QueryStatus(); - expectedResponse.setResourceID(targetResourceId); - - ProxyPostEndpointMocker.start(wireMockRule).withPath("/query").withRequestBody(postedRequest).withResponseBody(expectedResponse) - .withStatusCode(201).commit(); - - QueryStatus actual = subject.query(originalRequest); - - // equality isn't defined for QueryRequest, and I'm scared to define it, so let's - // just compare resource IDs - assertEquals(expectedResponse.getResourceID(), actual.getResourceID()); - } - - @Test - public void shouldPostQueryStatus() { - UUID targetResourceId = UUID.fromString(mockProperties.getTargetResourceId()); - Map query = new HashMap<>(); - query.put("q", "I seek the holy grail."); - query.put("expectedResultType", "COUNT"); - GeneralQueryRequest originalRequest = createRequest(query, Map.of("name", "King Arthur"), UUID.randomUUID()); - GeneralQueryRequest postedRequest = createRequest(query, Map.of("name", "King Arthur"), targetResourceId); - - QueryStatus expectedResponse = new QueryStatus(); - expectedResponse.setResourceID(targetResourceId); - - UUID randomUUID = UUID.randomUUID(); - String requestUUID = randomUUID.toString(); - - ProxyPostEndpointMocker.start(wireMockRule).withPath("/query/" + requestUUID + "/status").withRequestBody(postedRequest) - .withResponseBody(expectedResponse).withStatusCode(200).commit(); - - QueryStatus actual = subject.queryStatus(randomUUID, originalRequest); - - // equality isn't defined for QueryRequest, and I'm scared to define it, so let's - // just compare resource IDs - assertEquals(expectedResponse.getResourceID(), actual.getResourceID()); - } - - @Test - public void shouldPostQueryResult() { - UUID targetResourceId = UUID.fromString(mockProperties.getTargetResourceId()); - Map query = new HashMap<>(); - query.put("q", "I seek the holy grail."); - query.put("expectedResultType", "COUNT"); - GeneralQueryRequest originalRequest = createRequest(query, Map.of("name", "King Arthur"), UUID.randomUUID()); - GeneralQueryRequest postedRequest = createRequest(query, Map.of("name", "King Arthur"), targetResourceId); - - Response expectedResponse = new OutboundJaxrsResponse(Response.Status.OK, new OutboundMessageContext()); - - UUID randomUUID = UUID.randomUUID(); - String requestUUID = randomUUID.toString(); - - ProxyPostEndpointMocker.start(wireMockRule).withPath("/query/" + requestUUID + "/result").withRequestBody(postedRequest) - .withResponseBody(expectedResponse).withStatusCode(200).commit(); - - Response actual = subject.queryResult(randomUUID, originalRequest); - - assertEquals(expectedResponse.getStatus(), actual.getStatus()); - } - - @Test - public void shouldHandleErrorResponse() { - UUID targetResourceId = UUID.fromString(mockProperties.getTargetResourceId()); - Map query = new HashMap<>(); - query.put("q", "I seek the holy grail."); - query.put("expectedResultType", "COUNT"); - GeneralQueryRequest originalRequest = createRequest(query, Map.of("name", "Sir Lancelot"), UUID.randomUUID()); - GeneralQueryRequest postedRequest = createRequest(query, Map.of("name", "Sir Lancelot"), targetResourceId); - - QueryStatus expectedResponse = new QueryStatus(); - expectedResponse.setResourceID(targetResourceId); - - ProxyPostEndpointMocker.start(wireMockRule).withPath("/query").withRequestBody(postedRequest).withResponseBody(expectedResponse) - .withStatusCode(500).commit(); - - - ResourceInterfaceException exception = null; - - try { - subject.query(originalRequest); - } catch (ResourceInterfaceException ex) { - exception = ex; - } - - assertNotNull(exception); - } - - private static GeneralQueryRequest createRequest(Object query, Map credentials, UUID resourceUUID) { - GeneralQueryRequest originalRequest = new GeneralQueryRequest(); - originalRequest.setQuery(query); - originalRequest.setResourceCredentials(credentials); - originalRequest.setResourceUUID(resourceUUID); - return originalRequest; - } - - @Test(expected = ProtocolException.class) - public void testMissingExpectedResultType() throws IOException { - GeneralQueryRequest request = getTestQuery(); - @SuppressWarnings("unchecked") - Map queryMap = (Map) request.getQuery(); - queryMap.remove("expectedResultType"); - request.setQuery(queryMap); - subject.querySync(request); - } - - @Test - public void testCrossCountQueryModifiesRequest() throws IOException { - // Mock /search for consents - // We need to escape backslashes for Java string literals and JSON - // JSON: "\\PHENO\\CONSENT1\\" -> Java String: "\"\\\\PHENO\\\\CONSENT1\\\\\"" - String consentResponseJson = "{\"results\": {\"phenotypes\": {\"\\\\PHENO\\\\CONSENT1\\\\\": {}, \"\\\\PHENO\\\\CONSENT2\\\\\": {}}}}"; - - wireMockRule.stubFor( - post(urlEqualTo("/search")) - .withRequestBody(matchingJsonPath("$.query", containing("_studies_consents"))) - .willReturn(aResponse().withStatus(200).withBody(consentResponseJson)) - ); - - // Mock /query/sync - wireMockRule.stubFor( - post(urlEqualTo("/query/sync")) - .willReturn(aResponse().withStatus(200).withBody("{}")) - ); - - GeneralQueryRequest request = getTestQuery(); - @SuppressWarnings("unchecked") - Map queryMap = (Map) request.getQuery(); - queryMap.put("expectedResultType", "CROSS_COUNT"); - // We don't care about existing crossCountFields as they will be overwritten - request.setQuery(queryMap); - - subject.querySync(request); - - // Verify /query/sync called with modified body - verify(postRequestedFor(urlEqualTo("/query/sync")) - .withRequestBody(matchingJsonPath("$.query.crossCountFields", containing("CONSENT1"))) - .withRequestBody(matchingJsonPath("$.query.crossCountFields", containing("CONSENT2"))) - .withRequestBody(matchingJsonPath("$.query.expectedResultType", equalTo("CROSS_COUNT"))) - ); - } - - @Test - public void testCrossCountQueryModifiesRequestV3() throws IOException { - // Mock /search for consents - String consentResponseJson = "{\"results\": {\"phenotypes\": {\"\\\\PHENO\\\\CONSENT1\\\\\": {}, \"\\\\PHENO\\\\CONSENT2\\\\\": {}}}}"; - - wireMockRule.stubFor( - post(urlEqualTo("/search")) - .withRequestBody(matchingJsonPath("$.query", containing("_studies_consents"))) - .willReturn(aResponse().withStatus(200).withBody(consentResponseJson)) - ); - - // Mock /v3/query/sync (V3 appends /v3 prefix to path in getHttpResponse) - wireMockRule.stubFor( - post(urlEqualTo("/v3/query/sync")) - .willReturn(aResponse().withStatus(200).withBody("{}")) - ); - - GeneralQueryRequest request = getTestQuery(); - @SuppressWarnings("unchecked") - Map queryMap = (Map) request.getQuery(); - queryMap.put("expectedResultType", "CROSS_COUNT"); - request.setQuery(queryMap); - - subjectV3.querySync(request); - - // Verify /v3/query/sync called with modified body using "select" - verify(postRequestedFor(urlEqualTo("/v3/query/sync")) - .withRequestBody(matchingJsonPath("$.query.select", containing("CONSENT1"))) - .withRequestBody(matchingJsonPath("$.query.select", containing("CONSENT2"))) - .withRequestBody(matchingJsonPath("$.query.expectedResultType", equalTo("CROSS_COUNT"))) - ); - } - - @Test - public void testOtherQueryTypeDoesNotModifyRequest() throws IOException { - wireMockRule.stubFor( - post(urlEqualTo("/query/sync")) - .willReturn(aResponse().withStatus(200).withBody("100")) - ); - - GeneralQueryRequest request = getTestQuery(); - @SuppressWarnings("unchecked") - Map queryMap = (Map) request.getQuery(); - queryMap.put("expectedResultType", "COUNT"); - queryMap.remove("crossCountFields"); - request.setQuery(queryMap); - - subject.querySync(request); - - verify(postRequestedFor(urlEqualTo("/query/sync")) - .withRequestBody(matchingJsonPath("$.query.expectedResultType", equalTo("COUNT"))) - .withRequestBody(notMatching(".*crossCountFields.*")) - ); - } - -} diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/java/edu/harvard/hms/dbmi/avillach/ObfuscatedCountShapeTest.java b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/java/edu/harvard/hms/dbmi/avillach/ObfuscatedCountShapeTest.java deleted file mode 100644 index 074f2145d..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/java/edu/harvard/hms/dbmi/avillach/ObfuscatedCountShapeTest.java +++ /dev/null @@ -1,160 +0,0 @@ -package edu.harvard.hms.dbmi.avillach; - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertTrue; -import static org.mockito.Mockito.mock; -import static org.mockito.Mockito.when; - -import java.util.Optional; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; - -import org.junit.Before; -import org.junit.Test; - -/** - * Verifies that the obfuscation methods produce the rich {count, display} shape - * required by the visualization-resource for Plotly-compatible chart values. - * - * Exercises both V1 and V3 implementations since they carry parallel copies. - */ -public class ObfuscatedCountShapeTest { - - private AggregateDataSharingResourceRS subject; - private AggregateDataSharingResourceRSV3 subjectV3; - - @Before - public void setup() { - ApplicationProperties props = mock(ApplicationProperties.class); - when(props.getTargetPicsureObfuscationThreshold()).thenReturn(10); - when(props.getTargetPicsureObfuscationVariance()).thenReturn(3); - when(props.getTargetPicsureObfuscationSalt()).thenReturn("salt-for-test"); - subject = new AggregateDataSharingResourceRS(props); - subjectV3 = new AggregateDataSharingResourceRSV3(props); - } - - @Test - public void applyThresholdFloor_belowThreshold_returnsZeroCountWithThresholdBandAndLessThanDisplay() { - Optional result = subject.applyThresholdFloor(3); - - assertTrue("Below-threshold counts must be obfuscated", result.isPresent()); - assertEquals(0, result.get().count()); - assertEquals("< 10", result.get().display()); - assertEquals("Band [max(0, 0-9), 0+9] renders 0..threshold-1", Integer.valueOf(9), result.get().variance()); - } - - @Test - public void applyThresholdFloor_zero_returnsZeroCountWithThresholdBandAndLessThanDisplay() { - Optional result = subject.applyThresholdFloor(0); - - assertTrue("Zero is treated as below-threshold (privacy floor)", result.isPresent()); - assertEquals(0, result.get().count()); - assertEquals("< 10", result.get().display()); - assertEquals(Integer.valueOf(9), result.get().variance()); - } - - @Test - public void applyThresholdFloor_atOrAboveThreshold_returnsEmpty() { - assertTrue(subject.applyThresholdFloor(10).isEmpty()); - assertTrue(subject.applyThresholdFloor(999).isEmpty()); - } - - @Test - public void applyThresholdFloor_stringOverload_nonNumeric_returnsEmpty() { - assertTrue(subject.applyThresholdFloor("not-a-number").isEmpty()); - } - - @Test - public void randomize_appliesVariance_returnsNumericDisplayAndVariance() { - ObfuscatedCount result = subject.randomize(100, 2); - - assertEquals("count must be the numeric obfuscated value", 102, result.count()); - assertEquals("display must carry the formatted variance string", "102 ±3", result.display()); - assertEquals("variance must carry the configured band half-width", Integer.valueOf(3), result.variance()); - } - - @Test - public void randomize_floorsAtThreshold_whenVarianceTakesItBelow() { - ObfuscatedCount result = subject.randomize(10, -5); - - assertEquals("Floored at threshold so the numeric stays >= threshold", 10, result.count()); - assertEquals("10 ±3", result.display()); - assertEquals(Integer.valueOf(3), result.variance()); - } - - @Test - public void v3_applyThresholdFloor_belowThreshold_sameContract() { - Optional result = subjectV3.applyThresholdFloor(5); - - assertTrue(result.isPresent()); - assertEquals(0, result.get().count()); - assertEquals("< 10", result.get().display()); - assertEquals(Integer.valueOf(9), result.get().variance()); - } - - @Test - public void v3_randomize_sameContract() { - ObfuscatedCount result = subjectV3.randomize(200, 1); - - assertEquals(201, result.count()); - assertEquals("201 ±3", result.display()); - assertEquals(Integer.valueOf(3), result.variance()); - } - - @Test - public void toInt_acceptsAllJacksonNumberRuntimeTypes() { - // Jackson deserializes JSON numbers into Integer when they fit, Long for larger magnitudes, Double when - // decimal. The previous innerValue.toString() shape silently accepted all of these via Integer.parseInt - // (well, except Double — which it would have crashed on anyway). The replacement must not narrow. - assertEquals(42, AggregateDataSharingResourceRS.toInt(Integer.valueOf(42))); - assertEquals(42, AggregateDataSharingResourceRS.toInt(Long.valueOf(42L))); - assertEquals(42, AggregateDataSharingResourceRS.toInt(Double.valueOf(42.0))); - assertEquals(42, AggregateDataSharingResourceRS.toInt(Short.valueOf((short) 42))); - assertEquals(42, AggregateDataSharingResourceRS.toInt("42")); - } - - @Test - public void ofInt_factory_producesStringifiedDisplayAndNullVariance() { - ObfuscatedCount result = ObfuscatedCount.ofInt(45000); - - assertEquals(45000, result.count()); - assertEquals("45000", result.display()); - assertEquals("Exact (authorized) values carry no uncertainty band", null, result.variance()); - } - - /** - * Pins the JSON wire shape that visualization-resource (and any other consumer) deserializes against. - * If field names ever drift (e.g. someone renames the record component), this test fails BEFORE the - * cross-repo contract silently breaks in production. - */ - @Test - public void jsonShape_serializesAsCountDisplayAndVarianceFields() throws JsonProcessingException { - ObjectMapper mapper = new ObjectMapper(); - ObfuscatedCount value = new ObfuscatedCount(222, "222 ±3", 3); - - String json = mapper.writeValueAsString(value); - - // Exact-match assertion on serialized form. Field order is conventional for clarity but not load-bearing - // for consumers; we accept either ordering by JSON equality below. - assertEquals("{\"count\":222,\"display\":\"222 ±3\",\"variance\":3}", json); - - // Round-trip back through the mapper, asserting all fields survived. - ObfuscatedCount roundTripped = mapper.readValue(json, ObfuscatedCount.class); - assertEquals(value, roundTripped); - } - - /** - * Exact (authorized) values serialize variance as an explicit null, and below-threshold values pin - * the {count: 0, variance: threshold-1} encoding the frontend's band rule depends on. - */ - @Test - public void jsonShape_nullVarianceAndBelowThresholdEncoding() throws JsonProcessingException { - ObjectMapper mapper = new ObjectMapper(); - - assertEquals("{\"count\":45000,\"display\":\"45000\",\"variance\":null}", mapper.writeValueAsString(ObfuscatedCount.ofInt(45000))); - - ObfuscatedCount belowThreshold = subject.applyThresholdFloor(3).orElseThrow(IllegalStateException::new); - assertEquals("{\"count\":0,\"display\":\"< 10\",\"variance\":9}", mapper.writeValueAsString(belowThreshold)); - } -} diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/java/edu/harvard/hms/dbmi/avillach/ProxyPostEndpointMocker.java b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/java/edu/harvard/hms/dbmi/avillach/ProxyPostEndpointMocker.java deleted file mode 100644 index 256382d50..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/java/edu/harvard/hms/dbmi/avillach/ProxyPostEndpointMocker.java +++ /dev/null @@ -1,67 +0,0 @@ -package edu.harvard.hms.dbmi.avillach; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.github.tomakehurst.wiremock.client.WireMock; -import com.github.tomakehurst.wiremock.junit.WireMockClassRule; - -/** - * Prettier interface for mocking a http response. Only supports POST rn. - */ -public class ProxyPostEndpointMocker { - private WireMockClassRule rule; - - private String responseBody; - - private int status; - - private String requestBody; - - private String path; - - - public static ProxyPostEndpointMocker start(WireMockClassRule rule) { - ProxyPostEndpointMocker mock = new ProxyPostEndpointMocker(); - mock.rule = rule; - return mock; - } - - public ProxyPostEndpointMocker withPath(String path) { - this.path = path; - return this; - } - - public ProxyPostEndpointMocker withResponseBody(Object body) { - this.responseBody = toJsonString(body); - return this; - } - - public ProxyPostEndpointMocker withRequestBody(Object body) { - this.requestBody = toJsonString(body); - return this; - } - - public ProxyPostEndpointMocker withStatusCode(int status) { - this.status = status; - return this; - } - - public void commit() { - rule.stubFor(WireMock.post(WireMock.urlEqualTo(path)) - .withRequestBody(WireMock.equalToJson(requestBody)) - .willReturn(WireMock.aResponse() - .withStatus(status) - .withBody(responseBody) - ) - ); - } - - private String toJsonString(Object o) { - try { - return new ObjectMapper().writeValueAsString(o); - } catch (JsonProcessingException e) { - throw new RuntimeException(e); - } - } - -} diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/all_less_ten_open_access_cross_count_result.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/all_less_ten_open_access_cross_count_result.json deleted file mode 100644 index 0cbd4ecf2..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/all_less_ten_open_access_cross_count_result.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "\\all\\a\\": "3", - "\\all\\a\\1\\": "6", - "\\all\\b\\": "5", - "\\all\\b\\1\\": "2", - "\\all\\b\\2\\": "4", - "\\all\\c\\": "6", - "\\all\\c\\1\\": "3", - "\\all\\c\\2\\": "2", - "\\all\\c\\3\\": "1", - "\\all\\d\\": "8", - "\\all\\d\\1\\": "1", - "\\all\\d\\2\\": "2", - "\\all\\d\\3\\": "7", - "\\all\\d\\4\\": "6", - "\\all\\": "9" -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/all_ten_open_access_cross_count_obfuscated_result.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/all_ten_open_access_cross_count_obfuscated_result.json deleted file mode 100644 index b0fad4c8d..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/all_ten_open_access_cross_count_obfuscated_result.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "\\all\\a\\": "12 ±3", - "\\all\\a\\1\\": "12 ±3", - "\\all\\b\\": "12 ±3", - "\\all\\b\\1\\": "12 ±3", - "\\all\\b\\2\\": "12 ±3", - "\\all\\c\\": "12 ±3", - "\\all\\c\\1\\": "12 ±3", - "\\all\\c\\2\\": "12 ±3", - "\\all\\c\\3\\": "12 ±3", - "\\all\\d\\": "12 ±3", - "\\all\\d\\1\\": "12 ±3", - "\\all\\d\\2\\": "12 ±3", - "\\all\\d\\3\\": "12 ±3", - "\\all\\d\\4\\": "12 ±3", - "\\all\\": "12 ±3" -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/all_ten_open_access_cross_count_result.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/all_ten_open_access_cross_count_result.json deleted file mode 100644 index ca8bd2872..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/all_ten_open_access_cross_count_result.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "\\all\\a\\": "10", - "\\all\\a\\1\\": "10", - "\\all\\b\\": "10", - "\\all\\b\\1\\": "10", - "\\all\\b\\2\\": "10", - "\\all\\c\\": "10", - "\\all\\c\\1\\": "10", - "\\all\\c\\2\\": "10", - "\\all\\c\\3\\": "10", - "\\all\\d\\": "10", - "\\all\\d\\1\\": "10", - "\\all\\d\\2\\": "10", - "\\all\\d\\3\\": "10", - "\\all\\d\\4\\": "10", - "\\all\\": "10" -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/all_zero_open_access_cross_count_result.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/all_zero_open_access_cross_count_result.json deleted file mode 100644 index f87e4195a..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/all_zero_open_access_cross_count_result.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "\\all\\a\\": "0", - "\\all\\a\\1\\": "0", - "\\all\\b\\": "0", - "\\all\\b\\1\\": "0", - "\\all\\b\\2\\": "0", - "\\all\\c\\": "0", - "\\all\\c\\1\\": "0", - "\\all\\c\\2\\": "0", - "\\all\\c\\3\\": "0", - "\\all\\d\\": "0", - "\\all\\d\\1\\": "0", - "\\all\\d\\2\\": "0", - "\\all\\d\\3\\": "0", - "\\all\\d\\4\\": "0", - "\\all\\": "0" -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/large_open_access_cross_count_obfuscated_result.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/large_open_access_cross_count_obfuscated_result.json deleted file mode 100644 index f3d86d077..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/large_open_access_cross_count_obfuscated_result.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "\\all\\a\\": "25 ±3", - "\\all\\a\\1\\": "14 ±3", - "\\all\\b\\": "91 ±3", - "\\all\\b\\1\\": "36 ±3", - "\\all\\b\\2\\": "80 ±3", - "\\all\\c\\": "66 ±3", - "\\all\\c\\1\\": "25 ±3", - "\\all\\c\\2\\": "14 ±3", - "\\all\\c\\3\\": "36 ±3", - "\\all\\d\\": "58 ±3", - "\\all\\d\\1\\": "36 ±3", - "\\all\\d\\2\\": "25 ±3", - "\\all\\d\\3\\": "14 ±3", - "\\all\\d\\4\\": "25 ±3", - "\\all\\": "336 ±3" -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/large_open_access_cross_count_result.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/large_open_access_cross_count_result.json deleted file mode 100644 index f7775ab62..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/large_open_access_cross_count_result.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "\\all\\a\\": "22", - "\\all\\a\\1\\": "11", - "\\all\\b\\": "88", - "\\all\\b\\1\\": "33", - "\\all\\b\\2\\": "77", - "\\all\\c\\": "63", - "\\all\\c\\1\\": "22", - "\\all\\c\\2\\": "11", - "\\all\\c\\3\\": "33", - "\\all\\d\\": "55", - "\\all\\d\\1\\": "33", - "\\all\\d\\2\\": "22", - "\\all\\d\\3\\": "11", - "\\all\\d\\4\\": "22", - "\\all\\": "333" -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/middle_less_ten_obfuscated_open_access_cross_count_obfuscated_result.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/middle_less_ten_obfuscated_open_access_cross_count_obfuscated_result.json deleted file mode 100644 index f72329f77..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/middle_less_ten_obfuscated_open_access_cross_count_obfuscated_result.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "\\all\\a\\": "23 ±3", - "\\all\\a\\1\\": "12 ±3", - "\\all\\b\\": "< 10", - "\\all\\b\\1\\": "< 10", - "\\all\\b\\2\\": "< 10", - "\\all\\c\\": "64 ±3", - "\\all\\c\\1\\": "23 ±3", - "\\all\\c\\2\\": "< 10", - "\\all\\c\\3\\": "34 ±3", - "\\all\\d\\": "56 ±3", - "\\all\\d\\1\\": "34 ±3", - "\\all\\d\\2\\": "< 10", - "\\all\\d\\3\\": "< 10", - "\\all\\d\\4\\": "23 ±3", - "\\all\\": "334 ±3" -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/middle_less_ten_obfuscated_open_access_cross_count_result.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/middle_less_ten_obfuscated_open_access_cross_count_result.json deleted file mode 100644 index d3156e4df..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/middle_less_ten_obfuscated_open_access_cross_count_result.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "\\all\\a\\": "22", - "\\all\\a\\1\\": "11", - "\\all\\b\\": "9", - "\\all\\b\\1\\": "5", - "\\all\\b\\2\\": "7", - "\\all\\c\\": "63", - "\\all\\c\\1\\": "22", - "\\all\\c\\2\\": "3", - "\\all\\c\\3\\": "33", - "\\all\\d\\": "55", - "\\all\\d\\1\\": "33", - "\\all\\d\\2\\": "6", - "\\all\\d\\3\\": "7", - "\\all\\d\\4\\": "22", - "\\all\\": "333" -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/obfuscated_all_less_ten_open_access_cross_count_result.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/obfuscated_all_less_ten_open_access_cross_count_result.json deleted file mode 100644 index 0539422e4..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/obfuscated_all_less_ten_open_access_cross_count_result.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "\\all\\a\\": "< 10", - "\\all\\a\\1\\": "< 10", - "\\all\\b\\": "< 10", - "\\all\\b\\1\\": "< 10", - "\\all\\b\\2\\": "< 10", - "\\all\\c\\": "< 10", - "\\all\\c\\1\\": "< 10", - "\\all\\c\\2\\": "< 10", - "\\all\\c\\3\\": "< 10", - "\\all\\d\\": "< 10", - "\\all\\d\\1\\": "< 10", - "\\all\\d\\2\\": "< 10", - "\\all\\d\\3\\": "< 10", - "\\all\\d\\4\\": "< 10", - "\\all\\": "< 10" -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/obfuscated_cross_count_query.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/obfuscated_cross_count_query.json deleted file mode 100644 index cb3edffba..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/obfuscated_cross_count_query.json +++ /dev/null @@ -1,33 +0,0 @@ -{ - "resourceUUID": "7bec1300-ae93-5ffc-11eb-0242a0c83702", - "query": { - "categoryFilters": {}, - "numericFilters": {}, - "requiredFields": [], - "anyRecordOf": [], - "variantInfoFilters": [ - { - "categoryVariantInfoFilters": {}, - "numericVariantInfoFilters": {} - } - ], - "expectedResultType": "CROSS_COUNT", - "crossCountFields": [ - "\\all\\a\\", - "\\all\\a\\1\\", - "\\all\\b\\", - "\\all\\b\\1\\", - "\\all\\b\\2\\", - "\\all\\c\\", - "\\all\\c\\1\\", - "\\all\\c\\2\\", - "\\all\\c\\3\\", - "\\all\\d\\", - "\\all\\d\\1\\", - "\\all\\d\\2\\", - "\\all\\d\\3\\", - "\\all\\d\\4\\", - "\\all\\" - ] - } -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/obfuscated_cross_count_query2.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/obfuscated_cross_count_query2.json deleted file mode 100644 index 86e7ce9ce..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/obfuscated_cross_count_query2.json +++ /dev/null @@ -1,33 +0,0 @@ -{ - "resourceUUID": "7bec1300-ae93-5ffc-11eb-0242a0c83702", - "query": { - "categoryFilters": {"something":["something"]}, - "numericFilters": {}, - "requiredFields": [], - "anyRecordOf": [], - "variantInfoFilters": [ - { - "categoryVariantInfoFilters": {}, - "numericVariantInfoFilters": {} - } - ], - "expectedResultType": "CROSS_COUNT", - "crossCountFields": [ - "\\all\\a\\", - "\\all\\a\\1\\", - "\\all\\b\\", - "\\all\\b\\1\\", - "\\all\\b\\2\\", - "\\all\\c\\", - "\\all\\c\\1\\", - "\\all\\c\\2\\", - "\\all\\c\\3\\", - "\\all\\d\\", - "\\all\\d\\1\\", - "\\all\\d\\2\\", - "\\all\\d\\3\\", - "\\all\\d\\4\\", - "\\all\\" - ] - } -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/one_obfuscated_open_access_cross_count_obfuscated_result.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/one_obfuscated_open_access_cross_count_obfuscated_result.json deleted file mode 100644 index 6464e7b3f..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/one_obfuscated_open_access_cross_count_obfuscated_result.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "\\all\\a\\": "22 ±3", - "\\all\\a\\1\\": "11 ±3", - "\\all\\b\\": "88 ±3", - "\\all\\b\\1\\": "33 ±3", - "\\all\\b\\2\\": "77 ±3", - "\\all\\c\\": "63 ±3", - "\\all\\c\\1\\": "22 ±3", - "\\all\\c\\2\\": "< 10", - "\\all\\c\\3\\": "33 ±3", - "\\all\\d\\": "55 ±3", - "\\all\\d\\1\\": "33 ±3", - "\\all\\d\\2\\": "22 ±3", - "\\all\\d\\3\\": "11 ±3", - "\\all\\d\\4\\": "22 ±3", - "\\all\\": "333 ±3" -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/one_obfuscated_open_access_cross_count_result.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/one_obfuscated_open_access_cross_count_result.json deleted file mode 100644 index 7f4e2896d..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/one_obfuscated_open_access_cross_count_result.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "\\all\\a\\": "22", - "\\all\\a\\1\\": "11", - "\\all\\b\\": "88", - "\\all\\b\\1\\": "33", - "\\all\\b\\2\\": "77", - "\\all\\c\\": "63", - "\\all\\c\\1\\": "22", - "\\all\\c\\2\\": "3", - "\\all\\c\\3\\": "33", - "\\all\\d\\": "55", - "\\all\\d\\1\\": "33", - "\\all\\d\\2\\": "22", - "\\all\\d\\3\\": "11", - "\\all\\d\\4\\": "22", - "\\all\\": "333" -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/one_obfuscated_open_access_cross_count_result_without_obfuscated_elements.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/one_obfuscated_open_access_cross_count_result_without_obfuscated_elements.json deleted file mode 100644 index 163137a46..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/one_obfuscated_open_access_cross_count_result_without_obfuscated_elements.json +++ /dev/null @@ -1,14 +0,0 @@ -{ - "\\all\\a\\": "22", - "\\all\\a\\1\\": "11", - "\\all\\b\\": "88", - "\\all\\b\\1\\": "33", - "\\all\\b\\2\\": "77", - "\\all\\c\\1\\": "22", - "\\all\\c\\3\\": "33", - "\\all\\d\\": "55", - "\\all\\d\\1\\": "33", - "\\all\\d\\2\\": "22", - "\\all\\d\\3\\": "11", - "\\all\\d\\4\\": "22" -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/one_obfuscated_open_access_cross_count_unsorted_obfuscated_result.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/one_obfuscated_open_access_cross_count_unsorted_obfuscated_result.json deleted file mode 100644 index f0fb52aa9..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/one_obfuscated_open_access_cross_count_unsorted_obfuscated_result.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "\\all\\a\\1\\": "11 ±3", - "\\all\\b\\": "88 ±3", - "\\all\\b\\2\\": "77 ±3", - "\\all\\c\\": "63 ±3", - "\\all\\b\\1\\": "33 ±3", - "\\all\\c\\1\\": "22 ±3", - "\\all\\c\\2\\": "< 10", - "\\all\\d\\2\\": "22 ±3", - "\\all\\a\\": "22 ±3", - "\\all\\c\\3\\": "33 ±3", - "\\all\\d\\3\\": "11 ±3", - "\\all\\d\\": "55 ±3", - "\\all\\d\\1\\": "33 ±3", - "\\all\\d\\4\\": "22 ±3", - "\\all\\": "333 ±3" -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/one_obfuscated_open_access_cross_count_unsorted_result.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/one_obfuscated_open_access_cross_count_unsorted_result.json deleted file mode 100644 index 6ab277c87..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/one_obfuscated_open_access_cross_count_unsorted_result.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "\\all\\a\\1\\": "11", - "\\all\\b\\": "88", - "\\all\\b\\2\\": "77", - "\\all\\c\\": "63", - "\\all\\b\\1\\": "33", - "\\all\\c\\1\\": "22", - "\\all\\c\\2\\": "3", - "\\all\\d\\2\\": "22", - "\\all\\a\\": "22", - "\\all\\c\\3\\": "33", - "\\all\\d\\3\\": "11", - "\\all\\d\\": "55", - "\\all\\d\\1\\": "33", - "\\all\\d\\4\\": "22", - "\\all\\": "333" -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/open_access_search_result.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/open_access_search_result.json deleted file mode 100644 index 484674391..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/open_access_search_result.json +++ /dev/null @@ -1,23 +0,0 @@ -{ - "results": { - "phenotypes": { - "\\all\\a\\": {}, - "\\all\\a\\1\\": {}, - "\\all\\b\\": {}, - "\\all\\b\\1\\": {}, - "\\all\\b\\2\\": {}, - "\\all\\c\\": {}, - "\\all\\c\\1\\": {}, - "\\all\\c\\2\\": {}, - "\\all\\c\\3\\": {}, - "\\all\\d\\": {}, - "\\all\\d\\1\\": {}, - "\\all\\d\\2\\": {}, - "\\all\\d\\3\\": {}, - "\\all\\d\\4\\": {}, - "\\all\\": {} - }, - "info": {} - }, - "searchQuery": "\\all\\" -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/test_cross_count_query.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/test_cross_count_query.json deleted file mode 100644 index e38b0ea4a..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/test_cross_count_query.json +++ /dev/null @@ -1,33 +0,0 @@ -{ - "resourceUUID": "70c837be-5ffc-11eb-ae93-0242ac130002", - "query": { - "categoryFilters":{}, - "numericFilters":{}, - "requiredFields": [], - "anyRecordOf": [], - "variantInfoFilters": [ - { - "categoryVariantInfoFilters":{}, - "numericVariantInfoFilters":{} - } - ], - "expectedResultType": "CROSS_COUNT", - "crossCountFields": [ - "\\all\\a\\", - "\\all\\a\\1\\", - "\\all\\b\\", - "\\all\\b\\1\\", - "\\all\\b\\2\\", - "\\all\\c\\", - "\\all\\c\\1\\", - "\\all\\c\\2\\", - "\\all\\c\\3\\", - "\\all\\d\\", - "\\all\\d\\1\\", - "\\all\\d\\2\\", - "\\all\\d\\3\\", - "\\all\\d\\4\\", - "\\all\\" - ] - } -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/test_minimum_threshold.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/test_minimum_threshold.json deleted file mode 100644 index d8e87a089..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/test_minimum_threshold.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "\\all\\a\\": "22", - "\\all\\a\\1\\": "11", - "\\all\\b\\": "9", - "\\all\\b\\1\\": "5", - "\\all\\b\\2\\": "7", - "\\all\\c\\": "63", - "\\all\\c\\1\\": "22", - "\\all\\c\\2\\": "3", - "\\all\\c\\3\\": "33", - "\\all\\d\\": "10", - "\\all\\d\\1\\": "4", - "\\all\\d\\2\\": "3", - "\\all\\d\\3\\": "2", - "\\all\\d\\4\\": "1", - "\\all\\": "333" -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/two_obfuscated_open_access_cross_count_obfuscated_result.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/two_obfuscated_open_access_cross_count_obfuscated_result.json deleted file mode 100644 index 26f7668e8..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/two_obfuscated_open_access_cross_count_obfuscated_result.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "\\all\\a\\": "23 ±3", - "\\all\\a\\1\\": "12 ±3", - "\\all\\b\\": "89 ±3", - "\\all\\b\\1\\": "34 ±3", - "\\all\\b\\2\\": "78 ±3", - "\\all\\c\\": "64 ±3", - "\\all\\c\\1\\": "23 ±3", - "\\all\\c\\2\\": "< 10", - "\\all\\c\\3\\": "34 ±3", - "\\all\\d\\": "56 ±3", - "\\all\\d\\1\\": "34 ±3", - "\\all\\d\\2\\": "< 10", - "\\all\\d\\3\\": "< 10", - "\\all\\d\\4\\": "23 ±3", - "\\all\\": "334 ±3" -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/two_obfuscated_open_access_cross_count_result.json b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/two_obfuscated_open_access_cross_count_result.json deleted file mode 100644 index b82fc1bb8..000000000 --- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/test/resources/two_obfuscated_open_access_cross_count_result.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "\\all\\a\\": "22", - "\\all\\a\\1\\": "11", - "\\all\\b\\": "88", - "\\all\\b\\1\\": "33", - "\\all\\b\\2\\": "77", - "\\all\\c\\": "63", - "\\all\\c\\1\\": "22", - "\\all\\c\\2\\": "3", - "\\all\\c\\3\\": "33", - "\\all\\d\\": "55", - "\\all\\d\\1\\": "33", - "\\all\\d\\2\\": "6", - "\\all\\d\\3\\": "7", - "\\all\\d\\4\\": "22", - "\\all\\": "333" -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-passthrough-resource/README.md b/pic-sure-resources/pic-sure-passthrough-resource/README.md deleted file mode 100644 index 486d5155b..000000000 --- a/pic-sure-resources/pic-sure-passthrough-resource/README.md +++ /dev/null @@ -1,9 +0,0 @@ -### PIC-SURE Passthrough Resource - -A proxy resource that makes queries on behalf of users using the Common Area Service User Account Token for each institution. -Query submitted to the target resource should not be modified EXCEPT the resource UUID must match the target resource UUID - -This will require three configurations: -1. common area service account token -2. target resource UUID -3. target PIC-SURE URL diff --git a/pic-sure-resources/pic-sure-passthrough-resource/pom.xml b/pic-sure-resources/pic-sure-passthrough-resource/pom.xml deleted file mode 100644 index c0a6e250d..000000000 --- a/pic-sure-resources/pic-sure-passthrough-resource/pom.xml +++ /dev/null @@ -1,83 +0,0 @@ - - - 4.0.0 - - edu.harvard.hms.dbmi.avillach - pic-sure-resources - 2.2.0-SNAPSHOT - - pic-sure-passthrough-resource - pic-sure-passthrough-resource - war - - 13.0.0.Final - ${project.build.directory}/wildfly-${wildfly.version} - UTF-8 - - - - edu.harvard.hms.dbmi.avillach - pic-sure-resource-api - ${project.version} - - - edu.harvard.hms.dbmi.avillach - pic-sure-util - ${project.version} - - - javax - javaee-api - provided - - - org.apache.httpcomponents - httpclient - - - com.fasterxml.jackson.core - jackson-databind - - - commons-io - commons-io - - - org.apache.commons - commons-lang3 - - - org.junit.jupiter - junit-jupiter - test - - - org.mockito - mockito-core - test - - - org.mockito - mockito-junit-jupiter - test - - - org.glassfish.jersey.core - jersey-common - test - - - - ${project.artifactId} - - - org.apache.maven.plugins - maven-war-plugin - - false - - - - - diff --git a/pic-sure-resources/pic-sure-passthrough-resource/src/main/java/edu/harvard/hms/dbmi/avillach/resource/passthru/ApplicationProperties.java b/pic-sure-resources/pic-sure-passthrough-resource/src/main/java/edu/harvard/hms/dbmi/avillach/resource/passthru/ApplicationProperties.java deleted file mode 100644 index 760628b01..000000000 --- a/pic-sure-resources/pic-sure-passthrough-resource/src/main/java/edu/harvard/hms/dbmi/avillach/resource/passthru/ApplicationProperties.java +++ /dev/null @@ -1,63 +0,0 @@ -package edu.harvard.hms.dbmi.avillach.resource.passthru; - -import java.io.IOException; -import java.io.Serializable; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.Properties; - -import javax.enterprise.context.ApplicationScoped; - -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.exception.PicsureQueryException; - -@ApplicationScoped -public class ApplicationProperties implements Serializable { - - private String contextPath; - private String targetPicsureUrl; - private String targetResourceId; - private String targetPicsureToken; - - public String getContextPath() { - return contextPath; - } - - public String getTargetPicsureToken() { - return targetPicsureToken; - } - - public String getTargetPicsureUrl() { - return targetPicsureUrl; - } - - public String getTargetResourceId() { - return targetResourceId; - } - - public void init(String contextPath) { - this.contextPath = contextPath; - - Path configFile = Path.of(System.getProperty("jboss.server.config.dir"), "passthru", contextPath, - "resource.properties"); - Properties properties = null; - try { - properties = new Properties(); - properties.load(Files.newInputStream(configFile)); - } catch (IOException e) { - throw new ApplicationException("Error while reading resource properties file: " + configFile, e); - } - - targetPicsureUrl = properties.getProperty("target.picsure.url"); - if (targetPicsureUrl == null) - throw new PicsureQueryException("target.picsure.url property must be set."); - - targetResourceId = properties.getProperty("target.resource.id"); - if (targetResourceId == null) - throw new PicsureQueryException("target.resource.id property must be set."); - - targetPicsureToken = properties.getProperty("target.picsure.token"); - if (targetPicsureToken == null) - throw new PicsureQueryException("target.picsure.token property must be set."); - } -} diff --git a/pic-sure-resources/pic-sure-passthrough-resource/src/main/java/edu/harvard/hms/dbmi/avillach/resource/passthru/JAXRSConfiguration.java b/pic-sure-resources/pic-sure-passthrough-resource/src/main/java/edu/harvard/hms/dbmi/avillach/resource/passthru/JAXRSConfiguration.java deleted file mode 100755 index 9cfa5e1b4..000000000 --- a/pic-sure-resources/pic-sure-passthrough-resource/src/main/java/edu/harvard/hms/dbmi/avillach/resource/passthru/JAXRSConfiguration.java +++ /dev/null @@ -1,30 +0,0 @@ -package edu.harvard.hms.dbmi.avillach.resource.passthru; - -import javax.inject.Inject; -import javax.servlet.ServletContext; -import javax.servlet.ServletContextEvent; -import javax.servlet.ServletContextListener; -import javax.servlet.annotation.WebListener; -import javax.ws.rs.ApplicationPath; -import javax.ws.rs.core.Application; - -@ApplicationPath("pic-sure") -@WebListener -public class JAXRSConfiguration extends Application implements ServletContextListener { - - @Inject - private ApplicationProperties appProperties; - - @Override - public void contextInitialized(ServletContextEvent event) { - ServletContext servletContext = event.getServletContext(); - appProperties.init(servletContext.getContextPath()); - servletContext.setInitParameter("resteasy.resources", "org.jboss.resteasy.plugins.stats.RegistryStatsResource"); - } - - @Override - public void contextDestroyed(ServletContextEvent event) { - // NOOP. - } - -} diff --git a/pic-sure-resources/pic-sure-passthrough-resource/src/main/java/edu/harvard/hms/dbmi/avillach/resource/passthru/PassThroughResourceRS.java b/pic-sure-resources/pic-sure-passthrough-resource/src/main/java/edu/harvard/hms/dbmi/avillach/resource/passthru/PassThroughResourceRS.java deleted file mode 100644 index c2f8b4f8a..000000000 --- a/pic-sure-resources/pic-sure-passthrough-resource/src/main/java/edu/harvard/hms/dbmi/avillach/resource/passthru/PassThroughResourceRS.java +++ /dev/null @@ -1,357 +0,0 @@ -package edu.harvard.hms.dbmi.avillach.resource.passthru; - -import java.io.IOException; -import java.nio.charset.StandardCharsets; -import java.util.UUID; - -import javax.inject.Inject; -import javax.ws.rs.*; -import javax.ws.rs.core.HttpHeaders; -import javax.ws.rs.core.Response; - -import edu.harvard.dbmi.avillach.util.HttpClientUtil; -import org.apache.http.Header; -import org.apache.http.HttpResponse; -import org.apache.http.impl.conn.PoolingHttpClientConnectionManager; -import org.apache.http.message.BasicHeader; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import edu.harvard.dbmi.avillach.domain.*; -import edu.harvard.dbmi.avillach.service.IResourceRS; -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; -import static edu.harvard.dbmi.avillach.service.ResourceWebClient.QUERY_METADATA_FIELD; -import static edu.harvard.dbmi.avillach.util.HttpClientUtil.closeHttpResponse; - -@Path("/passthru") -@Produces("application/json") -@Consumes("application/json") -public class PassThroughResourceRS implements IResourceRS { - - private static final String BEARER_STRING = "Bearer "; - - private static final ObjectMapper objectMapper = new ObjectMapper(); - private static final Logger logger = LoggerFactory.getLogger(PassThroughResourceRS.class); - - @Inject - private ApplicationProperties properties; - - private final HttpClientUtil httpClient; - - public PoolingHttpClientConnectionManager getConnectionManager() { - PoolingHttpClientConnectionManager connectionManager; - connectionManager = new PoolingHttpClientConnectionManager(); - connectionManager.setMaxTotal(100); // Maximum total connections - connectionManager.setDefaultMaxPerRoute(20); // Maximum connections per route - return connectionManager; - } - - public PassThroughResourceRS() { - this.httpClient = HttpClientUtil.getInstance(getConnectionManager()); - } - - @Inject - public PassThroughResourceRS(ApplicationProperties applicationProperties) { - this.properties = applicationProperties; - this.httpClient = HttpClientUtil.getInstance(getConnectionManager()); - } - - public PassThroughResourceRS(ApplicationProperties properties, HttpClientUtil httpClient) { - this.properties = properties; - this.httpClient = httpClient; - } - - @POST - @Path("/info") - public ResourceInfo info(QueryRequest infoRequest) { - String pathName = "/info"; - - HttpResponse response = null; - try { - QueryRequest chainRequest = new GeneralQueryRequest(); - if (infoRequest != null) { - chainRequest.setQuery(infoRequest.getQuery()); - chainRequest.setResourceCredentials(infoRequest.getResourceCredentials()); - } - chainRequest.setResourceUUID(UUID.fromString(properties.getTargetResourceId())); - - String payload = objectMapper.writeValueAsString(chainRequest); - - response = httpClient - .retrievePostResponse(HttpClientUtil.composeURL(properties.getTargetPicsureUrl(), pathName), createAuthHeader(), payload); - if (response.getStatusLine().getStatusCode() != 200) { - logger.error( - "{}{} did not return a 200: {} {} ", properties.getTargetPicsureUrl(), pathName, - response.getStatusLine().getStatusCode(), response.getStatusLine().getReasonPhrase() - ); - HttpClientUtil.throwInternalResponseError(response, properties.getTargetPicsureUrl()); - } - - ResourceInfo resourceInfo = HttpClientUtil.readObjectFromResponse(response, ResourceInfo.class); - if (infoRequest != null && infoRequest.getResourceUUID() != null) { - resourceInfo.setId(infoRequest.getResourceUUID()); - } - return resourceInfo; - } catch (IOException e) { - throw new ApplicationException("Error encoding query for resource with id " + infoRequest.getResourceUUID()); - } catch (ClassCastException | IllegalArgumentException e) { - logger.error(e.getMessage()); - throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); - } finally { - closeHttpResponse(response); - } - } - - @POST - @Path("/query") - public QueryStatus query(QueryRequest queryRequest) { - if (queryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - Object search = queryRequest.getQuery(); - if (search == null) { - throw new ProtocolException((ProtocolException.MISSING_DATA)); - } - - String pathName = "/query"; - HttpResponse response = null; - try { - QueryRequest chainRequest = queryRequest.copy(); - chainRequest.setResourceUUID(UUID.fromString(properties.getTargetResourceId())); - - String payload = objectMapper.writeValueAsString(chainRequest); - response = httpClient - .retrievePostResponse(httpClient.composeURL(properties.getTargetPicsureUrl(), pathName), createAuthHeader(), payload); - if (response.getStatusLine().getStatusCode() != 200) { - logger.error( - "{}{} calling resource with id {} did not return a 200: {} {} ", properties.getTargetPicsureUrl(), pathName, - chainRequest.getResourceUUID(), response.getStatusLine().getStatusCode(), response.getStatusLine().getReasonPhrase() - ); - httpClient.throwInternalResponseError(response, properties.getTargetPicsureUrl()); - } - QueryStatus queryStatus = httpClient.readObjectFromResponse(response, QueryStatus.class); - queryStatus.setResourceID(queryRequest.getResourceUUID()); - return queryStatus; - } catch (IOException e) { - throw new ApplicationException("Error encoding query for resource with id " + queryRequest.getResourceUUID()); - } catch (ClassCastException | IllegalArgumentException e) { - logger.error(e.getMessage()); - throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); - } finally { - closeHttpResponse(response); - } - } - - @POST - @Path("/query/{resourceQueryId}/result") - public Response queryResult(@PathParam("resourceQueryId") String queryId, QueryRequest resultRequest) { - if (resultRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - - String pathName = "/query/" + queryId + "/result"; - - HttpResponse response = null; - try { - QueryRequest chainRequest = new GeneralQueryRequest(); - chainRequest.setQuery(resultRequest.getQuery()); - chainRequest.setResourceCredentials(resultRequest.getResourceCredentials()); - chainRequest.setResourceUUID(UUID.fromString(properties.getTargetResourceId())); - - String payload = objectMapper.writeValueAsString(chainRequest); - response = httpClient - .retrievePostResponse(httpClient.composeURL(properties.getTargetPicsureUrl(), pathName), createAuthHeader(), payload); - byte[] content = httpClient.readBytesFromResponse(response); - if (response.getStatusLine().getStatusCode() != 200) { - logger.error( - "{}{} calling resource with id {} did not return a 200: {} {} ", properties.getTargetPicsureUrl(), pathName, - chainRequest.getResourceUUID(), response.getStatusLine().getStatusCode(), response.getStatusLine().getReasonPhrase() - ); - httpClient.throwInternalResponseError(response, properties.getTargetPicsureUrl()); - } - - return Response.ok(content).build(); - } catch (IOException e) { - throw new ApplicationException("Error encoding query for resource with id " + resultRequest.getResourceUUID()); - } catch (ClassCastException | IllegalArgumentException e) { - logger.error(e.getMessage()); - throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); - } finally { - closeHttpResponse(response); - } - } - - @POST - @Path("/query/{resourceQueryId}/status") - public QueryStatus queryStatus(@PathParam("resourceQueryId") String queryId, QueryRequest statusRequest) { - // JNix: Retaining for future use... - if (statusRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - - String pathName = "/query/" + queryId + "/status"; - HttpResponse response = null; - try { - QueryRequest chainRequest = new GeneralQueryRequest(); - chainRequest.setQuery(statusRequest.getQuery()); - chainRequest.setResourceCredentials(statusRequest.getResourceCredentials()); - chainRequest.setResourceUUID(UUID.fromString(properties.getTargetResourceId())); - - String payload = objectMapper.writeValueAsString(chainRequest); - response = httpClient - .retrievePostResponse(httpClient.composeURL(properties.getTargetPicsureUrl(), pathName), createAuthHeader(), payload); - if (response.getStatusLine().getStatusCode() != 200) { - logger.error( - "{}{} calling resource with id {} did not return a 200: {} {} ", properties.getTargetPicsureUrl(), pathName, - chainRequest.getResourceUUID(), response.getStatusLine().getStatusCode(), response.getStatusLine().getReasonPhrase() - ); - httpClient.throwInternalResponseError(response, properties.getTargetPicsureUrl()); - } - QueryStatus queryStatus = httpClient.readObjectFromResponse(response, QueryStatus.class); - queryStatus.setResourceID(statusRequest.getResourceUUID()); - return queryStatus; - } catch (IOException e) { - throw new ApplicationException("Error encoding query for resource with id " + statusRequest.getResourceUUID()); - } catch (ClassCastException | IllegalArgumentException e) { - logger.error(e.getMessage()); - throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); - } finally { - closeHttpResponse(response); - } - } - - @POST - @Path("/query/sync") - @Override - public Response querySync(QueryRequest queryRequest) { - if (queryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - Object search = queryRequest.getQuery(); - if (search == null) { - throw new ProtocolException((ProtocolException.MISSING_DATA)); - } - - String pathName = "/query/sync"; - - HttpResponse response = null; - try { - QueryRequest chainRequest = new GeneralQueryRequest(); - chainRequest.setQuery(queryRequest.getQuery()); - chainRequest.setResourceCredentials(queryRequest.getResourceCredentials()); - chainRequest.setResourceUUID(UUID.fromString(properties.getTargetResourceId())); - - String payload = objectMapper.writeValueAsString(chainRequest); - response = httpClient - .retrievePostResponse(httpClient.composeURL(properties.getTargetPicsureUrl(), pathName), createAuthHeader(), payload); - if (response.getStatusLine().getStatusCode() != 200) { - logger.error( - "{}{} calling resource with id {} did not return a 200: {} {} ", properties.getTargetPicsureUrl(), pathName, - chainRequest.getResourceUUID(), response.getStatusLine().getStatusCode(), response.getStatusLine().getReasonPhrase() - ); - httpClient.throwInternalResponseError(response, properties.getTargetPicsureUrl()); - } - - if (response.containsHeader(QUERY_METADATA_FIELD)) { - Header metadataHeader = ((Header[]) response.getHeaders(QUERY_METADATA_FIELD))[0]; - logger.debug("Found Header[] : " + metadataHeader.getValue()); - return Response.ok(response.getEntity().getContent()).header(QUERY_METADATA_FIELD, metadataHeader.getValue()).build(); - } - - return Response.ok(response.getEntity().getContent()).build(); - } catch (IOException e) { - throw new ApplicationException("Error encoding query for resource with id " + queryRequest.getResourceUUID()); - } catch (ClassCastException | IllegalArgumentException e) { - logger.error(e.getMessage()); - throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); - } finally { - closeHttpResponse(response); - } - } - - @POST - @Path("/search") - public SearchResults search(QueryRequest searchRequest) { - if (searchRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - Object search = searchRequest.getQuery(); - if (search == null) { - throw new ProtocolException((ProtocolException.MISSING_DATA)); - } - - HttpResponse response = null; - String pathName = "/search/" + properties.getTargetResourceId(); - try { - QueryRequest chainRequest = new GeneralQueryRequest(); - chainRequest.setQuery(searchRequest.getQuery()); - chainRequest.setResourceCredentials(searchRequest.getResourceCredentials()); - chainRequest.setResourceUUID(UUID.fromString(properties.getTargetResourceId())); - - String payload = objectMapper.writeValueAsString(chainRequest); - response = httpClient - .retrievePostResponse(httpClient.composeURL(properties.getTargetPicsureUrl(), pathName), createAuthHeader(), payload); - if (response.getStatusLine().getStatusCode() != 200) { - logger.error( - "{}{} did not return a 200: {} {} ", properties.getTargetPicsureUrl(), pathName, - response.getStatusLine().getStatusCode(), response.getStatusLine().getReasonPhrase() - ); - httpClient.throwInternalResponseError(response, properties.getTargetPicsureUrl()); - } - return httpClient.readObjectFromResponse(response, SearchResults.class); - } catch (IOException e) { - // Note: this shouldn't ever happen - logger.error("Error encoding search payload", e); - throw new ApplicationException("Error encoding search for resource with id " + searchRequest.getResourceUUID()); - } finally { - closeHttpResponse(response); - } - } - - @Override - public Response queryFormat(QueryRequest queryRequest) { - if (queryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - Object search = queryRequest.getQuery(); - if (search == null) { - throw new ProtocolException((ProtocolException.MISSING_DATA)); - } - - String pathName = "/query/format"; - HttpResponse response = null; - try { - QueryRequest chainRequest = new GeneralQueryRequest(); - chainRequest.setQuery(queryRequest.getQuery()); - chainRequest.setResourceCredentials(queryRequest.getResourceCredentials()); - chainRequest.setResourceUUID(UUID.fromString(properties.getTargetResourceId())); - - String payload = objectMapper.writeValueAsString(chainRequest); - response = httpClient - .retrievePostResponse(httpClient.composeURL(properties.getTargetPicsureUrl(), pathName), createAuthHeader(), payload); - if (response.getStatusLine().getStatusCode() != 200) { - logger.error( - "{}{} calling resource with id {} did not return a 200: {} {} ", properties.getTargetPicsureUrl(), pathName, - chainRequest.getResourceUUID(), response.getStatusLine().getStatusCode(), response.getStatusLine().getReasonPhrase() - ); - httpClient.throwInternalResponseError(response, properties.getTargetPicsureUrl()); - } - - return Response.ok(response.getEntity().getContent()).build(); - } catch (IOException e) { - throw new ApplicationException("Error encoding query for resource with id " + queryRequest.getResourceUUID()); - } catch (ClassCastException | IllegalArgumentException e) { - logger.error(e.getMessage()); - throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); - } finally { - closeHttpResponse(response); - } - } - - private Header[] createAuthHeader() { - return new Header[] {new BasicHeader(HttpHeaders.AUTHORIZATION, BEARER_STRING + properties.getTargetPicsureToken())}; - } -} diff --git a/pic-sure-resources/pic-sure-passthrough-resource/src/main/resources/META-INF/persistence.xml b/pic-sure-resources/pic-sure-passthrough-resource/src/main/resources/META-INF/persistence.xml deleted file mode 100644 index 307ff0024..000000000 --- a/pic-sure-resources/pic-sure-passthrough-resource/src/main/resources/META-INF/persistence.xml +++ /dev/null @@ -1,7 +0,0 @@ - - - - - diff --git a/pic-sure-resources/pic-sure-passthrough-resource/src/main/resources/webapp/META-INF/context.xml b/pic-sure-resources/pic-sure-passthrough-resource/src/main/resources/webapp/META-INF/context.xml deleted file mode 100755 index 6d30046dd..000000000 --- a/pic-sure-resources/pic-sure-passthrough-resource/src/main/resources/webapp/META-INF/context.xml +++ /dev/null @@ -1,3 +0,0 @@ - - - \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-passthrough-resource/src/main/resources/webapp/WEB-INF/beans.xml b/pic-sure-resources/pic-sure-passthrough-resource/src/main/resources/webapp/WEB-INF/beans.xml deleted file mode 100755 index 1c97df0e3..000000000 --- a/pic-sure-resources/pic-sure-passthrough-resource/src/main/resources/webapp/WEB-INF/beans.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-passthrough-resource/src/main/resources/webapp/WEB-INF/web.xml b/pic-sure-resources/pic-sure-passthrough-resource/src/main/resources/webapp/WEB-INF/web.xml deleted file mode 100644 index c29b44b53..000000000 --- a/pic-sure-resources/pic-sure-passthrough-resource/src/main/resources/webapp/WEB-INF/web.xml +++ /dev/null @@ -1,20 +0,0 @@ - - - JAX-RS Simple Service - JAX-RS Simple Service - - contextConfigLocation - webapp/WEB-INF/beans.xml - - - resteasy.scan - true - - - org.springframework.web.context.ContextLoaderListener - - diff --git a/pic-sure-resources/pic-sure-passthrough-resource/src/test/java/edu/harvard/hms/dbmi/avillach/resource/passthru/Filter.java b/pic-sure-resources/pic-sure-passthrough-resource/src/test/java/edu/harvard/hms/dbmi/avillach/resource/passthru/Filter.java deleted file mode 100644 index 3db9a5a0d..000000000 --- a/pic-sure-resources/pic-sure-passthrough-resource/src/test/java/edu/harvard/hms/dbmi/avillach/resource/passthru/Filter.java +++ /dev/null @@ -1,102 +0,0 @@ -package edu.harvard.hms.dbmi.avillach.resource.passthru; - -public interface Filter { - public boolean apply(T value); - - public static class DoubleFilter implements Filter { - - Double min, max; - - public Double getMin() { - return min; - } - - public void setMin(Double min) { - this.min = min; - } - - public Double getMax() { - return max; - } - - public void setMax(Double max) { - this.max = max; - } - - public DoubleFilter() { - - } - - public DoubleFilter(Double min, Double max) { - this.min = min; - this.max = max; - } - - public boolean apply(Double value) { - return value >= min && value <= max; - } - - public String toString() { - String strVal = ""; - if (min != null) { - strVal = "Greater than " + min; - if (max != null) { - strVal += " and "; - } - } - if (max != null) { - strVal += "Less than " + max; - } - return strVal; - } - } - - public static class FloatFilter implements Filter { - - Float min, max; - - public Float getMin() { - return min; - } - - public void setMin(Float min) { - this.min = min; - } - - public Float getMax() { - return max; - } - - public void setMax(Float max) { - this.max = max; - } - - public FloatFilter() { - - } - - public FloatFilter(Float min, Float max) { - this.min = min; - this.max = max; - } - - public boolean apply(Float value) { - return value >= min && value <= max; - } - - public String toString() { - String strVal = ""; - if (min != null) { - strVal = "Greater than " + min; - if (max != null) { - strVal += " and "; - } - } - if (max != null) { - strVal += "Less than " + max; - } - return strVal; - } - } - -} diff --git a/pic-sure-resources/pic-sure-passthrough-resource/src/test/java/edu/harvard/hms/dbmi/avillach/resource/passthru/PassThroughResourceRSTest.java b/pic-sure-resources/pic-sure-passthrough-resource/src/test/java/edu/harvard/hms/dbmi/avillach/resource/passthru/PassThroughResourceRSTest.java deleted file mode 100644 index 18859271c..000000000 --- a/pic-sure-resources/pic-sure-passthrough-resource/src/test/java/edu/harvard/hms/dbmi/avillach/resource/passthru/PassThroughResourceRSTest.java +++ /dev/null @@ -1,342 +0,0 @@ -package edu.harvard.hms.dbmi.avillach.resource.passthru; - -import static org.junit.jupiter.api.Assertions.*; -import static org.mockito.ArgumentMatchers.*; -import static org.mockito.Mockito.lenient; -import static org.mockito.Mockito.mock; -import static org.mockito.Mockito.when; - -import java.io.InputStream; -import java.nio.charset.StandardCharsets; -import java.util.Collections; -import java.util.HashMap; -import java.util.Map; -import java.util.UUID; - -import edu.harvard.dbmi.avillach.domain.*; -import edu.harvard.dbmi.avillach.util.HttpClientUtil; -import org.apache.commons.io.IOUtils; -import org.apache.http.Header; -import org.apache.http.HeaderElement; -import org.apache.http.HttpResponse; -import org.apache.http.ParseException; -import org.apache.http.StatusLine; -import org.apache.http.entity.StringEntity; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.mockito.junit.jupiter.MockitoExtension; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; -import edu.harvard.dbmi.avillach.util.exception.ResourceInterfaceException; - -@ExtendWith(MockitoExtension.class) -class PassThroughResourceRSTest { - - HttpClientUtil httpClient; - PassThroughResourceRS resource; - ObjectMapper objectMapper = new ObjectMapper(); - - @BeforeEach - void init() { - ApplicationProperties appProperties = mock(ApplicationProperties.class); - lenient().when(appProperties.getTargetPicsureToken()).thenReturn("/tmp/unit_test"); - lenient().when(appProperties.getTargetPicsureUrl()).thenReturn("http://test"); - lenient().when(appProperties.getTargetResourceId()).thenReturn(UUID.randomUUID().toString()); - - httpClient = mock(HttpClientUtil.class); - - resource = new PassThroughResourceRS(appProperties, httpClient); - } - - @Test - void testInfo() throws Exception { - // setup http response mocks - HttpResponse httpResponse = mock(HttpResponse.class); - StringEntity httpResponseEntity = new StringEntity(""); - StatusLine statusLine = mock(StatusLine.class); - when(httpResponse.getStatusLine()).thenReturn(statusLine); - when(httpResponse.getEntity()).thenReturn(httpResponseEntity); - when(httpClient.retrievePostResponse(anyString(), any(Header[].class), anyString())).thenReturn(httpResponse); - - when(statusLine.getStatusCode()).thenReturn(500); - assertThrows(ResourceInterfaceException.class, () -> { - resource.info(new GeneralQueryRequest()); - }, "Downstream Resource returned 500 and should cause 'ResourceInterfaceException'"); - - when(statusLine.getStatusCode()).thenReturn(401); - assertThrows(ResourceInterfaceException.class, () -> { - resource.info(new GeneralQueryRequest()); - }, "Downstream Resource returned 401 and should cause 'ResourceInterfaceException'"); - - when(statusLine.getStatusCode()).thenReturn(200); - ResourceInfo resourceInfo = newResourceInfo(); - httpResponseEntity = new StringEntity(new String(objectMapper.writeValueAsBytes(resourceInfo))); - when(httpResponse.getEntity()).thenReturn(httpResponseEntity); - ResourceInfo returnVal = resource.info(new GeneralQueryRequest()); - assertEquals(resourceInfo.getId(), returnVal.getId(), "Downstream ResourceInfo Id should match output"); - assertEquals(resourceInfo.getName(), returnVal.getName(), "Downstream ResourceInfo Name should match output"); - assertEquals( - resourceInfo.getQueryFormats().size(), returnVal.getQueryFormats().size(), - "Downstream ResourceInfo QueryFormats should match output" - ); - } - - @Test - void testQuery() throws Exception { - // setup http response mocks - HttpResponse httpResponse = mock(HttpResponse.class); - StringEntity httpResponseEntity = new StringEntity(""); - StatusLine statusLine = mock(StatusLine.class); - when(statusLine.getStatusCode()).thenReturn(200); - when(httpResponse.getStatusLine()).thenReturn(statusLine); - when(httpResponse.getEntity()).thenReturn(httpResponseEntity); - when(httpClient.retrievePostResponse(anyString(), any(Header[].class), anyString())).thenReturn(httpResponse); - - assertThrows(ProtocolException.class, () -> { - resource.query(null); - }, "QueryRequest is required"); - - assertThrows(ProtocolException.class, () -> { - resource.query(new GeneralQueryRequest()); - }, "Query is required"); - - when(statusLine.getStatusCode()).thenReturn(500); - assertThrows(ResourceInterfaceException.class, () -> { - resource.query(newQueryRequest("test")); - }, "Downstream Resource returned 500 and should cause 'ResourceInterfaceException'"); - - when(statusLine.getStatusCode()).thenReturn(401); - assertThrows(ResourceInterfaceException.class, () -> { - resource.query(newQueryRequest("test")); - }, "Downstream Resource returned 401 and should cause 'ResourceInterfaceException'"); - - when(statusLine.getStatusCode()).thenReturn(200); - QueryStatus queryStatus = newQueryStatus(null); - httpResponseEntity = new StringEntity(new String(objectMapper.writeValueAsBytes(queryStatus))); - when(httpResponse.getEntity()).thenReturn(httpResponseEntity); - GeneralQueryRequest queryRequest = newQueryRequest("test"); - QueryStatus returnVal = resource.query(queryRequest); - assertEquals(queryRequest.getResourceUUID(), returnVal.getResourceID()); - } - - @Test - void testQueryResult() throws Exception { - // setup http response mocks - HttpResponse httpResponse = mock(HttpResponse.class); - StringEntity httpResponseEntity = new StringEntity(""); - StatusLine statusLine = mock(StatusLine.class); - when(statusLine.getStatusCode()).thenReturn(200); - when(httpResponse.getStatusLine()).thenReturn(statusLine); - when(httpResponse.getEntity()).thenReturn(httpResponseEntity); - when(httpClient.retrievePostResponse(anyString(), any(Header[].class), anyString())).thenReturn(httpResponse); - byte[] byteResponse = {101}; - when(httpClient.readBytesFromResponse(any(HttpResponse.class))).thenReturn(byteResponse); - - assertThrows(ProtocolException.class, () -> { - resource.queryResult("", null); - }, "QueryID is required"); - - assertThrows(ProtocolException.class, () -> { - resource.queryResult(UUID.randomUUID().toString(), null); - }, "QueryRequest is required"); - - when(statusLine.getStatusCode()).thenReturn(500); - assertThrows(ResourceInterfaceException.class, () -> { - resource.queryResult(UUID.randomUUID().toString(), newQueryRequest(null)); - }, "Downstream Resource returned 500 and should cause 'ResourceInterfaceException'"); - - when(statusLine.getStatusCode()).thenReturn(401); - assertThrows(ResourceInterfaceException.class, () -> { - resource.queryResult(UUID.randomUUID().toString(), newQueryRequest(null)); - }, "Downstream Resource returned 401 and should cause 'ResourceInterfaceException'"); - - when(statusLine.getStatusCode()).thenReturn(200); - String resultId = UUID.randomUUID().toString(); - UUID queryId = UUID.randomUUID(); - lenient().when(httpResponse.getFirstHeader("resultId")).thenReturn(newHeader("resultId", resultId)); - httpResponseEntity = new StringEntity("4"); - when(httpResponse.getEntity()).thenReturn(httpResponseEntity); - GeneralQueryRequest queryRequest = newQueryRequest(null); - javax.ws.rs.core.Response returnVal = resource.queryResult(queryId.toString(), queryRequest); - assertArrayEquals(byteResponse, (byte[]) returnVal.getEntity()); - // assertEquals(resultId, returnVal.getHeaderString("resultId")); - } - - @Test - void testQueryStatus() throws Exception { - // setup http response mocks - HttpResponse httpResponse = mock(HttpResponse.class); - StringEntity httpResponseEntity = new StringEntity(""); - StatusLine statusLine = mock(StatusLine.class); - when(statusLine.getStatusCode()).thenReturn(200); - when(httpResponse.getStatusLine()).thenReturn(statusLine); - when(httpResponse.getEntity()).thenReturn(httpResponseEntity); - when(httpClient.retrievePostResponse(anyString(), any(Header[].class), anyString())).thenReturn(httpResponse); - - assertThrows(ProtocolException.class, () -> { - resource.queryStatus("", null); - }, "QueryID is required"); - - assertThrows(ProtocolException.class, () -> { - resource.queryStatus(UUID.randomUUID().toString(), null); - }, "QueryRequest is required"); - - when(statusLine.getStatusCode()).thenReturn(500); - assertThrows(ResourceInterfaceException.class, () -> { - resource.queryStatus(UUID.randomUUID().toString(), newQueryRequest(null)); - }, "Downstream Resource returned 500 and should cause 'ResourceInterfaceException'"); - - when(statusLine.getStatusCode()).thenReturn(401); - assertThrows(ResourceInterfaceException.class, () -> { - resource.queryStatus(UUID.randomUUID().toString(), newQueryRequest(null)); - }, "Downstream Resource returned 401 and should cause 'ResourceInterfaceException'"); - - when(statusLine.getStatusCode()).thenReturn(200); - UUID queryId = UUID.randomUUID(); - QueryStatus queryStatus = newQueryStatus(queryId); - httpResponseEntity = new StringEntity(new String(objectMapper.writeValueAsBytes(queryStatus))); - when(httpResponse.getEntity()).thenReturn(httpResponseEntity); - GeneralQueryRequest queryRequest = newQueryRequest(null); - QueryStatus returnVal = resource.queryStatus(queryId.toString(), queryRequest); - assertEquals(queryId, returnVal.getPicsureResultId()); - assertEquals(queryStatus.getStatus(), returnVal.getStatus()); - assertEquals(queryStatus.getResourceStatus(), returnVal.getResourceStatus()); - } - - @Test - void testQuerySync() throws Exception { - // setup http response mocks - HttpResponse httpResponse = mock(HttpResponse.class); - StringEntity httpResponseEntity = new StringEntity(""); - StatusLine statusLine = mock(StatusLine.class); - when(statusLine.getStatusCode()).thenReturn(200); - when(httpResponse.getStatusLine()).thenReturn(statusLine); - when(httpResponse.getEntity()).thenReturn(httpResponseEntity); - when(httpClient.retrievePostResponse(anyString(), any(Header[].class), anyString())).thenReturn(httpResponse); - - assertThrows(ProtocolException.class, () -> { - resource.querySync(null); - }, "QueryRequest is required"); - - assertThrows(ProtocolException.class, () -> { - resource.querySync(new GeneralQueryRequest()); - }, "Query is required"); - - when(statusLine.getStatusCode()).thenReturn(500); - assertThrows(ResourceInterfaceException.class, () -> { - resource.querySync(newQueryRequest("test")); - }, "Downstream Resource returned 500 and should cause 'ResourceInterfaceException'"); - - when(statusLine.getStatusCode()).thenReturn(401); - assertThrows(ResourceInterfaceException.class, () -> { - resource.querySync(newQueryRequest("test")); - }, "Downstream Resource returned 401 and should cause 'ResourceInterfaceException'"); - - when(statusLine.getStatusCode()).thenReturn(200); - String resultId = UUID.randomUUID().toString(); - lenient().when(httpResponse.getFirstHeader("resultId")).thenReturn(newHeader("resultId", resultId)); - httpResponseEntity = new StringEntity("4"); - when(httpResponse.getEntity()).thenReturn(httpResponseEntity); - GeneralQueryRequest queryRequest = newQueryRequest(newQuery()); - javax.ws.rs.core.Response returnVal = resource.querySync(queryRequest); - assertEquals("4", IOUtils.toString((InputStream) returnVal.getEntity(), StandardCharsets.UTF_8)); - // assertEquals(resultId, returnVal.getHeaderString("resultId")); - } - - @Test - void testSearch() throws Exception { - // setup http response mocks - HttpResponse httpResponse = mock(HttpResponse.class); - StringEntity httpResponseEntity = new StringEntity(""); - StatusLine statusLine = mock(StatusLine.class); - when(statusLine.getStatusCode()).thenReturn(200); - when(httpResponse.getStatusLine()).thenReturn(statusLine); - when(httpResponse.getEntity()).thenReturn(httpResponseEntity); - when(httpClient.retrievePostResponse(anyString(), any(Header[].class), anyString())).thenReturn(httpResponse); - - assertThrows(ProtocolException.class, () -> { - resource.search(null); - }, "QueryRequest is required"); - - assertThrows(ProtocolException.class, () -> { - resource.search(new GeneralQueryRequest()); - }, "Query is required"); - - when(statusLine.getStatusCode()).thenReturn(500); - assertThrows(ResourceInterfaceException.class, () -> { - resource.search(newQueryRequest("test")); - }, "Downstream Resource returned 500 and should cause 'ResourceInterfaceException'"); - - when(statusLine.getStatusCode()).thenReturn(401); - assertThrows(ResourceInterfaceException.class, () -> { - resource.search(newQueryRequest("test")); - }, "Downstream Resource returned 401 and should cause 'ResourceInterfaceException'"); - - String queryText = "test"; - when(statusLine.getStatusCode()).thenReturn(200); - SearchResults searchResults = new SearchResults(); - searchResults.setSearchQuery(queryText); - httpResponseEntity = new StringEntity(new String(objectMapper.writeValueAsBytes(searchResults))); - when(httpResponse.getEntity()).thenReturn(httpResponseEntity); - GeneralQueryRequest queryRequest = newQueryRequest(queryText); - SearchResults returnVal = resource.search(queryRequest); - assertEquals(queryText, returnVal.getSearchQuery()); - } - - private ResourceInfo newResourceInfo() { - ResourceInfo info = new ResourceInfo(); - info.setName("PhenoCube v1.0-SNAPSHOT"); - info.setId(UUID.randomUUID()); - info.setQueryFormats( - Collections.singletonList(new QueryFormat().setDescription("PhenoCube Query Format").setName("PhenoCube Query Format")) - ); - return info; - } - - private QueryStatus newQueryStatus(UUID picsureResultId) { - QueryStatus status = new QueryStatus(); - status.setStatus(PicSureStatus.QUEUED); - status.setResourceID(UUID.randomUUID()); - status.setResourceStatus("PENDING"); - status.setPicsureResultId(picsureResultId); - status.setResourceResultId(UUID.randomUUID().toString()); - return status; - } - - private GeneralQueryRequest newQueryRequest(Object query) { - GeneralQueryRequest request = new GeneralQueryRequest(); - request.setResourceUUID(UUID.randomUUID()); - request.setQuery(query); - return request; - } - - // replace with Map - private Map newQuery() { - Map queryMap = new HashMap<>(); - queryMap.put("requiredFields", "\\TEST"); - queryMap.put("expectedResultType", "COUNT"); - return queryMap; - } - - private Header newHeader(final String name, final String value) { - return new Header() { - @Override - public String getValue() { - return value; - } - - @Override - public String getName() { - return name; - } - - @Override - public HeaderElement[] getElements() throws ParseException { - return null; - } - }; - } -} diff --git a/pic-sure-resources/pic-sure-resource-api/pom.xml b/pic-sure-resources/pic-sure-resource-api/pom.xml deleted file mode 100755 index 2d15aaa99..000000000 --- a/pic-sure-resources/pic-sure-resource-api/pom.xml +++ /dev/null @@ -1,75 +0,0 @@ - - - 4.0.0 - - edu.harvard.hms.dbmi.avillach - pic-sure-resources - 2.2.0-SNAPSHOT - - pic-sure-resource-api - pic-sure-resource-api - http://maven.apache.org - jar - - UTF-8 - - - - edu.harvard.hms.dbmi.avillach - pic-sure-util - ${project.version} - - - javax - javaee-api - provided - - - com.fasterxml.jackson.core - jackson-databind - - - org.apache.httpcomponents - httpcore - - - org.apache.httpcomponents - httpclient - - - commons-io - commons-io - - - org.mockito - mockito-core - test - - - com.github.tomakehurst - wiremock-standalone - test - - - org.glassfish.jersey.core - jersey-common - test - - - io.swagger.core.v3 - swagger-annotations - - - org.junit.vintage - junit-vintage-engine - test - - - edu.harvard.hms.dbmi.avillach - pic-sure-api-data - ${project.version} - - - - diff --git a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/QueryFormatDeserializer.java b/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/QueryFormatDeserializer.java deleted file mode 100644 index e2e7b08c0..000000000 --- a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/QueryFormatDeserializer.java +++ /dev/null @@ -1,46 +0,0 @@ -package edu.harvard.dbmi.avillach; - -import com.fasterxml.jackson.core.JsonParser; -import com.fasterxml.jackson.databind.*; -import edu.harvard.dbmi.avillach.domain.QueryFormat; - -import java.io.IOException; -import java.util.*; - -public class QueryFormatDeserializer extends JsonDeserializer { - - private final static ObjectMapper mapper = new ObjectMapper(); - //All extra fields are just shoved into specification - //TODO Not sure this is the format we want this in actually but for now it's readable at least - @Override - public QueryFormat deserialize(JsonParser jp, DeserializationContext context) throws IOException{ - JsonNode node = jp.getCodec().readTree(jp); - QueryFormat qf = new QueryFormat(); - - Iterator> fields = node.fields(); - HashMap extraFields = new HashMap<>(); - List> examples = new ArrayList<>(); - while (fields.hasNext()){ - Map.Entry field = fields.next(); - if (field.getKey().equalsIgnoreCase("name")){ - qf.setName(field.getValue().asText()); - } else if (field.getKey().equalsIgnoreCase("description")){ - qf.setDescription(field.getValue().asText()); - } else if (field.getKey().equalsIgnoreCase("examples")){ - List> test = mapper.convertValue(field.getValue(), ArrayList.class); - examples = test; - } else { - extraFields.put(field.getKey(), mapper.convertValue(field.getValue(), Object.class)); - } - } - if (!extraFields.isEmpty()){ - qf.setSpecification(extraFields); - } - if (!examples.isEmpty()){ - qf.setExamples(examples); - } - return qf; - } - - -} diff --git a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/FederatedQueryRequest.java b/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/FederatedQueryRequest.java deleted file mode 100644 index e0695f28f..000000000 --- a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/FederatedQueryRequest.java +++ /dev/null @@ -1,137 +0,0 @@ -package edu.harvard.dbmi.avillach.domain; - -import io.swagger.v3.oas.annotations.media.Schema; - -import java.util.HashMap; -import java.util.Map; -import java.util.UUID; - -// spotless:off -@Schema(name = "QueryRequest", description = "Object containing credentials map under 'resourceCredentials' and query" + - " object under 'query'. The query object expectedResultType can be on of the following " + - "\"COUNT\", \"CROSS_COUNT\", \"INFO_COLUMN_LISTING\", \"OBSERVATION_COUNT\", \"OBSERVATION_CROSS_COUNT\", \"DATAFRAME\". ", - example = "{\n" + - " \"resourceUUID\": \"\",\n" + - " \"query\": {\n" + - " \"categoryFilters\": {\n" + - " \"\\\\demographics\\\\SEX\\\\\": [\n" + - " \"female\",\n" + - " \"male\"\n" + - " ]\n" + - " },\n" + - " \"numericFilters\": {\n" + - " \"\\\\demographics\\\\AGE\\\\\": {\n" + - " \"min\": \"0\",\n" + - " \"max\": \"85\"\n" + - " }\n" + - " },\n" + - " \"requiredFields\": [],\n" + - " \"anyRecordOf\": [\n" + - " \"\\\\demographics\\\\RACE\\\\\"\n" + - " ],\n" + - " \"variantInfoFilters\": [\n" + - " {\n" + - " \"categoryVariantInfoFilters\": {},\n" + - " \"numericVariantInfoFilters\": {}\n" + - " }\n" + - " ],\n" + - " \"expectedResultType\": \"DATAFRAME\",\n" + - " \"fields\": []\n" + - " }\n" + - "}") - -//spotless:on - -/* - * QueryRequests for vanilla GIC PIC-SURE. Includes details about the source of the request, the requester, and any unifying identifiers for - * sharing - */ -public class FederatedQueryRequest implements QueryRequest { - - @Schema(hidden = true) - private Map resourceCredentials = new HashMap<>(); - - @Schema(hidden = true) - private Object query; - - @Schema(hidden = true) - private UUID resourceUUID; - - @Schema(hidden = true) - private UUID commonAreaUUID; - - @Schema(hidden = true) - private String institutionOfOrigin; - - @Schema(hidden = true) - private String requesterEmail; - - @Override - public Map getResourceCredentials() { - return resourceCredentials; - } - - @Override - public FederatedQueryRequest setResourceCredentials(Map resourceCredentials) { - this.resourceCredentials = resourceCredentials; - return this; - } - - @Override - public Object getQuery() { - return query; - } - - @Override - public FederatedQueryRequest setQuery(Object query) { - this.query = query; - return this; - } - - @Override - public UUID getResourceUUID() { - return resourceUUID; - } - - @Override - public void setResourceUUID(UUID resourceUUID) { - this.resourceUUID = resourceUUID; - } - - @Override - public FederatedQueryRequest copy() { - FederatedQueryRequest request = new FederatedQueryRequest(); - request.setQuery(getQuery()); - request.setResourceCredentials(getResourceCredentials()); - request.setResourceUUID(getResourceUUID()); - request.setCommonAreaUUID(getCommonAreaUUID()); - request.setInstitutionOfOrigin(getInstitutionOfOrigin()); - request.setRequesterEmail(getRequesterEmail()); - - return request; - } - - public UUID getCommonAreaUUID() { - return commonAreaUUID; - } - - public void setCommonAreaUUID(UUID commonAreaUUID) { - this.commonAreaUUID = commonAreaUUID; - } - - public String getInstitutionOfOrigin() { - return institutionOfOrigin; - } - - public void setInstitutionOfOrigin(String institutionOfOrigin) { - this.institutionOfOrigin = institutionOfOrigin; - } - - public String getRequesterEmail() { - return requesterEmail; - } - - public void setRequesterEmail(String requesterEmail) { - this.requesterEmail = requesterEmail; - } -} diff --git a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/GeneralQueryRequest.java b/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/GeneralQueryRequest.java deleted file mode 100644 index c636a0a40..000000000 --- a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/GeneralQueryRequest.java +++ /dev/null @@ -1,98 +0,0 @@ -package edu.harvard.dbmi.avillach.domain; - -import com.fasterxml.jackson.annotation.JsonIgnoreProperties; -import io.swagger.v3.oas.annotations.media.Schema; - -import java.util.HashMap; -import java.util.Map; -import java.util.UUID; - -@Schema(name = "QueryRequest", description = "Object containing credentials map under 'resourceCredentials' and query" + - " object under 'query'. The query object expectedResultType can be on of the following " + - "\"COUNT\", \"CROSS_COUNT\", \"INFO_COLUMN_LISTING\", \"OBSERVATION_COUNT\", \"OBSERVATION_CROSS_COUNT\", \"DATAFRAME\". ", - example = "{\n" + - " \"resourceUUID\": \"\",\n" + - " \"query\": {\n" + - " \"categoryFilters\": {\n" + - " \"\\\\demographics\\\\SEX\\\\\": [\n" + - " \"female\",\n" + - " \"male\"\n" + - " ]\n" + - " },\n" + - " \"numericFilters\": {\n" + - " \"\\\\demographics\\\\AGE\\\\\": {\n" + - " \"min\": \"0\",\n" + - " \"max\": \"85\"\n" + - " }\n" + - " },\n" + - " \"requiredFields\": [],\n" + - " \"anyRecordOf\": [\n" + - " \"\\\\demographics\\\\RACE\\\\\"\n" + - " ],\n" + - " \"variantInfoFilters\": [\n" + - " {\n" + - " \"categoryVariantInfoFilters\": {},\n" + - " \"numericVariantInfoFilters\": {}\n" + - " }\n" + - " ],\n" + - " \"expectedResultType\": \"DATAFRAME\",\n" + - " \"fields\": []\n" + - " }\n" + - "}") - -/* - * QueryRequests for vanilla PIC-SURE - */ -public class GeneralQueryRequest implements QueryRequest { - - @Schema(hidden = true) - private Map resourceCredentials = new HashMap<>(); - - @Schema(hidden = true) - private Object query; - - @Schema(hidden = true) - private UUID resourceUUID; - - @Override - public Map getResourceCredentials() { - return resourceCredentials; - } - - @Override - public GeneralQueryRequest setResourceCredentials(Map resourceCredentials) { - this.resourceCredentials = resourceCredentials; - return this; - } - - @Override - public Object getQuery() { - return query; - } - - @Override - public GeneralQueryRequest setQuery(Object query) { - this.query = query; - return this; - } - - @Override - public UUID getResourceUUID() { - return resourceUUID; - } - - @Override - public void setResourceUUID(UUID resourceUUID) { - this.resourceUUID = resourceUUID; - } - - @Override - public GeneralQueryRequest copy() { - GeneralQueryRequest request = new GeneralQueryRequest(); - request.setQuery(getQuery()); - request.setResourceCredentials(getResourceCredentials()); - request.setResourceUUID(getResourceUUID()); - - return request; - } -} diff --git a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/QueryFormat.java b/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/QueryFormat.java deleted file mode 100644 index a6b704333..000000000 --- a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/QueryFormat.java +++ /dev/null @@ -1,60 +0,0 @@ -package edu.harvard.dbmi.avillach.domain; - -import com.fasterxml.jackson.annotation.JsonInclude; -import com.fasterxml.jackson.databind.annotation.JsonDeserialize; -import edu.harvard.dbmi.avillach.QueryFormatDeserializer; -import io.swagger.v3.oas.annotations.media.Schema; - -import java.util.List; -import java.util.Map; - -@Schema(description = "Information about the query format supported by a resource.") -@JsonDeserialize(using = QueryFormatDeserializer.class) -@JsonInclude(JsonInclude.Include.NON_NULL) -public class QueryFormat { - - @Schema(description = "The name of the query format.") - private String name; - - @Schema(description = "A description of the query format.") - private String description; - - @Schema(description = "A specification of the query format.") - private Map specification; - - @Schema(description = "A list of examples of the query format.") - private List> examples; - - public String getName() { - return name; - } - public QueryFormat setName(String name) { - this.name = name; - return this; - } - - public String getDescription() { - return description; - } - public QueryFormat setDescription(String description) { - this.description = description; - return this; - } - - public Map getSpecification() { - return specification; - } - public QueryFormat setSpecification(Map specification) { - this.specification = specification; - return this; - } - - public List> getExamples() { - return examples; - } - public QueryFormat setExamples(List> examples) { - this.examples = examples; - return this; - } - -} diff --git a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/ResourceInfo.java b/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/ResourceInfo.java deleted file mode 100644 index 59288f475..000000000 --- a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/ResourceInfo.java +++ /dev/null @@ -1,51 +0,0 @@ -package edu.harvard.dbmi.avillach.domain; - -import com.fasterxml.jackson.annotation.JsonInclude; -import io.swagger.v3.oas.annotations.media.Schema; - -import java.util.ArrayList; -import java.util.List; -import java.util.UUID; - -/** - * Information about interacting with a specific resource. - * - */ -@Schema(description = "Information about interacting with a specific resource.") -@JsonInclude(JsonInclude.Include.NON_NULL) -public class ResourceInfo { - - @Schema(description = "The UUID of the resource.") - private UUID id; - - @Schema(description = "The name of the resource.") - private String name; - - @Schema(description = "The query formats supported by the resource.") - private List queryFormats; - public UUID getId() { - return id; - } - public ResourceInfo setId(UUID id) { - this.id = id; - return this; - } - public String getName() { - return name; - } - public ResourceInfo setName(String name) { - this.name = name; - return this; - } - public List getQueryFormats() { - if(queryFormats == null) { - queryFormats = new ArrayList<>(); - } - return queryFormats; - } - public ResourceInfo setQueryFormats(List queryFormats) { - this.queryFormats = queryFormats; - return this; - } - -} diff --git a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/SearchResults.java b/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/SearchResults.java deleted file mode 100644 index d8bcfc440..000000000 --- a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/SearchResults.java +++ /dev/null @@ -1,31 +0,0 @@ -package edu.harvard.dbmi.avillach.domain; - -import io.swagger.v3.oas.annotations.media.Schema; - -@Schema(description = "A search results object") -public class SearchResults { - - @Schema(description = "The results of the search.") - Object results; - - @Schema(description = "The query that was used to generate the results.") - String searchQuery; - - public Object getResults() { - return results; - } - - public SearchResults setResults(Object results) { - this.results = results; - return this; - } - - public String getSearchQuery() { - return searchQuery; - } - - public SearchResults setSearchQuery(String searchQuery) { - this.searchQuery = searchQuery; - return this; - } -} diff --git a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/service/IResourceRS.java b/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/service/IResourceRS.java deleted file mode 100644 index 8f9fb13ab..000000000 --- a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/service/IResourceRS.java +++ /dev/null @@ -1,107 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import javax.ws.rs.*; -import javax.ws.rs.core.Response; - -import edu.harvard.dbmi.avillach.domain.*; -import io.swagger.v3.oas.annotations.Operation; - -import java.util.Map; -import java.util.UUID; - -@Path("/pic-sure") -@Produces("application/json") -@Consumes("application/json") -public interface IResourceRS -{ - - @POST - @Path("/info") - @Operation(hidden = true) - default ResourceInfo info(QueryRequest queryRequest) { - throw new NotSupportedException(); - } - - @POST - @Path("/search") - @Operation(hidden = true) - default SearchResults search(QueryRequest searchJson) { - throw new NotSupportedException(); - } - - @POST - @Path("/query") - @Operation(hidden = true) - default QueryStatus query(QueryRequest queryJson) { - throw new NotSupportedException(); - } - - @POST - @Path("/query/{resourceQueryId}/status") - @Operation(hidden = true) - default QueryStatus queryStatus(UUID queryId, QueryRequest statusRequest) { - throw new NotSupportedException(); - } - - @POST - @Path("/query/{resourceQueryId}/result") - @Operation(hidden = true) - default Response queryResult(UUID queryId, QueryRequest resultRequest) { - throw new NotSupportedException(); - } - - @POST - @Path("/query/sync") - @Operation(hidden = true) - default Response querySync(QueryRequest resultRequest) { - throw new NotSupportedException("Query Sync is not implemented in this resource. Please use query"); - } - - @POST - @Path("/query/format") - @Operation(hidden = true) - default Response queryFormat(QueryRequest resultRequest) { - throw new NotSupportedException("Query formatting is not implemented in this resource."); - } - - @GET - @Path("/search/values/") - default PaginatedSearchResult searchGenomicConceptValues( - @QueryParam("genomicConceptPath") String genomicConceptPath, - @QueryParam("query") String query, - @QueryParam("page") int page, - @QueryParam("size") int size - ) { - throw new NotSupportedException(); - } - - @POST - @Path("/bin/continuous") - @Operation(hidden = true) - default Response generateContinuousBin(QueryRequest continuousData) { - throw new NotSupportedException(); - } - - - @POST - @Path("/proxy/{container}/{request : .+}") - @Operation(hidden = true) - default Response postProxy( - @PathParam("containerId") String containerId, - @PathParam("request") String request, - String body - ) { - throw new NotSupportedException(); - } - - @GET - @Path("/proxy/{container}/{request : .+}") - @Operation(hidden = true) - default Response getProxy( - @PathParam("containerId") String containerId, - @PathParam("request") String request - ) { - throw new NotSupportedException(); - } - -} diff --git a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/service/ProxyWebClient.java b/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/service/ProxyWebClient.java deleted file mode 100644 index fce25a394..000000000 --- a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/service/ProxyWebClient.java +++ /dev/null @@ -1,189 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import edu.harvard.dbmi.avillach.data.repository.ResourceRepository; -import edu.harvard.dbmi.avillach.util.HttpClientUtil; -import edu.harvard.dbmi.avillach.util.Utilities; -import org.apache.http.Header; -import org.apache.http.HttpResponse; -import org.apache.http.NameValuePair; -import org.apache.http.client.HttpClient; -import org.apache.http.client.methods.HttpGet; -import org.apache.http.client.methods.HttpPost; -import org.apache.http.client.methods.HttpRequestBase; -import org.apache.http.client.utils.URIBuilder; -import org.apache.http.entity.StringEntity; -import org.apache.http.impl.conn.PoolingHttpClientConnectionManager; -import org.apache.http.message.BasicNameValuePair; -import org.apache.http.util.EntityUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.enterprise.context.ApplicationScoped; -import javax.inject.Inject; -import javax.ws.rs.core.HttpHeaders; -import javax.ws.rs.core.MultivaluedMap; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; -import javax.ws.rs.core.StreamingOutput; -import java.io.IOException; -import java.io.InputStream; -import java.net.URI; -import java.net.URISyntaxException; -import java.util.Arrays; -import java.util.Collections; -import java.util.List; -import java.util.Set; -import java.util.stream.Collectors; - -@ApplicationScoped -public class ProxyWebClient { - private static final Logger LOG = LoggerFactory.getLogger(ProxyWebClient.class); - HttpClient client; - - @Inject - ResourceRepository resourceRepository; - - public ProxyWebClient() { - PoolingHttpClientConnectionManager connectionManager; - - connectionManager = new PoolingHttpClientConnectionManager(); - connectionManager.setMaxTotal(100); // Maximum total connections - connectionManager.setDefaultMaxPerRoute(50); // Maximum connections per route - connectionManager.setValidateAfterInactivity(5000); // Validate idle connections before reuse - - client = HttpClientUtil.getConfiguredHttpClient(connectionManager); - } - - public Response postProxy( - String containerId, String path, String body, MultivaluedMap queryParams, HttpHeaders headers - ) { - if (containerIsNOTAResource(containerId)) { - return Response.status(400, "container name not trustworthy").build(); - } - - String requestSource = Utilities.getRequestSourceFromHeader(headers); - LOG.info( - "path={}, requestSource={}, containerId={}, body={}, queryParams={}, ", path, requestSource, containerId, body, queryParams - ); - - try { - URI uri = - new URIBuilder().setScheme("http").setHost(containerId).setPath(path).setParameters(processParams(queryParams)).build(); - HttpPost request = new HttpPost(uri); - request.setEntity(new StringEntity(body)); - request.addHeader("Content-Type", "application/json"); - forwardHeaders(headers, request); - return getResponse(request); - } catch (URISyntaxException e) { - LOG.warn("Failed to construct URI. Container: {} Path: {}", containerId, path); - throw new RuntimeException(e); - } catch (IOException e) { - throw new RuntimeException(e); - } - } - - public Response getProxy(String containerId, String path, MultivaluedMap queryParams, HttpHeaders headers) { - if (containerIsNOTAResource(containerId)) { - return Response.status(400, "container name not trustworthy").build(); - } - - String requestSource = Utilities.getRequestSourceFromHeader(headers); - LOG.info("path={}, requestSource={}, containerId={}, queryParams={}", path, requestSource, containerId, queryParams); - - try { - URI uri = - new URIBuilder().setScheme("http").setHost(containerId).setPath(path).setParameters(processParams(queryParams)).build(); - HttpGet request = new HttpGet(uri); - forwardHeaders(headers, request); - return getResponse(request); - } catch (URISyntaxException e) { - LOG.warn("Failed to construct URI. Container: {} Path: {}", containerId, path); - throw new RuntimeException(e); - } catch (IOException e) { - throw new RuntimeException(e); - } - } - - private NameValuePair[] processParams(MultivaluedMap params) { - return params.entrySet().stream().flatMap(e -> e.getValue().stream().map(v -> new BasicNameValuePair(e.getKey(), v))) - .toArray(NameValuePair[]::new); - } - - private static final String DEFAULT_FORWARDED_HEADERS = "authorization,x-api-key,x-request-id,x-session-id,x-client-type"; - - private static final Set FORWARDED_HEADERS = initForwardedHeaders(); - - private static Set initForwardedHeaders() { - String configured = System.getenv("PROXY_FORWARDED_HEADERS"); - String headerList = configured != null ? configured : DEFAULT_FORWARDED_HEADERS; - return Collections.unmodifiableSet( - Arrays.stream(headerList.split(",")).map(String::trim).filter(s -> !s.isEmpty()).map(String::toLowerCase) - .collect(Collectors.toSet()) - ); - } - - private void forwardHeaders(HttpHeaders headers, HttpRequestBase request) { - if (headers == null) { - return; - } - for (String headerName : FORWARDED_HEADERS) { - List values = headers.getRequestHeader(headerName); - if (values != null && !values.isEmpty()) { - request.addHeader(headerName, values.get(0)); - } - } - } - - private boolean containerIsNOTAResource(String container) { - return resourceRepository.getByColumn("name", container).isEmpty(); - } - - // Responses larger than 10MB are streamed instead of buffered to avoid OOM - private static final long MAX_BUFFERED_BYTES = 10 * 1024 * 1024; - - private Response getResponse(HttpRequestBase request) throws IOException { - HttpResponse response = client.execute(request); - int status = response.getStatusLine().getStatusCode(); - - if (status >= 500) { - LOG.warn("Upstream server error: status={}, host={}, path={}", status, request.getURI().getHost(), request.getURI().getPath()); - } else if (status >= 400) { - LOG.debug("Upstream client error: status={}, host={}, path={}", status, request.getURI().getHost(), request.getURI().getPath()); - } - - Header contentTypeHeader = response.getEntity().getContentType(); - String contentType = contentTypeHeader != null ? contentTypeHeader.getValue() : MediaType.APPLICATION_OCTET_STREAM; - - long contentLength = response.getEntity().getContentLength(); - if (contentLength > MAX_BUFFERED_BYTES || contentLength == -1) { - // Large or unknown-size response: stream via StreamingOutput so RESTEasy - // flushes chunks instead of buffering the entire body in heap. - // The connection stays checked out until the client finishes reading. - String sizeDesc = contentLength == -1 ? "unknown" : (contentLength / (1024 * 1024)) + "MB"; - LOG.info("Large upstream response ({}), streaming instead of buffering", sizeDesc); - StreamingOutput stream = outputStream -> { - try (InputStream in = response.getEntity().getContent()) { - byte[] buffer = new byte[8192]; - int bytesRead; - while ((bytesRead = in.read(buffer)) != -1) { - outputStream.write(buffer, 0, bytesRead); - outputStream.flush(); - } - } finally { - request.releaseConnection(); - } - }; - return Response.status(status).entity(stream).type(contentType).build(); - } - - // Normal case: buffer the response so the connection is released immediately - try { - byte[] body = EntityUtils.toByteArray(response.getEntity()); - return Response.status(status).entity(body).type(contentType).build(); - } catch (IOException e) { - // Ensure the connection is released back to the pool on read failure - request.releaseConnection(); - throw e; - } - } -} diff --git a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/service/ResourceWebClient.java b/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/service/ResourceWebClient.java deleted file mode 100644 index 13d2f968c..000000000 --- a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/service/ResourceWebClient.java +++ /dev/null @@ -1,454 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; -import edu.harvard.dbmi.avillach.domain.*; -import edu.harvard.dbmi.avillach.util.HttpClientUtil; -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; -import edu.harvard.dbmi.avillach.util.exception.ResourceInterfaceException; -import edu.harvard.dbmi.avillach.util.exception.NotAuthorizedException; -import org.apache.http.Header; -import org.apache.http.HttpResponse; -import org.apache.http.client.utils.URIBuilder; -import org.apache.http.impl.conn.PoolingHttpClientConnectionManager; -import org.apache.http.message.BasicHeader; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.enterprise.context.ApplicationScoped; -import javax.ws.rs.core.HttpHeaders; -import javax.ws.rs.core.Response; -import java.io.*; -import java.net.URISyntaxException; -import java.nio.charset.StandardCharsets; -import java.util.Map; - -import static edu.harvard.dbmi.avillach.util.HttpClientUtil.closeHttpResponse; - - -/** - * The ResourceWebClient class implements the client side logic for the endpoints specified in IResourceRS.

The PicsureInfoService, - * PicsureQueryService and PicsureSearchService would then use this class to serve calls from their methods to each configured Resource - * target url after looking up the target url from the ResourceRepository. - */ -@ApplicationScoped -public class ResourceWebClient { - - private final Logger logger = LoggerFactory.getLogger(this.getClass()); - private final static ObjectMapper json = new ObjectMapper(); - public static final String BEARER_STRING = "Bearer "; - public static final String BEARER_TOKEN_KEY = "BEARER_TOKEN"; - public static final String QUERY_METADATA_FIELD = "queryMetadata"; - - private final HttpClientUtil httpClientUtil; - - public ResourceWebClient() { - PoolingHttpClientConnectionManager connectionManager; - - connectionManager = new PoolingHttpClientConnectionManager(); - connectionManager.setMaxTotal(100); // Maximum total connections - connectionManager.setDefaultMaxPerRoute(20); // Maximum connections per route - - this.httpClientUtil = HttpClientUtil.getInstance(connectionManager); - } - - public ResourceInfo info(String rsURL, QueryRequest queryRequest) { - logger.debug("Calling ResourceWebClient info()"); - HttpResponse resourcesResponse = null; - try { - if (queryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - if (queryRequest.getResourceCredentials() == null) { - throw new NotAuthorizedException(NotAuthorizedException.MISSING_CREDENTIALS); - } - if (rsURL == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - logger.debug("Calling /info at ResourceURL: {}", rsURL); - String pathName = "/info"; - String body = json.writeValueAsString(queryRequest); - resourcesResponse = httpClientUtil.retrievePostResponse( - httpClientUtil.composeURL(rsURL, pathName), createHeaders(queryRequest.getResourceCredentials()), body - ); - if (resourcesResponse.getStatusLine().getStatusCode() != 200) { - logger.error("ResourceRS did not return a 200"); - httpClientUtil.throwResponseError(resourcesResponse, rsURL); - } - return httpClientUtil.readObjectFromResponse(resourcesResponse, ResourceInfo.class); - } catch (JsonProcessingException e) { - throw new NotAuthorizedException("Unable to encode resource credentials", e); - } finally { - closeHttpResponse(resourcesResponse); - } - } - - public PaginatedSearchResult searchConceptValues( - String rsURL, QueryRequest queryRequest, String conceptPath, String query, Integer page, Integer size - ) { - HttpResponse resourcesResponse = null; - try { - logger.debug("Calling /search/values at ResourceURL: {}"); - URIBuilder uriBuilder = new URIBuilder(rsURL); - String pathName = "search/values/"; - uriBuilder.setPath(uriBuilder.getPath() + pathName); - uriBuilder.addParameter("genomicConceptPath", conceptPath); - uriBuilder.addParameter("query", query); - if (page != null) { - uriBuilder.addParameter("page", page.toString()); - } - if (size != null) { - uriBuilder.addParameter("size", size.toString()); - } - Map resourceCredentials = queryRequest != null ? queryRequest.getResourceCredentials() : Map.of(); - resourcesResponse = httpClientUtil.retrieveGetResponse(uriBuilder.build().toString(), createHeaders(resourceCredentials)); - if (resourcesResponse.getStatusLine().getStatusCode() != 200) { - logger.error("ResourceRS did not return a 200"); - httpClientUtil.throwResponseError(resourcesResponse, rsURL); - } - return httpClientUtil.readObjectFromResponse(resourcesResponse, PaginatedSearchResult.class); - } catch (URISyntaxException e) { - throw new ApplicationException("rsURL invalid : " + rsURL, e); - } finally { - closeHttpResponse(resourcesResponse); - } - } - - public SearchResults search(String rsURL, QueryRequest searchQueryRequest) { - logger.debug("Calling ResourceWebClient search()"); - HttpResponse resourcesResponse = null; - try { - if (searchQueryRequest == null || searchQueryRequest.getQuery() == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - if (rsURL == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - - if (searchQueryRequest.getResourceCredentials() == null) { - throw new NotAuthorizedException(NotAuthorizedException.MISSING_CREDENTIALS); - } - String pathName = "/search"; - String body = json.writeValueAsString(searchQueryRequest); - - resourcesResponse = httpClientUtil.retrievePostResponse( - httpClientUtil.composeURL(rsURL, pathName), createHeaders(searchQueryRequest.getResourceCredentials()), body - ); - if (resourcesResponse.getStatusLine().getStatusCode() != 200) { - logger.error("ResourceRS did not return a 200"); - httpClientUtil.throwResponseError(resourcesResponse, rsURL); - } - return httpClientUtil.readObjectFromResponse(resourcesResponse, SearchResults.class); - } catch (JsonProcessingException e) { - logger.error("Unable to serialize search query"); - // TODO Write custom exception - throw new ProtocolException("Unable to serialize search query", e); - } finally { - closeHttpResponse(resourcesResponse); - } - } - - public QueryStatus query(String rsURL, QueryRequest dataQueryRequest) { - logger.debug("Calling ResourceWebClient query()"); - HttpResponse resourcesResponse = null; - try { - if (rsURL == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - if (dataQueryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - if (dataQueryRequest.getResourceCredentials() == null) { - throw new NotAuthorizedException("Missing credentials"); - } - String pathName = "/query"; - String body = json.writeValueAsString(dataQueryRequest); - resourcesResponse = httpClientUtil.retrievePostResponse( - httpClientUtil.composeURL(rsURL, pathName), createHeaders(dataQueryRequest.getResourceCredentials()), body - ); - if (resourcesResponse.getStatusLine().getStatusCode() != 200) { - logger.error("ResourceRS did not return a 200"); - httpClientUtil.throwResponseError(resourcesResponse, rsURL); - } - return httpClientUtil.readObjectFromResponse(resourcesResponse, QueryStatus.class); - } catch (JsonProcessingException e) { - logger.error("Unable to encode data query"); - throw new ProtocolException("Unable to encode data query", e); - } finally { - closeHttpResponse(resourcesResponse); - } - } - - public QueryStatus queryStatus(String rsURL, String queryId, QueryRequest queryRequest) { - logger.debug("Calling ResourceWebClient query()"); - HttpResponse resourcesResponse = null; - try { - if (queryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - if (queryRequest.getResourceCredentials() == null) { - throw new NotAuthorizedException("Missing credentials"); - } - if (rsURL == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - if (queryId == null) { - throw new ProtocolException("Missing query id"); - } - String pathName = "/query/" + queryId + "/status"; - String body = json.writeValueAsString(queryRequest); - logger.debug(httpClientUtil.composeURL(rsURL, pathName)); - logger.debug(body); - resourcesResponse = httpClientUtil.retrievePostResponse( - httpClientUtil.composeURL(rsURL, pathName), createHeaders(queryRequest.getResourceCredentials()), body - ); - if (resourcesResponse.getStatusLine().getStatusCode() != 200) { - logger.error("ResourceRS did not return a 200"); - httpClientUtil.throwResponseError(resourcesResponse, rsURL); - } - return httpClientUtil.readObjectFromResponse(resourcesResponse, QueryStatus.class); - } catch (JsonProcessingException e) { - logger.error("Unable to encode resource credentials"); - throw new ProtocolException("Unable to encode resource credentials", e); - } finally { - closeHttpResponse(resourcesResponse); - } - } - - public Response queryResult(String rsURL, String queryId, QueryRequest queryRequest) { - logger.debug("Calling ResourceWebClient query()"); - - HttpResponse resourcesResponse = null; - try { - if (queryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - if (queryRequest.getResourceCredentials() == null) { - throw new NotAuthorizedException("Missing credentials"); - } - if (rsURL == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - if (queryId == null) { - throw new ProtocolException(ProtocolException.MISSING_QUERY_ID); - } - String pathName = "/query/" + queryId + "/result"; - String body = json.writeValueAsString(queryRequest); - resourcesResponse = httpClientUtil.retrievePostResponse( - HttpClientUtil.composeURL(rsURL, pathName), createHeaders(queryRequest.getResourceCredentials()), body - ); - - byte[] content = httpClientUtil.readBytesFromResponse(resourcesResponse); - if (resourcesResponse.getStatusLine().getStatusCode() != 200) { - logger.error("ResourceRS did not return a 200"); - HttpClientUtil.throwResponseError(resourcesResponse, rsURL); - } - return Response.ok(content).build(); - } catch (JsonProcessingException e) { - logger.error("Unable to encode resource credentials"); - throw new NotAuthorizedException("Unable to encode resource credentials", e); - } finally { - closeHttpResponse(resourcesResponse); - } - } - - public Response queryResultSignedUrl(String rsURL, String queryId, QueryRequest queryRequest) { - logger.debug("Calling ResourceWebClient querySignedUrl()"); - HttpResponse resourcesResponse = null; - try { - if (queryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - if (queryRequest.getResourceCredentials() == null) { - throw new NotAuthorizedException("Missing credentials"); - } - if (rsURL == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - if (queryId == null) { - throw new ProtocolException(ProtocolException.MISSING_QUERY_ID); - } - String pathName = "/query/" + queryId + "/signed-url"; - String body = json.writeValueAsString(queryRequest); - resourcesResponse = httpClientUtil.retrievePostResponse( - httpClientUtil.composeURL(rsURL, pathName), createHeaders(queryRequest.getResourceCredentials()), body - ); - - if (resourcesResponse.getStatusLine().getStatusCode() != 200) { - logger.error("ResourceRS did not return a 200"); - httpClientUtil.throwResponseError(resourcesResponse, rsURL); - } - - String content = httpClientUtil.readObjectFromResponse(resourcesResponse, StandardCharsets.UTF_8); - return Response.ok(content).build(); - } catch (JsonProcessingException e) { - logger.error("Unable to encode resource credentials"); - throw new NotAuthorizedException("Unable to encode resource credentials", e); - } finally { - closeHttpResponse(resourcesResponse); - } - } - - - public Response queryFormat(String rsURL, QueryRequest queryRequest) { - logger.debug("Calling ResourceWebClient queryFormat()"); - HttpResponse resourcesResponse = null; - try { - if (queryRequest == null) { - throw new ProtocolException(ProtocolException.MISSING_DATA); - } - if (queryRequest.getResourceCredentials() == null) { - throw new NotAuthorizedException("Missing credentials"); - } - if (rsURL == null) { - throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH); - } - String pathName = "/query/format"; - String body = json.writeValueAsString(queryRequest); - resourcesResponse = httpClientUtil.retrievePostResponse( - httpClientUtil.composeURL(rsURL, pathName), createHeaders(queryRequest.getResourceCredentials()), body - ); - - String content = httpClientUtil.readObjectFromResponse(resourcesResponse, StandardCharsets.UTF_8); - int status = resourcesResponse.getStatusLine().getStatusCode(); - if (status != 200) { - logger.error("Query format request did not return a 200: {}", resourcesResponse.getStatusLine().getStatusCode()); - return Response.status(status).entity(content).build(); - } - return Response.ok(content).build(); - } catch (JsonProcessingException e) { - logger.error("Unable to encode resource credentials"); - throw new NotAuthorizedException("Unable to encode resource credentials", e); - } finally { - closeHttpResponse(resourcesResponse); - } - } - - public Response querySync(String rsURL, QueryRequest queryRequest, String requestSource) { - logger.debug("Calling ResourceWebClient querySync()"); - HttpResponse resourcesResponse = null; - try { - if (queryRequest == null) { - throw new ProtocolException("Missing query data"); - } - if (queryRequest.getResourceCredentials() == null) { - throw new NotAuthorizedException("Missing credentials"); - } - if (rsURL == null) { - throw new ApplicationException("Missing resource URL"); - } - - String pathName = "/query/sync"; - String body = json.writeValueAsString(queryRequest); - - - Header[] headers = createHeaders(queryRequest.getResourceCredentials()); - if (requestSource != null) { - Header sourceHeader = new BasicHeader("request-source", requestSource); - - // Add the source header to the headers array. - Header[] newHeaders = new Header[headers.length + 1]; - System.arraycopy(headers, 0, newHeaders, 0, headers.length); - newHeaders[headers.length] = sourceHeader; - headers = newHeaders; - } - - resourcesResponse = httpClientUtil.retrievePostResponse(httpClientUtil.composeURL(rsURL, pathName), headers, body); - if (resourcesResponse.getStatusLine().getStatusCode() != 200) { - throwError(resourcesResponse, rsURL); - } - - String content = httpClientUtil.readObjectFromResponse(resourcesResponse, StandardCharsets.UTF_8); - if (resourcesResponse.containsHeader(QUERY_METADATA_FIELD)) { - Header metadataHeader = ((Header[]) resourcesResponse.getHeaders(QUERY_METADATA_FIELD))[0]; - return Response.ok(content).header(QUERY_METADATA_FIELD, metadataHeader.getValue()).build(); - } - return Response.ok(content).build(); - } catch (JsonProcessingException e) { - logger.error("Unable to encode resource credentials"); - throw new NotAuthorizedException("Unable to encode resource credentials", e); - } finally { - closeHttpResponse(resourcesResponse); - } - } - - /** - * This method is used to call the /bin/continuous endpoint on the ResourceRS. The /bin/continuous endpoint is used to retrieve binned - * continuous data from the visualization resource. - * - * @param rsURL The URL of the ResourceRS - * @param queryRequest The query request object - * @param requestSource The request source - * @return The response from the ResourceRS - */ - public Response queryContinuous(String rsURL, QueryRequest queryRequest, String requestSource) { - logger.debug("Calling ResourceWebClient queryContinuous()"); - HttpResponse resourcesResponse = null; - try { - if (queryRequest == null) { - throw new ProtocolException("Missing query data"); - } - if (queryRequest.getResourceCredentials() == null) { - throw new NotAuthorizedException("Missing credentials"); - } - if (rsURL == null) { - throw new ApplicationException("Missing resource URL"); - } - - String pathName = "/bin/continuous"; - String body = json.writeValueAsString(queryRequest); - - Header[] headers = createHeaders(queryRequest.getResourceCredentials()); - if (requestSource != null) { - Header sourceHeader = new BasicHeader("request-source", requestSource); - - // Add the source header to the headers array. - Header[] newHeaders = new Header[headers.length + 1]; - System.arraycopy(headers, 0, newHeaders, 0, headers.length); - newHeaders[headers.length] = sourceHeader; - headers = newHeaders; - } - - logger.debug("Calling ResourceWebClient queryContinuous() with body: " + body + " and headers: " + queryRequest); - resourcesResponse = httpClientUtil.retrievePostResponse(HttpClientUtil.composeURL(rsURL, pathName), headers, body); - if (resourcesResponse.getStatusLine().getStatusCode() != 200) { - throwError(resourcesResponse, rsURL); - } - - String content = httpClientUtil.readObjectFromResponse(resourcesResponse, StandardCharsets.UTF_8); - return Response.ok(content).build(); - } catch (JsonProcessingException e) { - throw new RuntimeException(e); - } finally { - closeHttpResponse(resourcesResponse); - } - } - - private void throwError(HttpResponse response, String baseURL) { - logger.error("ResourceRS did not return a 200"); - String errorMessage = baseURL + " " + response.getStatusLine().getStatusCode() + " " + response.getStatusLine().getReasonPhrase(); - try { - JsonNode responseNode = json.readTree(response.getEntity().getContent()); - if (responseNode != null && responseNode.has("message")) { - errorMessage += "/n" + responseNode.get("message").asText(); - } - } catch (IOException e) { - logger.error(e.getMessage()); - } - if (response.getStatusLine().getStatusCode() == 401) { - throw new NotAuthorizedException(errorMessage); - } - throw new ResourceInterfaceException(errorMessage); - - } - - private Header[] createHeaders(Map resourceCredentials) { - Header authorizationHeader = new BasicHeader(HttpHeaders.AUTHORIZATION, BEARER_STRING + resourceCredentials.get(BEARER_TOKEN_KEY)); - Header contentTypeHeader = new BasicHeader(HttpHeaders.CONTENT_TYPE, "application/json"); - Header[] headers = {authorizationHeader, contentTypeHeader}; - return headers; - } - -} diff --git a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/util/exception/ResourceCommunicationException.java b/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/util/exception/ResourceCommunicationException.java deleted file mode 100644 index 63ef0f47d..000000000 --- a/pic-sure-resources/pic-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/util/exception/ResourceCommunicationException.java +++ /dev/null @@ -1,15 +0,0 @@ -package edu.harvard.dbmi.avillach.util.exception; - -public class ResourceCommunicationException extends RuntimeException { - - private static final long serialVersionUID = -3039213913753996987L; - - public ResourceCommunicationException(String targetIrctUrl, Exception e) { - super("An error has occurred attempting to process a request for " + targetIrctUrl, e); - } - - public ResourceCommunicationException(String targetIrctUrl, String message){ - super("An error has occurred attempting to process a request for " + targetIrctUrl + ": " + message); - } - -} diff --git a/pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/AppTest.java b/pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/AppTest.java deleted file mode 100755 index d8ae15963..000000000 --- a/pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/AppTest.java +++ /dev/null @@ -1,38 +0,0 @@ -package edu.harvard.dbmi.avillach; - -import junit.framework.Test; -import junit.framework.TestCase; -import junit.framework.TestSuite; - -/** - * Unit test for simple App. - */ -public class AppTest - extends TestCase -{ - /** - * Create the test case - * - * @param testName name of the test case - */ - public AppTest( String testName ) - { - super( testName ); - } - - /** - * @return the suite of tests being tested - */ - public static Test suite() - { - return new TestSuite( AppTest.class ); - } - - /** - * Rigourous Test :-) - */ - public void testApp() - { - assertTrue( true ); - } -} diff --git a/pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/domain/QueryRequestTest.java b/pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/domain/QueryRequestTest.java deleted file mode 100644 index 9e52a3580..000000000 --- a/pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/domain/QueryRequestTest.java +++ /dev/null @@ -1,72 +0,0 @@ -package edu.harvard.dbmi.avillach.domain; - - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; -import org.junit.Assert; -import org.junit.Test; - -import java.util.HashMap; -import java.util.UUID; - -public class QueryRequestTest { - private static final ObjectMapper mapper = new ObjectMapper(); - - @Test - public void shouldSerializeGeneralQueryRequest() throws JsonProcessingException { - GeneralQueryRequest expected = new GeneralQueryRequest(); - expected.setQuery(null); - expected.setResourceCredentials(new HashMap<>()); - expected.setResourceUUID(UUID.randomUUID()); - String json = mapper.writeValueAsString(expected); - - QueryRequest actual = mapper.readValue(json, QueryRequest.class); - - Assert.assertEquals(GeneralQueryRequest.class, actual.getClass()); - Assert.assertEquals(expected.getResourceUUID(), actual.getResourceUUID()); - } - - @Test - public void shouldSerializeGICRequest() throws JsonProcessingException { - FederatedQueryRequest expected = new FederatedQueryRequest(); - expected.setQuery(null); - expected.setResourceCredentials(new HashMap<>()); - expected.setResourceUUID(UUID.randomUUID()); - expected.setCommonAreaUUID(UUID.randomUUID()); - expected.setInstitutionOfOrigin("Top secret institution (shh!)"); - String json = mapper.writeValueAsString(expected); - - QueryRequest actual = mapper.readValue(json, QueryRequest.class); - - Assert.assertEquals(FederatedQueryRequest.class, actual.getClass()); - Assert.assertEquals(expected.getResourceUUID(), actual.getResourceUUID()); - } - - @Test - public void shouldSerializeRequestWithNoType() throws JsonProcessingException { - // Make sure json without the @Type annotation doesn't break this - String json = "{\"resourceCredentials\":{},\"query\":null,\"resourceUUID\":\"e4513cca-12c0-4fe2-b2fd-5d05b821056c\"}"; - QueryRequest actual = mapper.readValue(json, QueryRequest.class); - - Assert.assertEquals(GeneralQueryRequest.class, actual.getClass()); - } - - @Test - public void shouldSerializeRequestWithNoTypeWithGICFields() throws JsonProcessingException { - String json = "{\"resourceCredentials\":{},\"query\":null,\"resourceUUID\":\"716d744f-9c89-40af-b572-222c1b20848f\",\"commonAreaUUID\":\"a79e3da0-e1fa-4626-9873-41cffd5e9115\",\"institutionOfOrigin\":\"Top secret institution (shh!)\"}"; - QueryRequest actual = mapper.readValue(json, QueryRequest.class); - - // This is for backwards compatibility. An un-updated client should handle unknown fields gracefully - Assert.assertEquals(GeneralQueryRequest.class, actual.getClass()); - } - - @Test - public void shouldSerializeRequestWithGICTypeAndExtraField() throws JsonProcessingException { - String json = "{\"@type\":\"FederatedQueryRequest\",\"madeUpField\":0,\"resourceCredentials\":{},\"query\":null,\"resourceUUID\":\"716d744f-9c89-40af-b572-222c1b20848f\",\"commonAreaUUID\":\"a79e3da0-e1fa-4626-9873-41cffd5e9115\",\"institutionOfOrigin\":\"Top secret institution (shh!)\"}"; - QueryRequest actual = mapper.readValue(json, QueryRequest.class); - - // This is for backwards compatibility. - // An un-updated client should handle unknown fields gracefully, even when it's a GIC request - Assert.assertEquals(FederatedQueryRequest.class, actual.getClass()); - } -} \ No newline at end of file diff --git a/pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/service/HttpClientUtilTest.java b/pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/service/HttpClientUtilTest.java deleted file mode 100644 index 53afc1d12..000000000 --- a/pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/service/HttpClientUtilTest.java +++ /dev/null @@ -1,33 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import static org.junit.Assert.assertEquals; - -import edu.harvard.dbmi.avillach.util.HttpClientUtil; -import org.junit.Test; - -public class HttpClientUtilTest { - - @Test - public void testComposeUrl() { - String test = HttpClientUtil.composeURL("http://foo.bar.com/pic-sure", "info"); - assertEquals("http://foo.bar.com/pic-sure/info", test); - - test = HttpClientUtil.composeURL("http://foo.bar.com/pic-sure/", "info"); - assertEquals("http://foo.bar.com/pic-sure/info", test); - - test = HttpClientUtil.composeURL("http://foo.bar.com/pic-sure///", "//info"); - assertEquals("http://foo.bar.com/pic-sure/info", test); - - test = HttpClientUtil.composeURL("http://foo.bar.com/pic-sure", "info/something/something"); - assertEquals("http://foo.bar.com/pic-sure/info/something/something", test); - - test = HttpClientUtil.composeURL("http://foo.bar.com/pic-sure/", "/info"); - assertEquals("http://foo.bar.com/pic-sure/info", test); - - test = HttpClientUtil.composeURL("http://localhost:8080", "/info"); - assertEquals("http://localhost:8080/info", test); - - test = HttpClientUtil.composeURL("http://localhost:8080/", "/info"); - assertEquals("http://localhost:8080/info", test); - } -} diff --git a/pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/service/ProxyWebClientTest.java b/pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/service/ProxyWebClientTest.java deleted file mode 100644 index 6d894d865..000000000 --- a/pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/service/ProxyWebClientTest.java +++ /dev/null @@ -1,328 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import edu.harvard.dbmi.avillach.data.entity.Resource; -import edu.harvard.dbmi.avillach.data.repository.ResourceRepository; -import org.apache.http.Header; -import org.apache.http.HttpEntity; -import org.apache.http.HttpResponse; -import org.apache.http.StatusLine; -import org.apache.http.message.BasicHeader; -import org.apache.http.client.HttpClient; -import org.apache.http.client.methods.HttpGet; -import org.apache.http.client.methods.HttpPost; -import org.junit.Assert; -import org.junit.Test; -import org.junit.runner.RunWith; -import org.mockito.InjectMocks; -import org.mockito.Mock; -import org.mockito.Mockito; -import org.mockito.junit.MockitoJUnitRunner; - -import javax.ws.rs.core.HttpHeaders; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.MultivaluedHashMap; -import javax.ws.rs.core.Response; -import javax.ws.rs.core.StreamingOutput; -import java.io.ByteArrayInputStream; -import java.io.ByteArrayOutputStream; -import java.io.IOException; -import java.io.InputStream; -import java.util.List; - -import static org.junit.Assert.*; - -@RunWith(MockitoJUnitRunner.class) -public class ProxyWebClientTest { - - @Mock - private HttpClient client; - - @Mock - private HttpResponse response; - - @Mock - private HttpEntity entity; - - @Mock - private StatusLine statusLine; - - @Mock - private ResourceRepository resourceRepository; - - @InjectMocks - private ProxyWebClient subject; - - @Test - public void shouldPostToProxy() throws IOException { - Mockito.when(client.execute(Mockito.any(HttpPost.class))).thenReturn(response); - Mockito.when(response.getStatusLine()).thenReturn(statusLine); - Mockito.when(statusLine.getStatusCode()).thenReturn(200); - Mockito.when(response.getEntity()).thenReturn(entity); - Mockito.when(response.getStatusLine()).thenReturn(statusLine); - Mockito.when(statusLine.getStatusCode()).thenReturn(200); - Mockito.when(entity.getContent()).thenReturn(new ByteArrayInputStream("{}".getBytes())); - Mockito.when(entity.getContentLength()).thenReturn(2L); - Mockito.when(resourceRepository.getByColumn("name", "foo")).thenReturn(List.of(new Resource())); - subject.client = client; - - Response actual = subject.postProxy("foo", "/my/cool/path", "{}", new MultivaluedHashMap<>(), null); - - Assert.assertEquals(200, actual.getStatus()); - } - - @Test - public void shouldGetToProxy() throws IOException { - Mockito.when(client.execute(Mockito.any(HttpGet.class))).thenReturn(response); - Mockito.when(response.getStatusLine()).thenReturn(statusLine); - Mockito.when(statusLine.getStatusCode()).thenReturn(200); - Mockito.when(response.getEntity()).thenReturn(entity); - Mockito.when(response.getStatusLine()).thenReturn(statusLine); - Mockito.when(statusLine.getStatusCode()).thenReturn(200); - Mockito.when(entity.getContent()).thenReturn(new ByteArrayInputStream("{}".getBytes())); - Mockito.when(entity.getContentLength()).thenReturn(2L); - Mockito.when(resourceRepository.getByColumn("name", "bar")).thenReturn(List.of(new Resource())); - subject.client = client; - - Response actual = subject.getProxy("bar", "/my/cool/path", new MultivaluedHashMap<>(), null); - - Assert.assertEquals(200, actual.getStatus()); - } - - @Test - public void shouldRejectNastyHost() { - Mockito.when(resourceRepository.getByColumn("name", "an.evil.domain")).thenReturn(List.of()); - - Response actual = subject.postProxy("an.evil.domain", "hax", null, new MultivaluedHashMap<>(), null); - assertEquals(400, actual.getStatus()); - - actual = subject.getProxy("an.evil.domain", "hax", new MultivaluedHashMap<>(), null); - assertEquals(400, actual.getStatus()); - } - - @Test - public void shouldForwardApiKeyHeader() throws IOException { - Mockito.when(resourceRepository.getByColumn("name", "foo")).thenReturn(List.of(new Resource())); - Mockito.when(client.execute(Mockito.argThat(request -> { - if (request instanceof HttpPost) { - HttpPost post = (HttpPost) request; - return post.getFirstHeader("X-API-Key") != null && "my-secret-key".equals(post.getFirstHeader("X-API-Key").getValue()); - } - return false; - }))).thenReturn(response); - Mockito.when(response.getStatusLine()).thenReturn(statusLine); - Mockito.when(statusLine.getStatusCode()).thenReturn(200); - Mockito.when(response.getEntity()).thenReturn(entity); - Mockito.when(entity.getContent()).thenReturn(new ByteArrayInputStream("{}".getBytes())); - subject.client = client; - - HttpHeaders headers = Mockito.mock(HttpHeaders.class); - Mockito.when(headers.getRequestHeader("x-api-key")).thenReturn(List.of("my-secret-key")); - - Response actual = subject.postProxy("foo", "/audit", "{}", new MultivaluedHashMap<>(), headers); - assertEquals(200, actual.getStatus()); - } - - @Test - public void shouldForwardAuthorizationHeader() throws IOException { - Mockito.when(resourceRepository.getByColumn("name", "foo")).thenReturn(List.of(new Resource())); - Mockito.when(client.execute(Mockito.argThat(request -> { - if (request instanceof HttpPost) { - HttpPost post = (HttpPost) request; - return post.getFirstHeader("authorization") != null - && "Bearer token123".equals(post.getFirstHeader("authorization").getValue()); - } - return false; - }))).thenReturn(response); - Mockito.when(response.getStatusLine()).thenReturn(statusLine); - Mockito.when(statusLine.getStatusCode()).thenReturn(200); - Mockito.when(response.getEntity()).thenReturn(entity); - Mockito.when(entity.getContent()).thenReturn(new ByteArrayInputStream("{}".getBytes())); - subject.client = client; - - HttpHeaders headers = Mockito.mock(HttpHeaders.class); - Mockito.when(headers.getRequestHeader("authorization")).thenReturn(List.of("Bearer token123")); - - Response actual = subject.postProxy("foo", "/audit", "{}", new MultivaluedHashMap<>(), headers); - assertEquals(200, actual.getStatus()); - } - - @Test - public void shouldForwardSessionIdHeader() throws IOException { - Mockito.when(resourceRepository.getByColumn("name", "foo")).thenReturn(List.of(new Resource())); - Mockito.when(client.execute(Mockito.argThat(request -> { - if (request instanceof HttpPost) { - HttpPost post = (HttpPost) request; - return post.getFirstHeader("x-session-id") != null - && "sess-abc-123".equals(post.getFirstHeader("x-session-id").getValue()); - } - return false; - }))).thenReturn(response); - Mockito.when(response.getStatusLine()).thenReturn(statusLine); - Mockito.when(statusLine.getStatusCode()).thenReturn(200); - Mockito.when(response.getEntity()).thenReturn(entity); - Mockito.when(entity.getContent()).thenReturn(new ByteArrayInputStream("{}".getBytes())); - subject.client = client; - - HttpHeaders headers = Mockito.mock(HttpHeaders.class); - Mockito.when(headers.getRequestHeader("x-session-id")).thenReturn(List.of("sess-abc-123")); - - Response actual = subject.postProxy("foo", "/audit", "{}", new MultivaluedHashMap<>(), headers); - assertEquals(200, actual.getStatus()); - } - - @Test - public void shouldForwardClientTypeHeader() throws IOException { - Mockito.when(resourceRepository.getByColumn("name", "foo")).thenReturn(List.of(new Resource())); - Mockito.when(client.execute(Mockito.argThat(request -> { - if (request instanceof HttpPost) { - HttpPost post = (HttpPost) request; - return post.getFirstHeader("x-client-type") != null - && "PYTHON_ADAPTER".equals(post.getFirstHeader("x-client-type").getValue()); - } - return false; - }))).thenReturn(response); - Mockito.when(response.getStatusLine()).thenReturn(statusLine); - Mockito.when(statusLine.getStatusCode()).thenReturn(200); - Mockito.when(response.getEntity()).thenReturn(entity); - Mockito.when(entity.getContent()).thenReturn(new ByteArrayInputStream("{}".getBytes())); - subject.client = client; - - HttpHeaders headers = Mockito.mock(HttpHeaders.class); - Mockito.when(headers.getRequestHeader("x-client-type")).thenReturn(List.of("PYTHON_ADAPTER")); - - Response actual = subject.postProxy("foo", "/audit", "{}", new MultivaluedHashMap<>(), headers); - assertEquals(200, actual.getStatus()); - } - - @Test - public void shouldNotFailWithNullHeaders() throws IOException { - Mockito.when(client.execute(Mockito.any(HttpPost.class))).thenReturn(response); - Mockito.when(response.getStatusLine()).thenReturn(statusLine); - Mockito.when(statusLine.getStatusCode()).thenReturn(200); - Mockito.when(response.getEntity()).thenReturn(entity); - Mockito.when(entity.getContent()).thenReturn(new ByteArrayInputStream("{}".getBytes())); - Mockito.when(resourceRepository.getByColumn("name", "foo")).thenReturn(List.of(new Resource())); - subject.client = client; - - Response actual = subject.postProxy("foo", "/audit", "{}", new MultivaluedHashMap<>(), null); - assertEquals(200, actual.getStatus()); - } - - @Test - public void shouldPostWithParams() throws IOException { - Mockito.when(client.execute(Mockito.any(HttpPost.class))).thenReturn(response); - Mockito.when(response.getStatusLine()).thenReturn(statusLine); - Mockito.when(statusLine.getStatusCode()).thenReturn(200); - Mockito.when(response.getEntity()).thenReturn(entity); - Mockito.when(response.getStatusLine()).thenReturn(statusLine); - Mockito.when(statusLine.getStatusCode()).thenReturn(200); - Mockito.when(entity.getContent()).thenReturn(new ByteArrayInputStream("{}".getBytes())); - Mockito.when(entity.getContentLength()).thenReturn(2L); - Mockito.when(resourceRepository.getByColumn("name", "foo")).thenReturn(List.of(new Resource())); - subject.client = client; - - MultivaluedHashMap params = new MultivaluedHashMap<>(); - params.put("site", List.of("bch")); - Response actual = subject.postProxy("foo", "/my/cool/path", "{}", params, null); - - Assert.assertEquals(200, actual.getStatus()); - } - - @Test - public void shouldBufferSmallResponse() throws IOException { - Mockito.when(client.execute(Mockito.any(HttpGet.class))).thenReturn(response); - Mockito.when(response.getEntity()).thenReturn(entity); - Mockito.when(response.getStatusLine()).thenReturn(statusLine); - Mockito.when(statusLine.getStatusCode()).thenReturn(200); - Mockito.when(entity.getContent()).thenReturn(new ByteArrayInputStream("{}".getBytes())); - Mockito.when(entity.getContentLength()).thenReturn(2L); - Mockito.when(resourceRepository.getByColumn("name", "bar")).thenReturn(List.of(new Resource())); - subject.client = client; - - Response actual = subject.getProxy("bar", "/my/cool/path", new MultivaluedHashMap<>(), null); - - Assert.assertEquals(200, actual.getStatus()); - // Small responses should be buffered as a byte array - assertTrue(actual.getEntity() instanceof byte[]); - } - - @Test - public void shouldStreamLargeResponse() throws IOException { - ByteArrayInputStream largeBody = new ByteArrayInputStream("{}".getBytes()); - Mockito.when(client.execute(Mockito.any(HttpGet.class))).thenReturn(response); - Mockito.when(response.getEntity()).thenReturn(entity); - Mockito.when(response.getStatusLine()).thenReturn(statusLine); - Mockito.when(statusLine.getStatusCode()).thenReturn(200); - Mockito.when(entity.getContent()).thenReturn(largeBody); - Mockito.when(entity.getContentLength()).thenReturn(20 * 1024 * 1024L); - Mockito.when(resourceRepository.getByColumn("name", "bar")).thenReturn(List.of(new Resource())); - subject.client = client; - - Response actual = subject.getProxy("bar", "/my/cool/path", new MultivaluedHashMap<>(), null); - - Assert.assertEquals(200, actual.getStatus()); - // Large responses should use StreamingOutput for true chunked streaming - assertTrue(actual.getEntity() instanceof StreamingOutput); - ByteArrayOutputStream out = new ByteArrayOutputStream(); - ((StreamingOutput) actual.getEntity()).write(out); - assertEquals("{}", out.toString()); - } - - @Test - public void shouldStreamWhenContentLengthUnknown() throws IOException { - ByteArrayInputStream body = new ByteArrayInputStream("{}".getBytes()); - Mockito.when(client.execute(Mockito.any(HttpGet.class))).thenReturn(response); - Mockito.when(response.getEntity()).thenReturn(entity); - Mockito.when(response.getStatusLine()).thenReturn(statusLine); - Mockito.when(statusLine.getStatusCode()).thenReturn(200); - Mockito.when(entity.getContent()).thenReturn(body); - Mockito.when(entity.getContentLength()).thenReturn(-1L); - Mockito.when(resourceRepository.getByColumn("name", "bar")).thenReturn(List.of(new Resource())); - subject.client = client; - - Response actual = subject.getProxy("bar", "/my/cool/path", new MultivaluedHashMap<>(), null); - - Assert.assertEquals(200, actual.getStatus()); - // Unknown content length (-1) should use StreamingOutput to be safe - assertTrue(actual.getEntity() instanceof StreamingOutput); - ByteArrayOutputStream out = new ByteArrayOutputStream(); - ((StreamingOutput) actual.getEntity()).write(out); - assertEquals("{}", out.toString()); - } - - @Test - public void shouldForwardContentType() throws IOException { - Mockito.when(client.execute(Mockito.any(HttpGet.class))).thenReturn(response); - Mockito.when(response.getEntity()).thenReturn(entity); - Mockito.when(response.getStatusLine()).thenReturn(statusLine); - Mockito.when(statusLine.getStatusCode()).thenReturn(200); - Mockito.when(entity.getContent()).thenReturn(new ByteArrayInputStream("{}".getBytes())); - Mockito.when(entity.getContentLength()).thenReturn(2L); - Mockito.when(entity.getContentType()).thenReturn(new BasicHeader("Content-Type", "application/json")); - Mockito.when(resourceRepository.getByColumn("name", "bar")).thenReturn(List.of(new Resource())); - subject.client = client; - - Response actual = subject.getProxy("bar", "/my/cool/path", new MultivaluedHashMap<>(), null); - - Assert.assertEquals(200, actual.getStatus()); - assertEquals("application/json", actual.getMediaType().toString()); - } - - @Test - public void shouldDefaultContentTypeWhenMissing() throws IOException { - Mockito.when(client.execute(Mockito.any(HttpGet.class))).thenReturn(response); - Mockito.when(response.getEntity()).thenReturn(entity); - Mockito.when(response.getStatusLine()).thenReturn(statusLine); - Mockito.when(statusLine.getStatusCode()).thenReturn(200); - Mockito.when(entity.getContent()).thenReturn(new ByteArrayInputStream("{}".getBytes())); - Mockito.when(entity.getContentLength()).thenReturn(2L); - // entity.getContentType() returns null by default (no mock) - Mockito.when(resourceRepository.getByColumn("name", "bar")).thenReturn(List.of(new Resource())); - subject.client = client; - - Response actual = subject.getProxy("bar", "/my/cool/path", new MultivaluedHashMap<>(), null); - - Assert.assertEquals(200, actual.getStatus()); - assertEquals(MediaType.APPLICATION_OCTET_STREAM, actual.getMediaType().toString()); - } -} diff --git a/pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/service/ResourceWebClientTest.java b/pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/service/ResourceWebClientTest.java deleted file mode 100644 index b3ea54b1b..000000000 --- a/pic-sure-resources/pic-sure-resource-api/src/test/java/edu/harvard/dbmi/avillach/service/ResourceWebClientTest.java +++ /dev/null @@ -1,436 +0,0 @@ -package edu.harvard.dbmi.avillach.service; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.github.tomakehurst.wiremock.junit.WireMockClassRule; -import edu.harvard.dbmi.avillach.domain.*; -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; -import org.glassfish.jersey.internal.RuntimeDelegateImpl; -import org.junit.BeforeClass; -import org.junit.Rule; -import org.junit.Test; -import org.junit.runner.RunWith; -import org.mockito.junit.MockitoJUnitRunner; - -import javax.ws.rs.core.Response; -import javax.ws.rs.ext.RuntimeDelegate; -import java.util.HashMap; -import java.util.Map; -import java.util.UUID; - -import static com.github.tomakehurst.wiremock.client.WireMock.*; -import static org.junit.Assert.*; - -@RunWith(MockitoJUnitRunner.class) -public class ResourceWebClientTest { - - private final static ObjectMapper json = new ObjectMapper(); - private final static String token = "testToken"; - private final static int port = 8079; - private final static String testURL = "http://localhost:" + port; - private final ResourceWebClient cut = new ResourceWebClient(); - - @Rule - public WireMockClassRule wireMockRule = new WireMockClassRule(port); - - @BeforeClass - public static void beforeClass() { - - // Need to be able to throw exceptions without container so we can verify correct errors are being thrown - RuntimeDelegate runtimeDelegate = new RuntimeDelegateImpl(); - RuntimeDelegate.setInstance(runtimeDelegate); - } - - @Test - public void testInfo() throws JsonProcessingException { - String resourceInfo = json.writeValueAsString(new ResourceInfo()); - - wireMockRule.stubFor(any(urlEqualTo("/info")).willReturn(aResponse().withStatus(200).withBody(resourceInfo))); - - // Any targetURL that matches /info will trigger wiremock - String targetURL = "/info"; - // Should throw an error if any parameters are missing - try { - cut.info(testURL, null); - fail(); - } catch (ProtocolException e) { - assertEquals(ProtocolException.MISSING_DATA, e.getContent()); - } - GeneralQueryRequest queryRequest = new GeneralQueryRequest(); - Map credentials = new HashMap<>(); - credentials.put(ResourceWebClient.BEARER_TOKEN_KEY, token); - queryRequest.setResourceCredentials(credentials); - // queryRequest.setTargetURL(targetURL); - // Obviously should fail without the rsURL - try { - cut.info(null, queryRequest); - fail(); - } catch (ApplicationException e) { - assertEquals(ApplicationException.MISSING_RESOURCE_PATH, e.getContent()); - } - - // Should fail without a targetURL - - // queryRequest.setTargetURL(null); - // try { - // cut.info(testURL, queryRequest); - // fail(); - // } catch (ApplicationException e) { - // assertEquals(ApplicationException.MISSING_TARGET_URL, e.getContent()); - // } - - // Assuming everything goes right - // queryRequest.setTargetURL(targetURL); - ResourceInfo result = cut.info(testURL, queryRequest); - assertNotNull("Result should not be null", result); - - // What if the resource has a problem? - wireMockRule.stubFor(any(urlEqualTo("/info")).willReturn(aResponse().withStatus(500))); - - try { - cut.info(testURL, queryRequest); - fail(); - } catch (Exception e) { - assertTrue(e.getMessage().contains("500 Server Error")); - } - - // What if resource returns the wrong type of object for some reason? - String incorrectResponse = json.writeValueAsString(new SearchResults()); - wireMockRule.stubFor(any(urlEqualTo("/info")).willReturn(aResponse().withStatus(200).withBody(incorrectResponse))); - - try { - cut.info(testURL, queryRequest); - fail(); - } catch (Exception e) { - assertTrue(e.getMessage().contains("Incorrect object type returned")); - } - } - - @Test - public void testSearch() throws JsonProcessingException { - String searchResults = json.writeValueAsString(new SearchResults()); - - wireMockRule.stubFor(any(urlEqualTo("/search")).willReturn(aResponse().withStatus(200).withBody(searchResults))); - - // Should throw an error if any parameters are missing - try { - cut.search(testURL, null); - fail(); - } catch (ProtocolException e) { - assertEquals(ProtocolException.MISSING_DATA, e.getContent()); - } - - GeneralQueryRequest request = new GeneralQueryRequest(); - try { - cut.search(testURL, request); - fail(); - } catch (ProtocolException e) { - assertEquals(ProtocolException.MISSING_DATA, e.getContent()); - } - - request.setQuery("query"); - - // try { - // cut.search(testURL, request); - // fail(); - // } catch (ApplicationException e) { - // assertEquals(ApplicationException.MISSING_TARGET_URL, e.getContent()); - // } - - String targetURL = "/search"; - // request.setTargetURL(targetURL); - - try { - cut.search(null, request); - fail(); - } catch (ApplicationException e) { - assertEquals(ApplicationException.MISSING_RESOURCE_PATH, e.getContent()); - } - - // //Should fail if no credentials given - // request.setQuery("query"); - // request.setTargetURL(targetURL); - // try { - // cut.search(testURL, request); - // fail(); - // } catch (Exception e) { - // assertEquals("HTTP 401 Unauthorized", e.getMessage()); - // } - - // With credentials but not search term - /* - * Map credentials = new HashMap<>(); credentials.put(ResourceWebClient.BEARER_TOKEN_KEY, token); - * request.setQuery(null); request.setResourceCredentials(credentials); try { cut.search(testURL, request); fail(); } catch - * (ProtocolException e) { assertEquals(ProtocolException.MISSING_DATA, e.getContent()); } - */ - - // Should fail with no targetURL - Map credentials = new HashMap<>(); - credentials.put(ResourceWebClient.BEARER_TOKEN_KEY, token); - request.setResourceCredentials(credentials); - // request.setTargetURL(null); - request.setQuery("%blood%"); - // try { - // cut.search(testURL, request); - // fail(); - // } catch (ApplicationException e) { - // assertEquals(ApplicationException.MISSING_TARGET_URL, e.getContent()); - // } - - // request.setTargetURL(targetURL); - SearchResults result = cut.search(testURL, request); - assertNotNull("Result should not be null", result); - - // What if the resource has a problem? - wireMockRule.stubFor(any(urlEqualTo("/search")).willReturn(aResponse().withStatus(500))); - - try { - cut.search(testURL, request); - fail(); - } catch (Exception e) { - assertTrue(e.getMessage().contains("500 Server Error")); - } - - // What if resource returns the wrong type of object for some reason? - ResourceInfo incorrectResponse = new ResourceInfo(); - incorrectResponse.setName("resource name"); - incorrectResponse.setId(new UUID(1L, 1L)); - wireMockRule.stubFor( - any(urlEqualTo("/search")).willReturn(aResponse().withStatus(200).withBody(json.writeValueAsString(incorrectResponse))) - ); - - try { - cut.search(testURL, request); - fail(); - } catch (Exception e) { - assertTrue(e.getMessage().contains("Incorrect object type returned")); - } - } - - @Test - public void testQuery() throws JsonProcessingException { - String queryResults = json.writeValueAsString(new QueryStatus()); - - wireMockRule.stubFor(any(urlEqualTo("/query")).willReturn(aResponse().withStatus(200).withBody(queryResults))); - - // Should fail if any parameters are missing - try { - cut.query(testURL, null); - fail(); - } catch (ProtocolException e) { - assertEquals(ProtocolException.MISSING_DATA, e.getContent()); - } - GeneralQueryRequest request = new GeneralQueryRequest(); - // request.setTargetURL("/query"); - - try { - cut.query(null, request); - fail(); - } catch (ApplicationException e) { - assertEquals(ApplicationException.MISSING_RESOURCE_PATH, e.getContent()); - } - - // Should fail if no credentials given - // try { - // cut.query(testURL, request); - // fail(); - // } catch (Exception e) { - // assertEquals("HTTP 401 Unauthorized", e.getMessage()); - // } - - Map credentials = new HashMap<>(); - request.setResourceCredentials(credentials); - // request.setTargetURL(null); - // Should fail without a targetURL - // try { - // cut.query(testURL, request); - // fail(); - // } catch (ApplicationException e) { - // assertEquals(ApplicationException.MISSING_TARGET_URL, e.getContent()); - // } - - // request.setTargetURL("/query"); - - // Everything goes correctly - QueryStatus result = cut.query(testURL, request); - assertNotNull("Result should not be null", result); - - // What if the resource has a problem? - wireMockRule.stubFor(any(urlEqualTo("/query")).willReturn(aResponse().withStatus(500))); - - try { - cut.query(testURL, request); - fail(); - } catch (Exception e) { - assertTrue(e.getMessage().contains("500 Server Error")); - } - - // What if resource returns the wrong type of object for some reason? - ResourceInfo incorrectResponse = new ResourceInfo(); - incorrectResponse.setName("resource name"); - incorrectResponse.setId(new UUID(1L, 1L)); - wireMockRule.stubFor( - any(urlEqualTo("/query")).willReturn(aResponse().withStatus(200).withBody(json.writeValueAsString(incorrectResponse))) - ); - - try { - cut.query(testURL, request); - fail(); - } catch (Exception e) { - assertTrue(e.getMessage().contains("Incorrect object type returned")); - } - } - - @Test - public void testQueryResult() throws JsonProcessingException { - String testId = "230048"; - byte[] mockResult = new byte[] {}; - - - - wireMockRule.stubFor(any(urlMatching("/query/.*/result")).willReturn(aResponse().withStatus(200).withBody(mockResult))); - - // Should fail if missing any parameters - // try { - // cut.queryResult(testURL, testId, null); - // fail(); - // } catch (ProtocolException e) { - // assertEquals(ProtocolException.MISSING_DATA, e.getContent()); - // } - GeneralQueryRequest queryRequest = new GeneralQueryRequest(); - Map credentials = new HashMap<>(); - credentials.put(ResourceWebClient.BEARER_TOKEN_KEY, token); - queryRequest.setResourceCredentials(credentials); - // String targetURL = "/query/13452134/result"; - //// queryRequest.setTargetURL(targetURL); - // - // try { - // cut.queryResult(testURL, null, queryRequest); - // fail(); - // } catch (ProtocolException e) { - // assertEquals(ProtocolException.MISSING_QUERY_ID, e.getContent()); - // } - // try { - // cut.queryResult(null, testId, queryRequest); - // fail(); - // } catch (ApplicationException e) { - // assertEquals(ApplicationException.MISSING_RESOURCE_PATH, e.getContent()); - // } - - //// queryRequest.setTargetURL(null); - // //Should fail without a targetURL - // try { - // cut.queryResult(testURL, testId, queryRequest); - // fail(); - // } catch (ApplicationException e) { - // assertEquals(ApplicationException.MISSING_TARGET_URL, e.getContent()); - // } - // - //// queryRequest.setTargetURL(targetURL); - - - // Everything should work here - Response result = cut.queryResult(testURL, testId, queryRequest); - assertNotNull("Result should not be null", result); - // String resultContent = IOUtils.toString((InputStream) result.getEntity(), "UTF-8"); - byte[] resultContent = (byte[]) result.getEntity(); - assertArrayEquals("Result should match " + mockResult, mockResult, resultContent); - - // What if the resource has a problem? - wireMockRule.stubFor(any(urlMatching("/query/.*/result")).willReturn(aResponse().withStatus(500))); - - try { - cut.queryResult(testURL, testId, queryRequest); - fail(); - } catch (Exception e) { - assertTrue(e.getMessage().contains("500 Server Error")); - } - } - - @Test - public void testQueryStatus() throws JsonProcessingException { - String testId = "230048"; - QueryStatus testResult = new QueryStatus(); - testResult.setStatus(PicSureStatus.PENDING); - testResult.setResourceStatus("RUNNING"); - String queryStatus = json.writeValueAsString(testResult); - - wireMockRule.stubFor(any(urlMatching("/query/.*/status")).willReturn(aResponse().withStatus(200).withBody(queryStatus))); - - // Fails with any missing parameters - try { - cut.queryStatus(testURL, testId, null); - fail(); - } catch (ProtocolException e) { - assertEquals(ProtocolException.MISSING_DATA, e.getContent()); - } - GeneralQueryRequest queryRequest = new GeneralQueryRequest(); - Map credentials = new HashMap<>(); - credentials.put(ResourceWebClient.BEARER_TOKEN_KEY, token); - queryRequest.setResourceCredentials(credentials); - // String targetURL = "/query/13452134/result"; - // queryRequest.setTargetURL(targetURL); - - try { - cut.queryStatus(testURL, null, queryRequest); - fail(); - } catch (ProtocolException e) { - assertEquals(ProtocolException.MISSING_QUERY_ID, e.getContent()); - } - try { - cut.queryStatus(null, testId, queryRequest); - fail(); - } catch (ApplicationException e) { - assertEquals(ApplicationException.MISSING_RESOURCE_PATH, e.getContent()); - } - - // queryRequest.setTargetURL(null); - - // Should fail without a targetURL - // try { - // cut.queryStatus(testURL, testId, queryRequest); - // fail(); - // } catch (ApplicationException e) { - // assertEquals(ApplicationException.MISSING_TARGET_URL, e.getContent()); - // } - - - - // queryRequest.setTargetURL(targetURL); - - // Everything should work here - QueryStatus result = cut.queryStatus(testURL, testId, queryRequest); - assertNotNull("Result should not be null", result); - // Make sure all necessary fields are present - assertNotNull("Duration should not be null", result.getDuration()); - assertNotNull("Expiration should not be null", result.getExpiration()); - assertNotNull("ResourceStatus should not be null", result.getResourceStatus()); - assertNotNull("Status should not be null", result.getStatus()); - - // What if the resource has a problem? - wireMockRule.stubFor(any(urlMatching("/query/.*/status")).willReturn(aResponse().withStatus(500))); - - try { - cut.queryStatus(testURL, testId, queryRequest); - fail(); - } catch (Exception e) { - assertTrue(e.getMessage().contains("500 Server Error")); - } - - // What if resource returns the wrong type of object for some reason? - ResourceInfo incorrect = new ResourceInfo(); - incorrect.setName("resource name"); - incorrect.setId(new UUID(1L, 1L)); - wireMockRule.stubFor( - any(urlMatching("/query/.*/status")).willReturn(aResponse().withStatus(200).withBody(json.writeValueAsString(incorrect))) - ); - - try { - cut.queryStatus(testURL, testId, queryRequest); - fail(); - } catch (Exception e) { - assertTrue(e.getMessage().contains("Incorrect object type returned")); - } - } -} diff --git a/pic-sure-resources/pom.xml b/pic-sure-resources/pom.xml deleted file mode 100644 index 3d53cff18..000000000 --- a/pic-sure-resources/pom.xml +++ /dev/null @@ -1,75 +0,0 @@ - - - 4.0.0 - - pic-sure-api - edu.harvard.hms.dbmi.avillach - 2.2.0-SNAPSHOT - - pic-sure-resources - pom - pic-sure-resources - - pic-sure-resource-api - pic-sure-passthrough-resource - pic-sure-aggregate-data-sharing-resource - - - - - org.slf4j - slf4j-api - - - org.slf4j - slf4j-jdk14 - - - - - - - org.apache.maven.plugins - maven-compiler-plugin - - 9 - 9 - - - - org.apache.maven.plugins - maven-dependency-plugin - - - retrieve-mysql-driver - generate-sources - - copy - - false - - - - com.mysql - mysql-connector-j - 8.0.32 - jar - true - ${project.build.directory}/modules/system/layers/base/com/sql/mysql/main/ - - - - - - - - org.apache.maven.plugins - maven-war-plugin - - false - - - - - - diff --git a/pic-sure-util/pom.xml b/pic-sure-util/pom.xml deleted file mode 100644 index 4806886db..000000000 --- a/pic-sure-util/pom.xml +++ /dev/null @@ -1,49 +0,0 @@ - - - - pic-sure-api - edu.harvard.hms.dbmi.avillach - 2.2.0-SNAPSHOT - - 4.0.0 - pic-sure-util - - - com.fasterxml.jackson.core - jackson-core - - - javax - javaee-api - provided - - - com.fasterxml.jackson.core - jackson-databind - - - - org.slf4j - slf4j-api - - - - org.slf4j - slf4j-jdk14 - - - org.apache.httpcomponents - httpcore - - - org.apache.httpcomponents - httpclient - - - commons-io - commons-io - - - diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/HttpClientUtil.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/HttpClientUtil.java deleted file mode 100644 index 6be9785a7..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/HttpClientUtil.java +++ /dev/null @@ -1,350 +0,0 @@ -package edu.harvard.dbmi.avillach.util; - -import static edu.harvard.dbmi.avillach.util.Utilities.buildHttpClientContext; - -import java.io.*; -import java.net.URI; -import java.net.URISyntaxException; -import java.nio.charset.Charset; -import java.nio.charset.StandardCharsets; -import java.security.KeyManagementException; -import java.security.NoSuchAlgorithmException; -import java.util.*; -import java.util.function.Predicate; -import java.util.stream.Collectors; - -import javax.net.ssl.SSLContext; -import javax.ws.rs.NotAuthorizedException; -import javax.ws.rs.core.HttpHeaders; -import javax.ws.rs.core.MediaType; - -import org.apache.http.Header; -import org.apache.http.HttpResponse; -import org.apache.http.client.HttpClient; -import org.apache.http.client.config.RequestConfig; -import org.apache.http.client.methods.HttpGet; -import org.apache.http.client.methods.HttpPost; -import org.apache.http.conn.HttpClientConnectionManager; -import org.apache.http.conn.ssl.SSLConnectionSocketFactory; -import org.apache.http.entity.StringEntity; -import org.apache.http.impl.client.HttpClientBuilder; -import org.apache.http.impl.client.HttpClients; -import org.apache.http.message.BasicHeader; -import org.apache.http.ssl.SSLContexts; -import org.apache.http.util.EntityUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.core.type.TypeReference; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; - -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.exception.ResourceInterfaceException; - -public class HttpClientUtil { - private static final ObjectMapper json = new ObjectMapper(); - - private static final Logger logger = LoggerFactory.getLogger(HttpClientUtil.class); - - private final HttpClient httpClient; - - public HttpClientUtil(HttpClient httpClient) { - this.httpClient = httpClient; - } - - public static boolean is2xx(HttpResponse response) { - return response.getStatusLine().getStatusCode() / 100 == 2; - } - - /** - * resource level get, which will throw a ResourceInterfaceException if cannot get response back from the url - * - * @param uri - * @param headers - * @return - */ - public HttpResponse retrieveGetResponse(String uri, Header[] headers) { - try { - logger.debug("HttpClientUtil retrieveGetResponse()"); - - // HttpClient client = getConfiguredHttpClient(); - return simpleGet(httpClient, uri, headers); - } catch (ApplicationException e) { - throw new ResourceInterfaceException(uri, e); - } - } - - public static String composeURL(String baseURL, String pathName) { - return composeURL(baseURL, pathName, null); - } - - public static String composeURL(String baseURL, String pathName, String query) { - try { - URI uri = new URI(baseURL); - List basePathComponents = Arrays.asList(uri.getPath().split("/")); - List pathNameComponents = Arrays.asList(pathName.split("/")); - List allPathComponents = new LinkedList<>(); - Predicate nonEmpty = (segment) -> { - return !segment.isEmpty(); - }; - allPathComponents.addAll(basePathComponents.stream().filter(nonEmpty).collect(Collectors.toList())); - allPathComponents.addAll(pathNameComponents.stream().filter(nonEmpty).collect(Collectors.toList())); - String queryString = query == null ? uri.getQuery() : query; - return new URI( - uri.getScheme(), uri.getUserInfo(), uri.getHost(), uri.getPort(), "/" + String.join("/", allPathComponents), queryString, - uri.getFragment() - ).toString(); - } catch (URISyntaxException e) { - throw new ApplicationException("baseURL invalid : " + baseURL, e); - } - } - - /** - * resource level post, which will throw a ResourceInterfaceException if cannot get response back from the url - * - * @param uri - * @param headers - * @return - */ - public HttpResponse retrievePostResponse(String uri, Header[] headers, String body) { - try { - logger.debug("HttpClientUtil retrievePostResponse()"); - - List

headerList = new ArrayList<>(); - - if (headers != null) headerList = new ArrayList<>(Arrays.asList(headers)); - headerList.add(new BasicHeader(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON)); - - // HttpClient client = getConfiguredHttpClient(); - return simplePost(uri, httpClient, new StringEntity(body), headerList.toArray(new Header[headerList.size()])); - } catch (ApplicationException | UnsupportedEncodingException e) { - throw new ResourceInterfaceException(uri, e); - } - } - - public HttpResponse retrievePostResponse(String uri, List
headers, String body) { - return retrievePostResponse(uri, headers.toArray(new Header[headers.size()]), body); - } - - public List readListFromResponse(HttpResponse response, Class expectedElementType) { - logger.debug("HttpClientUtil readListFromResponse()"); - try { - String responseBody = EntityUtils.toString(response.getEntity(), StandardCharsets.UTF_8); - return json.readValue(responseBody, new TypeReference>() {}); - } catch (IOException e) { - throw new ApplicationException("Incorrect list type returned"); - } - } - - public String readObjectFromResponse(HttpResponse response, Charset charset) { - logger.debug("HttpClientUtil readObjectFromResponse(HttpResponse response)"); - try { - String responseBody = EntityUtils.toString(response.getEntity(), charset); - logger.debug("readObjectFromResponse() responseBody {}", responseBody); - return responseBody; - } catch (IOException e) { - throw new ApplicationException("Incorrect object type returned", e); - } - } - - public byte[] readBytesFromResponse(HttpResponse response) { - logger.debug("HttpClientUtil readObjectFromResponse(HttpResponse response)"); - try { - byte[] responseBody = EntityUtils.toByteArray(response.getEntity()); - logger.debug("readObjectFromResponse() responseBody {}", responseBody); - return responseBody; - } catch (IOException e) { - throw new ApplicationException("Incorrect object type returned", e); - } - } - - public static T readObjectFromResponse(HttpResponse response, Class expectedElementType) { - logger.debug("HttpClientUtil readObjectFromResponse()"); - try (InputStream is = response.getEntity().getContent(); - /* - * Note: We previously used EntityUtils.toString(), which was convenient because it automatically removed the UTF-8 BOM (Byte - * Order Mark) and decoded the content. However, it buffers the entire response into memory, which is inefficient for large - * payloads. To support streaming while maintaining BOM safety for downstream clients (e.g., R's gsub, which fails if a BOM is - * present), we now manually strip the BOM using a PushbackInputStream before passing the stream to Jackson for deserialization. - */ - PushbackInputStream pbis = new PushbackInputStream(is, 3) - ) { - - byte[] bom = new byte[3]; - int bytesRead = pbis.read(bom, 0, bom.length); - if (!(bytesRead == 3 && bom[0] == (byte) 0xEF && bom[1] == (byte) 0xBB && bom[2] == (byte) 0xBF)) { - pbis.unread(bom, 0, bytesRead); - } - - Reader reader = new InputStreamReader(pbis, StandardCharsets.UTF_8); - return json.readValue(reader, json.getTypeFactory().constructType(expectedElementType)); - } catch (IOException e) { - throw new ApplicationException("Incorrect object type returned", e); - } - } - - public static void throwResponseError(HttpResponse response, String baseURL) { - String errorMessage = baseURL + " " + response.getStatusLine().getStatusCode() + " " + response.getStatusLine().getReasonPhrase(); - try { - JsonNode responseNode = json.readTree(response.getEntity().getContent()); - if (responseNode != null && responseNode.has("message")) { - errorMessage += "/n" + responseNode.get("message").asText(); - } - } catch (IOException e) { - // That's fine, there's no message - } - if (response.getStatusLine().getStatusCode() == 401) { - throw new NotAuthorizedException(errorMessage); - } - throw new ResourceInterfaceException(errorMessage); - } - - public static void throwInternalResponseError(HttpResponse response, String baseURL) { - // We don't want to propagate 401s. A site 401ing is a server side error and should - // 500 in the common area. - String errorMessage = baseURL + " " + response.getStatusLine().getStatusCode() + " " + response.getStatusLine().getReasonPhrase(); - try { - JsonNode responseNode = json.readTree(response.getEntity().getContent()); - if (responseNode != null && responseNode.has("message")) { - errorMessage += "/n" + responseNode.get("message").asText(); - } - } catch (IOException e) { - // That's fine, there's no message - } - throw new ResourceInterfaceException(errorMessage); - } - - /** - * Basic and general post function using Apache Http Client - * - * @param uri - * @param client - * @param requestBody - * @param headers - * @return HttpResponse - * @throws ApplicationException - */ - public HttpResponse simplePost(String uri, HttpClient client, StringEntity requestBody, Header... headers) throws ApplicationException { - - HttpPost post = new HttpPost(uri); - post.setHeaders(headers); - post.setEntity(requestBody); - - try { - return httpClient.execute(post, buildHttpClientContext()); - } catch (IOException ex) { - logger.error("simplePost() Exception: {}, cannot get response by POST from url: {}", ex.getMessage(), uri); - throw new ApplicationException("Inner problem, please contact system admin and check the server log"); - } - } - - /** - * Basic and general post function using Apache Http Client - * - * @param uri - * @param requestBody - * @param client - * @param headers - * @return InputStream - */ - public InputStream simplePost(String uri, StringEntity requestBody, HttpClient client, Header... headers) { - HttpResponse response = simplePost(uri, client, requestBody, headers); - - try { - return response.getEntity().getContent(); - } catch (IOException ex) { - logger.error("simplePost() cannot get content by POST from url: {} - " + ex.getLocalizedMessage(), uri); - throw new ApplicationException("Inner problem, please contact system admin and check the server log"); - } - } - - /** - * for general and basic use of GET function using Apache Http Client - * - * @param client - * @param uri - * @param headers - * @return - * @throws ApplicationException - */ - public HttpResponse simpleGet(HttpClient client, String uri, Header... headers) throws ApplicationException { - HttpGet get = new HttpGet(uri); - get.setHeaders(headers); - - try { - return httpClient.execute(get, buildHttpClientContext()); - } catch (IOException ex) { - logger.error("HttpResponse simpleGet() cannot get response by GET from url: {} - " + ex.getLocalizedMessage(), uri); - throw new ApplicationException("Inner problem, please contact system admin and check the server log"); - } - } - - public InputStream simpleGet(String uri, HttpClient client, Header... headers) { - return simpleGetWithConfig(uri, client, null, headers); - } - - public InputStream simpleGetWithConfig(String uri, HttpClient client, RequestConfig config, Header... headers) - throws ApplicationException { - HttpGet get = new HttpGet(uri); - get.setHeaders(headers); - if (config != null) { - get.setConfig(config); - } - - try { - return httpClient.execute(get, buildHttpClientContext()).getEntity().getContent(); - } catch (IOException ex) { - logger.error("InputStream simpleGet() cannot get response by GET from url: {} - " + ex.getLocalizedMessage(), uri); - throw new ApplicationException("Inner problem, please contact system admin and check the server log"); - } - } - - public static HttpClient getConfiguredHttpClient(HttpClientConnectionManager connectionManager) { - try { - int timeout = 60; - RequestConfig config = RequestConfig.custom().setConnectTimeout(timeout * 1000).setConnectionRequestTimeout(timeout * 1000) - .setSocketTimeout(timeout * 1000).build(); - - SSLConnectionSocketFactory.getSocketFactory(); - SSLContext sslContext = SSLContext.getInstance("TLSv1.2"); - sslContext.init(null, null, null); - String[] defaultCiphers = sslContext.getServerSocketFactory().getDefaultCipherSuites(); - - List limited = new LinkedList(); - for (String suite : defaultCiphers) { - // filter out Diffie-Hellman ciphers - if (!(suite.contains("_DHE_") || suite.contains("_DH_"))) { - limited.add(suite); - } - } - - return HttpClients.custom() - .setSSLSocketFactory( - new SSLConnectionSocketFactory( - SSLContexts.createSystemDefault(), new String[] {"TLSv1.2"}, limited.toArray(new String[limited.size()]), - SSLConnectionSocketFactory.getDefaultHostnameVerifier() - ) - ).setConnectionManager(connectionManager).setDefaultRequestConfig(config).build(); - } catch (NoSuchAlgorithmException | KeyManagementException e) { - logger.warn("Unable to establish SSL context. using default client", e); - } - - // default - return HttpClientBuilder.create().useSystemProperties().build(); - } - - public static HttpClientUtil getInstance(HttpClientConnectionManager connectionManager) { - return new HttpClientUtil(getConfiguredHttpClient(connectionManager)); - } - - public static void closeHttpResponse(HttpResponse resourcesResponse) { - if (resourcesResponse != null) { - try { - EntityUtils.consume(resourcesResponse.getEntity()); - } catch (IOException e) { - logger.error("Failed to close HttpResponse entity", e); - } - } - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/PicsureNaming.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/PicsureNaming.java deleted file mode 100644 index c1c31bc16..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/PicsureNaming.java +++ /dev/null @@ -1,35 +0,0 @@ -package edu.harvard.dbmi.avillach.util; - -import java.lang.reflect.Field; -import java.util.ArrayList; -import java.util.List; - -public class PicsureNaming { - - public static class RoleNaming{ - - /** - * please NOTICE: - * This ROLE_SYSTEM is used across different projects - * if this ROLE_SYSTEM naming changed, it will affect other projects, like picsure-micro-auth-app, - * the suggestion is, if you want to change the naming of role_system, - * please either create a new role named PIC_SURE_SYSTEM_ADMIN - * or not use this naming in other project (this naming is not designed to use in other projects originally) - */ - public static final String ROLE_SYSTEM = "ROLE_SYSTEM"; - - public static final String ROLE_RESEARCH = "ROLE_RESEARCH"; - public static final String ROLE_USER = "ROLE_USER"; - public static final String ROLE_TOKEN_INTROSPECTION = "ROLE_TOKEN_INTROSPECTION"; - public static final String ROLE_INTROSPECTION_USER = "ROLE_INTROSPECTION_USER"; - - - public static List allRoles(){ - List roles = new ArrayList<>(); - for (Field field : RoleNaming.class.getFields()){ - roles.add(field.getName()); - } - return roles; - } - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/Utilities.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/Utilities.java deleted file mode 100644 index 5e63be454..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/Utilities.java +++ /dev/null @@ -1,57 +0,0 @@ -package edu.harvard.dbmi.avillach.util; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; -import org.apache.http.auth.AuthScope; -import org.apache.http.auth.UsernamePasswordCredentials; -import org.apache.http.client.CredentialsProvider; -import org.apache.http.client.protocol.HttpClientContext; -import org.apache.http.impl.client.BasicCredentialsProvider; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.ws.rs.core.HttpHeaders; -import java.util.Optional; - -public class Utilities { - - private static final Logger logger = LoggerFactory.getLogger(Utilities.class); - - public static HttpClientContext buildHttpClientContext() { - HttpClientContext httpClientContext = null; - String proxyUser = System.getProperty("http.proxyUser"); // non-standard - String proxyPass = System.getProperty("http.proxyPassword"); // non-standard - if (proxyUser != null && proxyPass != null) { - httpClientContext = HttpClientContext.create(); - CredentialsProvider credentialsProvider = new BasicCredentialsProvider(); - credentialsProvider.setCredentials(AuthScope.ANY, new UsernamePasswordCredentials(proxyUser, proxyPass)); - httpClientContext.setCredentialsProvider(credentialsProvider); - } - return httpClientContext; - } - - /** - * This method is used to get the request source from the request header. It is used for logging purposes. - * - * @param headers the request headers - * @return the request source - */ - public static String getRequestSourceFromHeader(HttpHeaders headers) { - if (headers == null) return "headers are null"; - return headers.getHeaderString("request-source") == null ? "request-source header is null" : headers.getHeaderString("request-source"); - } - - public static String convertQueryRequestToString(ObjectMapper mapper, Object searchQueryRequest) { - if (mapper == null || searchQueryRequest == null) { - logger.info("Error converting query request to string: mapper or searchQueryRequest is null"); - return ""; - } - try { - return mapper.writeValueAsString(searchQueryRequest); - } catch (JsonProcessingException e) { - logger.info("Error converting query request to string: " + e.getMessage()); - return ""; - } - } - -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java deleted file mode 100644 index ed32a921a..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/VisualizationUtil.java +++ /dev/null @@ -1,118 +0,0 @@ -package edu.harvard.dbmi.avillach.util; - -import java.util.*; -import java.util.function.Supplier; -import java.util.stream.Collectors; -import java.util.stream.Stream; - -public class VisualizationUtil { - - protected static final String CONSENTS_KEY = "\\_consents\\"; - protected static final String HARMONIZED_CONSENT_KEY = "\\_harmonized_consent\\"; - protected static final String TOPMED_CONSENTS_KEY = "\\_topmed_consents\\"; - protected static final String PARENT_CONSENTS_KEY = "\\_parent_consents\\"; - private static final int MAX_X_LABEL_LINE_LENGTH = 45; - private static final boolean LIMITED = true; - private static final int LIMIT_SIZE = 7; - - public static boolean skipKey(String key) { - return key.equals(CONSENTS_KEY) || - key.equals(HARMONIZED_CONSENT_KEY) || - key.equals(TOPMED_CONSENTS_KEY) || - key.equals(PARENT_CONSENTS_KEY); - } - - public static Map processResults(Map axisMap) { - Map convertedAxisMap = new HashMap<>(); - for (Map.Entry entry : axisMap.entrySet()) { - if (entry.getValue() instanceof Integer) { - convertedAxisMap.put(entry.getKey(), (Integer) entry.getValue()); - } - } - Map stringIntegerMap = doProcessResults(convertedAxisMap); - return new HashMap<>(stringIntegerMap); - } - - /** - * Sorts the map and if there is more than the LIMIT_SIZE then we also get the greatest 7 categories and then combines - * the others into an "other" category. Also replace long column names with shorter version. - * - * @param axisMap - Map of the categories and their counts - * @return Map - sorted map of the categories and their counts with the "other" category added if necessary - */ - public static Map doProcessResults(Map axisMap) { - Map finalAxisMap = axisMap; - if (LIMITED && axisMap.size() > (LIMIT_SIZE + 1)) { - //Create Other bar and sort - Supplier>> stream = () -> finalAxisMap.entrySet().stream().sorted(Collections.reverseOrder(Map.Entry.comparingByValue())); - Integer otherSum = stream.get().skip(LIMIT_SIZE).mapToInt(Map.Entry::getValue).sum(); - axisMap = stream.get().limit(LIMIT_SIZE).collect(Collectors.toMap(Map.Entry::getKey, Map.Entry::getValue, (e1, e2) -> e2, LinkedHashMap::new)); - axisMap = limitKeySize(axisMap).entrySet() - .stream() - .sorted(Collections.reverseOrder(Map.Entry.comparingByValue())) - .collect(Collectors.toMap( - Map.Entry::getKey, - Map.Entry::getValue, - (e1, e2) -> e2, - LinkedHashMap::new)); - axisMap.put("Other", otherSum); - } else { - axisMap = limitKeySize(finalAxisMap).entrySet() - .stream() - .sorted(Collections.reverseOrder(Map.Entry.comparingByValue())) - .collect(Collectors.toMap(Map.Entry::getKey, - Map.Entry::getValue, - (e1, e2) -> e2, - LinkedHashMap::new)); - } - return axisMap; - } - - /** - * This method is used to limit the size of the keys in the axisMap to a maximum of 45 characters. If the key is longer - * than 45 characters, it will be shortened to 45 characters and the last 3 characters will be replaced with "...". - * If the shortened key is not unique, we will create a unique one - *

- * - * @param axisMap - Map of the categories and their counts - * @return Map - Map of the categories and their counts with the keys limited to 45 characters - */ - public static Map limitKeySize(Map axisMap) { - if (axisMap == null) { - throw new IllegalArgumentException("axisMap cannot be null"); - } - - Map newAxisMap = new HashMap<>(); - HashSet keys = new HashSet<>(); - axisMap.forEach((key, value) -> { - String adjustedKey = key.length() < MAX_X_LABEL_LINE_LENGTH ? key : createAdjustedKey(axisMap, keys, key); - newAxisMap.put(adjustedKey, value); - keys.add(adjustedKey); - }); - return newAxisMap; - } - - private static String createAdjustedKey(Map axisMap, HashSet keys, String key) { - String keyPrefix = key.substring(0, MAX_X_LABEL_LINE_LENGTH); - return isKeyPrefixInAxisMap(axisMap, keyPrefix) ? generateUniqueKey(keys, key) : appendEllipsis(keyPrefix); - } - - private static boolean isKeyPrefixInAxisMap(Map axisMap, String keyPrefix) { - return axisMap.keySet().stream().anyMatch(k -> k.startsWith(keyPrefix)); - } - - private static String generateUniqueKey(HashSet keys, String key) { - int countFromEnd = 6; - String proposedKey; - do { - proposedKey = String.format("%s...%s", key.substring(0, MAX_X_LABEL_LINE_LENGTH - 3 - countFromEnd), key.substring(key.length() - countFromEnd)); - countFromEnd++; - } while (keys.contains(proposedKey)); - return proposedKey; - } - - private static String appendEllipsis(String keyPrefixAdjusted) { - return String.format("%s...", keyPrefixAdjusted); - } - -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/converter/UUIDParamConverter.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/converter/UUIDParamConverter.java deleted file mode 100644 index 9bc7adb80..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/converter/UUIDParamConverter.java +++ /dev/null @@ -1,23 +0,0 @@ -package edu.harvard.dbmi.avillach.util.converter; - -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; - -import javax.ws.rs.ext.ParamConverter; -import java.util.UUID; - -public class UUIDParamConverter implements ParamConverter { - - @Override - public UUID fromString(String value) { - try { - return UUID.fromString(value); - } catch (IllegalArgumentException e) { - throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST); - } - } - - @Override - public String toString(UUID value) { - return value.toString(); - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/converter/UUIDParamConverterProvider.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/converter/UUIDParamConverterProvider.java deleted file mode 100644 index 05b804951..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/converter/UUIDParamConverterProvider.java +++ /dev/null @@ -1,18 +0,0 @@ -package edu.harvard.dbmi.avillach.util.converter; - -import javax.ws.rs.ext.ParamConverter; -import javax.ws.rs.ext.ParamConverterProvider; -import javax.ws.rs.ext.Provider; -import java.util.UUID; - -@Provider -public class UUIDParamConverterProvider implements ParamConverterProvider { - - @Override - public ParamConverter getConverter(Class rawType, java.lang.reflect.Type genericType, java.lang.annotation.Annotation[] annotations) { - if (rawType.equals(UUID.class)) { - return (ParamConverter) new UUIDParamConverter(); - } - return null; - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/ApplicationException.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/ApplicationException.java deleted file mode 100644 index 3100e8e05..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/ApplicationException.java +++ /dev/null @@ -1,51 +0,0 @@ -package edu.harvard.dbmi.avillach.util.exception; - -import javax.ws.rs.WebApplicationException; -import javax.ws.rs.core.Response; - -/** - * Will end up to return an application error - * - * Common errors are included as public final strings - * - * @see edu.harvard.dbmi.avillach.util.response.PICSUREResponse - */ -public class ApplicationException extends WebApplicationException{ - - public final static String MISSING_TARGET_URL = "Resource is missing target URL"; - public final static String MISSING_RESOURCE_PATH = "Resource is missing resourceRS path"; - public final static String MISSING_RESOURCE = "Query is missing Resource"; - - private Object content; - - public ApplicationException() { - super(Response.Status.INTERNAL_SERVER_ERROR); - } - - public ApplicationException(Response.Status status) { - super(status); - } - - public ApplicationException(Object content) { - super(Response.Status.INTERNAL_SERVER_ERROR); - this.content = content; - } - - public ApplicationException(Response.Status status, Object content) { - super(status); - this.content = content; - } - - public ApplicationException(String message, Exception exception) { - super(message, exception); - } - - - public Object getContent() { - return content; - } - - public void setContent(Object content) { - this.content = content; - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/NotAuthorizedException.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/NotAuthorizedException.java deleted file mode 100644 index 74d6df795..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/NotAuthorizedException.java +++ /dev/null @@ -1,50 +0,0 @@ -package edu.harvard.dbmi.avillach.util.exception; - -import com.fasterxml.jackson.annotation.JsonIgnore; - -import javax.ws.rs.WebApplicationException; -import javax.ws.rs.core.Response; - -public class NotAuthorizedException extends WebApplicationException { - - public static final String MISSING_CREDENTIALS = "Missing credentials"; - - @JsonIgnore - private Response.Status status; - - private Object content; - - public NotAuthorizedException() { - this.status = Response.Status.UNAUTHORIZED; - } - - public NotAuthorizedException(Response.Status status) { - this.status = status; - } - - public NotAuthorizedException(Object content) { - super(Response.Status.UNAUTHORIZED); - this.content = content; - } - - public NotAuthorizedException(String message, Throwable cause) { - super(message, cause); - } - - public NotAuthorizedException(Response.Status status, Object content) { - this.status = status; - this.content = content; - } - - public Response.Status getStatus() { - return status; - } - - public Object getContent() { - return content; - } - - public void setContent(Object content) { - this.content = content; - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/PicsureQueryException.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/PicsureQueryException.java deleted file mode 100644 index e8c8d71a6..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/PicsureQueryException.java +++ /dev/null @@ -1,50 +0,0 @@ -package edu.harvard.dbmi.avillach.util.exception; - -import javax.ws.rs.WebApplicationException; - -public class PicsureQueryException extends WebApplicationException { - private Object content; - - public PicsureQueryException() { - } - - public PicsureQueryException(Object content) { - this.content = content; - } - - /** - * Create a Resource Interface Exception with the given message - * - * @param message Messsage - */ - public PicsureQueryException(String message) { - super(message); - } - - /** - * Create a Resource Interface Exception - * - * @param exception Exception - */ - public PicsureQueryException(Exception exception) { - super(exception); - } - - /** - * Create a Resource Interface Exception with the given message - * - * @param message Message - * @param exception Exception - */ - public PicsureQueryException(String message, Exception exception) { - super(message, exception); - } - - public Object getContent() { - return content; - } - - public void setContent(Object content) { - this.content = content; - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/ProtocolException.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/ProtocolException.java deleted file mode 100644 index 46377e630..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/ProtocolException.java +++ /dev/null @@ -1,62 +0,0 @@ -package edu.harvard.dbmi.avillach.util.exception; - -import com.fasterxml.jackson.annotation.JsonIgnore; - -import javax.ws.rs.WebApplicationException; -import javax.ws.rs.core.Response; - -/** - * Will end up to return a protocol error - * - * Common errors are included as public final strings - * - * @see edu.harvard.dbmi.avillach.util.response.PICSUREResponse - */ -public class ProtocolException extends WebApplicationException { - - public final static String MISSING_RESOURCE_ID = "Missing resource id"; - public final static String RESOURCE_NOT_FOUND = "No resource with id: "; - public final static String MISSING_DATA = "Missing query request data"; - public final static String MISSING_QUERY_ID = "Missing query id"; - public final static String QUERY_NOT_FOUND = "No query with id: "; - public static final String INCORRECTLY_FORMATTED_REQUEST = "Incorrectly formatted query request data"; - - @JsonIgnore - private Response.Status status; - - private Object content; - - public ProtocolException() { - this.status = Response.Status.INTERNAL_SERVER_ERROR; - } - - public ProtocolException(Response.Status status) { - this.status = status; - } - - public ProtocolException(Object content) { - super(Response.Status.INTERNAL_SERVER_ERROR); - this.content = content; - } - - public ProtocolException(String message, Throwable cause) { - super(message, cause); - } - - public ProtocolException(Response.Status status, Object content) { - this.status = status; - this.content = content; - } - - public Response.Status getStatus() { - return status; - } - - public Object getContent() { - return content; - } - - public void setContent(Object content) { - this.content = content; - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/ResourceInterfaceException.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/ResourceInterfaceException.java deleted file mode 100644 index 9b99f18e8..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/ResourceInterfaceException.java +++ /dev/null @@ -1,57 +0,0 @@ -package edu.harvard.dbmi.avillach.util.exception; - -import javax.ws.rs.WebApplicationException; - -/** - * Will end up to return a RI error - * - * @see edu.harvard.dbmi.avillach.util.response.PICSUREResponse - */ -public class ResourceInterfaceException extends WebApplicationException { - private static final long serialVersionUID = -4688536480746747740L; - - private Object content; - - public ResourceInterfaceException() { - } - - public ResourceInterfaceException(Object content) { - this.content = content; - } - - /** - * Create a Resource Interface Exception with the given message - * - * @param message Messsage - */ - public ResourceInterfaceException(String message) { - super(message); - } - - /** - * Create a Resource Interface Exception - * - * @param exception Exception - */ - public ResourceInterfaceException(Exception exception) { - super(exception); - } - - /** - * Create a Resource Interface Exception with the given message - * - * @param message Message - * @param exception Exception - */ - public ResourceInterfaceException(String message, Exception exception) { - super(message, exception); - } - - public Object getContent() { - return content; - } - - public void setContent(Object content) { - this.content = content; - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/ApplicationExceptionMapper.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/ApplicationExceptionMapper.java deleted file mode 100644 index 2c64d742a..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/ApplicationExceptionMapper.java +++ /dev/null @@ -1,17 +0,0 @@ -package edu.harvard.dbmi.avillach.util.exception.mapper; - -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.response.PICSUREResponse; - -import javax.ws.rs.core.Response; -import javax.ws.rs.ext.ExceptionMapper; -import javax.ws.rs.ext.Provider; - -@Provider -public class ApplicationExceptionMapper implements ExceptionMapper{ - - @Override - public Response toResponse(ApplicationException exception) { - return PICSUREResponse.applicationError(exception.getContent()); - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/IllegalArgumentExceptionMapper.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/IllegalArgumentExceptionMapper.java deleted file mode 100644 index f7816674b..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/IllegalArgumentExceptionMapper.java +++ /dev/null @@ -1,21 +0,0 @@ -package edu.harvard.dbmi.avillach.util.exception.mapper; - -import edu.harvard.dbmi.avillach.util.response.PICSUREResponse; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.ws.rs.core.Response; -import javax.ws.rs.ext.ExceptionMapper; -import javax.ws.rs.ext.Provider; - -@Provider -public class IllegalArgumentExceptionMapper implements ExceptionMapper{ - - private static final Logger logger = LoggerFactory.getLogger(IllegalArgumentExceptionMapper.class); - - @Override - public Response toResponse(IllegalArgumentException exception) { - logger.error("Uncaught exception", exception); - return PICSUREResponse.protocolError(exception.getMessage()); - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/NotAuthorizedExceptionMapper.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/NotAuthorizedExceptionMapper.java deleted file mode 100644 index 421bece03..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/NotAuthorizedExceptionMapper.java +++ /dev/null @@ -1,17 +0,0 @@ -package edu.harvard.dbmi.avillach.util.exception.mapper; - -import edu.harvard.dbmi.avillach.util.response.PICSUREResponse; - -import javax.ws.rs.NotAuthorizedException; -import javax.ws.rs.core.Response; -import javax.ws.rs.ext.ExceptionMapper; -import javax.ws.rs.ext.Provider; - -@Provider -public class NotAuthorizedExceptionMapper implements ExceptionMapper{ - @Override - public Response toResponse(NotAuthorizedException exception) { - return PICSUREResponse.protocolError(Response.Status.UNAUTHORIZED, - exception.getChallenges().toString()); - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/NotSupportedExceptionMapper.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/NotSupportedExceptionMapper.java deleted file mode 100644 index 31562d594..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/NotSupportedExceptionMapper.java +++ /dev/null @@ -1,19 +0,0 @@ -package edu.harvard.dbmi.avillach.util.exception.mapper; - -import edu.harvard.dbmi.avillach.util.exception.ApplicationException; -import edu.harvard.dbmi.avillach.util.response.PICSUREResponse; - -import javax.ws.rs.NotSupportedException; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; -import javax.ws.rs.ext.ExceptionMapper; -import javax.ws.rs.ext.Provider; - -@Provider -public class NotSupportedExceptionMapper implements ExceptionMapper{ - - @Override - public Response toResponse(NotSupportedException exception) { - return PICSUREResponse.error(Response.Status.NOT_IMPLEMENTED, exception.getMessage(), MediaType.APPLICATION_JSON_TYPE); - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/NullPointerExceptionMapper.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/NullPointerExceptionMapper.java deleted file mode 100644 index 92f9f90f2..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/NullPointerExceptionMapper.java +++ /dev/null @@ -1,21 +0,0 @@ -package edu.harvard.dbmi.avillach.util.exception.mapper; - -import edu.harvard.dbmi.avillach.util.response.PICSUREResponse; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.ws.rs.core.Response; -import javax.ws.rs.ext.ExceptionMapper; -import javax.ws.rs.ext.Provider; - -@Provider -public class NullPointerExceptionMapper implements ExceptionMapper{ - - private static final Logger logger = LoggerFactory.getLogger(NullPointerExceptionMapper.class); - - @Override - public Response toResponse(NullPointerException exception) { - logger.error("Uncaught exception", exception); - return PICSUREResponse.applicationError("An inner problem pops up, no worry, please contact your admin to see the logs in server"); - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/PersistenceExceptionMapper.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/PersistenceExceptionMapper.java deleted file mode 100644 index 77b945494..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/PersistenceExceptionMapper.java +++ /dev/null @@ -1,22 +0,0 @@ -package edu.harvard.dbmi.avillach.util.exception.mapper; - -import edu.harvard.dbmi.avillach.util.response.PICSUREResponse; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.persistence.PersistenceException; -import javax.ws.rs.core.Response; -import javax.ws.rs.ext.ExceptionMapper; -import javax.ws.rs.ext.Provider; - -@Provider -public class PersistenceExceptionMapper implements ExceptionMapper{ - - private static final Logger logger = LoggerFactory.getLogger(PersistenceExceptionMapper.class); - - @Override - public Response toResponse(PersistenceException exception) { - logger.error("Uncaught exception", exception); - return PICSUREResponse.applicationError(exception.getMessage()); - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/PicsureQueryExceptionMapper.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/PicsureQueryExceptionMapper.java deleted file mode 100644 index 0010ae6a0..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/PicsureQueryExceptionMapper.java +++ /dev/null @@ -1,16 +0,0 @@ -package edu.harvard.dbmi.avillach.util.exception.mapper; - -import edu.harvard.dbmi.avillach.util.exception.PicsureQueryException; -import edu.harvard.dbmi.avillach.util.response.PICSUREResponse; - -import javax.ws.rs.core.Response; -import javax.ws.rs.ext.ExceptionMapper; - -public class PicsureQueryExceptionMapper implements ExceptionMapper { - - @Override - public Response toResponse(PicsureQueryException exception) { - return PICSUREResponse.riError(exception.getClass().getSimpleName() + " - " + exception.getMessage() - + exception.getCause()==null?"":", cause: " + exception.getCause().getClass().getSimpleName() + " - " + exception.getCause().getMessage()); - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/ProtocolExceptionMapper.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/ProtocolExceptionMapper.java deleted file mode 100644 index 582f276d3..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/ProtocolExceptionMapper.java +++ /dev/null @@ -1,17 +0,0 @@ -package edu.harvard.dbmi.avillach.util.exception.mapper; - -import edu.harvard.dbmi.avillach.util.exception.ProtocolException; -import edu.harvard.dbmi.avillach.util.response.PICSUREResponse; - -import javax.ws.rs.core.Response; -import javax.ws.rs.ext.ExceptionMapper; -import javax.ws.rs.ext.Provider; - -@Provider -public class ProtocolExceptionMapper implements ExceptionMapper{ - - @Override - public Response toResponse(ProtocolException exception) { - return PICSUREResponse.protocolError(exception.getStatus(), exception.getContent()); - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/ResourceInterfaceExceptionMapper.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/ResourceInterfaceExceptionMapper.java deleted file mode 100644 index cf3879044..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/ResourceInterfaceExceptionMapper.java +++ /dev/null @@ -1,16 +0,0 @@ -package edu.harvard.dbmi.avillach.util.exception.mapper; - -import edu.harvard.dbmi.avillach.util.exception.ResourceInterfaceException; -import edu.harvard.dbmi.avillach.util.response.PICSUREResponse; - -import javax.ws.rs.core.Response; -import javax.ws.rs.ext.ExceptionMapper; -import javax.ws.rs.ext.Provider; - -@Provider -public class ResourceInterfaceExceptionMapper implements ExceptionMapper{ - @Override - public Response toResponse(ResourceInterfaceException exception) { - return PICSUREResponse.riError(exception.getMessage()); - } -} \ No newline at end of file diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/UnsupportedOperationExceptionMapper.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/UnsupportedOperationExceptionMapper.java deleted file mode 100644 index 2cc06286b..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/exception/mapper/UnsupportedOperationExceptionMapper.java +++ /dev/null @@ -1,17 +0,0 @@ -package edu.harvard.dbmi.avillach.util.exception.mapper; - -import edu.harvard.dbmi.avillach.util.response.PICSUREResponse; - -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; -import javax.ws.rs.ext.ExceptionMapper; -import javax.ws.rs.ext.Provider; - -@Provider -public class UnsupportedOperationExceptionMapper implements ExceptionMapper{ - - @Override - public Response toResponse(UnsupportedOperationException exception) { - return PICSUREResponse.error(Response.Status.NOT_IMPLEMENTED, exception.getMessage(), MediaType.APPLICATION_JSON_TYPE); - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/response/PICSUREResponse.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/response/PICSUREResponse.java deleted file mode 100644 index 125550c62..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/response/PICSUREResponse.java +++ /dev/null @@ -1,157 +0,0 @@ -package edu.harvard.dbmi.avillach.util.response; - -import javax.validation.constraints.NotEmpty; -import javax.validation.constraints.NotNull; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; - -/** - * Provide ability of creating IRCT own response methods - * - *

- * Notice: When implementing, several cases should be considered: - *

  • - * success response (status 200): users get what they want - *
    • - *
  • - * protocol error (400, 401, etc.): users' fault - *
    • - *
  • - * application error (500): IRCT application's fault - *
    • - *
  • - * RI error (500): IRCT thinks users are acting well, - * but resource interfaces return errors - *
    • - *

    - * - */ -public class PICSUREResponse { - - private static final MediaType DEFAULT_MEDIA_TYPE = MediaType.APPLICATION_JSON_TYPE; - private static final Response.Status DEFAULT_RESPONSE_ERROR_CODE = Response.Status.INTERNAL_SERVER_ERROR; - - public static Response success(){ - return Response.ok().build(); - } - - public static Response success(Object content){ - return success(content, DEFAULT_MEDIA_TYPE); - } - - public static Response success(String message, Object content){ - return success(message, content, DEFAULT_MEDIA_TYPE); - } - - public static Response success(Object content, MediaType type){ - return Response.ok(content, type) - .build(); - } - - public static Response success(String message, Object content, MediaType type){ - return Response.ok(new PICSUREResponseOKwithMsgAndContent(message, content), type) - .build(); - } - - public static Response error(Object content) { - return error(content, MediaType.APPLICATION_JSON_TYPE); - } - - public static Response error(String message, Object content) { - return error(DEFAULT_RESPONSE_ERROR_CODE, null, message, content, DEFAULT_MEDIA_TYPE); - } - - public static Response error(Object content, MediaType type){ - return error(DEFAULT_RESPONSE_ERROR_CODE, content, type); - } - - public static Response error(Response.Status status, Object content){ - return error(status, content, MediaType.APPLICATION_JSON_TYPE); - } - - public static Response error(Response.Status status, Object content, MediaType type){ - if(status==null) status = DEFAULT_RESPONSE_ERROR_CODE; - return error(status, null, content, type); - } - - private static Response error(Response.Status status, String errorType, Object content, MediaType type){ - return Response.status(status.getStatusCode()) - .entity(new PICSUREResponseError(errorType, content)) - .type(type) - .build(); - } - - private static Response error(Response.Status status, String errorType, String message, Object content, MediaType type){ - return Response.status(status.getStatusCode()) - .entity(new PICSUREResponseErrorWithMsgAndContent(errorType, message, content)) - .type(type) - .build(); - } - - /** - * if IRCT application encountered some errors which is not users' fault, - * this method should be used - * @param content - * @return - */ - public static Response applicationError(Object content){ - return error(DEFAULT_RESPONSE_ERROR_CODE, "application_error", content, DEFAULT_MEDIA_TYPE); - } - - public static Response applicationError(String message, Object content){ - return error(DEFAULT_RESPONSE_ERROR_CODE, "application_error", message, content, DEFAULT_MEDIA_TYPE); - } - - /** - * if the resource interface get some error back from the resource - * when the user is requesting, which means IRCT think users are doing well, - * and IRCT is acting well, but resources still return errors, - * this method should be called. - * @param content - * @return - */ - public static Response riError(Object content){ - return error(DEFAULT_RESPONSE_ERROR_CODE, "ri_error", content, DEFAULT_MEDIA_TYPE); - } - - public static Response riError(String message, Object content){ - return error(DEFAULT_RESPONSE_ERROR_CODE, "ri_error", message, content, DEFAULT_MEDIA_TYPE); - } - - /** - * Default method for protocol Error means client side has entered something wrong, - * the default error status is 400 - * @param content error content - * @return - */ - public static Response protocolError(Object content){ - return error(Response.Status.BAD_REQUEST, content, MediaType.APPLICATION_JSON_TYPE); - } - - public static Response protocolError(String message, Object content){ - return error(Response.Status.BAD_REQUEST, message, content, MediaType.APPLICATION_JSON_TYPE); - } - - /** - * @param status giving the flexibility of pointing out what specific status to return - * @param content error content - * @return - */ - public static Response protocolError(Response.Status status, Object content){ - return error(status, content, MediaType.APPLICATION_JSON_TYPE); - } - - /** - * status code is 401 - * @param content - * @return - */ - public static Response unauthorizedError(Object content) { - return error(Response.Status.UNAUTHORIZED, "Unauthorized", content, DEFAULT_MEDIA_TYPE); - } - - public static Response unauthorizedError(String message, Object content) { - return error(Response.Status.UNAUTHORIZED, "Unauthorized", message, content, DEFAULT_MEDIA_TYPE); - } - -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/response/PICSUREResponseError.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/response/PICSUREResponseError.java deleted file mode 100644 index 4bf0dd70e..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/response/PICSUREResponseError.java +++ /dev/null @@ -1,46 +0,0 @@ -package edu.harvard.dbmi.avillach.util.response; - -import com.fasterxml.jackson.databind.annotation.JsonSerialize; - -import java.io.Serializable; - -@JsonSerialize -public class PICSUREResponseError implements Serializable { - - private String errorType = "error"; - - private Object message; - - public PICSUREResponseError() { - } - - public PICSUREResponseError(String errorType) { - this.errorType = errorType; - } - - public PICSUREResponseError(Object message) { - this.message = message; - } - - public PICSUREResponseError(String errorType, Object message) { - if (errorType != null && !errorType.isEmpty()) - this.errorType = errorType; - this.message = message; - } - - public String getErrorType() { - return errorType; - } - - public void setErrorType(String errorType) { - this.errorType = errorType; - } - - public Object getMessage() { - return message; - } - - public void setMessage(Object message) { - this.message = message; - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/response/PICSUREResponseErrorWithMsgAndContent.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/response/PICSUREResponseErrorWithMsgAndContent.java deleted file mode 100644 index 883db95c6..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/response/PICSUREResponseErrorWithMsgAndContent.java +++ /dev/null @@ -1,46 +0,0 @@ -package edu.harvard.dbmi.avillach.util.response; - -import com.fasterxml.jackson.annotation.JsonInclude; -import com.fasterxml.jackson.databind.annotation.JsonSerialize; - -@JsonSerialize -@JsonInclude(JsonInclude.Include.NON_NULL) -public class PICSUREResponseErrorWithMsgAndContent { - - private String errorType = "error"; - - private String message; - - private Object content; - - public PICSUREResponseErrorWithMsgAndContent(String errorType, String message, Object content) { - if (errorType != null && !errorType.isEmpty()) - this.errorType = errorType; - this.message = message; - this.content = content; - } - - public String getErrorType() { - return errorType; - } - - public void setErrorType(String errorType) { - this.errorType = errorType; - } - - public String getMessage() { - return message; - } - - public void setMessage(String message) { - this.message = message; - } - - public Object getContent() { - return content; - } - - public void setContent(Object content) { - this.content = content; - } -} diff --git a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/response/PICSUREResponseOKwithMsgAndContent.java b/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/response/PICSUREResponseOKwithMsgAndContent.java deleted file mode 100644 index 56e5554f3..000000000 --- a/pic-sure-util/src/main/java/edu/harvard/dbmi/avillach/util/response/PICSUREResponseOKwithMsgAndContent.java +++ /dev/null @@ -1,34 +0,0 @@ -package edu.harvard.dbmi.avillach.util.response; - -import com.fasterxml.jackson.annotation.JsonInclude; -import com.fasterxml.jackson.databind.annotation.JsonSerialize; - -@JsonSerialize -@JsonInclude(JsonInclude.Include.NON_NULL) -public class PICSUREResponseOKwithMsgAndContent { - - private String message; - - private Object content; - - public PICSUREResponseOKwithMsgAndContent(String message, Object content) { - this.message = message; - this.content = content; - } - - public String getMessage() { - return message; - } - - public void setMessage(String message) { - this.message = message; - } - - public Object getContent() { - return content; - } - - public void setContent(Object content) { - this.content = content; - } -} diff --git a/picsure2.jpeg b/picsure2.jpeg deleted file mode 100644 index 640e8ea8e..000000000 Binary files a/picsure2.jpeg and /dev/null differ diff --git a/platform/README.md b/platform/README.md new file mode 100644 index 000000000..68105817f --- /dev/null +++ b/platform/README.md @@ -0,0 +1,84 @@ +# platform + +Bill of Materials (BOM) for `pic-sure`. This module publishes a single, centralized set of dependency versions so every service and library in the repo — and any external consumer — can stay in sync without hardcoding versions individually. + +## What this module is + +`platform` is a `pom`-packaged module containing **only** a `` block. It does not contain source code, does not get deployed as a runnable artifact, and does not carry build/plugin configuration (that belongs in the parent POM, not here). + +Its sole job: **pin versions**, for two categories of dependencies used across `pic-sure`: + +- **Third-party libraries** used across the monorepo, primarily via the imported `spring-boot-dependencies` and `spring-cloud-dependencies` BOMs +- **Internal artifacts** published from this repo (`pic-sure-api-model`, `pic-sure-hpds-model`, `pic-sure-logging-client`), so services always align on the current in-repo version + +> **This BOM is standalone by design** — it has no ``. The root parent POM imports this BOM, so a `` pointing back at the root would create a model-resolution cycle. Its version properties (`spring-boot.version`, `spring-cloud.version`) are therefore duplicated from the root pom and must be bumped in lockstep. + +## Why a separate module from the parent POM + +Two different concerns get conflated if you don't split them: + +| | `platform` (BOM) | parent POM | +|---|---|---| +| Purpose | Version pinning only | Shared plugin/build config, Java version, linting | +| Mechanism | `import` | `` inheritance | +| Can combine multiple? | Yes — import several BOMs | No — only one parent | +| Affects plugins/build? | No | Yes | + +Keeping them separate means a module can pull in consistent versions via this BOM **without** being forced to inherit all of the monorepo's internal build/plugin conventions — useful for any library here that may eventually be consumed or published outside this repo. + +## How to consume it + +**Inside this repo (modules under the root parent):** do nothing. The root parent imports this BOM in its ``, and every child module inherits it. Declare dependencies **without a version**: + +```xml + + + com.fasterxml.jackson.core + jackson-databind + + + edu.harvard.hms.dbmi.avillach + pic-sure-api-model + + +``` + +**Outside this repo (sibling repos, not-yet-migrated services):** import the published BOM directly in your own `` — you get the same versions without inheriting this repo's parent or build config: + +```xml + + + + edu.harvard.hms.dbmi.avillach + pic-sure-bom + 3.0.0 + pom + import + + + +``` + +## Adding or updating a version + +1. Open `pom.xml` in this module. +2. Add or update the relevant entry inside ``. +3. Bump the `platform` module's own version if this repo uses independent (non-lockstep) versioning; skip this step if versions are managed lockstep via `${revision}`. +4. Every consuming module picks up the change on its next build — no per-module edits required. + +**Guidelines:** +- One version per artifact, defined once, here — never override a BOM-managed version locally in a consuming module's `pom.xml` unless there's a documented, temporary reason (leave a comment explaining why if you do). +- Keep third-party and internal-module entries grouped and commented for readability as the list grows. +- If bumping a widely-used dependency (e.g. Spring Boot, Jackson major version), coordinate with module owners before merging — a BOM change can affect every service in the repo at once. + +## What does *not* belong here + +- Actual source code or logic +- Plugin configuration, compiler settings, checkstyle/spotless rules → these belong in the parent POM +- Environment- or profile-specific configuration +- Dependencies that only one or two modules use and aren't shared broadly (just declare those locally with an explicit version in the consuming module) + +## Related + +- Root aggregator `pom.xml` — lists all modules including this one +- Parent POM — shared build/plugin configuration inherited separately from this BOM \ No newline at end of file diff --git a/platform/pom.xml b/platform/pom.xml new file mode 100644 index 000000000..8102b2dc4 --- /dev/null +++ b/platform/pom.xml @@ -0,0 +1,118 @@ + + + 4.0.0 + + edu.harvard.hms.dbmi.avillach + pic-sure-bom + 3.0.0 + pom + PIC-SURE BOM + Bill of Materials for PIC-SURE API dependencies + + + 3.5.16 + 2025.0.0 + + 3.0.0 + 3.0.0 + 3.0.0 + 3.0.0 + 3.0.0 + 3.0.0 + + 3.10.0 + + 5.5.2 + + 8.1 + + + + + org.springframework.boot + spring-boot-dependencies + ${spring-boot.version} + pom + import + + + org.springframework.cloud + spring-cloud-dependencies + ${spring-cloud.version} + pom + import + + + + edu.harvard.hms.dbmi.avillach + pic-sure-api-model + ${pic-sure-api-model.version} + + + edu.harvard.hms.dbmi.avillach.hpds + pic-sure-hpds-model + ${pic-sure-hpds-model.version} + + + + edu.harvard.dbmi.avillach + pic-sure-logging-client + ${pic-sure-logging-client.version} + + + edu.harvard.hms.dbmi.avillach + pic-sure-spring-commons + ${pic-sure-spring-commons.version} + + + edu.harvard.hms.dbmi.avillach + pic-sure-operations-service + ${pic-sure-operations-service.version} + + + edu.harvard.hms.dbmi.avillach + pic-sure-hpds-query-service + ${pic-sure-hpds-query-service.version} + + + + org.wiremock + wiremock-standalone + ${wiremock.version} + + + + org.apache.httpcomponents.client5 + httpclient5 + ${httpclient5.version} + + + net.logstash.logback + logstash-logback-encoder + ${logstash-logback-encoder.version} + + + + com.squareup.okio + okio + 3.6.0 + + + + + + github + GitHub HMS-DBMI Apache Maven Packages + https://maven.pkg.github.com/hms-dbmi/pic-sure + + + diff --git a/pom.xml b/pom.xml index 97fac3bbc..0610f50b0 100644 --- a/pom.xml +++ b/pom.xml @@ -1,358 +1,235 @@ - 4.0.0 - edu.harvard.hms.dbmi.avillach - pic-sure-api - 2.2.0-SNAPSHOT - pom - pic-sure-api - - pic-sure-api-war - pic-sure-api-data - pic-sure-resources - pic-sure-util - - - - github - GitHub HMS-DBMI Apache Maven Packages - https://maven.pkg.github.com/hms-dbmi/pic-sure-common - - true - - - - - 2.18.6 - 5.6.2 - 3.5.10 - 3.5.10 - 5.3.31 - 6.4.0.Final - 4.5.13 - 2.15.1 - 1.18.30 - 2.41.1 - - - - - - com.diffplug.spotless - spotless-maven-plugin - ${spotless.version} - - - - 4.26 - code-formatting/eclipse-formatter.xml - - - - - - - org.apache.maven.plugins - maven-compiler-plugin - 3.11.0 - - 11 - - - - org.apache.maven.plugins - maven-war-plugin - 3.2.0 - - false - - - - org.apache.maven.plugins - maven-surefire-plugin - 2.22.0 - - - --illegal-access=permit - - - - - - - - - junit - junit - 4.13.2 - test - - - - - - com.fasterxml.jackson.core - jackson-core - ${jackson.version} - - - com.fasterxml.jackson.core - jackson-databind - ${jackson.version} - - - com.fasterxml.jackson.core - jackson-annotations - ${jackson.version} - - - io.jsonwebtoken - jjwt - 0.9.0 - - - javax - javaee-api - 8.0 - provided - - - javax.xml.bind - jaxb-api - 2.3.0 - - - com.sun.xml.bind - jaxb-core - 2.3.0 - - - com.sun.xml.bind - jaxb-impl - 2.3.0 - - - - org.hibernate.javax.persistence - hibernate-jpa-2.1-api - 1.0.2.Final - provided - - - org.hibernate - hibernate-annotations - 3.5.6-Final - provided - - - org.hibernate.javax.persistence - hibernate-jpa-2.0-api - - - - - - org.slf4j - slf4j-api - 1.7.25 - - - org.apache.commons - commons-lang3 - 3.7 - compile - - - org.slf4j - slf4j-log4j12 - 1.7.25 - test - - - - - org.apache.logging.log4j - log4j-core - 2.18.0 - - - - - org.hibernate - hibernate-core - ${hibernate-core.version} - provided - - - org.apache.httpcomponents - httpcore - 4.4.4 - - - org.apache.httpcomponents - httpclient - ${httpclient.version} - - - commons-io - commons-io - ${commons-io.version} - - - com.github.tomakehurst - wiremock-standalone - 2.14.0 - test - - - org.glassfish.jersey.core - jersey-common - 2.39.1 - test - - - org.jboss.resteasy - resteasy-jaxb-provider - 3.0.8.Final - - - org.mockito - mockito-core - ${mockito-core.version} - test - - - org.jboss.resteasy - resteasy-jackson2-provider - 3.15.6.Final - - - - io.swagger.core.v3 - swagger-jaxrs2 - 2.2.7 - - - io.swagger.core.v3 - swagger-jaxrs2-servlet-initializer-v2 - 2.2.7 - - - io.swagger.core.v3 - swagger-annotations - 2.2.8 - - - org.apache.cxf - cxf-rt-frontend-jaxrs - 3.4.1 - test - - - com.github.tomakehurst - wiremock-jre8 - 2.27.2 - test - - - org.junit.jupiter - junit-jupiter - ${junit-jupiter.version} - test - - - org.mockito - mockito-junit-jupiter - ${mockito-junit-jupiter.version} - test - - - commons-cli - commons-cli - 1.4 - - - org.slf4j - slf4j-jdk14 - 1.7.32 - - - junit - junit - 4.13.1 - test - - - org.junit.vintage - junit-vintage-engine - 5.9.3 - test - - - org.reactivestreams - reactive-streams - 1.0.4 - - - org.projectlombok - lombok - ${lombok.version} - - - org.knowm.xchart - xchart - 3.8.1 - - - com.fasterxml.jackson.jaxrs - jackson-jaxrs-json-provider - 2.13.1 - - - org.springframework - spring-core - ${spring.version} - - - org.springframework - spring-web - ${spring.version} - - - org.junit.jupiter - junit-jupiter-api - 5.9.0 - test - - - org.apache.commons - commons-math3 - 3.6.1 - - - org.apache.cxf - cxf-rt-transports-http - 3.4.1 - compile - - - edu.harvard.dbmi.avillach - pic-sure-logging-client - 1.1.0 - - - edu.harvard.hms.dbmi.avillach - pic-sure-api-model - 1.0.0-SNAPSHOT - - - - - - github - GitHub HMS-DBMI Apache Maven Packages - https://maven.pkg.github.com/hms-dbmi/pic-sure - - + xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> + 4.0.0 + edu.harvard.hms.dbmi.avillach + pic-sure-api + ${revision} + pom + pic-sure-api + + platform + libs/pic-sure-commons + libs/pic-sure-logging-client + libs/pic-sure-spring-commons + services/pic-sure-gateway + services/pic-sure-operations-service + services/pic-sure-hpds-query-service + + services/pic-sure-visualization-service + services/pic-sure-services/info-service + services/pic-sure-services/uploader + services/picsure-dictionary + services/picsure-dictionary/aggregate + services/picsure-dictionary/dictionaryweights + services/pic-sure-logging + services/pic-sure-auth-microapp + services/pic-sure-hpds + + + + 3.0.0 + 25 + + + 3.5.16 + 2025.0.0 + 2.46.1 + UTF-8 + + + + github + GitHub HMS-DBMI Apache Maven Packages + https://maven.pkg.github.com/hms-dbmi/pic-sure-common + + true + + + + + + + + edu.harvard.hms.dbmi.avillach + pic-sure-bom + ${revision} + pom + import + + + + + + + + maven-clean-plugin + 3.5.0 + + + maven-resources-plugin + 3.3.1 + + + maven-compiler-plugin + 3.14.0 + + ${java.version} + + + + org.apache.maven.plugins + maven-surefire-plugin + 3.5.3 + + + maven-jar-plugin + 3.4.2 + + + maven-install-plugin + 3.1.4 + + + maven-deploy-plugin + 3.1.4 + + + org.springframework.boot + spring-boot-maven-plugin + + + ${spring-boot.version} + + + com.diffplug.spotless + spotless-maven-plugin + ${spotless.version} + + + + 4.35 + ${maven.multiModuleProjectDirectory}/code-formatting/eclipse-formatter.xml + + + + + + + org.codehaus.mojo + flatten-maven-plugin + 1.6.0 + + + org.apache.maven.plugins + maven-enforcer-plugin + 3.5.0 + + + + + + + org.apache.maven.plugins + maven-enforcer-plugin + + + enforce-jdk-25 + + enforce + + + + + [25,26) + + + + + + + ban-duplicate-responsibility-libs + + enforce + + + + + + commons-httpclient:commons-httpclient + org.json:json + + true + + + + + + + + ban-direct-duplicate-libs + + enforce + + + + + + + junit:junit + com.squareup.okhttp3:okhttp + + false + + + + + + + + + org.codehaus.mojo + flatten-maven-plugin + + true + resolveCiFriendliesOnly + + + + flatten + process-resources + + flatten + + + + flatten.clean + clean + + clean + + + + + + + + + github + GitHub HMS-DBMI Apache Maven Packages + https://maven.pkg.github.com/hms-dbmi/pic-sure + + diff --git a/services/pic-sure-auth-microapp/.github/release.yml b/services/pic-sure-auth-microapp/.github/release.yml new file mode 100644 index 000000000..0db6cd02d --- /dev/null +++ b/services/pic-sure-auth-microapp/.github/release.yml @@ -0,0 +1,20 @@ +changelog: + exclude: + labels: + - ignore-for-release + categories: + - title: Breaking Changes + labels: + - breaking-change + - title: Features + labels: + - feature + - title: Enhancements + labels: + - enhancement + - title: Bug Fixes + labels: + - bug + - title: Other Changes + labels: + - "*" diff --git a/services/pic-sure-auth-microapp/.github/workflows/github-actions-test.yml b/services/pic-sure-auth-microapp/.github/workflows/github-actions-test.yml new file mode 100644 index 000000000..f81f41466 --- /dev/null +++ b/services/pic-sure-auth-microapp/.github/workflows/github-actions-test.yml @@ -0,0 +1,23 @@ +name: Maven Run Tests + +on: + push: + branches: [ "main", "release" ] + pull_request: + branches: [ "main", "release" ] + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd #v6.0.2 + - name: Set up JDK 25 + uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 #v5.2.0 + with: + java-version: '25' + distribution: 'temurin' + - name: Test with Maven + run: mvn test + env: + GITHUB_TOKEN: ${{ github.token }} \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/.github/workflows/label-checker.yml b/services/pic-sure-auth-microapp/.github/workflows/label-checker.yml new file mode 100644 index 000000000..4806967a4 --- /dev/null +++ b/services/pic-sure-auth-microapp/.github/workflows/label-checker.yml @@ -0,0 +1,21 @@ +name: Label Checker +on: + pull_request: + types: + - opened + - synchronize + - reopened + - labeled + - unlabeled + +jobs: + + check_labels: + name: Check labels + runs-on: ubuntu-latest + steps: + - uses: agilepathway/label-checker@c3d16ad512e7cea5961df85ff2486bb774caf3c5 # v1.6.65 + with: + one_of: breaking-change,enhancement,bug,documentation,ignore-for-release,dependencies + repo_token: ${{ secrets.GITHUB_TOKEN }} + diff --git a/services/pic-sure-auth-microapp/.gitignore b/services/pic-sure-auth-microapp/.gitignore new file mode 100644 index 000000000..ca3c22122 --- /dev/null +++ b/services/pic-sure-auth-microapp/.gitignore @@ -0,0 +1,37 @@ +target/ +.idea/ +.vscode/ +*.iml +pom.xml.tag +pom.xml.releaseBackup +pom.xml.versionsBackup +pom.xml.next +release.properties +dependency-reduced-pom.xml +buildNumber.properties +.mvn/timing.properties + +# Avoid ignoring Maven wrapper jar file (.jar files are usually ignored) +!/.mvn/wrapper/maven-wrapper.jar + + +httpd/pic-sure-auth-ui-webapp.zip + +.project +.settings/ +.classpath +.vscode/ + +.env +.DS_Store +.idea + +.docker-compose.yml.swp +pic-sure-auth-services.war +pic-sure-auth-services.war.deployed +*.war +*.deployed +*.failed + +.m2 +!.m2/README.md \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/.m2/README.md b/services/pic-sure-auth-microapp/.m2/README.md new file mode 100644 index 000000000..c6bc8a5a4 --- /dev/null +++ b/services/pic-sure-auth-microapp/.m2/README.md @@ -0,0 +1,4 @@ +The .m2 dir is used to pass proxy args to Jenkins +for environments that access the outside internet via +an HTTP proxy + diff --git a/services/pic-sure-auth-microapp/.sdkmanrc b/services/pic-sure-auth-microapp/.sdkmanrc new file mode 100644 index 000000000..d2344323e --- /dev/null +++ b/services/pic-sure-auth-microapp/.sdkmanrc @@ -0,0 +1 @@ +java=25.0.3-tem diff --git a/services/pic-sure-auth-microapp/CODE_OF_CONDUCT.md b/services/pic-sure-auth-microapp/CODE_OF_CONDUCT.md new file mode 100644 index 000000000..e0cf97b8f --- /dev/null +++ b/services/pic-sure-auth-microapp/CODE_OF_CONDUCT.md @@ -0,0 +1,128 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, religion, or sexual identity +and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the + overall community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or + advances of any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email + address, without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official e-mail address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +avillach_lab_developers@googlegroups.com. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series +of actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or +permanent ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within +the community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.0, available at +https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. + +Community Impact Guidelines were inspired by [Mozilla's code of conduct +enforcement ladder](https://github.com/mozilla/diversity). + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see the FAQ at +https://www.contributor-covenant.org/faq. Translations are available at +https://www.contributor-covenant.org/translations. diff --git a/services/pic-sure-auth-microapp/Jenkinsfile.fence b/services/pic-sure-auth-microapp/Jenkinsfile.fence new file mode 100644 index 000000000..602efae05 --- /dev/null +++ b/services/pic-sure-auth-microapp/Jenkinsfile.fence @@ -0,0 +1,55 @@ +pipeline { + agent any + + parameters { + string(name: 'DOCKER_REGISTRY', description: 'Docker registry URL (e.g., ECR URL)', defaultValue: 'hms-dbmi') + string(name: 'REPOSITORY_NAME', description: 'Docker repository name', defaultValue: 'psama') + string(name: 'DATASOURCE_URL', description: 'Datasource URL', defaultValue: '${database_host_address}') + string(name: 'DATASOURCE_USERNAME', description: 'Datasource username', defaultValue: '${database_app_user_secret_name}') + string(name: 'STACK_SPECIFIC_APPLICATION_ID', description: 'Application ID for base query', defaultValue: '${application_id_for_base_query}') + string(name: 'TARGET_STACK', description: 'Target stack for application deployment.') + string(name: 'STACK_S3_BUCKET', description: 'The s3 bucket', defaultValue: '${stack_s3_bucket}') + } + + environment { + DOCKER_BUILD_ARGS = "-f ./pic-sure-auth-services/bdc.Dockerfile" + GIT_BRANCH_SHORT = sh(script: 'echo ${GIT_BRANCH} | cut -d "/" -f 2', returnStdout: true).trim() + GIT_COMMIT_SHORT = sh(script: 'echo ${GIT_COMMIT} | cut -c1-7', returnStdout: true).trim() + IMAGE_TAG = "${GIT_BRANCH_SHORT}_${GIT_COMMIT_SHORT}" + LATEST_TAG = "latest" + } + + stages { + stage('Maven Build') { + steps { + sh '''docker run --rm \ + -v "/var/jenkins_home/workspace/${JOB_NAME}/:/app:z" \ + -v maven_m2_cache:/root/.m2 \ + -w /app/services/pic-sure-auth-microapp \ + --platform=linux/amd64 \ + maven:3.9-amazoncorretto-25 \ + sh -lc "mvn clean install -DskipTests"''' + } + } + + stage('Build Docker Image') { + steps { + script { + // Define the build args + def buildArgs = " --build-arg DATASOURCE_URL=${env.DATASOURCE_URL} " + + " --build-arg DATASOURCE_USERNAME=${env.DATASOURCE_USERNAME} " + + " --build-arg STACK_SPECIFIC_APPLICATION_ID=${env.STACK_SPECIFIC_APPLICATION_ID} " + + sh "docker build --load ${DOCKER_BUILD_ARGS} ${buildArgs} -t ${params.DOCKER_REGISTRY}/${params.REPOSITORY_NAME}:${IMAGE_TAG} services/pic-sure-auth-microapp" + sh "docker tag ${params.DOCKER_REGISTRY}/${params.REPOSITORY_NAME}:${IMAGE_TAG} ${params.DOCKER_REGISTRY}/${params.REPOSITORY_NAME}:${LATEST_TAG}" + } + } + } + stage('Deploy Docker Image') { + steps { + sh "docker save ${params.DOCKER_REGISTRY}/${params.REPOSITORY_NAME}:${LATEST_TAG} | gzip > psama.tar.gz" + sh "aws s3 --sse=AES256 cp psama.tar.gz s3://$STACK_S3_BUCKET/$TARGET_STACK/containers/psama.tar.gz" + } + } + } +} diff --git a/services/pic-sure-auth-microapp/LICENSE b/services/pic-sure-auth-microapp/LICENSE new file mode 100644 index 000000000..261eeb9e9 --- /dev/null +++ b/services/pic-sure-auth-microapp/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We offer implementations for both [CentOS](https://github.com/hms-dbmi/pic-sure-all-in-one/tree/master) and [Redhat](https://github.com/hms-dbmi/pic-sure-all-in-one/tree/feature/redhat) based operating systems. To get started, please consult the [README](https://github.com/hms-dbmi/pic-sure-all-in-one/tree/master#readme) section of the [All-In-One](https://github.com/hms-dbmi/pic-sure-all-in-one) repository. + +Before contributing code, please set up our git hook: +`cp code-formatting/pre-commit.sh .git/hooks/pre-commit` +To skip formatting on a block of code, wrap in `spotless:off`, `spotless:on` comments + + + +#### To add an initial top admin user in the system +If you follow the steps above, spins up the docker containers and you can see the login page in the browser, you are almost there. + +You just need to add a top admin user in the system to be able to play with all features. + +There is a sql script in source code for adding the top admin user with some initial setup, you can import the script +into your database. + +Open the file under `/{{root_pic-sure-auth-microapp}}/pic-sure-auth-db/db/tools/first_time_run_the_system_and_insert_admin_user.sql`, +modify the configuration data - `@user_email` with your own google email + +#### Terms of Service + +The content of the terms of service is stored in the termsOfService table in the database. This is html that is rendered on the page. +Some example termsOfService content would be: + +```aidl +These are the terms of service. +
    +This box must be checked +
    + + +``` + +#### Email templates configuration + +PSAMA has mechanism of sending various emails to the users and admins depending of the action. +MailService.class is responsible for compiling Mustache templates and populating it with required information based on parameters. There are few settings configured in standalone.xml for that. + +Email Template Path is where email templates could be stored, so that it can be configured per stack if needed. +``` + +``` +Email Template Path can be mapped as a volume in a container, so that application can discover it, where directory matching the one from standalone.xml: +``` +volumes: + - $PWD/config/psama/emailTemplates:/usr/local/shared/applications +``` + +Denied Email Enabled is flag to enable sending email to admin if user has not been added to system and trying to login. +``` + +``` + +List of admin email configured as below. Provide comma separated list of admin. +``` + +``` diff --git a/services/pic-sure-auth-microapp/cache.http b/services/pic-sure-auth-microapp/cache.http new file mode 100644 index 000000000..8b380736c --- /dev/null +++ b/services/pic-sure-auth-microapp/cache.http @@ -0,0 +1,12 @@ +# This class can be used to interact with the CacheController in the PSAMA API +# The CacheController must be enable in the application.properties file +# You can enable it by setting the following property: +# app.cache.inspect.enabled=true +# If you are using a environment variable to set the property, you can set it like this: +# CACHE_INSPECT_ENABLED=true + +### GET /cache - Get a list of all caches in the application +GET https://dev.picsure.biodatacatalyst.nhlbi.nih.gov/psama/cache + +### GET /cache/{cacheName} - Get the contents of a specific cache +GET https://dev.picsure.biodatacatalyst.nhlbi.nih.gov/psama/cache/mergedRulesCache \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/code-formatting/eclipse-formatter.xml b/services/pic-sure-auth-microapp/code-formatting/eclipse-formatter.xml new file mode 100644 index 000000000..e7cfababf --- /dev/null +++ b/services/pic-sure-auth-microapp/code-formatting/eclipse-formatter.xml @@ -0,0 +1,402 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/services/pic-sure-auth-microapp/code-formatting/pre-commit.sh b/services/pic-sure-auth-microapp/code-formatting/pre-commit.sh new file mode 100755 index 000000000..ed051d182 --- /dev/null +++ b/services/pic-sure-auth-microapp/code-formatting/pre-commit.sh @@ -0,0 +1,28 @@ +#!/bin/sh -e +CWD=$(pwd) +cd $(git rev-parse --show-toplevel) +format_cmd="" + +# skip if NO_VERIFY env var set +if [ "$NO_VERIFY" ]; then + echo 'code formatting skipped' 1>&2 + exit 0 +fi + +# I'm not great at bash, so this is a bit ugly, but I'll explain each pipe +# 1. Get all staged files +# 2. Reduce to just .java files +# 3. Replace newlines with commas (this was really hard to do in sed) +# 4. Replace commas with $,^.* +# 5. Crop off the last 4 chars +# This results in foo.java$,^.*bar.java$,^.*baz.java$ +# I then append ^.* to the beginning of that. +STAGED_JAVA_FILES_AS_REGEX=$(git diff --staged --name-only --diff-filter=ACMR | grep '.java$' | tr '\n' ',' | sed -e 's/,/$,^.*/g' | sed 's/.\{4\}$//') +FILES_TO_RESTAGE=$(git diff --staged --name-only --diff-filter=ACMR) +if [ -n "$STAGED_JAVA_FILES_AS_REGEX" ]; then + echo "Found the following staged java files to format: $STAGED_JAVA_FILES_AS_REGEX" + mvn spotless:apply -DspotlessFiles=^.*$STAGED_JAVA_FILES_AS_REGEX + git add $FILES_TO_RESTAGE +fi + +cd $CWD \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/config/psama/bdc/psama-db-config.properties b/services/pic-sure-auth-microapp/config/psama/bdc/psama-db-config.properties new file mode 100644 index 000000000..4d0461862 --- /dev/null +++ b/services/pic-sure-auth-microapp/config/psama/bdc/psama-db-config.properties @@ -0,0 +1,4 @@ +spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.MySQL8Dialect +spring.datasource.driver-class-name=com.amazonaws.secretsmanager.sql.AWSSecretsManagerMySQLDriver +spring.datasource.url=jdbc-secretsmanager:mysql://${DATASOURCE_URL}/auth?useUnicode=true&characterEncoding=UTF-8&autoReconnect=true&autoReconnectForPools=true +spring.datasource.username=${DATASOURCE_USERNAME} \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/config/psama/emailTemplates/accessEmail.mustache b/services/pic-sure-auth-microapp/config/psama/emailTemplates/accessEmail.mustache new file mode 100644 index 000000000..8b699bc69 --- /dev/null +++ b/services/pic-sure-auth-microapp/config/psama/emailTemplates/accessEmail.mustache @@ -0,0 +1,17 @@ +Access Changed: + +{{#rolesExists}} +You have been granted access to {{systemName}} with the following roles: +{{/rolesExists}} +{{#roles}} +{{name}} : {{#privileges}} {{description}} {{/privileges}} +{{/roles}} +{{^roles}} +Currently NO roles have been granted for you to {{systemName}}. +{{/roles}} + {{#documentation}} +You can find documentation at the following links: + {{.}} +{{/documentation}} + +Have a good day! \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/config/psama/emailTemplates/deniedAccessEmail.mustache b/services/pic-sure-auth-microapp/config/psama/emailTemplates/deniedAccessEmail.mustache new file mode 100644 index 000000000..abab886ba --- /dev/null +++ b/services/pic-sure-auth-microapp/config/psama/emailTemplates/deniedAccessEmail.mustache @@ -0,0 +1,6 @@ +The following user has been denied access to the {{systemName}} environment because their user has not been configured. + +First Name : {{given_name}} +Last Name : {{family_name}} +Email : {{email}} +ID : {{nickname}} diff --git a/services/pic-sure-auth-microapp/config/psama/psama.env b/services/pic-sure-auth-microapp/config/psama/psama.env new file mode 100644 index 000000000..9c519b745 --- /dev/null +++ b/services/pic-sure-auth-microapp/config/psama/psama.env @@ -0,0 +1,32 @@ +# This is a template file that can be used to configure the application. Pass this to the dockerfile and +# the application will be configured with the values provided in this file. + +# These properties are used to configure our applications JWT token. +# The JWT token is used to authenticate the user and authorize them to access the application +# after initial login. +APPLICATION_CLIENT_SECRET= +APPLICATION_CLIENT_SECRET_IS_BASE_64=false +STACK_SPECIFIC_APPLICATION_ID= + +# Fence IDP Configuration +FENCE_IDP_PROVIDER_IS_ENABLED=false +FENCE_CLIENT_ID= +FENCE_CLIENT_SECRET= +FENCE_IDP_PROVIDER_URI= + +# AIM AHEAD Authorized Access (A4) OKTA IDP Configuration +A4_OKTA_IDP_PROVIDER_IS_ENABLED=false +A4_OKTA_CLIENT_SECRET= +A4_OKTA_CLIENT_ID= +A4_OKTA_CONNECTION_ID= +A4_OKTA_IDP_PROVIDER_URI= + +# Auth0 IDP Configuration (Generally, this is used for the All-In-One and Authorized Access) +AUTH0_IDP_PROVIDER_IS_ENABLED=false +AUTH0_HOST= +AUTH0_DENIED_EMAIL_ENABLED= + +# Open Access IDP Configuration +OPEN_IDP_PROVIDER_IS_ENABLED=false + +SYSTEM_NAME=PIC-SURE BioDataCatalyst \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/docker-compose.dev.yml b/services/pic-sure-auth-microapp/docker-compose.dev.yml new file mode 100644 index 000000000..4fba9d733 --- /dev/null +++ b/services/pic-sure-auth-microapp/docker-compose.dev.yml @@ -0,0 +1,52 @@ +version: '3.8' +services: + pic-sure-auth-service: + build: + context: . + dockerfile: ./pic-sure-auth-services/dev.Dockerfile + environment: + JAVA_OPTS: "-Xmx1024m -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=*:5005" + # Note: To use this you will need to set ENVIRONMENT variables for the application.properties + ports: + - "8090:8090" # Application port + - "5005:5005" # Debug port + depends_on: + auth-flyway: + condition: service_started + + picsure-db: + build: + context: ./pic-sure-auth-db/ + dockerfile: Dockerfile + environment: + MYSQL_DATABASE: auth + MYSQL_ROOT_PASSWORD: password + ports: + - "3306:3306" # MySQL port + command: + - --default-authentication-plugin=mysql_native_password # Required for MySQL 8.0 + healthcheck: + test: ["CMD", "mysqladmin" ,"ping", "-h", "localhost"] + interval: 10s + timeout: 5s + retries: 5 + + auth-flyway: + image: flyway/flyway:latest + volumes: + - ./pic-sure-auth-db/db/sql:/flyway/sql + # linux/amd64 + platform: linux/amd64 + environment: + - FLYWAY_URL=jdbc:mysql://picsure-db:3306/auth?useSSL=false + - FLYWAY_USER=root + - FLYWAY_PASSWORD=password + - FLYWAY_SCHEMAS=auth + - FLYWAY_LOCATIONS=filesystem:/flyway/sql + - FLYWAY_IGNORE_MISSING_MIGRATIONS=true + - FLYWAY_BASELINE_ON_MIGRATE=true + command: + - migrate + depends_on: + picsure-db: + condition: service_healthy \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/docker-compose.yml b/services/pic-sure-auth-microapp/docker-compose.yml new file mode 100644 index 000000000..2e121f1cb --- /dev/null +++ b/services/pic-sure-auth-microapp/docker-compose.yml @@ -0,0 +1,52 @@ +version: '3' +services: + picsureauth: + build: + context: pic-sure-auth-services + dockerfile: Dockerfile + command: --debug *:8787 + depends_on: + - picsureauthdb + environment: + - AUTH_CLIENT_SECRET=${AUTH_CLIENT_SECRET:-secret} + - AUTH_CLIENT_ID=${AUTH_CLIENT_ID:-client_id} + - AUTH_USER_ID_CLAIM=sub + - AUTH_MYSQLADDRESS=picsureauthdb + - AUTH0TOKEN=${AUTH0TOKEN:-nothing} + - AUTH0HOST=https://avillachlab.auth0.com + - systemName=${systemName:-PICSURE} + - EMAIL_TEMPLATE_PATH=${EMAIL_TEMPLATE_PATH:-/opt/jboss/wildfly/emailTemplates}/ + - DENIED_EMAIL_ENABLED=${DENIED_EMAIL_ENABLED:-false} + - COMMA_SEPARATED_EMAILS=${COMMA_SEPARATED_EMAILS:-dummyemail} + - accessGrantEmailSubject=Testing + - MAIL_USERNAME=${MAIL_USERNAME:-emailuser@avillach.lab} + - MAIL_PASSWORD=${MAIL_PASSWORD:-email_password} + - TOS_ENABLED:false + ports: + - 8787:8787 + expose: + - 8080 + volumes: + - ./pic-sure-auth-services/src/main/resources/emailTemplates:${EMAIL_TEMPLATE_PATH:-/opt/jboss/wildfly/emailTemplates} + networks: + - public + env_file: + - .env + + picsureauthdb: + build: + context: pic-sure-auth-db + dockerfile: Dockerfile + environment: + - MYSQL_ROOT_PASSWORD=${AUTH_MYSQL_ROOT_PASSWORD:-password} + - MYSQL_DATABASE=auth + restart: always + expose: + - 3306 + ports: + - 3306:3306 + networks: + - public + +networks: + public: diff --git a/services/pic-sure-auth-microapp/jenkinsfile b/services/pic-sure-auth-microapp/jenkinsfile new file mode 100644 index 000000000..3c657ff3e --- /dev/null +++ b/services/pic-sure-auth-microapp/jenkinsfile @@ -0,0 +1,83 @@ +pipeline { + agent any + + parameters { + string(name: 'DOCKER_REGISTRY', description: 'Docker registry URL (e.g., ECR URL)', defaultValue: 'hms-dbmi') + string(name: 'REPOSITORY_NAME', description: 'Docker repository name', defaultValue: 'psama') + booleanParam(name: 'DEPLOY', description: 'Deploy the image to the registry', defaultValue: true) + } + + environment { + LATEST_TAG = "LATEST" + EMAIL_TEMPLATE_VOLUME = "-v $DOCKER_CONFIG_DIR/wildfly/emailTemplates:/opt/jboss/wildfly/standalone/configuration/emailTemplates" + TRUSTSTORE_VOLUME = "-v $DOCKER_CONFIG_DIR/wildfly/application.truststore:/opt/jboss/wildfly/standalone/configuration/application.truststore" + PSAMA_OPTS = "-Xms1g -Xmx2g -XX:MetaspaceSize=96M -XX:MaxMetaspaceSize=256m -Djava.net.preferIPv4Stack=true" + TRUSTSTORE_JAVA_OPTS = "-Djavax.net.ssl.trustStore=/opt/jboss/wildfly/standalone/configuration/application.truststore -Djavax.net.ssl.trustStorePassword=password" + + // If you need proxy args during docker build + DOCKER_BUILD_ARGS = "-f ./pic-sure-auth-services/Dockerfile " + + "--build-arg http_proxy=$http_proxy --build-arg https_proxy=$http_proxy --build-arg no_proxy=\"$no_proxy\" " + + "--build-arg HTTP_PROXY=$http_proxy --build-arg HTTPS_PROXY=$http_proxy --build-arg NO_PROXY=\"$no_proxy\"" + } + + stages { + stage('init') { + steps { + script { + env.GIT_BRANCH_SHORT = sh(script: 'echo "${GIT_BRANCH}" | awk -F/ \'{print $NF}\'', returnStdout: true).trim() + env.GIT_COMMIT_SHORT = sh(script: 'echo "${GIT_COMMIT}" | cut -c1-7', returnStdout: true).trim() + env.IMAGE_TAG = "${env.GIT_BRANCH_SHORT}_${env.GIT_COMMIT_SHORT}" + env.IMAGE_NAME = "${params.DOCKER_REGISTRY}/${params.REPOSITORY_NAME}" + } + } + } + + stage('build jar (docker run)') { + steps { + sh ''' + set -euo pipefail + + # Build in a Maven container, output goes into the mounted workspace (target/ created here) + docker run --rm \ + -v "$DOCKER_CONFIG_DIR/jenkins_home/workspace/$JOB_NAME/:/app" \ + -v maven_m2_cache:/root/.m2 \ + -w /app/services/pic-sure-auth-microapp \ + maven:3.9-amazoncorretto-25 \ + sh -lc "mvn clean install -B -T 1C -DskipTests" + + ls -lah services/pic-sure-auth-microapp/pic-sure-auth-services/target || true + ''' + } + } + + stage('build image') { + steps { + sh ''' + set -euo pipefail + docker build ${DOCKER_BUILD_ARGS} -t "${IMAGE_NAME}:${IMAGE_TAG}" services/pic-sure-auth-microapp + docker tag "${IMAGE_NAME}:${IMAGE_TAG}" "${IMAGE_NAME}:${LATEST_TAG}" + ''' + } + } + + stage('deploy') { + when { expression { return params.DEPLOY } } + steps { + sh ''' + set +e + docker stop psama + docker rm psama + set -e + + docker run --name=psama --restart always \ + --network=picsure \ + --env-file /usr/local/docker-config/psama/psama.env \ + ${EMAIL_TEMPLATE_VOLUME} \ + ${TRUSTSTORE_VOLUME} \ + -e JAVA_OPTS="${PSAMA_OPTS} ${TRUSTSTORE_JAVA_OPTS}" \ + -d "${IMAGE_NAME}:${IMAGE_TAG}" + ''' + } + } + } +} diff --git a/pic-sure-resources/pic-sure-aggregate-resource/.gitignore b/services/pic-sure-auth-microapp/pic-sure-auth-db/.gitignore similarity index 100% rename from pic-sure-resources/pic-sure-aggregate-resource/.gitignore rename to services/pic-sure-auth-microapp/pic-sure-auth-db/.gitignore diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/Dockerfile b/services/pic-sure-auth-microapp/pic-sure-auth-db/Dockerfile new file mode 100644 index 000000000..b9f5cc3b2 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/Dockerfile @@ -0,0 +1,9 @@ +FROM mysql:8.2.0 + +RUN mkdir /tempsql/ +COPY db/picsure-auth-dump-initial.sql /tempsql/picsure-auth-dump-initial.sql + +EXPOSE 3306 + +ENTRYPOINT ["docker-entrypoint.sh"] +CMD ["mysqld","--init-file","/tempsql/picsure-auth-dump-initial.sql"] \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/create_db_auth.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/create_db_auth.sql new file mode 100644 index 000000000..bbaa8b7dc --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/create_db_auth.sql @@ -0,0 +1,222 @@ +DROP DATABASE IF EXISTS `auth`; + +CREATE DATABASE IF NOT EXISTS `auth` /*!40100 DEFAULT CHARACTER SET utf8 COLLATE utf8_bin */; +USE `auth`; +-- MySQL dump 10.13 Distrib 5.7.17, for macos10.12 (x86_64) +-- +-- Host: 127.0.0.1 Database: auth +-- ------------------------------------------------------ +-- Server version 5.7.20 + +/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; +/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; +/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */; +/*!40101 SET NAMES utf8 */; +/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */; +/*!40103 SET TIME_ZONE='+00:00' */; +/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */; +/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */; +/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */; +/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; + +-- +-- Table structure for table `privilege` +-- + +-- DROP TABLE IF EXISTS `privilege`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `privilege` ( + `uuid` binary(16) NOT NULL, + `description` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `application_id` binary(16) DEFAULT NULL, + `queryTemplate` varchar(8192) DEFAULT NULL, + `queryScope` varchar(512) DEFAULT NULL, + PRIMARY KEY (`uuid`), + UNIQUE KEY `UK_h7iwbdg4ev8mgvmij76881tx8` (`name`), + KEY `FK61h3jewffk70b5ni4tsi5rhoy` (`application_id`), + CONSTRAINT `FK61h3jewffk70b5ni4tsi5rhoy` FOREIGN KEY (`application_id`) REFERENCES `application` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `role` +-- + +-- DROP TABLE IF EXISTS `role`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `role` ( + `uuid` binary(16) NOT NULL, + `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `description` varchar(255) COLLATE utf8_bin DEFAULT NULL, + PRIMARY KEY (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `role_privilege` +-- + +-- DROP TABLE IF EXISTS `role_privilege`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `role_privilege` ( + `role_id` binary(16) NOT NULL, + `privilege_id` binary(16) NOT NULL, + PRIMARY KEY (`role_id`,`privilege_id`), + KEY `FKdkwbrwb5r8h74m1v7dqmhp99c` (`privilege_id`), + CONSTRAINT `FKdkwbrwb5r8h74m1v7dqmhp99c` FOREIGN KEY (`privilege_id`) REFERENCES `privilege` (`uuid`), + CONSTRAINT `FKsykrtrdngu5iexmbti7lu9xa` FOREIGN KEY (`role_id`) REFERENCES `role` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `user` +-- + +-- DROP TABLE IF EXISTS `user`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `user` ( + `uuid` binary(16) NOT NULL, + `auth0_metadata` varchar(8000) COLLATE utf8_bin DEFAULT NULL, + `general_metadata` varchar(9000) COLLATE utf8_bin DEFAULT NULL, + `acceptedTOS` datetime COLLATE utf8_bin DEFAULT NULL, + `connectionId` binary(16) DEFAULT NULL, + `email` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `matched` bit(1) NOT NULL DEFAULT FALSE, + `subject` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `is_active` bit(1) NOT NULL DEFAULT TRUE, + `long_term_token` varchar(4000) COLLATE utf8_bin DEFAULT NULL, + PRIMARY KEY (`uuid`), + UNIQUE KEY `UK_r8xpakluitn685ua7pt8xjy9r` (`subject`), + UNIQUE KEY `email_UNIQUE` (`email`), + KEY `FKn8bku0vydfcnuwbqwgnbgg8ry` (`connectionId`), + CONSTRAINT `FKn8bku0vydfcnuwbqwgnbgg8ry` FOREIGN KEY (`connectionId`) REFERENCES `connection` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `userMetadataMapping` +-- + +-- DROP TABLE IF EXISTS `userMetadataMapping`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `userMetadataMapping` ( + `uuid` binary(16) NOT NULL, + `auth0MetadataJsonPath` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `connectionId` binary(16) DEFAULT NULL, + `generalMetadataJsonPath` varchar(255) COLLATE utf8_bin DEFAULT NULL, + PRIMARY KEY (`uuid`), + KEY `FKayr8vrvvwpgsdhxdyryt6k590` (`connectionId`), + CONSTRAINT `FKayr8vrvvwpgsdhxdyryt6k590` FOREIGN KEY (`connectionId`) REFERENCES `connection` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `user_role` +-- + +-- DROP TABLE IF EXISTS `user_role`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `user_role` ( + `user_id` binary(16) NOT NULL, + `role_id` binary(16) NOT NULL, + PRIMARY KEY (`user_id`,`role_id`), + KEY `FKa68196081fvovjhkek5m97n3y` (`role_id`), + CONSTRAINT `FK859n2jvi8ivhui0rl0esws6o` FOREIGN KEY (`user_id`) REFERENCES `user` (`uuid`), + CONSTRAINT `FKa68196081fvovjhkek5m97n3y` FOREIGN KEY (`role_id`) REFERENCES `role` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; +/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; + +CREATE TABLE `termsOfService` ( + `uuid` binary(16) NOT NULL, + `dateUpdated` timestamp, + `content` varchar(9000) COLLATE utf8_bin DEFAULT NULL, + PRIMARY KEY (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `connection` ( + `uuid` binary(16) NOT NULL, + `label` varchar(255) COLLATE utf8_bin NOT NULL, + `id` varchar(255) COLLATE utf8_bin NOT NULL, + `subprefix` varchar(255) COLLATE utf8_bin NOT NULL, + `requiredFields` varchar(9000) COLLATE utf8_bin NOT NULL, + PRIMARY KEY (`uuid`), + UNIQUE KEY `id` (`id`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +CREATE TABLE `application` ( + `uuid` binary(16) NOT NULL, + `description` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `enable` bit(1) NOT NULL DEFAULT b'1', + `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `token` varchar(2000) COLLATE utf8_bin DEFAULT NULL, + `url` varchar(500) COLLATE utf8_bin DEFAULT NULL, + PRIMARY KEY (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +CREATE TABLE `access_rule` ( + `uuid` binary(16) NOT NULL, + `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `description` varchar(2000) COLLATE utf8_bin DEFAULT NULL, + `rule` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `type` int(11) DEFAULT NULL, + `value` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `checkMapKeyOnly` bit(1) NOT NULL, + `checkMapNode` bit(1) NOT NULL, + `subAccessRuleParent_uuid` binary(16) DEFAULT NULL, + `isGateAnyRelation` bit(1) NOT NULL, + `isEvaluateOnlyByGates` bit(1) NOT NULL, + PRIMARY KEY (`uuid`), + KEY `FK8rovvx363ui99ce21sksmg6uy` (`subAccessRuleParent_uuid`), + CONSTRAINT `FK8rovvx363ui99ce21sksmg6uy` FOREIGN KEY (`subAccessRuleParent_uuid`) REFERENCES `access_rule` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +CREATE TABLE `accessRule_privilege` ( + `privilege_id` binary(16) NOT NULL, + `accessRule_id` binary(16) NOT NULL, + PRIMARY KEY (`privilege_id`,`accessRule_id`), + KEY `FK89rf30kbf9d246jty2dd7qk99` (`accessRule_id`), + CONSTRAINT `FK7x47w81gpua380qd7lp9x94l1` FOREIGN KEY (`privilege_id`) REFERENCES `privilege` (`uuid`), + CONSTRAINT `FK89rf30kbf9d246jty2dd7qk99` FOREIGN KEY (`accessRule_id`) REFERENCES `access_rule` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +CREATE TABLE `accessRule_gate` ( + `accessRule_id` binary(16) NOT NULL, + `gate_id` binary(16) NOT NULL, + PRIMARY KEY (`accessRule_id`,`gate_id`), + KEY `FK6re4kcq9tyl45jv9yg584doem` (`gate_id`), + CONSTRAINT `FK6re4kcq9tyl45jv9yg584doem` FOREIGN KEY (`gate_id`) REFERENCES `access_rule` (`uuid`), + CONSTRAINT `FKe6l5ee7f207958mm3anpsmqom` FOREIGN KEY (`accessRule_id`) REFERENCES `access_rule` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +CREATE OR REPLACE VIEW `management_view` +AS SELECT + `role`.`uuid` AS `uuid`, + `role`.`name` AS `role_name`, + `privilege`.`name` AS `privilege_name` + FROM + ((`role` JOIN `role_privilege`) JOIN `privilege`) + WHERE + ((`role`.`uuid` = `role_privilege`.`role_id`) + AND + (`privilege`.`uuid` = `role_privilege`.`privilege_id`)); + +/*!40101 SET SQL_MODE=@OLD_SQL_MODE */; +/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */; +/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */; +/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */; +/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */; +/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; +/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; + +-- Dump completed on 2018-10-16 19:48:56 diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/insert_connection_Google.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/insert_connection_Google.sql new file mode 100644 index 000000000..da4de9e61 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/insert_connection_Google.sql @@ -0,0 +1,20 @@ + +START TRANSACTION; + +SET @uuidConnection = REPLACE(uuid(),'-',''); + +INSERT INTO `connection` ( + `uuid`, + `label`, + `id`, + `subprefix`, + `requiredFields` +) VALUES ( + unhex(@uuidConnection), + 'Google', + 'google-oauth2', + 'google-oauth2|', + '[{\"label\":\"Email\", \"id\":\"email\"}]' +); + +COMMIT; diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/insert_privilege_ADMIN.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/insert_privilege_ADMIN.sql new file mode 100644 index 000000000..559084785 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/insert_privilege_ADMIN.sql @@ -0,0 +1,23 @@ +# +# Create a connection definition in the database +# of Google type. This example requires the Email +# field in the authentication definition to exist +# +START TRANSACTION; + +SET @uuidPrivilege = REPLACE(uuid(),'-',''); + +INSERT INTO `privilege` ( + `uuid`, + `name`, + `description`, + `application_id` +) +VALUES ( + unhex(@uuidPrivilege), + 'ADMIN', + 'PIC-SURE Auth admin for managing users.', + NULL +); + +COMMIT; diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/insert_privilege_SUPER_ADMIN.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/insert_privilege_SUPER_ADMIN.sql new file mode 100644 index 000000000..d611b7fbf --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/insert_privilege_SUPER_ADMIN.sql @@ -0,0 +1,23 @@ +# +# Create a connection definition in the database +# of Google type. This example requires the Email +# field in the authentication definition to exist +# +START TRANSACTION; + +SET @uuidPrivilege = REPLACE(uuid(),'-',''); + +INSERT INTO `privilege` ( + `uuid`, + `name`, + `description`, + `application_id` +) +VALUES ( + unhex(@uuidPrivilege), + 'SUPER_ADMIN', + 'PIC-SURE Auth super admin for managing roles/privileges/application/connections', + NULL +); + +COMMIT; diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/insert_role_TOPADMIN.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/insert_role_TOPADMIN.sql new file mode 100644 index 000000000..0962139e2 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/insert_role_TOPADMIN.sql @@ -0,0 +1,39 @@ +# +# Create a role, which is a collection of privileges +# +START TRANSACTION; + +SET @uuidRole = REPLACE(uuid(),'-',''); + +# This is an example, where the SUPERUSER role is added. +INSERT INTO `role` ( + `uuid`, + `name`, + `description` +) +VALUES ( + unhex(@uuidRole), + 'PIC-SURE Top Admin', + 'PIC-SURE Auth Micro App Top admin including Admin and super Admin' +); + +# This is an example, where the role is associated with the 'SUPER_ADMIN' privilege +INSERT INTO `role_privilege` ( + `role_id`, + `privilege_id` +) +VALUES ( + unhex(@uuidRole), + (SELECT uuid FROM `privilege` WHERE `name` = 'SUPER_ADMIN') +); + +INSERT INTO `role_privilege` ( + `role_id`, + `privilege_id` +) +VALUES ( + unhex(@uuidRole), + (SELECT uuid FROM `privilege` WHERE `name` = 'ADMIN') +); + +COMMIT; diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/insert_user_ADMINGMAIL.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/insert_user_ADMINGMAIL.sql new file mode 100644 index 000000000..69ccaff7e --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/insert_user_ADMINGMAIL.sql @@ -0,0 +1,64 @@ +# +# This script will insert the initial superuser account +# and corresponding information into the appropriate tables. +# Assuming, that all objects (tables and views) have been +# created, and the initial privileges and roles have been +# inserted into the appropriate tables already. +# +# Just in case clearing the underlying tables is required +# One might execute the folloring scripts, but BEWARE that +# these commands will remove ALL user information from +# the database. +# +# +# DELETE FROM `user_role`; +# DELETE FROM `user`; +# DELETE FROM `userMetadataMapping`; +# DELETE FROM `connection`; +# +# +START TRANSACTION; + +#configuration for connection table +SET @uuidUser = REPLACE(uuid(),'-',''); + +INSERT INTO user ( + `uuid`, + `general_metadata`, + `connectionId`, + `matched` +) VALUES ( + unhex(@uuidUser), + "{\"email\":\"__SUPERUSER_GMAIL_ADDRESS__\"}", + (SELECT `uuid` FROM `connection` WHERE `label` = 'Google'), + false +); + +# Add the initial ADMIN role for the user. +# Assuming, that all superuser privileges have been +# assigned to this role, already, during creation +# of the database. +INSERT INTO user_role ( + `user_id`, + `role_id` +) VALUES ( + UNHEX(@uuidUser), + (SELECT `uuid` FROM `role` WHERE name = 'PIC-SURE Top Admin') +); + +#### insert into userMetadataMapping +SET @uuidMetaData = REPLACE(uuid(),'-',''); + +INSERT INTO `userMetadataMapping` ( + `uuid`, + `auth0MetadataJsonPath`, + `connectionId`, + `generalMetadataJsonPath` +) VALUES ( + unhex(@uuidMetaData), + '$.email', + (SELECT `uuid` FROM `connection` WHERE `label` = 'Google'), + '$.email' +); + +COMMIT; diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/picsure-auth-dump-initial.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/picsure-auth-dump-initial.sql new file mode 100644 index 000000000..37be5c779 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/picsure-auth-dump-initial.sql @@ -0,0 +1,208 @@ +CREATE DATABASE IF NOT EXISTS `auth` /*!40100 DEFAULT CHARACTER SET utf8 COLLATE utf8_bin */; +USE `auth`; +-- MySQL dump 10.13 Distrib 5.7.17, for macos10.12 (x86_64) +-- +-- Host: 127.0.0.1 Database: auth +-- ------------------------------------------------------ +-- Server version 5.7.20 + +/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; +/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; +/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */; +/*!40101 SET NAMES utf8 */; +/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */; +/*!40103 SET TIME_ZONE='+00:00' */; +/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */; +/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */; +/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */; +/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; + +-- +-- Table structure for table `privilege` +-- + +-- DROP TABLE IF EXISTS `privilege`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `privilege` ( + `uuid` binary(16) NOT NULL, + `description` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `application_id` binary(16) DEFAULT NULL, + `queryTemplate` varchar(8192) DEFAULT NULL, + `queryScope` varchar(512) DEFAULT NULL, + PRIMARY KEY (`uuid`), + UNIQUE KEY `UK_h7iwbdg4ev8mgvmij76881tx8` (`name`), + KEY `FK61h3jewffk70b5ni4tsi5rhoy` (`application_id`), + CONSTRAINT `FK61h3jewffk70b5ni4tsi5rhoy` FOREIGN KEY (`application_id`) REFERENCES `application` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `role` +-- + +-- DROP TABLE IF EXISTS `role`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `role` ( + `uuid` binary(16) NOT NULL, + `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `description` varchar(255) COLLATE utf8_bin DEFAULT NULL, + PRIMARY KEY (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `role_privilege` +-- + +-- DROP TABLE IF EXISTS `role_privilege`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `role_privilege` ( + `role_id` binary(16) NOT NULL, + `privilege_id` binary(16) NOT NULL, + PRIMARY KEY (`role_id`,`privilege_id`), + KEY `FKdkwbrwb5r8h74m1v7dqmhp99c` (`privilege_id`), + CONSTRAINT `FKdkwbrwb5r8h74m1v7dqmhp99c` FOREIGN KEY (`privilege_id`) REFERENCES `privilege` (`uuid`), + CONSTRAINT `FKsykrtrdngu5iexmbti7lu9xa` FOREIGN KEY (`role_id`) REFERENCES `role` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `user` +-- + +-- DROP TABLE IF EXISTS `user`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `user` ( + `uuid` binary(16) NOT NULL, + `auth0_metadata` varchar(8000) COLLATE utf8_bin DEFAULT NULL, + `general_metadata` varchar(9000) COLLATE utf8_bin DEFAULT NULL, + `acceptedTOS` datetime COLLATE utf8_bin DEFAULT NULL, + `connectionId` binary(16) DEFAULT NULL, + `email` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `matched` bit(1) NOT NULL DEFAULT FALSE, + `subject` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `is_active` bit(1) NOT NULL DEFAULT TRUE, + `long_term_token` varchar(4000) COLLATE utf8_bin DEFAULT NULL, + `isGateAnyRelation` bit(1) NOT NULL DEFAULT TRUE, + PRIMARY KEY (`uuid`), + UNIQUE KEY `UK_r8xpakluitn685ua7pt8xjy9r` (`subject`), + KEY `FKn8bku0vydfcnuwbqwgnbgg8ry` (`connectionId`), + CONSTRAINT `FKn8bku0vydfcnuwbqwgnbgg8ry` FOREIGN KEY (`connectionId`) REFERENCES `connection` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `userMetadataMapping` +-- + +-- DROP TABLE IF EXISTS `userMetadataMapping`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `userMetadataMapping` ( + `uuid` binary(16) NOT NULL, + `auth0MetadataJsonPath` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `connectionId` binary(16) DEFAULT NULL, + `generalMetadataJsonPath` varchar(255) COLLATE utf8_bin DEFAULT NULL, + PRIMARY KEY (`uuid`), + KEY `FKayr8vrvvwpgsdhxdyryt6k590` (`connectionId`), + CONSTRAINT `FKayr8vrvvwpgsdhxdyryt6k590` FOREIGN KEY (`connectionId`) REFERENCES `connection` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `user_role` +-- + +-- DROP TABLE IF EXISTS `user_role`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `user_role` ( + `user_id` binary(16) NOT NULL, + `role_id` binary(16) NOT NULL, + PRIMARY KEY (`user_id`,`role_id`), + KEY `FKa68196081fvovjhkek5m97n3y` (`role_id`), + CONSTRAINT `FK859n2jvi8ivhui0rl0esws6o` FOREIGN KEY (`user_id`) REFERENCES `user` (`uuid`), + CONSTRAINT `FKa68196081fvovjhkek5m97n3y` FOREIGN KEY (`role_id`) REFERENCES `role` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; +/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; + +CREATE TABLE `termsOfService` ( + `uuid` binary(16) NOT NULL, + `dateUpdated` timestamp, + `content` varchar(9000) COLLATE utf8_bin DEFAULT NULL, + PRIMARY KEY (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `connection` ( + `uuid` binary(16) NOT NULL, + `label` varchar(255) COLLATE utf8_bin NOT NULL, + `id` varchar(255) COLLATE utf8_bin NOT NULL, + `subprefix` varchar(255) COLLATE utf8_bin NOT NULL, + `requiredFields` varchar(9000) COLLATE utf8_bin NOT NULL, + PRIMARY KEY (`uuid`), + UNIQUE KEY `id` (`id`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +CREATE TABLE `application` ( + `uuid` binary(16) NOT NULL, + `description` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `enable` bit(1) NOT NULL DEFAULT b'1', + `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `token` varchar(2000) COLLATE utf8_bin DEFAULT NULL, + `url` varchar(500) COLLATE utf8_bin DEFAULT NULL, + PRIMARY KEY (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +CREATE TABLE `access_rule` ( + `uuid` binary(16) NOT NULL, + `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `description` varchar(2000) COLLATE utf8_bin DEFAULT NULL, + `rule` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `type` int(11) DEFAULT NULL, + `value` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `checkMapKeyOnly` bit(1) NOT NULL, + `checkMapNode` bit(1) NOT NULL, + `subAccessRuleParent_uuid` binary(16) DEFAULT NULL, + `isGateAnyRelation` bit(1) NOT NULL, + `isEvaluateOnlyByGates` bit(1) NOT NULL, + PRIMARY KEY (`uuid`), + KEY `FK8rovvx363ui99ce21sksmg6uy` (`subAccessRuleParent_uuid`), + CONSTRAINT `FK8rovvx363ui99ce21sksmg6uy` FOREIGN KEY (`subAccessRuleParent_uuid`) REFERENCES `access_rule` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +CREATE TABLE `accessRule_privilege` ( + `privilege_id` binary(16) NOT NULL, + `accessRule_id` binary(16) NOT NULL, + PRIMARY KEY (`privilege_id`,`accessRule_id`), + KEY `FK89rf30kbf9d246jty2dd7qk99` (`accessRule_id`), + CONSTRAINT `FK7x47w81gpua380qd7lp9x94l1` FOREIGN KEY (`privilege_id`) REFERENCES `privilege` (`uuid`), + CONSTRAINT `FK89rf30kbf9d246jty2dd7qk99` FOREIGN KEY (`accessRule_id`) REFERENCES `access_rule` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +CREATE TABLE `accessRule_gate` ( + `accessRule_id` binary(16) NOT NULL, + `gate_id` binary(16) NOT NULL, + PRIMARY KEY (`accessRule_id`,`gate_id`), + KEY `FK6re4kcq9tyl45jv9yg584doem` (`gate_id`), + CONSTRAINT `FK6re4kcq9tyl45jv9yg584doem` FOREIGN KEY (`gate_id`) REFERENCES `access_rule` (`uuid`), + CONSTRAINT `FKe6l5ee7f207958mm3anpsmqom` FOREIGN KEY (`accessRule_id`) REFERENCES `access_rule` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +/*!40101 SET SQL_MODE=@OLD_SQL_MODE */; +/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */; +/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */; +/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */; +/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */; +/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; +/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; + +-- Dump completed on 2018-10-16 19:48:56 diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/psama_fence_setup.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/psama_fence_setup.sql new file mode 100644 index 000000000..37be5c779 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/psama_fence_setup.sql @@ -0,0 +1,208 @@ +CREATE DATABASE IF NOT EXISTS `auth` /*!40100 DEFAULT CHARACTER SET utf8 COLLATE utf8_bin */; +USE `auth`; +-- MySQL dump 10.13 Distrib 5.7.17, for macos10.12 (x86_64) +-- +-- Host: 127.0.0.1 Database: auth +-- ------------------------------------------------------ +-- Server version 5.7.20 + +/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; +/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; +/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */; +/*!40101 SET NAMES utf8 */; +/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */; +/*!40103 SET TIME_ZONE='+00:00' */; +/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */; +/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */; +/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */; +/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; + +-- +-- Table structure for table `privilege` +-- + +-- DROP TABLE IF EXISTS `privilege`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `privilege` ( + `uuid` binary(16) NOT NULL, + `description` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `application_id` binary(16) DEFAULT NULL, + `queryTemplate` varchar(8192) DEFAULT NULL, + `queryScope` varchar(512) DEFAULT NULL, + PRIMARY KEY (`uuid`), + UNIQUE KEY `UK_h7iwbdg4ev8mgvmij76881tx8` (`name`), + KEY `FK61h3jewffk70b5ni4tsi5rhoy` (`application_id`), + CONSTRAINT `FK61h3jewffk70b5ni4tsi5rhoy` FOREIGN KEY (`application_id`) REFERENCES `application` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `role` +-- + +-- DROP TABLE IF EXISTS `role`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `role` ( + `uuid` binary(16) NOT NULL, + `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `description` varchar(255) COLLATE utf8_bin DEFAULT NULL, + PRIMARY KEY (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `role_privilege` +-- + +-- DROP TABLE IF EXISTS `role_privilege`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `role_privilege` ( + `role_id` binary(16) NOT NULL, + `privilege_id` binary(16) NOT NULL, + PRIMARY KEY (`role_id`,`privilege_id`), + KEY `FKdkwbrwb5r8h74m1v7dqmhp99c` (`privilege_id`), + CONSTRAINT `FKdkwbrwb5r8h74m1v7dqmhp99c` FOREIGN KEY (`privilege_id`) REFERENCES `privilege` (`uuid`), + CONSTRAINT `FKsykrtrdngu5iexmbti7lu9xa` FOREIGN KEY (`role_id`) REFERENCES `role` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `user` +-- + +-- DROP TABLE IF EXISTS `user`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `user` ( + `uuid` binary(16) NOT NULL, + `auth0_metadata` varchar(8000) COLLATE utf8_bin DEFAULT NULL, + `general_metadata` varchar(9000) COLLATE utf8_bin DEFAULT NULL, + `acceptedTOS` datetime COLLATE utf8_bin DEFAULT NULL, + `connectionId` binary(16) DEFAULT NULL, + `email` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `matched` bit(1) NOT NULL DEFAULT FALSE, + `subject` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `is_active` bit(1) NOT NULL DEFAULT TRUE, + `long_term_token` varchar(4000) COLLATE utf8_bin DEFAULT NULL, + `isGateAnyRelation` bit(1) NOT NULL DEFAULT TRUE, + PRIMARY KEY (`uuid`), + UNIQUE KEY `UK_r8xpakluitn685ua7pt8xjy9r` (`subject`), + KEY `FKn8bku0vydfcnuwbqwgnbgg8ry` (`connectionId`), + CONSTRAINT `FKn8bku0vydfcnuwbqwgnbgg8ry` FOREIGN KEY (`connectionId`) REFERENCES `connection` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `userMetadataMapping` +-- + +-- DROP TABLE IF EXISTS `userMetadataMapping`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `userMetadataMapping` ( + `uuid` binary(16) NOT NULL, + `auth0MetadataJsonPath` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `connectionId` binary(16) DEFAULT NULL, + `generalMetadataJsonPath` varchar(255) COLLATE utf8_bin DEFAULT NULL, + PRIMARY KEY (`uuid`), + KEY `FKayr8vrvvwpgsdhxdyryt6k590` (`connectionId`), + CONSTRAINT `FKayr8vrvvwpgsdhxdyryt6k590` FOREIGN KEY (`connectionId`) REFERENCES `connection` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `user_role` +-- + +-- DROP TABLE IF EXISTS `user_role`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `user_role` ( + `user_id` binary(16) NOT NULL, + `role_id` binary(16) NOT NULL, + PRIMARY KEY (`user_id`,`role_id`), + KEY `FKa68196081fvovjhkek5m97n3y` (`role_id`), + CONSTRAINT `FK859n2jvi8ivhui0rl0esws6o` FOREIGN KEY (`user_id`) REFERENCES `user` (`uuid`), + CONSTRAINT `FKa68196081fvovjhkek5m97n3y` FOREIGN KEY (`role_id`) REFERENCES `role` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; +/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; + +CREATE TABLE `termsOfService` ( + `uuid` binary(16) NOT NULL, + `dateUpdated` timestamp, + `content` varchar(9000) COLLATE utf8_bin DEFAULT NULL, + PRIMARY KEY (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `connection` ( + `uuid` binary(16) NOT NULL, + `label` varchar(255) COLLATE utf8_bin NOT NULL, + `id` varchar(255) COLLATE utf8_bin NOT NULL, + `subprefix` varchar(255) COLLATE utf8_bin NOT NULL, + `requiredFields` varchar(9000) COLLATE utf8_bin NOT NULL, + PRIMARY KEY (`uuid`), + UNIQUE KEY `id` (`id`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +CREATE TABLE `application` ( + `uuid` binary(16) NOT NULL, + `description` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `enable` bit(1) NOT NULL DEFAULT b'1', + `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `token` varchar(2000) COLLATE utf8_bin DEFAULT NULL, + `url` varchar(500) COLLATE utf8_bin DEFAULT NULL, + PRIMARY KEY (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +CREATE TABLE `access_rule` ( + `uuid` binary(16) NOT NULL, + `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `description` varchar(2000) COLLATE utf8_bin DEFAULT NULL, + `rule` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `type` int(11) DEFAULT NULL, + `value` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `checkMapKeyOnly` bit(1) NOT NULL, + `checkMapNode` bit(1) NOT NULL, + `subAccessRuleParent_uuid` binary(16) DEFAULT NULL, + `isGateAnyRelation` bit(1) NOT NULL, + `isEvaluateOnlyByGates` bit(1) NOT NULL, + PRIMARY KEY (`uuid`), + KEY `FK8rovvx363ui99ce21sksmg6uy` (`subAccessRuleParent_uuid`), + CONSTRAINT `FK8rovvx363ui99ce21sksmg6uy` FOREIGN KEY (`subAccessRuleParent_uuid`) REFERENCES `access_rule` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +CREATE TABLE `accessRule_privilege` ( + `privilege_id` binary(16) NOT NULL, + `accessRule_id` binary(16) NOT NULL, + PRIMARY KEY (`privilege_id`,`accessRule_id`), + KEY `FK89rf30kbf9d246jty2dd7qk99` (`accessRule_id`), + CONSTRAINT `FK7x47w81gpua380qd7lp9x94l1` FOREIGN KEY (`privilege_id`) REFERENCES `privilege` (`uuid`), + CONSTRAINT `FK89rf30kbf9d246jty2dd7qk99` FOREIGN KEY (`accessRule_id`) REFERENCES `access_rule` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +CREATE TABLE `accessRule_gate` ( + `accessRule_id` binary(16) NOT NULL, + `gate_id` binary(16) NOT NULL, + PRIMARY KEY (`accessRule_id`,`gate_id`), + KEY `FK6re4kcq9tyl45jv9yg584doem` (`gate_id`), + CONSTRAINT `FK6re4kcq9tyl45jv9yg584doem` FOREIGN KEY (`gate_id`) REFERENCES `access_rule` (`uuid`), + CONSTRAINT `FKe6l5ee7f207958mm3anpsmqom` FOREIGN KEY (`accessRule_id`) REFERENCES `access_rule` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +/*!40101 SET SQL_MODE=@OLD_SQL_MODE */; +/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */; +/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */; +/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */; +/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */; +/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; +/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; + +-- Dump completed on 2018-10-16 19:48:56 diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V1__CREATE_AUTH_INITIAL.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V1__CREATE_AUTH_INITIAL.sql new file mode 100644 index 000000000..885e45082 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V1__CREATE_AUTH_INITIAL.sql @@ -0,0 +1,216 @@ +USE `auth`; +-- MySQL dump 10.13 Distrib 5.7.17, for macos10.12 (x86_64) +-- +-- Host: 127.0.0.1 Database: auth +-- ------------------------------------------------------ +-- Server version 5.7.20 + +/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; +/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; +/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */; +/*!40101 SET NAMES utf8 */; +/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */; +/*!40103 SET TIME_ZONE='+00:00' */; +/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */; +/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */; +/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */; +/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; + +-- +-- Table structure for table `privilege` +-- + +-- DROP TABLE IF EXISTS `privilege`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `privilege` ( + `uuid` binary(16) NOT NULL, + `description` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `application_id` binary(16) DEFAULT NULL, + PRIMARY KEY (`uuid`), + UNIQUE KEY `UK_h7iwbdg4ev8mgvmij76881tx8` (`name`), + KEY `FK61h3jewffk70b5ni4tsi5rhoy` (`application_id`), + CONSTRAINT `FK61h3jewffk70b5ni4tsi5rhoy` FOREIGN KEY (`application_id`) REFERENCES `application` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `role` +-- + +-- DROP TABLE IF EXISTS `role`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `role` ( + `uuid` binary(16) NOT NULL, + `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `description` varchar(255) COLLATE utf8_bin DEFAULT NULL, + PRIMARY KEY (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `role_privilege` +-- + +-- DROP TABLE IF EXISTS `role_privilege`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `role_privilege` ( + `role_id` binary(16) NOT NULL, + `privilege_id` binary(16) NOT NULL, + PRIMARY KEY (`role_id`,`privilege_id`), + KEY `FKdkwbrwb5r8h74m1v7dqmhp99c` (`privilege_id`), + CONSTRAINT `FKdkwbrwb5r8h74m1v7dqmhp99c` FOREIGN KEY (`privilege_id`) REFERENCES `privilege` (`uuid`), + CONSTRAINT `FKsykrtrdngu5iexmbti7lu9xa` FOREIGN KEY (`role_id`) REFERENCES `role` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `user` +-- + +-- DROP TABLE IF EXISTS `user`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `user` ( + `uuid` binary(16) NOT NULL, + `auth0_metadata` varchar(8000) COLLATE utf8_bin DEFAULT NULL, + `general_metadata` varchar(9000) COLLATE utf8_bin DEFAULT NULL, + `acceptedTOS` datetime COLLATE utf8_bin DEFAULT NULL, + `connectionId` binary(16) DEFAULT NULL, + `email` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `matched` bit(1) NOT NULL DEFAULT FALSE, + `subject` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `is_active` bit(1) NOT NULL DEFAULT TRUE, + `long_term_token` varchar(4000) COLLATE utf8_bin DEFAULT NULL, + PRIMARY KEY (`uuid`), + UNIQUE KEY `UK_r8xpakluitn685ua7pt8xjy9r` (`subject`), + KEY `FKn8bku0vydfcnuwbqwgnbgg8ry` (`connectionId`), + CONSTRAINT `FKn8bku0vydfcnuwbqwgnbgg8ry` FOREIGN KEY (`connectionId`) REFERENCES `connection` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `userMetadataMapping` +-- + +-- DROP TABLE IF EXISTS `userMetadataMapping`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `userMetadataMapping` ( + `uuid` binary(16) NOT NULL, + `auth0MetadataJsonPath` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `connectionId` binary(16) DEFAULT NULL, + `generalMetadataJsonPath` varchar(255) COLLATE utf8_bin DEFAULT NULL, + PRIMARY KEY (`uuid`), + KEY `FKayr8vrvvwpgsdhxdyryt6k590` (`connectionId`), + CONSTRAINT `FKayr8vrvvwpgsdhxdyryt6k590` FOREIGN KEY (`connectionId`) REFERENCES `connection` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `user_role` +-- + +-- DROP TABLE IF EXISTS `user_role`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `user_role` ( + `user_id` binary(16) NOT NULL, + `role_id` binary(16) NOT NULL, + PRIMARY KEY (`user_id`,`role_id`), + KEY `FKa68196081fvovjhkek5m97n3y` (`role_id`), + CONSTRAINT `FK859n2jvi8ivhui0rl0esws6o` FOREIGN KEY (`user_id`) REFERENCES `user` (`uuid`), + CONSTRAINT `FKa68196081fvovjhkek5m97n3y` FOREIGN KEY (`role_id`) REFERENCES `role` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; +/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; + +CREATE TABLE `termsOfService` ( + `uuid` binary(16) NOT NULL, + `dateUpdated` timestamp, + `content` varchar(9000) COLLATE utf8_bin DEFAULT NULL, + PRIMARY KEY (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `connection` ( + `uuid` binary(16) NOT NULL, + `label` varchar(255) COLLATE utf8_bin NOT NULL, + `id` varchar(255) COLLATE utf8_bin NOT NULL, + `subprefix` varchar(255) COLLATE utf8_bin NOT NULL, + `requiredFields` varchar(9000) COLLATE utf8_bin NOT NULL, + PRIMARY KEY (`uuid`), + UNIQUE KEY `id` (`id`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +CREATE TABLE `application` ( + `uuid` binary(16) NOT NULL, + `description` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `enable` bit(1) NOT NULL DEFAULT b'1', + `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `token` varchar(2000) COLLATE utf8_bin DEFAULT NULL, + `url` varchar(500) COLLATE utf8_bin DEFAULT NULL, + PRIMARY KEY (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +CREATE TABLE `access_rule` ( + `uuid` binary(16) NOT NULL, + `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `description` varchar(2000) COLLATE utf8_bin DEFAULT NULL, + `rule` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `type` int(11) DEFAULT NULL, + `value` varchar(255) COLLATE utf8_bin DEFAULT NULL, + `checkMapKeyOnly` bit(1) NOT NULL, + `checkMapNode` bit(1) NOT NULL, + `subAccessRuleParent_uuid` binary(16) DEFAULT NULL, + `isGateAnyRelation` bit(1) NOT NULL, + `isEvaluateOnlyByGates` bit(1) NOT NULL, + PRIMARY KEY (`uuid`), + KEY `FK8rovvx363ui99ce21sksmg6uy` (`subAccessRuleParent_uuid`), + CONSTRAINT `FK8rovvx363ui99ce21sksmg6uy` FOREIGN KEY (`subAccessRuleParent_uuid`) REFERENCES `access_rule` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +CREATE TABLE `accessRule_privilege` ( + `privilege_id` binary(16) NOT NULL, + `accessRule_id` binary(16) NOT NULL, + PRIMARY KEY (`privilege_id`,`accessRule_id`), + KEY `FK89rf30kbf9d246jty2dd7qk99` (`accessRule_id`), + CONSTRAINT `FK7x47w81gpua380qd7lp9x94l1` FOREIGN KEY (`privilege_id`) REFERENCES `privilege` (`uuid`), + CONSTRAINT `FK89rf30kbf9d246jty2dd7qk99` FOREIGN KEY (`accessRule_id`) REFERENCES `access_rule` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +CREATE TABLE `accessRule_gate` ( + `accessRule_id` binary(16) NOT NULL, + `gate_id` binary(16) NOT NULL, + PRIMARY KEY (`accessRule_id`,`gate_id`), + KEY `FK6re4kcq9tyl45jv9yg584doem` (`gate_id`), + CONSTRAINT `FK6re4kcq9tyl45jv9yg584doem` FOREIGN KEY (`gate_id`) REFERENCES `access_rule` (`uuid`), + CONSTRAINT `FKe6l5ee7f207958mm3anpsmqom` FOREIGN KEY (`accessRule_id`) REFERENCES `access_rule` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +CREATE OR REPLACE VIEW `management_view` +AS SELECT + `role`.`uuid` AS `uuid`, + `role`.`name` AS `role_name`, + `privilege`.`name` AS `privilege_name` + FROM + ((`role` JOIN `role_privilege`) JOIN `privilege`) + WHERE + ((`role`.`uuid` = `role_privilege`.`role_id`) + AND + (`privilege`.`uuid` = `role_privilege`.`privilege_id`)); + +/*!40101 SET SQL_MODE=@OLD_SQL_MODE */; +/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */; +/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */; +/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */; +/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */; +/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; +/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; + +-- Dump completed on 2018-10-16 19:48:56 diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V2__MODIFY_USER_TABLE_COLUMNS.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V2__MODIFY_USER_TABLE_COLUMNS.sql new file mode 100644 index 000000000..de6b13ed0 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V2__MODIFY_USER_TABLE_COLUMNS.sql @@ -0,0 +1,4 @@ +USE `auth`; + +ALTER TABLE `user` MODIFY auth0_metadata LONGTEXT; +ALTER TABLE `user` MODIFY general_metadata LONGTEXT; diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V3__ADD_COLUMNS_PRIVILEGE_TABLE.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V3__ADD_COLUMNS_PRIVILEGE_TABLE.sql new file mode 100644 index 000000000..f815752a0 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V3__ADD_COLUMNS_PRIVILEGE_TABLE.sql @@ -0,0 +1,4 @@ +USE `auth`; + +alter table `privilege` ADD COLUMN (queryScope VARCHAR(8192)); +alter table `privilege` ADD COLUMN (queryTemplate VARCHAR(8192)); diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V4__ADD_CREATE_USER_STORED_PROCEDURE.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V4__ADD_CREATE_USER_STORED_PROCEDURE.sql new file mode 100644 index 000000000..af57999c5 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V4__ADD_CREATE_USER_STORED_PROCEDURE.sql @@ -0,0 +1,43 @@ +USE `auth`; + +DROP PROCEDURE IF EXISTS CreateUserWithRole; +DELIMITER // +CREATE PROCEDURE CreateUserWithRole( + IN user_email VARCHAR(255), + IN connection_id VARCHAR(255), + IN role_name VARCHAR(255), + IN user_general_metadata varchar(255) +) +BEGIN + -- Attempt to retrieve the UUIDs for the user and role based on the provided information + SELECT @userUUID := uuid FROM auth.user WHERE email = user_email AND connectionId = connection_id; + SELECT @roleUUID := uuid FROM auth.role WHERE name = role_name; + SELECT @picsureUserRoleId := uuid FROM auth.role WHERE name = 'PIC-SURE User'; + +-- If the user does not exist, create a new user entry + IF @userUUID IS NULL THEN + set @baseUUID = UUID(); + -- Generate a new UUID for the user + SET @userUUID = UNHEX(REPLACE(@baseUUID, '-', '')); + -- Retrieve the UUID for the connection + SELECT @connectionUUID := uuid FROM auth.connection WHERE id = connection_id; + SELECT @connectionSubPrefix := subPrefix FROM auth.connection WHERE id = connection_id; +-- Insert the new user record into the user table + INSERT INTO auth.user (uuid, general_metadata, acceptedTOS, connectionId, email, matched, subject, is_active, + long_term_token) + VALUES (@userUUID, user_general_metadata, CURRENT_TIMESTAMP, @connectionUUID, user_email, 0, + concat(@connectionSubPrefix, REPLACE(@baseUUID, '-', '')), 1, NULL); + END IF; + + -- If the role exists, associate the user with the role + IF @roleUUID IS NOT NULL THEN + INSERT INTO auth.user_role (user_id, role_id) VALUES (@userUUID, @roleUUID); + END IF; + + -- If the role is not PIC-SURE User, associate the user with the PIC-SURE User role as well + -- All users must have the PIC-SURE User role + IF @roleUUID IS NOT NULL AND @roleUUID != @picsureUserRoleId THEN + INSERT INTO auth.user_role (user_id, role_id) VALUES (@userUUID, @picsureUserRoleId); + END IF; +END// +DELIMITER ; \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V5__MIGRATE_TO_ACCESSRULE_JOINTABLE.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V5__MIGRATE_TO_ACCESSRULE_JOINTABLE.sql new file mode 100644 index 000000000..9c1c67c92 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V5__MIGRATE_TO_ACCESSRULE_JOINTABLE.sql @@ -0,0 +1,31 @@ +# When merging the FENCE (Also consider the BDC specific) specific pic-sure-auth-micro-app and the more general +# pic-sure-auth-micro-app, we need to remove the circular dependency between the access_rule table and itself. +# We could have supported both, but the same functionality is already supported by the accessRule_subRule join table. +# This script will remove the circular dependency and replace it with a reference to the join table. + +-- Step 1: Create the join table +-- +-- Table structure for table `accessRule_subRule` +-- +CREATE TABLE `accessRule_subRule` +( + `accessRule_id` binary(16) NOT NULL, + `subRule_id` binary(16) NOT NULL, + PRIMARY KEY (`accessRule_id`, `subRule_id`), + KEY (`subRule_id`), + CONSTRAINT FOREIGN KEY (`subRule_id`) REFERENCES `access_rule` (`uuid`), + CONSTRAINT FOREIGN KEY (`accessRule_id`) REFERENCES `access_rule` (`uuid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; + +-- Step 2: Insert data from the circular dependency into the join table +INSERT INTO accessRule_subRule (accessRule_id, subRule_id) +SELECT ar.uuid, ar.subAccessRuleParent_uuid +FROM access_rule ar +WHERE ar.subAccessRuleParent_uuid IS NOT NULL; + +-- Step 3: Update references in the original table to point to the join table +UPDATE access_rule ar + JOIN accessRule_subRule ars ON ars.accessRule_id = ar.uuid + SET ar.subAccessRuleParent_uuid = NULL; -- Remove circular dependency reference so it can be dropped + +-- Step 4: Drop the column from the original table \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V6__UPDATE_EXISTING_ROLE_PRIVILEGE_RULE_NAMES.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V6__UPDATE_EXISTING_ROLE_PRIVILEGE_RULE_NAMES.sql new file mode 100644 index 000000000..e32a94fb0 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V6__UPDATE_EXISTING_ROLE_PRIVILEGE_RULE_NAMES.sql @@ -0,0 +1,28 @@ +# We have migrated our naming convention away from "FENCE_" to a more generalized "MANAGED_". + +-- Update roles table +UPDATE role +SET name = REPLACE(name, 'FENCE', 'MANAGED') +WHERE name LIKE '%FENCE%'; + +UPDATE role +SET description = REPLACE(description, 'FENCE', 'MANAGED') +WHERE description LIKE '%FENCE%'; + +-- Update privileges table +UPDATE privilege +SET name = REPLACE(name, 'FENCE', 'MANAGED') +WHERE name LIKE '%FENCE%'; + +UPDATE privilege +SET description = REPLACE(description, 'FENCE', 'MANAGED') +WHERE description LIKE '%FENCE%'; + +-- Update access rules table +UPDATE access_rule +SET name = REPLACE(name, 'FENCE', 'MANAGED') +WHERE name LIKE '%FENCE%'; + +UPDATE access_rule +SET description = REPLACE(description, 'FENCE', 'MANAGED') +WHERE description LIKE '%FENCE%'; \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V7__Add_Passport_User_Col.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V7__Add_Passport_User_Col.sql new file mode 100644 index 000000000..1fd4e2d65 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V7__Add_Passport_User_Col.sql @@ -0,0 +1 @@ +ALTER TABLE user ADD COLUMN passport TEXT; \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V8__ADD_USER_EMAIL_UNIQUE_CONSTRAINT.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V8__ADD_USER_EMAIL_UNIQUE_CONSTRAINT.sql new file mode 100644 index 000000000..f845b89d6 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V8__ADD_USER_EMAIL_UNIQUE_CONSTRAINT.sql @@ -0,0 +1,3 @@ +USE `auth`; + +ALTER TABLE `user` ADD CONSTRAINT `email_UNIQUE` UNIQUE (`email`, `connectionId`); diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V9__ADD_USER_CONSENT_TABLE.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V9__ADD_USER_CONSENT_TABLE.sql new file mode 100644 index 000000000..498569368 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/sql/V9__ADD_USER_CONSENT_TABLE.sql @@ -0,0 +1,7 @@ +CREATE TABLE user_consents ( + `uuid` binary(16) NOT NULL UNIQUE, + `user_id` binary(16) NOT NULL UNIQUE, + `consents` JSON, + FOREIGN KEY (`user_id`) REFERENCES user(`uuid`) + ON DELETE CASCADE +); \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/first_time_run_the_system_and_insert_admin_user.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/first_time_run_the_system_and_insert_admin_user.sql new file mode 100644 index 000000000..ee946a32f --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/first_time_run_the_system_and_insert_admin_user.sql @@ -0,0 +1,45 @@ +#configuration for user table +#for quick usage, please use a google user +#otherwise you need to modify connection configuration as well + +#if you choose to use a google user for login, this user_email is the only place to change +set @user_email='change_me_to_your_email'; + +set @user_uuid=replace(uuid(),'-',''); +set @matched=false; + +#configuration for connection table +set @connection_uuid=unhex(replace(uuid(),'-','')); +set @label='Google'; +set @id='google-oauth2'; +set @subprefix='google-oauth2|'; +set @requiredFields='[{\"label\":\"Email\", \"id\":\"email\"}]'; + +#configuration for userMetadataMapping table +set @userMetadataMapping_uuid=unhex(replace(uuid(),'-','')); +set @authMetadata='$.email'; +set @generalMetadata='$.email'; + +begin; +#### insert into connection table +insert into `connection` values (@connection_uuid, @label, @id, @subprefix, @requiredFields); + +#### insert into user table +create or replace view management_view as +select +role.uuid, role.name as role_name, privilege.name as privilege_name +from +role, role_privilege, privilege +where + +role.uuid = role_privilege.role_id +and privilege.uuid = role_privilege.privilege_id; + +insert into user (`uuid`,`general_metadata`,`connectionId`,`email`,`matched`) values (unhex(@user_uuid), CONCAT("{\"email\":\"", @user_email, "\"}"), @connection_uuid, @user_email, @matched); +insert into user_role (`user_id`,`role_id`) values (unhex(@user_uuid), +(select min(uuid) from management_view where privilege_name like 'ADMIN')) ; + +#### insert into userMetadataMapping +insert into `userMetadataMapping` values (@userMetadataMapping_uuid, @authMetadata, @connection_uuid, @generalMetadata); +commit; + diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/for_dev/grant_access.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/for_dev/grant_access.sql new file mode 100644 index 000000000..3205b02ef --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/for_dev/grant_access.sql @@ -0,0 +1,4 @@ +GRANT ALL PRIVILEGES +ON *.* +TO 'root'@'%' +IDENTIFIED BY 'password'; \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/for_dev/init_mysql.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/for_dev/init_mysql.sql new file mode 100644 index 000000000..7a146a036 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/for_dev/init_mysql.sql @@ -0,0 +1,2 @@ + +ALTER USER 'root'@'localhost' IDENTIFIED BY 'password'; \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/insert_admin_user.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/insert_admin_user.sql new file mode 100644 index 000000000..cb08506ac --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/insert_admin_user.sql @@ -0,0 +1,19 @@ +set @user_uuid='91124ef7df204412b4f399565c547bd9'; +set @user_subject='{{change_me}}'; +set @connection_uuid='{{change_me}}'; +set @matched=true; + +create or replace view management_view as +select +role.uuid, role.name as role_name, privilege.name as privilege_name +from +role, role_privilege, privilege +where +role.uuid = role_privilege.role_id +and privilege.uuid = role_privilege.privilege_id; + +begin; +insert into user (`uuid`,`subject`,`connectionId`,`matched`) values (unhex(@user_uuid), @user_subject, @connection_uuid, true); +insert into user_role (`user_id`,`role_id`) values (unhex(@user_uuid), +(select min(uuid) from management_view where privilege_name like 'ADMIN')) ; +commit; \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/insert_connection.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/insert_connection.sql new file mode 100644 index 000000000..3f7bce7bb --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/insert_connection.sql @@ -0,0 +1,9 @@ +set @uuid=0x2a3966ea7d024041975d784322b48342; +set @label='Google'; +set @id='google-oauth2'; +set @subprefix='google-oauth2|'; +set @requiredFields='[{\"label\":\"Email\", \"id\":\"email\"}]'; + +begin; +insert into `connection` values (@uuid, @label, @id, @subprefix, @requiredFields); +commit; diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/insert_privileges_for_transmart.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/insert_privileges_for_transmart.sql new file mode 100644 index 000000000..a99a6cee2 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/insert_privileges_for_transmart.sql @@ -0,0 +1,67 @@ +# +# Create the privileges used for i2b2/tranSmart application +# +START TRANSACTION; + +SET @uuidPrivilege = REPLACE(uuid(),'-',''); + +INSERT INTO `privilege` ( + `uuid`, + `name`, + `description`, + `application_id` +) +VALUES ( + unhex(@uuidPrivilege), + 'TM_ADMIN', + 'Administrator privilege for i2b2/tranSmart application', + (SELECT `uuid` FROM `application` WHERE `name` = 'TRANSMART') +); + +SET @uuidPrivilege = REPLACE(uuid(),'-',''); + +INSERT INTO `privilege` ( + `uuid`, + `name`, + `description`, + `application_id` +) +VALUES ( + unhex(@uuidPrivilege), + 'TM_STUDY_OWNER', + 'Level1 priveilege for i2b2/tranSmart user, allowing download functionality, in addition to Level1 privileges.', + (SELECT `uuid` FROM `application` WHERE `name` = 'TRANSMART') +); + +SET @uuidPrivilege = REPLACE(uuid(),'-',''); + +INSERT INTO `privilege` ( + `uuid`, + `name`, + `description`, + `application_id` +) +VALUES ( + unhex(@uuidPrivilege), + 'TM_DATASET_EXPLORER', + 'Level2 privilege for i2b2/tranSmart user, allowing to run advanced statistics, but no download or grid view.', + (SELECT `uuid` FROM `application` WHERE `name` = 'TRANSMART') +); + +SET @uuidPrivilege = REPLACE(uuid(),'-',''); + +INSERT INTO `privilege` ( + `uuid`, + `name`, + `description`, + `application_id` +) +VALUES ( + unhex(@uuidPrivilege), + 'TM_PUBLIC_USER', + 'Base level privilege, for i2b2/tranSmart, allowing the user to log in, and see counts.', + (SELECT `uuid` FROM `application` WHERE `name` = 'TRANSMART') +); + + +COMMIT; diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/insert_role_for_transmart.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/insert_role_for_transmart.sql new file mode 100644 index 000000000..565a1b3c9 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/insert_role_for_transmart.sql @@ -0,0 +1,60 @@ +# +# Create a role, which is a collection of privileges +# +START TRANSACTION; + +SET @uuidRole = REPLACE(uuid(),'-',''); + +# This is an example, where the SUPERUSER role is added. +INSERT INTO `role` ( + `uuid`, + `name`, + `description` +) +VALUES ( + unhex(@uuidRole), + 'TM_ADMIN', + 'i2b2/tranSmart administrator role.' +); + +# The i2b2/tranSmart administrator role has ADMIN and PUBLIC_USER privileges +INSERT INTO `role_privilege` ( + `role_id`, + `privilege_id` +) +VALUES ( + unhex(@uuidRole), + (SELECT uuid FROM `privilege` WHERE `name` = 'TM_ADMIN') +); + +# The i2b2/tranSmart level1 role has STUDY_OWNER and PUBLIC_USER privileges +INSERT INTO `role_privilege` ( + `role_id`, + `privilege_id` +) +VALUES ( + unhex(@uuidRole), + (SELECT uuid FROM `privilege` WHERE `name` = 'TM_STUDY_OWNER') +); + +# The i2b2/tranSmart level2 role has DATASET_EXPLORER and PUBLIC_USER privileges +INSERT INTO `role_privilege` ( + `role_id`, + `privilege_id` +) +VALUES ( + unhex(@uuidRole), + (SELECT uuid FROM `privilege` WHERE `name` = 'TM_DATASET_EXPLORER') +); + +# The i2b2/tranSmart level0 (authenticated, but not authorized for data access) role has only PUBLIC_USER privileges +INSERT INTO `role_privilege` ( + `role_id`, + `privilege_id` +) +VALUES ( + unhex(@uuidRole), + (SELECT uuid FROM `privilege` WHERE `name` = 'TM_PUBLIC_USER') +); + +COMMIT; diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/insert_userMetadataMapping.sql b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/insert_userMetadataMapping.sql new file mode 100644 index 000000000..6b472d648 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-db/db/tools/insert_userMetadataMapping.sql @@ -0,0 +1,18 @@ + +START TRANSACTION; + +INSERT INTO `userMetadataMapping` ( + `uuid`, + `auth0MetadataJsonPath`, + `connectionId`, + `generalMetadataJsonPath` +) +VALUES ( + (SELECT uuid FROM user WHERE email = '__SUPERUSER_GMAIL__'), + '$.email', + (SELECT uuid FROM connection WHERE label = 'Google'), + '$.email' +); + +COMMIT; + diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/Dockerfile b/services/pic-sure-auth-microapp/pic-sure-auth-services/Dockerfile new file mode 100644 index 000000000..a678255d5 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/Dockerfile @@ -0,0 +1,12 @@ +FROM amazoncorretto:25-alpine + +# Copy jar and access token from maven build +COPY pic-sure-auth-services/target/pic-sure-auth-services-*.jar /pic-sure-auth-service.jar + +# Copy the AWS certificate +COPY pic-sure-auth-services/aws_certs/certificate.der /certificate.der + +# Import the certificate into the Java trust store +RUN keytool -noprompt -import -alias aws_cert -keystore $JAVA_HOME/lib/security/cacerts -storepass changeit -file /certificate.der + +ENTRYPOINT ["sh", "-c", "java ${JAVA_OPTS} -jar /pic-sure-auth-service.jar"] \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/README.md b/services/pic-sure-auth-microapp/pic-sure-auth-services/README.md new file mode 100644 index 000000000..4ddfa9ca5 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/README.md @@ -0,0 +1,2 @@ +# pic-sure-auth-services + diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/WebContent/META-INF/MANIFEST.MF b/services/pic-sure-auth-microapp/pic-sure-auth-services/WebContent/META-INF/MANIFEST.MF new file mode 100644 index 000000000..5e9495128 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/WebContent/META-INF/MANIFEST.MF @@ -0,0 +1,3 @@ +Manifest-Version: 1.0 +Class-Path: + diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/aws_certs/certificate.der b/services/pic-sure-auth-microapp/pic-sure-auth-services/aws_certs/certificate.der new file mode 100644 index 000000000..dab9aedbc Binary files /dev/null and b/services/pic-sure-auth-microapp/pic-sure-auth-services/aws_certs/certificate.der differ diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/bdc.Dockerfile b/services/pic-sure-auth-microapp/pic-sure-auth-services/bdc.Dockerfile new file mode 100644 index 000000000..7668eb208 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/bdc.Dockerfile @@ -0,0 +1,26 @@ +FROM amazoncorretto:25-alpine + +ARG DATASOURCE_URL +ARG DATASOURCE_USERNAME +ARG STACK_SPECIFIC_APPLICATION_ID + +ENV DATASOURCE_URL=${DATASOURCE_URL} +ENV DATASOURCE_USERNAME=${DATASOURCE_USERNAME} +ENV STACK_SPECIFIC_APPLICATION_ID=${STACK_SPECIFIC_APPLICATION_ID} + +# Copy jar from pre-built workspace +COPY pic-sure-auth-services/target/pic-sure-auth-services-*.jar /pic-sure-auth-service.jar + +# Copy additional bdc configuration files. Root of the project +COPY config/psama/bdc/psama-db-config.properties /config/psama-db-config.properties + +# Set SPRING_CONFIG_ADDITIONAL_LOCATION +ENV SPRING_CONFIG_ADDITIONAL_LOCATION=file:/config/psama-db-config.properties + +# Copy the AWS certificate +COPY pic-sure-auth-services/aws_certs/certificate.der /certificate.der + +# Import the certificate into the Java trust store +RUN keytool -noprompt -import -alias aws_cert -keystore $JAVA_HOME/lib/security/cacerts -storepass changeit -file /certificate.der + +ENTRYPOINT ["sh", "-c", "java ${JAVA_OPTS} -jar /pic-sure-auth-service.jar"] \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/dev.Dockerfile b/services/pic-sure-auth-microapp/pic-sure-auth-services/dev.Dockerfile new file mode 100644 index 000000000..cd33af84d --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/dev.Dockerfile @@ -0,0 +1,20 @@ +FROM maven:3.9-amazoncorretto-25 AS build + +# Copy the source code into the container +COPY ../ /app + +# Change the working directory +WORKDIR /app + +# Build the jar +RUN mvn clean install -DskipTests + +FROM amazoncorretto:25-alpine + +# Copy jar and access token from maven build +#COPY target/pic-sure-auth-services.jar /pic-sure-auth-service.jar +COPY --from=build /app/pic-sure-auth-services/target/pic-sure-auth-services-*.jar /pic-sure-auth-service.jar + +EXPOSE 8090 + +ENTRYPOINT ["sh", "-c", "java ${JAVA_OPTS} -jar /pic-sure-auth-service.jar"] \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/pom.xml b/services/pic-sure-auth-microapp/pic-sure-auth-services/pom.xml new file mode 100644 index 000000000..b135ccd78 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/pom.xml @@ -0,0 +1,183 @@ + + + 4.0.0 + + edu.harvard.hms.dbmi.avillach + pic-sure-api + ${revision} + ../../../pom.xml + + edu.harvard.hms.dbmi.avillach + pic-sure-auth-services + pic-sure-auth-services + jar + + + org.springframework.boot + spring-boot-starter + + + org.springframework.boot + spring-boot-starter-web + + + org.springframework.boot + spring-boot-starter-data-jpa + + + org.springframework.boot + spring-boot-devtools + true + + + org.springframework.boot + spring-boot-starter-cache + + + org.springframework + spring-context + + + org.springframework.boot + spring-boot-starter-test + + + org.springframework.boot + spring-boot-starter-security + + + org.springframework.boot + spring-boot-starter-actuator + + + com.github.spullara.mustache.java + compiler + 0.9.5 + + + com.sun.mail + jakarta.mail + 2.0.2 + + + jakarta.mail + jakarta.mail-api + 2.1.3 + + + io.swagger.core.v3 + swagger-jaxrs2-jakarta + 2.2.21 + + + io.swagger.core.v3 + swagger-jaxrs2-servlet-initializer-jakarta + 2.2.21 + + + io.swagger.core.v3 + swagger-annotations-jakarta + 2.2.21 + + + jakarta.xml.bind + jakarta.xml.bind-api + + + org.glassfish.jaxb + jaxb-runtime + + + org.glassfish.jaxb + jaxb-core + + + com.fasterxml.jackson.core + jackson-databind + + + com.fasterxml.jackson.core + jackson-core + + + com.fasterxml.jackson.core + jackson-annotations + + + net.bytebuddy + byte-buddy + + + com.mysql + mysql-connector-j + + + com.amazonaws.secretsmanager + aws-secretsmanager-jdbc + 2.0.2 + + + com.jayway.jsonpath + json-path + + + io.jsonwebtoken + jjwt-api + 0.12.5 + + + io.jsonwebtoken + jjwt-impl + 0.12.5 + runtime + + + io.jsonwebtoken + jjwt-jackson + 0.12.5 + runtime + + + com.auth0 + auth0 + 2.10.1 + + + + org.apache.httpcomponents.client5 + httpclient5 + + + org.apache.httpcomponents.core5 + httpcore5 + + + org.mockito + mockito-core + test + + + org.mockito + mockito-subclass + test + + + edu.harvard.hms.dbmi.avillach.hpds + pic-sure-hpds-model + + + edu.harvard.dbmi.avillach + pic-sure-logging-client + + + + + + + org.springframework.boot + spring-boot-maven-plugin + + + + diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/Application.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/Application.java new file mode 100644 index 000000000..4e84ce903 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/Application.java @@ -0,0 +1,17 @@ +package edu.harvard.hms.dbmi.avillach.auth; + +import org.springframework.boot.SpringApplication; +import org.springframework.boot.autoconfigure.SpringBootApplication; +import org.springframework.boot.autoconfigure.security.servlet.SecurityAutoConfiguration; +import org.springframework.boot.autoconfigure.security.servlet.UserDetailsServiceAutoConfiguration; +import org.springframework.data.jpa.repository.config.EnableJpaRepositories; +import org.springframework.scheduling.annotation.EnableScheduling; + +@SpringBootApplication(exclude = {SecurityAutoConfiguration.class, UserDetailsServiceAutoConfiguration.class}) +@EnableJpaRepositories +@EnableScheduling +public class Application { + public static void main(String[] args) { + SpringApplication.run(Application.class); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/config/ApplicationConfig.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/config/ApplicationConfig.java new file mode 100644 index 000000000..a15047140 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/config/ApplicationConfig.java @@ -0,0 +1,47 @@ +package edu.harvard.hms.dbmi.avillach.auth.config; + +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.CustomUserDetailService; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.cache.annotation.EnableCaching; +import org.springframework.cache.interceptor.KeyGenerator; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.security.authentication.AuthenticationManager; +import org.springframework.security.authentication.AuthenticationProvider; +import org.springframework.security.authentication.dao.DaoAuthenticationProvider; +import org.springframework.security.config.annotation.authentication.configuration.AuthenticationConfiguration; + +@Configuration +@EnableCaching +public class ApplicationConfig { + + private final CustomUserDetailService customUserDetailService; + + @Autowired + public ApplicationConfig(CustomUserDetailService customUserDetailService) { + this.customUserDetailService = customUserDetailService; + } + + @Bean + public AuthenticationManager authenticationManager(AuthenticationConfiguration authenticationConfiguration) throws Exception { + return authenticationConfiguration.getAuthenticationManager(); + } + + @Bean + public AuthenticationProvider authenticationProvider() { + DaoAuthenticationProvider provider = new DaoAuthenticationProvider(); + provider.setUserDetailsService(customUserDetailService); + return provider; + } + + @Bean("customKeyGenerator") + public KeyGenerator generator() { + return new CustomKeyGenerator(); + } + + @Bean + public ObjectMapper objectMapper() { + return new ObjectMapper(); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/config/CustomKeyGenerator.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/config/CustomKeyGenerator.java new file mode 100644 index 000000000..75485f4ac --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/config/CustomKeyGenerator.java @@ -0,0 +1,20 @@ +package edu.harvard.hms.dbmi.avillach.auth.config; + +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import org.springframework.cache.interceptor.KeyGenerator; + +import java.lang.reflect.Method; + +public class CustomKeyGenerator implements KeyGenerator { + + @Override + public Object generate(Object target, Method method, Object... params) { + for (Object param : params) { + if (param instanceof User user) { + return user.getSubject(); + } + } + + throw new IllegalArgumentException("No valid params found. Cannot generate cache key"); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/config/CustomLogoutHandler.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/config/CustomLogoutHandler.java new file mode 100644 index 000000000..9d11961cd --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/config/CustomLogoutHandler.java @@ -0,0 +1,55 @@ +package edu.harvard.hms.dbmi.avillach.auth.config; + +import edu.harvard.hms.dbmi.avillach.auth.service.impl.CacheEvictionService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.UserService; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuditAttributes; +import edu.harvard.hms.dbmi.avillach.auth.utils.JWTUtil; +import io.jsonwebtoken.Claims; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.security.core.Authentication; +import org.springframework.security.web.authentication.logout.LogoutHandler; +import org.springframework.stereotype.Component; + +@Component +public class CustomLogoutHandler implements LogoutHandler { + + private final Logger logger = LoggerFactory.getLogger(CustomLogoutHandler.class); + private final UserService userService; + private final CacheEvictionService cacheEvictionService; + private final JWTUtil jwtUtil; + + public CustomLogoutHandler(UserService userService, CacheEvictionService cacheEvictionService, JWTUtil jwtUtil) { + this.userService = userService; + this.cacheEvictionService = cacheEvictionService; + this.jwtUtil = jwtUtil; + } + + @Override + public void logout(HttpServletRequest request, HttpServletResponse response, Authentication authentication) { + String bearer = request.getHeader("Authorization"); + if (!bearer.startsWith("Bearer ")) { + return; + } + + String token = bearer.substring(7); + if (StringUtils.isBlank(token)) { + return; + } + + Claims payload = jwtUtil.parseToken(token).getPayload(); + String subject = payload.getSubject(); + + if (StringUtils.isNotBlank(subject)) { + logger.info("logout() Logging out User: {}", subject); + this.cacheEvictionService.evictCache(subject); + this.userService.removeUserPassport(subject); + + // Populate AuditAttributes for the AuditLoggingFilter to include in its event + AuditAttributes.putMetadata(request, "user_subject", subject); + } + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/config/LoggingConfig.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/config/LoggingConfig.java new file mode 100644 index 000000000..84edcf49d --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/config/LoggingConfig.java @@ -0,0 +1,28 @@ +package edu.harvard.hms.dbmi.avillach.auth.config; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingClientFactory; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuditInterceptor; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.web.servlet.config.annotation.InterceptorRegistry; +import org.springframework.web.servlet.config.annotation.WebMvcConfigurer; + +@Configuration +public class LoggingConfig implements WebMvcConfigurer { + + @Bean + public LoggingClient loggingClient() { + return LoggingClientFactory.create("pic-sure-auth-microapp"); + } + + @Bean + public AuditInterceptor auditInterceptor() { + return new AuditInterceptor(); + } + + @Override + public void addInterceptors(InterceptorRegistry registry) { + registry.addInterceptor(auditInterceptor()); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/config/SecurityConfig.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/config/SecurityConfig.java new file mode 100644 index 000000000..db5c24e79 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/config/SecurityConfig.java @@ -0,0 +1,87 @@ +package edu.harvard.hms.dbmi.avillach.auth.config; + +import edu.harvard.hms.dbmi.avillach.auth.filter.AuditLoggingFilter; +import edu.harvard.hms.dbmi.avillach.auth.filter.JWTFilter; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.CacheEvictionService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.UserService; +import edu.harvard.hms.dbmi.avillach.auth.utils.JWTUtil; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.security.authentication.AuthenticationProvider; +import org.springframework.security.config.annotation.method.configuration.EnableMethodSecurity; +import org.springframework.security.config.annotation.web.builders.HttpSecurity; +import org.springframework.security.config.annotation.web.configuration.EnableWebSecurity; +import org.springframework.security.config.annotation.web.configurers.AbstractHttpConfigurer; +import org.springframework.security.config.core.GrantedAuthorityDefaults; +import org.springframework.security.web.SecurityFilterChain; +import org.springframework.security.web.authentication.UsernamePasswordAuthenticationFilter; +import org.springframework.security.web.authentication.logout.LogoutFilter; + +import static org.springframework.security.config.http.SessionCreationPolicy.STATELESS; + +@Configuration +@EnableMethodSecurity(prePostEnabled = false, jsr250Enabled = true) +@EnableWebSecurity +public class SecurityConfig { + + private final JWTFilter jwtFilter; + private final AuditLoggingFilter auditLoggingFilter; + private final CacheEvictionService cacheEvictionService; + private final AuthenticationProvider authenticationProvider; + private final UserService userService; + private final JWTUtil jwtUtil; + + @Autowired + public SecurityConfig( + JWTFilter jwtFilter, AuditLoggingFilter auditLoggingFilter, AuthenticationProvider authenticationProvider, UserService userService, + CacheEvictionService cacheEvictionService, JWTUtil jwtUtil + ) { + this.jwtFilter = jwtFilter; + this.auditLoggingFilter = auditLoggingFilter; + this.authenticationProvider = authenticationProvider; + this.userService = userService; + this.jwtUtil = jwtUtil; + this.cacheEvictionService = cacheEvictionService; + } + + @Bean + public CustomLogoutHandler customLogoutHandler() { + return new CustomLogoutHandler(userService, cacheEvictionService, jwtUtil); + } + + @Bean + public SecurityFilterChain securityFilterChain(HttpSecurity http) throws Exception { + http.csrf(AbstractHttpConfigurer::disable).sessionManagement((session) -> session.sessionCreationPolicy(STATELESS)) + .authenticationProvider(authenticationProvider) + .authorizeHttpRequests( + (authorizeRequests) -> authorizeRequests.requestMatchers( + "/actuator/health", "/actuator/info", "/authentication", "/authentication/**", "/swagger.yaml", "/swagger.json", + "/user/me/queryTemplate", "/user/me/queryTemplate/**", "/tos/latest", "/open/validate", "/logout", "/cache/**" + ).permitAll().anyRequest().authenticated() + ).httpBasic(AbstractHttpConfigurer::disable).formLogin(AbstractHttpConfigurer::disable) + // AuditLoggingFilter must wrap the entire chain (including LogoutFilter and JWTFilter) + // so its try/finally captures events even when JWTFilter short-circuits or LogoutFilter handles /logout + .addFilterBefore(auditLoggingFilter, LogoutFilter.class) + .addFilterBefore(jwtFilter, UsernamePasswordAuthenticationFilter.class) + .logout( + (logout) -> logout.logoutUrl("/logout").addLogoutHandler(customLogoutHandler()) + .logoutSuccessHandler((request, response, authentication) -> { + // We don't want to redirect to a login page, we just want to return a 200 + // We leave it to the client to handle the redirect + response.setStatus(200); + }) + ); + + return http.build(); + } + + /** + * Remove the default "ROLE_" prefix so that hasRole("ADMIN") and @RolesAllowed("ADMIN") match a GrantedAuthority("ADMIN"). + */ + @Bean + public GrantedAuthorityDefaults grantedAuthorityDefaults() { + return new GrantedAuthorityDefaults(""); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/AccessRule.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/AccessRule.java new file mode 100644 index 000000000..5c5034340 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/AccessRule.java @@ -0,0 +1,288 @@ +package edu.harvard.hms.dbmi.avillach.auth.entity; + +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.FetchType; +import jakarta.persistence.JoinColumn; +import jakarta.persistence.JoinTable; +import jakarta.persistence.ManyToMany; +import jakarta.persistence.Transient; + +import java.lang.reflect.Field; +import java.util.HashSet; +import java.util.LinkedHashMap; +import java.util.Map; +import java.util.Set; + +/** + *

    + *

    Thoughts on design:

    the AccessRule is designed to fulfilled the requirements + * of complicated scenarios that includes AND/OR or nested AND/OR cases of jsonPath authorization + *

    + *
    + *
    + * Attribute Explanations: + *
  • checkMapNode - after retrieving the value by jsonPath rule, if the value is a map, + * this flag will let the evaluation go through all the map nodes and their children nodes
    • + *
  • checkMapKeyOnly - only take effective when checkMapNode flag is turned on. This flag will + * let the evaluation only check the key of current map node, it will stop the evaluation to go into + * the children nodes
    • + *
  • gateAnyRelation - true: gates are evaluated as ANY relationship, false: gates are evaluated as AND relationship
    • + *
  • evaluateOnlyByGates - this flag means no matter what rules and values are set, + * the evaluation will based on whether the gates are passed or not, which means if gates are passed, + * then evaluation result is true, not passed, return false. The use case for this flag is sometimes, we + * need to meet the requirements of some nested AND/OR gates like gateA && gateB && (gateC || gateD), + * in this example, (gateC || gateD) has to be together in a gate and not evaluate by the values and rules
    • + * + */ +@Entity(name = "access_rule") +public class AccessRule extends BaseEntity { + /** + * please do not modify the existing values, in case the value has + * already saved in the database. But you can add more constant values, or + * update the keys. + */ + public static class TypeNaming { +// public static final int CONTAINS = 0; + public static final int NOT_CONTAINS = 1; + public static final int NOT_CONTAINS_IGNORE_CASE = 2; + public static final int NOT_EQUALS = 3; + public static final int ALL_EQUALS = 4; + public static final int ALL_CONTAINS = 5; + public static final int ALL_CONTAINS_IGNORE_CASE = 6; + public static final int ANY_CONTAINS = 7; + public static final int NOT_EQUALS_IGNORE_CASE = 8; + public static final int ALL_EQUALS_IGNORE_CASE = 9; + public static final int ANY_EQUALS = 10; + public static final int ALL_REG_MATCH = 11; + public static final int ANY_REG_MATCH = 12; + public static final int IS_EMPTY = 13; + public static final int IS_NOT_EMPTY = 14; + public static final int ALL_CONTAINS_OR_EMPTY = 15; + public static final int ALL_CONTAINS_OR_EMPTY_IGNORE_CASE = 16; + public static final int USER_CONSENT_ACCESS = 17; + + public static Map getTypeNameMap(){ + Map map = new LinkedHashMap<>(); + for (Field f : AccessRule.TypeNaming.class.getDeclaredFields()){ + f.setAccessible(true); + try { + map.put(f.getName(), (Integer)f.get(null)); + } catch (IllegalAccessException e){ + continue; + } + } + return map; + } + } + + private String name; + + private String description; + + /** + * for check how to do with the retrieved value + * + * + * NOTICE: please don't change this back to int + * we need to support a null input, + * otherwise, the update mechanism will be broken + * + * + * @see TypeNaming + */ + private Integer type; + + /** + * The jsonpath rule to retrieve values, kind of the route to the data. + * The possible value will be String, JSONObject, JSONArray, etc. + */ + private String rule; + + /** + * The value for checking + */ + private String value; + + /** + * only inner use for merge accessRule + * This field should neither be saved to database + * nor seen by a user + */ + @Transient + private Set mergedValues = new HashSet<>(); + + /** + * This attribute will not be seen by either endpoint users or database. + * It is a intermediate product that generated on the fly for supporting + * auto-merging functionality of accessRules when doing authorization. + */ + @Transient + private String mergedName = ""; + + /** + * Guideline of using gates: if null or empty, will skip checking gate + * to pass gate settings, every gate in the set needs to be passed, + * which means if only part of the gate set is passed, the gate still + * not passed + */ + @ManyToMany(fetch = FetchType.EAGER) + @JoinTable(name = "accessRule_gate", + joinColumns = {@JoinColumn(name = "accessRule_id", nullable = false)}, + inverseJoinColumns = {@JoinColumn(name = "gate_id", nullable = false)}) + private Set gates; + + /** + * this attribute is for determining the relationship between gates + * the default value is false, means gates are AND relationship, + * meaning all gates need to be passed to check the actual rules + * + * NOTICE: please don't change this back to boolean + * we need to support a null input, + * otherwise, the update mechanism will be broken + */ + @Column(name = "isGateAnyRelation") + private Boolean gateAnyRelation; + + /** + * this attribute is to tell if the accessRule passes only based on + * the gates passes or not + * + * NOTICE: please don't change this back to boolean + * we need to support a null input, + * otherwise, the update mechanism will be broken + */ + @Column(name = "isEvaluateOnlyByGates") + private Boolean evaluateOnlyByGates; + + /** + * introduce sub-accessRule to enable the ability of more complex problem, essentially it is an AND relationship. + */ + @ManyToMany(fetch = FetchType.EAGER) + @JoinTable(name = "accessRule_subRule", + joinColumns = {@JoinColumn(name = "accessRule_id", nullable = false)}, + inverseJoinColumns = {@JoinColumn(name = "subRule_id", nullable = false)}) + private Set subAccessRule; + + /** + * NOTICE: please don't change this back to boolean + * we need to support a null input, + * otherwise, the auto update mechanism will be broken + */ + private Boolean checkMapNode; + + /** + * NOTICE: please don't change this back to boolean + * we need to support a null input, + * otherwise, the auto update mechanism will be broken + */ + private Boolean checkMapKeyOnly; + + public Integer getType() { + return type; + } + + public void setType(Integer type) { + this.type = type; + } + + public String getRule() { + return rule; + } + + public void setRule(String rule) { + this.rule = rule; + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public String getDescription() { + return description; + } + + public void setDescription(String description) { + this.description = description; + } + + public Set getGates() { + return gates; + } + + public void setGates(Set gates) { + this.gates = gates; + } + + public Boolean getEvaluateOnlyByGates() { + return evaluateOnlyByGates; + } + + public void setEvaluateOnlyByGates(Boolean evaluateOnlyByGates) { + this.evaluateOnlyByGates = evaluateOnlyByGates; + } + + public Set getSubAccessRule() { + return subAccessRule; + } + + public void setSubAccessRule(Set subAccessRule) { + this.subAccessRule = subAccessRule; + } + + public Boolean getCheckMapNode() { + return checkMapNode; + } + + public void setCheckMapNode(Boolean checkMapNode) { + this.checkMapNode = checkMapNode; + } + + public Boolean getCheckMapKeyOnly() { + return checkMapKeyOnly; + } + + public void setCheckMapKeyOnly(Boolean checkMapKeyOnly) { + this.checkMapKeyOnly = checkMapKeyOnly; + } + + public Set getMergedValues() { + return mergedValues; + } + + public void setMergedValues(Set mergedValues) { + this.mergedValues = mergedValues; + } + + public String getMergedName() { + return mergedName; + } + + public void setMergedName(String mergedName) { + this.mergedName = mergedName; + } + + public Boolean getGateAnyRelation() { + return gateAnyRelation; + } + + public void setGateAnyRelation(Boolean gateAnyRelation) { + this.gateAnyRelation = gateAnyRelation; + } + + public String toString() { + return uuid.toString() + " ___ " + name + " ___ " + description + " ___ " + rule + " ___ " + type + " ___ " + value; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/Application.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/Application.java new file mode 100644 index 000000000..a58856dee --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/Application.java @@ -0,0 +1,143 @@ +package edu.harvard.hms.dbmi.avillach.auth.entity; + +import com.fasterxml.jackson.annotation.JsonInclude; +import jakarta.persistence.*; + +import java.security.Principal; +import java.util.Objects; +import java.util.Set; +import java.util.stream.Collectors; + +/** + *

    Defines a model for a registered application's behavior and provides application-level privilege management.

    + */ +@JsonInclude(JsonInclude.Include.NON_EMPTY) +@Entity(name = "application") +public class Application extends BaseEntity implements Principal { + + @Column(unique = true) + private String name; + private String description; + private String token; + private String url; + private boolean enable = true; + + @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL) + @JoinColumn(name = "application_id", referencedColumnName = "uuid") + private Set privileges; + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public String getDescription() { + return description; + } + + public void setDescription(String description) { + this.description = description; + } + + public String getToken() { + return token; + } + + public void setToken(String token) { + this.token = token; + } + + public boolean isEnable() { + return enable; + } + + public void setEnable(boolean enable) { + this.enable = enable; + } + + public Set getPrivileges() { + return privileges; + } + + public void setPrivileges(Set privileges) { + if (this.privileges != null) { + this.privileges.clear(); + this.privileges.addAll(privileges); + } else { + this.privileges = privileges; + } + } + + public String getUrl() { + return url; + } + + public void setUrl(String url) { + this.url = url; + } + + /** + *

    Inner class that returns limited attributes back to an application user.

    + */ + @JsonInclude(JsonInclude.Include.NON_EMPTY) + public static class ApplicationForDisplay { + String uuid; + String name; + String description; + String url; + boolean enable; + + public String getName() { + return name; + } + + public ApplicationForDisplay setName(String name) { + this.name = name; + return this; + } + + public String getDescription() { + return description; + } + + public ApplicationForDisplay setDescription(String description) { + this.description = description; + return this; + } + + public boolean isEnable() { + return enable; + } + + public ApplicationForDisplay setEnable(boolean enable) { + this.enable = enable; + return this; + } + + public String getUuid() { + return uuid; + } + + public ApplicationForDisplay setUuid(String uuid) { + this.uuid = uuid; + return this; + } + + public String getUrl() { + return url; + } + + public ApplicationForDisplay setUrl(String url) { + this.url = url; + return this; + } + } + + public String toString() { + return uuid.toString() + " ___ " + name + " ___ " + description + " ___ " + enable + " ___ " + url + " ___ " + (privileges==null?"NO PRIVILEGES DEFINED" : privileges.stream().map(Privilege::toString).collect(Collectors.joining(","))); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/BaseEntity.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/BaseEntity.java new file mode 100644 index 000000000..6e681ec3a --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/BaseEntity.java @@ -0,0 +1,53 @@ +package edu.harvard.hms.dbmi.avillach.auth.entity; + +import jakarta.persistence.Column; +import jakarta.persistence.GeneratedValue; +import jakarta.persistence.Id; +import jakarta.persistence.MappedSuperclass; +import org.hibernate.annotations.GenericGenerator; + +import java.util.Objects; +import java.util.UUID; + +@MappedSuperclass +public abstract class BaseEntity { + @Id + @GeneratedValue(generator = "UUID") + @GenericGenerator( + name = "UUID", + strategy = "org.hibernate.id.UUIDGenerator") + @Column(columnDefinition = "BINARY(16)") + protected UUID uuid; + + public UUID getUuid() { + return uuid; + } + + public void setUuid(UUID uuid) { + this.uuid = uuid; + } + + @Override + public int hashCode() { + return Objects.hash(uuid); + } + + @Override + public boolean equals(Object obj) { + if (obj == this) return true; + if (!(obj instanceof BaseEntity entity)) { + return false; + } + if (this.uuid == null){ + return false; + } + + return this.uuid.equals(entity.uuid); + } + + @Override + public String toString() { + return this.uuid.toString(); + } +} + diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/Connection.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/Connection.java new file mode 100644 index 000000000..c4e4db8fc --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/Connection.java @@ -0,0 +1,67 @@ +package edu.harvard.hms.dbmi.avillach.auth.entity; + +import jakarta.persistence.Column; +import jakarta.persistence.Entity; + +import java.io.Serializable; + +/** + *

    Defines a model of different supporting connections for the login process.

    + *

    This class will eventually reflect changes in the ConnectionManagement page.

    + */ +@Entity(name = "connection") +public class Connection extends BaseEntity implements Serializable { + + private String label; + + @Column(unique = true) + private String id; + private String subPrefix; + + private String requiredFields; + + public String getLabel() { + return label; + } + + public Connection setLabel(String label) { + this.label = label; + return this; + } + + public String getId() { + return id; + } + + public Connection setId(String id) { + this.id = id; + return this; + } + + public String getSubPrefix() { + return subPrefix; + } + + public Connection setSubPrefix(String subPrefix) { + this.subPrefix = subPrefix; + return this; + } + + public String getRequiredFields() { + return requiredFields; + } + + public Connection setRequiredFields(String requiredFields) { + this.requiredFields = requiredFields; + return this; + } + + public String toString() { + if(uuid == null) { + return "No UUID assgned___ " + id + " ___ " + subPrefix + " ___ " + label + " ___ " + requiredFields; + } + return uuid.toString() + " ___ " + id + " ___ " + subPrefix + " ___ " + label + " ___ " + requiredFields; + } +} + + diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/Privilege.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/Privilege.java new file mode 100644 index 000000000..83dca989d --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/Privilege.java @@ -0,0 +1,114 @@ +package edu.harvard.hms.dbmi.avillach.auth.entity; + +import com.fasterxml.jackson.annotation.JsonIgnore; +import com.fasterxml.jackson.annotation.JsonInclude; +import com.fasterxml.jackson.annotation.JsonProperty; +import jakarta.persistence.*; + +import java.util.Set; +import java.util.stream.Collectors; + +/** + *

    Models the authorization layer along with Role/AccessRule.

    + */ +@JsonInclude(JsonInclude.Include.NON_EMPTY) +@Entity(name = "privilege") +public class Privilege extends BaseEntity { + + @Column(unique = true) + private String name; + + private String description; + + @ManyToOne(fetch = FetchType.EAGER) + @JoinColumn(name = "application_id") + private Application application; + + @ManyToMany(fetch = FetchType.LAZY) + @JoinTable(name = "accessRule_privilege", + joinColumns = {@JoinColumn(name = "privilege_id")}, + inverseJoinColumns = {@JoinColumn(name = "accessRule_id")}) + private Set accessRules; + + /** + * We only support a JSON Object format for now, + * since it will return a merged JSON in the end, + * if saving as a JSON array, later processing will + * throw exception + */ + private String queryTemplate; + + /** + * This is a field that will be retrieved by the pic-sure-ui, + * so the UI will understand what data should be filtered when + * doing a search, to furthermore prevent invalid queries because + * no invalid search results will be shown. + */ + private String queryScope; + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public String getDescription() { + return description; + } + + public void setDescription(String description) { + this.description = description; + } + + @JsonIgnore + public Application getApplication() { + return application; + } + + @JsonProperty("application") + public void setApplication(Application application) { + this.application = application; + } + + public Set getAccessRules() { + return accessRules; + } + + public void setAccessRules(Set accessRules) { + this.accessRules = accessRules; + } + + public String getQueryTemplate() { + return queryTemplate; + } + + public void setQueryTemplate(String queryTemplate) { + this.queryTemplate = queryTemplate; + } + + public String getQueryScope() { + return queryScope; + } + + public void setQueryScope(String queryScope) { + this.queryScope = queryScope; + } + + @JsonProperty("application") + public Application.ApplicationForDisplay getApplicationForDisplay(){ + if (application != null) + return new Application.ApplicationForDisplay() + .setDescription(application.getDescription()) + .setName(application.getName()) + .setEnable(application.isEnable()) + .setUuid(application.getUuid().toString()); + + return null; + } + + public String toString() { + return uuid.toString() + " ___ " + name + " ___ " + description + " ___ Application UUID : " + (application==null ? "NO APPLICATION AFFILIATED" : application.getUuid()) + "} ___ ({"+ (accessRules==null ? "NO ACCESS RULES DEFINED" :accessRules.stream().map(AccessRule::toString).collect(Collectors.joining("},{"))) + "})"; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/Role.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/Role.java new file mode 100644 index 000000000..aa0fd91fd --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/Role.java @@ -0,0 +1,54 @@ +package edu.harvard.hms.dbmi.avillach.auth.entity; + +import com.fasterxml.jackson.annotation.JsonInclude; +import jakarta.persistence.*; + +import java.util.Set; +import java.util.stream.Collectors; + +/** + *

    Models the authorization layer along with Privilege/AccessRule.

    + */ +@JsonInclude(JsonInclude.Include.NON_EMPTY) +@Entity(name = "role") +public class Role extends BaseEntity { + + private String name; + + private String description; + + @ManyToMany(fetch = FetchType.EAGER) + @JoinTable(name = "role_privilege", + joinColumns = {@JoinColumn(name = "role_id")}, + inverseJoinColumns = {@JoinColumn(name = "privilege_id")}) + private Set privileges; + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public String getDescription() { + return description; + } + + public void setDescription(String description) { + this.description = description; + } + + public Set getPrivileges() { + return privileges; + } + + public void setPrivileges(Set privileges) { + this.privileges = privileges; + } + + public String toString() { + return uuid.toString() + " ___ " + name + " ___ " + description + " ___ (" + (privileges==null?"NO PRIVILEGES DEFINED":privileges.stream().map(Privilege::toString).collect(Collectors.joining("},{"))) + ")"; + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/TermsOfService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/TermsOfService.java new file mode 100644 index 000000000..8843cfec6 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/TermsOfService.java @@ -0,0 +1,39 @@ +package edu.harvard.hms.dbmi.avillach.auth.entity; + +import jakarta.persistence.Entity; +import jakarta.persistence.PrePersist; + +import java.util.Date; + +/** + *

    Defines a model for terms of service.

    + */ +@Entity(name = "termsOfService") +public class TermsOfService extends BaseEntity { + + private String content; + + private Date dateUpdated; + + public String getContent() { + return content; + } + + @PrePersist + protected void onCreate() { + dateUpdated = new Date(); + } + public TermsOfService setContent(String content) { + this.content = content; + return this; + } + + public Date getDateUpdated() { + return dateUpdated; + } + + public TermsOfService setDateUpdated(Date date){ + this.dateUpdated = date; + return this; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/User.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/User.java new file mode 100644 index 000000000..8de7800c7 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/User.java @@ -0,0 +1,373 @@ +package edu.harvard.hms.dbmi.avillach.auth.entity; + +import com.fasterxml.jackson.annotation.JsonIgnore; +import com.fasterxml.jackson.annotation.JsonInclude; +import jakarta.persistence.*; + +import java.io.Serializable; +import java.security.Principal; +import java.util.*; +import java.util.stream.Collectors; + +/** + * Defines a model of User behavior. + */ +@JsonInclude(JsonInclude.Include.NON_EMPTY) +@Table( + uniqueConstraints = @UniqueConstraint(columnNames = { "email", "connectionId" }) +) +@Entity(name = "user") +public class User extends BaseEntity implements Serializable, Principal { + + @Column(unique = true) + private String subject; + + @ManyToMany(fetch = FetchType.EAGER) + @JoinTable(name = "user_role", + joinColumns = {@JoinColumn(name = "user_id", nullable = false, referencedColumnName = "uuid")}, + inverseJoinColumns = {@JoinColumn(name = "role_id", nullable = false, referencedColumnName = "uuid")}) + private Set roles; + + private String email; + + public User(User user) { + this.uuid = user.getUuid(); + this.subject = user.getSubject(); + this.roles = user.getRoles(); + this.email = user.getEmail(); + this.connection = user.getConnection(); + this.matched = user.isMatched(); + this.acceptedTOS = user.getAcceptedTOS(); + this.auth0metadata = user.getAuth0metadata(); + this.generalMetadata = user.getGeneralMetadata(); + this.active = user.isActive(); + this.token = user.getToken(); + } + + /** + *

    NOTICE

    + *

    + * When you update or create a user, + * please use connection.id as the input. The UserService is specifically using connection.id. + *

    + *
    + *

    + * Note: This is because of the checkAssociation() method in UserService. + *


    + */ + @ManyToOne + @JoinColumn(name = "connectionId") + private Connection connection; + + private boolean matched; + + @Column(nullable = true) + private Date acceptedTOS; + + @Column(name = "auth0_metadata") + private String auth0metadata; + + @Column(name = "general_metadata") + private String generalMetadata; + + @Column(name = "is_active") + private boolean active = true; + + @Column(name = "long_term_token") + private String token; + + /** + * This is a passport for the user represented as a string. See the Passport class for more information. + */ + @Column(name = "passport") + private String passport; + + public User() { + + } + + public String getSubject() { + return subject; + } + + public User setSubject(String subject) { + this.subject = subject; + return this; + } + + public Set getRoles() { + return roles; + } + + public User setRoles(Set roles) { + this.roles = roles; + return this; + } + + /** + * @return set of privileges + */ + @JsonIgnore + public Set getTotalPrivilege(){ + if (roles == null) + return null; + + Set privileges = new HashSet<>(); + roles.forEach(r -> privileges.addAll(r.getPrivileges())); + return privileges; + } + + /** + * return all privileges in the roles as a set + * @return set of privileges + */ + @JsonIgnore + public Set getTotalAccessRule(){ + if (roles == null) + return null; + + Set accessRules = new HashSet<>(); + roles.forEach(r -> r.getPrivileges().forEach(p -> accessRules.addAll(p.getAccessRules()))); + return accessRules; + } + + /** + * return all privilege name in each role as a set. + * + * @return set of privilege names + */ + @JsonIgnore + public Set getPrivilegeNameSet(){ + Set totalPrivilegeSet = getTotalPrivilege(); + + if (totalPrivilegeSet == null) + return new HashSet<>(); + + Set nameSet = new HashSet<>(); + totalPrivilegeSet.forEach(p -> nameSet.add(p.getName())); + return nameSet; + } + + /** + * return privilege names in each role as a set based on Application given. + * + * @return set of privilege names + */ + @JsonIgnore + public Set getPrivilegeNameSetByApplication(Application application){ + Set totalPrivilegeSet = getTotalPrivilege(); + + if (totalPrivilegeSet == null) + return new HashSet<>(); + + Set nameSet = new HashSet<>(); + if (application == null) + return nameSet; + + for (Privilege appPrivilege : application.getPrivileges()) { + for (Privilege userPrivilege : totalPrivilegeSet) { + if (appPrivilege.equals(userPrivilege)) + nameSet.add(userPrivilege.getName()); + } + } + return nameSet; + } + + /** + * return privileges in each role as a set based on Application given. + * + * @return set of privileges + */ + @JsonIgnore + public Set getPrivilegesByApplication(Application application){ + if (application == null || application.getUuid() == null){ + return getTotalPrivilege(); + } + + if (roles == null) + return null; + + Set privileges = new HashSet<>(); + roles.forEach(r -> privileges.addAll(r.getPrivileges() + .stream() + .filter(p -> application.getUuid() + .equals((p.getApplication()==null)? + null: + p.getApplication().getUuid())) + .collect(Collectors.toSet()))); + return privileges; + } + + @JsonIgnore + public String getPrivilegeString(){ + Set totalPrivilegeSet = getTotalPrivilege(); + + if (totalPrivilegeSet == null) + return null; + + return totalPrivilegeSet.stream().map(Privilege::getName).collect(Collectors.joining(",")); + } + + @JsonIgnore + public String getRoleString(){ + return (roles==null)?null:roles.stream().map(Role::getName) + .collect(Collectors.joining(",")); + } + + public String getAuth0metadata() { + return auth0metadata; + } + + public User setAuth0metadata(String auth0metadata) { + this.auth0metadata = auth0metadata; + return this; + } + + public String getGeneralMetadata() { + return generalMetadata; + } + + public User setGeneralMetadata(String generalMetadata) { + this.generalMetadata = generalMetadata; + return this; + } + + public String getEmail() { + return email; + } + + public void setEmail(String email) { + this.email = email; + } + + public Connection getConnection() { + return connection; + } + + public User setConnection(Connection connection) { + this.connection = connection; + return this; + } + + public boolean isMatched() { + return matched; + } + + public void setMatched(boolean matched) { + this.matched = matched; + } + + public Date getAcceptedTOS() { + return acceptedTOS; + } + + public void setAcceptedTOS(Date acceptedTOS) { + this.acceptedTOS = acceptedTOS; + } + + @JsonIgnore + @Override + public String getName() { + return this.subject; + } + + public boolean isActive() { + return active; + } + + public void setActive(boolean active) { + this.active = active; + } + + public String getToken() { + return token; + } + + public void setToken(String token) { + this.token = token; + } + + public String getPassport() { + return passport; + } + + public void setPassport(String passport) { + this.passport = passport; + } + + /** + *

    Inner class defining limited user attributes returned from the User endpoint.

    + */ + @JsonInclude(JsonInclude.Include.NON_EMPTY) + public static class UserForDisplay { + String uuid; + String email; + Set privileges; + String token; + Set queryScopes; + private boolean acceptedTOS; + + public UserForDisplay() { + } + + public String getEmail() { + return email; + } + + public UserForDisplay setEmail(String email) { + this.email = email; + return this; + } + + public Set getPrivileges() { + return privileges; + } + + public UserForDisplay setPrivileges(Set privileges) { + this.privileges = privileges; + return this; + } + + public String getUuid() { + return uuid; + } + + public UserForDisplay setUuid(String uuid) { + this.uuid = uuid; + return this; + } + + public String getToken() { + return token; + } + + public UserForDisplay setToken(String token) { + this.token = token; + return this; + } + + public Set getQueryScopes() { + return queryScopes; + } + + public void setQueryScopes(Set queryScopes) { + this.queryScopes = queryScopes; + } + + public boolean getAcceptedTOS() { + return acceptedTOS; + } + + public UserForDisplay setAcceptedTOS(boolean acceptedTOS) { + this.acceptedTOS = acceptedTOS; + return this; + } + } + + public String toString() { + if(uuid == null) { + return "No UUID assigned___ " + subject + " ___ " + email + " ___ " + generalMetadata + " ___ " + auth0metadata + " ___ {" + ((connection==null)?null:connection.toString()) + "}"; + } + return uuid.toString() + " ___ " + subject + " ___ " + email + " ___ " + generalMetadata + " ___ " + auth0metadata + " ___ {" + ((connection==null)?null:connection.toString()) + "}"; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/UserClaims.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/UserClaims.java new file mode 100644 index 000000000..14174adb0 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/UserClaims.java @@ -0,0 +1,119 @@ +package edu.harvard.hms.dbmi.avillach.auth.entity; + +import java.util.HashMap; +import java.util.List; + +public class UserClaims { + + private String uuid; + private String name; + private String email; + private String sub; + + // RAS, AIM-AHEAD, AUTH0, FENCE, etc + private String idp; + + // Non-study roles. There are far too many study roles to include them in the claims. + private List roles; + + // These claims are RAS specific + private String userid; + private String era_commons_id; + private String preferred_username; + private String user_permission_group; + + public String getUuid() { + return uuid; + } + + public void setUuid(String uuid) { + this.uuid = uuid; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public String getEmail() { + return email; + } + + public void setEmail(String email) { + this.email = email; + } + + public String getSub() { + return sub; + } + + public void setSub(String sub) { + this.sub = sub; + } + + public String getIdp() { + return idp; + } + + public void setIdp(String idp) { + this.idp = idp; + } + + public List getRoles() { + return roles; + } + + public void setRoles(List roles) { + this.roles = roles; + } + + public String getUserid() { + return userid; + } + + public void setUserid(String userid) { + this.userid = userid; + } + + public String getEra_commons_id() { + return era_commons_id; + } + + public void setEra_commons_id(String era_commons_id) { + this.era_commons_id = era_commons_id; + } + + public String getPreferred_username() { + return preferred_username; + } + + public void setPreferred_username(String preferred_username) { + this.preferred_username = preferred_username; + } + + public String getUser_permission_group() { + return user_permission_group; + } + + public void setUser_permission_group(String user_permission_group) { + this.user_permission_group = user_permission_group; + } + + public HashMap toHashMap() { + HashMap map = new HashMap<>(); + if (uuid != null) map.put("uuid", uuid); + if (name != null) map.put("name", name); + if (email != null) map.put("email", email); + if (sub != null) map.put("sub", sub); + if (idp != null) map.put("idp", idp); + if (roles != null) map.put("roles", roles); + if (userid != null) map.put("userid", userid); + if (era_commons_id != null) map.put("era_commons_id", era_commons_id); + if (preferred_username != null) map.put("preferred_username", preferred_username); + if (user_permission_group != null) map.put("user_permission_group", user_permission_group); + return map; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/UserConsents.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/UserConsents.java new file mode 100644 index 000000000..bf8aa2f46 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/UserConsents.java @@ -0,0 +1,64 @@ +package edu.harvard.hms.dbmi.avillach.auth.entity; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.core.type.TypeReference; +import com.fasterxml.jackson.databind.ObjectMapper; +import jakarta.persistence.*; + +import java.io.Serializable; +import java.security.Principal; +import java.util.Map; +import java.util.Set; +import java.util.UUID; + +@Entity(name = "user_consents") +public class UserConsents extends BaseEntity { + + @Column(unique = true, name = "user_id") + private UUID userId; + + + @Convert(converter = ConsentsJsonConverter.class) + private Map> consents; + + public UUID getUserId() { + return userId; + } + + public UserConsents setUserId(UUID userId) { + this.userId = userId; + return this; + } + + public Map> getConsents() { + return consents; + } + + public UserConsents setConsents(Map> consents) { + this.consents = consents; + return this; + } + + protected static class ConsentsJsonConverter implements AttributeConverter>, String> { + private static final ObjectMapper objectMapper = new ObjectMapper(); + private static final TypeReference>> SET_OF_STRING_TYPE_REF = new TypeReference>>() {}; + + @Override + public String convertToDatabaseColumn(Map> strings) { + try { + return objectMapper.writeValueAsString(strings); + } catch (JsonProcessingException e) { + throw new RuntimeException(e); + } + } + + @Override + public Map> convertToEntityAttribute(String s) { + try { + return objectMapper.readValue(s, SET_OF_STRING_TYPE_REF); + } catch (JsonProcessingException e) { + throw new RuntimeException(e); + } + } + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/UserMetadataMapping.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/UserMetadataMapping.java new file mode 100644 index 000000000..6d67d2ad6 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/UserMetadataMapping.java @@ -0,0 +1,52 @@ +package edu.harvard.hms.dbmi.avillach.auth.entity; + +import jakarta.persistence.Entity; +import jakarta.persistence.FetchType; +import jakarta.persistence.JoinColumn; +import jakarta.persistence.ManyToOne; + +/** + *

    Model defining how to map an admin added user to an Oauth user profile.

    + */ +@Entity(name="userMetadataMapping") +public class UserMetadataMapping extends BaseEntity { + + @ManyToOne(fetch = FetchType.EAGER) + @JoinColumn(name = "connectionId") + private Connection connection; + + private String generalMetadataJsonPath; + + private String auth0MetadataJsonPath; + + public String getGeneralMetadataJsonPath() { + return generalMetadataJsonPath; + } + + public UserMetadataMapping setGeneralMetadataJsonPath(String generalMetadataJsonPath) { + this.generalMetadataJsonPath = generalMetadataJsonPath; + return this; + } + + public String getAuth0MetadataJsonPath() { + return auth0MetadataJsonPath; + } + + public UserMetadataMapping setAuth0MetadataJsonPath(String auth0MetadataJsonPath) { + this.auth0MetadataJsonPath = auth0MetadataJsonPath; + return this; + } + + public Connection getConnection() { + return connection; + } + + public UserMetadataMapping setConnection(Connection connection) { + this.connection = connection; + return this; + } + + public String toString() { + return uuid.toString() + " ___ {" + connection.toString() + "} ___ " + generalMetadataJsonPath + " ___ " + auth0MetadataJsonPath; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/package-info.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/package-info.java new file mode 100644 index 000000000..a3ef54e20 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/entity/package-info.java @@ -0,0 +1,4 @@ +/** + * Contains the entity objects for PSAMA. + */ +package edu.harvard.hms.dbmi.avillach.auth.entity; \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/enums/PassportValidationResponse.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/enums/PassportValidationResponse.java new file mode 100644 index 000000000..ec5e486fc --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/enums/PassportValidationResponse.java @@ -0,0 +1,45 @@ +package edu.harvard.hms.dbmi.avillach.auth.enums; + +public enum PassportValidationResponse { + // The Visa’s signature is valid, the Visa has not expired, a valid txn claim is present + VALID("Valid"), + // The encoded Visa’s signature failed validation, is missing or incorrect + INVALID("Invalid"), + // The Passport payload or Visa parameter is missing + MISSING("Missing"), + // The format of the Passport or Visa is incorrect + INVALID_PASSPORT("Invalid Passport"), + // The Visa has expired (as indicated by the “exp” claim) + VISA_EXPIRED("Visa Expired"), + // The Transaction claim (txn) has an error or is missing + TXN_ERROR("Txn Error"), + // The Expiration claim (exp) has an error or is missing + EXPIRATION_ERROR("Expiration Error"), + // A DB related validation error occurred + VALIDATION_ERROR("Validation Error"), + // The Visa was expired because the required polling time was exceeded + EXPIRED_POLLING("Expired Polling"), + // There is a change in the dbGaP permissions associated with the user + PERMISSION_UPDATE("Permission Update"); + + private final String value; + + PassportValidationResponse(String value) { + this.value = value; + } + + // FromValue + public static PassportValidationResponse fromValue(String value) { + for (PassportValidationResponse response : PassportValidationResponse.values()) { + if (response.getValue().equals(value)) { + return response; + } + } + return null; + } + + public String getValue() { + return value; + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/exceptions/GlobalExceptionHandler.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/exceptions/GlobalExceptionHandler.java new file mode 100644 index 000000000..90545b484 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/exceptions/GlobalExceptionHandler.java @@ -0,0 +1,182 @@ +package edu.harvard.hms.dbmi.avillach.auth.exceptions; + +import edu.harvard.hms.dbmi.avillach.auth.model.response.PICSUREResponse; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.dao.DataIntegrityViolationException; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.security.access.AccessDeniedException; +import org.springframework.security.core.userdetails.UsernameNotFoundException; +import org.springframework.web.bind.annotation.ExceptionHandler; +import org.springframework.web.bind.annotation.RestControllerAdvice; +import org.springframework.web.client.HttpClientErrorException; +import org.springframework.web.client.HttpServerErrorException; + +import java.sql.SQLIntegrityConstraintViolationException; + +/** + * Global exception handler for the PICSURE Auth application. + * Provides centralized exception handling for various types of exceptions. + */ +@RestControllerAdvice +public class GlobalExceptionHandler { + + private static final Logger logger = LoggerFactory.getLogger(GlobalExceptionHandler.class); + + /** + * Handles database constraint violations which occur when trying to delete + * records that are referenced by other entities through foreign keys. + * + * @param ex The exception thrown by the database or Spring's data layer + * @return A response with HTTP 409 Conflict status and explanatory message + */ + @ExceptionHandler({SQLIntegrityConstraintViolationException.class, DataIntegrityViolationException.class}) + public ResponseEntity handleConstraintViolation(Exception ex) { + logger.error("Database constraint violation: {}", ex.getMessage()); + return PICSUREResponse.error( + HttpStatus.CONFLICT, + "Cannot delete this resource as it's referenced by other entities in the system", + "This resource is still being used by other records in the database. You must remove those references before deleting this item." + ); + } + + /** + * Handles cases where a user attempts an operation they don't have permission for. + * + * @param ex The access denied exception + * @return A response with HTTP 403 Forbidden status and explanatory message + */ + @ExceptionHandler(AccessDeniedException.class) + public ResponseEntity handleAccessDenied(AccessDeniedException ex) { + logger.warn("Access denied: {}", ex.getMessage()); + return PICSUREResponse.error( + HttpStatus.FORBIDDEN, + "You do not have permission to perform this operation", + ex.getMessage() + ); + } + + /** + * Handles NotAuthorizedException which is thrown when a user is not authorized + * to perform certain operations. + * + * @param ex The not authorized exception + * @return A response with HTTP 401 Unauthorized status and explanatory message + */ + @ExceptionHandler(NotAuthorizedException.class) + public ResponseEntity handleNotAuthorized(NotAuthorizedException ex) { + logger.warn("Not authorized: {}", ex.getMessage()); + return PICSUREResponse.error( + HttpStatus.UNAUTHORIZED, + "Authorization failed", + ex.getMessage() + ); + } + + /** + * Handles IllegalArgumentException, which is commonly used for validation errors. + * + * @param ex The exception + * @return A response with HTTP 400 Bad Request status + */ + @ExceptionHandler(IllegalArgumentException.class) + public ResponseEntity handleIllegalArgument(IllegalArgumentException ex) { + logger.warn("Invalid request argument: {}", ex.getMessage()); + return PICSUREResponse.error( + HttpStatus.BAD_REQUEST, + "Invalid request", + ex.getMessage() + ); + } + + /** + * Handles NullPointerException, often indicating a system error. + * + * @param ex The exception + * @return A response with HTTP 500 Internal Server Error status + */ + @ExceptionHandler(NullPointerException.class) + public ResponseEntity handleNullPointer(NullPointerException ex) { + logger.error("Null pointer exception: ", ex); + return PICSUREResponse.error( + HttpStatus.INTERNAL_SERVER_ERROR, + "An internal server error occurred", + "Please contact the system administrator with the time this error occurred." + ); + } + + /** + * Handles UsernameNotFoundException thrown during authentication. + * + * @param ex The exception + * @return A response with HTTP 401 Unauthorized status + */ + @ExceptionHandler(UsernameNotFoundException.class) + public ResponseEntity handleUsernameNotFound(UsernameNotFoundException ex) { + logger.warn("Username not found: {}", ex.getMessage()); + return PICSUREResponse.error( + HttpStatus.UNAUTHORIZED, + "Authentication failed", + ex.getMessage() + ); + } + + /** + * Handles HTTP client errors from external API calls. + * + * @param ex The HTTP client error exception + * @return A response with the appropriate HTTP status from the exception + */ + @ExceptionHandler({HttpClientErrorException.class, HttpServerErrorException.class}) + public ResponseEntity handleHttpClientError(Exception ex) { + HttpStatus status = HttpStatus.BAD_GATEWAY; + String errorMsg = ex.getMessage(); + + if (ex instanceof HttpClientErrorException clientEx) { + status = HttpStatus.valueOf(clientEx.getStatusCode().value()); + logger.error("HTTP client error: {} - {}", status, clientEx.getMessage()); + } else if (ex instanceof HttpServerErrorException serverEx) { + status = HttpStatus.valueOf(serverEx.getStatusCode().value()); + logger.error("HTTP server error: {} - {}", status, serverEx.getMessage()); + } + + return PICSUREResponse.error( + status, + "Error communicating with external service", + errorMsg + ); + } + + /** + * Handles RuntimeException, which includes many business logic errors. + * + * @param ex The runtime exception + * @return A response with HTTP 500 Internal Server Error status + */ + @ExceptionHandler(RuntimeException.class) + public ResponseEntity handleRuntime(RuntimeException ex) { + logger.error("Runtime exception: ", ex); + return PICSUREResponse.error( + HttpStatus.INTERNAL_SERVER_ERROR, + "An error occurred while processing your request", + ex.getMessage() + ); + } + + /** + * Fallback handler for all other exceptions that aren't specifically handled. + * + * @param ex The exception + * @return A response with HTTP 500 Internal Server Error status + */ + @ExceptionHandler(Exception.class) + public ResponseEntity handleGenericException(Exception ex) { + logger.error("Unhandled exception: ", ex); + return PICSUREResponse.error( + HttpStatus.INTERNAL_SERVER_ERROR, + "An unexpected error occurred", + "Please contact the system administrator with the time this error occurred." + ); + } +} \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/exceptions/NotAuthorizedException.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/exceptions/NotAuthorizedException.java new file mode 100644 index 000000000..050b6de05 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/exceptions/NotAuthorizedException.java @@ -0,0 +1,7 @@ +package edu.harvard.hms.dbmi.avillach.auth.exceptions; + +public class NotAuthorizedException extends RuntimeException { + public NotAuthorizedException(String message) { + super(message); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/filter/AuditLoggingFilter.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/filter/AuditLoggingFilter.java new file mode 100644 index 000000000..2e15fecbb --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/filter/AuditLoggingFilter.java @@ -0,0 +1,175 @@ +package edu.harvard.hms.dbmi.avillach.auth.filter; + +import java.io.IOException; +import java.util.HashMap; +import java.util.Map; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.dbmi.avillach.logging.RequestInfo; +import edu.harvard.dbmi.avillach.logging.SessionIdResolver; +import edu.harvard.hms.dbmi.avillach.auth.model.CustomApplicationDetails; +import edu.harvard.hms.dbmi.avillach.auth.model.CustomUserDetails; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuditAttributes; +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.core.annotation.Order; +import org.springframework.lang.NonNull; +import org.springframework.security.core.Authentication; +import org.springframework.security.core.context.SecurityContextHolder; +import org.springframework.stereotype.Component; +import org.springframework.web.filter.OncePerRequestFilter; + +@Component +@Order(2) +public class AuditLoggingFilter extends OncePerRequestFilter { + + private static final Logger logger = LoggerFactory.getLogger(AuditLoggingFilter.class); + + private static final String AUDIT_START_TIME = "audit_start_time"; + + @Value("${DEST_IP:#{null}}") + private String destIp; + + @Value("${DEST_PORT:#{null}}") + private Integer destPort; + + private final LoggingClient loggingClient; + + @Autowired + public AuditLoggingFilter(LoggingClient loggingClient) { + this.loggingClient = loggingClient; + } + + @Override + protected void doFilterInternal( + @NonNull HttpServletRequest request, @NonNull HttpServletResponse response, @NonNull FilterChain filterChain + ) throws ServletException, IOException { + request.setAttribute(AUDIT_START_TIME, System.currentTimeMillis()); + + try { + filterChain.doFilter(request, response); + } finally { + logRequest(request, response); + } + } + + private void logRequest(HttpServletRequest request, HttpServletResponse response) { + try { + if (loggingClient == null || !loggingClient.isEnabled()) { + return; + } + + String path = request.getRequestURI(); + + // Strip context path (e.g., /auth) + String contextPath = request.getContextPath(); + if (contextPath != null && !contextPath.isEmpty() && path.startsWith(contextPath)) { + path = path.substring(contextPath.length()); + } + + // Skip paths that should not be logged + if ( + path.startsWith("/actuator/") || path.endsWith("/swagger.yaml") || path.endsWith("/swagger.json") + || path.endsWith("/openapi.json") + ) { + return; + } + + // Calculate duration + Long startTime = (Long) request.getAttribute(AUDIT_START_TIME); + long duration = 0L; + if (startTime != null) { + duration = System.currentTimeMillis() - startTime; + } + + // Read event type and action from request attributes (set by AuditInterceptor from @AuditEvent annotations) + String method = request.getMethod(); + String eventType = (String) request.getAttribute(AuditAttributes.EVENT_TYPE); + String action = (String) request.getAttribute(AuditAttributes.ACTION); + if (eventType == null) eventType = "OTHER"; + if (action == null) action = method.toLowerCase(); + + // Determine source IP + String srcIp = AuditAttributes.extractClientIp(request); + + // Determine dest IP and port + String resolvedDestIp = destIp != null ? destIp : request.getLocalAddr(); + int resolvedDestPort = destPort != null ? destPort : request.getLocalPort(); + + // Response info + int responseStatus = response.getStatus(); + String contentType = response.getContentType(); + + // Build RequestInfo + RequestInfo requestInfo = RequestInfo.builder().method(method).url(request.getRequestURI()).srcIp(srcIp).destIp(resolvedDestIp) + .destPort(resolvedDestPort).httpUserAgent(request.getHeader("User-Agent")).status(responseStatus).duration(duration) + .httpContentType(contentType).build(); + + // Build metadata + Map metadata = new HashMap<>(); + + // Extract user info from security context + Authentication authentication = SecurityContextHolder.getContext().getAuthentication(); + if (authentication != null && authentication.getPrincipal() != null) { + Object principal = authentication.getPrincipal(); + if (principal instanceof CustomUserDetails userDetails) { + metadata.put("user_id", userDetails.getUser().getUuid().toString()); + if (userDetails.getUser().getEmail() != null) { + metadata.put("user_email", userDetails.getUser().getEmail()); + } + } else if (principal instanceof CustomApplicationDetails appDetails) { + if (appDetails.getApplication() != null) { + metadata.put("app_id", appDetails.getApplication().getUuid().toString()); + metadata.put("app_name", appDetails.getApplication().getName()); + } + } + } + + // Session ID + String sessionId = SessionIdResolver.resolve(request.getHeader("X-Session-Id"), srcIp, request.getHeader("User-Agent")); + + // Merge domain-specific metadata from AuditAttributes (set by services). + // Filter-managed keys take precedence over AuditAttributes values. + AuditAttributes.getMetadata(request).forEach(metadata::putIfAbsent); + + // Build error map for 4xx/5xx + Map errorMap = null; + if (responseStatus >= 400) { + errorMap = new HashMap<>(); + errorMap.put("status", responseStatus); + errorMap.put("error_type", responseStatus >= 500 ? "server_error" : "client_error"); + } + + // Build the event + LoggingEvent.Builder eventBuilder = + LoggingEvent.builder(eventType).action(action).sessionId(sessionId).request(requestInfo).metadata(metadata); + + if (errorMap != null) { + eventBuilder.error(errorMap); + } + + LoggingEvent event = eventBuilder.build(); + + // Send the event with bearer token passthrough + String authHeader = request.getHeader("Authorization"); + String requestId = request.getHeader("X-Request-Id"); + + if (authHeader != null || requestId != null) { + loggingClient.send(event, authHeader, requestId); + } else { + loggingClient.send(event); + } + + } catch (Exception e) { + logger.warn("AuditLoggingFilter failed to log request", e); + } + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/filter/JWTFilter.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/filter/JWTFilter.java new file mode 100755 index 000000000..e166b12cc --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/filter/JWTFilter.java @@ -0,0 +1,263 @@ +package edu.harvard.hms.dbmi.avillach.auth.filter; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Application; +import edu.harvard.hms.dbmi.avillach.auth.entity.Privilege; +import edu.harvard.hms.dbmi.avillach.auth.entity.Role; +import edu.harvard.hms.dbmi.avillach.auth.exceptions.NotAuthorizedException; +import edu.harvard.hms.dbmi.avillach.auth.model.CustomApplicationDetails; +import edu.harvard.hms.dbmi.avillach.auth.model.CustomUserDetails; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.CustomUserDetailService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.TOSService; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuditAttributes; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming; +import edu.harvard.hms.dbmi.avillach.auth.utils.JWTUtil; +import io.jsonwebtoken.Claims; +import io.jsonwebtoken.Jws; +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.core.annotation.Order; +import org.springframework.lang.NonNull; +import org.springframework.security.authentication.UsernamePasswordAuthenticationToken; +import org.springframework.security.core.context.SecurityContextHolder; +import org.springframework.security.web.authentication.WebAuthenticationDetailsSource; +import org.springframework.stereotype.Component; +import org.springframework.util.CollectionUtils; +import org.springframework.web.filter.OncePerRequestFilter; + +import java.io.IOException; +import java.util.Set; +import java.util.stream.Collectors; + + +/** + * The main gate for PSAMA that filters all incoming requests against PSAMA.

    Design Logic

    • All incoming requests pass + * through this filter.
    • To pass this filter, the incoming request needs a valid bearer token in its HTTP Authorization Header to + * represent a valid identity behind the token.
    • In some cases, the incoming request doesn't need to hold a token. For example, + * when the request is to the authentication endpoint, swagger.json, or swagger.html.
    + */ + +@Component +@Order(1) +public class JWTFilter extends OncePerRequestFilter { + + private final static Logger logger = LoggerFactory.getLogger(JWTFilter.class); + + private final TOSService tosService; + + private final String userClaimId; + + private final JWTUtil jwtUtil; + private final CustomUserDetailService customUserDetailService; + + @Autowired + public JWTFilter( + TOSService tosService, @Value("${application.user.id.claim}") String userClaimId, JWTUtil jwtUtil, + CustomUserDetailService customUserDetailService + ) { + this.tosService = tosService; + this.userClaimId = userClaimId; + this.jwtUtil = jwtUtil; + this.customUserDetailService = customUserDetailService; + } + + /** + * Filter that performs authentication and authorization checks based on the provided request headers. The filter checks for the + * presence of the "Authorization" header and validates the token. It sets the appropriate security context based on the type of token + * (long-term token or PSAMA application token) and performs the necessary checks to ensure that the user or application is authorized + * to access the requested resource. This filter is called by the configured security filter chain in the SecurityConfig class. + * + * @param request the HttpServletRequest object + * @param response the HttpServletResponse object + * @param filterChain the FilterChain object + * @throws IOException if an I/O error occurs during the execution of the filter + */ + @Override + protected void doFilterInternal(HttpServletRequest request, @NonNull HttpServletResponse response, @NonNull FilterChain filterChain) + throws IOException, ServletException { + // Get headers from the request + String authorizationHeader = request.getHeader("Authorization"); + + if (!StringUtils.isNotBlank(authorizationHeader)) { + // If the header is not present, we allow the request to pass through + // without any authentication or authorization checks + filterChain.doFilter(request, response); + } else { + String token = authorizationHeader.substring(6).trim(); + Jws jws; + try { + jws = this.jwtUtil.parseToken(token); + } catch (Exception e) { + logger.error("Failed to parse JWT token.", e); + sendAuthFailure(request, "invalid_token", e.getMessage()); + response.sendError(HttpServletResponse.SC_UNAUTHORIZED, "Invalid token."); + return; + } + String userId = jws.getPayload().get(this.userClaimId, String.class); + + if (userId.startsWith(AuthNaming.LONG_TERM_TOKEN_PREFIX)) { + // For profile information, we do indeed allow a long-term token to be a valid token. + if (request.getRequestURI().startsWith("/auth/user/me")) { + String realClaimsSubject = jws.getPayload().getSubject().substring(AuthNaming.LONG_TERM_TOKEN_PREFIX.length() + 1); + + setSecurityContextForUser(request, response, realClaimsSubject); + } else { + logger.error("the long term token with subject, {}, cannot access to PSAMA.", userId); + sendAuthFailure(request, "long_term_token_rejected", "Long term token on non-/me endpoint"); + response.sendError(HttpServletResponse.SC_UNAUTHORIZED, "Long term tokens cannot be used to access to PSAMA."); + } + } else if (userId.startsWith(AuthNaming.PSAMA_APPLICATION_TOKEN_PREFIX)) { + logger.info("User Authentication Starts with {}", AuthNaming.PSAMA_APPLICATION_TOKEN_PREFIX); + + // Check if the user is attempting to access the correct introspection endpoint. If not reject the request, + // log an error indicating the user's token may be being used by a malicious actor. + if (!request.getRequestURI().endsWith("token/inspect") && !request.getRequestURI().endsWith("open/validate")) { + logger.error("{} attempted to perform request {} token may be compromised.", userId, request.getRequestURI()); + sendAuthFailure(request, "compromised_token", "App token on wrong endpoint"); + response.sendError(HttpServletResponse.SC_UNAUTHORIZED, "User is deactivated"); + } + + String applicationId = userId.split("\\|")[1]; + logger.info("Application ID: {}", applicationId); + + // Create custom application details. Will be used to set the correct security context. + CustomApplicationDetails customApplicationDetails = + (CustomApplicationDetails) this.customUserDetailService.loadUserByUsername("application:" + applicationId); + if (customApplicationDetails.getApplication() == null) { + logger.error("Cannot find an application by userId: {}", applicationId); + sendAuthFailure(request, "application_not_found", "No application for ID: " + applicationId); + response.sendError( + HttpServletResponse.SC_UNAUTHORIZED, "Your token doesn't contain valid identical information, please contact admin." + ); + return; + } + + Application application = customApplicationDetails.getApplication(); + + if (!application.getToken().equals(token)) { + logger.error( + "filter() incoming application token - {} - is not the same as record, might because the token has been refreshed. Subject: {}", + token, userId + ); + sendAuthFailure(request, "token_mismatch", "Application token does not match record"); + response.sendError( + HttpServletResponse.SC_UNAUTHORIZED, + "Your token has been inactivated, please contact admin to grab you the latest one." + ); + } + + // This is the application token that is being used to authenticate the user by other applications + // Set the security context for the application + setSecurityContextForApplication(request, customApplicationDetails); + } else { + logger.info("UserID: {} is not a long term token and not a PSAMA application token.", userId); + // Authenticate as User + setSecurityContextForUser(request, response, jws.getPayload().getSubject()); + } + + filterChain.doFilter(request, response); + } + } + + private void setSecurityContextForApplication(HttpServletRequest request, CustomApplicationDetails authenticatedApplication) { + logger.debug("Setting security context for application: {}", authenticatedApplication.getApplication().getName()); + UsernamePasswordAuthenticationToken authentication = + new UsernamePasswordAuthenticationToken(authenticatedApplication, null, authenticatedApplication.getAuthorities()); + authentication.setDetails(new WebAuthenticationDetailsSource().buildDetails(request)); + logger.debug( + "Created authenticationToken object {} for application: {}", authentication, authenticatedApplication.getApplication().getName() + ); + SecurityContextHolder.getContext().setAuthentication(authentication); + } + + /** + * Sets the security context for the given user. This method is responsible for validating the user claims. It checks if the user is + * active, ensuring the user has accepted the terms of service (if enabled), validating user roles and privileges, and setting the user + * object as an attribute in the security context. + * + * @param request the HttpServletRequest object + * @param response the HttpServletResponse object + * @param realClaimsSubject the subject of the user's claims in the JWT token + */ + private void setSecurityContextForUser(HttpServletRequest request, HttpServletResponse response, String realClaimsSubject) { + logger.debug("Setting security context for user: {}", realClaimsSubject); + + CustomUserDetails authenticatedUser = (CustomUserDetails) this.customUserDetailService.loadUserByUsername(realClaimsSubject); + + if (authenticatedUser == null) { + logger.error("Cannot validate user claims, based on information stored in the JWT token."); + sendAuthFailure(request, "invalid_token", "Cannot validate user claims"); + throw new IllegalArgumentException("Cannot validate user claims, based on information stored in the JWT token."); + } + + logger.debug("User with email: {} is found.", authenticatedUser.getUser().getEmail()); + + if (!authenticatedUser.getUser().isActive()) { + logger.warn("User with ID: {} is deactivated.", authenticatedUser.getUser().getUuid()); + sendAuthFailure(request, "user_deactivated", "User is deactivated"); + throw new NotAuthorizedException("User is deactivated"); + } + + logger.debug("User with ID: {} is active.", authenticatedUser.getUser().getUuid()); + logger.debug("Checking if user has accepted the latest terms of service."); + + if ( + !request.getRequestURI().endsWith("/tos/accept") && !tosService.hasUserAcceptedLatest(authenticatedUser.getUser().getSubject()) + ) { + logger.info("User with ID: {} has not accepted the latest terms of service.", authenticatedUser.getUser().getUuid()); + sendAuthFailure(request, "tos_not_accepted", "User must accept terms of service"); + // If user has not accepted terms of service and is attempted to get information other than the terms of service, don't + // authenticate + try { + response.sendError(HttpServletResponse.SC_FORBIDDEN, "User must accept terms of service"); + // Return early to prevent setting up security context + return; + } catch (IOException e) { + logger.error("Failed to send response.", e); + } + } + + Set userRoles = authenticatedUser.getUser().getRoles(); + if ( + userRoles == null || userRoles.isEmpty() || userRoles.stream().allMatch(role -> CollectionUtils.isEmpty(role.getPrivileges())) + ) { + logger.error("User doesn't have any roles or privileges."); + sendAuthFailure(request, "no_roles_or_privileges", "User has no roles or privileges"); + try { + response.sendError(HttpServletResponse.SC_UNAUTHORIZED, "User doesn't have any roles or privileges."); + // Return early to prevent setting up security context + return; + } catch (IOException e) { + logger.error("Failed to send response.", e); + } + } + + logger.debug( + "User with email {} has privileges {}.", authenticatedUser.getUser().getEmail(), + authenticatedUser.getUser().getTotalPrivilege().stream().map(Privilege::getName).collect(Collectors.joining(",")) + ); + UsernamePasswordAuthenticationToken authentication = + new UsernamePasswordAuthenticationToken(authenticatedUser, null, authenticatedUser.getAuthorities()); + authentication.setDetails(new WebAuthenticationDetailsSource().buildDetails(request)); + SecurityContextHolder.getContext().setAuthentication(authentication); + + // Populate AuditAttributes for the AuditLoggingFilter to include in its event. + // user_id and user_email are read from SecurityContext by the filter directly. + AuditAttributes.putMetadata(request, "auth_result", "success"); + } + + private void sendAuthFailure(HttpServletRequest request, String reason, String message) { + AuditAttributes.putMetadata(request, "auth_result", "failure"); + AuditAttributes.putMetadata(request, "auth_failure_reason", reason); + if (message != null) { + AuditAttributes.putMetadata(request, "auth_failure_message", message); + } + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/AccessEmail.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/AccessEmail.java new file mode 100644 index 000000000..31825de94 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/AccessEmail.java @@ -0,0 +1,61 @@ +package edu.harvard.hms.dbmi.avillach.auth.model; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Role; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; + +import java.util.Set; + +/** + *

    Provides attributes for generating email notifications.

    + */ +public class AccessEmail { + + private String systemName = null; + private String documentation = null; + + private String username; + private Set roles; + private boolean rolesExists; + + public AccessEmail(User u, String systemName) { + this.username = u.getName(); + this.roles = u.getRoles(); + this.systemName = systemName; + } + + public String getUsername() { + return username; + } + + public void setUsername(String username) { + this.username = username; + } + + public Set getRoles() { + return roles; + } + + public void setRoles(Set roles) { + this.roles = roles; + } + + public String getDocumentation() { + return documentation; + } + + public void setDocumentation(String documentation) { + this.documentation = documentation; + } + + public String getSystemName() { + return systemName; + } + + public void setSystemName(String systemName) { + this.systemName = systemName; + } + + public boolean isRolesExists() { + return (roles != null) && (!roles.isEmpty()); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/AccessRuleEvaluationNode.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/AccessRuleEvaluationNode.java new file mode 100644 index 000000000..1273a6ab1 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/AccessRuleEvaluationNode.java @@ -0,0 +1,70 @@ +package edu.harvard.hms.dbmi.avillach.auth.model; + +import edu.harvard.hms.dbmi.avillach.auth.entity.AccessRule; + +import java.util.ArrayList; +import java.util.List; + +public class AccessRuleEvaluationNode { + private final AccessRule rule; + private final String nodeName; + private final boolean isGate; + private final boolean isSubRule; + private final boolean isOrRelationship; + private final List children = new ArrayList<>(); + private boolean result; + private String failureReason; + private int depth = 0; + + public AccessRuleEvaluationNode(AccessRule rule, boolean isGate, boolean isSubRule, boolean isOrRelationship) { + this.rule = rule; + this.nodeName = rule.getMergedName().isEmpty() ? rule.getName() : rule.getMergedName(); + this.isGate = isGate; + this.isSubRule = isSubRule; + this.isOrRelationship = isOrRelationship; + } + + public void addChild(AccessRuleEvaluationNode child) { + child.depth = this.depth + 1; + children.add(child); + } + + public void setResult(boolean result) { + this.result = result; + } + + public void setFailureReason(String failureReason) { + this.failureReason = failureReason; + } + + public String generateTreeString() { + StringBuilder sb = new StringBuilder(); + generateTreeString(sb, "", true); + return sb.toString(); + } + + private void generateTreeString(StringBuilder sb, String prefix, boolean isTail) { + String nodeType = isGate ? "GATE" : (isSubRule ? "SUB_RULE" : "RULE"); + String relationshipType = isOrRelationship ? "OR" : "AND"; + String resultStr = result ? "✓ PASS" : "✗ FAIL"; + String failureInfo = failureReason != null ? " - Reason: " + failureReason : ""; + + sb.append(prefix) + .append(isTail ? "└── " : "├── ") + .append("[").append(nodeType).append("|").append(relationshipType).append("] ") + .append(nodeName) + .append(" (").append(resultStr).append(")") + .append(failureInfo) + .append("\n"); + + for (int i = 0; i < children.size(); i++) { + boolean isLastChild = (i == children.size() - 1); + children.get(i).generateTreeString(sb, prefix + (isTail ? " " : "│ "), isLastChild); + } + } + + public AccessRule getRule() { return rule; } + public boolean isResult() { return result; } + public List getChildren() { return children; } + public String getFailureReason() { return failureReason; } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/CustomApplicationDetails.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/CustomApplicationDetails.java new file mode 100644 index 000000000..56c4bd6ea --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/CustomApplicationDetails.java @@ -0,0 +1,56 @@ +package edu.harvard.hms.dbmi.avillach.auth.model; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Application; +import org.springframework.security.core.GrantedAuthority; +import org.springframework.security.core.userdetails.UserDetails; + +import java.util.Collection; +import java.util.List; + +public class CustomApplicationDetails implements UserDetails { + + private final Application application; + + public CustomApplicationDetails(Application authenticatedApplication) { + this.application = authenticatedApplication; + } + + @Override + public Collection getAuthorities() { + return List.of(); + } + + @Override + public String getPassword() { + return null; + } + + @Override + public String getUsername() { + return this.application.getName(); + } + + @Override + public boolean isAccountNonExpired() { + return true; + } + + @Override + public boolean isAccountNonLocked() { + return true; + } + + @Override + public boolean isCredentialsNonExpired() { + return true; + } + + @Override + public boolean isEnabled() { + return true; + } + + public Application getApplication() { + return application; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/CustomUserDetails.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/CustomUserDetails.java new file mode 100644 index 000000000..cbd591128 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/CustomUserDetails.java @@ -0,0 +1,65 @@ +package edu.harvard.hms.dbmi.avillach.auth.model; + +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import org.springframework.security.core.GrantedAuthority; +import org.springframework.security.core.authority.SimpleGrantedAuthority; +import org.springframework.security.core.userdetails.UserDetails; + +import java.util.ArrayList; +import java.util.Collection; + +public class CustomUserDetails implements UserDetails { + + private final User user; + private final Collection authorities; + + public CustomUserDetails(User user) { + this.user = user; + if (user != null && user.getRoles() != null) { + this.authorities = new ArrayList<>(user.getTotalPrivilege().stream() + .map(privilege-> new SimpleGrantedAuthority(privilege.getName())) + .toList()); + } else { + this.authorities = new ArrayList<>(); + } + } + + @Override + public Collection getAuthorities() { + return this.authorities; + } + + @Override + public String getPassword() { + return null; + } + + @Override + public String getUsername() { + return this.user.getEmail(); + } + + @Override + public boolean isAccountNonExpired() { + return true; + } + + @Override + public boolean isAccountNonLocked() { + return true; + } + + @Override + public boolean isCredentialsNonExpired() { + return true; + } + + @Override + public boolean isEnabled() { + return true; + } + + public User getUser() { + return user; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/EvaluateAccessRuleResult.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/EvaluateAccessRuleResult.java new file mode 100644 index 000000000..177a82034 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/EvaluateAccessRuleResult.java @@ -0,0 +1,11 @@ +package edu.harvard.hms.dbmi.avillach.auth.model; + +import edu.harvard.hms.dbmi.avillach.auth.entity.AccessRule; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; + +import java.util.Optional; +import java.util.Set; + +public record EvaluateAccessRuleResult(boolean result, Set failedRules, String passRuleName, + Optional query) { +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/InvalidRefreshToken.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/InvalidRefreshToken.java new file mode 100644 index 000000000..a738d25aa --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/InvalidRefreshToken.java @@ -0,0 +1,4 @@ +package edu.harvard.hms.dbmi.avillach.auth.model; + +public record InvalidRefreshToken(String error) implements RefreshToken { +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/RefreshToken.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/RefreshToken.java new file mode 100644 index 000000000..f42a8248f --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/RefreshToken.java @@ -0,0 +1,5 @@ +package edu.harvard.hms.dbmi.avillach.auth.model; + +public sealed interface RefreshToken permits ValidRefreshToken, InvalidRefreshToken { +} + diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/TokenInspection.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/TokenInspection.java new file mode 100644 index 000000000..cebf2e8ba --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/TokenInspection.java @@ -0,0 +1,48 @@ +package edu.harvard.hms.dbmi.avillach.auth.model; + +import io.jsonwebtoken.Claims; + +import java.util.HashMap; +import java.util.Map; + +/** + * inner used token introspection class with active:false included + */ +public class TokenInspection { + + Map responseMap = new HashMap<>(); + String message = null; + + public TokenInspection() { + responseMap.put("active", false); + } + + public TokenInspection(String message) { + responseMap.put("active", false); + this.message = message; + } + + public Map getResponseMap() { + return responseMap; + } + + public void setResponseMap(Map responseMap) { + this.responseMap = responseMap; + } + + public String getMessage() { + return message; + } + + public void setMessage(String message) { + this.message = message; + } + + public void addField(String key, Object value) { + responseMap.put(key, value); + } + + public void addAllFields(Claims body) { + responseMap.putAll(body); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/ValidRefreshToken.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/ValidRefreshToken.java new file mode 100644 index 000000000..9cc1211ec --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/ValidRefreshToken.java @@ -0,0 +1,4 @@ +package edu.harvard.hms.dbmi.avillach.auth.model; + +public record ValidRefreshToken(String token, String expirationDate) implements RefreshToken { +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/fenceMapping/BioDataCatalyst.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/fenceMapping/BioDataCatalyst.java new file mode 100644 index 000000000..79475c4d5 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/fenceMapping/BioDataCatalyst.java @@ -0,0 +1,19 @@ +package edu.harvard.hms.dbmi.avillach.auth.model.fenceMapping; + +import com.fasterxml.jackson.annotation.JsonProperty; + +import java.util.List; + +public class BioDataCatalyst { + + @JsonProperty("bio_data_catalyst") + private List studyMetaData; + + public List getStudyMetaData() { + return studyMetaData; + } + + public void setStudyMetaData(List studyMetaData) { + this.studyMetaData = studyMetaData; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/fenceMapping/IsHarmonizedDeserializer.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/fenceMapping/IsHarmonizedDeserializer.java new file mode 100644 index 000000000..510998e38 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/fenceMapping/IsHarmonizedDeserializer.java @@ -0,0 +1,15 @@ +package edu.harvard.hms.dbmi.avillach.auth.model.fenceMapping; + +import com.fasterxml.jackson.core.JsonParser; +import com.fasterxml.jackson.databind.DeserializationContext; +import com.fasterxml.jackson.databind.JsonDeserializer; + +import java.io.IOException; + +public class IsHarmonizedDeserializer extends JsonDeserializer { + @Override + public Boolean deserialize(JsonParser jsonParser, DeserializationContext deserializationContext) throws IOException { + String text = jsonParser.getText(); + return "Y".equalsIgnoreCase(text) || "Yes".equalsIgnoreCase(text); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/fenceMapping/StudyMetaData.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/fenceMapping/StudyMetaData.java new file mode 100644 index 000000000..06163c3c8 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/fenceMapping/StudyMetaData.java @@ -0,0 +1,328 @@ +package edu.harvard.hms.dbmi.avillach.auth.model.fenceMapping; + +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; +import org.apache.commons.lang3.builder.ToStringBuilder; + +import java.util.Objects; + +public class StudyMetaData { + + @JsonProperty("study_identifier") + private String studyIdentifier; + + @JsonProperty("study_type") + private String studyType; + + @JsonProperty("abbreviated_name") + private String abbreviatedName; + + @JsonProperty("full_study_name") + private String fullStudyName; + + @JsonProperty("consent_group_code") + private String consentGroupCode; + + @JsonProperty("consent_group_name_abv") + private String consentGroupNameAbv; + + @JsonProperty("consent_group_name") + private String consentGroupName; + + @JsonProperty("request_access") + private String requestAccess; + + @JsonProperty("data_type") + private String dataType; + + @JsonProperty("clinical_variable_count") + private int clinicalVariableCount; + + @JsonProperty("genetic_sample_size") + private int geneticSampleSize; + + @JsonProperty("clinical_sample_size") + private int clinicalSampleSize; + + @JsonProperty("raw_clinical_variable_count") + private int rawClinicalVariableCount; + + @JsonProperty("raw_genetic_sample_size") + private int rawGeneticSampleSize; + + @JsonProperty("raw_clinical_sample_size") + private int rawClinicalSampleSize; + + @JsonProperty("study_version") + private String studyVersion; + + @JsonProperty("study_phase") + private String studyPhase; + + @JsonProperty("top_level_path") + private String topLevelPath; + + @JsonProperty("is_harmonized") + @JsonDeserialize(using = IsHarmonizedDeserializer.class) + private Boolean isHarmonized; + + @JsonProperty("study_focus") + private String studyFocus; + + @JsonProperty("study_design") + private String studyDesign; + + @JsonProperty("authZ") + private String authZ; + + @JsonProperty("additional_information") + private String additionalInformation; + + public String getStudyIdentifier() { + return studyIdentifier; + } + + public StudyMetaData setStudyIdentifier(String studyIdentifier) { + this.studyIdentifier = studyIdentifier; + return this; + } + + public String getStudyType() { + return studyType; + } + + public StudyMetaData setStudyType(String studyType) { + this.studyType = studyType; + return this; + } + + public String getAbbreviatedName() { + return abbreviatedName; + } + + public StudyMetaData setAbbreviatedName(String abbreviatedName) { + this.abbreviatedName = abbreviatedName; + return this; + } + + public String getFullStudyName() { + return fullStudyName; + } + + public StudyMetaData setFullStudyName(String fullStudyName) { + this.fullStudyName = fullStudyName; + return this; + } + + public String getConsentGroupCode() { + return consentGroupCode; + } + + public StudyMetaData setConsentGroupCode(String consentGroupCode) { + this.consentGroupCode = consentGroupCode; + return this; + } + + public String getConsentGroupNameAbv() { + return consentGroupNameAbv; + } + + public StudyMetaData setConsentGroupNameAbv(String consentGroupNameAbv) { + this.consentGroupNameAbv = consentGroupNameAbv; + return this; + } + + public String getConsentGroupName() { + return consentGroupName; + } + + public StudyMetaData setConsentGroupName(String consentGroupName) { + this.consentGroupName = consentGroupName; + return this; + } + + public String getRequestAccess() { + return requestAccess; + } + + public StudyMetaData setRequestAccess(String requestAccess) { + this.requestAccess = requestAccess; + return this; + } + + public String getDataType() { + return dataType; + } + + public StudyMetaData setDataType(String dataType) { + this.dataType = dataType; + return this; + } + + public int getClinicalVariableCount() { + return clinicalVariableCount; + } + + public StudyMetaData setClinicalVariableCount(int clinicalVariableCount) { + this.clinicalVariableCount = clinicalVariableCount; + return this; + } + + public int getGeneticSampleSize() { + return geneticSampleSize; + } + + public StudyMetaData setGeneticSampleSize(int geneticSampleSize) { + this.geneticSampleSize = geneticSampleSize; + return this; + } + + public int getClinicalSampleSize() { + return clinicalSampleSize; + } + + public StudyMetaData setClinicalSampleSize(int clinicalSampleSize) { + this.clinicalSampleSize = clinicalSampleSize; + return this; + } + + public int getRawClinicalVariableCount() { + return rawClinicalVariableCount; + } + + public StudyMetaData setRawClinicalVariableCount(int rawClinicalVariableCount) { + this.rawClinicalVariableCount = rawClinicalVariableCount; + return this; + } + + public int getRawGeneticSampleSize() { + return rawGeneticSampleSize; + } + + public StudyMetaData setRawGeneticSampleSize(int rawGeneticSampleSize) { + this.rawGeneticSampleSize = rawGeneticSampleSize; + return this; + } + + public int getRawClinicalSampleSize() { + return rawClinicalSampleSize; + } + + public StudyMetaData setRawClinicalSampleSize(int rawClinicalSampleSize) { + this.rawClinicalSampleSize = rawClinicalSampleSize; + return this; + } + + public String getStudyVersion() { + return studyVersion; + } + + public StudyMetaData setStudyVersion(String studyVersion) { + this.studyVersion = studyVersion; + return this; + } + + public String getStudyPhase() { + return studyPhase; + } + + public StudyMetaData setStudyPhase(String studyPhase) { + this.studyPhase = studyPhase; + return this; + } + + public String getTopLevelPath() { + return topLevelPath; + } + + public StudyMetaData setTopLevelPath(String topLevelPath) { + this.topLevelPath = topLevelPath; + return this; + } + + public Boolean getIsHarmonized() { + return isHarmonized; + } + + public StudyMetaData setHarmonized(Boolean harmonized) { + isHarmonized = harmonized; + return this; + } + + public String getStudyFocus() { + return studyFocus; + } + + public StudyMetaData setStudyFocus(String studyFocus) { + this.studyFocus = studyFocus; + return this; + } + + public String getStudyDesign() { + return studyDesign; + } + + public StudyMetaData setStudyDesign(String studyDesign) { + this.studyDesign = studyDesign; + return this; + } + + public String getAuthZ() { + return authZ; + } + + public StudyMetaData setAuthZ(String authZ) { + this.authZ = authZ; + return this; + } + + public String getAdditionalInformation() { + return additionalInformation; + } + + public StudyMetaData setAdditionalInformation(String additionalInformation) { + this.additionalInformation = additionalInformation; + return this; + } + + @Override + public String toString() { + return new ToStringBuilder(this).append("studyIdentifier", studyIdentifier).append("studyType", studyType) + .append("abbreviatedName", abbreviatedName).append("fullStudyName", fullStudyName).append("consentGroupCode", consentGroupCode) + .append("consentGroupNameAbv", consentGroupNameAbv).append("consentGroupName", consentGroupName) + .append("requestAccess", requestAccess).append("dataType", dataType).append("clinicalVariableCount", clinicalVariableCount) + .append("geneticSampleSize", geneticSampleSize).append("clinicalSampleSize", clinicalSampleSize) + .append("rawClinicalVariableCount", rawClinicalVariableCount).append("rawGeneticSampleSize", rawGeneticSampleSize) + .append("rawClinicalSampleSize", rawClinicalSampleSize).append("studyVersion", studyVersion).append("studyPhase", studyPhase) + .append("topLevelPath", topLevelPath).append("isHarmonized", isHarmonized).append("studyFocus", studyFocus) + .append("studyDesign", studyDesign).append("authZ", authZ).append("additionalInformation", additionalInformation).toString(); + } + + @Override + public boolean equals(Object o) { + if (o == null || getClass() != o.getClass()) return false; + StudyMetaData that = (StudyMetaData) o; + return clinicalVariableCount == that.clinicalVariableCount && geneticSampleSize == that.geneticSampleSize + && clinicalSampleSize == that.clinicalSampleSize && rawClinicalVariableCount == that.rawClinicalVariableCount + && rawGeneticSampleSize == that.rawGeneticSampleSize && rawClinicalSampleSize == that.rawClinicalSampleSize + && Objects.equals(studyIdentifier, that.studyIdentifier) && Objects.equals(studyType, that.studyType) + && Objects.equals(abbreviatedName, that.abbreviatedName) && Objects.equals(fullStudyName, that.fullStudyName) + && Objects.equals(consentGroupCode, that.consentGroupCode) && Objects.equals(consentGroupNameAbv, that.consentGroupNameAbv) + && Objects.equals(consentGroupName, that.consentGroupName) && Objects.equals(requestAccess, that.requestAccess) + && Objects.equals(dataType, that.dataType) && Objects.equals(studyVersion, that.studyVersion) + && Objects.equals(studyPhase, that.studyPhase) && Objects.equals(topLevelPath, that.topLevelPath) + && Objects.equals(isHarmonized, that.isHarmonized) && Objects.equals(studyFocus, that.studyFocus) + && Objects.equals(studyDesign, that.studyDesign) && Objects.equals(authZ, that.authZ) + && Objects.equals(additionalInformation, that.additionalInformation); + } + + @Override + public int hashCode() { + return Objects.hash( + studyIdentifier, studyType, abbreviatedName, fullStudyName, consentGroupCode, consentGroupNameAbv, consentGroupName, + requestAccess, dataType, clinicalVariableCount, geneticSampleSize, clinicalSampleSize, rawClinicalVariableCount, + rawGeneticSampleSize, rawClinicalSampleSize, studyVersion, studyPhase, topLevelPath, isHarmonized, studyFocus, studyDesign, + authZ, additionalInformation + ); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/ras/Ga4ghPassportV1.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/ras/Ga4ghPassportV1.java new file mode 100644 index 000000000..741fff86b --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/ras/Ga4ghPassportV1.java @@ -0,0 +1,121 @@ +package edu.harvard.hms.dbmi.avillach.auth.model.ras; + +import com.fasterxml.jackson.annotation.JsonProperty; + +import java.util.ArrayList; +import java.util.List; + +/** + * The Ga4ghPassportV1 class is a model for the GA4GH Passport V1 object. + * passport-claim + * + *

    + * Description + *
    + * The GA4GH Passport V1 object is a JSON Web Token (JWT) that contains information about a user's identity, the signing entity (ga4ghVisaV1), and + * the permissions they have been granted (RasDbgapPermissions). + *

    + */ +public class Ga4ghPassportV1 { + + private String iss; + private String sub; + private long iat; + private long exp; + private String scope; + private String jti; + private String txn; + + @JsonProperty("ga4gh_visa_v1") + private Ga4ghVisaV1 ga4ghVisaV1; + + @JsonProperty("ras_dbgap_permissions") + private List rasDbgapPermissions = new ArrayList<>(); + + public String getIss() { + return iss; + } + + public void setIss(String iss) { + this.iss = iss; + } + + public String getSub() { + return sub; + } + + public void setSub(String sub) { + this.sub = sub; + } + + public long getIat() { + return iat; + } + + public void setIat(long iat) { + this.iat = iat; + } + + public long getExp() { + return exp; + } + + public void setExp(long exp) { + this.exp = exp; + } + + public String getScope() { + return scope; + } + + public void setScope(String scope) { + this.scope = scope; + } + + public String getJti() { + return jti; + } + + public void setJti(String jti) { + this.jti = jti; + } + + public String getTxn() { + return txn; + } + + public void setTxn(String txn) { + this.txn = txn; + } + + public Ga4ghVisaV1 getGa4ghVisaV1() { + return ga4ghVisaV1; + } + + public void setGa4ghVisaV1(Ga4ghVisaV1 ga4ghVisaV1) { + this.ga4ghVisaV1 = ga4ghVisaV1; + } + + public List getRasDbgagPermissions() { + return rasDbgapPermissions; + } + + public void setRasDbgapPermissions(List rasDbgapPermissions) { + this.rasDbgapPermissions = rasDbgapPermissions != null ? rasDbgapPermissions : new ArrayList<>(); + } + + @Override + public String toString() { + return "Ga4ghPassportV1{" + + "iss='" + iss + '\'' + + ", sub='" + sub + '\'' + + ", iat=" + iat + + ", exp=" + exp + + ", scope='" + scope + '\'' + + ", jti='" + jti + '\'' + + ", txn='" + txn + '\'' + + ", ga4ghVisaV1=" + ga4ghVisaV1 + + ", rasDbgapPermissions=" + rasDbgapPermissions + + '}'; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/ras/Ga4ghVisaV1.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/ras/Ga4ghVisaV1.java new file mode 100644 index 000000000..1bb6534c8 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/ras/Ga4ghVisaV1.java @@ -0,0 +1,54 @@ +package edu.harvard.hms.dbmi.avillach.auth.model.ras; + +/** + * The Ga4ghVisaV1 class is a model for the GA4GH Visa V1 object. + * ga4gh_passport_v1.md#visa-claim + */ +public class Ga4ghVisaV1 { + + private String type; + private long asserted; + private String value; + private String source; + private String by; + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } + + public long getAsserted() { + return asserted; + } + + public void setAsserted(long asserted) { + this.asserted = asserted; + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } + + public String getSource() { + return source; + } + + public void setSource(String source) { + this.source = source; + } + + public String getBy() { + return by; + } + + public void setBy(String by) { + this.by = by; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/ras/Passport.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/ras/Passport.java new file mode 100644 index 000000000..5f31963db --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/ras/Passport.java @@ -0,0 +1,100 @@ +package edu.harvard.hms.dbmi.avillach.auth.model.ras; + +import com.fasterxml.jackson.annotation.JsonProperty; + +import java.util.List; + +/** + * The RAS Passport JWT as defined by RAS in their developer documentation. + * Contains a list of claims about the user and the user's identity and a list of GA4Gh Passports as defined in the GA4GH standard. + */ +public class Passport { + + private String sub; + private String jti; + private String scope; + private String txn; + private String iss; + private long iat; + private long exp; + + @JsonProperty("ga4gh_passport_v1") + private List ga4ghPassportV1; + + public String getSub() { + return sub; + } + + public void setSub(String sub) { + this.sub = sub; + } + + public String getJti() { + return jti; + } + + public void setJti(String jti) { + this.jti = jti; + } + + public String getScope() { + return scope; + } + + public void setScope(String scope) { + this.scope = scope; + } + + public String getTxn() { + return txn; + } + + public void setTxn(String txn) { + this.txn = txn; + } + + public String getIss() { + return iss; + } + + public void setIss(String iss) { + this.iss = iss; + } + + public long getIat() { + return iat; + } + + public void setIat(long iat) { + this.iat = iat; + } + + public long getExp() { + return exp; + } + + public void setExp(long exp) { + this.exp = exp; + } + + public List getGa4ghPassportV1() { + return ga4ghPassportV1; + } + + public void setGa4ghPassportV1(List ga4ghPassportV1) { + this.ga4ghPassportV1 = ga4ghPassportV1; + } + + @Override + public String toString() { + return "Passport{" + + "exp=" + exp + + ", iat=" + iat + + ", iss='" + iss + '\'' + + ", txn='" + txn + '\'' + + ", scope='" + scope + '\'' + + ", jti='" + jti + '\'' + + ", sub='" + sub + '\'' + + '}'; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/ras/RasDbgapPermission.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/ras/RasDbgapPermission.java new file mode 100644 index 000000000..8e97beba5 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/ras/RasDbgapPermission.java @@ -0,0 +1,109 @@ +package edu.harvard.hms.dbmi.avillach.auth.model.ras; + +import com.fasterxml.jackson.annotation.JsonProperty; + +import java.util.Objects; + +/** + * The RasDbgapPermission class is a model for the RAS dbGaP Permission object. An example of this object is: This is not a real study, but + * an example of what the object looks like. 
     { "consent_name": "Unrestricted", "phs_id": "phs000123", "version": "v1",
+ * "participant_set": "p1", "consent_group": "c1", "role": "pi", "expiration": 1234567890 }
    + */ +public class RasDbgapPermission { + + @JsonProperty("consent_name") + private String consentName; + @JsonProperty("phs_id") + private String phsId; + private String version; + @JsonProperty("participant_set") + private String participantSet; + @JsonProperty("consent_group") + private String consentGroup; + private String role; + private long expiration; + + public String getConsentName() { + return consentName; + } + + public RasDbgapPermission setConsentName(String consentName) { + this.consentName = consentName; + return this; + } + + public String getPhsId() { + return phsId; + } + + public RasDbgapPermission setPhsId(String phsId) { + this.phsId = phsId; + return this; + } + + public String getVersion() { + return version; + } + + public RasDbgapPermission setVersion(String version) { + this.version = version; + return this; + } + + public String getParticipantSet() { + return participantSet; + } + + public RasDbgapPermission setParticipantSet(String participantSet) { + this.participantSet = participantSet; + return this; + } + + public String getConsentGroup() { + return consentGroup; + } + + public RasDbgapPermission setConsentGroup(String consentGroup) { + this.consentGroup = consentGroup; + return this; + } + + public String getRole() { + return role; + } + + public RasDbgapPermission setRole(String role) { + this.role = role; + return this; + } + + public long getExpiration() { + return expiration; + } + + public RasDbgapPermission setExpiration(long expiration) { + this.expiration = expiration; + return this; + } + + @Override + public String toString() { + return "RasDbgapPermission{" + "consentName='" + consentName + '\'' + ", phsId='" + phsId + '\'' + ", version='" + version + '\'' + + ", participantSet='" + participantSet + '\'' + ", consentGroup='" + consentGroup + '\'' + ", role='" + role + '\'' + + ", expiration=" + expiration + '}'; + } + + @Override + public boolean equals(Object o) { + if (o == null || getClass() != o.getClass()) return false; + RasDbgapPermission that = (RasDbgapPermission) o; + return expiration == that.expiration && Objects.equals(consentName, that.consentName) && Objects.equals(phsId, that.phsId) + && Objects.equals(version, that.version) && Objects.equals(participantSet, that.participantSet) + && Objects.equals(consentGroup, that.consentGroup) && Objects.equals(role, that.role); + } + + @Override + public int hashCode() { + return Objects.hash(consentName, phsId, version, participantSet, consentGroup, role, expiration); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/response/PICSUREResponse.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/response/PICSUREResponse.java new file mode 100644 index 000000000..24202da09 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/response/PICSUREResponse.java @@ -0,0 +1,78 @@ +package edu.harvard.hms.dbmi.avillach.auth.model.response; + +import org.springframework.http.HttpStatus; +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import java.util.HashMap; +import java.util.Map; + +public class PICSUREResponse { + + private static final MediaType DEFAULT_MEDIA_TYPE = MediaType.APPLICATION_JSON; + private static final HttpStatus DEFAULT_RESPONSE_ERROR_CODE = HttpStatus.INTERNAL_SERVER_ERROR; + + public static ResponseEntity success() { + return new ResponseEntity<>(HttpStatus.OK); + } + + public static ResponseEntity success(T content) { + return ResponseEntity.ok(content); + } + + public static ResponseEntity> success(String message, T content) { + PicSureResponseBody body = new PicSureResponseBody<>(message, content); + return new ResponseEntity<>(body, HttpStatus.OK); + } + + public static ResponseEntity error(T content) { + return error(DEFAULT_RESPONSE_ERROR_CODE, content); + } + + public static ResponseEntity> error(String message, T content) { + return error(DEFAULT_RESPONSE_ERROR_CODE, message, content); + } + + public static ResponseEntity error(HttpStatus status, T content) { + if (status == null) { + status = DEFAULT_RESPONSE_ERROR_CODE; + } + return new ResponseEntity<>(content, status); + } + + public static ResponseEntity> error(HttpStatus status, String message, T content) { + return new ResponseEntity<>(new PicSureResponseBody<>(message, content), status); + } + + public static ResponseEntity> applicationError(T content) { + return error(DEFAULT_RESPONSE_ERROR_CODE, "Application error", content); + } + + public static ResponseEntity> applicationError(String message, T content) { + return error(DEFAULT_RESPONSE_ERROR_CODE, message, content); + } + + public static ResponseEntity> riError(T content) { + return error(DEFAULT_RESPONSE_ERROR_CODE, "RI error", content); + } + + public static ResponseEntity> riError(String message, T content) { + return error(DEFAULT_RESPONSE_ERROR_CODE, message, content); + } + + public static ResponseEntity protocolError(T content) { + return error(HttpStatus.BAD_REQUEST, content); + } + + public static ResponseEntity> protocolError(String message, T content) { + return error(HttpStatus.BAD_REQUEST, message, content); + } + + public static ResponseEntity> unauthorizedError(T content) { + return error(HttpStatus.UNAUTHORIZED, "Unauthorized", content); + } + + public static ResponseEntity> unauthorizedError(String message, T content) { + return error(HttpStatus.UNAUTHORIZED, message, content); + } +} + diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/response/PicSureResponseBody.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/response/PicSureResponseBody.java new file mode 100644 index 000000000..a3b878215 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/response/PicSureResponseBody.java @@ -0,0 +1,4 @@ +package edu.harvard.hms.dbmi.avillach.auth.model.response; + +public record PicSureResponseBody(String message, T content) { +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/package-info.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/package-info.java new file mode 100644 index 000000000..36de4fcac --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/package-info.java @@ -0,0 +1,4 @@ +/** + * Provides all the basic configuration classes and acts as a container for the other packages. + */ +package edu.harvard.hms.dbmi.avillach.auth; \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/AccessRuleRepository.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/AccessRuleRepository.java new file mode 100644 index 000000000..a97dce8c3 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/AccessRuleRepository.java @@ -0,0 +1,28 @@ +package edu.harvard.hms.dbmi.avillach.auth.repository; + +import edu.harvard.hms.dbmi.avillach.auth.entity.AccessRule; +import org.springframework.data.jpa.repository.JpaRepository; +import org.springframework.data.jpa.repository.Query; +import org.springframework.data.repository.query.Param; +import org.springframework.stereotype.Repository; + +import java.util.List; +import java.util.Set; +import java.util.UUID; + +/** + *

    Provides operations for the AccessRule entity to interact with a database.

    + * + * @see AccessRule + */ +@Repository +public interface AccessRuleRepository extends JpaRepository { + + AccessRule findByName(String name); + + @Query("SELECT p.accessRules FROM privilege p WHERE p.uuid = :uuid") + Set findAccessRulesByPrivilegeId(@Param("uuid") UUID uuid); + + @Query("SELECT p.accessRules FROM privilege p WHERE p.uuid IN :privilegeIds") + List getAccessRulesByPrivilegeIds(@Param("privilegeIds") List privilegeIds); +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/ApplicationRepository.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/ApplicationRepository.java new file mode 100644 index 000000000..15fb729d7 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/ApplicationRepository.java @@ -0,0 +1,23 @@ +package edu.harvard.hms.dbmi.avillach.auth.repository; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Application; +import org.springframework.data.jpa.repository.JpaRepository; +import org.springframework.stereotype.Repository; + +import java.util.Optional; +import java.util.UUID; + +/** + *

    Provides operations for the Application entity to interact with a database.

    > + * + * @see Application + */ + +@Repository +public interface ApplicationRepository extends JpaRepository { + + Application findByName(String name); + + Optional findByUuid(UUID uuid); + +} \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/ConnectionRepository.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/ConnectionRepository.java new file mode 100644 index 000000000..93f6d0813 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/ConnectionRepository.java @@ -0,0 +1,24 @@ +package edu.harvard.hms.dbmi.avillach.auth.repository; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Connection; +import org.springframework.data.jpa.repository.JpaRepository; +import org.springframework.stereotype.Repository; + +import java.util.Optional; +import java.util.UUID; + +/** + *

    Provides operations for the Connection entity to interact with a database.

    + * + * @see Connection + */ +@Repository +public interface ConnectionRepository extends JpaRepository { + + Connection findByLabel(String label); + + Optional findById(String id); + + void deleteById(String id); + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/PrivilegeRepository.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/PrivilegeRepository.java new file mode 100644 index 000000000..4a1a2dcb2 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/PrivilegeRepository.java @@ -0,0 +1,25 @@ +package edu.harvard.hms.dbmi.avillach.auth.repository; + +import edu.harvard.hms.dbmi.avillach.auth.entity.AccessRule; +import edu.harvard.hms.dbmi.avillach.auth.entity.Privilege; +import jakarta.transaction.Transactional; +import org.springframework.data.jpa.repository.JpaRepository; +import org.springframework.data.jpa.repository.Modifying; +import org.springframework.data.jpa.repository.Query; +import org.springframework.data.repository.query.Param; +import org.springframework.stereotype.Repository; + +import java.util.Set; +import java.util.UUID; + +/** + *

    Provides operations for the Privilege entity to interact with a database.

    + * @see Privilege + */ + +@Repository +public interface PrivilegeRepository extends JpaRepository { + + Privilege findByName(String name); + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/RoleRepository.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/RoleRepository.java new file mode 100644 index 000000000..084ec1a00 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/RoleRepository.java @@ -0,0 +1,26 @@ +package edu.harvard.hms.dbmi.avillach.auth.repository; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Role; +import org.springframework.data.jpa.repository.JpaRepository; +import org.springframework.stereotype.Repository; + +import java.util.Set; +import java.util.UUID; + +/** + *

    Provides operations for the Role entity to interact with a database.

    + * @see Role + */ + +@Repository +public interface RoleRepository extends JpaRepository { + + Role findByName(String name); + + // find all user roles where uuid is in the list of uuids + Set findByUuidIn(Set uuids); + + Set findByNameIn(Set names); + + Set findByNameNotIn(Set names); +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/TermsOfServiceRepository.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/TermsOfServiceRepository.java new file mode 100644 index 000000000..47bc83161 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/TermsOfServiceRepository.java @@ -0,0 +1,23 @@ +package edu.harvard.hms.dbmi.avillach.auth.repository; + +import edu.harvard.hms.dbmi.avillach.auth.entity.TermsOfService; +import org.springframework.data.jpa.repository.JpaRepository; +import org.springframework.stereotype.Repository; + +import java.util.Optional; +import java.util.UUID; + +/** + *

    Provides operations for the TermsOfService entity to interact with a database.

    + * @see TermsOfService + */ +@Repository +public interface TermsOfServiceRepository extends JpaRepository { + + /** + *

    Find the latest TermsOfService by date updated.

    + * @return TermsOfService + */ + Optional findTopByOrderByDateUpdatedDesc(); + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/UserConsentsRepository.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/UserConsentsRepository.java new file mode 100644 index 000000000..85b0c3c52 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/UserConsentsRepository.java @@ -0,0 +1,18 @@ +package edu.harvard.hms.dbmi.avillach.auth.repository; + +import edu.harvard.hms.dbmi.avillach.auth.entity.UserConsents; +import org.springframework.data.jpa.repository.JpaRepository; +import org.springframework.data.jpa.repository.Query; +import org.springframework.data.repository.query.Param; +import org.springframework.stereotype.Repository; + +import java.util.UUID; + +@Repository +public interface UserConsentsRepository extends JpaRepository { + + @Query("SELECT uc FROM user_consents uc WHERE uc.userId = :userId") + UserConsents findByUserId(@Param("userId") UUID userId); + + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/UserMetadataMappingRepository.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/UserMetadataMappingRepository.java new file mode 100644 index 000000000..36a457d6d --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/UserMetadataMappingRepository.java @@ -0,0 +1,21 @@ +package edu.harvard.hms.dbmi.avillach.auth.repository; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Connection; +import edu.harvard.hms.dbmi.avillach.auth.entity.UserMetadataMapping; +import org.springframework.data.jpa.repository.JpaRepository; +import org.springframework.stereotype.Repository; + +import java.util.List; +import java.util.UUID; + +/** + *

    Provides operations for the UserMetadataMapping entity to interact with a database.

    + * @see UserMetadataMapping + */ + +@Repository +public interface UserMetadataMappingRepository extends JpaRepository { + + List findByConnection(Connection connection); + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/UserRepository.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/UserRepository.java new file mode 100644 index 000000000..585ef1ad0 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/UserRepository.java @@ -0,0 +1,51 @@ +package edu.harvard.hms.dbmi.avillach.auth.repository; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Connection; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import org.springframework.data.jpa.repository.EntityGraph; +import org.springframework.data.jpa.repository.JpaRepository; +import org.springframework.data.jpa.repository.Modifying; +import org.springframework.data.jpa.repository.Query; +import org.springframework.data.repository.PagingAndSortingRepository; +import org.springframework.data.repository.query.Param; +import org.springframework.stereotype.Repository; +import org.springframework.transaction.annotation.Transactional; + +import java.util.List; +import java.util.Optional; +import java.util.Set; +import java.util.UUID; + +/** + *

    Provides operations for the User entity to interact with a database.

    + * + * @see User + */ + +@Repository +public interface UserRepository extends JpaRepository { + + User findBySubject(String subject); + + User findBySubjectAndConnection(String subject, Connection connection); + + List findByConnectionAndMatched(Connection connection, boolean matched); + + /** + *

    Find a user by email.

    + * + * @param email the email to search for + * @return User + */ + User findByEmail(String email); + + Optional findByEmailAndConnectionId(String email, String id); + + Set findByPassportIsNotNull(); + + @Modifying + @Query(value = "DELETE FROM user_role where role_id in (:roleIDs)", nativeQuery = true) + @Transactional + void deleteUserRoles(@Param("roleIDs") List roleIDs); + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/package-info.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/package-info.java new file mode 100644 index 000000000..6ab62fffc --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/repository/package-info.java @@ -0,0 +1,4 @@ +/** + * Defines which entity objects should persist in the database. + */ +package edu.harvard.hms.dbmi.avillach.auth.repository; \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/AccessRuleController.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/AccessRuleController.java new file mode 100644 index 000000000..931f8054a --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/AccessRuleController.java @@ -0,0 +1,116 @@ +package edu.harvard.hms.dbmi.avillach.auth.rest; + +import edu.harvard.hms.dbmi.avillach.auth.entity.AccessRule; +import edu.harvard.hms.dbmi.avillach.auth.model.response.PICSUREResponse; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.AccessRuleService; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuditAttributes; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import io.swagger.v3.oas.annotations.*; +import io.swagger.v3.oas.annotations.tags.Tag; +import jakarta.annotation.security.RolesAllowed; +import jakarta.servlet.http.HttpServletRequest; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.*; + +import java.util.List; +import java.util.Map; +import java.util.Optional; + +import static edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming.AuthRoleNaming.ADMIN; +import static edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming.AuthRoleNaming.SUPER_ADMIN; + +/** + *

    Endpoint for service handling business logic for access rules.

    + *

    Note: Only users with the super admin role can access this endpoint.

    + *

    + * Path: /accessRule + */ +@Tag(name = "Access Rule Management") +@Controller +@RequestMapping(value = "/accessRule") +public class AccessRuleController { + + private final AccessRuleService accessRuleService; + + @Autowired + public AccessRuleController(AccessRuleService accessRuleService) { + this.accessRuleService = accessRuleService; + } + + @Operation(description = "GET information of one AccessRule with the UUID, requires ADMIN or SUPER_ADMIN role") + @AuditEvent(type = "OTHER", action = "access_rule.read") + @RolesAllowed({ADMIN, SUPER_ADMIN}) + @GetMapping(value = "/{accessRuleId}") + public ResponseEntity getAccessRuleById( + @Parameter(description = "The UUID of the accessRule to fetch information about") + @PathVariable("accessRuleId") String accessRuleId) { + Optional entityById = this.accessRuleService.getAccessRuleById(accessRuleId); + + if (entityById.isEmpty()) { + return PICSUREResponse.error("AccessRule not found", 404); + } + + return PICSUREResponse.success(entityById.get()); + } + + @Operation(description = "GET a list of existing AccessRules, requires ADMIN or SUPER_ADMIN role") + @AuditEvent(type = "OTHER", action = "access_rule.list") + @RolesAllowed({ADMIN, SUPER_ADMIN}) + @GetMapping("") + public ResponseEntity> getAccessRuleAll() { + List allAccessRules = this.accessRuleService.getAllAccessRules(); + return PICSUREResponse.success(allAccessRules); + } + + @Operation(description = "POST a list of AccessRules, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "access_rule.modify") + @RolesAllowed(SUPER_ADMIN) + @PostMapping(consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) + public ResponseEntity addAccessRule( + @Parameter(required = true, description = "A list of AccessRule in JSON format") + @RequestBody List accessRules, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "access_rule_count", String.valueOf(accessRules.size())); + accessRules = this.accessRuleService.addAccessRule(accessRules); + + if (accessRules.isEmpty()) { + return PICSUREResponse.protocolError("No access rules added", 400); + } + + return PICSUREResponse.success(accessRules); + } + + @Operation(description = "Update a list of AccessRules, will only update the fields listed, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "access_rule.modify") + @RolesAllowed(SUPER_ADMIN) + @PutMapping(consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) + public ResponseEntity> updateAccessRule( + @Parameter(required = true, description = "A list of AccessRule with fields to be updated in JSON format") + @RequestBody List accessRules, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "access_rule_count", String.valueOf(accessRules.size())); + accessRules = this.accessRuleService.updateAccessRules(accessRules); + return PICSUREResponse.success(accessRules); + } + + @Operation(description = "DELETE an AccessRule by Id only if the accessRule is not associated by others, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "access_rule.delete") + @RolesAllowed(SUPER_ADMIN) + @DeleteMapping(path = "/{accessRuleId}") + public ResponseEntity> removeById( + @Parameter(required = true, description = "A valid accessRule Id") + @PathVariable("accessRuleId") final String accessRuleId, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "access_rule_id", accessRuleId); + return PICSUREResponse.success(this.accessRuleService.removeAccessRuleById(accessRuleId)); + } + + @Operation(description = "GET all types listed for the rule in accessRule that could be used, requires SUPER_ADMIN role") + @AuditEvent(type = "OTHER", action = "access_rule.types") + @RolesAllowed(SUPER_ADMIN) + @GetMapping(path = "/allTypes", produces = MediaType.APPLICATION_JSON_VALUE, consumes = MediaType.APPLICATION_JSON_VALUE) + public ResponseEntity> getAllTypes() { + return PICSUREResponse.success(AccessRule.TypeNaming.getTypeNameMap()); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/ApplicationController.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/ApplicationController.java new file mode 100644 index 000000000..b9faeb0a8 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/ApplicationController.java @@ -0,0 +1,115 @@ +package edu.harvard.hms.dbmi.avillach.auth.rest; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Application; +import edu.harvard.hms.dbmi.avillach.auth.model.response.PICSUREResponse; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.ApplicationService; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuditAttributes; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import io.swagger.v3.oas.annotations.Operation; +import io.swagger.v3.oas.annotations.Parameter; +import io.swagger.v3.oas.annotations.tags.Tag; +import jakarta.annotation.security.RolesAllowed; +import jakarta.servlet.http.HttpServletRequest; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.*; + +import java.util.List; +import java.util.Map; +import java.util.Optional; + +import static edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming.AuthRoleNaming.SUPER_ADMIN; + +/** + *

    Endpoint for registering and administering applications. + *
    + * Note: Only users with the super admin role can access this endpoint.

    + */ +@Tag(name = "Application Management") +@Controller +@RequestMapping(value = "/application") +public class ApplicationController { + + private final ApplicationService applicationService; + + @Autowired + public ApplicationController(ApplicationService applicationService) { + this.applicationService = applicationService; + } + + @Operation(description = "GET information of one Application with the UUID, no role restrictions") + @AuditEvent(type = "OTHER", action = "application.read") + @GetMapping(value = "/{applicationId}") + public ResponseEntity getApplicationById( + @Parameter(required = true, description = "The UUID of the application to fetch information about") + @PathVariable("applicationId") String applicationId) { + Optional entityById = applicationService.getApplicationByID(applicationId); + + if (entityById.isEmpty()) { + return PICSUREResponse.protocolError("Application is not found by given Application ID: " + applicationId); + } + + return PICSUREResponse.success(entityById.get()); + } + + @Operation(description = "GET a list of existing Applications, no role restrictions") + @AuditEvent(type = "OTHER", action = "application.list") + @GetMapping + public ResponseEntity> getApplicationAll() { + return PICSUREResponse.success(applicationService.getAllApplications()); + } + + @Operation(description = "POST a list of Applications, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "application.modify") + @RolesAllowed({SUPER_ADMIN}) + @PostMapping(consumes = "application/json", produces = "application/json") + public ResponseEntity> addApplication( + @Parameter(required = true, description = "A list of AccessRule in JSON format") + @RequestBody List applications, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "app_count", String.valueOf(applications.size())); + applications = applicationService.addNewApplications(applications); + return PICSUREResponse.success(applications); + } + + @Operation(description = "Update a list of Applications, will only update the fields listed, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "application.modify") + @RolesAllowed({SUPER_ADMIN}) + @PutMapping(consumes = "application/json", produces = "application/json") + public ResponseEntity> updateApplication( + @Parameter(required = true, description = "A list of AccessRule with fields to be updated in JSON format") + @RequestBody List applications, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "app_count", String.valueOf(applications.size())); + applications = applicationService.updateApplications(applications); + return PICSUREResponse.success(applications); + } + + @Operation(description = "Refresh a token of an application by application Id, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "application.token_refresh") + @RolesAllowed({SUPER_ADMIN}) + @GetMapping(value = "/refreshToken/{applicationId}") + public ResponseEntity> refreshApplicationToken( + @Parameter(required = true, description = "A valid application Id") + @PathVariable("applicationId") String applicationId, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "app_id", applicationId); + String newApplicationToken = applicationService.refreshApplicationToken(applicationId); + return PICSUREResponse.success(Map.of("token", newApplicationToken)); + } + + @Operation(description = "DELETE an Application by Id only if the application is not associated by others, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "application.delete") + @RolesAllowed({SUPER_ADMIN}) + @DeleteMapping(value = "/{applicationId}") + public ResponseEntity removeById( + @Parameter(required = true, description = "A valid accessRule Id") + @PathVariable("applicationId") final String applicationId, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "app_id", applicationId); + try { + List applications = applicationService.deleteApplicationById(applicationId); + return PICSUREResponse.success(applications); + } catch (IllegalArgumentException e) { + return PICSUREResponse.protocolError(e.getMessage()); + } + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/AuthenticationController.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/AuthenticationController.java new file mode 100644 index 000000000..83b4de59b --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/AuthenticationController.java @@ -0,0 +1,97 @@ +package edu.harvard.hms.dbmi.avillach.auth.rest; + +import edu.harvard.hms.dbmi.avillach.auth.model.response.PICSUREResponse; +import edu.harvard.hms.dbmi.avillach.auth.service.AuthenticationService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.SessionService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.authentication.AuthenticationServiceRegistry; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuditAttributes; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import io.swagger.v3.oas.annotations.Operation; +import io.swagger.v3.oas.annotations.Parameter; +import io.swagger.v3.oas.annotations.tags.Tag; +import jakarta.servlet.http.HttpServletRequest; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.util.CollectionUtils; +import org.springframework.web.bind.annotation.PathVariable; +import org.springframework.web.bind.annotation.PostMapping; +import org.springframework.web.bind.annotation.RequestBody; +import org.springframework.web.bind.annotation.RequestMapping; + +import java.io.IOException; +import java.util.HashMap; +import java.util.Map; + + +/** + *

    The authentication endpoint for PSAMA.

    + */ +@Tag(name = "Authentication") +@Controller +@RequestMapping("/") +public class AuthenticationController { + + private final static Logger logger = LoggerFactory.getLogger(AuthenticationController.class.getName()); + + private final AuthenticationServiceRegistry authenticationServiceRegistry; + private final SessionService sessionService; + + @Autowired + public AuthenticationController(AuthenticationServiceRegistry authenticationServiceRegistry, SessionService sessionService) { + this.authenticationServiceRegistry = authenticationServiceRegistry; + this.sessionService = sessionService; + } + + @Operation(description = "The authentication endpoint for retrieving a valid user token") + @AuditEvent(type = "AUTH", action = "auth.login") + @PostMapping(path = "/authentication/{idpProvider}", consumes = "application/json", produces = "application/json") + public ResponseEntity authentication( + @PathVariable("idpProvider") String idpProvider, + @Parameter(required = true, description = "A json object that includes all Oauth authentication needs, for example, access_token and redirectURI") + @RequestBody Map authRequest, HttpServletRequest request) throws IOException { + logger.debug("authentication() starting..."); + logger.debug("authentication() requestHost: {}", request.getServerName()); + + AuditAttributes.putMetadata(request, "idp", idpProvider); + + if (authRequest == null) { + logger.error("authentication() authRequest is null"); + AuditAttributes.putMetadata(request, "login_result", "failure"); + AuditAttributes.putMetadata(request, "reason", "null_request"); + return ResponseEntity.badRequest().body("authRequest is null"); + } + + AuthenticationService authenticationService = authenticationServiceRegistry.getAuthenticationService(idpProvider); + if (authenticationService == null) { + logger.error("authentication() authenticationService is null"); + AuditAttributes.putMetadata(request, "login_result", "failure"); + AuditAttributes.putMetadata(request, "reason", "unknown_idp"); + return ResponseEntity.badRequest().body("authenticationService is null"); + } + + HashMap authenticate = authenticationService.authenticate(authRequest, request.getServerName()); + if (!CollectionUtils.isEmpty(authenticate)) { + if (authenticate.containsKey("userId")) { + sessionService.startSession(authenticate.get("userId")); + } else { + logger.error("authentication() userId authentication is null"); + logger.error("User claims must contain a userId to start their session."); + AuditAttributes.putMetadata(request, "login_result", "failure"); + AuditAttributes.putMetadata(request, "reason", "missing_user_id"); + return PICSUREResponse.unauthorizedError("User not authenticated."); + } + logger.info("authentication() User authenticated successfully."); + AuditAttributes.putMetadata(request, "login_result", "success"); + AuditAttributes.putMetadata(request, "user_id", authenticate.get("userId")); + return PICSUREResponse.success(authenticate); + } + + logger.error("authentication() User not authenticated."); + AuditAttributes.putMetadata(request, "login_result", "failure"); + AuditAttributes.putMetadata(request, "reason", "authentication_failed"); + return PICSUREResponse.unauthorizedError("User not authenticated."); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/CacheController.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/CacheController.java new file mode 100644 index 000000000..b028e721c --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/CacheController.java @@ -0,0 +1,45 @@ +package edu.harvard.hms.dbmi.avillach.auth.rest; + +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression; +import org.springframework.cache.Cache; +import org.springframework.cache.CacheManager; +import org.springframework.web.bind.annotation.GetMapping; +import org.springframework.web.bind.annotation.PathVariable; +import org.springframework.web.bind.annotation.RequestMapping; +import org.springframework.web.bind.annotation.RestController; + +import java.util.Collection; + +@RestController +@ConditionalOnExpression("${app.cache.inspect.enabled:false}") +@RequestMapping("/cache") +public class CacheController { + + private final CacheManager cacheManager; + + @Autowired + public CacheController(CacheManager cacheManager) { + this.cacheManager = cacheManager; + } + + @AuditEvent(type = "OTHER", action = "cache.list") + @GetMapping + public Collection getCacheNames() { + return cacheManager.getCacheNames(); + } + + @AuditEvent(type = "OTHER", action = "cache.read") + @GetMapping("/{cacheName}") + public Object getCache(@PathVariable("cacheName") String cacheName) { + Cache cache = cacheManager.getCache(cacheName); + if (cache == null) { + throw new IllegalArgumentException("Cache not found: " + cacheName); + } + + return cache.getNativeCache(); + } + + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/ConnectionWebController.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/ConnectionWebController.java new file mode 100644 index 000000000..ceae75d7d --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/ConnectionWebController.java @@ -0,0 +1,106 @@ +package edu.harvard.hms.dbmi.avillach.auth.rest; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Connection; +import edu.harvard.hms.dbmi.avillach.auth.model.response.PICSUREResponse; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.ConnectionWebService; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuditAttributes; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import io.swagger.v3.oas.annotations.Operation; +import io.swagger.v3.oas.annotations.Parameter; +import io.swagger.v3.oas.annotations.tags.Tag; +import jakarta.annotation.security.RolesAllowed; +import jakarta.servlet.http.HttpServletRequest; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.*; + +import java.util.List; + +import static edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming.AuthRoleNaming.ADMIN; +import static edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming.AuthRoleNaming.SUPER_ADMIN; + +/** + *

    Endpoint for service handling business logic for connections to PSAMA.
    + * Note: Only users with the super admin role can access this endpoint.

    + */ +@Tag(name = "Connection Management") +@Controller +@RequestMapping("/connection") +public class ConnectionWebController { + + + private final ConnectionWebService connectionWebService; + + @Autowired + public ConnectionWebController(ConnectionWebService connectionWebSerivce) { + this.connectionWebService = connectionWebSerivce; + } + + @Operation(description = "GET information of one Connection with the UUID, requires ADMIN or SUPER_ADMIN role") + @AuditEvent(type = "OTHER", action = "connection.read") + @GetMapping(path = "/{connectionId}", produces = "application/json") + @RolesAllowed({SUPER_ADMIN, ADMIN}) + public ResponseEntity getConnectionById( + @Parameter(required = true, description = "The UUID of the Connection to fetch information about") + @PathVariable("connectionId") String connectionId) { + try { + Connection connectionById = connectionWebService.getConnectionById(connectionId); + return ResponseEntity.ok(connectionById); + } catch (IllegalArgumentException e) { + return PICSUREResponse.protocolError(e.getMessage()); + } + } + + @Operation(description = "GET a list of existing Connection, requires SUPER_ADMIN or ADMIN role") + @AuditEvent(type = "OTHER", action = "connection.list") + @GetMapping + @RolesAllowed({SUPER_ADMIN, ADMIN}) + public ResponseEntity> getAllConnections() { + List allConnections = connectionWebService.getAllConnections(); + return ResponseEntity.ok(allConnections); + } + + @Operation(description = "POST a list of Connections, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "connection.modify") + @RolesAllowed({SUPER_ADMIN}) + @PostMapping(produces = "application/json", consumes = "application/json") + public ResponseEntity addConnection( + @Parameter(required = true, description = "A list of Connections in JSON format") + @RequestBody List connections, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "connection_count", String.valueOf(connections.size())); + try { + connections = connectionWebService.addConnection(connections); + } catch (IllegalArgumentException e) { + return PICSUREResponse.protocolError(e.getMessage()); + } + + return PICSUREResponse.success("All connections are added.", connections); + } + + @Operation(description = "Update a list of Connections, will only update the fields listed, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "connection.modify") + @RolesAllowed({SUPER_ADMIN}) + @PutMapping(produces = "application/json", consumes = "application/json") + public ResponseEntity> updateConnection( + @Parameter(required = true, description = "A list of Connection with fields to be updated in JSON format") + @RequestBody List connections, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "connection_count", String.valueOf(connections.size())); + List responseEntity = connectionWebService.updateConnections(connections); + return ResponseEntity.ok(responseEntity); + } + + @Operation(description = "DELETE an Connection by Id only if the Connection is not associated by others, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "connection.delete") + @RolesAllowed({SUPER_ADMIN}) + @DeleteMapping(path = "/{connectionId}", produces = "application/json") + public ResponseEntity> removeById( + @Parameter(required = true, description = "A valid connection Id") + @PathVariable("connectionId") final String connectionId, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "connection_id", connectionId); + List connections = connectionWebService.removeConnectionById(connectionId); + return ResponseEntity.ok(connections); + } + + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/OpenAccessController.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/OpenAccessController.java new file mode 100644 index 000000000..237485d77 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/OpenAccessController.java @@ -0,0 +1,60 @@ +package edu.harvard.hms.dbmi.avillach.auth.rest; + +import edu.harvard.hms.dbmi.avillach.auth.service.impl.authorization.AuthorizationService; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuditAttributes; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import io.swagger.v3.oas.annotations.Parameter; +import jakarta.servlet.http.HttpServletRequest; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.RequestBody; +import org.springframework.web.bind.annotation.RequestMapping; + +import java.util.Map; + +@Controller +@RequestMapping(value = "/open") +public class OpenAccessController { + + private final AuthorizationService authorizationService; + private final boolean openIdpProviderIsEnabled; + + @Autowired + public OpenAccessController(AuthorizationService authorizationService, @Value("${open.idp.provider.is.enabled}") boolean openIdpProviderIsEnabled) { + this.authorizationService = authorizationService; + this.openIdpProviderIsEnabled = openIdpProviderIsEnabled; + } + + @AuditEvent(type = "ACCESS", action = "open.validate") + @RequestMapping(value = "/validate", produces = "application/json") + public ResponseEntity validate(@Parameter(required = true, description = "A JSON object that at least" + + " include a user the token for validation") + @RequestBody Map inputMap, HttpServletRequest request) { + if (!openIdpProviderIsEnabled) { + return ResponseEntity.ok(false); + } + + boolean isValid = authorizationService.openAccessRequestIsValid(inputMap); + AuditAttributes.putMetadata(request, "validation_result", String.valueOf(isValid)); + + Object requestObj = inputMap.get("request"); + if (requestObj instanceof Map requestDetails) { + Object targetService = requestDetails.get("Target Service"); + if (targetService != null) { + AuditAttributes.putMetadata(request, "target_service", targetService.toString()); + } + Object query = requestDetails.get("query"); + if (query instanceof Map queryMap) { + Object resourceUUID = queryMap.get("resourceUUID"); + if (resourceUUID != null) { + AuditAttributes.putMetadata(request, "resource_id", resourceUUID.toString()); + } + } + } + + return ResponseEntity.ok(isValid); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/PrivilegeController.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/PrivilegeController.java new file mode 100644 index 000000000..a320d9142 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/PrivilegeController.java @@ -0,0 +1,99 @@ +package edu.harvard.hms.dbmi.avillach.auth.rest; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Privilege; +import edu.harvard.hms.dbmi.avillach.auth.model.response.PICSUREResponse; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.PrivilegeService; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuditAttributes; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import io.swagger.v3.oas.annotations.tags.Tag; +import io.swagger.v3.oas.annotations.Operation; +import io.swagger.v3.oas.annotations.Parameter; +import jakarta.annotation.security.RolesAllowed; +import jakarta.servlet.http.HttpServletRequest; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.ResponseEntity; +import org.springframework.web.bind.annotation.*; + +import java.util.List; + +import static edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming.AuthRoleNaming.ADMIN; +import static edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming.AuthRoleNaming.SUPER_ADMIN; + +/** + *

    Endpoint for service handling business logic for privileges. + *
    Note: Only users with the super admin role can access this endpoint.

    + */ +@Tag(name = "Privilege Management") +@RestController +@RequestMapping("/privilege") +public class PrivilegeController { + + private final PrivilegeService privilegeService; + + @Autowired + public PrivilegeController(PrivilegeService privilegeService) { + this.privilegeService = privilegeService; + } + + @Operation(description = "GET information of one Privilege with the UUID, requires ADMIN or SUPER_ADMIN role") + @AuditEvent(type = "OTHER", action = "privilege.read") + @RolesAllowed({ADMIN, SUPER_ADMIN}) + @GetMapping(path = "/{privilegeId}", produces = "application/json") + public ResponseEntity getPrivilegeById( + @Parameter(description="The UUID of the privilege to fetch information about") + @PathVariable("privilegeId") String privilegeId) { + Privilege privilegeById = this.privilegeService.getPrivilegeById(privilegeId); + + if (privilegeById == null) { + return PICSUREResponse.protocolError("Privilege not found"); + } + + return PICSUREResponse.success(privilegeById); + } + + @Operation(description = "GET a list of existing privileges, requires ADMIN or SUPER_ADMIN role") + @AuditEvent(type = "OTHER", action = "privilege.list") + @RolesAllowed({ADMIN, SUPER_ADMIN}) + @GetMapping(produces = "application/json") + public ResponseEntity> getPrivilegeAll() { + List privilegesAll = this.privilegeService.getPrivilegesAll(); + return PICSUREResponse.success(privilegesAll); + } + + @Operation(description = "POST a list of privileges, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "privilege.modify") + @RolesAllowed({SUPER_ADMIN}) + @PostMapping(consumes = "application/json", produces = "application/json") + public ResponseEntity> addPrivilege( + @Parameter(required = true, description = "A list of privileges in JSON format") + @RequestBody List privileges, HttpServletRequest request){ + AuditAttributes.putMetadata(request, "privilege_count", String.valueOf(privileges.size())); + privileges = this.privilegeService.addPrivileges(privileges); + return PICSUREResponse.success(privileges); + } + + @Operation(description = "Update a list of privileges, will only update the fields listed, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "privilege.modify") + @RolesAllowed({SUPER_ADMIN}) + @PutMapping(consumes = "application/json", produces = "application/json") + public ResponseEntity> updatePrivilege( + @Parameter(required = true, description = "A list of privilege with fields to be updated in JSON format") + @RequestBody List privileges, HttpServletRequest request){ + AuditAttributes.putMetadata(request, "privilege_count", String.valueOf(privileges.size())); + privileges = this.privilegeService.updatePrivileges(privileges); + return ResponseEntity.ok(privileges); + } + + @Operation(description = "DELETE an privilege by Id only if the privilege is not associated by others, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "privilege.delete") + @RolesAllowed({SUPER_ADMIN}) + @DeleteMapping(path = "/{privilegeId}", produces = "application/json") + public ResponseEntity> removeById( + @Parameter(required = true, description = "A valid privilege Id") + @PathVariable("privilegeId") final String privilegeId, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "privilege_id", privilegeId); + List privileges = this.privilegeService.deletePrivilegeByPrivilegeId(privilegeId); + return ResponseEntity.ok(privileges); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/RoleController.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/RoleController.java new file mode 100644 index 000000000..e1def559c --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/RoleController.java @@ -0,0 +1,109 @@ +package edu.harvard.hms.dbmi.avillach.auth.rest; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Role; +import edu.harvard.hms.dbmi.avillach.auth.model.response.PICSUREResponse; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.RoleService; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuditAttributes; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import io.swagger.v3.oas.annotations.Operation; +import io.swagger.v3.oas.annotations.Parameter; +import io.swagger.v3.oas.annotations.tags.Tag; +import jakarta.annotation.security.RolesAllowed; +import jakarta.servlet.http.HttpServletRequest; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.*; + +import java.text.MessageFormat; +import java.util.List; +import java.util.Optional; + +import static edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming.AuthRoleNaming.ADMIN; +import static edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming.AuthRoleNaming.SUPER_ADMIN; + +/** + *

    Endpoint for service handling business logic for user roles. + *
    Note: Users with admin level access can view roles, but only super admin users can modify them.

    + */ +@Tag(name = "Role Management") +@Controller +@RequestMapping("/role") +public class RoleController { + + private final RoleService roleService; + + @Autowired + public RoleController(RoleService roleService) { + this.roleService = roleService; + } + + @Operation(description = "GET information of one Role with the UUID, requires ADMIN or SUPER_ADMIN role") + @AuditEvent(type = "OTHER", action = "role.read") + @RolesAllowed({ADMIN, SUPER_ADMIN}) + @GetMapping(produces = "application/json", path = "/{roleId}") + public ResponseEntity getRoleById( + @Parameter(description = "The UUID of the Role to fetch information about") + @PathVariable("roleId") String roleId) { + Optional optionalRole = this.roleService.getRoleById(roleId); + if (optionalRole.isEmpty()) { + return PICSUREResponse.protocolError("Role is not found by given role ID: " + roleId); + } + return PICSUREResponse.success(optionalRole.get()); + } + + @Operation(description = "GET a list of existing Roles, requires ADMIN or SUPER_ADMIN role") + @AuditEvent(type = "OTHER", action = "role.list") + @RolesAllowed({ADMIN, SUPER_ADMIN}) + @GetMapping + public ResponseEntity> getRoleAll() { + List allRoles = this.roleService.getAllRoles(); + return PICSUREResponse.success(allRoles); + } + + @Operation(description = "POST a list of Roles, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "role.modify") + @RolesAllowed({SUPER_ADMIN}) + @PostMapping(produces = "application/json") + public ResponseEntity addRole( + @Parameter(required = true, description = "A list of Roles in JSON format") + @RequestBody List roles, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "role_count", String.valueOf(roles.size())); + List savedRoles = this.roleService.addRoles(roles); + return PICSUREResponse.success("All roles are added.", savedRoles); + } + + @Operation(description = "Update a list of Roles, will only update the fields listed, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "role.modify") + @RolesAllowed({SUPER_ADMIN}) + @PutMapping(produces = "application/json") + public ResponseEntity updateRole( + @Parameter(required = true, description = "A list of Roles with fields to be updated in JSON format") + @RequestBody List roles, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "role_count", String.valueOf(roles.size())); + List updatedRoles = this.roleService.updateRoles(roles); + if (updatedRoles.isEmpty()) { + return PICSUREResponse.protocolError("No Role(s) has been updated."); + } + + return PICSUREResponse.success("All Roles are updated.", updatedRoles); + } + + @Operation(description = "DELETE an Role by Id only if the Role is not associated by others, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "role.delete") + @RolesAllowed({SUPER_ADMIN}) + @DeleteMapping(produces = "application/json", path = "/{roleId}") + public ResponseEntity removeById( + @Parameter(required = true, description = "A valid Role Id") + @PathVariable("roleId") final String roleId, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "role_id", roleId); + Optional> roles = this.roleService.removeRoleById(roleId); + if (roles.isEmpty()) { + return PICSUREResponse.protocolError("Role not found - uuid: " + roleId); + } + + return PICSUREResponse.success(MessageFormat.format("Successfully deleted role by id: {0}, listing rest of the role(s) as below", roleId), roles.get()); + } + + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/StudyAccessController.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/StudyAccessController.java new file mode 100644 index 000000000..16309dc72 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/StudyAccessController.java @@ -0,0 +1,54 @@ +package edu.harvard.hms.dbmi.avillach.auth.rest; + +import edu.harvard.hms.dbmi.avillach.auth.model.response.PICSUREResponse; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.StudyAccessService; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuditAttributes; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import io.swagger.v3.oas.annotations.Operation; +import io.swagger.v3.oas.annotations.Parameter; +import jakarta.annotation.security.RolesAllowed; +import jakarta.servlet.http.HttpServletRequest; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.transaction.annotation.Transactional; +import org.springframework.web.bind.annotation.PostMapping; +import org.springframework.web.bind.annotation.RequestBody; +import org.springframework.web.bind.annotation.RequestMapping; + + +import static edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming.AuthRoleNaming.ADMIN; +import static edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming.AuthRoleNaming.SUPER_ADMIN; + +/** + *

    Endpoint for service handling business logic for adding all the auth + * rules for a given study

    + *

    Note: Only users with the super admin role can access this endpoint.

    + */ +@Controller +@RequestMapping("/studyAccess") +public class StudyAccessController { + + private final StudyAccessService studyAccessService; + + @Autowired + public StudyAccessController(StudyAccessService studyAccessService) { + this.studyAccessService = studyAccessService; + } + + @Operation(description = "POST a single study and it creates the role, privs, and rules for it, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "study_access.create") + @Transactional + @RolesAllowed({SUPER_ADMIN, ADMIN}) + @PostMapping(consumes = "application/json") + public ResponseEntity addStudyAccess(@Parameter(description = "The Study Identifier of the new study from the metadata.json") + @RequestBody String studyIdentifier, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "study_identifier", studyIdentifier); + String status = studyAccessService.addStudyAccess(studyIdentifier); + if (status.contains("Error:")) { + return PICSUREResponse.error(status); + } else { + return PICSUREResponse.success(status); + } + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/TermsOfServiceController.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/TermsOfServiceController.java new file mode 100644 index 000000000..18d7efbbb --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/TermsOfServiceController.java @@ -0,0 +1,103 @@ +package edu.harvard.hms.dbmi.avillach.auth.rest; + +import edu.harvard.hms.dbmi.avillach.auth.entity.TermsOfService; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import edu.harvard.hms.dbmi.avillach.auth.model.CustomUserDetails; +import edu.harvard.hms.dbmi.avillach.auth.model.response.PICSUREResponse; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.TOSService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.UserService; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuditAttributes; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming; +import io.swagger.v3.oas.annotations.Operation; +import io.swagger.v3.oas.annotations.Parameter; +import io.swagger.v3.oas.annotations.tags.Tag; +import jakarta.annotation.security.RolesAllowed; +import jakarta.servlet.http.HttpServletRequest; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.ResponseEntity; +import org.springframework.security.core.context.SecurityContext; +import org.springframework.security.core.context.SecurityContextHolder; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.GetMapping; +import org.springframework.web.bind.annotation.PostMapping; +import org.springframework.web.bind.annotation.RequestMapping; +import org.springframework.web.bind.annotation.RequestBody; + +import java.util.List; +import java.util.Optional; + +import static edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming.AuthRoleNaming.SUPER_ADMIN; + +/** + *

    Endpoint for creating and updating terms of service entities. Records when a user accepts a term of service.

    + */ +@Tag(name = "Terms of Service Management") +@Controller +@RequestMapping("/tos") +public class TermsOfServiceController { + + private final Logger logger = LoggerFactory.getLogger(TermsOfServiceController.class); + private final TOSService tosService; + private final UserService userService; + + @Autowired + public TermsOfServiceController(TOSService tosService, UserService userService) { + this.tosService = tosService; + this.userService = userService; + } + + @Operation(description = "GET the latest Terms of Service") + @AuditEvent(type = "ACCESS", action = "tos.view") + @GetMapping(path = "/latest", produces = "text/html") + public ResponseEntity getLatestTermsOfService() { + logger.info("Getting latest Terms of Service"); + return PICSUREResponse.success(tosService.getLatest()); + } + + @Operation(description = "Update the Terms of Service html body") + @AuditEvent(type = "ADMIN", action = "tos.update") + @RolesAllowed({AuthNaming.AuthRoleNaming.ADMIN, SUPER_ADMIN}) + @PostMapping(path = "/update", consumes = "text/html", produces = "application/json") + public ResponseEntity updateTermsOfService(@RequestBody String html, HttpServletRequest request) { + SecurityContext context = SecurityContextHolder.getContext(); + CustomUserDetails customUserDetails = (CustomUserDetails) context.getAuthentication().getPrincipal(); + String userSubject = customUserDetails.getUser().getSubject(); + logger.info("User {} updating TOS", userSubject); + Optional termsOfService = tosService.updateTermsOfService(html); + if (termsOfService.isEmpty()) { + return PICSUREResponse.success(); + } + User user = tosService.acceptTermsOfService(userSubject); + userService.updateUser(List.of(user)); + AuditAttributes.putMetadata(request, "tos_updated", "true"); + return PICSUREResponse.success(termsOfService.get()); + } + + @Operation(description = "GET if current user has acceptted his TOS or not") + @AuditEvent(type = "ACCESS", action = "tos.view") + @GetMapping(produces = "text/plain") + public ResponseEntity hasUserAcceptedTOS() { + SecurityContext context = SecurityContextHolder.getContext(); + CustomUserDetails customUserDetails = (CustomUserDetails) context.getAuthentication().getPrincipal(); + String userSubject = customUserDetails.getUser().getSubject(); + logger.info("hasUserAcceptedTOS for user {}", userSubject); + return PICSUREResponse.success(tosService.hasUserAcceptedLatest(userSubject)); + } + + @Operation(description = "Endpoint for current user to accept his terms of service") + @AuditEvent(type = "ACCESS", action = "tos.accept") + @PostMapping(path = "/accept", produces = "application/json") + public ResponseEntity acceptTermsOfService(HttpServletRequest request) { + SecurityContext context = SecurityContextHolder.getContext(); + CustomUserDetails customUserDetails = (CustomUserDetails) context.getAuthentication().getPrincipal(); + String userSubject = customUserDetails.getUser().getSubject(); + User user = tosService.acceptTermsOfService(userSubject); + userService.updateUser(List.of(user)); + AuditAttributes.putMetadata(request, "tos_accepted", "true"); + return PICSUREResponse.success(); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/TokenController.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/TokenController.java new file mode 100644 index 000000000..d770a636f --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/TokenController.java @@ -0,0 +1,104 @@ +package edu.harvard.hms.dbmi.avillach.auth.rest; + +import edu.harvard.hms.dbmi.avillach.auth.model.InvalidRefreshToken; +import edu.harvard.hms.dbmi.avillach.auth.model.RefreshToken; +import edu.harvard.hms.dbmi.avillach.auth.model.ValidRefreshToken; +import edu.harvard.hms.dbmi.avillach.auth.model.response.PICSUREResponse; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.authorization.AuthorizationService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.TokenService; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuditAttributes; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import io.swagger.v3.oas.annotations.Operation; +import io.swagger.v3.oas.annotations.Parameter; +import io.swagger.v3.oas.annotations.tags.Tag; +import jakarta.servlet.http.HttpServletRequest; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.*; + +import java.util.Map; + +/** + *

    Token introspection endpoint called by an application to validate a user's token and permissions by request.

    + * + *

    Here, a registered application asks if the user behind a token is allowed to perform certain activities by showing this endpoint the + * token and where the user wants to go.

    To accomplish this, this endpoint validates the incoming token, then checks if the user + * behind the token is authorized to access the URLs they queried and send data along with them. The AuthorizationService class handles + * authorization {@link AuthorizationService} at the access rule level, but this endpoint handles token validation and pre-check at the + * privilege level.

    + */ +@Tag(name = "Token Management") +@Controller +@RequestMapping("/token") +public class TokenController { + + private final static Logger logger = LoggerFactory.getLogger(TokenController.class); + + private final TokenService tokenService; + + @Autowired + public TokenController(TokenService tokenService) { + this.tokenService = tokenService; + } + + @Operation(description = "Token introspection endpoint for user to retrieve a valid token") + @AuditEvent(type = "ACCESS", action = "token.introspect") + @PostMapping(path = "/inspect", produces = "application/json") + public ResponseEntity> inspectToken( + @Parameter(required = true, description = "A JSON object that at least" + + " include a user the token for validation") + @RequestBody Map inputMap, HttpServletRequest request) { + Map resultMap = this.tokenService.inspectToken(inputMap); + + boolean active = Boolean.TRUE.equals(resultMap.getOrDefault("active", false)); + AuditAttributes.putMetadata(request, "authz_result", active ? "granted" : "denied"); + AuditAttributes.putMetadata(request, "authz_user_sub", String.valueOf(resultMap.getOrDefault("sub", ""))); + if (resultMap.containsKey("message")) { + AuditAttributes.putMetadata(request, "authz_message", String.valueOf(resultMap.get("message"))); + } + if (resultMap.containsKey("tokenRefreshed")) { + AuditAttributes.putMetadata(request, "authz_token_refreshed", String.valueOf(resultMap.get("tokenRefreshed"))); + } + + Object requestObj = inputMap.get("request"); + if (requestObj instanceof Map requestDetails) { + Object targetService = requestDetails.get("Target Service"); + if (targetService != null) { + AuditAttributes.putMetadata(request, "target_service", targetService.toString()); + } + Object query = requestDetails.get("query"); + if (query instanceof Map queryMap) { + Object resourceUUID = queryMap.get("resourceUUID"); + if (resourceUUID != null) { + AuditAttributes.putMetadata(request, "resource_id", resourceUUID.toString()); + } + } + } + + return PICSUREResponse.success(resultMap); + } + + @Operation(description = "To refresh current user's token if the user is an active user") + @AuditEvent(type = "ACCESS", action = "token.refresh") + @GetMapping(path = "/refresh", produces = "application/json") + public ResponseEntity refreshToken(@RequestHeader("Authorization") String authorizationHeader, HttpServletRequest request) { + RefreshToken refreshTokenResp = this.tokenService.refreshToken(authorizationHeader); + + if (refreshTokenResp instanceof InvalidRefreshToken invalidRefreshToken) { + AuditAttributes.putMetadata(request, "token_refresh_result", "failure"); + AuditAttributes.putMetadata(request, "token_refresh_error", invalidRefreshToken.error()); + return PICSUREResponse.protocolError(invalidRefreshToken.error()); + } + + if (refreshTokenResp instanceof ValidRefreshToken validRefreshToken) { + AuditAttributes.putMetadata(request, "token_refresh_result", "success"); + return PICSUREResponse.success(Map.of("token", validRefreshToken.token(), "expirationDate", validRefreshToken.expirationDate())); + } + + return PICSUREResponse.success(); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/UserController.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/UserController.java new file mode 100644 index 000000000..460e5fda2 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/UserController.java @@ -0,0 +1,192 @@ +package edu.harvard.hms.dbmi.avillach.auth.rest; + +import edu.harvard.hms.dbmi.avillach.auth.entity.*; +import edu.harvard.hms.dbmi.avillach.auth.model.response.PICSUREResponse; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.UserService; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuditAttributes; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import io.swagger.v3.oas.annotations.Operation; +import io.swagger.v3.oas.annotations.Parameter; +import io.swagger.v3.oas.annotations.tags.Tag; +import jakarta.annotation.security.RolesAllowed; +import jakarta.servlet.http.HttpServletRequest; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.HttpHeaders; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.*; + +import java.util.*; + +import static edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming.AuthRoleNaming.ADMIN; +import static edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming.AuthRoleNaming.SUPER_ADMIN; + +/** + *

    Endpoint for service handling business logic for users.

    + */ +@Tag(name = "User Management") +@Controller +@RequestMapping("/user") +public class UserController { + + private final static Logger logger = LoggerFactory.getLogger(UserController.class); + + private final UserService userService; + + + @Autowired + public UserController(UserService userService) { + this.userService = userService; + } + + @Operation(description = "GET information of one user with the UUID, requires ADMIN or SUPER_ADMIN roles") + @AuditEvent(type = "OTHER", action = "user.read") + @RolesAllowed({ADMIN, SUPER_ADMIN}) + @GetMapping(path = "/{userId}", produces = "application/json") + public ResponseEntity getUserById( + @Parameter(required = true, description = "The UUID of the user to fetch information about") + @PathVariable("userId") String userId, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "target_user_id", userId); + User userById = this.userService.getUserById(userId); + return PICSUREResponse.success(userById); + } + + @Operation(description = "GET a list of existing users, requires ADMIN or SUPER_ADMIN roles") + @AuditEvent(type = "OTHER", action = "user.list") + @RolesAllowed({ADMIN, SUPER_ADMIN}) + @GetMapping(produces = "application/json") + public ResponseEntity> getUserAll() { + List entityAll = this.userService.getAllUsers(); + return PICSUREResponse.success(entityAll); + } + + @Operation(description = "POST a list of users, requires ADMIN role") + @AuditEvent(type = "ADMIN", action = "user.modify") + @RolesAllowed({ADMIN}) + @PostMapping(produces = "application/json") + public ResponseEntity addUser( + @Parameter(required = true, description = "A list of user in JSON format") + @RequestBody List users, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "target_user_count", String.valueOf(users.size())); + List addedUsers = this.userService.addUsers(users); + if (addedUsers == null) { + return PICSUREResponse.applicationError("Inner application error, please contact admin."); + } + + String message = this.userService.sendUserUpdateEmailsFromResponse(addedUsers); + if (message != null) { + return PICSUREResponse.success(message, addedUsers); + } + + return PICSUREResponse.success(addedUsers); + } + + @Operation(description = "Update a list of users, will only update the fields listed, requires ADMIN role") + @AuditEvent(type = "ADMIN", action = "user.modify") + @RolesAllowed({ADMIN}) + @PutMapping(produces = "application/json") + public ResponseEntity updateUser( + @RequestBody List users, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "target_user_count", String.valueOf(users.size())); + List updatedUsers = this.userService.updateUser(users); + if (updatedUsers == null) { + return PICSUREResponse.applicationError("Inner application error, please contact admin."); + } + + String message = this.userService.sendUserUpdateEmailsFromResponse(updatedUsers); + if (message != null) { + return PICSUREResponse.success(message, updatedUsers); + } + + return PICSUREResponse.success(updatedUsers); + } + + /** + * For the long term token, current logic is, every time a user hit this endpoint /me with the query parameter ?hasToken + * presented, it will refresh the long term token. + * + */ + @Operation(description = "Retrieve information of current user") + @AuditEvent(type = "ACCESS", action = "user.profile") + @GetMapping(produces = "application/json", path = "/me") + public ResponseEntity getCurrentUser( + @RequestHeader("Authorization") String authorizationHeader, + @Parameter(description = "Attribute that represents if a long term token will attach to the response") @RequestParam( + name = "hasToken", required = false + ) Boolean hasToken + ) { + logger.info("getCurrentUser() authorizationHeader: {}, hasToken {}", authorizationHeader, hasToken); + User.UserForDisplay currentUser = this.userService.getCurrentUser(authorizationHeader, hasToken); + + if (currentUser == null) { + return PICSUREResponse.applicationError("Inner application error, please contact admin."); + } + + return PICSUREResponse.success(currentUser); + } + + @Operation(description = "Retrieve the queryTemplate of certain application by given application Id for the currentUser ") + @AuditEvent(type = "ACCESS", action = "user.profile") + @GetMapping(path = "/me/queryTemplate/{applicationId}", produces = "application/json") + public ResponseEntity getQueryTemplate( + @Parameter(description = "Application Id for the returning queryTemplate") @PathVariable("applicationId") String applicationId + ) { + Optional mergedTemplate = this.userService.getQueryTemplate(applicationId); + + if (mergedTemplate.isEmpty()) { + logger.error("getDefaultQueryTemplate() cannot find corresponding application by UUID: {}", applicationId); + return PICSUREResponse.applicationError("Inner application error, please contact admin."); + } + + return PICSUREResponse.success(Map.of("queryTemplate", mergedTemplate.orElse(null))); + } + + @Operation(description = "Retrieve the queryTemplate of default application") + @AuditEvent(type = "ACCESS", action = "user.profile") + @GetMapping(value = {"/me/queryTemplate", "/me/queryTemplate/"}, produces = "application/json") + public ResponseEntity getQueryTemplate() { + Map defaultQueryTemplate = userService.getDefaultQueryTemplate(); + + if (defaultQueryTemplate == null) { + return PICSUREResponse.applicationError("Inner application error, please contact admin."); + } + + return PICSUREResponse.success(defaultQueryTemplate); + } + + /** + * For the long term token, current logic is, every time a user hit this endpoint /me with the query parameter ?hasToken presented, it + * will refresh the long term token. + * + * @param httpHeaders the http headers + * @return the refreshed long term token + */ + @Operation(description = "refresh the long term tokne of current user") + @AuditEvent(type = "ACCESS", action = "user.profile") + @GetMapping(path = "/me/refresh_long_term_token", produces = "application/json") + public ResponseEntity refreshUserToken( + @RequestHeader HttpHeaders httpHeaders, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "token_type", "long_term"); + Map stringStringMap = this.userService.refreshUserToken(httpHeaders); + if (stringStringMap != null) { + return PICSUREResponse.success(stringStringMap); + } + + return PICSUREResponse.applicationError("Inner application error, please contact admin."); + } + + @Operation(description = "Retrieve consents of current user") + @GetMapping(path = "/me/consents", produces = "application/json") + public ResponseEntity getUserConsents(@PathVariable("userId") UUID userId) { + UserConsents userConsents = this.userService.getUserConsents(userId); + + if (userConsents == null) { + return PICSUREResponse.applicationError("Inner application error, please contact admin."); + } + + return PICSUREResponse.success(userConsents); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/UserMetadataMappingWebController.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/UserMetadataMappingWebController.java new file mode 100644 index 000000000..ad76e3877 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/UserMetadataMappingWebController.java @@ -0,0 +1,102 @@ +package edu.harvard.hms.dbmi.avillach.auth.rest; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Connection; +import edu.harvard.hms.dbmi.avillach.auth.entity.UserMetadataMapping; +import edu.harvard.hms.dbmi.avillach.auth.model.response.PICSUREResponse; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.UserMetadataMappingService; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuditAttributes; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import io.swagger.v3.oas.annotations.Operation; +import io.swagger.v3.oas.annotations.Parameter; +import io.swagger.v3.oas.annotations.tags.Tag; +import jakarta.annotation.security.RolesAllowed; +import jakarta.servlet.http.HttpServletRequest; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.*; + +import java.util.List; + +import static edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming.AuthRoleNaming.ADMIN; +import static edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming.AuthRoleNaming.SUPER_ADMIN; + +/** + *

    Endpoint for service handling business logic for user metadata mapping.

    + *

    + */ +@Tag(name = "User Metadata Mapping Management") +@Controller +@RequestMapping("/mapping") +public class UserMetadataMappingWebController { + + private final UserMetadataMappingService mappingService; + + @Autowired + public UserMetadataMappingWebController(UserMetadataMappingService mappingService) { + this.mappingService = mappingService; + } + + @Operation(description = "GET information of one UserMetadataMapping with the UUID, requires ADMIN or SUPER_ADMIN role") + @AuditEvent(type = "OTHER", action = "mapping.read") + @RolesAllowed({ADMIN, SUPER_ADMIN}) + @GetMapping(path = "{connectionId}", produces = "application/json") + public ResponseEntity getMappingsForConnection(@PathVariable("connectionId") String connection) { + Connection allMappingsForConnection = this.mappingService.getAllMappingsForConnection(connection); + return PICSUREResponse.success(allMappingsForConnection); + } + + @Operation(description = "GET a list of existing UserMetadataMappings, requires ADMIN or SUPER_ADMIN role") + @AuditEvent(type = "OTHER", action = "mapping.list") + @RolesAllowed({ADMIN, SUPER_ADMIN}) + @GetMapping(produces = "application/json") + public ResponseEntity> getAllMappings() { + List allMappings = mappingService.getAllMappings(); + return PICSUREResponse.success(allMappings); + } + + @Operation(description = "POST a list of UserMetadataMappings, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "mapping.modify") + @RolesAllowed({SUPER_ADMIN}) + @PostMapping(consumes = "application/json", produces = "application/json") + public ResponseEntity addMapping( + @Parameter(required = true, description = "A list of UserMetadataMapping in JSON format") + @RequestBody List mappings, HttpServletRequest request) { + + AuditAttributes.putMetadata(request, "mapping_count", String.valueOf(mappings.size())); + try { + List userMetadataMappings = mappingService.addMappings(mappings); + return PICSUREResponse.success(userMetadataMappings); + } catch (IllegalArgumentException e) { + return PICSUREResponse.error(e.getMessage()); + } + } + + @Operation(description = "Update a list of UserMetadataMappings, will only update the fields listed, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "mapping.modify") + @RolesAllowed({SUPER_ADMIN}) + @PutMapping(consumes = "application/json", produces = "application/json") + public ResponseEntity updateMapping( + @Parameter(required = true, description = "A list of UserMetadataMapping with fields to be updated in JSON format") + @RequestBody List mappings, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "mapping_count", String.valueOf(mappings.size())); + List userMetadataMappings = this.mappingService.updateUserMetadataMappings(mappings); + + if (userMetadataMappings == null || userMetadataMappings.isEmpty()) { + return PICSUREResponse.error("No UserMetadataMapping found with the given Ids"); + } + return PICSUREResponse.success(userMetadataMappings); + } + + @Operation(description = "DELETE an UserMetadataMapping by Id only if the UserMetadataMapping is not associated by others, requires SUPER_ADMIN role") + @AuditEvent(type = "ADMIN", action = "mapping.delete") + @RolesAllowed({SUPER_ADMIN}) + @DeleteMapping(path = "/{mappingId}", produces = "application/json") + public ResponseEntity> removeById( + @Parameter(required = true, description = "A valid UserMetadataMapping Id") + @PathVariable("mappingId") final String mappingId, HttpServletRequest request) { + AuditAttributes.putMetadata(request, "mapping_id", mappingId); + List userMetadataMappings = this.mappingService.removeMetadataMappingByIdAndRetrieveAll(mappingId); + return PICSUREResponse.success(userMetadataMappings); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/package-info.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/package-info.java new file mode 100644 index 000000000..4265d3996 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/package-info.java @@ -0,0 +1,4 @@ +/** + * Defines RESTful endpoints users can access in PSAMA. + */ +package edu.harvard.hms.dbmi.avillach.auth.rest; \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/AuthenticationService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/AuthenticationService.java new file mode 100644 index 000000000..ff0e10045 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/AuthenticationService.java @@ -0,0 +1,15 @@ +package edu.harvard.hms.dbmi.avillach.auth.service; + +import java.io.IOException; +import java.util.HashMap; +import java.util.Map; + +public interface AuthenticationService { + + HashMap authenticate(Map authRequest, String requestHost) throws IOException; + + String getProvider(); + + boolean isEnabled(); + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/MailService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/MailService.java new file mode 100644 index 000000000..ef6542cc6 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/MailService.java @@ -0,0 +1,14 @@ +package edu.harvard.hms.dbmi.avillach.auth.service; + +import com.fasterxml.jackson.databind.JsonNode; +import com.github.mustachejava.Mustache; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import jakarta.mail.MessagingException; + +public interface MailService { + void sendUsersAccessEmail(User user) throws MessagingException; + + void sendDeniedAccessEmail(JsonNode userInfo) throws MessagingException; + + void sendEmail(Mustache emailTemplate, String to, String subject, Object scope) throws MessagingException; +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/AccessRuleService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/AccessRuleService.java new file mode 100644 index 000000000..3c6e7ba33 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/AccessRuleService.java @@ -0,0 +1,1162 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.jayway.jsonpath.JsonPath; +import com.jayway.jsonpath.PathNotFoundException; +import com.mysql.cj.xdevapi.JsonArray; +import edu.harvard.hms.dbmi.avillach.auth.entity.AccessRule; +import edu.harvard.hms.dbmi.avillach.auth.entity.Application; +import edu.harvard.hms.dbmi.avillach.auth.entity.Privilege; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import edu.harvard.hms.dbmi.avillach.auth.model.AccessRuleEvaluationNode; +import edu.harvard.hms.dbmi.avillach.auth.repository.AccessRuleRepository; +import io.micrometer.common.util.StringUtils; +import jakarta.annotation.PostConstruct; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.cache.annotation.CacheEvict; +import org.springframework.cache.annotation.Cacheable; +import org.springframework.stereotype.Service; +import org.springframework.transaction.annotation.Transactional; + +import java.util.*; +import java.util.concurrent.ConcurrentHashMap; +import java.util.stream.Collectors; + +@Service +public class AccessRuleService { + + private final Logger logger = LoggerFactory.getLogger(AccessRuleService.class); + + private final AccessRuleRepository accessRuleRepo; + private final ObjectMapper objectMapper = new ObjectMapper(); + + private final ConcurrentHashMap accessRuleCache = new ConcurrentHashMap<>(); + private Set allowQueryTypeRules; + private Set standardAccessRules; + + public static final String parentAccessionField = "\\\\_Parent Study Accession with Subject ID\\\\"; + private static final String topmedAccessionField = "\\\\_Topmed Study Accession with Subject ID\\\\"; + private final String fence_harmonized_consent_group_concept_path; + private final String fence_parent_consent_group_concept_path; + private final String fence_topmed_consent_group_concept_path; + private final String fence_standard_access_rules; + private final String fence_allowed_query_types; + private final String fence_harmonized_concept_path; + + private String[] underscoreFields; + + private final ThreadLocal> evaluationTreeStack = + ThreadLocal.withInitial(Stack::new); + private final ThreadLocal rootNode = new ThreadLocal<>(); + + @Autowired + public AccessRuleService(AccessRuleRepository accessRuleRepo, + @Value("${fence.harmonized.consent.group.concept.path}") String fenceHarmonizedConsentGroupConceptPath, + @Value("${fence.parent.consent.group.concept.path}") String fenceParentConceptPath, + @Value("${fence.topmed.consent.group.concept.path}") String fenceTopmedConceptPath, + @Value("${fence.standard.access.rules}") String fenceStandardAccessRules, + @Value("${fence.allowed.query.types}") String fenceAllowedQueryTypes, + @Value("${fence.consent.group.concept.path}") String fenceHarmonizedConceptPath) { + this.accessRuleRepo = accessRuleRepo; + this.fence_harmonized_consent_group_concept_path = fenceHarmonizedConsentGroupConceptPath; + this.fence_parent_consent_group_concept_path = fenceParentConceptPath; + this.fence_topmed_consent_group_concept_path = fenceTopmedConceptPath; + this.fence_standard_access_rules = fenceStandardAccessRules; + this.fence_allowed_query_types = fenceAllowedQueryTypes; + this.fence_harmonized_concept_path = fenceHarmonizedConceptPath; + } + + @PostConstruct + public void init() { + // We need to set the underscoreFields here so that we can use them in the access rules during PostConstruct + // If we don't set them here, we will get a NullPointerException when we try to use them in the access rules + underscoreFields = new String[]{ + parentAccessionField, + topmedAccessionField, + fence_harmonized_consent_group_concept_path, + fence_parent_consent_group_concept_path, + fence_topmed_consent_group_concept_path, + "\\\\_VCF Sample Id\\\\", + "\\\\_studies\\\\", + "\\\\_studies_consents\\\\", //used to provide consent-level counts for open access + "\\\\_parent_consents\\\\", //parent consents not used for auth (use combined _consents) + "\\\\_Consents\\\\" + }; + + logger.info("fence_standard_access_rules: {}", fence_standard_access_rules); + logger.info("fence_allowed_query_types: {}", fence_allowed_query_types); + logger.info("fence_harmonized_consent_group_concept_path: {}", fence_harmonized_consent_group_concept_path); + logger.info("fence_parent_consent_group_concept_path: {}", fence_parent_consent_group_concept_path); + logger.info("fence_topmed_consent_group_concept_path: {}", fence_topmed_consent_group_concept_path); + logger.info("fence_harmonized_concept_path: {}", fence_harmonized_concept_path); + logger.info("underscoreFields: {}", Arrays.toString(underscoreFields)); + } + + public Optional getAccessRuleById(String accessRuleId) { + return accessRuleRepo.findById(UUID.fromString(accessRuleId)); + } + + public List getAllAccessRules() { + return accessRuleRepo.findAll(); + } + + public List addAccessRule(List accessRules) { + accessRules.forEach(accessRule -> { + if (accessRule.getEvaluateOnlyByGates() == null) + accessRule.setEvaluateOnlyByGates(false); + + if (accessRule.getCheckMapKeyOnly() == null) + accessRule.setCheckMapKeyOnly(false); + + if (accessRule.getCheckMapNode() == null) + accessRule.setCheckMapNode(false); + + if (accessRule.getGateAnyRelation() == null) + accessRule.setGateAnyRelation(false); + }); + + return this.accessRuleRepo.saveAll(accessRules); + } + + public List updateAccessRules(List accessRules) { + return this.accessRuleRepo.saveAll(accessRules); + } + + @Transactional + public List removeAccessRuleById(String accessRuleId) { + this.accessRuleRepo.deleteById(UUID.fromString(accessRuleId)); + return this.accessRuleRepo.findAll(); + } + + public AccessRule save(AccessRule accessRule) { + // if the access rule exists in the AccessRule cache, update it + if (accessRuleCache.containsKey(accessRule.getName())) { + accessRuleCache.put(accessRule.getName(), accessRule); + } + return this.accessRuleRepo.save(accessRule); + } + + /** + * Prints the evaluation tree for the most recently evaluated access rule. + * This method should be called after evaluateAccessRule() has been called. + * + * @return A string representation of the evaluation tree + */ + public String printEvaluationTree() { + AccessRuleEvaluationNode root = rootNode.get(); + if (root == null) { + return "No evaluation tree available"; + } + + + return "ACCESS RULE EVALUATION TREE:\n" + root.generateTreeString(); + } + + /** + * Clears the evaluation tree data. + * This should be called after processing is complete to prevent memory leaks. + */ + public void clearEvaluationTree() { + rootNode.remove(); + evaluationTreeStack.remove(); + } + + public AccessRule getAccessRuleByName(String arName) { + return this.accessRuleRepo.findByName(arName); + } + + @Cacheable(value = "mergedRulesCache", keyGenerator = "customKeyGenerator") + public Set getAccessRulesForUserAndApp(User user, Application application) { + try { + Set privileges = user.getPrivilegesByApplication(application); + if (privileges == null || privileges.isEmpty()) { + return new HashSet<>(); + } + + Set detachedMergedRules = new HashSet<>(); + for (AccessRule rule : preProcessAccessRules(privileges)) { + detachedMergedRules.add(objectMapper.readValue(objectMapper.writeValueAsString(rule), AccessRule.class)); + } + + return detachedMergedRules; + } catch (Exception e) { + logger.error("Error populating or retrieving data from cache: ", e); + } + + return new HashSet<>(); + } + + @CacheEvict(value = "mergedRulesCache") + public void evictFromMergedAccessRuleCache(String userSubject) { + if (StringUtils.isBlank(userSubject)) { + logger.warn("evictFromMergedAccessRuleCache() was called with a null or empty email"); + return; + } + logger.info("evictFromMergedAccessRuleCache() evicting cache for user: {}", userSubject); + } + + @Cacheable(value = "preProcessedAccessRules", keyGenerator = "customKeyGenerator") + public Set cachedPreProcessAccessRules(User user, Set privileges) { + Set accessRules = new HashSet<>(); + for (Privilege privilege : privileges) { + accessRules.addAll(privilege.getAccessRules()); + } + + return preProcessARBySortedKeys(accessRules); + } + + public Set preProcessAccessRules(Set privileges) { + Set accessRules = new HashSet<>(); + for (Privilege privilege : privileges) { + accessRules.addAll(privilege.getAccessRules()); + } + + return preProcessARBySortedKeys(accessRules); + } + + @CacheEvict(value = "preProcessedAccessRules") + public void evictFromPreProcessedAccessRules(String userSubject) { + if (userSubject == null || userSubject.isEmpty()) { + logger.warn("evictFromPreProcessedAccessRules() was called with a null or empty email"); + return; + } + logger.info("evictFromPreProcessedAccessRules() evicting cache for user: {}", userSubject); + } + + public Set preProcessARBySortedKeys(Set accessRules) { + Map> accessRuleMap = new HashMap<>(); + + for (AccessRule accessRule : accessRules) { + + // 1st generate the key by grabbing all related string and put them together in order + // we use a treeSet here to put orderly combine Strings together + Set keys = new TreeSet<>(); + + // the current accessRule rule + keys.add(accessRule.getRule()); + + // all gates' UUID as strings + keys.add(accessRule.getType().toString()); + + if (accessRule.getGates() != null) { + for (AccessRule gate : accessRule.getGates()) { + keys.add(gate.getUuid().toString()); + } + } + + // all sub accessRule rules + if (accessRule.getSubAccessRule() != null) { + for (AccessRule subAccessRule : accessRule.getSubAccessRule()) { + keys.add(subAccessRule.getRule()); + } + } + Boolean checkMapKeyOnly = accessRule.getCheckMapKeyOnly(), + checkMapNode = accessRule.getCheckMapNode(), + evaluateOnlyByGates = accessRule.getEvaluateOnlyByGates(), + gateAnyRelation = accessRule.getGateAnyRelation(); + + keys.add(checkMapKeyOnly == null ? "null" : Boolean.toString(checkMapKeyOnly)); + keys.add(checkMapNode == null ? "null" : Boolean.toString(checkMapNode)); + keys.add(evaluateOnlyByGates == null ? "null" : Boolean.toString(evaluateOnlyByGates)); + keys.add(gateAnyRelation == null ? "null" : Boolean.toString(gateAnyRelation)); + + String key = String.join("", keys); + if (accessRuleMap.containsKey(key)) { + accessRuleMap.get(key).add(accessRule); + } else { + Set accessRuleSet = new HashSet<>(); + accessRuleSet.add(accessRule); + accessRuleMap.put(key, accessRuleSet); + } + } + + return mergeSameKeyAccessRules(accessRuleMap.values()); + } + + private Set mergeSameKeyAccessRules(Collection> accessRuleMap) { + Set accessRules = new HashSet<>(); + for (Set accessRulesSet : accessRuleMap) { + AccessRule accessRule = null; + for (AccessRule innerAccessRule : accessRulesSet) { + accessRule = mergeAccessRules(accessRule, innerAccessRule); + } + if (accessRule != null) { + accessRules.add(accessRule); + } + } + return accessRules; + } + + private AccessRule mergeAccessRules(AccessRule baseAccessRule, AccessRule accessRuleToBeMerged) { + if (baseAccessRule == null) { + accessRuleToBeMerged.getMergedValues().add(accessRuleToBeMerged.getValue()); + return accessRuleToBeMerged; + } + + if (baseAccessRule.getSubAccessRule() != null && accessRuleToBeMerged.getSubAccessRule() != null) { + baseAccessRule.getSubAccessRule().addAll(accessRuleToBeMerged.getSubAccessRule()); + } else if (baseAccessRule.getSubAccessRule() == null && accessRuleToBeMerged.getSubAccessRule() != null) { + baseAccessRule.setSubAccessRule(accessRuleToBeMerged.getSubAccessRule()); + } + + baseAccessRule.getMergedValues().add(accessRuleToBeMerged.getValue()); + if (baseAccessRule.getMergedName().startsWith("Merged|")) { + baseAccessRule.setMergedName(baseAccessRule.getMergedName() + "|" + accessRuleToBeMerged.getName()); + } else { + baseAccessRule.setMergedName("Merged|" + baseAccessRule.getName() + "|" + accessRuleToBeMerged.getName()); + } + + return baseAccessRule; + } + + public boolean evaluateAccessRule(Object parsedRequestBody, AccessRule accessRule) { + String ruleName = accessRule.getMergedName().isEmpty() ? + accessRule.getName() : + accessRule.getMergedName(); + + boolean isGate = !evaluationTreeStack.get().isEmpty() && + evaluationTreeStack.get().peek().getRule().getGates() != null && + evaluationTreeStack.get().peek().getRule().getGates().contains(accessRule); + boolean isSubRule = !evaluationTreeStack.get().isEmpty() && + evaluationTreeStack.get().peek().getRule().getSubAccessRule() != null && + evaluationTreeStack.get().peek().getRule().getSubAccessRule().contains(accessRule); + boolean isOrRelationship = accessRule.getGateAnyRelation() != null && accessRule.getGateAnyRelation(); + + AccessRuleEvaluationNode currentNode = new AccessRuleEvaluationNode(accessRule, isGate, isSubRule, isOrRelationship); + + if (evaluationTreeStack.get().isEmpty()) { + rootNode.set(currentNode); + } else { + evaluationTreeStack.get().peek().addChild(currentNode); + } + + evaluationTreeStack.get().push(currentNode); + + try { + logger.trace("evaluateAccessRule() starting with: {}", parsedRequestBody); + logger.debug("evaluateAccessRule() evaluating rule: {}", ruleName); + + Set gates = accessRule.getGates(); + boolean gatesPassed = true; + + // depends on the flag getGateAnyRelation is true or false, + // the logic of checking if apply gate will be changed + // the following cases are gate passed: + // 1. if gates are null or empty + // 2. if getGateAnyRelation is false, all gates passed + // 3. if getGateAnyRelation is true, one of the gate passed + if (gates != null && !gates.isEmpty()) { + if (accessRule.getGateAnyRelation() == null || !accessRule.getGateAnyRelation()) { + // All gates are AND relationship + // means one fails all fail + for (AccessRule gate : gates) { + if (!evaluateAccessRule(parsedRequestBody, gate)) { + logger.info("evaluateAccessRule() gate {} failed", gate.getName()); + gatesPassed = false; + break; + } + } + } else { + // All gates are OR relationship + // means one passes all pass + gatesPassed = false; + for (AccessRule gate : gates) { + if (evaluateAccessRule(parsedRequestBody, gate)) { + logger.debug("evaluateAccessRule() gate {} passed", gate.getName()); + gatesPassed = true; + break; + } + } + + if (!gatesPassed) { + logger.debug("All OR gates failed"); + } + } + } + + boolean result = false; + if (accessRule.getEvaluateOnlyByGates() != null && accessRule.getEvaluateOnlyByGates()) { + logger.debug("evaluateAccessRule() eval only by gates"); + result = gatesPassed; + currentNode.setResult(result); + if (!result) { + currentNode.setFailureReason("Gates evaluation failed"); + } + return result; + } + + if (gatesPassed) { + logger.debug("evaluateAccessRule() gates passed"); + if (!extractAndCheckRule(accessRule, parsedRequestBody)) { + logger.debug("Query Rejected by rule(1) {}, with request body {}", accessRule, parsedRequestBody); + currentNode.setResult(false); + currentNode.setFailureReason("Rule check failed: " + accessRule.getRule()); + return false; + } else { + if (accessRule.getSubAccessRule() != null) { + // We need to check all the sub rules as merged rules; they can overlap + Set mergedSubRules = preProcessARBySortedKeys(accessRule.getSubAccessRule()); + for (AccessRule subAccessRule : mergedSubRules) { + if (!evaluateAccessRule(parsedRequestBody, subAccessRule)) { + logger.debug("Query Rejected by rule(2) {}", subAccessRule); + currentNode.setResult(false); + currentNode.setFailureReason("Sub-rule check failed"); + return false; + } + } + } + } + } else { + logger.debug("evaluateAccessRule() gates failed"); + currentNode.setResult(false); + currentNode.setFailureReason("Gates evaluation failed"); + return false; + } + + currentNode.setResult(true); + return true; + } finally { + evaluationTreeStack.get().pop(); + } + } + + public boolean extractAndCheckRule(AccessRule accessRule, Object parsedRequestBody) { + String rule = accessRule.getRule(); + + if (rule == null || rule.isEmpty()) + return true; + + rule = rule.stripLeading(); + + Object requestBodyValue; + int accessRuleType = accessRule.getType(); + + try { + logger.trace("extractAndCheckRule() -> JsonPath.parse().read() with parsedRequestBody - {} - {}", parsedRequestBody, rule); + requestBodyValue = JsonPath.parse(parsedRequestBody).read(rule); + + if (accessRule.getCheckMapNode() != null && accessRule.getCheckMapNode()) { + // Json parse will always return a list even when we want a map (to check keys) + if (requestBodyValue instanceof JsonArray && ((JsonArray) requestBodyValue).size() == 1) { + requestBodyValue = ((JsonArray) requestBodyValue).get(0); + } + } + } catch (PathNotFoundException ex) { + if (accessRuleType == AccessRule.TypeNaming.IS_EMPTY) { + // We could return true directly, but we want to log the reason + logger.debug("extractAndCheckRule() -> JsonPath.parse().read() PathNotFound; passing rule {} for type {}", rule, accessRuleType); + return true; + } + + if (accessRuleType == AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY || + accessRuleType == AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY_IGNORE_CASE) { + logger.debug("extractAndCheckRule() -> JsonPath.parse().read() PathNotFound; passing rule {} for type {}", rule, accessRuleType); + return true; + } + + logger.info("extractAndCheckRule() -> JsonPath.parse().read() throws exception with parsedRequestBody - {} : {} - {}", parsedRequestBody, ex.getClass().getSimpleName(), ex.getMessage()); + + // Record failure reason in the evaluation tree + if (!evaluationTreeStack.get().isEmpty()) { + AccessRuleEvaluationNode currentNode = evaluationTreeStack.get().peek(); + currentNode.setFailureReason("Path not found: " + rule + " - " + ex.getMessage()); + } + + return false; + } + + if (accessRuleType == AccessRule.TypeNaming.IS_EMPTY + || accessRuleType == AccessRule.TypeNaming.IS_NOT_EMPTY) { + if (requestBodyValue == null + || (requestBodyValue instanceof String && ((String) requestBodyValue).isEmpty()) + || (requestBodyValue instanceof Collection && ((Collection) requestBodyValue).isEmpty()) + || (requestBodyValue instanceof Map && ((Map) requestBodyValue).isEmpty())) { + boolean result = accessRuleType == AccessRule.TypeNaming.IS_EMPTY; + if (!result && !evaluationTreeStack.get().isEmpty()) { + AccessRuleEvaluationNode currentNode = evaluationTreeStack.get().peek(); + currentNode.setFailureReason("Expected empty path but found value: " + requestBodyValue); + } + return result; + } else { + boolean result = accessRuleType == AccessRule.TypeNaming.IS_NOT_EMPTY; + if (!result && !evaluationTreeStack.get().isEmpty()) { + AccessRuleEvaluationNode currentNode = evaluationTreeStack.get().peek(); + currentNode.setFailureReason("Expected non-empty path but found empty value"); + } + return result; + } + } + + boolean result = evaluateNode(requestBodyValue, accessRule); + if (!result && !evaluationTreeStack.get().isEmpty()) { + AccessRuleEvaluationNode currentNode = evaluationTreeStack.get().peek(); + if (currentNode.getFailureReason() == null) { + currentNode.setFailureReason("Rule evaluation failed for path: " + rule); + } + } + return result; + } + + private boolean evaluateNode(Object requestBodyValue, AccessRule accessRule) { + logger.trace("evaluateNode() starting: {} :: {} :: {}", accessRule.getRule(), accessRule.getType(), accessRule.getMergedValues().isEmpty() ? accessRule.getValue() : ("Merged " + Arrays.deepToString(accessRule.getMergedValues().toArray()))); + logger.trace("evaluateNode() requestBody {} {}", requestBodyValue.getClass().getName(), requestBodyValue instanceof Collection ? + Arrays.deepToString(((Collection) requestBodyValue).toArray()) : + requestBodyValue.toString()); + + return switch (requestBodyValue) { + case String s -> decisionMaker(accessRule, s); + case Collection collection -> evaluateCollection(collection, accessRule); + case Map map when accessRule.getCheckMapNode() != null && accessRule.getCheckMapNode() -> + evaluateMap(requestBodyValue, accessRule); + default -> true; + }; + } + + private boolean evaluateMap(Object requestBodyValue, AccessRule accessRule) { + logger.trace("evaluateMap() access rule:{}", accessRule.getName()); + logger.trace("evaluateMap() request body value:{}", requestBodyValue); + + switch (accessRule.getType()) { + case (AccessRule.TypeNaming.ANY_EQUALS): + case (AccessRule.TypeNaming.ANY_CONTAINS): + case (AccessRule.TypeNaming.ANY_REG_MATCH): + for (Map.Entry entry : ((Map) requestBodyValue).entrySet()) { + if (decisionMaker(accessRule, (String) entry.getKey())) + return true; + + if ((accessRule.getCheckMapKeyOnly() == null || !accessRule.getCheckMapKeyOnly()) + && evaluateNode(entry.getValue(), accessRule)) + return true; + } + return false; + default: + if (((Map) requestBodyValue).isEmpty()) { + return switch (accessRule.getType()) { + case (AccessRule.TypeNaming.ALL_EQUALS_IGNORE_CASE), (AccessRule.TypeNaming.ALL_EQUALS), + (AccessRule.TypeNaming.ALL_CONTAINS), (AccessRule.TypeNaming.ALL_CONTAINS_IGNORE_CASE) -> + false; + default -> true; + }; + } + for (Map.Entry entry : ((Map) requestBodyValue).entrySet()) { + if (!decisionMaker(accessRule, (String) entry.getKey())) + return false; + + if ((accessRule.getCheckMapKeyOnly() == null || !accessRule.getCheckMapKeyOnly()) + && !evaluateNode(entry.getValue(), accessRule)) + return false; + } + + } + + return true; + } + + private Boolean evaluateCollection(Collection requestBodyValue, AccessRule accessRule) { + logger.debug("evaluateCollection()"); + logger.trace("evaluateCollection() access rule:{}", accessRule.getName()); + logger.trace("evaluateCollection() request body value:{}", requestBodyValue); + + switch (accessRule.getType()) { + case (AccessRule.TypeNaming.ANY_EQUALS): + case (AccessRule.TypeNaming.ANY_CONTAINS): + case (AccessRule.TypeNaming.ANY_REG_MATCH): + for (Object item : requestBodyValue) { + if (item instanceof String) { + if (decisionMaker(accessRule, (String) item)) { + return true; + } + } else { + if (evaluateNode(item, accessRule)) { + return true; + } + } + } + return false; + default: + if (requestBodyValue.isEmpty()) { + switch (accessRule.getType()) { + case (AccessRule.TypeNaming.ALL_EQUALS_IGNORE_CASE): + case (AccessRule.TypeNaming.ALL_EQUALS): + case (AccessRule.TypeNaming.ALL_CONTAINS): + case (AccessRule.TypeNaming.ALL_CONTAINS_IGNORE_CASE): + return false; + case (AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY): + case (AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY_IGNORE_CASE): + default: + return true; + } + } + + for (Object item : requestBodyValue) { + if (item instanceof String) { + if (!decisionMaker(accessRule, (String) item)) { + return false; + } + } else { + if (!evaluateNode(item, accessRule)) + return false; + } + } + } + + return true; + } + + public boolean decisionMaker(AccessRule accessRule, String requestBodyValue) { + if (accessRule.getMergedValues().isEmpty()) { + String value = accessRule.getValue(); + logger.debug("decisionMaker No Merged values: {}, request body: {}, access rule: {}", value, requestBodyValue, accessRule); + if (value == null) { + return requestBodyValue == null; + } + return _decisionMaker(accessRule, requestBodyValue, value); + } + + // recursively check the values + // until one of them is true + // if there is only one element in the merged value set + // the operation equals to _decisionMaker(accessRule, requestBodyValue, value) + boolean res = false; + logger.debug("Checking {} in collection {}", requestBodyValue, Arrays.deepToString(accessRule.getMergedValues().toArray())); + for (String s : accessRule.getMergedValues()) { + // check the special case value is null + // if value is null, the check will stop here and + // not goes to _decisionMaker() + if (s == null) { + if (requestBodyValue == null) { + res = true; + break; + } else { + continue; + } + } + + // all the merged values are OR relationship + // means if you pass one of them, you pass the rule + if (_decisionMaker(accessRule, requestBodyValue, s)) { + res = true; + logger.info("Returning true for {} in collection {}", s, Arrays.deepToString(accessRule.getMergedValues().toArray())); + break; + } + } + return res; + } + + private boolean _decisionMaker(AccessRule accessRule, String requestBodyValue, String value) { + boolean decision = switch (accessRule.getType()) { + case AccessRule.TypeNaming.NOT_CONTAINS -> !requestBodyValue.contains(value); + case AccessRule.TypeNaming.NOT_CONTAINS_IGNORE_CASE -> + !requestBodyValue.toLowerCase().contains(value.toLowerCase()); + case (AccessRule.TypeNaming.NOT_EQUALS) -> !value.equals(requestBodyValue); + case (AccessRule.TypeNaming.ANY_EQUALS), (AccessRule.TypeNaming.ALL_EQUALS) -> + value.equals(requestBodyValue); + case (AccessRule.TypeNaming.ALL_CONTAINS), (AccessRule.TypeNaming.ANY_CONTAINS), + (AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY) -> requestBodyValue.contains(value); + case (AccessRule.TypeNaming.ALL_CONTAINS_IGNORE_CASE), + (AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY_IGNORE_CASE) -> + requestBodyValue.toLowerCase().contains(value.toLowerCase()); + case (AccessRule.TypeNaming.NOT_EQUALS_IGNORE_CASE) -> !value.equalsIgnoreCase(requestBodyValue); + case (AccessRule.TypeNaming.ALL_EQUALS_IGNORE_CASE) -> value.equalsIgnoreCase(requestBodyValue); + case (AccessRule.TypeNaming.ALL_REG_MATCH), (AccessRule.TypeNaming.ANY_REG_MATCH) -> + requestBodyValue.matches(value); + default -> { + logger.warn("evaluateAccessRule() incoming accessRule type is out of scope. Just return true."); + yield true; + } + }; + + if (decision) { + logger.info("_decisionMaker() returning true for request body: {} access rule: {} value: {}", requestBodyValue, accessRule, value); + } + + return decision; + } + + /** + * Configures the AccessRule with gates and sub-rules. + * + * @param ar The AccessRule to configure. + * @param studyIdentifier The study identifier. + * @param consent_group The consent group. + * @param conceptPath The concept path. + * @param projectAlias The project alias. + */ + protected void configureAccessRule(AccessRule ar, String studyIdentifier, String consent_group, String conceptPath, String projectAlias) { + ar.setGates(new HashSet<>(getGates(true, false, false))); + + addUniqueSubRules(ar, getAllowedQueryTypeRules()); + addUniqueSubRules(ar, getPhenotypeSubRules(studyIdentifier, conceptPath, projectAlias)); + addUniqueSubRules(ar, getTopmedRestrictedSubRules()); + } + + + /** + * Configures the harmonized AccessRule with gates and sub-rules. + * + * @param ar The AccessRule to configure. + * @param studyIdentifier The study identifier. + * @param conceptPath The concept path. + * @param projectAlias The project alias. + */ + protected void configureHarmonizedAccessRule(AccessRule ar, String studyIdentifier, String conceptPath, String projectAlias) { + ar.setGates(new HashSet<>(Collections.singleton(upsertConsentGate("HARMONIZED_CONSENT", "$.query.query.categoryFilters." + fence_harmonized_consent_group_concept_path + "[*]", true, "harmonized data")))); + + addUniqueSubRules(ar, getAllowedQueryTypeRules()); + addUniqueSubRules(ar, getHarmonizedSubRules()); + addUniqueSubRules(ar, getPhenotypeSubRules(studyIdentifier, conceptPath, projectAlias)); + } + + protected AccessRule configureClinicalAccessRuleWithPhenoSubRule(AccessRule ar, String studyIdentifier, String consent_group, String conceptPath, String projectAlias) { + ar.setGates(new HashSet<>(getGates(true, false, true))); + + addUniqueSubRules(ar, getAllowedQueryTypeRules()); + addUniqueSubRules(ar, getPhenotypeSubRules(studyIdentifier, conceptPath, projectAlias)); + addUniqueSubRules(ar, Collections.singleton(createPhenotypeSubRule(fence_topmed_consent_group_concept_path, "ALLOW_TOPMED_CONSENT", "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "", true))); + + return ar; + } + + protected Set getAllowedQueryTypeRules() { + if (allowQueryTypeRules == null) { + allowQueryTypeRules = loadAllowedQueryTypeRules(); + } + + return allowQueryTypeRules; + } + + /** + * Retrieves or creates AccessRules for allowed query types. + * + * @return A set of AccessRules for allowed query types. + */ + private Set loadAllowedQueryTypeRules() { + // Initialize a set to hold the AccessRules + Set rules = new HashSet<>(); + // Split the allowed query types from the configuration + String[] allowedTypes = this.fence_allowed_query_types.split(","); + + // Iterate over each allowed query type + for (String queryType : allowedTypes) { + // Construct the AccessRule name + String ar_name = "AR_ALLOW_" + queryType; + + // Log the creation of a new AccessRule + AccessRule ar = getOrCreateAccessRule( + ar_name, + "MANAGED SUB AR to allow " + queryType + " Queries", + "$.query.query.expectedResultType", + AccessRule.TypeNaming.ALL_EQUALS, + queryType, + false, + false, + false, + false + ); + + // Add the newly created rule to the set + rules.add(ar); + } + // Return the set of AccessRules + return rules; + } + + + private Collection getTopmedRestrictedSubRules() { + Set rules = new HashSet(); + rules.add(upsertTopmedRestrictedSubRule("CATEGORICAL", "$.query.query.variantInfoFilters[*].categoryVariantInfoFilters.*")); + rules.add(upsertTopmedRestrictedSubRule("NUMERIC", "$.query.query.variantInfoFilters[*].numericVariantInfoFilters.*")); + + return rules; + } + + /** + * Creates and returns a restricted sub-rule AccessRule for Topmed. + * topmed restriction rules don't need much configuration. Just deny all access. + * + * @param type The type of the Topmed restriction. + * @param rule The rule expression. + * @return The created AccessRule. + */ + private AccessRule upsertTopmedRestrictedSubRule(String type, String rule) { + // Construct the AccessRule name + String ar_name = "AR_TOPMED_RESTRICTED_" + type; + // Check if the AccessRule already exists + AccessRule ar = this.getAccessRuleByName(ar_name); + if (ar != null) { + // Log and return the existing rule + logger.trace("Found existing rule: {}", ar.getName()); + return ar; + } + + // Log the creation of a new AccessRule + // Create the AccessRule using the createAccessRule method + return getOrCreateAccessRule( + ar_name, + "MANAGED SUB AR for restricting " + type + " genomic concepts", + rule, + AccessRule.TypeNaming.IS_EMPTY, + null, + false, + false, + false, + false + ); + } + + protected Collection getPhenotypeSubRules(String studyIdentifier, String conceptPath, String alias) { + Set rules = new HashSet(); + //categorical filters will always contain at least one entry (for the consent groups); it will never be empty + rules.add(createPhenotypeSubRule(fence_parent_consent_group_concept_path, "ALLOW_PARENT_CONSENT", "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "", true)); + + for (String underscorePath : underscoreFields) { + rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.fields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "FIELDS", false)); + rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "CATEGORICAL", true)); + rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.requiredFields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "REQ_FIELDS", false)); + rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.anyRecordOf.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "ANY_RECORD_OF", false)); + rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.anyRecordOfMulti.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "ANY_RECORD_OF_MULTI", false)); + } + + rules.add(createPhenotypeSubRule(conceptPath, alias + "_" + studyIdentifier, "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "CATEGORICAL", true)); + rules.add(createPhenotypeSubRule(conceptPath, alias + "_" + studyIdentifier, "$.query.query.numericFilters", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "NUMERIC", true)); + rules.add(createPhenotypeSubRule(conceptPath, alias + "_" + studyIdentifier, "$.query.query.fields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "FIELDS", false)); + rules.add(createPhenotypeSubRule(conceptPath, alias + "_" + studyIdentifier, "$.query.query.requiredFields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "REQUIRED_FIELDS", false)); + rules.add(createPhenotypeSubRule(conceptPath, alias + "_" + studyIdentifier, "$.query.query.anyRecordOf.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "ANY_RECORD_OF", false)); + rules.add(createPhenotypeSubRule(conceptPath, alias + "_" + studyIdentifier, "$.query.query.anyRecordOfMulti.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "ANY_RECORD_OF_MULTI", false)); + + return rules; + } + + /** + * Harmonized rules should allow the user to supply paretn and top med consent groups; this allows a single harmonized + * rules instead of splitting between a topmed+harmonized and parent+harmonized + * + * @return + */ + private Collection getHarmonizedSubRules() { + + Set rules = new HashSet(); + //categorical filters will always contain at least one entry (for the consent groups); it will never be empty + rules.add(createPhenotypeSubRule(fence_parent_consent_group_concept_path, "ALLOW_PARENT_CONSENT", "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "", true)); + rules.add(createPhenotypeSubRule(fence_harmonized_consent_group_concept_path, "ALLOW_HARMONIZED_CONSENT", "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "", true)); + rules.add(createPhenotypeSubRule(fence_topmed_consent_group_concept_path, "ALLOW_TOPMED_CONSENT", "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "", true)); + + for (String underscorePath : underscoreFields) { + rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.fields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "FIELDS", false)); + rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "CATEGORICAL", true)); + rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.requiredFields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "REQ_FIELDS", false)); + rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.anyRecordOf.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "ANY_RECORD_OF", false)); + rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.anyRecordOfMulti.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "ANY_RECORD_OF_MULTI", false)); + } + + rules.add(createPhenotypeSubRule(fence_harmonized_concept_path, "HARMONIZED", "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "CATEGORICAL", true)); + rules.add(createPhenotypeSubRule(fence_harmonized_concept_path, "HARMONIZED", "$.query.query.numericFilters", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "NUMERIC", true)); + rules.add(createPhenotypeSubRule(fence_harmonized_concept_path, "HARMONIZED", "$.query.query.fields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "FIELDS", false)); + rules.add(createPhenotypeSubRule(fence_harmonized_concept_path, "HARMONIZED", "$.query.query.requiredFields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "REQUIRED_FIELDS", false)); + rules.add(createPhenotypeSubRule(fence_harmonized_concept_path, "HARMONIZED", "$.query.query.anyRecordOf.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "ANY_RECORD_OF", false)); + rules.add(createPhenotypeSubRule(fence_harmonized_concept_path, "HARMONIZED", "$.query.query.anyRecordOfMulti.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "ANY_RECORD_OF_MULTI", false)); + + return rules; + } + + + /** + * generate and return a set of rules that disallow access to phenotype data (only genomic filters allowed) + * + * @return + */ + protected Collection getPhenotypeRestrictedSubRules(String studyIdentifier, String consentCode, String alias) { + Set rules = new HashSet(); + //categorical filters will always contain at least one entry (for the consent groups); it will never be empty + rules.add(createPhenotypeSubRule(fence_topmed_consent_group_concept_path, "ALLOW_TOPMED_CONSENT", "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "", true)); + + for (String underscorePath : underscoreFields) { + rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.fields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "FIELDS", false)); + rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "CATEGORICAL", true)); + rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.requiredFields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "REQ_FIELDS", false)); + rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.anyRecordOf.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "ANY_RECORD_OF", false)); + rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.anyRecordOfMulti.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "ANY_RECORD_OF_MULTI", false)); + } + + rules.add(createPhenotypeSubRule(null, alias + "_" + studyIdentifier + "_" + consentCode, "$.query.query.numericFilters.[*]", AccessRule.TypeNaming.IS_EMPTY, "DISALLOW_NUMERIC", false)); + rules.add(createPhenotypeSubRule(null, alias + "_" + studyIdentifier + "_" + consentCode, "$.query.query.requiredFields.[*]", AccessRule.TypeNaming.IS_EMPTY, "DISALLOW_REQUIRED_FIELDS", false)); + + return rules; + } + + /** + * Return a set of gates that identify which consent values have been provided. the boolean parameters indicate + * if a value in the specified consent location should allow this gate to pass. + * + * @param parent + * @param harmonized + * @param topmed + * @return + */ + private Collection getGates(boolean parent, boolean harmonized, boolean topmed) { + Set gates = new HashSet(); + gates.add(upsertConsentGate("PARENT_CONSENT", "$.query.query.categoryFilters." + fence_parent_consent_group_concept_path + "[*]", parent, "parent study data")); + gates.add(upsertConsentGate("HARMONIZED_CONSENT", "$.query.query.categoryFilters." + fence_harmonized_consent_group_concept_path + "[*]", harmonized, "harmonized data")); + gates.add(upsertConsentGate("TOPMED_CONSENT", "$.query.query.categoryFilters." + fence_topmed_consent_group_concept_path + "[*]", topmed, "Topmed data")); + + return gates; + } + + protected AccessRule populateTopmedAccessRule(AccessRule rule, boolean includeParent) { + rule.setGates(new HashSet<>(getGates(includeParent, false, true))); + addUniqueSubRules(rule, getAllowedQueryTypeRules()); + + return rule; + } + + protected AccessRule populateHarmonizedAccessRule(AccessRule rule, String parentConceptPath, String studyIdentifier, String projectAlias) { + rule.setGates(new HashSet<>(Collections.singletonList( + upsertConsentGate("HARMONIZED_CONSENT", "$.query.query.categoryFilters." + fence_harmonized_consent_group_concept_path + "[*]", true, "harmonized data") + ))); + + addUniqueSubRules(rule, getAllowedQueryTypeRules()); + addUniqueSubRules(rule, getHarmonizedSubRules()); + addUniqueSubRules(rule, getPhenotypeSubRules(studyIdentifier, parentConceptPath, projectAlias)); + + return rule; + } + + + /** + * The set of standard access rules that are added to all privileges. + * This set is cached to avoid loading the rules multiple times. + * + * @return The set of standard access rules. + */ + protected Set addStandardAccessRules() { + if (standardAccessRules != null && !standardAccessRules.isEmpty()) { + return standardAccessRules; + } + + standardAccessRules = new HashSet<>(); + for (String arName : fence_standard_access_rules.split(",")) { + if (arName.startsWith("AR_")) { + AccessRule ar = this.getAccessRuleByName(arName); + if (ar != null) { + standardAccessRules.add(ar); + } else { + logger.warn("Unable to find an access rule with name {}", arName); + } + } else { + logger.info("Skipping AccessRule {} as it does not start with AR_", arName); + } + } + + logger.info("Added {} standard access rules to privilege", standardAccessRules.size()); + return standardAccessRules; + } + + + /** + * Creates and returns a consent access rule AccessRule. + * Generates Main rule only; gates & sub-rules attached after calling this + * prentRule should be null if this is the main rule, or the appropriate value if this is a sub-rule + * + * @param studyIdentifier The study identifier. + * @param consent_group The consent group. + * @param label The label for the rule. + * @param consent_path The consent path. + * @return The created AccessRule. + */ + protected AccessRule createConsentAccessRule(String studyIdentifier, String consent_group, String label, String consent_path) { + String ar_name = (consent_group != null && !consent_group.isEmpty()) ? "AR_CONSENT_" + studyIdentifier + "_" + consent_group + "_" + label : "AR_CONSENT_" + studyIdentifier; + String description = (consent_group != null && !consent_group.isEmpty()) ? "MANAGED AR for " + studyIdentifier + "." + consent_group + " clinical concepts" : "MANAGED AR for " + studyIdentifier + " clinical concepts"; + String ruleText = "$.query.query.categoryFilters." + consent_path + "[*]"; + String arValue = (consent_group != null && !consent_group.isEmpty()) ? studyIdentifier + "." + consent_group : studyIdentifier; + + return getOrCreateAccessRule( + ar_name, + description, + ruleText, + AccessRule.TypeNaming.ALL_CONTAINS, + arValue, + false, + false, + false, + false + ); + } + + /** + * Creates and returns a Topmed access rule AccessRule. + * Generates Main Rule only; gates & sub-rules attached by calling method + * + * @param project_name The name of the project. + * @param consent_group The consent group. + * @param label The label for the rule. + * @return The created AccessRule. + */ + protected AccessRule upsertTopmedAccessRule(String project_name, String consent_group, String label) { + String ar_name = (consent_group != null && !consent_group.isEmpty()) ? "AR_TOPMED_" + project_name + "_" + consent_group + "_" + label : "AR_TOPMED_" + project_name + "_" + label; + String description = "MANAGED AR for " + project_name + "." + consent_group + " Topmed data"; + + String conceptPath = fence_topmed_consent_group_concept_path; + // Check if the conceptPath has `\\\\` present. This technically represents `\\`. + if (conceptPath != null && conceptPath.contains("\\\\")) { + // This will convert all `\\\\` to `\\`. + conceptPath = conceptPath.replaceAll("\\\\\\\\", "\\\\"); + } + + String ruleText = "$.query.query.categoryFilters." + conceptPath + "[*]"; + String arValue = (consent_group != null && !consent_group.isEmpty()) ? project_name + "." + consent_group : project_name; + + return getOrCreateAccessRule( + ar_name, + description, + ruleText, + AccessRule.TypeNaming.ALL_CONTAINS, + arValue, + false, + false, + false, + false + ); + } + + /** + * Creates and returns a harmonized access rule AccessRule for Topmed. + * Generates Main Rule only; gates & sub rules attached by calling method + * + * @param project_name The name of the project. + * @param consent_group The consent group. + * @return The created AccessRule. + */ + protected AccessRule upsertHarmonizedAccessRule(String project_name, String consent_group) { + String ar_name = "AR_TOPMED_" + project_name + "_" + consent_group + "_" + "HARMONIZED"; + logger.trace("upsertHarmonizedAccessRule() Creating new access rule {}", ar_name); + String description = "MANAGED AR for " + project_name + "." + consent_group + " Topmed data"; + String ruleText = "$.query.query.categoryFilters." + fence_harmonized_consent_group_concept_path + "[*]"; + String arValue = project_name + "." + consent_group; + + return getOrCreateAccessRule( + ar_name, + description, + ruleText, + AccessRule.TypeNaming.ALL_CONTAINS, + arValue, + false, + false, + false, + false + ); + } + + /** + * Creates and returns a consent gate AccessRule. + * Insert a new gate (if it doesn't exist yet) to identify if consent values are present in the query. + * return an existing gate named GATE_{gateName}_(PRESENT|MISSING) if it exists. + * + * @param gateName The name of the gate. + * @param rule The rule expression. + * @param is_present Whether the gate is for present or missing consent. + * @param description The description of the gate. + * @return The created AccessRule. + */ + private AccessRule upsertConsentGate(String gateName, String rule, boolean is_present, String description) { + gateName = "GATE_" + gateName + "_" + (is_present ? "PRESENT" : "MISSING"); + + escapePath(rule); + + return getOrCreateAccessRule( + gateName, + "MANAGED GATE for " + description + " consent " + (is_present ? "present" : "missing"), + rule, + is_present ? AccessRule.TypeNaming.IS_NOT_EMPTY : AccessRule.TypeNaming.IS_EMPTY, + null, + false, + false, + false, + false + ); + } + + protected AccessRule createPhenotypeSubRule(String conceptPath, String alias, String rule, int ruleType, String label, boolean useMapKey) { + String ar_name = "AR_PHENO_" + alias + "_" + label; + logger.trace("createPhenotypeSubRule() Creating new access rule {}", ar_name); + + // Check if the conceptPath has `\\\\` present. This technically represents `\\`. + if (conceptPath != null && conceptPath.contains("\\\\")) { + // This will convert all `\\\\` to `\\`. + conceptPath = conceptPath.replaceAll("\\\\\\\\", "\\\\"); + } + + return getOrCreateAccessRule( + ar_name, + "MANAGED SUB AR for " + alias + " " + label + " clinical concepts", + rule, + ruleType, + ruleType == AccessRule.TypeNaming.IS_NOT_EMPTY ? null : conceptPath, + useMapKey, + useMapKey, + false, + false + ); + } + + protected AccessRule getOrCreateAccessRule(String name, String description, String rule, int type, String value, boolean checkMapKeyOnly, boolean checkMapNode, boolean evaluateOnlyByGates, boolean gateAnyRelation) { + return accessRuleCache.computeIfAbsent(name, key -> { + AccessRule ar = this.getAccessRuleByName(key); + if (ar == null) { + logger.trace("Creating new access rule {}", key); + ar = new AccessRule(); + + ar.setName(name); + ar.setDescription(description); + ar.setRule(rule); + ar.setType(type); + ar.setValue(value); + ar.setCheckMapKeyOnly(checkMapKeyOnly); + ar.setCheckMapNode(checkMapNode); + ar.setEvaluateOnlyByGates(evaluateOnlyByGates); + ar.setGateAnyRelation(gateAnyRelation); + ar = this.save(ar); + } + + return ar; + }); + } + + private String escapePath(String path) { + if (path != null && !path.contains("\\\\")) { + return path.replaceAll("\\\\", "\\\\\\\\"); + } + return path; + } + + public List getAccessRulesByPrivilegeIds(List privilegeIds) { + return this.accessRuleRepo.getAccessRulesByPrivilegeIds(privilegeIds); + } + + /** + * Adds unique sub-rules to the provided parent access rule. This method ensures that duplicate sub-rules, + * based on their names, are not added to the parent access rule. + * + * @param accessRule the parent access rule to which the sub-rules are added + * @param subRulesToAdd the collection of sub-rules to be added to the parent access rule + */ + private void addUniqueSubRules(AccessRule accessRule, Collection subRulesToAdd) { + if (accessRule.getSubAccessRule() == null) { + accessRule.setSubAccessRule(new HashSet<>()); + } + + Set existingRuleNames = accessRule.getSubAccessRule().stream() + .map(AccessRule::getName) + .collect(Collectors.toSet()); + + for (AccessRule subRule : subRulesToAdd) { + if (!existingRuleNames.contains(subRule.getName())) { + accessRule.getSubAccessRule().add(subRule); + existingRuleNames.add(subRule.getName()); + } + } + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/ApplicationService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/ApplicationService.java new file mode 100644 index 000000000..0c8c862fd --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/ApplicationService.java @@ -0,0 +1,166 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Application; +import edu.harvard.hms.dbmi.avillach.auth.entity.Privilege; +import edu.harvard.hms.dbmi.avillach.auth.repository.ApplicationRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.PrivilegeRepository; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming; +import edu.harvard.hms.dbmi.avillach.auth.utils.JWTUtil; +import org.hibernate.Hibernate; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.security.core.userdetails.UserDetails; +import org.springframework.security.core.userdetails.UserDetailsService; +import org.springframework.security.core.userdetails.UsernameNotFoundException; +import org.springframework.stereotype.Service; +import org.springframework.transaction.annotation.Transactional; + +import java.util.*; + +@Service +public class ApplicationService implements UserDetailsService { + + private final static Logger logger = LoggerFactory.getLogger(ApplicationService.class); + private final ApplicationRepository applicationRepo; + private final PrivilegeRepository privilegeRepo; + private final JWTUtil jwtUtil; + + @Autowired + public ApplicationService(ApplicationRepository applicationRepo, PrivilegeRepository privilegeRepo, JWTUtil jwtUtil) { + this.applicationRepo = applicationRepo; + this.privilegeRepo = privilegeRepo; + this.jwtUtil = jwtUtil; + } + + /** + * Retrieves an entity by its ID. + * + * @param applicationId the ID of the entity to retrieve + * @return a ResponseEntity representing the result of the operation + */ + @Transactional + public Optional getApplicationByID(String applicationId) { + return applicationRepo.findById(UUID.fromString(applicationId)); + } + + /** + * Retrieves an entity by its ID with its privileges. This method is used to avoid lazy loading exception. + * + * @param applicationName + * @return + */ + @Transactional + public Optional getApplicationByIdWithPrivileges(String applicationName) { + Optional byId = this.applicationRepo.findById(UUID.fromString(applicationName)); + + if (byId.isEmpty()) { + return Optional.empty(); + } + + Application application = byId.get(); + Hibernate.initialize(application.getPrivileges()); + return Optional.of(application); + } + + public List getAllApplications() { + return this.applicationRepo.findAll(); + } + + @Transactional + public List addNewApplications(List applications) { + checkAssociation(applications); + List appEntities = this.applicationRepo.saveAll(applications); + for (Application application : appEntities) { + application.setToken( + generateApplicationToken(application) + ); + } + + return this.applicationRepo.saveAll(appEntities); + } + + @Transactional + public List deleteApplicationById(String applicationId) { + Optional application = applicationRepo.findById(UUID.fromString(applicationId)); + + if (application.isEmpty()) { + logger.error("deleteApplicationById() cannot find the application by applicationId: {}", applicationId); + throw new IllegalArgumentException("Cannot find application by the given applicationId: " + applicationId); + } + + this.applicationRepo.delete(application.get()); + return this.applicationRepo.findAll(); + } + + @Transactional + public List updateApplications(List applications) { + checkAssociation(applications); + return this.applicationRepo.saveAll(applications); + } + + public String refreshApplicationToken(String applicationId) throws NullPointerException, IllegalArgumentException { + Optional application = applicationRepo.findById(UUID.fromString(applicationId)); + + if (application.isEmpty()) { + logger.error("refreshApplicationToken() cannot find the application by applicationId: {}", applicationId); + throw new IllegalArgumentException("Cannot find application by the given applicationId: " + applicationId); + } + + String newApplicationToken = generateApplicationToken(application.orElse(null)); + if (newApplicationToken == null) { + logger.error("refreshApplicationToken() failed to generate new application token for applicationId: {}", applicationId); + throw new NullPointerException("Failed to generate new application token for applicationId: " + applicationId); + } + + application.get().setToken(newApplicationToken); + this.applicationRepo.save(application.get()); + return newApplicationToken; + } + + private void checkAssociation(List applications) { + for (Application application : applications) { + if (application.getPrivileges() != null) { + Set privileges = new HashSet<>(); + application.getPrivileges().forEach(p -> { + Optional optionalPrivilege = privilegeRepo.findById(p.getUuid()); + if (optionalPrivilege.isPresent()) { + Privilege privilege = optionalPrivilege.get(); + privilege.setApplication(application); + privileges.add(privilege); + } else { + logger.error("Didn't find privilege by uuid: {}", p.getUuid()); + } + }); + + application.setPrivileges(privileges); + } + } + } + + public String generateApplicationToken(Application application) { + if (application == null || application.getUuid() == null) { + logger.error("generateApplicationToken() application is null or uuid is missing to generate the application token"); + throw new NullPointerException("Cannot generate application token, please contact admin"); + } + + return this.jwtUtil.createJwtToken( + null, null, + new HashMap<>( + Map.of( + "user_id", AuthNaming.PSAMA_APPLICATION_TOKEN_PREFIX + "|" + application.getName() + ) + ), + AuthNaming.PSAMA_APPLICATION_TOKEN_PREFIX + "|" + application.getUuid().toString(), 365L * 1000 * 60 * 60 * 24); + } + + @Override + public UserDetails loadUserByUsername(String username) throws UsernameNotFoundException { + return null; + } + + public Application getApplicationByName(String picsure) { + return applicationRepo.findByName(picsure); + } +} + diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/BasicMailService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/BasicMailService.java new file mode 100644 index 000000000..f55a8d79b --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/BasicMailService.java @@ -0,0 +1,139 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import java.io.FileNotFoundException; +import java.io.FileReader; +import java.io.StringWriter; +import java.util.Map; + +import edu.harvard.hms.dbmi.avillach.auth.model.AccessEmail; +import edu.harvard.hms.dbmi.avillach.auth.service.MailService; +import jakarta.mail.MessagingException; +import jakarta.mail.internet.MimeMessage; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.mail.javamail.JavaMailSender; +import org.springframework.mail.javamail.MimeMessageHelper; +import org.springframework.stereotype.Service; +import org.springframework.util.StringUtils; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.github.mustachejava.DefaultMustacheFactory; +import com.github.mustachejava.Mustache; +import com.github.mustachejava.MustacheFactory; + +import edu.harvard.hms.dbmi.avillach.auth.entity.User; + +/** + *

    Service class for sending email notifications.

    + */ +@Service +public class BasicMailService implements MailService { + private static final Logger logger = LoggerFactory.getLogger(BasicMailService.class); + private static final MustacheFactory mf = new DefaultMustacheFactory(); + private Mustache accessTemplate = compileTemplate("accessEmail.mustache"); + private Mustache deniedTemplate = compileTemplate("deniedAccessEmail.mustache"); + private final JavaMailSender mailSender; + private final String templatePath; + private final String systemName; + private final String accessGrantEmailSubject; + private final String adminUsers; + + + @Autowired + public BasicMailService(JavaMailSender mailSender, + @Value("${application.template.path}") String templatePath, + @Value("${application.system.name}") String systemName, + @Value("${application.access.grant.email.subject") String accessGrantEmailSubject, + @Value("${application.admin.users}") String adminUsers) { + this.mailSender = mailSender; + this.templatePath = templatePath; + this.systemName = systemName; + this.accessGrantEmailSubject = accessGrantEmailSubject; + this.adminUsers = adminUsers; + } + + /** + * Compile mustache template from templateFile + */ + Mustache compileTemplate(String templateFile) { + try { + FileReader reader = new FileReader(templatePath + templateFile); + return mf.compile(reader, templateFile); + } catch (FileNotFoundException e) { + logger.warn("email template not found for " + templateFile); + return null; + } + } + + /** + * Send email to user about changes in user Roles + * @param user User object + */ + @Override + public void sendUsersAccessEmail(User user) throws MessagingException { + if(accessTemplate == null) { + logger.debug("No template defined for new user access email, not sending"); + }else if (StringUtils.isEmpty(user.getEmail())) { + logger.error("User " + (user.getSubject() != null ? user.getSubject() : "") + " has no email address."); + } else { + String subject = "Your Access To " + this.systemName; + if (this.accessGrantEmailSubject != null && !this.accessGrantEmailSubject.isEmpty() && !this.accessGrantEmailSubject.equals("none")){ + subject = this.accessGrantEmailSubject; + } + sendEmail(accessTemplate, user.getEmail(),subject, new AccessEmail(user, this.systemName)); + } + } + + /** + * Send email to admin about user being denied access to the system + * @param userInfo User info object returned by authentication provider + */ + @Override + public void sendDeniedAccessEmail(JsonNode userInfo) throws MessagingException { + if(deniedTemplate == null) { + logger.debug("No template for Access Denied email, not sending"); + } else { + userInfo.get("email"); + logger.info(userInfo.get("email").asText()); + ObjectMapper mapper = new ObjectMapper(); + Map scope = mapper.convertValue(userInfo, Map.class); + scope.put("systemName", this.systemName); + sendEmail(deniedTemplate, this.adminUsers, "User denied access to " + this.systemName, scope); + } + } + + /** + * Generate email from template and send it. + * @param emailTemplate Name of the template. + * @param to Recipients + * @param subject Subject of the email + * @param scope Object that contains attributes for template. e.g.: Map + */ + @Override + public void sendEmail(Mustache emailTemplate, String to, String subject, Object scope) throws MessagingException { + logger.debug("sendEmail(String, String, String, Object) - start"); + if (StringUtils.isEmpty(to) || StringUtils.isEmpty(subject) || scope == null || emailTemplate == null) { + logger.error("One of the required parameters is null. Can't send email."); + return; + } + + MimeMessage message = mailSender.createMimeMessage(); + MimeMessageHelper helper = new MimeMessageHelper(message); + helper.setFrom(to); + helper.setSubject(subject); + helper.setText(emailTemplate.execute(new StringWriter(), scope).toString(), true); + mailSender.send(message); + logger.debug("sendEmail() finished"); + } + + public void setDeniedTemplate(Mustache deniedTemplate) { + this.deniedTemplate = deniedTemplate; + } + + public void setAccessTemplate(Mustache accessTemplate) { + this.accessTemplate = accessTemplate; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/CacheEvictionService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/CacheEvictionService.java new file mode 100644 index 000000000..2c7dcc90d --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/CacheEvictionService.java @@ -0,0 +1,49 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Service; + +@Service +public class CacheEvictionService { + + private static final Logger log = LoggerFactory.getLogger(CacheEvictionService.class); + private final SessionService sessionService; + private final UserService userService; + private final AccessRuleService accessRuleService; + + @Autowired + public CacheEvictionService(SessionService sessionService, UserService userService, AccessRuleService accessRuleService) { + this.sessionService = sessionService; + this.userService = userService; + this.accessRuleService = accessRuleService; + } + + public void evictCache(String userSubject) { + this.sessionService.endSession(userSubject); + this.userService.evictFromCache(userSubject); + this.accessRuleService.evictFromMergedAccessRuleCache(userSubject); + this.accessRuleService.evictFromPreProcessedAccessRules(userSubject); + // No audit logging here — evictCache is called from multiple paths (logout, + // passport invalidation, login flows) and each caller logs its own domain-specific event. + } + + public void evictCache(User user) { + if (user == null) { + log.error("User is null, cannot evict cache"); + return; + } + + String userSubject = user.getSubject(); + if (StringUtils.isBlank(userSubject)) { + log.error("User subject is blank, cannot evict cache"); + return; + } + + evictCache(userSubject); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/ConnectionWebService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/ConnectionWebService.java new file mode 100644 index 000000000..9c595e449 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/ConnectionWebService.java @@ -0,0 +1,73 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Connection; +import edu.harvard.hms.dbmi.avillach.auth.entity.UserMetadataMapping; +import edu.harvard.hms.dbmi.avillach.auth.repository.ConnectionRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserMetadataMappingRepository; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Service; +import org.springframework.transaction.annotation.Transactional; + +import java.util.List; +import java.util.Optional; + +@Service +public class ConnectionWebService { + + private final ConnectionRepository connectionRepo; + private final UserMetadataMappingRepository userMetadataMappingRepo; + + @Autowired + protected ConnectionWebService(ConnectionRepository connectionRepo, UserMetadataMappingRepository userMetadataMappingRepo) { + this.connectionRepo = connectionRepo; + this.userMetadataMappingRepo = userMetadataMappingRepo; + } + + @Transactional + public List addConnection(List connections) throws IllegalArgumentException { + for (Connection c : connections){ + if (c.getSubPrefix() == null || c.getRequiredFields() == null || c.getLabel() == null || c.getId() == null){ + throw new IllegalArgumentException("Id, Label, Subprefix, and RequiredFields cannot be null"); + } + Optional conn = connectionRepo.findById(c.getId()); + if (conn.isPresent()){ + throw new IllegalArgumentException("Id must be unique, a connection with id " + c.getId() + " already exists in the database"); + } + } + + List savedConnections = this.connectionRepo.saveAll(connections); + + List mappings = savedConnections.stream() + .map(c -> new UserMetadataMapping() + .setConnection(c) + .setGeneralMetadataJsonPath("$.email") + .setAuth0MetadataJsonPath("$.email")) + .toList(); + this.userMetadataMappingRepo.saveAll(mappings); + + return savedConnections; + } + + public Connection getConnectionById(String connectionId) { + return this.connectionRepo.findById(connectionId) + .orElseThrow(() -> new IllegalArgumentException("Connection with id " + connectionId + " not found")); + } + + public List getAllConnections() { + return this.connectionRepo.findAll(); + } + + public List updateConnections(List connections) { + return this.connectionRepo.saveAll(connections); + } + + @Transactional + public List removeConnectionById(String connectionId) { + this.connectionRepo.deleteById(connectionId); + return this.getAllConnections(); + } + + public Connection getConnectionByLabel(String fence) { + return this.connectionRepo.findByLabel(fence); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/CustomUserDetailService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/CustomUserDetailService.java new file mode 100644 index 000000000..93bd19022 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/CustomUserDetailService.java @@ -0,0 +1,54 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Application; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import edu.harvard.hms.dbmi.avillach.auth.model.CustomApplicationDetails; +import edu.harvard.hms.dbmi.avillach.auth.model.CustomUserDetails; +import org.hibernate.Hibernate; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.security.core.userdetails.UserDetails; +import org.springframework.security.core.userdetails.UserDetailsService; +import org.springframework.security.core.userdetails.UsernameNotFoundException; +import org.springframework.stereotype.Service; + +import java.util.Optional; + +@Service +public class CustomUserDetailService implements UserDetailsService { + + private final Logger logger = LoggerFactory.getLogger(CustomUserDetailService.class); + + private final UserService userService; + private final ApplicationService applicationService; + + @Autowired + public CustomUserDetailService(UserService userService, ApplicationService applicationService) { + this.userService = userService; + this.applicationService = applicationService; + } + + @Override + public UserDetails loadUserByUsername(String username) throws UsernameNotFoundException { + if (username.startsWith("application:")) { + String applicationName = username.substring(12); + Optional applicationByID = applicationService.getApplicationByIdWithPrivileges(applicationName); + if (applicationByID.isEmpty()) { + throw new UsernameNotFoundException("Application not found"); + } + + // Initialize the privileges of the application proxy object to avoid lazy loading exception + Hibernate.initialize(applicationByID.get().getPrivileges()); + return new CustomApplicationDetails(applicationByID.get()); + } else { + logger.info("Loading user by username: {}", username); + User user = this.userService.findBySubject(username); + if (user == null) { + throw new UsernameNotFoundException("User not found with email: " + username); + } + + return new CustomUserDetails(user); + } + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/OauthUserMatchingService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/OauthUserMatchingService.java new file mode 100644 index 000000000..f8ab36f92 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/OauthUserMatchingService.java @@ -0,0 +1,129 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import java.util.List; +import java.util.Optional; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.jayway.jsonpath.*; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Connection; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import edu.harvard.hms.dbmi.avillach.auth.entity.UserMetadataMapping; +import edu.harvard.hms.dbmi.avillach.auth.repository.ConnectionRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserRepository; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Service; + +/** + *

    Matches users created by admins with user profiles created by a 3rd party Oauth provider.

    + */ +@Service +public class OauthUserMatchingService { + + private final Logger logger = LoggerFactory.getLogger(OauthUserMatchingService.class); + + private final UserRepository userRepo; + + private final UserService userService; + + private final UserMetadataMappingService mappingService; + + private final ConnectionRepository connectionRepo; + + private final ObjectMapper mapper = new ObjectMapper(); + + @Autowired + public OauthUserMatchingService(UserRepository userRepo, UserService userService, UserMetadataMappingService mappingService, ConnectionRepository connectionRepo) { + this.userRepo = userRepo; + this.userService = userService; + this.mappingService = mappingService; + this.connectionRepo = connectionRepo; + } + + /** + * Retrieve a user profile by access_token and match it to a pre-created user in the database using + * pre-configured matching rules. + * + * @param userInfo UserInfo returned from auth0 + * @return The user that was matched or null if no match was possible. + */ + public User matchTokenToUser(JsonNode userInfo) { + // This retrieves a map of UserInfo as JSON. + try { + String userInfoString = mapper.writeValueAsString(userInfo); + logger.info("Attempting to find match for user with info: {}", userInfo); + + //Parse this once so it doesn't get re-parsed every time we read from it + Configuration conf = Configuration.defaultConfiguration().addOptions(Option.DEFAULT_PATH_LEAF_TO_NULL).addOptions(Option.ALWAYS_RETURN_LIST); + Object parsedInfo = conf.jsonProvider().parse(userInfoString); + //Return lists or null so that we don't have to worry about whether it's a single object or an array, or catch errors + List connections = JsonPath.using(conf).parse(parsedInfo).read("$.identities[0].connection"); + String connectionId = connections.getFirst(); + Optional connection = connectionRepo.findById(connectionId); + if (connection.isEmpty()) { + //We don't have a connection for this user + logger.warn("Unable to find connection with id {}", connectionId); + return null; + } + + List mappings = mappingService.getAllMappingsForConnection(connection.get()); + + if (mappings == null || mappings.isEmpty()) { + //We don't have any mappings for this connection yet + logger.warn("Unable to find user metadata mappings for connectionId {}", connection); + return null; + } + + //We only care about unmatched users + List users = userRepo.findByConnectionAndMatched(connection.get(), false); + if (users == null || users.isEmpty()) { + logger.info("No unmatched users exist with connectionId {}", connection); + return null; + } + for (UserMetadataMapping umm : mappings) { + List auth0values = JsonPath.using(conf).parse(parsedInfo).read(umm.getAuth0MetadataJsonPath()); + if (auth0values == null || auth0values.isEmpty()) { + //Well, nothing found, let's move on. + logger.info("Fetched data has no value at {}", umm.getAuth0MetadataJsonPath()); + break; + } + String auth0value = auth0values.get(0); + for (User u : users) { + List values = null; + try{ + values = JsonPath.using(conf).parse(u.getGeneralMetadata()).read(umm.getGeneralMetadataJsonPath()); + } catch (JsonPathException e) { + logger.warn("User {} has invalid general metadata: {}", u.getUuid(), u.getGeneralMetadata()); + continue; + } + if (values == null || values.isEmpty()) { + logger.warn("User {} has no value at {}", u.getUuid(), umm.getGeneralMetadataJsonPath()); + continue; + } + String generalValue = values.get(0); + if (auth0value.equalsIgnoreCase(generalValue)) { + //Match found!! + String userId = JsonPath.read(parsedInfo, "$.user_id"); + logger.info("Matching user with user_id {}", userId); + u.setAuth0metadata(userInfoString); + u.setMatched(true); + u.setSubject(userId); + userService.save(u); + return u; + } + } + } + } catch (JsonProcessingException e ){ + logger.error("Unable to read UserInfo"); + } + //No user found + logger.info("No matching user found"); + return null; + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/PrivilegeService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/PrivilegeService.java new file mode 100644 index 000000000..51888a973 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/PrivilegeService.java @@ -0,0 +1,461 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.hms.dbmi.avillach.auth.entity.AccessRule; +import edu.harvard.hms.dbmi.avillach.auth.entity.Application; +import edu.harvard.hms.dbmi.avillach.auth.entity.Privilege; +import edu.harvard.hms.dbmi.avillach.auth.entity.Role; +import edu.harvard.hms.dbmi.avillach.auth.model.fenceMapping.StudyMetaData; +import edu.harvard.hms.dbmi.avillach.auth.repository.PrivilegeRepository; +import jakarta.annotation.PostConstruct; +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.context.event.ApplicationContextEvent; +import org.springframework.context.event.EventListener; +import org.springframework.security.core.context.SecurityContext; +import org.springframework.security.core.context.SecurityContextHolder; +import org.springframework.stereotype.Service; +import org.springframework.transaction.annotation.Transactional; + +import java.util.*; +import java.util.regex.Matcher; +import java.util.regex.Pattern; +import java.util.stream.Collectors; + +import static edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming.AuthRoleNaming.ADMIN; + +@Service +public class PrivilegeService { + + private final static Logger logger = LoggerFactory.getLogger(PrivilegeService.class.getName()); + + private final PrivilegeRepository privilegeRepository; + private final ApplicationService applicationService; + private final AccessRuleService accessRuleService; + + private Application picSureApp; + private final String variantAnnotationColumns; + + private final String fence_harmonized_consent_group_concept_path; + private final String fence_parent_consent_group_concept_path; + private final String fence_topmed_consent_group_concept_path; + + private String fence_harmonized_concept_path; + private static final String topmedAccessionField = "\\\\_Topmed Study Accession with Subject ID\\\\"; + + @Autowired + protected PrivilegeService(PrivilegeRepository privilegeRepository, + ApplicationService applicationService, + AccessRuleService accessRuleService, + @Value("${fence.variant.annotation.columns}") String variantAnnotationColumns, + @Value("${fence.harmonized.consent.group.concept.path}") String fenceHarmonizedConsentGroupConceptPath, + @Value("${fence.parent.consent.group.concept.path}") String fenceParentConceptPath, + @Value("${fence.topmed.consent.group.concept.path}") String fenceTopmedConceptPath, + @Value("${fence.consent.group.concept.path}") String fenceHarmonizedConceptPath) { + this.privilegeRepository = privilegeRepository; + this.applicationService = applicationService; + this.accessRuleService = accessRuleService; + this.variantAnnotationColumns = variantAnnotationColumns; + this.fence_harmonized_consent_group_concept_path = fenceHarmonizedConsentGroupConceptPath; + this.fence_parent_consent_group_concept_path = fenceParentConceptPath; + this.fence_topmed_consent_group_concept_path = fenceTopmedConceptPath; + this.fence_harmonized_concept_path = fenceHarmonizedConceptPath; + } + + @PostConstruct + private void init() { + picSureApp = applicationService.getApplicationByName("PICSURE"); + logger.info("variantAnnotationColumns: {}", variantAnnotationColumns); + } + + @Transactional + @EventListener(ApplicationContextEvent.class) + protected void onContextRefreshedEvent() { + updateAllPrivilegesOnStartup(); + } + + @Transactional + public List deletePrivilegeByPrivilegeId(String privilegeId) { + Optional privilege = this.privilegeRepository.findById(UUID.fromString(privilegeId)); + + // Get security context with spring security context + SecurityContext securityContext = SecurityContextHolder.getContext(); + // Get the principal name from the security context + String principalName = securityContext.getAuthentication().getName(); + + if (ADMIN.equals(privilege.get().getName())) { + logger.info("User: {}, is trying to remove the system admin privilege: " + ADMIN, principalName); + throw new RuntimeException("System Admin privilege cannot be removed - uuid: " + privilege.get().getUuid().toString() + + ", name: " + privilege.get().getName()); + } + + this.privilegeRepository.deleteById(UUID.fromString(privilegeId)); + return this.getPrivilegesAll(); + } + + public List updatePrivileges(List privileges) { + this.privilegeRepository.saveAll(privileges); + return this.getPrivilegesAll(); + } + + public List addPrivileges(List privileges) { + return this.privilegeRepository.saveAll(privileges); + } + + public List getPrivilegesAll() { + return this.privilegeRepository.findAll(); + } + + public Privilege getPrivilegeById(String privilegeId) { + return this.privilegeRepository.findById(UUID.fromString(privilegeId)).orElse(null); + } + + public Privilege findByName(String privilegeName) { + return this.privilegeRepository.findByName(privilegeName); + } + + public Privilege save(Privilege privilege) { + return this.privilegeRepository.save(privilege); + } + + public Set addPrivileges(Role r, Map fenceMapping) { + String roleName = r.getName(); + logger.debug("addPrivilege() starting, adding privilege(s) to role {}", roleName); + + //each project can have up to three privileges: Parent | Harmonized | Topmed + //harmonized has 2 ARs for parent + harmonized and harmonized only + //Topmed has up to three ARs for topmed / topmed + parent / topmed + harmonized + Set privs = r.getPrivileges(); + if (privs == null) { + privs = new HashSet(); + } + + //e.g. MANAGED_phs0000xx_c2 or MANAGED_tutorial-biolinc_camp + String project_name = extractProject(roleName); + if (project_name.isEmpty()) { + logger.warn("addPrivileges() role name: {} returned an empty project name", roleName); + } + String consent_group = extractConsentGroup(roleName); + if (!consent_group.isEmpty()) { + logger.warn("addPrivileges() role name: {} returned an empty consent group", roleName); + } + logger.debug("addPrivileges() project name: {} consent group: {}", project_name, consent_group); + + // Look up the metadata by consent group. + StudyMetaData projectMetadata = getStudyMappingForProjectAndConsent(project_name, consent_group, fenceMapping); + + if (projectMetadata == null) { + //no privileges means no access to this project. just return existing set of privs. + logger.warn("No metadata available for project {}.{}", project_name, consent_group); + return privs; + } + + String dataType = projectMetadata.getDataType(); + Boolean isHarmonized = projectMetadata.getIsHarmonized(); + String concept_path = projectMetadata.getTopLevelPath(); + String projectAlias = projectMetadata.getAbbreviatedName(); + + // Need to add the escape sequence back in to the path for parsing later (also need to doubly escape the regex). + // Need to do this for the query Template and scopes, but should NOT do this for the rules. + if (concept_path != null) { + concept_path = concept_path.replaceAll("\\\\", "\\\\\\\\"); + } + + if (dataType != null && dataType.contains("G")) { + //insert genomic/topmed privs - this will also add rules for including harmonized & parent data if applicable + privs.add(upsertTopmedPrivilege(project_name, projectAlias, consent_group, concept_path, isHarmonized)); + } + + if (dataType != null && dataType.contains("P")) { + //insert clinical privs + logger.debug("addPrivileges() project:{} consent_group:{} concept_path:{}", project_name, consent_group, concept_path); + privs.add(upsertClinicalPrivilege(project_name, projectAlias, consent_group, concept_path, false)); + + //if harmonized study, also create harmonized privileges + if (Boolean.TRUE.equals(isHarmonized)) { + privs.add(upsertClinicalPrivilege(project_name, projectAlias, consent_group, concept_path, true)); + } + } + + //projects without G or P in data_type are skipped + if (dataType == null || (!dataType.contains("P") && !dataType.contains("G"))) { + logger.warn("Missing study type for {} {}. Skipping.", project_name, consent_group); + } + + logger.info("addPrivileges() Finished"); + return privs; + } + + /** + * Creates a privilege with a set of access rules that allow queries containing a consent group to pass if the query only contains valid entries that match conceptPath. If the study is harmonized, + * this also creates an access rule to allow access when using the harmonized consent concept path. + * Privileges created with this method will deny access if any genomic filters (topmed data) are included. + * + * @param studyIdentifier The study identifier + * @param consent_group The consent group + * @param conceptPath The concept path + * @param isHarmonized Whether the study is harmonized + * @return The created privilege + */ + private Privilege upsertClinicalPrivilege(String studyIdentifier, String projectAlias, String consent_group, String conceptPath, boolean isHarmonized) { + // Construct the privilege name + String privilegeName = (consent_group != null && !consent_group.isEmpty()) ? + "PRIV_MANAGED_" + studyIdentifier + "_" + consent_group + (isHarmonized ? "_HARMONIZED" : "") : + "PRIV_MANAGED_" + studyIdentifier + (isHarmonized ? "_HARMONIZED" : ""); + + // Check if the Privilege already exists + Privilege priv = this.findByName(privilegeName); + if (priv == null) { + priv = new Privilege(); + } + + try { + priv.setApplication(picSureApp); + priv.setName(privilegeName); + + // In BioData Catalyst this is either \\_harmonized_consent\\_ or \\_consents\\ we need to escape the slashes + String consent_concept_path = isHarmonized ? fence_harmonized_consent_group_concept_path : fence_parent_consent_group_concept_path; + consent_concept_path = escapePath(consent_concept_path); + fence_harmonized_concept_path = escapePath(fence_harmonized_concept_path); + + priv.setQueryTemplate(createClinicalQueryTemplate(studyIdentifier, consent_group, consent_concept_path)); + priv.setQueryScope(isHarmonized ? String.format("[\"%s\",\"_\",\"%s\"]", conceptPath, fence_harmonized_concept_path) : String.format("[\"%s\",\"_\"]", conceptPath)); + + Set accessRules = new HashSet<>(); + accessRules.add(createClinicalParentAccessRule(studyIdentifier, consent_group, conceptPath, projectAlias)); + accessRules.add(createClinicalTopmedParentAccessRule(studyIdentifier, consent_group, conceptPath, projectAlias)); + if (isHarmonized) { + accessRules.add(createClinicalHarmonizedAccessRule(studyIdentifier, consent_group, conceptPath, projectAlias)); + } + accessRules.addAll(this.accessRuleService.addStandardAccessRules()); + priv.setAccessRules(accessRules); + + priv = this.save(priv); + logger.info("Added new privilege {} to DB", priv.getName()); + } catch (Exception ex) { + logger.error("Could not save privilege", ex); + } + return priv; + } + + private static String createClinicalQueryTemplate(String studyIdentifier, String consent_group, String consent_concept_path) { + String studyIdentifierField = (consent_group != null && !consent_group.isEmpty()) ? studyIdentifier + "." + consent_group : studyIdentifier; + return String.format( + "{\"categoryFilters\": {\"%s\":[\"%s\"]},\"numericFilters\":{},\"requiredFields\":[],\"fields\":[\"%s\"],\"variantInfoFilters\":[{\"categoryVariantInfoFilters\":{},\"numericVariantInfoFilters\":{}}],\"expectedResultType\": \"COUNT\"}", + consent_concept_path, studyIdentifierField, AccessRuleService.parentAccessionField + ); + } + + private AccessRule createClinicalHarmonizedAccessRule(String studyIdentifier, String consentGroup, String conceptPath, String projectAlias) { + AccessRule ar = this.accessRuleService.createConsentAccessRule(studyIdentifier, consentGroup, "HARMONIZED", fence_harmonized_consent_group_concept_path); + ar.setSubAccessRule(new HashSet<>()); + this.accessRuleService.configureHarmonizedAccessRule(ar, studyIdentifier, conceptPath, projectAlias); + return this.accessRuleService.save(ar); + } + + private AccessRule createClinicalTopmedParentAccessRule(String studyIdentifier, String consentGroup, String conceptPath, String projectAlias) { + AccessRule ar = this.accessRuleService.upsertTopmedAccessRule(studyIdentifier, consentGroup, "TOPMED+PARENT"); + ar.setSubAccessRule(new HashSet<>()); + ar = this.accessRuleService.configureClinicalAccessRuleWithPhenoSubRule(ar, studyIdentifier, consentGroup, conceptPath, projectAlias); + return this.accessRuleService.save(ar); + } + + private AccessRule createClinicalParentAccessRule(String studyIdentifier, String consentGroup, String conceptPath, String projectAlias) { + AccessRule ar = this.accessRuleService.createConsentAccessRule(studyIdentifier, consentGroup, "PARENT", fence_parent_consent_group_concept_path); + ar.setSubAccessRule(new HashSet<>()); + this.accessRuleService.configureAccessRule(ar, studyIdentifier, consentGroup, conceptPath, projectAlias); + return this.accessRuleService.save(ar); + } + + /** + * Creates a privilege for Topmed access. This has (up to) three access rules: + * 1) topmed only 2) topmed + parent 3) topmed + harmonized. + * + * @param studyIdentifier The study identifier + * @param projectAlias The project alias + * @param consentGroup The consent group + * @param parentConceptPath The parent concept path + * @param isHarmonized Whether the study is harmonized + * @return Privilege + */ + private Privilege upsertTopmedPrivilege(String studyIdentifier, String projectAlias, String consentGroup, String parentConceptPath, boolean isHarmonized) { + String privilegeName = "PRIV_MANAGED_" + studyIdentifier + "_" + consentGroup + "_TOPMED"; + Privilege priv = this.findByName(privilegeName); + + if (priv == null) { + priv = new Privilege(); + } + + try { + buildPrivilegeObject(priv, privilegeName, studyIdentifier, consentGroup); + + Set accessRules = new HashSet<>(); + accessRules.add(createTopmedAccessRules(studyIdentifier, projectAlias, consentGroup)); + + if (parentConceptPath != null) { + accessRules.add(createTopmedParentAccessRule(studyIdentifier, consentGroup, parentConceptPath, projectAlias)); + if (isHarmonized) { + accessRules.add(createHarmonizedTopmedAccessRule(studyIdentifier, projectAlias, consentGroup, parentConceptPath)); + } + } + + accessRules.addAll(this.accessRuleService.addStandardAccessRules()); + + priv.setAccessRules(accessRules); + logger.info("upsertTopmedPrivilege() Added {} access_rules to privilege", accessRules.size()); + + priv = this.save(priv); + logger.info("upsertTopmedPrivilege() Added new privilege {} to DB", priv.getName()); + } catch (Exception ex) { + logger.error("upsertTopmedPrivilege() could not save privilege", ex); + } + + return priv; + } + + private AccessRule createHarmonizedTopmedAccessRule(String studyIdentifier, String projectAlias, String consentGroup, String parentConceptPath) { + AccessRule harmonizedRule = this.accessRuleService.upsertHarmonizedAccessRule(studyIdentifier, consentGroup); + harmonizedRule.setSubAccessRule(new HashSet<>()); + harmonizedRule = this.accessRuleService.populateHarmonizedAccessRule(harmonizedRule, parentConceptPath, studyIdentifier, projectAlias); + this.accessRuleService.save(harmonizedRule); + return harmonizedRule; + } + + private AccessRule createTopmedParentAccessRule(String studyIdentifier, String consentGroup, String parentConceptPath, String projectAlias) { + AccessRule topmedParentRule = this.accessRuleService.upsertTopmedAccessRule(studyIdentifier, consentGroup, "TOPMED+PARENT"); + topmedParentRule.setSubAccessRule(new HashSet<>()); + this.accessRuleService.populateTopmedAccessRule(topmedParentRule, true); + topmedParentRule.getSubAccessRule().addAll(this.accessRuleService.getPhenotypeSubRules(studyIdentifier, parentConceptPath, projectAlias)); + topmedParentRule.getSubAccessRule().add(this.accessRuleService.createPhenotypeSubRule(fence_topmed_consent_group_concept_path, "ALLOW_TOPMED_CONSENT", "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "", true)); + return this.accessRuleService.save(topmedParentRule); + } + + private AccessRule createTopmedAccessRules(String studyIdentifier, String projectAlias, String consentGroup) { + AccessRule topmedRule = this.accessRuleService.upsertTopmedAccessRule(studyIdentifier, consentGroup, "TOPMED"); + topmedRule = this.accessRuleService.populateTopmedAccessRule(topmedRule, false); + topmedRule.getSubAccessRule().addAll(this.accessRuleService.getPhenotypeRestrictedSubRules(studyIdentifier, consentGroup, projectAlias)); + return this.accessRuleService.save(topmedRule); + } + + private void buildPrivilegeObject(Privilege priv, String privilegeName, String studyIdentifier, String consentGroup) { + priv.setApplication(picSureApp); + priv.setName(privilegeName); + String consent = studyIdentifier + (StringUtils.isNotBlank(consentGroup) ? "." + consentGroup : ""); + priv.setDescription("MANAGED privilege for Topmed " + consent); + + String consentConceptPath = escapePath(fence_topmed_consent_group_concept_path); + fence_harmonized_concept_path = escapePath(fence_harmonized_concept_path); + + + String queryTemplateText = "{\"categoryFilters\": {\"" + consentConceptPath + "\":[\"" + consent + "\"]}," + + "\"numericFilters\":{},\"requiredFields\":[]," + + "\"fields\":[\"" + topmedAccessionField + "\"]," + + "\"variantInfoFilters\":[{\"categoryVariantInfoFilters\":{},\"numericVariantInfoFilters\":{}}]," + + "\"expectedResultType\": \"COUNT\"" + + "}"; + + priv.setQueryTemplate(queryTemplateText); + + priv.setQueryScope(buildQueryScope(this.variantAnnotationColumns)); + } + + private String escapePath(String path) { + if (path != null && !path.contains("\\\\")) { + return path.replaceAll("\\\\", "\\\\\\\\"); + } + return path; + } + + private String buildQueryScope(String variantColumns) { + if (variantColumns == null || variantColumns.isEmpty()) { + return "[\"_\"]"; + } + + return Arrays.stream(variantColumns.split(",")) + .map(path -> "\"" + path + "\"") + .collect(Collectors.joining(",", "[", ",\"_\"]")); + } + + private String extractProject(String roleName) { + String projectPattern = "MANAGED_(.*?)(?:_c\\d+)?$"; + if (roleName.startsWith("MANUAL_")) { + projectPattern = "MANUAL_(.*?)(?:_c\\d+)?$"; + } + Pattern projectRegex = Pattern.compile(projectPattern); + Matcher projectMatcher = projectRegex.matcher(roleName); + String project = ""; + if (projectMatcher.find()) { + project = projectMatcher.group(1).trim(); + } else { + logger.info("extractProject() Could not extract project from role name: {}", roleName); + String[] parts = roleName.split("_", 1); + if (parts.length > 0) { + project = parts[1]; + } + } + return project; + } + + private static String extractConsentGroup(String roleName) { + String consentPattern = "MANAGED_.*?_c(\\d+)$"; + if (roleName.startsWith("MANUAL_")) { + consentPattern = "MANUAL_.*?_c(\\d+)$"; + } + Pattern consentRegex = Pattern.compile(consentPattern); + Matcher consentMatcher = consentRegex.matcher(roleName); + String consentGroup = ""; + if (consentMatcher.find()) { + consentGroup = "c" + consentMatcher.group(1).trim(); + } + return consentGroup; + } + + private StudyMetaData getStudyMappingForProjectAndConsent(String projectId, String consent_group, Map fenceMapping) { + String consentVal = (consent_group != null && !consent_group.isEmpty()) ? projectId + "." + consent_group : projectId; + logger.debug("getStudyMappingForProjectAndConsent() looking up {}", consentVal); + + return fenceMapping.get(consentVal); + } + + public Optional findById(UUID uuid) { + return privilegeRepository.findById(uuid); + } + + /** + * This method will update all existing privileges with the standard access rules and allowed query types. + * This method will not remove any existing standard access rules If you need to remove a standard access rule, + * you will need to create a migration script. + */ + protected void updateAllPrivilegesOnStartup() { + List privileges = this.getPrivilegesAll(); + Set standardAccessRules = this.accessRuleService.addStandardAccessRules(); + if (standardAccessRules.isEmpty()) { + logger.error("No standard access rules found."); + return; + } else { + privileges.forEach(privilege -> + { + privilege.getAccessRules().addAll(standardAccessRules); + this.save(privilege); + }); + } + + List privilegeIds = privileges.stream().map(Privilege::getUuid).toList(); + List accessRules = this.accessRuleService.getAccessRulesByPrivilegeIds(privilegeIds); + + // find each access rule that has sub access rules that allow query types an update them + accessRules.parallelStream() + .filter(accessRule -> accessRule.getSubAccessRule().stream().anyMatch(subAccessRule -> subAccessRule.getName().startsWith("AR_ALLOW_"))) + .forEach(accessRule -> { + Set subAccessRules = accessRule.getSubAccessRule(); + subAccessRules.removeIf(subAccessRule -> subAccessRule.getName().startsWith("AR_ALLOW_")); + + // Add the currently allowed query types + subAccessRules.addAll(this.accessRuleService.getAllowedQueryTypeRules()); + accessRule.setSubAccessRule(subAccessRules); + this.accessRuleService.save(accessRule); + }); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/RASPassPortService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/RASPassPortService.java new file mode 100644 index 000000000..f7b7314ae --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/RASPassPortService.java @@ -0,0 +1,242 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import com.fasterxml.jackson.databind.JsonNode; +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import edu.harvard.hms.dbmi.avillach.auth.enums.PassportValidationResponse; +import edu.harvard.hms.dbmi.avillach.auth.model.ras.Ga4ghPassportV1; +import edu.harvard.hms.dbmi.avillach.auth.model.ras.Passport; +import edu.harvard.hms.dbmi.avillach.auth.model.ras.RasDbgapPermission; +import edu.harvard.hms.dbmi.avillach.auth.utils.JWTUtil; +import edu.harvard.hms.dbmi.avillach.auth.utils.RestClientUtil; +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.http.HttpEntity; +import org.springframework.http.ResponseEntity; +import org.springframework.scheduling.annotation.Scheduled; +import org.springframework.stereotype.Service; +import org.springframework.util.LinkedMultiValueMap; +import org.springframework.util.MultiValueMap; + +import java.time.Instant; +import java.util.*; +import java.util.function.Function; +import java.util.stream.Collectors; + +@Service +public class RASPassPortService { + + enum ValidationOutcome { VALIDATED, INVALIDATED, SKIPPED } + + private final Logger logger = LoggerFactory.getLogger(RASPassPortService.class); + private final RestClientUtil restClientUtil; + private final UserService userService; + private final String rasURI; + private final CacheEvictionService cacheEvictionService; + private final LoggingClient loggingClient; + + @Autowired + public RASPassPortService(RestClientUtil restClientUtil, + UserService userService, + @Value("${ras.idp.uri}") String rasURI, CacheEvictionService cacheEvictionService, + LoggingClient loggingClient) { + this.restClientUtil = restClientUtil; + this.userService = userService; + this.rasURI = rasURI.replaceAll("/$", ""); + this.cacheEvictionService = cacheEvictionService; + this.loggingClient = loggingClient; + + logger.info("RASPassPortService initialized with rasURI: {}", rasURI); + } + + /** + * We will run this nearly immediately after startup. We don't know how long it has been since the last auth micro app + * ran its validate. + */ + @Scheduled(initialDelay = 1000, fixedDelay = 300000) + public void validateAllUserPassports() { + logger.info("validateAllUserPassports() STARTING PASSPORT VALIDATION"); + + Set allUsersWithAPassport = this.userService.getAllUsersWithAPassport(); + if (allUsersWithAPassport.isEmpty()) { + logger.info("validateAllUserPassports() NO USERS WITH PASSPORTS FOUND"); + return; + } + + Map counts = allUsersWithAPassport.parallelStream() + .map(this::validateUserPassport) + .collect(Collectors.groupingBy(Function.identity(), Collectors.counting())); + + long totalValidated = counts.getOrDefault(ValidationOutcome.VALIDATED, 0L); + long totalInvalidated = counts.getOrDefault(ValidationOutcome.INVALIDATED, 0L); + + if (loggingClient != null && loggingClient.isEnabled()) { + try { + loggingClient.send(LoggingEvent.builder("AUTHZ").action("passport.validation_batch") + .metadata(Map.of("total_validated", totalValidated, "total_invalidated", totalInvalidated)) + .build()); + } catch (Exception e) { + logger.warn("Failed to send PASSPORT_VALIDATION_BATCH audit log event", e); + } + } + } + + ValidationOutcome validateUserPassport(User user) { + logger.info("validateAllUserPassports() ATTEMPTING TO VALIDATE PASSPORT ___ USER {}", user.getSubject()); + if (StringUtils.isBlank(user.getPassport())) { + logger.error("NO PASSPORT FOUND ___ USER {}", user.getSubject()); + return ValidationOutcome.SKIPPED; + } + + String encodedPassport = user.getPassport(); + Optional passportOptional = JWTUtil.parsePassportJWTV11(encodedPassport); + if (passportOptional.isEmpty()) { + logger.error("FAILED TO DECODE PASSPORT ___ USER: {}", user.getSubject()); + user.setPassport(null); + userService.save(user); + cacheEvictionService.evictCache(user); + sendInvalidatedEvent(user.getSubject(), "FAILED_TO_DECODE_PASSPORT"); + return ValidationOutcome.INVALIDATED; + } + + List ga4ghPassportV1 = passportOptional.get().getGa4ghPassportV1(); + for (String visa : ga4ghPassportV1) { + Optional parsedVisa = JWTUtil.parseGa4ghPassportV1(visa); + if (parsedVisa.isEmpty()) { + logger.error("validatePassport() ga4ghPassportV1 PASSPORT VISA IS EMPTY ___ USER {}", user.getSubject()); + return ValidationOutcome.SKIPPED; + } + + if (parsedVisa.get().getExp() < System.currentTimeMillis() / 1000) { + handleFailedValidationResponse(PassportValidationResponse.VISA_EXPIRED.getValue(), user); + sendInvalidatedEvent(user.getSubject(), PassportValidationResponse.VISA_EXPIRED.getValue()); + return ValidationOutcome.INVALIDATED; + } + + Optional response = validateVisa(visa); + if (response.isPresent()) { + boolean successfullyUpdated = handlePassportValidationResponse(response.get(), user); + if (!successfullyUpdated) { + logger.info("PASSPORT VALIDATION COMPLETE __ PASSPORT IS NO LONGER VALID ___ USER {} ___ USER LOGGED OUT", user.getSubject()); + sendInvalidatedEvent(user.getSubject(), response.get()); + return ValidationOutcome.INVALIDATED; + } else { + logger.info("PASSPORT VALIDATION COMPLETE __ PASSPORT IS VALID ___ USER {}", user.getSubject()); + return ValidationOutcome.VALIDATED; + } + } + } + + return ValidationOutcome.SKIPPED; + } + + private void sendInvalidatedEvent(String userSubject, String reason) { + if (loggingClient != null && loggingClient.isEnabled()) { + try { + loggingClient.send(LoggingEvent.builder("AUTHZ").action("passport.invalidated") + .metadata(Map.of("user_subject", userSubject, "reason", reason)) + .build()); + } catch (Exception e) { + logger.warn("Failed to send PASSPORT_INVALIDATED audit log event", e); + } + } + } + + private boolean handlePassportValidationResponse(String response, User user) { + PassportValidationResponse passportValidationResponse = PassportValidationResponse.fromValue(response); + if (passportValidationResponse == null) { + logger.error("handlePassportValidationResponse() VALIDATE PASSPORT RESPONSE WAS NULL ___ USER {}, ", user.getSubject()); + return false; + } + + return switch (passportValidationResponse) { + case VALID -> handleValidValidationResponse(response, user); + case PERMISSION_UPDATE, INVALID, MISSING, INVALID_PASSPORT, VISA_EXPIRED, TXN_ERROR, EXPIRATION_ERROR, VALIDATION_ERROR, + EXPIRED_POLLING -> handleFailedValidationResponse(response, user); + }; + } + + /** + * If a passport is anything but VALID the user will be logged out and their passport be cleared. + * + * @param validateResponse The response from the passport validation + * @param user The user to log out + * @return true if the user was successfully updated + */ + private boolean handleFailedValidationResponse(String validateResponse, User user) { + this.userService.save(user); + this.userService.logoutUser(user); + this.cacheEvictionService.evictCache(user); + this.logger.info("handleFailedValidationResponse - {} - USER LOGGED OUT - {}", validateResponse, user.getSubject()); + return false; + } + + private boolean handleValidValidationResponse(String validateResponse, User user) { + this.logger.info("handleValidValidationResponse PASSPORT VALIDATE RESPONSE ___ {} ___ USER {}", validateResponse, user.getSubject()); + return true; + } + + public Optional validateVisa(String visa) { + if (StringUtils.isBlank(visa)) { + logger.error("validatePassport() VISA IS EMPTY"); + return Optional.empty(); + } + + MultiValueMap queryParams = new LinkedMultiValueMap<>(); + queryParams.add("visa", visa); + HttpEntity> request = new HttpEntity<>(queryParams, null); + + String responseVal = PassportValidationResponse.VISA_EXPIRED.getValue(); + ResponseEntity resp; + try { + resp = this.restClientUtil.retrievePostResponse(this.rasURI + "/passport/validate", request); + responseVal = resp.getBody(); + } catch (Exception e) { + logger.error("validatePassport() FAILED TO VALIDATE VISA ___ {}", e.getMessage()); + } + + return Optional.ofNullable(responseVal); + } + + public Set ga4ghPassportToRasDbgapPermissions(Set> ga4ghPassports) { + if (ga4ghPassports == null) { + return null; + } + + logger.debug("Converting ga4ghPassports to RasDbgapPermissions"); + HashSet rasDbgapPermissions = new HashSet<>(); + long date = Instant.now().toEpochMilli() / 1000; + ga4ghPassports.forEach(ga4ghPassport -> { + if (ga4ghPassport.isPresent()) { + Ga4ghPassportV1 ga4ghPassportV1 = ga4ghPassport.get(); + List permissions = ga4ghPassportV1.getRasDbgagPermissions(); + rasDbgapPermissions.addAll(permissions.stream().filter(rasDbgapPermission -> date <= rasDbgapPermission.getExpiration()).collect(Collectors.toSet())); + } + }); + + return rasDbgapPermissions; + } + + public Optional extractPassport(JsonNode introspectResponse) { + if (introspectResponse == null) { + logger.error("extractPassport() introspectResponse is null"); + return Optional.empty(); + } + + if (!introspectResponse.has("passport_jwt_v11")) { + logger.error("extractPassport() introspectResponse does not have passport_jwt_v11"); + return Optional.empty(); + } + + return JWTUtil.parsePassportJWTV11(introspectResponse.get("passport_jwt_v11").toString()); + } + + public boolean isExpired(Passport passport) { + return passport.getExp() < System.currentTimeMillis() / 1000 && + passport.getIat() < System.currentTimeMillis() / 1000; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/RoleService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/RoleService.java new file mode 100644 index 000000000..996fa38c0 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/RoleService.java @@ -0,0 +1,373 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.hms.dbmi.avillach.auth.entity.Privilege; +import edu.harvard.hms.dbmi.avillach.auth.entity.Role; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import edu.harvard.hms.dbmi.avillach.auth.model.fenceMapping.StudyMetaData; +import edu.harvard.hms.dbmi.avillach.auth.model.ras.RasDbgapPermission; +import edu.harvard.hms.dbmi.avillach.auth.repository.RoleRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserRepository; +import edu.harvard.hms.dbmi.avillach.auth.utils.FenceMappingUtility; +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.context.ApplicationContext; +import org.springframework.context.event.ContextRefreshedEvent; +import org.springframework.context.event.EventListener; +import org.springframework.stereotype.Service; +import org.springframework.transaction.annotation.Transactional; + +import java.util.*; +import java.util.function.Function; +import java.util.stream.Collectors; + +@Service +public class RoleService { + + private final Logger logger = LoggerFactory.getLogger(RoleService.class); + private final UserRepository userRepository; + private final RoleRepository roleRepository; + private final PrivilegeService privilegeService; + private final FenceMappingUtility fenceMappingUtility; + public static final String MANAGED_OPEN_ACCESS_ROLE_NAME = "MANUAL_ROLE_OPEN_ACCESS"; + public static final String MANAGED_AUTH_ACCESS_ROLE_NAME = "MANUAL_ROLE_AUTH_ACCESS"; + public static final String MANAGED_ROLE_NAMED_DATASET = "MANUAL_ROLE_NAMED_DATASET"; + private final Set publicAccessRoles = new HashSet<>(); + + private final ApplicationContext applicationContext; + private final LoggingClient loggingClient; + + @Autowired + public RoleService(UserRepository userRepository, RoleRepository roleRepository, PrivilegeService privilegeService, FenceMappingUtility fenceMappingUtility, ApplicationContext applicationContext, LoggingClient loggingClient) { + this.userRepository = userRepository; + this.roleRepository = roleRepository; + this.privilegeService = privilegeService; + this.fenceMappingUtility = fenceMappingUtility; + this.applicationContext = applicationContext; + this.loggingClient = loggingClient; + } + + @EventListener(ContextRefreshedEvent.class) + public void createPermissionsForFenceMapping() { + if (this.fenceMappingUtility.getFENCEMapping() != null && this.fenceMappingUtility.getFenceMappingByAuthZ() != null + && !this.fenceMappingUtility.getFENCEMapping().isEmpty() && !this.fenceMappingUtility.getFenceMappingByAuthZ().isEmpty()) { + // Create all potential access rules using the fence mapping + Set roles = this.fenceMappingUtility.getFenceMappingByAuthZ().values().parallelStream() + .filter(this::projectMetaIsValid) + .map(this::extractRole) + .collect(Collectors.toSet()); + + RoleService roleService = applicationContext.getBean(RoleService.class); + roleService.cleanupRolesNotInMapping(roles); + + this.persistAll(roles); + + if (loggingClient != null && loggingClient.isEnabled()) { + try { + loggingClient.send(LoggingEvent.builder("AUTHZ").action("role.fence_sync") + .metadata(Map.of( + "roles_synced_count", String.valueOf(roles.size()) + )).build()); + } catch (Exception e) { + logger.warn("Failed to send FENCE role sync logging event", e); + } + } + } else { + logger.error("createPermissionsForFenceMapping() -> createAndUpsertRole could not find any studies in FENCE mapping"); + } + + String publicAccessRolesString = publicAccessRoles.stream().map(Role::getName).collect(Collectors.joining(", ")); + logger.info("Public access roles: {}", publicAccessRolesString); + logger.info("RoleService initialized..."); + } + + @Transactional + protected void cleanupRolesNotInMapping(Set roles) { + try { + // We only want to update MANAGED_ roles + Set roleNamesInMapping = roles.stream().map(Role::getName).filter(roleName -> roleName.startsWith("MANAGED_")).collect(Collectors.toSet()); + Set byNameNotIn = this.roleRepository.findByNameNotIn(roleNamesInMapping); + Set managedRoles = byNameNotIn.stream().filter(role -> role.getName().startsWith("MANAGED_")).collect(Collectors.toSet()); + logger.info("List of roles not in the fence mapping: {}", managedRoles.stream().map(Role::getName).collect(Collectors.joining(", "))); + + // First, delete the user-role associations + List roleIDs = managedRoles.stream().map(Role::getUuid).collect(Collectors.toList()); + if (!roleIDs.isEmpty()) { + this.userRepository.deleteUserRoles(roleIDs); + logger.info("Deleted user-role associations for {} roles", roleIDs.size()); + } + + // Then clear privileges from each role and delete them one by one + if (!managedRoles.isEmpty()) { + for (Role role : managedRoles) { + try { + // Clear privileges to remove entries from role_privilege table + if (role.getPrivileges() != null && !role.getPrivileges().isEmpty()) { + role.setPrivileges(new HashSet<>()); + roleRepository.save(role); + logger.debug("Cleared privileges for role: {}", role.getName()); + } + + // Now delete the role + roleRepository.delete(role); + logger.debug("Deleted role: {}", role.getName()); + } catch (Exception e) { + logger.error("Error deleting role {}: {}", role.getName(), e.getMessage(), e); + } + } + logger.info("Deleted {} roles", managedRoles.size()); + } + + if (loggingClient != null && loggingClient.isEnabled()) { + try { + loggingClient.send(LoggingEvent.builder("AUTHZ").action("role.cleanup") + .metadata(Map.of( + "roles_deleted", managedRoles.stream().map(Role::getName).collect(Collectors.joining(", ")), + "trigger", "fence_mapping_sync" + )).build()); + } catch (Exception e) { + logger.warn("Failed to send role cleanup logging event", e); + } + } + } catch (Exception e) { + logger.error("Error cleaning up roles not in mapping", e); + throw e; + } + } + + private boolean projectMetaIsValid(StudyMetaData projectMetadata) { + if (projectMetadata == null) { + logger.error("createPermissionsForFenceMapping() -> createAndUpsertRole could not find study in FENCE mapping SKIPPING: NULL"); + return false; + } + if (projectMetadata.getStudyIdentifier() == null || projectMetadata.getStudyIdentifier().isEmpty()) { + logger.error("createPermissionsForFenceMapping() -> createAndUpsertRole could not find study identifier in FENCE mapping SKIPPING: {}", projectMetadata); + return false; + } + if (projectMetadata.getAuthZ() == null || projectMetadata.getAuthZ().isEmpty()) { + logger.error("createPermissionsForFenceMapping() -> createAndUpsertRole could not find authZ in FENCE mapping SKIPPING: {}", projectMetadata); + return false; + } + return true; + } + + public Role extractRole(StudyMetaData projectMetadata) { + String projectId = projectMetadata.getStudyIdentifier(); + String consentCode = projectMetadata.getConsentGroupCode(); + String newRoleName = org.apache.commons.lang3.StringUtils.isNotBlank(consentCode) ? "MANAGED_" + projectId + "_" + consentCode : "MANAGED_" + projectId; + Role role = this.createRole(newRoleName, "MANAGED role " + newRoleName); + if (projectMetadata.getStudyType().equalsIgnoreCase("public")) { + publicAccessRoles.add(role); + } + return role; + } + + public Optional getRoleById(String roleId) { + return roleRepository.findById(UUID.fromString(roleId)); + } + + public Optional getRoleById(UUID roleId) { + return roleRepository.findById(roleId); + } + + public List getAllRoles() { + return roleRepository.findAll(); + } + + @Transactional + public List addRoles(List roles) { + checkPrivilegeAssociation(roles); + return roleRepository.saveAll(roles); + } + + /** + * check if the privileges under role is in the database or not, + * then retrieve it from database and attach it to role object + * + * @param roles list of roles + */ + private void checkPrivilegeAssociation(List roles) throws RuntimeException { + for (Role role : roles) { + if (role.getPrivileges() != null) { + Set privileges = new HashSet<>(); + for (Privilege p : role.getPrivileges()) { + Optional privilege = this.privilegeService.findById(p.getUuid()); + if (privilege.isEmpty()) { + throw new RuntimeException("Privilege not found - uuid: " + p.getUuid().toString()); + } + privileges.add(privilege.get()); + } + role.setPrivileges(privileges); + } + } + + } + + @Transactional + public List updateRoles(List roles) { + checkPrivilegeAssociation(roles); + return roleRepository.saveAll(roles); + } + + @Transactional + public Optional> removeRoleById(String roleId) { + Optional optionalRole = roleRepository.findById(UUID.fromString(roleId)); + if (optionalRole.isEmpty()) { + return Optional.empty(); + } + + roleRepository.deleteById(optionalRole.get().getUuid()); + return Optional.of(roleRepository.findAll()); + } + + public void addObjectToSet(Set roles, Role t) { + // check if the role exists in the database + Role role = roleRepository.findById(t.getUuid()).orElse(null); + if (role == null) { + throw new RuntimeException("Role not found - uuid: " + t.getUuid().toString()); + } + + roles.add(t); + } + + public Role getRoleByName(String roleName) { + return this.roleRepository.findByName(roleName); + } + + public Role save(Role r) { + return this.roleRepository.save(r); + } + + public Set getRolesByIds(Set roleUuids) { + return this.roleRepository.findByUuidIn(roleUuids); + } + + public List persistAll(List newRoles) { + return this.roleRepository.saveAll(newRoles); + } + + private List persistAll(Set newRoles) { + return this.roleRepository.saveAll(newRoles); + } + + public Role findByName(String roleName) { + return this.roleRepository.findByName(roleName); + } + + public Role getOrCreateRole(String roleName, String roleDescription) { + Role existingRole = this.roleRepository.findByName(roleName); + if (existingRole != null) { + return existingRole; + } + + return createRole(roleName, roleDescription); + } + + public Role createRole(String roleName, String roleDescription) { + if (roleName.isEmpty()) { + logger.info("createRole() roleName is empty"); + return null; + } + + Role role = findByName(roleName); + if (role != null) { + // Role already exists + logger.trace("upsertRole() role: {} already exists", role.getName()); + } else { + logger.info("createRole() New PSAMA role name:{}", roleName); + // This is a new Role + role = new Role(); + role.setName(roleName); + role.setDescription(roleDescription); + logger.info("createRole() created new role"); + } + + /* + * Even if a role already exists, there is a chance the privileges have changed. We need to update all + * roles' privileges out of precaution. + */ + role.setPrivileges(privilegeService.addPrivileges(role, this.fenceMappingUtility.getFENCEMapping())); + + return role; + } + + /** + * Insert or Update the User object's list of Roles in the database. + * + * @param u The User object the generated Role will be added to + * @param roleName Name of the Role + * @param roleDescription Description of the Role + * @return boolean Whether the Role was successfully added to the User or not + */ + public boolean upsertRole(User u, String roleName, String roleDescription) { + boolean status = false; + + // Get the User's list of Roles. The first time, this will be an empty Set. + // This method is called for every Role, and the User's list of Roles will + // be updated for all subsequent calls. + try { + Role r = null; + // Create the Role in the Servicesitory, if it does not exist. Otherwise, add it. + Role existing_role = this.getRoleByName(roleName); + if (existing_role != null) { + // Role already exists + logger.info("upsertRole() role already exists"); + r = existing_role; + } else { + // This is a new Role + r = new Role(); + r.setName(roleName); + r.setDescription(roleDescription); + // Since this is a new Role, we need to ensure that the + // corresponding Privilege (with gates) and AccessRule is added. + r.setPrivileges(privilegeService.addPrivileges(r, this.fenceMappingUtility.getFENCEMapping())); + this.save(r); + logger.info("upsertRole() created new role"); + } + if (u != null) { + u.getRoles().add(r); + } + status = true; + } catch (Exception ex) { + logger.error("upsertRole() Could not inser/update role {} to Service", roleName, ex); + } + + + logger.debug("upsertRole() finished"); + return status; + } + + public Set getRoleNamesForDbgapPermissions(Set dbgapPermissions) { + Set roles = new HashSet<>(); + if (dbgapPermissions == null || dbgapPermissions.isEmpty()) { + logger.info("getRoleNamesForDbgapPermissions() dbgapPermissions is empty"); + return roles; + } + + dbgapPermissions.forEach(dbgapPermission -> { + String roleName = StringUtils.isNotBlank(dbgapPermission.getConsentGroup()) ? + "MANAGED_" + dbgapPermission.getPhsId() + "_" + dbgapPermission.getConsentGroup() : + "MANAGED_" + dbgapPermission.getPhsId(); + roles.add(roleName); + }); + + return roles; + } + + public Set findByNameIn(Set roleNames) { + return this.roleRepository.findByNameIn(roleNames); + } + + public Map findByNames(Set roleNames) { + return this.findByNameIn(roleNames).stream() + .collect(Collectors.toMap(Role::getName, Function.identity())); + } + + public Set getPublicAccessRoles() { + return publicAccessRoles; + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/SessionService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/SessionService.java new file mode 100644 index 000000000..ebb89e87e --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/SessionService.java @@ -0,0 +1,75 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.cache.Cache; +import org.springframework.cache.CacheManager; +import org.springframework.cache.annotation.CacheEvict; +import org.springframework.cache.annotation.CachePut; +import org.springframework.stereotype.Service; + +import java.util.Map; +import java.util.Optional; + +@Service +public class SessionService { + + private static final Logger logger = LoggerFactory.getLogger(SessionService.class); + + private final long sessionMaxDuration; + private final CacheManager cacheManager; + private final LoggingClient loggingClient; + + public SessionService(@Value("${application.max.session.length}") long sessionMaxDuration, CacheManager cacheManager, + LoggingClient loggingClient) { + this.sessionMaxDuration = sessionMaxDuration > 0 ? sessionMaxDuration : 8 * 60 * 60 * 1000; // 8 hours in milliseconds + this.cacheManager = cacheManager; + this.loggingClient = loggingClient; + } + + @CachePut(value = "sessions") + public long startSession(String userSubject) { + if (loggingClient != null && loggingClient.isEnabled()) { + try { + loggingClient.send(LoggingEvent.builder("AUTH").action("session.start") + .metadata(Map.of("user_subject", userSubject)) + .build()); + } catch (Exception e) { + logger.warn("Failed to send SESSION_START audit log event", e); + } + } + return System.currentTimeMillis(); + } + + @CacheEvict(value = "sessions") + public void endSession(String userSubject) { + // No audit logging here — endSession is called from evictCache() which fires on + // logout, passport invalidation, and login flows. The callers log their own + // domain-specific events (LOGOUT, PASSPORT_INVALIDATED, LOGIN_SUCCESS). + } + + private Optional getCachedSessionStartTime(String userSubject) { + Cache cache = cacheManager.getCache("sessions"); + if (cache != null) { + Cache.ValueWrapper valueWrapper = cache.get(userSubject); + if (valueWrapper != null) { + return Optional.ofNullable((Long) valueWrapper.get()); + } + } + return Optional.empty(); + } + + /** + * If the user has been logged in longer than the max session duration. + * @param userSubject User::getSubject() + * @return boolean if the session exists or the length of the current session + */ + public boolean isSessionExpired(String userSubject) { + Optional sessionStartTime = getCachedSessionStartTime(userSubject); + return sessionStartTime.map(aLong -> System.currentTimeMillis() - aLong > sessionMaxDuration).orElse(true); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/StudyAccessService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/StudyAccessService.java new file mode 100644 index 000000000..0c03bed7d --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/StudyAccessService.java @@ -0,0 +1,66 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.hms.dbmi.avillach.auth.model.fenceMapping.StudyMetaData; +import edu.harvard.hms.dbmi.avillach.auth.utils.FenceMappingUtility; +import io.swagger.v3.oas.annotations.Parameter; +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Service; +import org.springframework.web.bind.annotation.RequestBody; +import java.util.Map; + +@Service +public class StudyAccessService { + private final Logger logger = LoggerFactory.getLogger(StudyAccessService.class); + + private final FenceMappingUtility fenceMappingUtility; + private final RoleService roleService; + + public static final String MANUAL = "MANUAL_"; + + @Autowired + public StudyAccessService(FenceMappingUtility fenceMappingUtility, RoleService roleService) { + this.fenceMappingUtility = fenceMappingUtility; + this.roleService = roleService; + } + + public String addStudyAccess(@Parameter(description="The Study Identifier of the new study from the metadata.json") + @RequestBody String studyIdentifier) { + if (StringUtils.isBlank(studyIdentifier)) { + return "Error: Study identifier cannot be blank"; + } + + StudyMetaData fenceMappingForStudy; + try { + Map fenceMapping = fenceMappingUtility.getFENCEMapping(); + if (fenceMapping == null) { + throw new Exception("Fence mapping is null"); + } + fenceMappingForStudy = fenceMapping.get(studyIdentifier); + } catch(Exception ex) { + logger.error(ex.toString()); + logger.error("addStudyAccess - Error occurred while fetching FENCE mapping"); + return "Error: occurred while fetching FENCE mapping"; + } + + if (fenceMappingForStudy == null) { + logger.error("addStudyAccess - Could not find study: {} in FENCE mapping", studyIdentifier); + return "Error: Could not find study with the provided identifier"; + } + + String projectId = fenceMappingForStudy.getStudyIdentifier(); + String consentCode = fenceMappingForStudy.getConsentGroupCode(); + String newRoleName = StringUtils.isNotBlank(consentCode) ? MANUAL+projectId+"_"+consentCode : MANUAL+projectId; + + logger.debug("addStudyAccess - New manual PSAMA role name: {}", newRoleName); + if (roleService.upsertRole(null, newRoleName, MANUAL + " role "+newRoleName)) { + logger.info("addStudyAccess - Updated user role. Now it includes `{}`", newRoleName); + return "Role '" + newRoleName + "' successfully created"; + } else { + logger.error("addStudyAccess - could not add {} role to to database", newRoleName); + return "Error: Could not add role '" + newRoleName + "' to database"; + } + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/TOSService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/TOSService.java new file mode 100644 index 000000000..4632ce2cf --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/TOSService.java @@ -0,0 +1,113 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.hms.dbmi.avillach.auth.entity.TermsOfService; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import edu.harvard.hms.dbmi.avillach.auth.repository.TermsOfServiceRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserRepository; +import edu.harvard.hms.dbmi.avillach.auth.rest.TermsOfServiceController; +import jakarta.annotation.Nullable; +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Service; + +import java.util.*; + +/** + *

    Provides business logic for the TermsOfService endpoint.

    > + * + * @see TermsOfServiceController + */ +@Service +public class TOSService { + + private final static Logger logger = LoggerFactory.getLogger(TOSService.class); + + + private final boolean isToSEnabled; + + private final TermsOfServiceRepository termsOfServiceRepo; + + private final UserRepository userRepo; + + + @Autowired + public TOSService( + TermsOfServiceRepository termsOfServiceRepo, UserRepository userRepo, @Value("${application.tos.enabled}") boolean isToSEnabled + ) { + this.termsOfServiceRepo = termsOfServiceRepo; + this.userRepo = userRepo; + this.isToSEnabled = isToSEnabled; + } + + + public boolean hasUserAcceptedLatest(String userSubj) { + logger.info("Checking if user {} has accepted the latest TOS", userSubj); + // If TOS is not enabled, then the user has accepted it + if (!isToSEnabled) { + logger.info("TOS is disabled"); + return true; + } + + // If there is no TOS, then the user has accepted it + if (getLatest() == null) { + logger.info("No TOS found in database"); + return true; + } + + return checkAgainstTOSDate(userSubj); + } + + public Optional updateTermsOfService(String html) { + TermsOfService updatedTOS = new TermsOfService(); + updatedTOS.setContent(html); + termsOfServiceRepo.save(updatedTOS); + return termsOfServiceRepo.findTopByOrderByDateUpdatedDesc(); + } + + public @Nullable String getLatest() { + Optional termsOfService = termsOfServiceRepo.findTopByOrderByDateUpdatedDesc(); + if (termsOfService.isPresent()) { + return termsOfService.get().getContent(); + } else { + logger.info("Terms Of Service disabled: No Terms of Service found in database"); + return null; + } + } + + public User acceptTermsOfService(String userSubj) { + logger.info("User {} accepting TOS", userSubj); + User user = userRepo.findBySubject(userSubj); + if (user == null) { + throw new RuntimeException("User does not exist"); + } + user.setAcceptedTOS(new Date()); + Optional tosDate = termsOfServiceRepo.findTopByOrderByDateUpdatedDesc(); + if (tosDate.isEmpty()) { + throw new RuntimeException("No Terms of Service found in database"); + } + + String userLogId = !StringUtils.isBlank(user.getEmail()) ? user.getEmail() : user.getGeneralMetadata(); + logger.info("TOS_LOG : User {} accepted the Terms of Service dated {}", userLogId, tosDate.get().getDateUpdated()); + return user; + } + + private boolean checkAgainstTOSDate(String userSubj) { + User user = this.userRepo.findBySubject(userSubj); + if (user == null) { + return false; + } + + Date acceptedTOS = user.getAcceptedTOS(); + logger.info("User {} accepted TOS on {}", userSubj, acceptedTOS); + if (acceptedTOS == null) { + return false; + } + + Optional latestTOS = this.termsOfServiceRepo.findTopByOrderByDateUpdatedDesc(); + return latestTOS.filter(termsOfService -> acceptedTOS.compareTo(termsOfService.getDateUpdated()) >= 0).isPresent(); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/TokenService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/TokenService.java new file mode 100644 index 000000000..f6d1029ed --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/TokenService.java @@ -0,0 +1,283 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.hms.dbmi.avillach.auth.entity.Application; +import edu.harvard.hms.dbmi.avillach.auth.entity.Privilege; +import edu.harvard.hms.dbmi.avillach.auth.entity.Role; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import edu.harvard.hms.dbmi.avillach.auth.exceptions.NotAuthorizedException; +import edu.harvard.hms.dbmi.avillach.auth.model.*; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserRepository; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.authorization.AuthorizationService; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming; +import edu.harvard.hms.dbmi.avillach.auth.utils.JWTUtil; +import io.jsonwebtoken.Claims; +import io.jsonwebtoken.Jws; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.security.core.context.SecurityContext; +import org.springframework.security.core.context.SecurityContextHolder; +import org.springframework.stereotype.Service; + +import java.time.ZoneOffset; +import java.time.ZonedDateTime; +import java.util.*; +import java.util.stream.Collectors; + + +@Service +public class TokenService { + + private final static Logger logger = LoggerFactory.getLogger(TokenService.class); + + private final AuthorizationService authorizationService; + + private final UserRepository userRepository; + + private final long tokenExpirationTime; + + // Default token expiration time set to 1 hour + private static final long defaultTokenExpirationTime = 1000L * 60 * 60; + private final JWTUtil jwtUtil; + private final SessionService sessionService; + private final UserService userService; + + @Autowired + public TokenService(AuthorizationService authorizationService, UserRepository userRepository, + @Value("${application.token.expiration.time}") long tokenExpirationTime, + JWTUtil jwtUtil, + SessionService sessionService, + UserService userService) { + this.authorizationService = authorizationService; + this.userRepository = userRepository; + this.tokenExpirationTime = tokenExpirationTime > 0 ? tokenExpirationTime : defaultTokenExpirationTime; + this.jwtUtil = jwtUtil; + this.sessionService = sessionService; + this.userService = userService; + } + + public Map inspectToken(Map inputMap) { + logger.info("TokenInspect starting..."); + TokenInspection tokenInspection; + try { + tokenInspection = validateToken(inputMap); + } catch (IllegalAccessException e) { + throw new RuntimeException(e); + } + if (tokenInspection.getMessage() != null) { + tokenInspection.addField("message", tokenInspection.getMessage()); + } + + logger.info("Finished token introspection."); + return tokenInspection.getResponseMap(); + } + + private TokenInspection validateToken(Map inputMap) throws IllegalAccessException { + logger.debug( + "_inspectToken, the incoming token map is: {}", + inputMap.entrySet().stream().map(entry -> entry.getKey() + " - " + entry.getValue()).collect(Collectors.joining(", ")) + ); + + TokenInspection tokenInspection = new TokenInspection(); + String token = (String) inputMap.get("token"); + if (token == null || token.isEmpty()) { + logger.error("Token - {} is blank", token); + tokenInspection.setMessage("Token not found"); + tokenInspection.addField("active", false); + return tokenInspection; + } + + // Parse token using client secret and verify signature + Jws jws; + try { + jws = this.jwtUtil.parseToken(token); + + // Remove token from inputMap to prevent accidental logging + inputMap.remove("token"); + } catch (NotAuthorizedException ex) { + // Log invalid token only when verification fails + logger.error("_inspectToken() the token - {} - is invalid with exception: {}", token, ex.getMessage()); + tokenInspection.setMessage(ex.getMessage()); + tokenInspection.addField("active", false); + return tokenInspection; + } + + Application application; + try { + CustomApplicationDetails customApplicationDetails = + (CustomApplicationDetails) SecurityContextHolder.getContext().getAuthentication().getPrincipal(); + application = customApplicationDetails.getApplication(); + } catch (ClassCastException ex) { + SecurityContext securityContext = SecurityContextHolder.getContext(); + String principalName = securityContext.getAuthentication().getName(); + logger.error( + "{} - {} - is trying to use token introspection endpoint, but it is not an application", principalName, principalName + ); + throw new IllegalAccessException("The application token does not associate with an application but " + principalName); + } + + // Verify application exists after JWT authentication + if (application == null) { + logger.error("_inspectToken() There is no application in securityContext, which shall not be."); + throw new NullPointerException("Inner application error, please ask admin to check the log."); + } + + String subject = jws.getPayload().getSubject(); + + // Extract user from token subject + User user; + + // Check for long-term token type + // Long-term tokens: + // - One per user stored in database + // - Must match database token exactly + // - Previous token invalidated on refresh + // Regular tokens remain valid after refresh + boolean isLongTermToken = false; + if (subject.startsWith(AuthNaming.LONG_TERM_TOKEN_PREFIX)) { + subject = subject.substring(AuthNaming.LONG_TERM_TOKEN_PREFIX.length() + 1); + isLongTermToken = true; + } + + user = this.userRepository.findBySubject(subject); + logger.info("_inspectToken() does user with subject - {} - exists in database", subject); + if (user == null) { + logger.error("_inspectToken() could not find user with subject {}", subject); + tokenInspection.setMessage("user doesn't exist"); + tokenInspection.addField("active", false); + return tokenInspection; + } + + // Verify token is active and authorized + boolean isAuthorizationPassed = false; + String errorMsg = null; + + // Verify long-term token matches database + boolean isLongTermTokenCompromised = false; + if (isLongTermToken && !token.equals(user.getToken())) { + isLongTermTokenCompromised = true; + logger.error( + "_inspectToken User {}|{}is sending a long term token that is not matching the record in database user table.", + user.getUuid(), user.getSubject() + ); + errorMsg = "Cannot find matched long term token, your token might have been refreshed."; + } + + // Authorize token based on application privileges + if (application.getPrivileges() == null || application.getPrivileges().isEmpty()) { + isAuthorizationPassed = true; + logger.info( + "ACCESS_LOG ___ {},{},{} ___ has been granted access to execute query ___ {} ___ in application ___ {} ___ NO APP PRIVILEGES DEFINED", + user.getUuid(), user.getEmail(), user.getName(), inputMap.get("request"), application.getName() + ); + } else if (!isLongTermTokenCompromised && user.getRoles() != null) { + EvaluateAccessRuleResult evaluateAccessRuleResult = + authorizationService.isAuthorized(application, inputMap.get("request"), user, isLongTermToken); + isAuthorizationPassed = evaluateAccessRuleResult.result(); + evaluateAccessRuleResult.query().ifPresent(query -> { + try { + tokenInspection.addField("query", new ObjectMapper().writeValueAsString(query)); + } catch (JsonProcessingException e) { + throw new RuntimeException(e); + } + }); + } else if (!isLongTermTokenCompromised) { + errorMsg = "User doesn't have enough privileges."; + } + + if (isLongTermToken && isAuthorizationPassed) { + tokenInspection.addField("active", true); + } else if (isAuthorizationPassed) { + tokenInspection.addField("active", true); + + // Refresh token if expiring soon + Date expiration = jws.getPayload().getExpiration(); + if (jwtUtil.shouldRefreshToken(expiration, tokenExpirationTime)) { + logger.info("_inspectToken() Token is about to expire, refreshing token..."); + RefreshToken refreshResponse = refreshToken(token); + if (refreshResponse instanceof ValidRefreshToken validRefreshToken) { + tokenInspection.addField("token", validRefreshToken.token()); + tokenInspection.addField("tokenRefreshed", true); + } else if (refreshResponse instanceof InvalidRefreshToken invalidRefreshToken) { + tokenInspection.setMessage(invalidRefreshToken.error()); + tokenInspection.addField("active", false); + } + } else { + tokenInspection.addField("tokenRefreshed", false); + } + } else { + tokenInspection.setMessage(errorMsg); + tokenInspection.addField("active", false); + } + + // Include token payload and privileges + tokenInspection.addAllFields(jws.getPayload()); + tokenInspection.addField("roles", user.getRoleString()); + Set userPrivileges = user.getPrivilegeNameSetByApplication(application); + userPrivileges.addAll(user.getPrivilegeNameSet()); + tokenInspection.addField("privileges", userPrivileges); + + logger.debug( + "_inspectToken() Successfully inspect and return response map: {}", + tokenInspection.getResponseMap().entrySet().stream().map(entry -> entry.getKey() + " - " + entry.getValue()) + .collect(Collectors.joining(", ")) + ); + + return tokenInspection; + } + + public RefreshToken refreshToken(String authorizationHeader) { + logger.debug("RefreshToken starting..."); + + String subject; + Jws jws; + try { + String token = JWTUtil.getTokenFromAuthorizationHeader(authorizationHeader) + .orElseThrow(() -> new NotAuthorizedException("Token not found")); + jws = this.jwtUtil.parseToken(token); + } catch (NotAuthorizedException ex) { + return new InvalidRefreshToken("Cannot parse original token."); + } + + Claims claims = jws.getPayload(); + subject = claims.getSubject(); + if (subject == null || subject.isEmpty()) { + logger.error("refreshToken() subject doesn't exist in the user."); + return new InvalidRefreshToken("Inner application error, please contact admin."); + } + + User loadUser = this.userRepository.findBySubject(subject); + if (loadUser == null) { + logger.error("refreshToken() When retrieving current user, it returned null, the user might be removed from database"); + return new InvalidRefreshToken("User doesn't exist anymore."); + } + + if (!loadUser.isActive()) { + logger.error("refreshToken() The user has just been deactivated."); + return new InvalidRefreshToken("User has been deactivated."); + } + + if (!JWTUtil.isLongTermToken(claims.getSubject()) && sessionService.isSessionExpired(claims.getSubject())) { + logger.info("refreshToken() The user has just is being logged out. The user's session has expired."); + return new InvalidRefreshToken("Your session has expired. Please log in again."); + } + + Map claimsMap = new HashMap<>(claims); + claimsMap.put("roles", userService.addRoleClaims(loadUser)); + + Date expirationDate = new Date(Calendar.getInstance().getTimeInMillis() + this.tokenExpirationTime); + String refreshedToken = this.jwtUtil.createJwtToken( + claims.getId(), + claims.getIssuer(), + claimsMap, + subject, + this.tokenExpirationTime); + + logger.debug("Finished RefreshToken and new token has been generated."); + return new ValidRefreshToken(refreshedToken, ZonedDateTime.ofInstant(expirationDate.toInstant(), ZoneOffset.UTC).toString()); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/UserMetadataMappingService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/UserMetadataMappingService.java new file mode 100644 index 000000000..1b98a95db --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/UserMetadataMappingService.java @@ -0,0 +1,72 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Connection; +import edu.harvard.hms.dbmi.avillach.auth.entity.UserMetadataMapping; +import edu.harvard.hms.dbmi.avillach.auth.repository.ConnectionRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserMetadataMappingRepository; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Service; +import org.springframework.transaction.annotation.Transactional; + +import java.util.List; +import java.util.Optional; +import java.util.UUID; + +/** + *

    Provides business logic for UserMetadataMapping endpoint.

    + */ +@Service +public class UserMetadataMappingService { + + private final UserMetadataMappingRepository userMetadataMappingRepo; + + private final ConnectionRepository connectionRepo; + + @Autowired + public UserMetadataMappingService(UserMetadataMappingRepository userMetadataMappingRepo, ConnectionRepository connectionRepo) { + this.userMetadataMappingRepo = userMetadataMappingRepo; + this.connectionRepo = connectionRepo; + } + + public List getAllMappingsForConnection(Connection connection) { + return userMetadataMappingRepo.findByConnection(connection); + } + + @Transactional + public List addMappings(List mappings) { + StringBuilder errorMessage = new StringBuilder("The following connectionIds do not exist:\n"); + boolean error = false; + for (UserMetadataMapping umm : mappings) { + Optional c = connectionRepo.findById(umm.getConnection().getId()); + if (c.isEmpty()) { + error = true; + errorMessage.append(umm.getConnection().getId()).append("\n"); + } else { + umm.setConnection(c.get()); + } + } + + if (error) { + throw new IllegalArgumentException(errorMessage.toString()); + } + + return this.userMetadataMappingRepo.saveAll(mappings); + } + + public List getAllMappings() { + return userMetadataMappingRepo.findAll(); + } + + public Connection getAllMappingsForConnection(String connectionId) { + return this.connectionRepo.findById(connectionId).orElseThrow(() -> new IllegalArgumentException("Connection not found")); + } + + public List updateUserMetadataMappings(List mappings) { + return this.userMetadataMappingRepo.saveAll(mappings); + } + + public List removeMetadataMappingByIdAndRetrieveAll(String mappingId) { + this.userMetadataMappingRepo.deleteById(UUID.fromString(mappingId)); + return this.userMetadataMappingRepo.findAll(); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/UserService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/UserService.java new file mode 100644 index 000000000..946270c4e --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/UserService.java @@ -0,0 +1,853 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.node.ObjectNode; +import edu.harvard.hms.dbmi.avillach.auth.entity.*; +import edu.harvard.hms.dbmi.avillach.auth.model.CustomUserDetails; +import edu.harvard.hms.dbmi.avillach.auth.model.ras.RasDbgapPermission; +import edu.harvard.hms.dbmi.avillach.auth.repository.ApplicationRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.ConnectionRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserConsentsRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserRepository; +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.authorization.BdcConsentsBuilder; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming; +import edu.harvard.hms.dbmi.avillach.auth.utils.FenceMappingUtility; +import edu.harvard.hms.dbmi.avillach.auth.utils.JWTUtil; +import edu.harvard.hms.dbmi.avillach.auth.utils.JsonUtils; +import io.jsonwebtoken.Claims; +import io.jsonwebtoken.Jws; +import jakarta.mail.MessagingException; +import jakarta.validation.constraints.NotNull; +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.cache.annotation.CacheEvict; +import org.springframework.cache.annotation.Cacheable; +import org.springframework.http.HttpHeaders; +import org.springframework.security.core.context.SecurityContext; +import org.springframework.security.core.context.SecurityContextHolder; +import org.springframework.stereotype.Service; +import org.springframework.transaction.annotation.Transactional; + +import java.io.IOException; +import java.time.ZoneOffset; +import java.time.ZonedDateTime; +import java.util.*; +import java.util.stream.Collectors; + +import static edu.harvard.hms.dbmi.avillach.auth.service.impl.RoleService.*; + +@Service +public class UserService { + + private final Logger logger = LoggerFactory.getLogger(UserService.class.getName()); + + private final BasicMailService basicMailService; + private final TOSService tosService; + private final UserRepository userRepository; + private final ConnectionRepository connectionRepository; + private final ApplicationRepository applicationRepository; + private final RoleService roleService; + private final long tokenExpirationTime; + private static final long defaultTokenExpirationTime = 1000L * 60 * 60; // 1 hour + private final boolean openAccessIsEnabled; + private final UserConsentsRepository userConsentsRepository; + private final FenceMappingUtility fenceMappingUtility; + + public long longTermTokenExpirationTime; + + private final String applicationUUID; + private final ObjectMapper objectMapper = new ObjectMapper(); + private final JWTUtil jwtUtil; + + private final List tokenInclusionRoles; + private final LoggingClient loggingClient; + + @Autowired + public UserService(BasicMailService basicMailService, TOSService tosService, + UserRepository userRepository, + ConnectionRepository connectionRepository, + ApplicationRepository applicationRepository, + RoleService roleService, + UserConsentsRepository userConsentsRepository, + FenceMappingUtility fenceMappingUtility, + @Value("${application.token.expiration.time}") long tokenExpirationTime, + @Value("${application.default.uuid}") String applicationUUID, + @Value("${application.long.term.token.expiration.time}") long longTermTokenExpirationTime, + JWTUtil jwtUtil, + @Value("${open.idp.provider.is.enabled}") boolean openIdpProviderIsEnabled, + @Value("${application.token.inclusionRoles}") String tokenInclusionRoles, + LoggingClient loggingClient) { + this.basicMailService = basicMailService; + this.tosService = tosService; + this.userRepository = userRepository; + this.connectionRepository = connectionRepository; + this.roleService = roleService; + this.userConsentsRepository = userConsentsRepository; + this.fenceMappingUtility = fenceMappingUtility; + this.tokenExpirationTime = tokenExpirationTime > 0 ? tokenExpirationTime : defaultTokenExpirationTime; + logger.info("Token Expiration Time : {}", tokenExpirationTime); + this.applicationRepository = applicationRepository; + this.applicationUUID = applicationUUID; + this.jwtUtil = jwtUtil; + + long defaultLongTermTokenExpirationTime = 1000L * 60 * 60 * 24 * 30; + this.longTermTokenExpirationTime = + longTermTokenExpirationTime > 0 ? longTermTokenExpirationTime : defaultLongTermTokenExpirationTime; + this.openAccessIsEnabled = openIdpProviderIsEnabled; + this.tokenInclusionRoles = Arrays.asList(tokenInclusionRoles.split(",")); + this.loggingClient = loggingClient; + } + + public HashMap getUserProfileResponse(UserClaims userClaims) { + if (StringUtils.isBlank(userClaims.getSub())) { + logger.warn("User subject is blank, cannot generate profile response"); + return null; + } + + logger.debug("getUserProfileResponse() started"); + HashMap responseMap = new HashMap(); + + HashMap claimsMap = userClaims.toHashMap(); + logger.debug("getUserProfileResponse() using claims:{}", claimsMap.toString()); + String token = this.jwtUtil.createJwtToken( + "whatever", + "edu.harvard.hms.dbmi.psama", + claimsMap, + userClaims.getSub(), + this.tokenExpirationTime + ); + + responseMap.put("token", token); + logger.debug("getUserProfileResponse() .usedId field is set"); + responseMap.put("userId", userClaims.getSub()); + + logger.debug("getUserProfileResponse() .email field is set"); + responseMap.put("email", userClaims.getEmail()); + + logger.debug("getUserProfileResponse() acceptedTOS is set"); + boolean acceptedTOS = tosService.hasUserAcceptedLatest(userClaims.getSub()); + responseMap.put("acceptedTOS", "" + acceptedTOS); + + logger.debug("getUserProfileResponse() expirationDate is set"); + Date expirationDate = new Date(Calendar.getInstance().getTimeInMillis() + this.tokenExpirationTime); + responseMap.put("expirationDate", ZonedDateTime.ofInstant(expirationDate.toInstant(), ZoneOffset.UTC).toString()); + + logger.debug("getUserProfileResponse() uuid field is set"); + responseMap.put("uuid", userClaims.getUuid()); + + logger.debug("getUserProfileResponse() finished"); + return responseMap; + } + + public List addRoleClaims(User user) { + if (user != null && user.getRoles() != null) { + return user.getRoles().stream() + .map(Role::getName) + .filter(tokenInclusionRoles::contains) + .collect(Collectors.toList()); + } + + return List.of(); + } + + public User getUserById(String userId) { + Optional user = this.userRepository.findById(UUID.fromString(userId)); + if (user.isEmpty()) { + logger.error("getUserById() cannot find user by UUID: {}", userId); + throw new IllegalArgumentException("Cannot find user by input UUID: " + userId); + } + + return user.get(); + } + + public List getAllUsers() { + return this.userRepository.findAll(); + } + + public List addUser(List users) { + return this.userRepository.saveAll(users); + } + + /** + * This check is to prevent non-super-admin user to create/remove a super admin role against a user(include themselves). Only super + * admin user could perform such actions. + * + *

    if operations not related to super admin role updates, this will return true.

    The logic here is checking the state of + * the super admin role in the input and output users, if the state is changed, check if the user is a super admin to determine if the + * user could perform the action. + * + * @param currentUser the user trying to perform the action + * @param inputUser the user that is going to be updated + * @param originalUser there could be no original user when adding a new user + * @return true if the user could perform the action, false otherwise + */ + private boolean allowUpdateSuperAdminRole(@NotNull User currentUser, @NotNull User inputUser, User originalUser) { + + // if current user is a super admin, this check will return true + for (Role role : currentUser.getRoles()) { + for (Privilege privilege : role.getPrivileges()) { + if (privilege.getName().equals(AuthNaming.AuthRoleNaming.SUPER_ADMIN)) { + return true; + } + } + } + + boolean inputUserHasSuperAdmin = false; + boolean originalUserHasSuperAdmin = false; + + for (Role role : inputUser.getRoles()) { + for (Privilege privilege : role.getPrivileges()) { + if (privilege.getName().equals(AuthNaming.AuthRoleNaming.SUPER_ADMIN)) { + inputUserHasSuperAdmin = true; + break; + } + } + } + + if (originalUser != null) { + for (Role role : originalUser.getRoles()) { + for (Privilege privilege : role.getPrivileges()) { + if (privilege.getName().equals(AuthNaming.AuthRoleNaming.SUPER_ADMIN)) { + originalUserHasSuperAdmin = true; + break; + } + } + } + + // when they equals, nothing has changed, a non super admin user could perform the action + return inputUserHasSuperAdmin == originalUserHasSuperAdmin; + } else { + // if inputUser has super admin, it should return false + return !inputUserHasSuperAdmin; + } + + } + + @Transactional + public List addUsers(List users) { + SecurityContext securityContext = SecurityContextHolder.getContext(); + CustomUserDetails customUserDetails = (CustomUserDetails) securityContext.getAuthentication().getPrincipal(); + if (customUserDetails == null || customUserDetails.getUser() == null && customUserDetails.getUser().getUuid() == null) { + logger.error("Security context didn't have a user stored."); + return null; + } + + User currentUser = customUserDetails.getUser(); + checkAssociation(users); + for (User user : users) { + logger.debug("Adding User {}", user); + if (!allowUpdateSuperAdminRole(currentUser, user, null)) { + logger.error( + "updateUser() user - {} - with roles [{}] - is not allowed to grant " + AuthNaming.AuthRoleNaming.SUPER_ADMIN + + " role when adding a user.", + currentUser.getUuid(), currentUser.getRoleString() + ); + throw new IllegalArgumentException( + "Not allowed to add a user with a " + AuthNaming.AuthRoleNaming.SUPER_ADMIN + " privilege associated." + ); + } + + if (user.getEmail() == null) { + try { + logger.info("Parsing metadata for email address"); + HashMap metadata = + new HashMap(new ObjectMapper().readValue(user.getGeneralMetadata(), Map.class)); + List emailKeys = metadata.keySet().stream().filter((key) -> key.toLowerCase().contains("email")).toList(); + if (!emailKeys.isEmpty()) { + user.setEmail(metadata.get(emailKeys.getFirst())); + } + } catch (IOException e) { + logger.error("Failed to parse metadata for email address", e); + } + } + } + + users = addUser(users); + return users; + } + + /** + * Check all referenced fields if they are already in a database. If they are in the database, then retrieve it by id and attach it to a + * user object. + * + * @param users A list of users + */ + private void checkAssociation(List users) { + for (User user : users) { + if (user.getRoles() != null && !user.getRoles().isEmpty()) { + Set roleUuids = user.getRoles().stream().map(Role::getUuid).collect(Collectors.toSet()); + Set rolesFromDb = this.roleService.getRolesByIds(roleUuids); + + // If the size of the roles from the database is different from the input role UUIDs, then + // we cannot find all roles by the input UUIDs. + if (rolesFromDb.size() != roleUuids.size()) { + logger.error("checkAssociation() cannot find all roles by UUIDs: {}", roleUuids); + throw new IllegalArgumentException("Cannot find all roles by input UUIDs: " + roleUuids); + } + + user.setRoles(rolesFromDb); + } else { + throw new IllegalArgumentException("User must have at least one role."); + } + + if (user.getConnection() != null) { + Optional connection = this.connectionRepository.findById(user.getConnection().getId()); + user.setConnection(connection.orElse(null)); + } + } + } + + @Transactional + public List updateUser(List users) { + SecurityContext securityContext = SecurityContextHolder.getContext(); + CustomUserDetails customUserDetails = (CustomUserDetails) securityContext.getAuthentication().getPrincipal(); + if (customUserDetails == null || customUserDetails.getUser() == null && customUserDetails.getUser().getUuid() == null) { + logger.error("Security context didn't have a user stored."); + return null; + } + + User currentUser = customUserDetails.getUser(); + checkAssociation(users); + boolean allowUpdate = true; + for (User user : users) { + Optional originalUser = this.userRepository.findById(user.getUuid()); + if (!allowUpdateSuperAdminRole(currentUser, user, originalUser.orElse(null))) { + allowUpdate = false; + break; + } + } + + if (allowUpdate) { + users = this.userRepository.saveAll(users); + return users; + } else { + logger.error( + "updateUser() user - {} - with roles [{}] - is not allowed to grant or remove " + AuthNaming.AuthRoleNaming.SUPER_ADMIN + + " privilege.", + currentUser.getUuid(), currentUser.getRoleString() + ); + throw new IllegalArgumentException( + "Not allowed to update a user with changes associated to " + AuthNaming.AuthRoleNaming.SUPER_ADMIN + " privilege." + ); + } + } + + public String sendUserUpdateEmailsFromResponse(List addedUsers) { + logger.debug("Sending email"); + try { + for (User user : addedUsers) { + try { + basicMailService.sendUsersAccessEmail(user); + } catch (MessagingException e) { + logger.error("Failed to send email! {}", e.getLocalizedMessage()); + logger.debug("Exception Trace: ", e); + return " WARN - could not send email to user " + user.getEmail() + " see logs for more info"; + } + } + } catch (Exception e) { + logger.error("Failed to send email - unhandled exception: ", e); + } + logger.debug("finished email sending method"); + return null; + } + + @Transactional + public User.UserForDisplay getCurrentUser(String authorizationHeader, Boolean hasToken) { + SecurityContext securityContext = SecurityContextHolder.getContext(); + Optional customUserDetails = + Optional.ofNullable((CustomUserDetails) securityContext.getAuthentication().getPrincipal()); + if (customUserDetails.isEmpty() || customUserDetails.get().getUser() == null) { + logger.error("Security context didn't have a user stored."); + return null; + } + + User user = customUserDetails.get().getUser(); + if (user == null) { + logger.error("When retrieving current user, it returned null"); + return null; + } + + logger.info("getCurrentUser() user found: {}", user.getEmail()); + User.UserForDisplay userForDisplay = new User.UserForDisplay().setEmail(user.getEmail()).setPrivileges(user.getPrivilegeNameSet()) + .setUuid(user.getUuid().toString()).setAcceptedTOS(this.tosService.hasUserAcceptedLatest(user.getSubject())); + + // currently, the queryScopes are simple combination of queryScope string together as a set. + // We are expecting the queryScope string as plain string. If it is a JSON, we could change the + // code to use JsonUtils.mergeTemplateMap(Map, Map) + Set privileges = user.getTotalPrivilege(); + if (privileges != null && !privileges.isEmpty()) { + Set scopes = new TreeSet<>(); + privileges.stream().filter(privilege -> privilege.getQueryScope() != null).forEach(privilege -> { + try { + Arrays.stream(objectMapper.readValue(privilege.getQueryScope(), String[].class)).filter(Objects::nonNull) + .forEach(scopes::add); + } catch (IOException e) { + logger.error("Parsing issue for privilege {} queryScope", privilege.getUuid(), e); + } + }); + userForDisplay.setQueryScopes(scopes); + } + + if (user.getToken() != null && !user.getToken().isEmpty()) { + userForDisplay.setToken(user.getToken()); + } else { + user.setToken(generateUserLongTermToken(authorizationHeader, user)); + this.userRepository.save(user); + userForDisplay.setToken(user.getToken()); + } + + return userForDisplay; + } + + public Optional getQueryTemplate(String applicationId) { + if (applicationId == null || applicationId.trim().isEmpty()) { + logger.error("getQueryTemplate() input application UUID is null or empty."); + throw new IllegalArgumentException("Input application UUID is incorrect."); + } + + SecurityContext securityContext = SecurityContextHolder.getContext(); + Optional customUserDetails = + Optional.ofNullable((CustomUserDetails) securityContext.getAuthentication().getPrincipal()); + if ((customUserDetails.isEmpty() || customUserDetails.get().getUser() == null) && openAccessIsEnabled) { + Optional application = this.applicationRepository.findById(UUID.fromString(applicationId)); + if (application.isEmpty()) { + logger.error("getQueryTemplate() cannot find corresponding application by UUID: {}", UUID.fromString(applicationId)); + throw new IllegalArgumentException("Cannot find application by input UUID: " + UUID.fromString(applicationId)); + } + + return Optional.ofNullable(openMergeTemplate(application.orElse(null))); + } else { + if (customUserDetails.isEmpty() || customUserDetails.get().getUser() == null) { + logger.error("Security context didn't have a user stored."); + return Optional.empty(); + } + + User user = customUserDetails.get().getUser(); + Optional application = this.applicationRepository.findById(UUID.fromString(applicationId)); + if (application.isEmpty()) { + logger.error("getQueryTemplate() cannot find corresponding application by UUID: {}", UUID.fromString(applicationId)); + throw new IllegalArgumentException("Cannot find application by input UUID: " + UUID.fromString(applicationId)); + } + + return Optional.ofNullable(mergeTemplate(user, application.orElse(null))); + } + } + + private String openMergeTemplate(Application application) { + Set applicationPrivileges = application.getPrivileges(); + Role openAccessRole = roleService.findByName(MANAGED_OPEN_ACCESS_ROLE_NAME); + Set privileges = openAccessRole.getPrivileges(); + privileges.addAll(applicationPrivileges); + Map mergedTemplateMap = getMergedQueryTemplateMap(privileges); + String resultJSON; + try { + resultJSON = objectMapper.writeValueAsString(mergedTemplateMap); + } catch (JsonProcessingException ex) { + logger.error("mergeTemplate() cannot convert map to json string. The map mergedTemplate is: {}", mergedTemplateMap); + throw new IllegalArgumentException("Inner application error, please contact admin."); + } + + return resultJSON; + } + + public Map getDefaultQueryTemplate() { + Optional mergedTemplate = getQueryTemplate(this.applicationUUID); + + if (mergedTemplate.isEmpty()) { + logger.error("getDefaultQueryTemplate() cannot find corresponding application by UUID: {}", this.applicationUUID); + return null; + } + + return Map.of("queryTemplate", mergedTemplate.orElse(null)); + } + + @Cacheable(value = "mergedTemplateCache", keyGenerator = "customKeyGenerator") + public String mergeTemplate(User user, Application application) { + String resultJSON; + Set privileges = user.getPrivilegesByApplication(application); + Map mergedTemplateMap = getMergedQueryTemplateMap(privileges); + + try { + resultJSON = objectMapper.writeValueAsString(mergedTemplateMap); + } catch (JsonProcessingException ex) { + logger.error("mergeTemplate() cannot convert map to json string. The map mergedTemplate is: {}", mergedTemplateMap); + throw new IllegalArgumentException("Inner application error, please contact admin."); + } + + return resultJSON; + } + + private Map getMergedQueryTemplateMap(Set privileges) { + Map mergedTemplateMap = null; + for (Privilege privilege : privileges) { + String template = privilege.getQueryTemplate(); + logger.debug("mergeTemplate() processing template:{}", template); + if (template == null || template.trim().isEmpty()) { + continue; + } + Map templateMap = null; + try { + templateMap = objectMapper.readValue(template, Map.class); + } catch (IOException ex) { + logger.error("mergeTemplate() cannot convert stored queryTemplate using Jackson, the queryTemplate is: {}", template); + throw new IllegalArgumentException("Inner application error, please contact admin."); + } + + if (templateMap == null) { + continue; + } + + if (mergedTemplateMap == null) { + mergedTemplateMap = templateMap; + continue; + } + + mergedTemplateMap = JsonUtils.mergeTemplateMap(mergedTemplateMap, templateMap); + } + return mergedTemplateMap; + } + + @CacheEvict(value = "mergedTemplateCache") + public void evictFromCache(String userSubject) { + if (userSubject == null || userSubject.isEmpty()) { + logger.warn("evictFromCache() was called with a null or empty email"); + return; + } + logger.info("evictFromCache() evicting cache for user: {}", userSubject); + } + + @Transactional + public Map refreshUserToken(HttpHeaders httpHeaders) { + SecurityContext securityContext = SecurityContextHolder.getContext(); + CustomUserDetails customUserDetails = (CustomUserDetails) securityContext.getAuthentication().getPrincipal(); + if (customUserDetails == null || customUserDetails.getUser() == null || customUserDetails.getUser().getUuid() == null) { + logger.error("Security context didn't have a user stored."); + return null; + } + + User user = customUserDetails.getUser(); + String authorizationHeader = httpHeaders.getFirst("Authorization"); + String longTermToken = generateUserLongTermToken(authorizationHeader, user); + user.setToken(longTermToken); + this.userRepository.save(user); + + return Map.of("userLongTermToken", longTermToken); + } + + /** + * Logic here is, retrieve the subject of the user from httpHeader. Then generate a long term one with LONG_TERM_TOKEN_PREFIX| in front + * of the subject to be able to distinguish with regular ones, since long term token only generated for accessing certain things to, in + * some degrees, decrease the insecurity. + * + * @param authorizationHeader the authorization header + * @return the long term token + * @throws IllegalArgumentException if the authorization header is not presented + */ + private String generateUserLongTermToken(String authorizationHeader, User user) { + if (!StringUtils.isNotBlank(authorizationHeader)) { + throw new IllegalArgumentException("Authorization header is not presented."); + } + + Optional token = JWTUtil.getTokenFromAuthorizationHeader(authorizationHeader); + if (token.isEmpty()) { + throw new IllegalArgumentException("Token is not presented in the authorization header."); + } + + Jws jws = this.jwtUtil.parseToken(token.get()); + + Claims claims = jws.getPayload(); + String tokenSubject = claims.getSubject(); + + if (tokenSubject.startsWith(AuthNaming.LONG_TERM_TOKEN_PREFIX + "|")) { + tokenSubject = tokenSubject.substring(AuthNaming.LONG_TERM_TOKEN_PREFIX.length() + 1); + } + + Map claimsMap = new HashMap<>(claims); + claimsMap.put("roles", addRoleClaims(user)); + + return this.jwtUtil.createJwtToken( + claims.getId(), + claims.getIssuer(), + claimsMap, + AuthNaming.LONG_TERM_TOKEN_PREFIX + "|" + tokenSubject, + this.longTermTokenExpirationTime); + } + + public User changeRole(User currentUser, Set roles) { + // set the users roles and merge the user + currentUser.setRoles(roles); + return this.userRepository.save(currentUser); + } + + public User findBySubject(String username) { + return this.userRepository.findBySubject(username); + } + + public User save(User user) { + return this.userRepository.save(user); + } + + public User findOrCreate(User newUser) { + logger.info( + "findOrCreate(), trying to find user: {subject: {}}, and found a user with uuid: {}, subject: {}", newUser.getSubject(), + newUser.getUuid(), newUser.getSubject() + ); + // check if the user exist by subject + Optional user = Optional.ofNullable(findBySubject(newUser.getSubject())); + if (user.isPresent()) { + return user.orElse(null); + } + + // check if the user exist by email and connection + user = userRepository.findByEmailAndConnectionId(newUser.getEmail(), newUser.getConnection().getId()); + if (user.isPresent()) { + if (StringUtils.isEmpty(user.get().getSubject())) { + user.get().setSubject(newUser.getSubject()); + user.get().setGeneralMetadata(newUser.getGeneralMetadata()); + } + + return user.orElse(null); + } + + user = Optional.ofNullable(save(newUser)); + logger.info( + "createUser created user, uuid: {}, subject: {}, role: {}, privilege: {}", user.get().getUuid(), newUser.getSubject(), + user.get().getRoleString(), user.get().getPrivilegeString() + ); + // create a new user + return user.orElse(null); + } + + public Optional findByEmailAndConnection(String email, String connectionId) { + return this.userRepository.findByEmailAndConnectionId(email, connectionId); + } + + public User findUserByUUID(String userUUID) { + return this.userRepository.findById(UUID.fromString(userUUID)).orElse(null); + } + + public User createOpenAccessUser(Role openAccessRole) { + User user = new User(); + + // Save the user to get a UUID + user = save(user); + user.setSubject("open_access|" + user.getUuid().toString()); + + if (user.getRoles() == null) { + user.setRoles(new HashSet<>()); + } + + if (openAccessRole != null) { + user.getRoles().add(openAccessRole); + } + + user.setEmail(user.getUuid() + "@open_access.com"); + user = save(user); + + logger.info("createOpenAccessUser() created user, uuid: {}, subject: {}, role: {}, privilege: {}", + user.getUuid(), user.getSubject(), user.getRoleString(), user.getPrivilegeString()); + + if (loggingClient != null && loggingClient.isEnabled()) { + try { + loggingClient.send(LoggingEvent.builder("AUTHZ").action("user.open_access_created") + .metadata(Map.of( + "user_uuid", user.getUuid().toString(), + "assigned_role", "MANAGED_OPEN_ACCESS" + )).build()); + } catch (Exception e) { + logger.warn("Failed to send open access user creation logging event", e); + } + } + + return user; + } + + /** + * Using the introspection token response, load the user from the database. If the user does not exist, we will reject their login + * attempt. For the RAS integration here is a sample payload. + * + * @param node The response from the introspect endpoint + * @return The user + */ + public Optional createRasUser(JsonNode node, Connection connection) { + try { + String userEmail = node.get("preferred_username").asText(); + logger.info("Loading user for sub: {}", userEmail); + + User new_user = new User(); + new_user.setSubject(connection.getSubPrefix() + userEmail); + new_user.setEmail(userEmail); + new_user.setConnection(connection); + User actual_user = this.findOrCreate(new_user); + + if (actual_user.getRoles() == null) { + actual_user.setRoles(new HashSet<>()); + } + + actual_user.setAcceptedTOS(new Date()); + logger.info("LOGIN SUCCESS ___ USER DATA: {}", actual_user); + return Optional.of(actual_user); + } catch (Exception e) { + logger.error("Failed to create user from introspect response", e); + return Optional.empty(); + } + } + + public Set getAllUsersWithAPassport() { + return this.userRepository.findByPassportIsNotNull(); + } + + /** + * Clears users session and merge template which effectively logs them out. + * + * @param user + */ + public void logoutUser(User user) { + this.removeUserPassport(user.getSubject()); + } + + /** + * Update the provided users roles based on the list of roleNames provided. This method will update the roles in place. Adding and + * removing roles from the current list of roles. + * + * @param current_user User to be updated + * @param roleNames Roles that should be assigned to the user. + */ + public User updateUserRoles(User current_user, Set roleNames) { + Set currentRoleNames = current_user.getRoles().stream().map(Role::getName).collect(Collectors.toSet()); + + Set rolesToRemove = current_user.getRoles().stream() + .filter( + role -> !roleNames.contains(role.getName()) && !role.getName().equals(MANAGED_OPEN_ACCESS_ROLE_NAME) + && !role.getName().equals(MANAGED_AUTH_ACCESS_ROLE_NAME) && !role.getName().startsWith("MANUAL_") + && !role.getName().equals("PIC-SURE Top Admin") && !role.getName().equals("Admin") + ).collect(Collectors.toSet()); + + if (!rolesToRemove.isEmpty()) { + current_user.getRoles().removeAll(rolesToRemove); + logger.debug("upsertRole() removed {} roles from user", rolesToRemove.size()); + logger.debug("User roles after removal: {}", current_user.getRoles().size()); + } + + // Bulk lookup for existing roles. By using a hashmap we avoid having to iterate over the set of roles each time. + Map existingRoles = roleService.findByNames(roleNames); + List newRoles = roleNames.stream().filter(roleName -> !currentRoleNames.contains(roleName)).map(existingRoles::get) + .filter(Objects::nonNull).collect(Collectors.toList()); + + if (!newRoles.isEmpty()) { + logger.debug("upsertRole() updated {} roles from user", newRoles.size()); + newRoles = roleService.persistAll(newRoles); + current_user.getRoles().addAll(newRoles); + } + + Role authAccessRole = roleService.findByName(MANAGED_AUTH_ACCESS_ROLE_NAME); + if (authAccessRole != null) { + current_user.getRoles().add(authAccessRole); + } else { + logger.warn("Unable to find fence AUTH ACCESS role"); + } + + if (loggingClient != null && loggingClient.isEnabled()) { + try { + String addedNames = newRoles.stream().map(Role::getName).collect(Collectors.joining(",")); + String removedNames = rolesToRemove.stream().map(Role::getName).collect(Collectors.joining(",")); + loggingClient.send(LoggingEvent.builder("AUTHZ").action("role.sync") + .metadata(Map.of( + "user_id", current_user.getUuid().toString(), + "user_email", current_user.getEmail() != null ? current_user.getEmail() : "", + "roles_added", addedNames, + "roles_removed", removedNames + )).build()); + } catch (Exception e) { + logger.warn("Failed to send role sync logging event", e); + } + } + + Role openAccessRole = roleService.findByName(MANAGED_OPEN_ACCESS_ROLE_NAME); + if (openAccessRole != null) { + current_user.getRoles().add(openAccessRole); + } else { + logger.warn("Unable to find fence OPEN ACCESS role"); + } + + Role role = roleService.findByName(MANAGED_ROLE_NAMED_DATASET); + if (role != null) { + current_user.getRoles().add(role); + } else { + logger.warn("upsertRole() Unable to find role named {}", MANAGED_ROLE_NAMED_DATASET); + } + + // Every user has access to public datasets by default. + current_user.getRoles().addAll(roleService.getPublicAccessRoles()); + + logger.debug( + "User roles: {}", current_user.getRoles().stream().filter(Objects::nonNull).map(Role::getName).collect(Collectors.joining(", ")) + ); + try { + current_user = this.changeRole(current_user, current_user.getRoles()); + logger.debug("upsertRole() updated user, who now has {} roles.", current_user.getRoles().size()); + return current_user; + } catch (Exception ex) { + logger.error("upsertRole() Could not add roles to user, because {}", ex.getMessage()); + } + + return null; + } + + + private String extractIdp(User current_user) { + try { + final ObjectNode node; + node = new ObjectMapper().readValue(current_user.getGeneralMetadata(), ObjectNode.class); + return node.get("idp").asText(); + } catch (JsonProcessingException e) { + logger.warn("Error parsing idp value from medatada", e); + return ""; + } + } + + public void removeUserPassport(String subject) { + User user = this.findBySubject(subject); + if (user != null) { + user.setPassport(null); + this.save(user); + } + } + + public User updateUserConsents(User user, Set userConsentStrings) { + Map> consents = new BdcConsentsBuilder(fenceMappingUtility.getFENCEMapping(), userConsentStrings).createConsents(); + UserConsents userConsents = userConsentsRepository.findByUserId(user.getUuid()); + if (userConsents == null) { + logger.info("Creating user consents"); + userConsents = new UserConsents() + .setConsents(consents) + .setUserId(user.getUuid()); + logger.info("{} User consents created", userConsents.getConsents().size()); + } + userConsents.setConsents(consents); + logger.info("Saving {} user consents", userConsents.getConsents().size()); + userConsentsRepository.save(userConsents); + + return user; + } + + public UserConsents getUserConsents(UUID userId) { + SecurityContext securityContext = SecurityContextHolder.getContext(); + CustomUserDetails customUserDetails = (CustomUserDetails) securityContext.getAuthentication().getPrincipal(); + if (customUserDetails == null || customUserDetails.getUser() == null || customUserDetails.getUser().getUuid() == null) { + logger.error("Security context didn't have a user stored."); + return null; + } else if (customUserDetails.getUser().getUuid() != userId) { + logger.error("User " + customUserDetails.getUser().getUuid() + " tried to access consents for user " + userId); + return null; + } + return userConsentsRepository.findByUserId(userId); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/AimAheadAuthenticationService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/AimAheadAuthenticationService.java new file mode 100644 index 000000000..79d7ab025 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/AimAheadAuthenticationService.java @@ -0,0 +1,230 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl.authentication; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.node.ObjectNode; +import edu.harvard.hms.dbmi.avillach.auth.entity.Role; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import edu.harvard.hms.dbmi.avillach.auth.entity.UserClaims; +import edu.harvard.hms.dbmi.avillach.auth.service.AuthenticationService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.RoleService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.UserService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.CacheEvictionService; +import edu.harvard.hms.dbmi.avillach.auth.utils.RestClientUtil; +import jakarta.persistence.NoResultException; +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Service; + +import java.util.*; + +import static edu.harvard.hms.dbmi.avillach.auth.service.impl.RoleService.MANAGED_AUTH_ACCESS_ROLE_NAME; +import static edu.harvard.hms.dbmi.avillach.auth.service.impl.RoleService.MANAGED_OPEN_ACCESS_ROLE_NAME; + +@Service +public class AimAheadAuthenticationService extends OktaAuthenticationService implements AuthenticationService { + + private final Logger logger = LoggerFactory.getLogger(this.getClass()); + + private final UserService userService; + private final RoleService roleService; + + private final String connectionId; + private final boolean isOktaEnabled; + + private final CacheEvictionService cacheEvictionService; + + /** + * Constructor for the OktaOAuthAuthenticationService + * @param userService The user service + * @param roleService The role service + * @param idp_provider_uri The IDP provider URI + * @param connectionId The connection ID + * @param clientId The client ID + * @param spClientSecret The client secret + */ + @Autowired + public AimAheadAuthenticationService(UserService userService, + RoleService roleService, + RestClientUtil restClientUtil, + @Value("${a4.okta.idp.provider.is.enabled}") boolean isOktaEnabled, + @Value("${a4.okta.idp.provider.uri}") String idp_provider_uri, + @Value("${a4.okta.connection.id}") String connectionId, + @Value("${a4.okta.client.id}") String clientId, + @Value("${a4.okta.client.secret}") String spClientSecret, CacheEvictionService cacheEvictionService) { + super(idp_provider_uri, clientId, spClientSecret, restClientUtil); + + this.userService = userService; + this.roleService = roleService; + this.connectionId = connectionId; + this.isOktaEnabled = isOktaEnabled; + this.cacheEvictionService = cacheEvictionService; + + logger.info("OktaOAuthAuthenticationService is enabled: {}", isOktaEnabled); + logger.info("OktaOAuthAuthenticationService initialized"); + logger.info("idp_provider_uri: {}", idp_provider_uri); + logger.info("connectionId: {}", connectionId); + } + + /** + * Authenticate the user using the code provided by the IDP. This code is exchanged for an access token. + * The access token is then used to introspect the user. The user is then loaded from the database. + * If the user does not exist, we will reject their login attempt. + * + * @param host The host of the request + * @param authRequest The request body + * @return The response from the authentication attempt + */ + @Override + public HashMap authenticate(Map authRequest, String host) { + logger.info("OKTA LOGIN ATTEMPT ___ {} ___", authRequest.get("code")); + + String code = authRequest.get("code"); + if (StringUtils.isNotBlank(code)) { + JsonNode userToken = super.handleCodeTokenExchange(host, code); +JsonNode introspectResponse = super.introspectToken(userToken); + User user = initializeUser(introspectResponse); + + if (user == null) { + return null; + } + + HashMap responseMap = createUserClaims(user); + if (responseMap != null) { + logger.info("LOGIN SUCCESS ___ {}:{} ___ Authorization will expire at ___ {}___", user.getEmail(), user.getUuid().toString(), responseMap.get("expirationDate")); + responseMap.put("oktaIdToken", userToken.get("id_token").asText()); + } + + return responseMap; + } + + logger.info("LOGIN FAILED ___ USER NOT AUTHENTICATED ___"); + return null; + } + + @Override + public String getProvider() { + return "aimAheadOkta"; + } + + @Override + public boolean isEnabled() { + return this.isOktaEnabled; + } + + private User initializeUser(JsonNode introspectResponse) { + if (introspectResponse == null) { + logger.info("FAILED TO INTROSPECT TOKEN ___ "); + return null; + } + + boolean isActive = introspectResponse.get("active").asBoolean(); + if (!isActive) { + logger.info("LOGIN FAILED ___ USER IS NOT ACTIVE ___ "); + return null; + } + + User user = loadUser(introspectResponse); + if (user == null) { + return null; + } + + cacheEvictionService.evictCache(user); + return user; + } + + /** + * Create user claims to return to the client + * + * @param user The user + * @return The user claims as a HashMap + */ + private HashMap createUserClaims(User user) { + UserClaims userClaims = new UserClaims(); + userClaims.setUuid(user.getUuid().toString()); + userClaims.setSub(user.getSubject()); + userClaims.setEmail(user.getEmail()); + userClaims.setName(user.getName()); + userClaims.setIdp(this.connectionId); + userClaims.setRoles(userService.addRoleClaims(user)); + return userService.getUserProfileResponse(userClaims); + } + + /** + * Using the introspection token response, load the user from the database. If the user does not exist, we + * will reject their login attempt. + * Documentation: response-example-success-access-token + * + * @param introspectResponse The response from the introspect endpoint + * @return The user + */ + private User loadUser(JsonNode introspectResponse) { + String userEmail = introspectResponse.get("sub").asText(); + try { + // connection id = okta + User user = userService.findByEmailAndConnection(userEmail, this.connectionId).orElse(null); + if (user == null) { + return null; + } + + // If the user does not yet have a subject, set it to the subject from the introspect response + if (user.getSubject() == null) { + user.setSubject("okta|" + introspectResponse.get("uid").asText()); + } + + Role authAccessRole = this.roleService.getRoleByName(MANAGED_AUTH_ACCESS_ROLE_NAME); + if (authAccessRole != null) { + logger.info("Adding auth access role to user: {}", user.getUuid()); + Set roles = user.getRoles(); + roles.add(authAccessRole); + user = userService.changeRole(user, roles); + userService.updateUserConsents(user, Set.of()); + } else { + logger.info("{} has not be created for this environment. Please create the role and its permissions before attempting to use auth access.", MANAGED_AUTH_ACCESS_ROLE_NAME); + } + + // All users that login through OKTA should have the fence_open_access role, or they will not be able to interact with the UI + Role openAccessRole = roleService.getRoleByName(MANAGED_OPEN_ACCESS_ROLE_NAME); + if (!user.getRoles().contains(openAccessRole)) { + logger.info("Adding fence_open_access role to user: {}", user.getUuid()); + Set roles = user.getRoles(); + roles.add(openAccessRole); + user = userService.changeRole(user, roles); + } + + user.setGeneralMetadata(generateUserMetadata(introspectResponse, user).toString()); + + userService.save(user); + logger.info("LOGIN SUCCESS ___ USER DATA: {}", user); + return user; + } catch (NoResultException ex) { + logger.info("LOGIN FAILED ___ USER NOT FOUND ___ {} ___", userEmail); + return null; + } + } + + /** + * Generate the user metadata that will be stored in the database. This metadata is used to determine the user's + * role and other information. + * + * @param introspectResponse The response from the introspect endpoint + * @param user The user + * @return The user metadata as an ObjectNode + */ + protected ObjectNode generateUserMetadata(JsonNode introspectResponse, User user) { + // JsonNode is immutable, so we need to convert it to an ObjectNode + ObjectNode objectNode = new ObjectMapper().createObjectNode(); + + objectNode.put("role", "user"); + objectNode.put("sub", introspectResponse.get("sub").asText()); + objectNode.put("user_id", user.getUuid().toString()); + objectNode.put("username", user.getEmail()); + objectNode.put("email", user.getEmail()); + + return objectNode; + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/Auth0AuthenticationService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/Auth0AuthenticationService.java new file mode 100644 index 000000000..8053307a0 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/Auth0AuthenticationService.java @@ -0,0 +1,187 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl.authentication; + +import java.io.IOException; +import java.util.*; + +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.hms.dbmi.avillach.auth.entity.Connection; +import edu.harvard.hms.dbmi.avillach.auth.entity.UserClaims; +import edu.harvard.hms.dbmi.avillach.auth.exceptions.NotAuthorizedException; +import edu.harvard.hms.dbmi.avillach.auth.repository.ConnectionRepository; +import edu.harvard.hms.dbmi.avillach.auth.service.AuthenticationService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.BasicMailService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.CacheEvictionService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.OauthUserMatchingService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.UserService; +import edu.harvard.hms.dbmi.avillach.auth.utils.RestClientUtil; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.JsonNode; + +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserRepository; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.http.HttpHeaders; +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Service; + +/** + * This class provides authentication functionality. This implements an authenticationService interface + * in the future to support different modes of authentication. + * + *

    Thoughts of design

    + * The main purpose of this class is returns a token that includes information of the roles of users. + */ + +@Service +public class Auth0AuthenticationService implements AuthenticationService { + + private final Logger logger = LoggerFactory.getLogger(Auth0AuthenticationService.class); + + private final OauthUserMatchingService matchingService; + private final UserRepository userRepository; + private final BasicMailService basicMailService; + private final UserService userService; + + private static final int AUTH_RETRY_LIMIT = 3; + private final boolean isAuth0Enabled; + private final CacheEvictionService cacheEvictionService; + + private boolean deniedEmailEnabled; + + private final String auth0host; + + private final ObjectMapper objectMapper = new ObjectMapper(); + private final ConnectionRepository connectionRepository; + private final RestClientUtil restClientUtil; + + @Autowired + public Auth0AuthenticationService(OauthUserMatchingService matchingService, + UserRepository userRepository, + BasicMailService basicMailService, + UserService userService, + ConnectionRepository connectionRepository, + RestClientUtil restClientUtil, + @Value("${auth0.idp.provider.is.enabled}") boolean isAuth0Enabled, + @Value("${auth0.denied.email.enabled}") boolean deniedEmailEnabled, + @Value("${auth0.host}") String auth0host, + CacheEvictionService cacheEvictionService) { + this.matchingService = matchingService; + this.userRepository = userRepository; + this.basicMailService = basicMailService; + this.userService = userService; + this.deniedEmailEnabled = deniedEmailEnabled; + this.auth0host = auth0host; + this.connectionRepository = connectionRepository; + this.restClientUtil = restClientUtil; + this.isAuth0Enabled = isAuth0Enabled; + this.cacheEvictionService = cacheEvictionService; + } + + @Override + public HashMap authenticate(Map authRequest, String requestHost) throws IOException { + String accessToken = authRequest.get("access_token"); + String redirectURI = authRequest.get("redirectURI"); + + if (accessToken == null || redirectURI == null || accessToken.isEmpty() || redirectURI.isEmpty()) { + throw new IllegalArgumentException("Missing accessToken or redirectURI in request body."); + } + + JsonNode userInfo = retrieveUserInfo(accessToken); + JsonNode userIdNode = userInfo.get("user_id"); + if (userIdNode == null) { + logger.error("getToken() cannot find user_id by retrieveUserInfo(), return json response: {}", userInfo.toString()); + throw new NotAuthorizedException("cannot get sufficient user information. Please contact admin."); + } + String userId = userIdNode.asText(); + + logger.info("Successfully retrieved userId, {}, from the provided code and redirectURI", userId); + String connectionId; + try { + connectionId = userInfo.get("identities").get(0).get("connection").asText(); + } catch (Exception e) { + logger.error("getToken() cannot find connection_id by retrieveUserInfo(), return json response: {}", userInfo.toString()); + throw new NotAuthorizedException("cannot get sufficient user information. Please contact admin."); + } + + Connection connection = connectionRepository.findById(connectionId).orElseThrow(() -> new NotAuthorizedException("No connection found for connection_id " + connectionId)); + //Do we have this user already? + User user = userRepository.findBySubjectAndConnection(userId, connection); + if (user == null) { + //Try to match + user = matchingService.matchTokenToUser(userInfo); + if (user == null) { + if (this.deniedEmailEnabled) { + try { + basicMailService.sendDeniedAccessEmail(userInfo); + } catch (jakarta.mail.MessagingException e) { + throw new RuntimeException(e); + } + } + throw new NotAuthorizedException("No user matching user_id " + userId + " present in database"); + } + } + + cacheEvictionService.evictCache(user); + UserClaims userClaims = new UserClaims(); + userClaims.setUuid(user.getUuid().toString()); + userClaims.setSub(userId); + userClaims.setEmail(user.getEmail()); + userClaims.setName(user.getName()); + userClaims.setIdp(connection.getId()); + userClaims.setRoles(userService.addRoleClaims(user)); + HashMap responseMap = userService.getUserProfileResponse(userClaims); + + if (responseMap != null) { + logger.info("LOGIN SUCCESS ___ {}:{} ___ Authorization will expire at ___ {}___", user.getEmail(), user.getUuid().toString(), responseMap.get("expirationDate")); + } + + return responseMap; + } + + @Override + public String getProvider() { + return "auth0"; + } + + @Override + public boolean isEnabled() { + return this.isAuth0Enabled; + } + + public JsonNode retrieveUserInfo(String accessToken) throws IOException { + String auth0UserInfoURI = this.auth0host + "/userinfo"; + HttpHeaders headers = new HttpHeaders(); + headers.setContentType(MediaType.APPLICATION_JSON); + headers.set("Authorization", "Bearer " + accessToken); + + JsonNode auth0Response = null; + + for (int i = 1; i <= AUTH_RETRY_LIMIT && auth0Response == null; i++) { + try { + ResponseEntity response = this.restClientUtil.retrieveGetResponseWithRequestConfiguration( + auth0UserInfoURI, + headers, + 2000 + ); + + auth0Response = objectMapper.readTree(response.getBody()); + } catch (Exception e) { + if (i < AUTH_RETRY_LIMIT) { + logger.warn("Failed to authenticate. Retrying"); + } else { + logger.error("Failed to authenticate. Giving up!"); + throw e; + } + } + } + return auth0Response; + } + + public void setDeniedEmailEnabled(boolean deniedEmailEnabled) { + this.deniedEmailEnabled = deniedEmailEnabled; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/AuthenticationServiceRegistry.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/AuthenticationServiceRegistry.java new file mode 100644 index 000000000..f744a5d07 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/AuthenticationServiceRegistry.java @@ -0,0 +1,42 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl.authentication; + +import edu.harvard.hms.dbmi.avillach.auth.service.AuthenticationService; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Component; + +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +@Component +public class AuthenticationServiceRegistry { + + private final Logger logger = LoggerFactory.getLogger(AuthenticationServiceRegistry.class); + + private final Map authenticationServices = new HashMap<>(); + + @Autowired + public AuthenticationServiceRegistry(List authenticationServices) { + authenticationServices.forEach(authenticationService -> { + logger.info("Registering authentication service: {}", authenticationService.getProvider()); + if (authenticationService.isEnabled()) { + this.authenticationServices.put(authenticationService.getProvider(), authenticationService); + logger.info("Registered authentication service: {}", authenticationService.getProvider()); + } else { + logger.info("Skipping registration of disabled authentication service: {}", authenticationService.getProvider()); + } + }); + } + + public AuthenticationService getAuthenticationService(String provider) { + // Check if the provider is registered by the provider name + if (!authenticationServices.containsKey(provider)) { + throw new IllegalArgumentException("No authentication service found for provider: " + provider); + } + + return authenticationServices.get(provider); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/FENCEAuthenticationService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/FENCEAuthenticationService.java new file mode 100644 index 000000000..b2892aa95 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/FENCEAuthenticationService.java @@ -0,0 +1,315 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl.authentication; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.hms.dbmi.avillach.auth.entity.Connection; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import edu.harvard.hms.dbmi.avillach.auth.entity.UserClaims; +import edu.harvard.hms.dbmi.avillach.auth.entity.UserConsents; +import edu.harvard.hms.dbmi.avillach.auth.exceptions.NotAuthorizedException; +import edu.harvard.hms.dbmi.avillach.auth.model.fenceMapping.StudyMetaData; +import edu.harvard.hms.dbmi.avillach.auth.service.AuthenticationService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.*; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.authorization.BdcConsentsBuilder; +import edu.harvard.hms.dbmi.avillach.auth.utils.FenceMappingUtility; +import edu.harvard.hms.dbmi.avillach.auth.utils.RestClientUtil; +import jakarta.annotation.PostConstruct; +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.http.HttpEntity; +import org.springframework.http.HttpHeaders; +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Service; +import org.springframework.util.LinkedMultiValueMap; +import org.springframework.util.MultiValueMap; +import org.springframework.web.client.HttpClientErrorException; + +import java.util.*; +import java.util.stream.Collectors; + +@Service +public class FENCEAuthenticationService implements AuthenticationService { + + private final Logger logger = LoggerFactory.getLogger(FENCEAuthenticationService.class); + + private final UserService userService; + private final ConnectionWebService connectionService; // We will need to investigate if the ConnectionWebService will need to be versioned as well. + private final FenceMappingUtility fenceMappingUtility; + private final CacheEvictionService cacheEvictionService; + + private Connection fenceConnection; + + private final boolean isFenceEnabled; + private final String idp_provider_uri; + private final String fence_client_id; + private final String fence_client_secret; + + + private final RestClientUtil restClientUtil; + + @Autowired + public FENCEAuthenticationService(UserService userService, + ConnectionWebService connectionService, + RestClientUtil restClientUtil, + @Value("${fence.idp.provider.is.enabled}") boolean isFenceEnabled, + @Value("${fence.idp.provider.uri}") String idpProviderUri, + @Value("${fence.client.id}") String fenceClientId, + @Value("${fence.client.secret}") String fenceClientSecret, + FenceMappingUtility fenceMappingUtility, CacheEvictionService cacheEvictionService) { + this.userService = userService; + this.connectionService = connectionService; + this.idp_provider_uri = idpProviderUri; + this.fence_client_id = fenceClientId; + this.fence_client_secret = fenceClientSecret; + this.restClientUtil = restClientUtil; + this.fenceMappingUtility = fenceMappingUtility; + this.isFenceEnabled = isFenceEnabled; + this.cacheEvictionService = cacheEvictionService; + } + + @PostConstruct + public void initializeFenceService() { + fenceConnection = connectionService.getConnectionByLabel("FENCE"); + logger.info("isFenceEnabled: {}", isFenceEnabled); + logger.info("idp_provider_uri: {}", idp_provider_uri); + } + + @Override + public HashMap authenticate(Map authRequest, String host) { + String callBackUrl = "https://" + host + "/login/loading/"; + + logger.debug("getFENCEProfile() starting..."); + String fence_code = authRequest.get("code"); + + // Validate that the fence code is alphanumeric + if (!fence_code.matches("[a-zA-Z0-9]+")) { + logger.error("getFENCEProfile() fence code is not alphanumeric"); + throw new NotAuthorizedException("The fence code is not alphanumeric"); + } + + JsonNode fence_user_profile; + // Get the Gen3/FENCE user profile. It is a JsonNode object + try { + logger.debug("getFENCEProfile() query FENCE for user profile with code"); + JsonNode tokenJson = getFENCEAccessToken(callBackUrl, fence_code); + JsonNode accessTokenNode = tokenJson.get("access_token"); + if (accessTokenNode == null || accessTokenNode.isNull() || accessTokenNode.asText().isBlank()) { + logger.error("getFENCEProfile() access_token missing in token response: {}", tokenJson.toString()); + throw new NotAuthorizedException("Token response missing access_token"); + } + String accessToken = accessTokenNode.asText(); + fence_user_profile = getFENCEUserProfile(accessToken); + + if (logger.isTraceEnabled()) { + // create object mapper instance + ObjectMapper mapper = new ObjectMapper(); + // `JsonNode` to JSON string + String prettyString = mapper.writerWithDefaultPrettyPrinter().writeValueAsString(fence_user_profile); + + logger.trace("getFENCEProfile() user profile structure:{}", prettyString); + } + logger.debug("getFENCEProfile() .username:{}", fence_user_profile.get("username")); + logger.debug("getFENCEProfile() .user_id:{}", fence_user_profile.get("user_id")); + logger.debug("getFENCEProfile() .email:{}", fence_user_profile.get("email")); + } catch (Exception ex) { + logger.error("getFENCEProfile() could not retrieve the user profile from the auth provider, because {}", ex.getMessage(), ex); + throw new NotAuthorizedException("Could not get the user profile " + + "from the Gen3 authentication provider." + ex.getMessage()); + } + + User currentUser; + try { + // Create or retrieve the user profile from our database, based on the the key + // in the Gen3/FENCE profile + currentUser = createUserFromFENCEProfile(fence_user_profile); + logger.info("getFENCEProfile() saved details for user with e-mail:{} and subject:{}", currentUser.getEmail(), currentUser.getSubject()); + cacheEvictionService.evictCache(currentUser); + } catch (Exception ex) { + logger.error("getFENCEToken() Could not persist the user information, because {}", ex.getMessage()); + throw new NotAuthorizedException("The user details could not be persisted. Please contact the administrator."); + } + + // Update the user's roles (or create them if none exists) + Iterator project_access_names = fence_user_profile.get("authz").fieldNames(); + Set roleNames = new HashSet<>(); + Set userConsentStrings = new HashSet<>(); + project_access_names.forEachRemaining(roleName -> { + // We need to add/remove the users roles based on what is in the project_access_names list + StudyMetaData projectMetadata = this.fenceMappingUtility.getFenceMappingByAuthZ().get(roleName); + if (projectMetadata == null) { + logger.error("getFENCEProfile() -> createAndUpsertRole could not find study in FENCE mapping SKIPPING: {}", roleName); + return; + } + + String projectId = projectMetadata.getStudyIdentifier(); + String consentCode = projectMetadata.getConsentGroupCode(); + String userConsent = projectId; + if (consentCode != null && !consentCode.isEmpty()) { + userConsent += "." + consentCode; + } + userConsentStrings.add(userConsent); + String newRoleName = StringUtils.isNotBlank(consentCode) ? "MANAGED_" + projectId + "_" + consentCode : "MANAGED_" + projectId; + + roleNames.add(newRoleName); + }); + + userService.updateUserConsents(currentUser, userConsentStrings); + + + currentUser = userService.updateUserRoles(currentUser, roleNames); + UserClaims userClaims = new UserClaims(); + userClaims.setUuid(currentUser.getUuid().toString()); + userClaims.setSub(currentUser.getSubject()); + userClaims.setEmail(currentUser.getEmail()); + userClaims.setName(fence_user_profile.has("name") ? fence_user_profile.get("name").asText() : currentUser.getName()); + userClaims.setIdp(this.fenceConnection.getLabel()); + userClaims.setRoles(userService.addRoleClaims(currentUser)); + HashMap responseMap = userService.getUserProfileResponse(userClaims); + + if (responseMap != null) { + logger.info("LOGIN SUCCESS ___ {}:{}:{} ___ WITH ROLES ___ {} ___ Authorization will expire at ___ {}___", + currentUser.getEmail(), + currentUser.getUuid().toString(), + currentUser.getSubject(), + currentUser.getRoles().stream().map(role -> role.getName().replace("MANAGED_", "")).collect(Collectors.joining(",")), + responseMap.get("expirationDate")); + logger.debug("getFENCEProfile() UserProfile response object has been generated"); + logger.debug("getFENCEToken() finished"); + } + + return responseMap; + } + + + @Override + public String getProvider() { + return "fence"; + } + + @Override + public boolean isEnabled() { + return this.isFenceEnabled; + } + + private JsonNode getFENCEUserProfile(String access_token) { + logger.debug("getFENCEUserProfile() starting"); + + HttpHeaders headers = new HttpHeaders(); + headers.setBearerAuth(access_token); + + String url = this.idp_provider_uri + "/user/user"; + logger.debug("getFENCEUserProfile() getting user profile from uri:{}", url); + + try { + ResponseEntity resp = this.restClientUtil.retrieveGetResponseWithRequestConfiguration( + url, + headers, + 10000 + ); + + if (!resp.getStatusCode().is2xxSuccessful()) { + logger.error("getFENCEUserProfile() non-2xx: status={}, body={}", resp.getStatusCode(), resp.getBody()); + throw new NotAuthorizedException("User profile request failed: " + resp.getStatusCode()); + } + String body = resp.getBody(); + if (body == null || body.isBlank()) { + logger.error("getFENCEUserProfile() empty response body"); + throw new NotAuthorizedException("Empty user profile response"); + } + JsonNode json = new ObjectMapper().readTree(body); + logger.debug("getFENCEUserProfile() finished, returning user profile: {}", json.toString()); + return json; + } catch (HttpClientErrorException e) { + logger.error("getFENCEUserProfile() HttpClientErrorException: status={}, body={}", e.getStatusCode(), e.getResponseBodyAsString()); + throw new NotAuthorizedException("User profile request failed: " + e.getStatusCode()); + } catch (Exception e) { + logger.error("getFENCEUserProfile() error: {}", e.getMessage(), e); + throw new NotAuthorizedException("Failed to parse user profile"); + } + } + + private JsonNode getFENCEAccessToken(String callback_url, String fence_code) { + logger.debug("getFENCEAccessToken() starting, using FENCE code"); + + HttpHeaders headers = new HttpHeaders(); + headers.setBasicAuth(this.fence_client_id, this.fence_client_secret); + headers.setContentType(MediaType.APPLICATION_FORM_URLENCODED); + + MultiValueMap queryMap = new LinkedMultiValueMap<>(); + queryMap.add("grant_type", "authorization_code"); + queryMap.add("code", fence_code); + queryMap.add("redirect_uri", callback_url); + + String fence_token_url = this.idp_provider_uri + "/user/oauth2/token"; + + HttpEntity> request = new HttpEntity<>(queryMap, headers); + + try { + ResponseEntity resp = this.restClientUtil.retrievePostResponse( + fence_token_url, + request + ); + + if (!resp.getStatusCode().is2xxSuccessful()) { + String body = resp.getBody(); + logger.error("getFENCEAccessToken() non-2xx from FENCE: status={}, body={}", resp.getStatusCode(), body); + throw new NotAuthorizedException("Token endpoint returned status " + resp.getStatusCode()); + } + + String body = resp.getBody(); + if (body == null || body.isBlank()) { + logger.error("getFENCEAccessToken() empty response body from FENCE token endpoint"); + throw new NotAuthorizedException("Empty response from token endpoint"); + } + + JsonNode respJson = new ObjectMapper().readTree(body); + logger.debug("getFENCEAccessToken() finished: {}", respJson.toString()); + return respJson; + + } catch (HttpClientErrorException e) { + String body = e.getResponseBodyAsString(); + logger.error("getFENCEAccessToken() HttpClientErrorException: status={}, body={}", e.getStatusCode(), body); + throw new NotAuthorizedException("Token request failed: " + e.getStatusCode() + ": " + e.getMessage()); + } catch (Exception ex) { + logger.error("getFENCEAccessToken() failed to call FENCE token service: {}", ex.getMessage(), ex); + throw new NotAuthorizedException("Token request failed: " + ex.getMessage()); + } + } + + /** + * Create or update a user record, based on the FENCE user profile, which is in JSON format. + * + * @param node User profile, as it is received from Gen3 FENCE, in JSON format + * @return User The actual entity, as it is persisted (if no errors) in the PSAMA database + */ + private User createUserFromFENCEProfile(JsonNode node) { + logger.debug("createUserFromFENCEProfile() starting..."); + + User newUser = new User(); + newUser.setSubject("fence|" + node.get("user_id").asText()); + // This is not always an email address, but it is the only attribute other than the sub claim + // that is guaranteed to be populated by Fence and which makes sense as a display name for a + // user. + newUser.setEmail(node.get("username").asText()); + newUser.setGeneralMetadata(node.toString()); + // This is a hack, but someone has to do it. + newUser.setAcceptedTOS(new Date()); + newUser.setConnection(fenceConnection); + logger.debug("createUserFromFENCEProfile() finished setting fields"); + + User actual_user = userService.findOrCreate(newUser); + + if (actual_user.getRoles() == null) { + actual_user.setRoles(new HashSet<>()); + } + + logger.debug("createUserFromFENCEProfile() finished, user record inserted"); + return actual_user; + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/OktaAuthenticationService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/OktaAuthenticationService.java new file mode 100644 index 000000000..6a0e8ff9f --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/OktaAuthenticationService.java @@ -0,0 +1,100 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl.authentication; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.hms.dbmi.avillach.auth.utils.RestClientUtil; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.http.HttpHeaders; +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; + +import java.util.Objects; + +public class OktaAuthenticationService { + + private final Logger logger = LoggerFactory.getLogger(this.getClass()); + + private final String idp_provider_uri; + private final String clientId; + private final String spClientSecret; + private final RestClientUtil restClientUtil; + + public OktaAuthenticationService(String idpProviderUri, String clientId, String spClientSecret, RestClientUtil restClientUtil) { + this.idp_provider_uri = idpProviderUri; + this.clientId = clientId; + this.spClientSecret = spClientSecret; + this.restClientUtil = restClientUtil; + } + + /** + * Exchange the code for an access token. This is a call to the OKTA token endpoint. + * Documentation: Token + * + * @param host The UriInfo object from the JAX-RS context + * @param code The code to exchange + * @return The response from the token endpoint as a JsonNode + */ + protected JsonNode handleCodeTokenExchange(String host, String code) { + String redirectUri = "https://" + host + "/login/loading"; + String queryString = "grant_type=authorization_code" + "&code=" + code + "&redirect_uri=" + redirectUri; + String oktaTokenUrl = "https://" + this.idp_provider_uri + "/oauth2/default/v1/token"; + + return doOktaRequest(oktaTokenUrl, queryString); + } + + /** + * Perform a request to the OKTA API using the provided URL and parameters. The request will be a POST request. + * It is using Authorization Basic authentication. The client ID and client secret are base64 encoded and sent + * in the Authorization header. + * + * @param requestUrl The URL to call + * @param requestParams The parameters to send + * @return The response from the OKTA API as a JsonNode + */ + private JsonNode doOktaRequest(String requestUrl, String requestParams) { + HttpHeaders headers = new HttpHeaders(); + headers.setBasicAuth(this.clientId, this.spClientSecret); + headers.setContentType(MediaType.APPLICATION_FORM_URLENCODED); + + ResponseEntity resp; + JsonNode response = null; + try { + resp = this.restClientUtil.retrievePostResponse(requestUrl, headers, requestParams); + response = new ObjectMapper().readTree(Objects.requireNonNull(resp.getBody()).toString()); + } catch (Exception ex) { + logger.error("handleCodeTokenExchange() failed to call OKTA token endpoint, {}", ex.getMessage()); + } + + logger.debug("getFENCEAccessToken() finished: {}", response); + return response; + } + + /** + * Introspect the token to get the user's email address. This is a call to the OKTA introspect endpoint. + * Documentation: /introspect + * + * @param userToken The token to introspect + * @return The response from the introspect endpoint as a JsonNode + */ + protected JsonNode introspectToken(JsonNode userToken) { + if (userToken == null) { + logger.error("USER TOKEN IS NULL. CODE EXCHANGE FAILED."); + return null; + } + JsonNode accessTokenNode = userToken.get("access_token"); + if (accessTokenNode == null) { + logger.info("USER TOKEN DOES NOT HAVE ACCESS TOKEN ___ {}", userToken); + return null; + } + + return this.introspectToken(accessTokenNode.asText()); + } + + protected JsonNode introspectToken(String accessToken) { + String oktaIntrospectUrl = "https://" + this.idp_provider_uri + "/oauth2/default/v1/introspect"; + String payload = "token_type_hint=access_token&token=" + accessToken; + return doOktaRequest(oktaIntrospectUrl, payload); + } + +} \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/RASAuthenticationService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/RASAuthenticationService.java new file mode 100644 index 000000000..c63ab4787 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/RASAuthenticationService.java @@ -0,0 +1,264 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl.authentication; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.node.ObjectNode; +import edu.harvard.hms.dbmi.avillach.auth.entity.Connection; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import edu.harvard.hms.dbmi.avillach.auth.entity.UserClaims; +import edu.harvard.hms.dbmi.avillach.auth.model.ras.Ga4ghPassportV1; +import edu.harvard.hms.dbmi.avillach.auth.model.ras.Passport; +import edu.harvard.hms.dbmi.avillach.auth.model.ras.RasDbgapPermission; +import edu.harvard.hms.dbmi.avillach.auth.service.AuthenticationService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.*; +import edu.harvard.hms.dbmi.avillach.auth.utils.JWTUtil; +import edu.harvard.hms.dbmi.avillach.auth.utils.RestClientUtil; +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Service; + +import java.util.*; +import java.util.stream.Collectors; + +@Service +public class RASAuthenticationService extends OktaAuthenticationService implements AuthenticationService { + + private final Logger logger = LoggerFactory.getLogger(this.getClass()); + + private final UserService userService; + private final boolean isEnabled; + private final RoleService roleService; + private final RASPassPortService rasPassPortService; + private final CacheEvictionService cacheEvictionService; + private Connection rasConnection; + private final String rasPassportIssuer; + + /** + * Constructor for the RASAuthenticationService + * + * @param userService The user service + * @param idp_provider_uri The IDP provider URI + * @param connectionId The connection ID + * @param clientId The client ID + * @param clientSecret The client secret + */ + @Autowired + public RASAuthenticationService(UserService userService, + RestClientUtil restClientUtil, + @Value("${ras.okta.idp.provider.is.enabled}") boolean isEnabled, + @Value("${ras.okta.idp.provider.uri}") String idp_provider_uri, + @Value("${ras.okta.connection.id}") String connectionId, + @Value("${ras.okta.client.id}") String clientId, + @Value("${ras.okta.client.secret}") String clientSecret, + @Value("${ras.passport.issuer}") String rasPassportIssuer, + RoleService roleService, + RASPassPortService rasPassPortService, + ConnectionWebService connectionService, CacheEvictionService cacheEvictionService) { + super(idp_provider_uri, clientId, clientSecret, restClientUtil); + + this.userService = userService; + this.isEnabled = isEnabled; + this.roleService = roleService; + this.rasPassPortService = rasPassPortService; + this.rasPassportIssuer = rasPassportIssuer; + + logger.info("RASAuthenticationService is enabled: {}", isEnabled); + logger.info("RASAuthenticationService initialized"); + logger.info("idp_provider_uri: {}", idp_provider_uri); + logger.info("connectionId: {}", connectionId); + + this.rasConnection = connectionService.getConnectionByLabel("RAS"); + this.cacheEvictionService = cacheEvictionService; + } + + /** + * Authenticate the user using the code provided by the IDP. This code is exchanged for an access token. + * The access token is then used to introspect the user. The user is then loaded from the database. + * If the user does not exist, we will reject their login attempt. + * + * @param host The host of the request + * @param authRequest The request body + * @return The response from the authentication attempt + */ + @Override + public HashMap authenticate(Map authRequest, String host) { + logger.info("RAS OKTA LOGIN ATTEMPT ___ CODE {}", authRequest.get("code")); + + JsonNode introspectResponse = null; + String idToken = null; + if (authRequest.containsKey("code") && StringUtils.isNotBlank(authRequest.get("code"))) { + JsonNode userToken = handleCodeTokenExchange(host, authRequest.get("code")); + introspectResponse = introspectToken(userToken); + idToken = userToken.get("id_token").asText(); + logger.debug("RAS OKTA LOGIN ATTEMPT ___ INTROSPECTION RESPONSE {}", introspectResponse); + } + + if (introspectResponse == null) { + logger.info("LOGIN FAILED ___ USER NOT AUTHENTICATED ___ INTROSPECTION RESPONSE {} ___ CODE {}", introspectResponse, authRequest.get("code")); + return null; + } + + Optional initializedUser = initializeUser(introspectResponse); + if (initializedUser.isEmpty()) { + logger.info("LOGIN FAILED ___ COULD NOT CREATE USER ___ INTROSPECTION RESPONSE {} ___ CODE {}", introspectResponse, authRequest.get("code")); + return null; + } + + User user = initializedUser.get(); + Optional rasPassport = extractAndVerifyPassport(authRequest, introspectResponse, user); + if (rasPassport.isEmpty()) return null; + user = updateRasUserRoles(authRequest.get("code"), user, rasPassport.get()); + setUserPassport(authRequest, introspectResponse, user); + UserClaims userClaims = buildUserClaims(user, introspectResponse, rasPassport.get()); + HashMap responseMap = userService.getUserProfileResponse(userClaims); + + if (responseMap != null) { + responseMap.put("oktaIdToken", idToken); + logger.info("LOGIN SUCCESS ___ USER {}:{} ___ WITH ROLES ___ {} ___ AUTHORIZATION WILL EXPIRE AT ___ {} ___ CODE {}", + user.getSubject(), user.getUuid().toString(), + user.getRoles().stream().map(role -> role.getName().replace("MANAGED_", "")).collect(Collectors.joining(",")), + responseMap.get("expirationDate"), authRequest.get("code")); + } + + return responseMap; + } + + private Optional extractAndVerifyPassport(Map authRequest, JsonNode introspectResponse, User user) { + Optional rasPassport = this.rasPassPortService.extractPassport(introspectResponse); + if (rasPassport.isEmpty()) { + logger.info("LOGIN FAILED ___ NO RAS PASSPORT FOUND ___ USER: {} ___ CODE {}", user.getSubject(), authRequest.get("code")); + return Optional.empty(); + } + + if (rasPassPortService.isExpired(rasPassport.get())) { + logger.error("validateRASPassport() LOGIN FAILED ___ PASSPORT IS EXPIRED ___ USER: {} ___ CODE {}", user.getSubject(), authRequest.get("code")); + return Optional.empty(); + } + + if (!rasPassport.get().getIss().equals(this.rasPassportIssuer)) { + logger.error("validateRASPassport() LOGIN FAILED ___ PASSPORT ISSUER IS NOT CORRECT ___ USER: {} ___ " + + "EXPECTED ISSUER {} ___ ACTUAL ISSUER {} ___ CODE {}", + user.getSubject(), this.rasPassportIssuer, rasPassport.get().getIss(), authRequest.get("code")); + return Optional.empty(); + } + return rasPassport; + } + + protected User updateRasUserRoles(String code, User user, Passport rasPassport) { + logger.info("RAS PASSPORT FOUND ___ USER: {} ___ PASSPORT: {} ___ CODE {}", user.getSubject(), rasPassport, code); + Set> ga4ghPassports = rasPassport.getGa4ghPassportV1().stream().map(JWTUtil::parseGa4ghPassportV1).filter(Optional::isPresent).collect(Collectors.toSet()); + Set dbgapPermissions = this.rasPassPortService.ga4ghPassportToRasDbgapPermissions(ga4ghPassports); + Set dbgapRoleNames = this.roleService.getRoleNamesForDbgapPermissions(dbgapPermissions); + user = userService.updateUserRoles(user, dbgapRoleNames); + + Set userConsentStrings = dbgapPermissions.stream() + .map(permission -> permission.getPhsId() + "." + permission.getConsentGroup()).collect(Collectors.toSet()); + user = userService.updateUserConsents(user, userConsentStrings); + logger.debug("USER {} ROLES UPDATED {} ___ CODE {}", + user.getSubject(), + user.getRoles().stream().map(role -> role.getName().replace("MANAGED_", "")).toArray(), + code); + return user; + } + + private Optional initializeUser(JsonNode introspectResponse) { + Optional user = userService.createRasUser(introspectResponse, this.rasConnection); + if (user.isEmpty()) { + logger.info("FAILED TO LOAD OR CREATE USER"); + return Optional.empty(); + } + + User currentUser = user.get(); + currentUser.setGeneralMetadata(generateRasUserMetadata(currentUser).toString()); + logger.info("USER METADATA SUCCESSFULLY ADDED - USER DATA: {}", currentUser.getGeneralMetadata()); + + cacheEvictionService.evictCache(currentUser); + return Optional.of(currentUser); + } + + /** + * Create user claims to return to the client + * + * @param user The user + * @param introspectResponse The OKTA introspect response + * @param rasPassport The RAS passport + * @return The user claims as a HashMap + */ + private UserClaims buildUserClaims(User user, JsonNode introspectResponse, Passport rasPassport) { + UserClaims userClaims = new UserClaims(); + userClaims.setUuid(user.getUuid().toString()); + userClaims.setSub(user.getSubject()); + userClaims.setEmail(user.getEmail()); + userClaims.setIdp(this.rasConnection.getLabel()); + userClaims.setName(user.getName()); + userClaims.setUserid(introspectResponse.get("userid").asText()); + userClaims.setPreferred_username(introspectResponse.get("preferred_username").asText()); + userClaims.setUser_permission_group(extractPermissionGroupFromPassport(rasPassport)); + userClaims.setRoles(userService.addRoleClaims(user)); + + return userClaims; + } + + private String extractPermissionGroupFromPassport(Passport rasPassport) { + try { + List ga4ghPassports = rasPassport.getGa4ghPassportV1(); + if (ga4ghPassports == null || ga4ghPassports.isEmpty()) { + return null; + } + Optional parsedPassport = JWTUtil.parseGa4ghPassportV1(ga4ghPassports.get(0)); + if (parsedPassport.isPresent() && parsedPassport.get().getGa4ghVisaV1() != null) { + return parsedPassport.get().getGa4ghVisaV1().getSource(); + } + } catch (Exception e) { + logger.error("Failed to extract permission group from passport: {}", e.getMessage()); + } + return null; + } + + /** + * Generate the user metadata that will be stored in the database. This metadata is used to determine the user's + * role and other information. + * + * @param user The user + * @return The user metadata as an ObjectNode + */ + protected ObjectNode generateRasUserMetadata(User user) { + // JsonNode is immutable, so we need to convert it to an ObjectNode + ObjectNode objectNode = new ObjectMapper().createObjectNode(); + + objectNode.put("role", "user"); + objectNode.put("sub", user.getSubject()); + objectNode.put("user_id", user.getUuid().toString()); + objectNode.put("username", user.getEmail()); + objectNode.put("email", user.getEmail()); + objectNode.put("idp", this.rasConnection.getLabel()); + + return objectNode; + } + + private void setUserPassport(Map authRequest, JsonNode introspectResponse, User user) { + String passport = introspectResponse.get("passport_jwt_v11").toString(); + user.setPassport(passport); + userService.save(user); + logger.info("RAS PASSPORT SUCCESSFULLY ADDED TO USER: {} ___ CODE {}", user.getSubject(), authRequest.get("code")); + } + + @Override + public String getProvider() { + return "ras"; + } + + @Override + public boolean isEnabled() { + return this.isEnabled; + } + + public void setRasConnection(Connection rasConnection) { + this.rasConnection = rasConnection; + } + + +} \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/AuthorizationService.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/AuthorizationService.java new file mode 100644 index 000000000..4d125309d --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/AuthorizationService.java @@ -0,0 +1,351 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl.authorization; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.JsonMappingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.hms.dbmi.avillach.auth.entity.*; +import edu.harvard.hms.dbmi.avillach.auth.model.EvaluateAccessRuleResult; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserConsentsRepository; +import edu.harvard.hms.dbmi.avillach.auth.rest.TokenController; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.AccessRuleService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.RoleService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.SessionService; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import io.micrometer.common.util.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Service; + +import java.util.*; +import java.util.regex.Pattern; +import java.util.stream.Collectors; + +import static edu.harvard.hms.dbmi.avillach.auth.service.impl.RoleService.*; + +/** + * This class handles authorization activities in the project. It decides if a user can send a request to certain applications based on what + * endpoint they are trying to hit and the content of the request body (in HTTP POST method).

    Thoughts on design:

    The core + * technology used here is jsonpath. In the {@link TokenController#inspectToken(Map)} class, other registered applications can hit the + * tokenIntrospection endpoint with a token they want PSAMA to introspect along with the URL the token holder is trying to hit and what data + * this token holder is trying to send. After checking if the token is valid or not, the authorization check in this class will start. + *

    Whether users are allowed access or not depends on their privileges, which depends on the accessRules underneath. + * AuthorizationService class will eventually use jsonpath to check if certain places in the incoming JSON meet the requirement of the + * preset rules in accessRules to determine if the token holder is authorized or not.

    + */ +@Service +public class AuthorizationService { + + private final Logger logger = LoggerFactory.getLogger(AuthorizationService.class); + + /** + * Matches clean HPDS-v3 (auth-backend) target service paths, e.g. {@code /hpds/auth/v3}, {@code /hpds/auth/v3/query}, + * {@code /hpds/auth/v3/query/abc/result}. Only the {@code auth} backend reaches this method — open-access requests are authorized via a + * separate endpoint — so the {@code open} backend is intentionally not matched. Segment-aware so it does NOT match things like + * {@code /hpds/auth/v30/query}, {@code /hpds/auth/v3ish/query}, {@code /hpds/v3/query}, {@code /foo/hpds/auth/v3/query}, or + * {@code /hpds/auth/v3-query}. + */ + private static final Pattern HPDS_V3_TARGET_SERVICE_PATTERN = Pattern.compile("^/hpds/auth/v3(/.*)?$"); + + protected AccessRuleService accessRuleService; + protected SessionService sessionService; + private final RoleService roleService; + + private final ConsentBasedAccessRuleEvaluator consentBasedAccessRuleEvaluator; + + /** + * Applications that have strict access control. If the application is strict a user must have both privileges and access rules. If the + * application is not strict, the user only needs privileges. Access rules are optional. + */ + private final Set strictConnections = new HashSet<>(); + + + private final UserConsentsRepository userConsentsRepository; + + @Autowired + public AuthorizationService( + AccessRuleService accessRuleService, SessionService sessionService, RoleService roleService, + ConsentBasedAccessRuleEvaluator consentBasedAccessRuleEvaluator, + @Value("${strict.authorization.applications.connections}") String strictConnections, UserConsentsRepository userConsentsRepository + ) { + this.accessRuleService = accessRuleService; + this.sessionService = sessionService; + this.roleService = roleService; + this.consentBasedAccessRuleEvaluator = consentBasedAccessRuleEvaluator; + if (strictConnections != null && !strictConnections.isEmpty()) { + this.strictConnections.addAll(Arrays.asList(strictConnections.split(","))); + } + this.userConsentsRepository = userConsentsRepository; + } + + /** + * Checking based on AccessRule in Privilege

    Thoughts on design:

    We have three layers here: role, privilege, + * accessRule.
    A role might have multiple privileges, a privilege might have multiple accessRules.
    Currently, we retrieve all + * accessRules together. Between AccessRules, they should be OR relationship, which means roles and privileges are OR relationship, pass + * one, and you are good.

    Inside each accessRule, there are subAccessRules and Gates.
    Only if all gates are applied will + * the accessRule be checked.
    The accessRule and subAccessRules are an AND relationship. + * + * @param application + * @param requestBody + * @param isLongTermToken + * @return + * @see Privilege + * @see AccessRule + */ + public EvaluateAccessRuleResult isAuthorized(Application application, Object requestBody, User user, boolean isLongTermToken) { + String applicationName = application.getName(); + String resourceId = "null"; + String targetService = "null"; + + if (user == null) { + logger.error("isAuthorized() User cannot be null"); + return new EvaluateAccessRuleResult(false, Set.of(), null, Optional.empty()); + } + + if (StringUtils.isBlank(user.getSubject())) { + logger.error("isAuthorized() Subject cannot be blank {}", user.getSubject()); + return new EvaluateAccessRuleResult(false, Set.of(), null, Optional.empty()); + } + + if (!isLongTermToken && sessionService.isSessionExpired(user.getSubject())) { + logger.error("isAuthorized() Session expired {}", user.getSubject()); + return new EvaluateAccessRuleResult(false, Set.of(), null, Optional.empty()); + } + + // in some cases, we don't go through the evaluation + if (requestBody == null) { + logger.debug( + "ACCESS_LOG ___ {},{},{} ___ has been granted access to application ___ {} ___ NO REQUEST BODY FORWARDED BY APPLICATION", + user.getUuid().toString(), user.getEmail(), user.getName(), applicationName + ); + return new EvaluateAccessRuleResult(true, Set.of(), null, Optional.empty()); + } + + try { + Map requestBodyMap = (Map) requestBody; + Map queryMap = (Map) requestBodyMap.get("query"); + resourceId = (String) queryMap.get("resourceUUID"); + targetService = (String) queryMap.get("Target Service"); + } catch (RuntimeException e) { + logger.debug("Error parsing resource and target service from request body."); + } + + String formattedQuery; + try { + formattedQuery = (String) ((Map) requestBody).get("formattedQuery"); + + if (formattedQuery == null) { + // fallback in case no formatted query info present + formattedQuery = new ObjectMapper().writeValueAsString(requestBody); + } + + } catch (ClassCastException | JsonProcessingException e1) { + logger.debug( + "ACCESS_LOG ___ {},{},{} ___ has been denied access to execute query ___ {} ___ in application ___ {} ___ UNABLE TO PARSE REQUEST", + user.getUuid().toString(), user.getEmail(), user.getName(), requestBody, applicationName + ); + logger.debug("isAuthorized() Stack Trace: ", e1); + return new EvaluateAccessRuleResult(false, Set.of(), null, Optional.empty()); + } + + Set accessRules; + String label = ""; + if (user.getConnection() != null) { + // Open Access doesn't currently use a connection + label = user.getConnection().getLabel(); + } + + if (this.strictConnections.contains(label)) { + accessRules = this.accessRuleService.getAccessRulesForUserAndApp(user, application); + if (accessRules.isEmpty()) { + logger.info( + "ACCESS_LOG ___ {},{},{} ___ has been denied access to execute query ___ {} ___ in application ___ {} ___ NO ACCESS RULES EVALUATED", + user.getUuid().toString(), user.getEmail(), user.getName(), formattedQuery, applicationName + ); + return new EvaluateAccessRuleResult(false, Set.of(), null, Optional.empty()); + } + } else { + Set privileges = user.getPrivilegesByApplication(application); + // List all privileges of the user + logger.info( + "ACCESS_LOG ___ {},{},{} ___ has the following privileges: {}", user.getUuid().toString(), user.getEmail(), user.getName(), + privileges.stream().map(Privilege::getName).collect(Collectors.joining(", ")) + ); + if (privileges == null || privileges.isEmpty()) { + logger.info( + "ACCESS_LOG ___ {},{},{} ___ has been denied access to execute query ___ {} ___ in application ___ {} __ USER HAS NO PRIVILEGES ASSOCIATED TO THE APPLICATION, BUT APPLICATION HAS PRIVILEGES", + user.getUuid().toString(), user.getEmail(), user.getName(), formattedQuery, applicationName + ); + return new EvaluateAccessRuleResult(false, Set.of(), null, Optional.empty()); + } + + accessRules = this.accessRuleService.cachedPreProcessAccessRules(user, privileges); + if (accessRules.isEmpty()) { + logger.info( + "ACCESS_LOG ___ {},{},{} ___ has been granted access to execute query ___ {} ___ in application ___ {} ___ NO ACCESS RULES EVALUATED", + user.getUuid().toString(), user.getEmail(), user.getName(), formattedQuery, applicationName + ); + return new EvaluateAccessRuleResult(true, Set.of(), null, Optional.empty()); + } + } + + logger.info( + "ACCESS_LOG ___ {},{},{} ___ has the following access rules: {}", user.getUuid().toString(), user.getEmail(), user.getName(), + accessRules.stream().map(AccessRule::toString).collect(Collectors.joining(", ")) + ); + + EvaluateAccessRuleResult evaluationResult = passesAccessRuleEvaluation(requestBody, accessRules, user); + boolean result = evaluationResult.result(); + String passRuleName = evaluationResult.passRuleName(); + Set failedRules = evaluationResult.failedRules(); + + logger.info( + "ACCESS_LOG ___ {},{},{} ___ has been {} access to execute query ___ {} ___ in application ___ {} ___ {}", + user.getUuid().toString(), user.getEmail(), user.getName(), (result ? "granted" : "denied"), formattedQuery, applicationName, + (result ? "passed by " + passRuleName + : "failed by rules: [" + failedRules.stream().map(ar -> (ar.getMergedName().isEmpty() ? ar.getName() : ar.getMergedName())) + .collect(Collectors.joining(", ")) + "]") + ); + + return evaluationResult; + } + + private EvaluateAccessRuleResult passesAccessRuleEvaluation(Object requestBody, Set accessRules, User user) { + // Current logic here is: among all accessRules, they are OR relationship + Set failedRules = new HashSet<>(); + AccessRule passByRule = null; + boolean result = false; + Query returnQuery = null; + + for (AccessRule accessRule : accessRules) { + try { + if (AccessRule.TypeNaming.USER_CONSENT_ACCESS == accessRule.getType()) { + UserConsents userConsents = userConsentsRepository.findByUserId(user.getUuid()); + + // This is an HPDS query inside a PIC-SURE query + Map queryMap = (Map) ((Map) requestBody).get("query"); + Object queryObject = queryMap.get("query"); + Query query; + + if (queryObject instanceof String) { + query = new ObjectMapper().readValue((String) queryObject, Query.class); + } else { + query = new ObjectMapper().convertValue(queryObject, Query.class); + } + + if (consentBasedAccessRuleEvaluator.evaluateAccessRule(query, accessRule, userConsents)) { + result = true; + passByRule = accessRule; + + returnQuery = consentBasedAccessRuleEvaluator.setAuthorizationFiltersForQuery(userConsents, query); + break; + } else { + failedRules.add(accessRule); + } + } else { + String targetService = (String) ((Map) requestBody).get("Target Service"); + logger.debug("Target service = " + targetService); + if (targetService != null && (targetService.startsWith("/v3") || isHpdsV3TargetService(targetService))) { + logger.debug("Skipping access rule {}", accessRule.getName()); + } else if (this.accessRuleService.evaluateAccessRule(requestBody, accessRule)) { + result = true; + passByRule = accessRule; + break; + } else { + failedRules.add(accessRule); + // Print the evaluation tree when a rule fails + if (logger.isInfoEnabled()) { + String ruleName = accessRule.getMergedName().isEmpty() ? accessRule.getName() : accessRule.getMergedName(); + logger.info( + "Rule evaluation tree for failed rule {}:\n{}", ruleName, this.accessRuleService.printEvaluationTree() + ); + } + } + } + } catch (JsonProcessingException e) { + throw new RuntimeException(e); + } finally { + // Clear the evaluation tree to prevent memory leaks + this.accessRuleService.clearEvaluationTree(); + } + } + + String passRuleName = null; + if (passByRule != null) { + if (passByRule.getMergedName().isEmpty()) + passRuleName = passByRule.getName(); + else + passRuleName = passByRule.getMergedName(); + } + + return new EvaluateAccessRuleResult(result, failedRules, passRuleName, Optional.ofNullable(returnQuery)); + } + + /** + * Returns true only when {@code targetService} is a clean HPDS-v3 (auth-backend) target service path, i.e. exactly + * {@code /hpds/auth/v3} or {@code /hpds/auth/v3/**}. Open-access requests never reach this method (they are authorized via a separate + * endpoint), so the {@code open} backend is not matched.

    This is intentionally segment/prefix-aware (not a loose + * {@code contains("hpds") && contains("v3")} check) so that consent-rule evaluation is skipped only for genuine HPDS-v3 calls, not for + * unrelated paths that happen to contain those substrings. + */ + static boolean isHpdsV3TargetService(String targetService) { + if (targetService == null) { + return false; + } + return HPDS_V3_TARGET_SERVICE_PATTERN.matcher(targetService).matches(); + } + + public boolean openAccessRequestIsValid(Map inputMap) { + + if (inputMap == null || inputMap.isEmpty()) { + logger.info( + "ACCESS_LOG ___ AN OPEN ACCESS USER ___ has been denied access to application ___ NO REQUEST BODY FORWARDED BY APPLICATION" + ); + return true; + } + + Object requestBody = inputMap.get("request"); + // If there is no request body, we can assume the request is valid + if (requestBody == null) { + logger.info( + "ACCESS_LOG ___ AN OPEN ACCESS USER ___ has been granted access to application ___ NO REQUEST BODY FORWARDED BY APPLICATION" + ); + return true; + } + + // Load the open access rules + Role openAccessRole = this.roleService.getRoleByName(MANAGED_OPEN_ACCESS_ROLE_NAME); + if (openAccessRole == null) { + logger.info( + "{} has not be created for this environment. Please create the role and its permissions before attempting to use open access.", + MANAGED_OPEN_ACCESS_ROLE_NAME + ); + return false; + } + + Set allOpenAccessRules = openAccessRole.getPrivileges().stream().map(Privilege::getAccessRules) + .collect(Collectors.toSet()).stream().flatMap(Collection::stream).collect(Collectors.toSet()); + + boolean result = false; + if (allOpenAccessRules.isEmpty()) { + result = true; + logger.info("ACCESS_LOG ___ AN OPEN ACCESS USER ___ has been granted access to application ___ NO ACCESS RULES EVALUATED"); + } else { + EvaluateAccessRuleResult evaluationResult = passesAccessRuleEvaluation(requestBody, allOpenAccessRules, null); + result = evaluationResult.result(); + String passRuleName = evaluationResult.passRuleName(); + Set failedRules = evaluationResult.failedRules(); + logger.info( + "ACCESS_LOG ___ AN OPEN ACCESS USER ___ has been {} access to execute query ___ {} ___ in application ___ OPEN ACCESS ___ {}", + (result ? "granted" : "denied"), requestBody, + (result ? "passed by " + passRuleName + : "failed by rules: [" + failedRules.stream() + .map(ar -> (ar.getMergedName().isEmpty() ? ar.getName() : ar.getMergedName())).collect(Collectors.joining(", ")) + + "]") + ); + } + + return result; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/BdcConsentBasedAccessRuleEvaluator.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/BdcConsentBasedAccessRuleEvaluator.java new file mode 100644 index 000000000..18a521922 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/BdcConsentBasedAccessRuleEvaluator.java @@ -0,0 +1,93 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl.authorization; + +import edu.harvard.hms.dbmi.avillach.auth.entity.AccessRule; +import edu.harvard.hms.dbmi.avillach.auth.entity.UserConsents; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.AuthorizationFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.stereotype.Component; + +import java.util.Collection; +import java.util.List; +import java.util.Objects; +import java.util.Set; +import java.util.stream.Collectors; + +@Component +public class BdcConsentBasedAccessRuleEvaluator implements ConsentBasedAccessRuleEvaluator { + + private final Logger log = LoggerFactory.getLogger(BdcConsentBasedAccessRuleEvaluator.class); + + private static final String GENOMIC_AUTHORIZATION_FILTER = "\\_topmed_consents\\"; + private static final String HARMONIZED_AUTHORIZATION_FILTER = "\\_harmonized_consent\\"; + private static final Set ALWAYS_ALLOWED_CONCEPT_ROOTS = Set.of("_Topmed Study Accession with Subject ID", "_Parent Study Accession with Subject ID", "_consents", "_harmonized_consent", "_topmed_consents"); + + @Override + public boolean evaluateAccessRule(Query query, AccessRule accessRule, UserConsents consents) { + Set userStudies = consents.getConsents().values().stream().flatMap(Collection::stream) + .map(consent -> consent.split("\\.")[0]).collect(Collectors.toSet()); + + for (PhenotypicFilter phenotypicFilter : query.allFilters()) { + if (!isConceptPathAuthorized(phenotypicFilter.conceptPath(), consents, userStudies)) return false; + } + + for (String conceptPath : query.select()) { + if (!isConceptPathAuthorized(conceptPath, consents, userStudies)) return false; + } + + if (!query.genomicFilters().isEmpty()) { + if (!consents.getConsents().containsKey(GENOMIC_AUTHORIZATION_FILTER)) { + log.debug( + "Genomic filters must contain the following authorization concepts: " + String.join(", ", GENOMIC_AUTHORIZATION_FILTER) + ); + return false; + } + } + + return true; + } + + private boolean isConceptPathAuthorized(String conceptPath, UserConsents consents, Set userStudies) { + // the 0th index of the array is empty because consents start with \\ + String[] split = conceptPath.split("\\\\"); + String filterConsent = split.length > 1 ? split[1] : split[0]; + + if (ALWAYS_ALLOWED_CONCEPT_ROOTS.contains(filterConsent)) { + return true; + } + if (filterConsent.equals("DCC Harmonized data set")) { + Set harmonizedConsents = consents.getConsents().getOrDefault(HARMONIZED_AUTHORIZATION_FILTER, Set.of()); + if (harmonizedConsents.isEmpty()) { + log.debug("User must have at least one consent in " + HARMONIZED_AUTHORIZATION_FILTER + " to use filter " + conceptPath); + return false; + } + } else if (!userStudies.contains(filterConsent)) { + log.debug("User does not have study: " + filterConsent + " to access " + conceptPath); + return false; + } + return true; + } + + @Override + public Query setAuthorizationFiltersForQuery(UserConsents userConsents, Query query) { + List authorizationFilter = userConsents.getConsents().entrySet().stream().filter(entry -> { + if (entry.getKey().equals(GENOMIC_AUTHORIZATION_FILTER) && query.genomicFilters().isEmpty()) { + return false; + } + if (entry.getKey().equals(HARMONIZED_AUTHORIZATION_FILTER)) { + long harmonizedFilterCount = + query.allFilters().stream().filter(filter -> filter.conceptPath().startsWith("\\DCC Harmonized data set\\")).count(); + // leave these consents if there are any filters on harmonized concept paths + return harmonizedFilterCount > 0; + } + return true; + }).map(entry -> new AuthorizationFilter(entry.getKey(), entry.getValue())).toList(); + + log.debug("Adding authorization filters to query:"); + authorizationFilter.stream().map(Objects::toString).forEach(log::debug); + + return query.setAuthorizationFilters(authorizationFilter); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/BdcConsentsBuilder.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/BdcConsentsBuilder.java new file mode 100644 index 000000000..0df7df48d --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/BdcConsentsBuilder.java @@ -0,0 +1,80 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl.authorization; + +import edu.harvard.hms.dbmi.avillach.auth.model.fenceMapping.StudyMetaData; +import edu.harvard.hms.dbmi.avillach.auth.model.ras.RasDbgapPermission; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.HashMap; +import java.util.HashSet; +import java.util.Map; +import java.util.Set; +import java.util.stream.Collectors; + +/** + * Builds BDC consents based on a user's RAS passport + */ +public class BdcConsentsBuilder { + + public static final String PUBLIC_STUDY_TYPE = "public"; + public static final String GENOMIC_DATA_TYPE_VALUE = "G"; + private final Logger log = LoggerFactory.getLogger(BdcConsentsBuilder.class); + + public static final String CONSENTS_KEY = "\\_consents\\"; + public static final String HARMONIZED_CONSENTS_KEY = "\\_harmonized_consent\\"; + public static final String TOPMED_CONSENTS_KEY = "\\_topmed_consents\\"; + private final Map fenceMappingByConsent; + + private final Set userConsentStrings; + + public BdcConsentsBuilder(Map fenceMappingByConsent, Set userConsentStrings) { + this.fenceMappingByConsent = fenceMappingByConsent; + this.userConsentStrings = userConsentStrings; + } + + public Map> createConsents() { + Map> result = new HashMap<>(); + result.put(CONSENTS_KEY, new HashSet<>()); + + userConsentStrings.forEach(consent -> { + StudyMetaData studyMetaData = fenceMappingByConsent.get(consent); + if (studyMetaData == null) { + log.debug(consent + " not found in fence mapping"); + return; + } + // all user consents go in the consents list + result.computeIfAbsent(CONSENTS_KEY, _ -> new HashSet<>()).add(consent); + + if (studyMetaData.getIsHarmonized()) { + Set harmonizedConsents = result.getOrDefault(HARMONIZED_CONSENTS_KEY, new HashSet<>()); + harmonizedConsents.add(consent); + result.put(HARMONIZED_CONSENTS_KEY, harmonizedConsents); + } + + if (studyMetaData.getDataType() != null && studyMetaData.getDataType().contains(GENOMIC_DATA_TYPE_VALUE)) { + Set topmedConsents = result.getOrDefault(TOPMED_CONSENTS_KEY, new HashSet<>()); + topmedConsents.add(consent); + result.put(TOPMED_CONSENTS_KEY, topmedConsents); + } + }); + + // Add all public studies to the consents list + fenceMappingByConsent.forEach((key, value) -> { + if (PUBLIC_STUDY_TYPE.equalsIgnoreCase(value.getStudyType())) { + result.computeIfAbsent(CONSENTS_KEY, _ -> new HashSet<>()).add(key); + + if (value.getDataType() != null && value.getDataType().contains(GENOMIC_DATA_TYPE_VALUE)) { + Set topmedConsents = result.getOrDefault(TOPMED_CONSENTS_KEY, new HashSet<>()); + topmedConsents.add(key); + result.put(TOPMED_CONSENTS_KEY, topmedConsents); + } + } + }); + + if (result.get(CONSENTS_KEY).isEmpty()) { + throw new IllegalStateException("No studies available for user"); + } + + return result; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/ConsentBasedAccessRuleEvaluator.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/ConsentBasedAccessRuleEvaluator.java new file mode 100644 index 000000000..e5fa29c84 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/ConsentBasedAccessRuleEvaluator.java @@ -0,0 +1,11 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl.authorization; + +import edu.harvard.hms.dbmi.avillach.auth.entity.AccessRule; +import edu.harvard.hms.dbmi.avillach.auth.entity.UserConsents; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; + +public interface ConsentBasedAccessRuleEvaluator { + boolean evaluateAccessRule(Query query, AccessRule accessRule, UserConsents consents); + + Query setAuthorizationFiltersForQuery(UserConsents userConsents, Query query); +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/package-info.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/package-info.java new file mode 100644 index 000000000..9a626b7e0 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/package-info.java @@ -0,0 +1 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/package-info.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/package-info.java new file mode 100644 index 000000000..fa0af555d --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/package-info.java @@ -0,0 +1,4 @@ +/** + * Defines internal business logic for RESTful endpoints. + */ +package edu.harvard.hms.dbmi.avillach.auth.service; \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/AuditAttributes.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/AuditAttributes.java new file mode 100644 index 000000000..5c1bfd371 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/AuditAttributes.java @@ -0,0 +1,43 @@ +package edu.harvard.hms.dbmi.avillach.auth.utils; + +import jakarta.servlet.http.HttpServletRequest; +import java.util.HashMap; +import java.util.Map; + +public final class AuditAttributes { + public static final String EVENT_TYPE = "audit.event_type"; + public static final String ACTION = "audit.action"; + private static final String METADATA_PREFIX = "audit.ctx."; + + private AuditAttributes() {} + + public static void putMetadata(HttpServletRequest request, String key, Object value) { + if (request != null && key != null && value != null) { + request.setAttribute(METADATA_PREFIX + key, value); + } + } + + public static Map getMetadata(HttpServletRequest request) { + Map result = new HashMap<>(); + if (request == null) { + return result; + } + var names = request.getAttributeNames(); + while (names.hasMoreElements()) { + String name = names.nextElement(); + if (name.startsWith(METADATA_PREFIX)) { + result.put(name.substring(METADATA_PREFIX.length()), request.getAttribute(name)); + } + } + return result; + } + + public static String extractClientIp(HttpServletRequest request) { + String xff = request.getHeader("X-Forwarded-For"); + if (xff != null && !xff.isEmpty()) { + return xff.split(",")[0].trim(); + } + return request.getRemoteAddr(); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/AuditInterceptor.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/AuditInterceptor.java new file mode 100644 index 000000000..2ebc52e1d --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/AuditInterceptor.java @@ -0,0 +1,21 @@ +package edu.harvard.hms.dbmi.avillach.auth.utils; + +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import org.springframework.web.method.HandlerMethod; +import org.springframework.web.servlet.HandlerInterceptor; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +public class AuditInterceptor implements HandlerInterceptor { + @Override + public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) { + if (handler instanceof HandlerMethod handlerMethod) { + AuditEvent auditEvent = handlerMethod.getMethodAnnotation(AuditEvent.class); + if (auditEvent != null) { + request.setAttribute(AuditAttributes.EVENT_TYPE, auditEvent.type()); + request.setAttribute(AuditAttributes.ACTION, auditEvent.action()); + } + } + return true; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/AuthNaming.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/AuthNaming.java new file mode 100644 index 000000000..28cca3749 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/AuthNaming.java @@ -0,0 +1,30 @@ +package edu.harvard.hms.dbmi.avillach.auth.utils; + +import java.lang.reflect.Field; +import java.util.ArrayList; +import java.util.List; + +/** + *

    Contains all preset PSAMA naming conventions.

    + */ +public class AuthNaming { + + public static final String LONG_TERM_TOKEN_PREFIX = "LONG_TERM_TOKEN"; + public static final String PSAMA_APPLICATION_TOKEN_PREFIX = "PSAMA_APPLICATION"; + + /** + *

    Constants used to in @RolesAllowed() annotations.

    + */ + public static class AuthRoleNaming { + public static final String ADMIN = "ADMIN"; + public static final String SUPER_ADMIN = "SUPER_ADMIN"; + + public static List allRoles(){ + List roles = new ArrayList<>(); + for (Field field : AuthRoleNaming.class.getFields()){ + roles.add(field.getName()); + } + return roles; + } + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/FenceMappingUtility.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/FenceMappingUtility.java new file mode 100644 index 000000000..f27ea6f7c --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/FenceMappingUtility.java @@ -0,0 +1,97 @@ +package edu.harvard.hms.dbmi.avillach.auth.utils; + +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.hms.dbmi.avillach.auth.model.fenceMapping.BioDataCatalyst; +import edu.harvard.hms.dbmi.avillach.auth.model.fenceMapping.StudyMetaData; +import io.micrometer.common.util.StringUtils; +import jakarta.annotation.PostConstruct; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Service; + +import java.io.File; +import java.util.*; +import java.util.concurrent.ConcurrentHashMap; + +@Service +public class FenceMappingUtility { + + private final Logger logger = LoggerFactory.getLogger(this.getClass()); + + private Map fenceMappingByConsent; + private Map fenceMappingByAuthZ; + private final String templatePath; + private ObjectMapper objectMapper; + + @Autowired + public FenceMappingUtility(@Value("${application.template.path}") String templatePath) { + this.templatePath = templatePath; + } + + @PostConstruct + public void init() { + if (StringUtils.isNotBlank(this.templatePath) && this.templatePath.endsWith(File.separator)) { + // Check if file exists + File file = new File(this.templatePath + "fence_mapping.json"); + if (!file.exists()) { + logger.error("FenceMappingUtility: fence_mapping.json not found in {}", this.templatePath); + } else { + logger.info("FenceMappingUtility: fence_mapping.json found in {}", this.templatePath); + objectMapper = new ObjectMapper(); + initializeFENCEMappings(); + } + + } else { + logger.error("FenceMappingUtility: templatePath is not set or does not end with a file separator"); + } + } + + private void initializeFENCEMappings() { + if (fenceMappingByConsent == null || fenceMappingByAuthZ == null) { + List studies = loadBioDataCatalystFenceMappingData(); + ConcurrentHashMap tempFenceMappingByConsent = new ConcurrentHashMap<>(); + ConcurrentHashMap tempFenceMappingByAuthZ = new ConcurrentHashMap<>(); + + studies.parallelStream().forEach(study -> { + String consentVal = (study.getConsentGroupCode() != null && !study.getConsentGroupCode().isEmpty()) ? + study.getStudyIdentifier() + "." + study.getConsentGroupCode() : + study.getStudyIdentifier(); + tempFenceMappingByConsent.put(consentVal, study); + tempFenceMappingByAuthZ.put(study.getAuthZ().replace("\\/", "/"), study); + }); + + fenceMappingByConsent = Collections.unmodifiableMap(tempFenceMappingByConsent); + fenceMappingByAuthZ = Collections.unmodifiableMap(tempFenceMappingByAuthZ); + } + } + + public Map getFENCEMapping() { + return fenceMappingByConsent; + } + + public Map getFenceMappingByAuthZ() { + return fenceMappingByAuthZ; + } + + private List loadBioDataCatalystFenceMappingData() { + BioDataCatalyst fenceMapping; + List studies; + try { + logger.debug("getFENCEMapping: loading FENCE mapping from {}", templatePath); + fenceMapping = objectMapper.readValue( + new File(String.join(File.separator, + new String[]{templatePath, "fence_mapping.json"})) + , BioDataCatalyst.class); + + studies = fenceMapping.getStudyMetaData(); + logger.debug("getFENCEMapping: found FENCE mapping with {} entries", studies.size()); + } catch (Exception e) { + logger.error("loadFenceMappingData: Non-fatal error parsing fence_mapping.json: {}", templatePath, e); + return new ArrayList<>(); + } + return studies; + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/JWTUtil.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/JWTUtil.java new file mode 100644 index 000000000..1d055c92b --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/JWTUtil.java @@ -0,0 +1,197 @@ +package edu.harvard.hms.dbmi.avillach.auth.utils; + +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.hms.dbmi.avillach.auth.exceptions.NotAuthorizedException; +import edu.harvard.hms.dbmi.avillach.auth.model.ras.Ga4ghPassportV1; +import edu.harvard.hms.dbmi.avillach.auth.model.ras.Passport; +import io.jsonwebtoken.*; +import io.jsonwebtoken.security.Keys; +import org.apache.tomcat.util.codec.binary.Base64; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Component; + +import javax.crypto.SecretKey; +import java.io.IOException; +import java.nio.charset.StandardCharsets; +import java.util.Date; +import java.util.Map; +import java.util.Optional; + +/** + *

    This class is for generating a JWT token and contains common methods for operations on JWT tokens.

    + *

    For more information on JWT tokens, see ...

    + */ +@Component +public class JWTUtil { + + private final static Logger logger = LoggerFactory.getLogger(JWTUtil.class); + + private static final long defaultTTLMillis = 1000L * 60 * 60 * 24 * 7; + + private final String clientSecret; + + private final boolean clientSecretIsBase64; + + private final static ObjectMapper objectMapper = new ObjectMapper(); + + public JWTUtil(@Value("${application.client.secret}") String clientSecret, + @Value("${application.client.secret.base64}") boolean clientSecretIsBase64) { + this.clientSecret = clientSecret; + this.clientSecretIsBase64 = clientSecretIsBase64; + } + + private String getDecodedClientSecret() { + if (clientSecretIsBase64) { + return new String(Base64.decodeBase64(clientSecret)); + } + + return clientSecret; + } + + /** + * @param id - id + * @param issuer - issuer + * @param claims - claims + * @param subject - subject + * @return JWT token + */ + public String createJwtToken(String id, String issuer, Map claims, String subject, long ttlMillis) { + logger.debug("createJwtToken() starting..."); + String jwt_token = null; + + if (ttlMillis < 0) { + ttlMillis = defaultTTLMillis; + } + + if (ttlMillis == 0) { + ttlMillis = 999L * 1000 * 60 * 60 * 24; + } + + long nowMillis = System.currentTimeMillis(); + Date now = new Date(nowMillis); + + String clientSecret = getDecodedClientSecret(); + SecretKey signingKey = Keys.hmacShaKeyFor(clientSecret.getBytes(StandardCharsets.UTF_8)); + + //Builds the JWT and serializes it to a compact, URL-safe string + JwtBuilder builder = Jwts.builder() + .claims(claims) + .id(id) + .issuedAt(now) + .subject(subject) + .issuer(issuer) + .signWith(signingKey); + + //if it has been specified, let's add the expiration + long expMillis = nowMillis + ttlMillis; + Date exp = new Date(expMillis); + builder.expiration(exp); + jwt_token = builder.compact(); + + return jwt_token; + } + + public Jws parseToken(String token) { + String clientSecret = getDecodedClientSecret(); + SecretKey signingKey = Keys.hmacShaKeyFor(clientSecret.getBytes(StandardCharsets.UTF_8)); + + Jws jws; + try { + jws = Jwts.parser().verifyWith(signingKey).build().parseSignedClaims(token); + } catch (JwtException | IllegalArgumentException e) { + logger.error("parseToken() throws: {}, {}", e.getClass().getSimpleName(), e.getMessage()); + throw new NotAuthorizedException(e.getClass().getSimpleName() + ": " + e.getMessage()); + } + + if (jws == null) { + logger.error("parseToken() get null for jws body by parsing Token - {}", token); + throw new NotAuthorizedException("Please contact admin to see the log"); + } + + return jws; + } + + public static Optional getTokenFromAuthorizationHeader(String authorizationHeader) { + if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { + return Optional.ofNullable(authorizationHeader); + } + + return Optional.of(authorizationHeader.substring("Bearer".length()).trim()); + } + + public static boolean isLongTermToken(String sub) { + return sub.startsWith(AuthNaming.LONG_TERM_TOKEN_PREFIX); + } + + public String setClientSecret(String clientSecret) { + return clientSecret; + } + + public boolean setClientSecretIsBase64(boolean clientSecretIsBase64) { + return clientSecretIsBase64; + } + + public boolean shouldRefreshToken(Date expiration, long tokenExpirationTime) { + long currentTime = System.currentTimeMillis(); + if (currentTime >= expiration.getTime()) { + return false; + } + + long halfExpirationTime = tokenExpirationTime / 2; + long refreshTime = expiration.getTime() - halfExpirationTime; + return currentTime >= refreshTime; + } + + /** + * Extract the payload from the ga4gh token and convert it to a Ga4ghPassportV1 + * @param ga4ghToken The ga4gh_passport_v1 extracted from the Passport + * @return Optional of a Ga4ghPassportV1. If empty we could not successfully extract the claims and map them to + * the class. + */ + public static Optional parseGa4ghPassportV1(String ga4ghToken) { + try { + String[] passports = ga4ghToken.split("\\."); + String base64EncodedPayload = passports[1]; + java.util.Base64.Decoder decoder = java.util.Base64.getDecoder(); + String payload = new String(decoder.decode(base64EncodedPayload)); + Ga4ghPassportV1 ga4ghPassportV1 = objectMapper.readValue(payload, Ga4ghPassportV1.class); + return Optional.ofNullable(ga4ghPassportV1); + } catch (IOException e) { + logger.error("parsePassport() throws: {}, {}", e.getClass().getSimpleName(), e.getMessage()); + } + + return Optional.empty(); + } + + public static Optional parsePassportJWTV11(String passportJWTV11) { + try { + String[] passports = passportJWTV11.split("\\."); + String base64EncodedPayload = passports[1]; + java.util.Base64.Decoder decoder = java.util.Base64.getDecoder(); + String payload = new String(decoder.decode(base64EncodedPayload)); + Passport passport = objectMapper.readValue(payload, Passport.class); + return Optional.ofNullable(passport); + } catch (IOException e) { + logger.error("parsePassport() throws: {}, {}", e.getClass().getSimpleName(), e.getMessage()); + } + + return Optional.empty(); + } + + public static Optional decodePassport(String passportJWTV11) { + try { + String[] passports = passportJWTV11.split("\\."); + String base64EncodedPayload = passports[1]; + java.util.Base64.Decoder decoder = java.util.Base64.getDecoder(); + String payload = new String(decoder.decode(base64EncodedPayload)); + return Optional.of(payload); + } catch (Exception e) { + logger.error("decodePassport() throws: {}, {}", e.getClass().getSimpleName(), e.getMessage()); + } + + return Optional.empty(); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/JsonUtils.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/JsonUtils.java new file mode 100644 index 000000000..03d5fa958 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/JsonUtils.java @@ -0,0 +1,188 @@ +package edu.harvard.hms.dbmi.avillach.auth.utils; + +import jakarta.validation.constraints.NotNull; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.*; +import java.util.stream.Collectors; + +/** + *

    + * The scope of this class is only for operations on string, list, map that are converted from JSONs. All + * map keys we deal with will only be String. There are only three types of data: string, list, map, + * since input maps are converted from JSONs. + *

    + *

    * Originally this class was designed for merging two JSON maps (inputs are two Maps), + * only the mergeTemplateMap class is public. Now, the private methods could be used as utility methods as well, + * so they were made public. + * However, these methods are not designed for general usage, but specifically for query template merging use cases. + * Use caution when using these methods for other use cases.

    + *

    + * Notice: the input Map or list are from the conversion of JSONs, which means only three possible formats + * will appear here: string, list, map. These classes are changed internally to allow some field consolidation, + * so it is safer to use 'Collection' instead of 'List' when referencing the returned map. + *

    + */ +public class JsonUtils { + + static Logger logger = LoggerFactory.getLogger(JsonUtils.class); + + /** + * The logic for this method here is: + *
  • + * Only takes JSON map as input - this could be extended as take any JSON format as input in the future + *
    • + *
  • + * When a JSON map merge with another map, it will recursively merge every level of JSON Objects. + *
    • + *
  • + * Data in the same level will be merged, which means data of level 3 in JSON map A will not be merged as level + * 2 in JSON map B. + *
    • + *
  • + * When a JSONArray element merges with another JSONArray element, a single copy of each string element is + * preserved. Each instance of other objects (e.g., Maps) are present in the resulting Collection. This means + * that merging multiple VariantInfoFilters is not currently supported. + *
    • + *
  • + * When a JSON Map merge into a Json Array, it will be either append or merge into one of the element that is a + * Json Map as well and has the same structure based on isMapMergeable method + *
    • + * @param originMap + * @param incomingMap + * @return + */ + public static Map mergeTemplateMap(@NotNull Map originMap, + @NotNull Map incomingMap){ + + Map mergedMap = originMap; + + for (Map.Entry entry : incomingMap.entrySet()){ + String key = entry.getKey(); + Object value = entry.getValue(); + + if (originMap.containsKey(key)){ + Object originValue = originMap.get(key); + + //first check for valid types. this will throw an exception if an unhandled type is used + if(! ( value instanceof String || value instanceof Map || value instanceof Collection) || + ! ( originValue instanceof String || originValue instanceof Map || originValue instanceof Collection)) { + logJsonTypeException(originValue); + } + + if (value instanceof String) { + + if (originValue instanceof String || originValue instanceof Map) { + originMap.put(key,mergeToNewSet(originValue, value)); + } else if (originValue instanceof Set) { //we are only adding sets to our map + ((Set)originValue).add(value); + } + } else if (value instanceof Collection) { //we don't know what the input will be, so check super type + if (originValue instanceof String || originValue instanceof Collection) { + originMap.put(key, mergeToNewSet(originValue, value)); + } else if (originValue instanceof Map) { + mergeMapToSet((Map)originValue, (Collection)value); + } + } else if (value instanceof Map) { + if (originValue instanceof Map){ + originMap.put(key, mergeTemplateMap((Map)originValue, (Map)value)); + } else if (originValue instanceof String){ + originMap.put(key, mergeToNewSet(originValue, value)); + } else if (originValue instanceof Collection) { + mergeMapToSet((Map)value, (Collection)originValue); + } + } + } else { + originMap.put(key, value); + } + } + + return mergedMap; + } + + /** + * merge two JSON into a new list. Example use case: merge two string together. if the argument + * is a collection, each element will be added to the returned Set + * + * @param a + * @param b + * @return a new list that contains two input JSONs + */ + public static Set mergeToNewSet(Object a, Object b){ + Set newSet = new HashSet(); + + if(a instanceof Collection) { + newSet.addAll((Collection)a); + } else { + newSet.add(a); + } + + if(b instanceof Collection) { + newSet.addAll((Collection)b); + } else { + newSet.add(b); + } + + return newSet; + } + + + /** + * attach or merge a map to a list, the list might contain many elements that are string, list or map that are converted from JSONs. + * The logic here is first check if there is any map element that has the same structure based on the method isMapMergeable, + * if true, merge, if false, simply attach. + * + * @param map a map that is converted from a JSON. + * @param collection a list that contains many elements that are string, list or map that are converted from JSONs. + * @return a new list that contains the merged map. + */ + public static Set mergeMapToSet(Map map, Collection collection){ + Set mergedSet = new HashSet(collection.size()); + + boolean merged = false; + for (Object element : collection) { + //only merge the map once if it matches another map. + if (!merged && element instanceof Map && isMapMergeable((Map)element, map)){ + mergedSet.add(mergeTemplateMap((Map)element, map)); + merged = true; + } else { + mergedSet.add(element); + } + } + + //if we didn't find a mergeable map, just add the given map to the Set. + if(!merged) { + mergedSet.add(map); + } + return mergedSet; + } + + /** + * only use for checking if two maps have the same keys. All keys will only be string. Otherwise, the map is not + * converted from a JSON, which is not in the scope of this util class. + * @param baseMap + * @param incomingMap + * @return + */ + public static boolean isMapMergeable(Map baseMap, Map incomingMap){ + Set baseMapKeys = new TreeSet<>(); + for (Object key : baseMap.keySet()){ + baseMapKeys.add((String)key); + } + + Set incomingMapKeys = new TreeSet<>(); + for (Object key : incomingMap.keySet()){ + incomingMapKeys.add((String)key); + } + + return baseMapKeys.stream().collect(Collectors.joining()) + .equals(incomingMapKeys.stream().collect(Collectors.joining())); + } + + private static void logJsonTypeException(Object value){ + logger.error("Incoming JSON Object is a type: " + value.getClass() + ", can only merge String, List and Map!"); + throw new IllegalArgumentException("Inner application error, please contact admin."); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/RestClientConfig.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/RestClientConfig.java new file mode 100644 index 000000000..d39a26f08 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/RestClientConfig.java @@ -0,0 +1,65 @@ +package edu.harvard.hms.dbmi.avillach.auth.utils; + + +import org.apache.hc.client5.http.auth.AuthScope; +import org.apache.hc.client5.http.auth.UsernamePasswordCredentials; +import org.apache.hc.client5.http.classic.HttpClient; +import org.apache.hc.client5.http.impl.auth.BasicCredentialsProvider; +import org.apache.hc.client5.http.impl.classic.HttpClients; +import org.apache.hc.core5.http.HttpHost; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.http.client.HttpComponentsClientHttpRequestFactory; +import org.springframework.util.StringUtils; +import org.springframework.web.client.RestClient; + +@Configuration +public class RestClientConfig { + + private static final Logger LOG = LoggerFactory.getLogger(RestClientConfig.class); + + @Value("${http.proxyHost:}") + private String proxyHost; + + @Value("${http.proxyPort:8080}") + private int proxyPort; + + @Value("${http.proxyUser:}") + private String proxyUser; + + @Value("${http.proxyPassword:}") + private String proxyPassword; + + @Bean + public HttpClient getHttpClient() { + if (!StringUtils.hasLength(proxyHost)) { + return HttpClients.createDefault(); + } else if (!StringUtils.hasLength(proxyUser)) { + LOG.info("Utilizing unauthenticated proxy: host={}", proxyHost); + return HttpClients.custom() + .setProxy(new HttpHost(proxyHost, proxyPort)) + .build(); + } else { + LOG.info("Utilizing authenticated proxy: host={}, user={}", proxyHost, proxyUser); + + BasicCredentialsProvider credentialsProvider = new BasicCredentialsProvider(); + credentialsProvider.setCredentials( + new AuthScope(proxyHost, proxyPort), + new UsernamePasswordCredentials(proxyUser, proxyPassword.toCharArray())); + + return HttpClients.custom() + .setDefaultCredentialsProvider(credentialsProvider) + .setProxy(new HttpHost(proxyHost, proxyPort)) + .build(); + } + } + + @Bean + public RestClient restClient(@Autowired HttpClient client) { + return RestClient.builder().requestFactory(new HttpComponentsClientHttpRequestFactory(client)).build(); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/RestClientUtil.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/RestClientUtil.java new file mode 100644 index 000000000..a3f1b6d01 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/RestClientUtil.java @@ -0,0 +1,62 @@ +package edu.harvard.hms.dbmi.avillach.auth.utils; + +import org.apache.hc.client5.http.classic.HttpClient; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.*; +import org.springframework.http.client.HttpComponentsClientHttpRequestFactory; +import org.springframework.stereotype.Component; +import org.springframework.util.MultiValueMap; +import org.springframework.web.client.HttpClientErrorException; +import org.springframework.web.client.RestClient; + +@Component +public class RestClientUtil { + + private static final Logger logger = LoggerFactory.getLogger(RestClientUtil.class); + private final RestClient restClient; + private final HttpClient httpClient; + + @Autowired + public RestClientUtil(RestClient restClient, HttpClient httpClient) { + this.restClient = restClient; + this.httpClient = httpClient; + } + + public ResponseEntity retrieveGetResponse(String uri, HttpHeaders headers) { + try { + return restClient.get().uri(uri).headers(h -> h.addAll(headers)).retrieve().toEntity(String.class); + } catch (HttpClientErrorException ex) { + logger.error("HttpClientErrorException: {}", ex.getMessage()); + throw ex; + } + } + + // The ability to set the timeout for a given request: a one-off client with a + // dedicated request factory, so the shared client's settings are never mutated. + public ResponseEntity retrieveGetResponseWithRequestConfiguration(String uri, HttpHeaders headers, int timeoutMs) { + try { + HttpComponentsClientHttpRequestFactory factory = new HttpComponentsClientHttpRequestFactory(httpClient); + factory.setConnectTimeout(timeoutMs); + factory.setConnectionRequestTimeout(timeoutMs); + RestClient timeoutBoundClient = RestClient.builder().requestFactory(factory).build(); + return timeoutBoundClient.get().uri(uri).headers(h -> h.addAll(headers)).retrieve().toEntity(String.class); + } catch (HttpClientErrorException ex) { + logger.error("HttpClientErrorException: {}", ex.getMessage()); + throw ex; + } + } + + + public ResponseEntity retrievePostResponse(String uri, HttpHeaders headers, String body) throws HttpClientErrorException { + logger.debug("HttpClientUtilSpring retrievePostResponse()"); + return restClient.post().uri(uri).headers(h -> h.addAll(headers)).body(body).retrieve().toEntity(String.class); + } + + public ResponseEntity retrievePostResponse(String uri, HttpEntity> requestEntity) + throws HttpClientErrorException { + return restClient.post().uri(uri).headers(h -> h.addAll(requestEntity.getHeaders())).body(requestEntity.getBody()).retrieve() + .toEntity(String.class); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/package-info.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/package-info.java new file mode 100644 index 000000000..76b757e4c --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/package-info.java @@ -0,0 +1,4 @@ +/** + * Contains useful utility classes + */ +package edu.harvard.hms.dbmi.avillach.auth.utils; \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/resources/META-INF/additional-spring-configuration-metadata.json b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/resources/META-INF/additional-spring-configuration-metadata.json new file mode 100644 index 000000000..f46e8011c --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/resources/META-INF/additional-spring-configuration-metadata.json @@ -0,0 +1,178 @@ +{ + "properties": [ + { + "name": "application.client.id", + "type": "java.lang.String", + "description": "Description for application.client.id." + }, + { + "name": "application.client.secret", + "type": "java.lang.String", + "description": "Description for application.client.secret." + }, + { + "name": "application.client.secret.base64", + "type": "java.lang.String", + "description": "Description for application.client.secret.base64." + }, + { + "name": "application.user.id.claim", + "type": "java.lang.String", + "description": "Description for application.user.id.claim." + }, + { + "name": "application.tos.enabled", + "type": "java.lang.String", + "description": "Description for application.tos.enabled." + }, + { + "name": "application.system.name", + "type": "java.lang.String", + "description": "Description for application.system.name." + }, + { + "name": "application.template.path", + "type": "java.lang.String", + "description": "Description for application.template.path." + }, + { + "name": "application.access.grant.email.subject", + "type": "java.lang.String", + "description": "Description for application.access.grant.email.subject." + }, + { + "name": "application.user.activation.reply.to", + "type": "java.lang.String", + "description": "Description for application.user.activation.reply.to." + }, + { + "name": "application.admin.users", + "type": "java.lang.String", + "description": "Description for application.admin.users." + }, + { + "name": "application.idp.provider", + "type": "java.lang.String", + "description": "Description for application.idp.provider." + }, + { + "name": "application.idp.provider.uri", + "type": "java.lang.String", + "description": "Description for application.idp.provider.uri." + }, + { + "name": "fence.client.id", + "type": "java.lang.String", + "description": "Description for fence.client.id." + }, + { + "name": "fence.client.secret", + "type": "java.lang.String", + "description": "Description for fence.client.secret." + }, + { + "name": "fence.redirect.url", + "type": "java.lang.String", + "description": "Description for fence.redirect.url." + }, + { + "name": "fence.consent.group.concept.path", + "type": "java.lang.String", + "description": "Description for fence.consent.group.concept.path." + }, + { + "name": "fence.standard.access.rules", + "type": "java.lang.String", + "description": "Description for fence.standard.access.rules." + }, + { + "name": "fence.harmonized.consent.group.concept.path", + "type": "java.lang.String", + "description": "Description for fence.harmonized.consent.group.concept.path." + }, + { + "name": "application.token.expiration.time", + "type": "java.lang.String", + "description": "Description for application.token.expiration.time." + }, + { + "name": "application.long.term.token.expiration.time", + "type": "java.lang.String", + "description": "Description for application.long.term.token.expiration.time." + }, + { + "name": "application.default.uuid", + "type": "java.lang.String", + "description": "Description for application.default.uuid." + }, + { + "name": "fence.parent.consent.group.concept.path", + "type": "java.lang.String", + "description": "Description for fence.parent.consent.group.concept.path." + }, + { + "name": "fence.topmed.consent.group.concept.path", + "type": "java.lang.String", + "description": "Description for fence.topmed.consent.group.concept.path." + }, + { + "name": "fence.allowed.query.types", + "type": "java.lang.String", + "description": "Description for fence.allowed.query.types." + }, + { + "name": "a4.okta.client.id", + "type": "java.lang.String", + "description": "Description for okta.client.id." + }, + { + "name": "a4.okta.client.secret", + "type": "java.lang.String", + "description": "Description for okta.client.secret." + }, + { + "name": "a4.okta.connection.id", + "type": "java.lang.String", + "description": "Description for okta.connection.id." + }, + { + "name": "fence.idp.provider.is.enabled", + "type": "java.lang.String", + "description": "If set to true, the Fence IDP provider is enabled." + }, + { + "name": "open.idp.provider.is.enabled", + "type": "java.lang.String", + "description": "If set to true, the Open IDP provider is enabled." + }, + { + "name": "auth0.host", + "type": "java.lang.String", + "description": "Description for auth0.host." + }, + { + "name": "auth0.denied.email.enabled", + "type": "java.lang.String", + "description": "Description for auth0.denied.email.enabled." + }, + { + "name": "fence.idp.provider.uri", + "type": "java.lang.String", + "description": "Description for fence.idp.provider.uri." + }, + { + "name": "a4.okta.idp.provider.is.enabled", + "type": "java.lang.String", + "description": "Description for a4.okta.idp.provider.is.enabled." + }, + { + "name": "a4.okta.idp.provider.uri", + "type": "java.lang.String", + "description": "Description for a4.okta.idp.provider.uri." + }, + { + "name": "application.max.session.length", + "type": "java.lang.String", + "description": "If a user has been signed in for this length of time they will be logged out." + } + ] } \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/resources/application.properties b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/resources/application.properties new file mode 100644 index 000000000..908d26f95 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/resources/application.properties @@ -0,0 +1,136 @@ +# Application server port and context path +server.port=${SERVER_PORT:8090} +server.servlet.context-path=/auth + +# Actuator: OFF BY DEFAULT. AIO's psama.env sets PICSURE_ACTUATOR_EXPOSURE=health to enable a shallow +# health probe (available at /auth/actuator/health). Spring Security still permit-lists /actuator/health +# and /actuator/info (see SecurityConfig); details stay hidden by default (PICSURE_ACTUATOR_DETAILS=never) +# so no component internals leak on the unauthenticated health endpoint. +management.endpoints.web.exposure.include=${PICSURE_ACTUATOR_EXPOSURE:none} +management.endpoint.health.show-details=${PICSURE_ACTUATOR_DETAILS:never} +management.endpoint.health.probes.enabled=true + +spring.datasource.url=${DATASOURCE_URL:jdbc:mysql://picsure-db:3306/auth?useUnicode=true&characterEncoding=UTF-8&autoReconnect=true&autoReconnectForPools=true&serverTimezone=UTC} +spring.datasource.username=${DATASOURCE_USERNAME:root} +spring.datasource.password=${DATASOURCE_PASSWORD:password} +# MySQL 8 driver +spring.datasource.driver-class-name=com.mysql.cj.jdbc.Driver +# MySQL 5 driver +#spring.datasource.driver-class-name=com.mysql.jdbc.Driver + +# JPA/Hibernate properties +#spring.jpa.show-sql=true +spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.MySQL8Dialect +#spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.MySQL5Dialect +#spring.jpa.hibernate.ddl-auto=create + +# By default, hibernate will convert camelCase to snake_case for table and column names. This property disables that behavior. +spring.jpa.hibernate.naming.physical-strategy=org.hibernate.boot.model.naming.PhysicalNamingStrategyStandardImpl + +# Logging +logging.level.org.springframework.security=${LOGGING_LEVEL_SECURITY:INFO} +logging.level.root=${LOGGING_LEVEL_ROOT:INFO} +logging.level.org.springframework.web=${LOGGING_LEVEL_SLF4J:INFO} +logging.level.edu.harvard.hms.dbmi.avillach.auth.service.impl.authentication.RASAuthenticationService=${LOGGING_LEVEL_RAS_AUTHENTICATION:INFO} +logging.level.edu.harvard.hms.dbmi.avillach.auth.service.impl.authentication.FENCEAuthenticationService=${LOGGING_LEVEL_FENCE_AUTHENTICATION:INFO} +logging.level.edu.harvard.hms.dbmi.avillach.auth.service.impl.AccessRuleService=${LOGGING_LEVEL_ACCESS_RULE_SERVICE:INFO} +logging.level.edu.harvard.hms.dbmi.avillach.auth.service.impl.RoleService=${LOGGING_LEVEL_ROLE_SERVICE:INFO} +logging.level.edu.harvard.hms.dbmi.avillach.auth.service.impl.UserService=${LOGGING_LEVEL_USER_SERVICE:INFO} +logging.level.org.springframework.cache=${LOGGING_LEVEL_CACHE:INFO} + +# Logging File Output https://docs.spring.io/spring-boot/reference/features/logging.html#features.logging.file-output +# If you are adding additional log files please add them to /var/log/ directory. +logging.file.name=/var/log/psama.log + +# Cache Controller Configuration. This is used to gain insight into the cache. +# This should never be enabled in production. +app.cache.inspect.enabled=${CACHE_INSPECT_ENABLED:false} + +# Mail session configuration (Assuming Gmail SMTP for example) +spring.mail.host=smtp.gmail.com +spring.mail.port=587 +spring.mail.username=${EMAIL_ADDRESS:your_email@gmail.com} +spring.mail.password=${EMAIL_PASSWORD:your_email_password} +spring.mail.properties.mail.smtp.auth=true +spring.mail.properties.mail.smtp.starttls.enable=true + +# Custom application properties +application.tos.enabled=${TOS_ENABLED:true} +application.default.uuid=${STACK_SPECIFIC_APPLICATION_ID:default_uuid} +application.system.name=${SYSTEM_NAME:PIC-SURE All-in-one} +application.template.path=${TEMPLATE_PATH:/config/} +application.access.grant.email.subject=${GRANT_EMAIL_SUBJECT:email_subject} +application.user.activation.reply.to=${USER_ACTIVATION_REPLY_TO:reply_to_email} +application.admin.users=${ADMIN_USERS:__ADMIN_USERS__} + +# Fence Configurations. These are used to configure the access rules for the application. +# If you intend to use a fence_mapping.json file you will need to set the following properties. +fence.consent.group.concept.path=\\DCC Harmonized data set\\ +fence.standard.access.rules=AR_ONLY_INFO,AR_ONLY_SEARCH,AR_INFO_COLUMN_LISTING,AR_DICTIONARY_REQUESTS,AR_LOGGING_REQUESTS +fence.allowed.query.types=${FENCE_ALLOWED_QUERY_TYPES:COUNT,CROSS_COUNT,CATEGORICAL_CROSS_COUNT,CONTINUOUS_CROSS_COUNT,DATAFRAME,DATAFRAME_PFB} +#COUNT,CROSS_COUNT,CATEGORICAL_CROSS_COUNT,CONTINUOUS_CROSS_COUNT,DATAFRAME,DATAFRAME_PFB + +fence.harmonized.consent.group.concept.path=\\_harmonized_consent\\ +fence.parent.consent.group.concept.path=\\_consents\\ +fence.topmed.consent.group.concept.path=\\_topmed_consents\\ +fence.variant.annotation.columns=Variant_consequence_calculated,Variant_class,Gene_with_variant,Variant_severity,Variant_frequency_in_gnomAD,Variant_frequency_as_text + +# We have two different authorization flows. One is strict and the other is not strict. +# Strict requires both access rules and privilege rules to be present for the user. +strict.authorization.applications.connections=${STRICT_AUTHORIZATION_APPLICATIONS:OKTA,FENCE,OPEN,RAS} + +# Application Token configurations. +# This configuration is used to generate a token for the application to access the PIC-SURE API. +application.client.secret=${APPLICATION_CLIENT_SECRET} +application.client.secret.base64=${APPLICATION_CLIENT_SECRET_IS_BASE_64:false} +application.user.id.claim=${USER_ID_CLAIM:sub} + +# Comma-separated list of role names to embed in JWT token claims +application.token.inclusionRoles=${TOKEN_INCLUSION_ROLES:ADMIN,SUPER_ADMIN} + +# IDLE Timeout 15 minutes by default +application.token.expiration.time=${TOKEN_EXPIRATION_TIME:900000} +# Max session length 8 hours by default +application.max.session.length=${MAX_SESSION_TIME:28800000} + +# 30 days in milliseconds +application.long.term.token.expiration.time=${LONG_TERM_TOKEN_EXPIRATION_TIME:2592000000} + +# Open IDP configurations +open.idp.provider.is.enabled=${OPEN_IDP_PROVIDER_IS_ENABLED:false} + +# OKTA configurations +a4.okta.idp.provider.is.enabled=${A4_OKTA_IDP_PROVIDER_IS_ENABLED:false} +a4.okta.client.id=${A4_OKTA_CLIENT_ID:false} +a4.okta.client.secret=${A4_OKTA_CLIENT_SECRET:false} +a4.okta.connection.id=${A4_OKTA_CONNECTION_ID:false} +a4.okta.idp.provider.uri=${A4_OKTA_IDP_PROVIDER_URI:false} + +# Fence IDP configurations +fence.idp.provider.is.enabled=${FENCE_IDP_PROVIDER_IS_ENABLED:false} +fence.idp.provider.uri=${FENCE_IDP_PROVIDER_URI:false} +fence.client.id=${FENCE_CLIENT_ID:false} +fence.client.secret=${FENCE_CLIENT_SECRET:false} + +# IDP Provider configurations +auth0.idp.provider.is.enabled=${AUTH0_IDP_PROVIDER_IS_ENABLED:false} +auth0.host=${AUTH0_HOST:false} +auth0.denied.email.enabled=${AUTH0_DENIED_EMAIL_ENABLED:false} + +# RAS Provider configurations +ras.okta.idp.provider.is.enabled=${RAS_OKTA_IDP_PROVIDER_IS_ENABLED:false} +ras.okta.idp.provider.uri=${RAS_OKTA_IDP_PROVIDER_URI:false} +ras.okta.connection.id=${RAS_OKTA_CONNECTION_ID:false} +ras.okta.client.id=${RAS_OKTA_CLIENT_ID:false} +ras.okta.client.secret=${RAS_OKTA_CLIENT_SECRET:false} +ras.idp.uri=${RAS_IDP_URI:false} +ras.passport.issuer=${RAS_PASSPORT_ISSUER:false} + +server.servlet.session.cookie.http-only=true +server.servlet.session.cookie.secure=true + +spring.devtools.remote.secret=${DEVTOOLS_SECRET:false} +spring.devtools.remote.context-path=/remote + +# Mail-send failures must not gate service health (SMTP unreachable in some envs); actuator mail indicator off. +management.health.mail.enabled=false diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/resources/emailTemplates/accessEmail.mustache b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/resources/emailTemplates/accessEmail.mustache new file mode 100644 index 000000000..8a9c8eeb8 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/main/resources/emailTemplates/accessEmail.mustache @@ -0,0 +1,10 @@ +You have been granted access to {{systemName}}, which permits you to run queries returning aggregate clinical and variant patient data. + +You may use the portal to ascertain counts of patients with particular phenotypic or genomic features and run statistical analysis. + +A quick start guid is here. + +Please contact us at BCHBiobank4Discovery@childrens.harvard.edu for questions. + +http://biobank.childrens.harvard.edu +http://www.childrenshospital.org/research/biobank \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/ApplicationServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/ApplicationServiceTest.java new file mode 100644 index 000000000..f9d4364dd --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/ApplicationServiceTest.java @@ -0,0 +1,63 @@ +package edu.harvard.hms.dbmi.avillach; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Application; +import edu.harvard.hms.dbmi.avillach.auth.repository.ApplicationRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.PrivilegeRepository; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.ApplicationService; +import edu.harvard.hms.dbmi.avillach.auth.utils.FenceMappingUtility; +import edu.harvard.hms.dbmi.avillach.auth.utils.JWTUtil; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.test.context.ContextConfiguration; + +import java.security.SecureRandom; +import java.util.Base64; +import java.util.UUID; + +import static org.mockito.Mockito.spy; + +@SpringBootTest +@ContextConfiguration(classes = {ApplicationService.class, JWTUtil.class}) +public class ApplicationServiceTest { + + private ApplicationService applicationService; + + @MockBean + private PrivilegeRepository privilegeRepository; + + @MockBean + private ApplicationRepository applicationRepository; + + @BeforeEach + public void init() { + JWTUtil jwtUtil = spy(new JWTUtil(generate256Base64Secret(), false)); + applicationService = new ApplicationService(applicationRepository, privilegeRepository, jwtUtil); + } + + @Test + public void testGenerateToken() { + Application application = new Application(); + application.setUuid(UUID.randomUUID()); + application.setName("Testing Application"); + application.setUrl("https://psama.hms.harvard.edu"); + + String token = applicationService.generateApplicationToken(application); + + Assertions.assertNotNull(token, "Token is null, given application: " + application.getUuid()); + Assertions.assertTrue(token.length() > 10, "Token is too short"); + } + + /** + * Do not use this method in production code. This is only for testing purposes. + * @return a 256-bit base64 encoded secret + */ + private static String generate256Base64Secret() { + SecureRandom random = new SecureRandom(); + byte[] secret = new byte[32]; + random.nextBytes(secret); + return Base64.getEncoder().encodeToString(secret); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/filter/AuditLoggingFilterTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/filter/AuditLoggingFilterTest.java new file mode 100644 index 000000000..1ff95721a --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/filter/AuditLoggingFilterTest.java @@ -0,0 +1,412 @@ +package edu.harvard.hms.dbmi.avillach.auth.filter; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.dbmi.avillach.logging.SessionIdResolver; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuditAttributes; +import jakarta.servlet.FilterChain; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.ArgumentCaptor; +import org.springframework.mock.web.MockHttpServletRequest; +import org.springframework.mock.web.MockHttpServletResponse; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + +class AuditLoggingFilterTest { + + private LoggingClient loggingClient; + private AuditLoggingFilter filter; + private FilterChain filterChain; + + @BeforeEach + void setUp() { + loggingClient = mock(LoggingClient.class); + when(loggingClient.isEnabled()).thenReturn(true); + filter = new AuditLoggingFilter(loggingClient); + filterChain = mock(FilterChain.class); + } + + @Test + void shouldCategorizeLoginEvent() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/authentication/ras"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "AUTH"); + request.setAttribute(AuditAttributes.ACTION, "auth.login"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + LoggingEvent event = captor.getValue(); + assertEquals("AUTH", event.getEventType()); + assertEquals("auth.login", event.getAction()); + } + + @Test + void shouldCategorizeLogoutEvent() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/logout"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "AUTH"); + request.setAttribute(AuditAttributes.ACTION, "auth.logout"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("AUTH", captor.getValue().getEventType()); + assertEquals("auth.logout", captor.getValue().getAction()); + } + + @Test + void shouldCategorizeTokenIntrospect() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/token/inspect"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "ACCESS"); + request.setAttribute(AuditAttributes.ACTION, "token.introspect"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("ACCESS", captor.getValue().getEventType()); + assertEquals("token.introspect", captor.getValue().getAction()); + } + + @Test + void shouldCategorizeUserProfile() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/user/me"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "ACCESS"); + request.setAttribute(AuditAttributes.ACTION, "user.profile"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("ACCESS", captor.getValue().getEventType()); + assertEquals("user.profile", captor.getValue().getAction()); + } + + @Test + void shouldCategorizeAdminUserModify() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/user"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "ADMIN"); + request.setAttribute(AuditAttributes.ACTION, "user.modify"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("ADMIN", captor.getValue().getEventType()); + assertEquals("user.modify", captor.getValue().getAction()); + } + + @Test + void shouldCategorizeRoleModify() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("PUT", "/role"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "ADMIN"); + request.setAttribute(AuditAttributes.ACTION, "role.modify"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("ADMIN", captor.getValue().getEventType()); + assertEquals("role.modify", captor.getValue().getAction()); + } + + @Test + void shouldCategorizeRoleDelete() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("DELETE", "/role/some-uuid"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "ADMIN"); + request.setAttribute(AuditAttributes.ACTION, "role.delete"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("ADMIN", captor.getValue().getEventType()); + assertEquals("role.delete", captor.getValue().getAction()); + } + + @Test + void shouldCategorizeConnectionModify() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/connection"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "ADMIN"); + request.setAttribute(AuditAttributes.ACTION, "connection.modify"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("ADMIN", captor.getValue().getEventType()); + assertEquals("connection.modify", captor.getValue().getAction()); + } + + @Test + void shouldCategorizeConnectionDelete() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("DELETE", "/connection/some-uuid"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "ADMIN"); + request.setAttribute(AuditAttributes.ACTION, "connection.delete"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("ADMIN", captor.getValue().getEventType()); + assertEquals("connection.delete", captor.getValue().getAction()); + } + + @Test + void shouldCategorizeApplicationModify() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("PUT", "/application"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "ADMIN"); + request.setAttribute(AuditAttributes.ACTION, "application.modify"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("ADMIN", captor.getValue().getEventType()); + assertEquals("application.modify", captor.getValue().getAction()); + } + + @Test + void shouldCategorizeApplicationTokenRefresh() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/application/refreshToken/some-uuid"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "ADMIN"); + request.setAttribute(AuditAttributes.ACTION, "application.token_refresh"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("ADMIN", captor.getValue().getEventType()); + assertEquals("application.token_refresh", captor.getValue().getAction()); + } + + @Test + void shouldCategorizeTosAccept() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/tos/accept"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "ACCESS"); + request.setAttribute(AuditAttributes.ACTION, "tos.accept"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("ACCESS", captor.getValue().getEventType()); + assertEquals("tos.accept", captor.getValue().getAction()); + } + + @Test + void shouldCategorizeTosUpdate() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/tos/update"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "ADMIN"); + request.setAttribute(AuditAttributes.ACTION, "tos.update"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("ADMIN", captor.getValue().getEventType()); + assertEquals("tos.update", captor.getValue().getAction()); + } + + @Test + void shouldCategorizeTokenRefresh() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/token/refresh"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "ACCESS"); + request.setAttribute(AuditAttributes.ACTION, "token.refresh"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("ACCESS", captor.getValue().getEventType()); + assertEquals("token.refresh", captor.getValue().getAction()); + } + + @Test + void shouldCategorizeOpenAccessValidate() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/open/validate"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "ACCESS"); + request.setAttribute(AuditAttributes.ACTION, "open.validate"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("ACCESS", captor.getValue().getEventType()); + assertEquals("open.validate", captor.getValue().getAction()); + } + + @Test + void shouldCategorizeStudyAccessCreate() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/studyAccess"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "ADMIN"); + request.setAttribute(AuditAttributes.ACTION, "study_access.create"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("ADMIN", captor.getValue().getEventType()); + assertEquals("study_access.create", captor.getValue().getAction()); + } + + @Test + void shouldCategorizeMappingDelete() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("DELETE", "/mapping/some-uuid"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "ADMIN"); + request.setAttribute(AuditAttributes.ACTION, "mapping.delete"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("ADMIN", captor.getValue().getEventType()); + assertEquals("mapping.delete", captor.getValue().getAction()); + } + + @Test + void shouldSkipActuatorHealth() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/actuator/health"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + verify(loggingClient, never()).send(any(LoggingEvent.class)); + } + + @Test + void shouldSkipSwagger() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/swagger.json"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + verify(loggingClient, never()).send(any(LoggingEvent.class)); + } + + @Test + void shouldNotLogWhenClientDisabled() throws Exception { + when(loggingClient.isEnabled()).thenReturn(false); + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/authentication/ras"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + verify(loggingClient, never()).send(any(LoggingEvent.class)); + } + + @Test + void shouldExtractClientIpFromXForwardedFor() { + MockHttpServletRequest request = new MockHttpServletRequest(); + request.addHeader("X-Forwarded-For", "1.2.3.4, 5.6.7.8"); + + assertEquals("1.2.3.4", AuditAttributes.extractClientIp(request)); + } + + @Test + void shouldFallbackToRemoteAddr() { + MockHttpServletRequest request = new MockHttpServletRequest(); + request.setRemoteAddr("10.0.0.1"); + + assertEquals("10.0.0.1", AuditAttributes.extractClientIp(request)); + } + + @Test + void shouldUseSessionIdHeader() { + assertEquals("my-session-123", SessionIdResolver.resolve("my-session-123", "10.0.0.1", "Mozilla/5.0")); + } + + @Test + void shouldGenerateSessionIdFromHash() { + String sessionId = SessionIdResolver.resolve(null, "10.0.0.1", "Mozilla/5.0"); + assertNotNull(sessionId); + assertFalse(sessionId.isEmpty()); + assertEquals(16, sessionId.length()); + } + + @Test + void shouldIncludeSessionIdOnEvent() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/some/endpoint"); + request.addHeader("X-Session-Id", "test-session"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("test-session", captor.getValue().getSessionId()); + } + + @Test + void shouldMergeAuditAttributesMetadata() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/some/endpoint"); + AuditAttributes.putMetadata(request, "custom_field", "custom_value"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("custom_value", captor.getValue().getMetadata().get("custom_field")); + } + + @Test + void shouldPassBearerTokenThrough() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/some/endpoint"); + request.addHeader("Authorization", "Bearer my-token"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, filterChain); + + verify(loggingClient).send(any(LoggingEvent.class), eq("Bearer my-token"), any()); + } + + @Test + void shouldIncludeErrorMapFor4xx() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/some/endpoint"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(403); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertNotNull(captor.getValue().getError()); + assertEquals("client_error", captor.getValue().getError().get("error_type")); + } + + @Test + void shouldIncludeErrorMapFor5xx() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/some/endpoint"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(500); + + filter.doFilter(request, response, filterChain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertNotNull(captor.getValue().getError()); + assertEquals("server_error", captor.getValue().getError().get("error_type")); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/model/AccessRuleEvaluationNodeDemo.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/model/AccessRuleEvaluationNodeDemo.java new file mode 100644 index 000000000..9b0fa357f --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/model/AccessRuleEvaluationNodeDemo.java @@ -0,0 +1,125 @@ +package edu.harvard.hms.dbmi.avillach.auth.model; + +import edu.harvard.hms.dbmi.avillach.auth.entity.AccessRule; +import org.junit.jupiter.api.Test; + +import java.util.HashSet; +import java.util.Set; +import java.util.UUID; + +/** + * Demonstration class for AccessRuleEvaluationNode. + * This class provides examples of how AccessRuleEvaluationNode is used to build and print + * the access rule and gate evaluation tree. + */ +public class AccessRuleEvaluationNodeDemo { + + @Test + public void demonstrateAccessRuleEvaluationNode() { + System.out.println("AccessRuleEvaluationNode Demo"); + System.out.println("============================="); + + demonstrateSimpleTree(); + demonstrateComplexTree(); + } + + /** + * Demonstrates a simple tree with a parent and two child nodes + */ + private static void demonstrateSimpleTree() { + System.out.println("\n1. Simple Tree Example"); + System.out.println("---------------------"); + + AccessRule parentRule = createSimpleRule("ParentRule", "$.parent", AccessRule.TypeNaming.ALL_EQUALS, "parentValue"); + AccessRuleEvaluationNode parentNode = new AccessRuleEvaluationNode(parentRule, false, false, false); + parentNode.setResult(true); + + AccessRule childRule1 = createSimpleRule("ChildRule1", "$.child1", AccessRule.TypeNaming.ALL_EQUALS, "childValue1"); + AccessRuleEvaluationNode childNode1 = new AccessRuleEvaluationNode(childRule1, false, true, false); + childNode1.setResult(true); + + AccessRule childRule2 = createSimpleRule("ChildRule2", "$.child2", AccessRule.TypeNaming.ALL_EQUALS, "childValue2"); + AccessRuleEvaluationNode childNode2 = new AccessRuleEvaluationNode(childRule2, false, true, false); + childNode2.setResult(false); + childNode2.setFailureReason("Value mismatch"); + + parentNode.addChild(childNode1); + parentNode.addChild(childNode2); + + String treeString = parentNode.generateTreeString(); + System.out.println(treeString); + } + + /** + * Demonstrates a complex tree with gates, sub-rules, and different relationship types + */ + private static void demonstrateComplexTree() { + System.out.println("\n2. Complex Tree Example"); + System.out.println("----------------------"); + + AccessRule rootRule = createSimpleRule("RootRule", "$.root", AccessRule.TypeNaming.ALL_EQUALS, "rootValue"); + AccessRuleEvaluationNode rootNode = new AccessRuleEvaluationNode(rootRule, false, false, false); + rootNode.setResult(true); + + AccessRule gateRule1 = createSimpleRule("GateRule1", "$.gate1", AccessRule.TypeNaming.ALL_EQUALS, "gateValue1"); + AccessRuleEvaluationNode gateNode1 = new AccessRuleEvaluationNode(gateRule1, true, false, false); + gateNode1.setResult(true); + + AccessRule gateRule2 = createSimpleRule("GateRule2", "$.gate2", AccessRule.TypeNaming.ALL_EQUALS, "gateValue2"); + AccessRuleEvaluationNode gateNode2 = new AccessRuleEvaluationNode(gateRule2, true, false, true); + gateNode2.setResult(false); + gateNode2.setFailureReason("Gate condition not met"); + + AccessRule subRule1 = createSimpleRule("SubRule1", "$.sub1", AccessRule.TypeNaming.ALL_EQUALS, "subValue1"); + AccessRuleEvaluationNode subNode1 = new AccessRuleEvaluationNode(subRule1, false, true, false); + subNode1.setResult(true); + + AccessRule subRule2 = createSimpleRule("SubRule2", "$.sub2", AccessRule.TypeNaming.ALL_EQUALS, "subValue2"); + AccessRuleEvaluationNode subNode2 = new AccessRuleEvaluationNode(subRule2, false, true, true); + subNode2.setResult(false); + subNode2.setFailureReason("Sub-rule condition not met"); + + AccessRule nestedRule = createSimpleRule("NestedRule", "$.nested", AccessRule.TypeNaming.ALL_EQUALS, "nestedValue"); + AccessRuleEvaluationNode nestedNode = new AccessRuleEvaluationNode(nestedRule, false, true, false); + nestedNode.setResult(true); + + AccessRule nestedChildRule = createSimpleRule("NestedChild", "$.nestedChild", AccessRule.TypeNaming.ALL_EQUALS, "nestedChildValue"); + AccessRuleEvaluationNode nestedChildNode = new AccessRuleEvaluationNode(nestedChildRule, true, false, false); + nestedChildNode.setResult(true); + + rootNode.addChild(gateNode1); + rootNode.addChild(gateNode2); + rootNode.addChild(subNode1); + rootNode.addChild(subNode2); + + subNode1.addChild(nestedNode); + nestedNode.addChild(nestedChildNode); + + String treeString = rootNode.generateTreeString(); + System.out.println(treeString); + + // Explanation of the tree structure + System.out.println("\nTree Structure Explanation:"); + System.out.println("- The root node is a regular RULE with AND relationship"); + System.out.println("- It has two GATE children (one with AND, one with OR relationship)"); + System.out.println("- It has two SUB_RULE children (one with AND, one with OR relationship)"); + System.out.println("- The first SUB_RULE has a nested SUB_RULE child"); + System.out.println("- The nested SUB_RULE has a GATE child"); + System.out.println("- Nodes marked with ✓ PASS have passed their evaluation"); + System.out.println("- Nodes marked with ✗ FAIL have failed their evaluation"); + System.out.println("- Failed nodes include a failure reason"); + } + + /** + * Helper method to create a simple AccessRule + */ + private static AccessRule createSimpleRule(String name, String rule, Integer type, String value) { + AccessRule accessRule = new AccessRule(); + accessRule.setUuid(UUID.randomUUID()); + accessRule.setName(name); + accessRule.setRule(rule); + accessRule.setType(type); + accessRule.setValue(value); + return accessRule; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/model/AccessRuleEvaluationNodeTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/model/AccessRuleEvaluationNodeTest.java new file mode 100644 index 000000000..cde56b5e4 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/model/AccessRuleEvaluationNodeTest.java @@ -0,0 +1,247 @@ +package edu.harvard.hms.dbmi.avillach.auth.model; + +import edu.harvard.hms.dbmi.avillach.auth.entity.AccessRule; +import org.junit.jupiter.api.Test; + +import java.util.HashSet; +import java.util.Set; +import java.util.UUID; + +import static org.junit.jupiter.api.Assertions.*; + +/** + * Test class for AccessRuleEvaluationNode. + * This class demonstrates how AccessRuleEvaluationNode is used to build and print + * the access rule and gate evaluation tree. + */ +public class AccessRuleEvaluationNodeTest { + + /** + * Test creating a simple node and verifying its properties + */ + @Test + public void testCreateSimpleNode() { + AccessRule rule = createSimpleRule("TestRule", "$.test", AccessRule.TypeNaming.ALL_EQUALS, "value"); + + AccessRuleEvaluationNode node = new AccessRuleEvaluationNode(rule, false, false, false); + + assertEquals(rule, node.getRule()); + assertFalse(node.isResult()); + assertTrue(node.getChildren().isEmpty()); + assertNull(node.getFailureReason()); + } + + /** + * Test setting result and failure reason + */ + @Test + public void testSetResultAndFailureReason() { + AccessRule rule = createSimpleRule("TestRule", "$.test", AccessRule.TypeNaming.ALL_EQUALS, "value"); + + AccessRuleEvaluationNode node = new AccessRuleEvaluationNode(rule, false, false, false); + + node.setResult(true); + assertTrue(node.isResult()); + + node.setFailureReason("Test failure reason"); + assertEquals("Test failure reason", node.getFailureReason()); + } + + /** + * Test adding child nodes + */ + @Test + public void testAddChildNodes() { + AccessRule parentRule = createSimpleRule("ParentRule", "$.parent", AccessRule.TypeNaming.ALL_EQUALS, "parentValue"); + AccessRule childRule1 = createSimpleRule("ChildRule1", "$.child1", AccessRule.TypeNaming.ALL_EQUALS, "childValue1"); + AccessRule childRule2 = createSimpleRule("ChildRule2", "$.child2", AccessRule.TypeNaming.ALL_EQUALS, "childValue2"); + + AccessRuleEvaluationNode parentNode = new AccessRuleEvaluationNode(parentRule, false, false, false); + AccessRuleEvaluationNode childNode1 = new AccessRuleEvaluationNode(childRule1, false, false, false); + AccessRuleEvaluationNode childNode2 = new AccessRuleEvaluationNode(childRule2, false, false, false); + + parentNode.addChild(childNode1); + parentNode.addChild(childNode2); + + assertEquals(2, parentNode.getChildren().size()); + assertTrue(parentNode.getChildren().contains(childNode1)); + assertTrue(parentNode.getChildren().contains(childNode2)); + } + + /** + * Test generating tree string for a simple node + */ + @Test + public void testGenerateTreeStringSimpleNode() { + AccessRule rule = createSimpleRule("TestRule", "$.test", AccessRule.TypeNaming.ALL_EQUALS, "value"); + + AccessRuleEvaluationNode node = new AccessRuleEvaluationNode(rule, false, false, false); + node.setResult(true); + + String treeString = node.generateTreeString(); + + System.out.println("Simple Node Tree:"); + System.out.println(treeString); + + assertTrue(treeString.contains("TestRule")); + assertTrue(treeString.contains("RULE")); + assertTrue(treeString.contains("AND")); + assertTrue(treeString.contains("✓ PASS")); + } + + /** + * Test generating tree string for a node with children + */ + @Test + public void testGenerateTreeStringWithChildren() { + AccessRule parentRule = createSimpleRule("ParentRule", "$.parent", AccessRule.TypeNaming.ALL_EQUALS, "parentValue"); + AccessRuleEvaluationNode parentNode = new AccessRuleEvaluationNode(parentRule, false, false, false); + parentNode.setResult(true); + + AccessRule childRule1 = createSimpleRule("ChildRule1", "$.child1", AccessRule.TypeNaming.ALL_EQUALS, "childValue1"); + AccessRuleEvaluationNode childNode1 = new AccessRuleEvaluationNode(childRule1, false, true, false); + childNode1.setResult(true); + + AccessRule childRule2 = createSimpleRule("ChildRule2", "$.child2", AccessRule.TypeNaming.ALL_EQUALS, "childValue2"); + AccessRuleEvaluationNode childNode2 = new AccessRuleEvaluationNode(childRule2, false, true, false); + childNode2.setResult(false); + childNode2.setFailureReason("Value mismatch"); + + parentNode.addChild(childNode1); + parentNode.addChild(childNode2); + + String treeString = parentNode.generateTreeString(); + + System.out.println("Tree with Children:"); + System.out.println(treeString); + + assertTrue(treeString.contains("ParentRule")); + assertTrue(treeString.contains("RULE")); + assertTrue(treeString.contains("✓ PASS")); + + assertTrue(treeString.contains("ChildRule1")); + assertTrue(treeString.contains("SUB_RULE")); + assertTrue(treeString.contains("✓ PASS")); + + assertTrue(treeString.contains("ChildRule2")); + assertTrue(treeString.contains("✗ FAIL")); + assertTrue(treeString.contains("Value mismatch")); + } + + /** + * Test generating tree string for a complex tree with gates and different relationship types + */ + @Test + public void testGenerateTreeStringComplexTree() { + AccessRule rootRule = createSimpleRule("RootRule", "$.root", AccessRule.TypeNaming.ALL_EQUALS, "rootValue"); + AccessRuleEvaluationNode rootNode = new AccessRuleEvaluationNode(rootRule, false, false, false); + rootNode.setResult(true); + + AccessRule gateRule1 = createSimpleRule("GateRule1", "$.gate1", AccessRule.TypeNaming.ALL_EQUALS, "gateValue1"); + AccessRuleEvaluationNode gateNode1 = new AccessRuleEvaluationNode(gateRule1, true, false, false); + gateNode1.setResult(true); + + AccessRule gateRule2 = createSimpleRule("GateRule2", "$.gate2", AccessRule.TypeNaming.ALL_EQUALS, "gateValue2"); + AccessRuleEvaluationNode gateNode2 = new AccessRuleEvaluationNode(gateRule2, true, false, true); + gateNode2.setResult(false); + gateNode2.setFailureReason("Gate condition not met"); + + AccessRule subRule1 = createSimpleRule("SubRule1", "$.sub1", AccessRule.TypeNaming.ALL_EQUALS, "subValue1"); + AccessRuleEvaluationNode subNode1 = new AccessRuleEvaluationNode(subRule1, false, true, false); + subNode1.setResult(true); + + AccessRule subRule2 = createSimpleRule("SubRule2", "$.sub2", AccessRule.TypeNaming.ALL_EQUALS, "subValue2"); + AccessRuleEvaluationNode subNode2 = new AccessRuleEvaluationNode(subRule2, false, true, true); + subNode2.setResult(false); + subNode2.setFailureReason("Sub-rule condition not met"); + + rootNode.addChild(gateNode1); + rootNode.addChild(gateNode2); + rootNode.addChild(subNode1); + rootNode.addChild(subNode2); + + String treeString = rootNode.generateTreeString(); + + System.out.println("Complex Tree:"); + System.out.println(treeString); + + assertTrue(treeString.contains("RootRule")); + assertTrue(treeString.contains("RULE")); + assertTrue(treeString.contains("AND")); + assertTrue(treeString.contains("✓ PASS")); + + assertTrue(treeString.contains("GateRule1")); + assertTrue(treeString.contains("GATE")); + assertTrue(treeString.contains("AND")); + assertTrue(treeString.contains("✓ PASS")); + + assertTrue(treeString.contains("GateRule2")); + assertTrue(treeString.contains("GATE")); + assertTrue(treeString.contains("OR")); + assertTrue(treeString.contains("✗ FAIL")); + assertTrue(treeString.contains("Gate condition not met")); + + assertTrue(treeString.contains("SubRule1")); + assertTrue(treeString.contains("SUB_RULE")); + assertTrue(treeString.contains("AND")); + assertTrue(treeString.contains("✓ PASS")); + + assertTrue(treeString.contains("SubRule2")); + assertTrue(treeString.contains("SUB_RULE")); + assertTrue(treeString.contains("OR")); + assertTrue(treeString.contains("✗ FAIL")); + assertTrue(treeString.contains("Sub-rule condition not met")); + } + + /** + * Test a deep tree structure with multiple levels + */ + @Test + public void testDeepTreeStructure() { + // Create a deep tree with multiple levels + AccessRule level1Rule = createSimpleRule("Level1", "$.level1", AccessRule.TypeNaming.ALL_EQUALS, "value1"); + AccessRuleEvaluationNode level1Node = new AccessRuleEvaluationNode(level1Rule, false, false, false); + level1Node.setResult(true); + + AccessRule level2Rule = createSimpleRule("Level2", "$.level2", AccessRule.TypeNaming.ALL_EQUALS, "value2"); + AccessRuleEvaluationNode level2Node = new AccessRuleEvaluationNode(level2Rule, true, false, false); + level2Node.setResult(true); + + AccessRule level3Rule = createSimpleRule("Level3", "$.level3", AccessRule.TypeNaming.ALL_EQUALS, "value3"); + AccessRuleEvaluationNode level3Node = new AccessRuleEvaluationNode(level3Rule, false, true, false); + level3Node.setResult(true); + + AccessRule level4Rule = createSimpleRule("Level4", "$.level4", AccessRule.TypeNaming.ALL_EQUALS, "value4"); + AccessRuleEvaluationNode level4Node = new AccessRuleEvaluationNode(level4Rule, true, false, true); + level4Node.setResult(false); + level4Node.setFailureReason("Deep level failure"); + + level1Node.addChild(level2Node); + level2Node.addChild(level3Node); + level3Node.addChild(level4Node); + + String treeString = level1Node.generateTreeString(); + + System.out.println("Deep Tree Structure:"); + System.out.println(treeString); + + assertTrue(treeString.contains("Level1")); + assertTrue(treeString.contains("Level2")); + assertTrue(treeString.contains("Level3")); + assertTrue(treeString.contains("Level4")); + assertTrue(treeString.contains("Deep level failure")); + } + + /** + * Helper method to create a simple AccessRule + */ + private AccessRule createSimpleRule(String name, String rule, Integer type, String value) { + AccessRule accessRule = new AccessRule(); + accessRule.setUuid(UUID.randomUUID()); + accessRule.setName(name); + accessRule.setRule(rule); + accessRule.setType(type); + accessRule.setValue(value); + return accessRule; + } +} \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/rest/ControllerAuditEventTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/rest/ControllerAuditEventTest.java new file mode 100644 index 000000000..d61cb1253 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/rest/ControllerAuditEventTest.java @@ -0,0 +1,190 @@ +package edu.harvard.hms.dbmi.avillach.auth.rest; + +import static org.junit.jupiter.api.Assertions.*; + +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import jakarta.servlet.http.HttpServletRequest; +import org.junit.jupiter.api.Test; +import org.springframework.http.HttpHeaders; + +import java.lang.reflect.Method; +import java.util.List; +import java.util.Map; + +class ControllerAuditEventTest { + + private void assertAuditEvent(Class controller, String methodName, Class[] params, String expectedType, String expectedAction) throws Exception { + Method method = controller.getMethod(methodName, params); + AuditEvent event = method.getAnnotation(AuditEvent.class); + assertNotNull(event, controller.getSimpleName() + "." + methodName + " missing @AuditEvent"); + assertEquals(expectedType, event.type(), controller.getSimpleName() + "." + methodName + " wrong type"); + assertEquals(expectedAction, event.action(), controller.getSimpleName() + "." + methodName + " wrong action"); + } + + @Test + void authenticationController() throws Exception { + Class c = AuthenticationController.class; + // authentication(String idpProvider, Map authRequest, HttpServletRequest request) + assertAuditEvent(c, "authentication", new Class[]{String.class, Map.class, HttpServletRequest.class}, "AUTH", "auth.login"); + } + + @Test + void tokenController() throws Exception { + Class c = TokenController.class; + // inspectToken(Map inputMap, HttpServletRequest request) + assertAuditEvent(c, "inspectToken", new Class[]{Map.class, HttpServletRequest.class}, "ACCESS", "token.introspect"); + // refreshToken(String authorizationHeader, HttpServletRequest request) + assertAuditEvent(c, "refreshToken", new Class[]{String.class, HttpServletRequest.class}, "ACCESS", "token.refresh"); + } + + @Test + void userController() throws Exception { + Class c = UserController.class; + // getUserById(String userId, HttpServletRequest request) + assertAuditEvent(c, "getUserById", new Class[]{String.class, HttpServletRequest.class}, "OTHER", "user.read"); + // getUserAll() + assertAuditEvent(c, "getUserAll", new Class[]{}, "OTHER", "user.list"); + // addUser(List users, HttpServletRequest request) + assertAuditEvent(c, "addUser", new Class[]{List.class, HttpServletRequest.class}, "ADMIN", "user.modify"); + // updateUser(List users, HttpServletRequest request) + assertAuditEvent(c, "updateUser", new Class[]{List.class, HttpServletRequest.class}, "ADMIN", "user.modify"); + // getCurrentUser(String authorizationHeader, Boolean hasToken) + assertAuditEvent(c, "getCurrentUser", new Class[]{String.class, Boolean.class}, "ACCESS", "user.profile"); + // getQueryTemplate(String applicationId) + assertAuditEvent(c, "getQueryTemplate", new Class[]{String.class}, "ACCESS", "user.profile"); + // getQueryTemplate() - no params + assertAuditEvent(c, "getQueryTemplate", new Class[]{}, "ACCESS", "user.profile"); + // refreshUserToken(HttpHeaders httpHeaders, HttpServletRequest request) + assertAuditEvent(c, "refreshUserToken", new Class[]{HttpHeaders.class, HttpServletRequest.class}, "ACCESS", "user.profile"); + } + + @Test + void roleController() throws Exception { + Class c = RoleController.class; + // getRoleById(String roleId) + assertAuditEvent(c, "getRoleById", new Class[]{String.class}, "OTHER", "role.read"); + // getRoleAll() + assertAuditEvent(c, "getRoleAll", new Class[]{}, "OTHER", "role.list"); + // addRole(List roles, HttpServletRequest request) + assertAuditEvent(c, "addRole", new Class[]{List.class, HttpServletRequest.class}, "ADMIN", "role.modify"); + // updateRole(List roles, HttpServletRequest request) + assertAuditEvent(c, "updateRole", new Class[]{List.class, HttpServletRequest.class}, "ADMIN", "role.modify"); + // removeById(String roleId, HttpServletRequest request) + assertAuditEvent(c, "removeById", new Class[]{String.class, HttpServletRequest.class}, "ADMIN", "role.delete"); + } + + @Test + void privilegeController() throws Exception { + Class c = PrivilegeController.class; + // getPrivilegeById(String privilegeId) + assertAuditEvent(c, "getPrivilegeById", new Class[]{String.class}, "OTHER", "privilege.read"); + // getPrivilegeAll() + assertAuditEvent(c, "getPrivilegeAll", new Class[]{}, "OTHER", "privilege.list"); + // addPrivilege(List privileges, HttpServletRequest request) + assertAuditEvent(c, "addPrivilege", new Class[]{List.class, HttpServletRequest.class}, "ADMIN", "privilege.modify"); + // updatePrivilege(List privileges, HttpServletRequest request) + assertAuditEvent(c, "updatePrivilege", new Class[]{List.class, HttpServletRequest.class}, "ADMIN", "privilege.modify"); + // removeById(String privilegeId, HttpServletRequest request) + assertAuditEvent(c, "removeById", new Class[]{String.class, HttpServletRequest.class}, "ADMIN", "privilege.delete"); + } + + @Test + void accessRuleController() throws Exception { + Class c = AccessRuleController.class; + // getAccessRuleById(String accessRuleId) + assertAuditEvent(c, "getAccessRuleById", new Class[]{String.class}, "OTHER", "access_rule.read"); + // getAccessRuleAll() + assertAuditEvent(c, "getAccessRuleAll", new Class[]{}, "OTHER", "access_rule.list"); + // addAccessRule(List accessRules, HttpServletRequest request) + assertAuditEvent(c, "addAccessRule", new Class[]{List.class, HttpServletRequest.class}, "ADMIN", "access_rule.modify"); + // updateAccessRule(List accessRules, HttpServletRequest request) + assertAuditEvent(c, "updateAccessRule", new Class[]{List.class, HttpServletRequest.class}, "ADMIN", "access_rule.modify"); + // removeById(String accessRuleId, HttpServletRequest request) + assertAuditEvent(c, "removeById", new Class[]{String.class, HttpServletRequest.class}, "ADMIN", "access_rule.delete"); + // getAllTypes() + assertAuditEvent(c, "getAllTypes", new Class[]{}, "OTHER", "access_rule.types"); + } + + @Test + void applicationController() throws Exception { + Class c = ApplicationController.class; + // getApplicationById(String applicationId) + assertAuditEvent(c, "getApplicationById", new Class[]{String.class}, "OTHER", "application.read"); + // getApplicationAll() + assertAuditEvent(c, "getApplicationAll", new Class[]{}, "OTHER", "application.list"); + // addApplication(List applications, HttpServletRequest request) + assertAuditEvent(c, "addApplication", new Class[]{List.class, HttpServletRequest.class}, "ADMIN", "application.modify"); + // updateApplication(List applications, HttpServletRequest request) + assertAuditEvent(c, "updateApplication", new Class[]{List.class, HttpServletRequest.class}, "ADMIN", "application.modify"); + // refreshApplicationToken(String applicationId, HttpServletRequest request) + assertAuditEvent(c, "refreshApplicationToken", new Class[]{String.class, HttpServletRequest.class}, "ADMIN", "application.token_refresh"); + // removeById(String applicationId, HttpServletRequest request) + assertAuditEvent(c, "removeById", new Class[]{String.class, HttpServletRequest.class}, "ADMIN", "application.delete"); + } + + @Test + void termsOfServiceController() throws Exception { + Class c = TermsOfServiceController.class; + // getLatestTermsOfService() + assertAuditEvent(c, "getLatestTermsOfService", new Class[]{}, "ACCESS", "tos.view"); + // updateTermsOfService(String html, HttpServletRequest request) + assertAuditEvent(c, "updateTermsOfService", new Class[]{String.class, HttpServletRequest.class}, "ADMIN", "tos.update"); + // hasUserAcceptedTOS() + assertAuditEvent(c, "hasUserAcceptedTOS", new Class[]{}, "ACCESS", "tos.view"); + // acceptTermsOfService(HttpServletRequest request) + assertAuditEvent(c, "acceptTermsOfService", new Class[]{HttpServletRequest.class}, "ACCESS", "tos.accept"); + } + + @Test + void openAccessController() throws Exception { + Class c = OpenAccessController.class; + // validate(Map inputMap, HttpServletRequest request) + assertAuditEvent(c, "validate", new Class[]{Map.class, HttpServletRequest.class}, "ACCESS", "open.validate"); + } + + @Test + void studyAccessController() throws Exception { + Class c = StudyAccessController.class; + // addStudyAccess(String studyIdentifier, HttpServletRequest request) + assertAuditEvent(c, "addStudyAccess", new Class[]{String.class, HttpServletRequest.class}, "ADMIN", "study_access.create"); + } + + @Test + void connectionWebController() throws Exception { + Class c = ConnectionWebController.class; + // getConnectionById(String connectionId) + assertAuditEvent(c, "getConnectionById", new Class[]{String.class}, "OTHER", "connection.read"); + // getAllConnections() + assertAuditEvent(c, "getAllConnections", new Class[]{}, "OTHER", "connection.list"); + // addConnection(List connections, HttpServletRequest request) + assertAuditEvent(c, "addConnection", new Class[]{List.class, HttpServletRequest.class}, "ADMIN", "connection.modify"); + // updateConnection(List connections, HttpServletRequest request) + assertAuditEvent(c, "updateConnection", new Class[]{List.class, HttpServletRequest.class}, "ADMIN", "connection.modify"); + // removeById(String connectionId, HttpServletRequest request) + assertAuditEvent(c, "removeById", new Class[]{String.class, HttpServletRequest.class}, "ADMIN", "connection.delete"); + } + + @Test + void userMetadataMappingWebController() throws Exception { + Class c = UserMetadataMappingWebController.class; + // getMappingsForConnection(String connection) + assertAuditEvent(c, "getMappingsForConnection", new Class[]{String.class}, "OTHER", "mapping.read"); + // getAllMappings() + assertAuditEvent(c, "getAllMappings", new Class[]{}, "OTHER", "mapping.list"); + // addMapping(List mappings, HttpServletRequest request) + assertAuditEvent(c, "addMapping", new Class[]{List.class, HttpServletRequest.class}, "ADMIN", "mapping.modify"); + // updateMapping(List mappings, HttpServletRequest request) + assertAuditEvent(c, "updateMapping", new Class[]{List.class, HttpServletRequest.class}, "ADMIN", "mapping.modify"); + // removeById(String mappingId, HttpServletRequest request) + assertAuditEvent(c, "removeById", new Class[]{String.class, HttpServletRequest.class}, "ADMIN", "mapping.delete"); + } + + @Test + void cacheController() throws Exception { + Class c = CacheController.class; + // getCacheNames() + assertAuditEvent(c, "getCacheNames", new Class[]{}, "OTHER", "cache.list"); + // getCache(String cacheName) + assertAuditEvent(c, "getCache", new Class[]{String.class}, "OTHER", "cache.read"); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/AccessRuleServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/AccessRuleServiceTest.java new file mode 100644 index 000000000..d7eec7675 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/AccessRuleServiceTest.java @@ -0,0 +1,126 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.hms.dbmi.avillach.auth.entity.AccessRule; +import edu.harvard.hms.dbmi.avillach.auth.repository.AccessRuleRepository; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockitoAnnotations; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.test.context.ContextConfiguration; + +import java.util.*; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.ArgumentMatchers.anyList; +import static org.mockito.Mockito.doNothing; +import static org.mockito.Mockito.when; + +@SpringBootTest +@ContextConfiguration(classes = {AccessRuleService.class}) +public class AccessRuleServiceTest { + + @MockBean + private AccessRuleRepository accessRuleRepo; + + @Autowired + private AccessRuleService accessRuleService; + + @BeforeEach + void setUp() { + MockitoAnnotations.openMocks(this); + } + + @Test + public void testGetAccessRuleById_found() { + UUID id = UUID.randomUUID(); + AccessRule accessRule = new AccessRule(); + when(accessRuleRepo.findById(id)).thenReturn(Optional.of(accessRule)); + + Optional result = accessRuleService.getAccessRuleById(id.toString()); + assertTrue(result.isPresent()); + assertSame(accessRule, result.get()); + } + + @Test + public void testGetAccessRuleById_notFound() { + UUID id = UUID.randomUUID(); + when(accessRuleRepo.findById(id)).thenReturn(Optional.empty()); + + Optional result = accessRuleService.getAccessRuleById(id.toString()); + assertFalse(result.isPresent()); + } + + @Test + public void testGetAllAccessRules_empty() { + when(accessRuleRepo.findAll()).thenReturn(Collections.emptyList()); + + List result = accessRuleService.getAllAccessRules(); + assertTrue(result.isEmpty()); + } + + @Test + public void testGetAllAccessRules_nonEmpty() { + List rules = Arrays.asList(new AccessRule(), new AccessRule()); + when(accessRuleRepo.findAll()).thenReturn(rules); + + List result = accessRuleService.getAllAccessRules(); + assertEquals(2, result.size()); + } + + + @Test + public void testAddAccessRule_withNullFields() { + AccessRule rule = new AccessRule(); // fields are null + List rules = Collections.singletonList(rule); + when(accessRuleRepo.saveAll(anyList())).thenAnswer(invocation -> invocation.getArgument(0)); + + List result = accessRuleService.addAccessRule(rules); + assertFalse(result.getFirst().getEvaluateOnlyByGates()); + assertFalse(result.getFirst().getCheckMapKeyOnly()); + assertFalse(result.getFirst().getCheckMapNode()); + assertFalse(result.getFirst().getGateAnyRelation()); + } + + @Test + public void testAddAccessRule_noNullFields() { + AccessRule rule = new AccessRule(); + rule.setEvaluateOnlyByGates(true); + rule.setCheckMapKeyOnly(true); + rule.setCheckMapNode(true); + rule.setGateAnyRelation(true); + List rules = Collections.singletonList(rule); + when(accessRuleRepo.saveAll(anyList())).thenReturn(rules); + + List result = accessRuleService.addAccessRule(rules); + assertTrue(result.getFirst().getEvaluateOnlyByGates()); + assertTrue(result.getFirst().getCheckMapKeyOnly()); + assertTrue(result.getFirst().getCheckMapNode()); + assertTrue(result.getFirst().getGateAnyRelation()); + } + + + @Test + public void testUpdateAccessRules() { + AccessRule rule = new AccessRule(); + List rules = Collections.singletonList(rule); + when(accessRuleRepo.saveAll(anyList())).thenReturn(rules); + + List result = accessRuleService.updateAccessRules(rules); + assertSame(rules, result); + } + + + @Test + public void testRemoveAccessRuleById() { + UUID id = UUID.randomUUID(); + List remainingRules = List.of(new AccessRule()); + doNothing().when(accessRuleRepo).deleteById(id); + when(accessRuleRepo.findAll()).thenReturn(remainingRules); + + List result = accessRuleService.removeAccessRuleById(id.toString()); + assertEquals(1, result.size()); + } + +} \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/ApplicationServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/ApplicationServiceTest.java new file mode 100644 index 000000000..3a1619892 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/ApplicationServiceTest.java @@ -0,0 +1,185 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Application; +import edu.harvard.hms.dbmi.avillach.auth.entity.Privilege; +import edu.harvard.hms.dbmi.avillach.auth.repository.ApplicationRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.PrivilegeRepository; +import edu.harvard.hms.dbmi.avillach.auth.utils.JWTUtil; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockitoAnnotations; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.test.context.ContextConfiguration; + +import java.util.*; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + +@SpringBootTest +@ContextConfiguration(classes = {ApplicationService.class}) +public class ApplicationServiceTest { + + @MockBean + private ApplicationRepository applicationRepo; + + @MockBean + private PrivilegeRepository privilegeRepo; + + @MockBean + private JWTUtil jwtUtil; + + @Autowired + private ApplicationService applicationService; + + @BeforeEach + public void setUp() { + MockitoAnnotations.openMocks(this); + } + + @Test + public void testGetApplicationByID_found() { + UUID id = UUID.randomUUID(); + Application app = new Application(); + app.setUuid(id); + when(applicationRepo.findById(id)).thenReturn(Optional.of(app)); + + Optional result = applicationService.getApplicationByID(id.toString()); + assertTrue(result.isPresent()); + assertSame(app, result.get()); + } + + @Test + public void testGetApplicationByID_notFound() { + UUID id = UUID.randomUUID(); + when(applicationRepo.findById(id)).thenReturn(Optional.empty()); + + Optional result = applicationService.getApplicationByID(id.toString()); + assertFalse(result.isPresent()); + } + + @Test + public void testGetApplicationByIdWithPrivileges_foundWithPrivileges() { + UUID id = UUID.randomUUID(); + Application app = new Application(); + app.setPrivileges(new HashSet<>()); + when(applicationRepo.findById(id)).thenReturn(Optional.of(app)); + when(privilegeRepo.findById(any())).thenReturn(Optional.of(new Privilege())); + + Optional result = applicationService.getApplicationByIdWithPrivileges(id.toString()); + assertTrue(result.isPresent()); + Assertions.assertNotNull(result.get().getPrivileges()); + } + + @Test + public void testGetApplicationByIdWithPrivileges_notFound() { + UUID id = UUID.randomUUID(); + when(applicationRepo.findById(id)).thenReturn(Optional.empty()); + + Optional result = applicationService.getApplicationByIdWithPrivileges(id.toString()); + assertFalse(result.isPresent()); + } + + @Test + public void testGetAllApplications_empty() { + when(applicationRepo.findAll()).thenReturn(Collections.emptyList()); + + List result = applicationService.getAllApplications(); + assertTrue(result.isEmpty()); + } + + @Test + public void testGetAllApplications_nonEmpty() { + when(applicationRepo.findAll()).thenReturn(Arrays.asList(new Application(), new Application())); + + List result = applicationService.getAllApplications(); + assertEquals(2, result.size()); + } + + @Test + public void testAddNewApplications_successfulWithToken() { + Application application = new Application(); + application.setUuid(UUID.randomUUID()); + List applications = Collections.singletonList(application); + when(applicationRepo.saveAll(applications)).thenReturn(applications); + when(jwtUtil.createJwtToken(any(), any(), any(), anyString(), anyLong())).thenReturn("token"); + + List savedApps = applicationService.addNewApplications(applications); + assertNotNull(savedApps); + assertFalse(savedApps.isEmpty()); + assertEquals("token", savedApps.getFirst().getToken()); + } + + @Test + public void testDeleteApplicationById_existing() { + UUID id = UUID.randomUUID(); + Application application = new Application(); + when(applicationRepo.findById(id)).thenReturn(Optional.of(application)); + + List remainingApps = applicationService.deleteApplicationById(id.toString()); + verify(applicationRepo, times(1)).delete(application); + assertNotNull(remainingApps); + } + + @Test + public void testDeleteApplicationById_notFound() { + UUID id = UUID.randomUUID(); + when(applicationRepo.findById(id)).thenReturn(Optional.empty()); + + assertThrows(IllegalArgumentException.class, () -> { + applicationService.deleteApplicationById(id.toString()); + }); + } + + @Test + public void testUpdateApplications() { + Application application = new Application(); + application.setUuid(UUID.randomUUID()); + List applications = Collections.singletonList(application); + when(applicationRepo.saveAll(anyList())).thenReturn(applications); + + List updatedApps = applicationService.updateApplications(applications); + Assertions.assertNotNull(updatedApps); + Assertions.assertEquals(applications.size(), updatedApps.size()); + } + + @Test + public void testRefreshApplicationToken_successful() { + UUID id = UUID.randomUUID(); + Application application = new Application(); + application.setUuid(id); + application.setName("App"); + when(applicationRepo.findById(id)).thenReturn(Optional.of(application)); + when(jwtUtil.createJwtToken(any(), any(), any(), anyString(), anyLong())).thenReturn("newToken"); + + String token = applicationService.refreshApplicationToken(id.toString()); + assertEquals("newToken", token); + } + + @Test + public void testRefreshApplicationToken_notFound() { + UUID id = UUID.randomUUID(); + when(applicationRepo.findById(id)).thenReturn(Optional.empty()); + + assertThrows(IllegalArgumentException.class, () -> { + applicationService.refreshApplicationToken(id.toString()); + }); + } + + @Test + public void testRefreshApplicationToken_failedToGenerateToken() { + UUID id = UUID.randomUUID(); + Application application = new Application(); + application.setUuid(id); + when(applicationRepo.findById(id)).thenReturn(Optional.of(application)); + when(jwtUtil.createJwtToken(any(), any(), any(), anyString(), anyLong())).thenReturn(null); + + + assertThrows(NullPointerException.class, () -> { + applicationService.refreshApplicationToken(id.toString()); + }); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/Auth0MatchingServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/Auth0MatchingServiceTest.java new file mode 100644 index 000000000..aa30b125b --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/Auth0MatchingServiceTest.java @@ -0,0 +1,209 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import com.fasterxml.jackson.core.type.TypeReference; +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.hms.dbmi.avillach.auth.entity.Connection; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import edu.harvard.hms.dbmi.avillach.auth.entity.UserMetadataMapping; +import edu.harvard.hms.dbmi.avillach.auth.repository.ConnectionRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserRepository; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockitoAnnotations; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.test.context.ContextConfiguration; + +import java.io.IOException; +import java.util.List; +import java.util.Map; +import java.util.Optional; +import java.util.stream.Collectors; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.ArgumentMatchers.*; +import static org.mockito.Mockito.doAnswer; + +@SpringBootTest +@ContextConfiguration(classes = {OauthUserMatchingService.class}) +public class Auth0MatchingServiceTest { + + private static final Logger log = LoggerFactory.getLogger(Auth0MatchingServiceTest.class); + + @MockBean + private UserRepository userRepo; + + @MockBean + private UserMetadataMappingService mappingService; + + @MockBean + private UserService userService; + + @MockBean + private ConnectionRepository connectionRepo; + + @Autowired + private OauthUserMatchingService cut; + + private User persistedUser; + private final ObjectMapper mapper = new ObjectMapper(); + + @BeforeEach + public void setUp() { + MockitoAnnotations.openMocks(this); + //Instead of calling the database + doAnswer(invocation -> (listUnmatchedByConnectionIdMock(invocation.getArgument(0)))). + when(userRepo).findByConnectionAndMatched(any(Connection.class), anyBoolean()); + doAnswer(invocation -> (getAllMappingsForConnectionMock(invocation.getArgument(0)))). + when(mappingService).getAllMappingsForConnection(any(Connection.class)); + + doAnswer(invocation -> { + String connectionId = invocation.getArgument(0); + log.info("Mocking connection with id: {}", connectionId); + return mockConnection(connectionId); + }).when(connectionRepo).findById(anyString()); + + //So we can check that the user is persisted + doAnswer(invocation -> { + persistedUser = invocation.getArgument(0); + return null; + }).when(userService).save(any(User.class)); + } + + @Test + public void testMatchTokenToUser() { + String ldapToken = "ldap-connector-access-token"; + String githubToken = "github-access-token"; + String nihToken = "nih-gov-prod-access-token"; + + try { + JsonNode userInfo = mockAuthAPIUserInfo(ldapToken); + + //Test when everything works fine + User result = cut.matchTokenToUser(userInfo); + log.info("Result: " + result); + assertNotNull(result); + assertNotNull(result.getAuth0metadata()); + assertNotNull(result.getSubject()); + assertEquals("ad|ldap-connector|blablablablablablablablablablablabla", result.getSubject()); + assertTrue(result.isMatched()); + assertNotNull(persistedUser); + assertNotNull(persistedUser.getAuth0metadata()); + assertEquals(persistedUser.getAuth0metadata(), result.getAuth0metadata()); + assertNotNull(persistedUser.getSubject()); + assertEquals("ad|ldap-connector|blablablablablablablablablablablabla", persistedUser.getSubject()); + assertTrue(persistedUser.isMatched()); + //Reset + persistedUser = null; + + //Test when multiple mappings in database + userInfo = mockAuthAPIUserInfo(githubToken); + result = cut.matchTokenToUser(userInfo); + assertNotNull(result); + assertNotNull(result.getAuth0metadata()); + assertNotNull(result.getSubject()); + assertEquals("github|0000000", result.getSubject()); + assertTrue(result.isMatched()); + assertNotNull(persistedUser); + assertNotNull(persistedUser.getAuth0metadata()); + assertEquals(persistedUser.getAuth0metadata(), result.getAuth0metadata()); + assertNotNull(persistedUser.getSubject()); + assertEquals("github|0000000", persistedUser.getSubject()); + assertTrue(persistedUser.isMatched()); + + persistedUser = null; + + //Test when path not found in user generalmetadata + userInfo = mockAuthAPIUserInfo(nihToken); + result = cut.matchTokenToUser(userInfo); + assertNotNull(result); + assertNotNull(result.getAuth0metadata()); + assertNotNull(result.getSubject()); + assertEquals("samlp|NOBODY", result.getSubject()); + assertTrue(result.isMatched()); + assertNotNull(persistedUser); + assertNotNull(persistedUser.getAuth0metadata()); + assertEquals(persistedUser.getAuth0metadata(), result.getAuth0metadata()); + assertNotNull(persistedUser.getSubject()); + assertEquals("samlp|NOBODY", persistedUser.getSubject()); + assertTrue(persistedUser.isMatched()); + + persistedUser = null; + + //Test when no user matches + userInfo = mockAuthAPIUserInfo("no-user-token"); + result = cut.matchTokenToUser(userInfo); + assertNull(result); + + //Test when path not found in auth0metadata -- This is a problem with the mapping data in the database + userInfo = mockAuthAPIUserInfo("invalid-path-token"); + result = cut.matchTokenToUser(userInfo); + assertNull(result); + + //Test when no mappings in database -- We have no mappings set up for this yet + userInfo = mockAuthAPIUserInfo("no-mapping-connection-token"); + result = cut.matchTokenToUser(userInfo); + assertNull(result); + + } catch (Exception e) { + e.printStackTrace(); + } + } + + private List listUnmatchedByConnectionIdMock(Connection connectionId) { + List allMappings = List.of( + new User().setConnection(new Connection().setId("ldap-connector")).setGeneralMetadata("{ \"email\": \"foo@childrens.harvard.edu\", \"fullName\" : \"Bruce Banner\"}"), + new User().setConnection(new Connection().setId("ldap-connector")).setGeneralMetadata("{ \"email\": \"foobar@childrens.harvard.edu\", \"fullName\" : \"Scott Lang\"}"), + new User().setConnection(new Connection().setId("nih-gov-prod")).setGeneralMetadata("{ \"email\": \"foo@nih.gov\", \"fullName\" : \"Piotr Rasputin\"}"), + new User().setConnection(new Connection().setId("nih-gov-prod")).setGeneralMetadata("{ \"email\": \"foobar@nih.gov\", \"fullName\" : \"Matthew Murdock\", \"nih-userid\" : \"NOBODY\"}"), + new User().setConnection(new Connection().setId("github")).setGeneralMetadata("{ \"email\": \"blablabla@gmail.com\", \"fullName\" : \"Some Girl\"}"), + new User().setConnection(new Connection().setId("github")).setGeneralMetadata("{ \"email\": \"blablabla@gmail.com\", \"fullName\" : \"Jean Grey\"}"), + new User().setConnection(new Connection().setId("no-mapping-connection")).setGeneralMetadata("{ \"email\": \"foo@bar.com\", \"fullName\" : \"Luke Cage\"}") + ); + return allMappings.stream().filter((User user) -> { + return user.getConnection().getId().equalsIgnoreCase(connectionId.getId()); + }).collect(Collectors.toList()); + } + + private List getAllMappingsForConnectionMock(Connection connection) { + log.info("Mocking mappings for connection with id: " + connection.getId()); + List allMappings = List.of( + new UserMetadataMapping().setConnection(new Connection().setId("ldap-connector")).setGeneralMetadataJsonPath("$.email").setAuth0MetadataJsonPath("$.email"), + new UserMetadataMapping().setConnection(new Connection().setId("nih-gov-prod")).setGeneralMetadataJsonPath("$.nih-userid").setAuth0MetadataJsonPath("$.identities[0].user_id"), + new UserMetadataMapping().setConnection(new Connection().setId("github")).setGeneralMetadataJsonPath("$.full_name").setAuth0MetadataJsonPath("$.name"), + new UserMetadataMapping().setConnection(new Connection().setId("github")).setGeneralMetadataJsonPath("$.email").setAuth0MetadataJsonPath("$.emails[?(@.primary == true)].email"), + new UserMetadataMapping().setConnection(new Connection().setId("no-user-connection")).setGeneralMetadataJsonPath("$.email").setAuth0MetadataJsonPath("$.email"), + new UserMetadataMapping().setConnection(new Connection().setId("invalid-path")).setGeneralMetadataJsonPath("$.email").setAuth0MetadataJsonPath("$.noPath") + + ); + return allMappings.stream().filter((UserMetadataMapping mapping) -> { + return mapping.getConnection().getId().equalsIgnoreCase(connection.getId()); + }).collect(Collectors.toList()); + } + + public JsonNode mockAuthAPIUserInfo(String accessToken) throws IOException { + Map map = Map.of("ldap-connector-access-token", + "{ \"name\": \"Guy,Some\", \"family_name\": \"Guy\", \"given_name\": \"Some\", \"nickname\": \"CH000000000\", \"groups\": [], \"emails\": [ \"foo@childrens.harvard.edu\" ], \"dn\": \"CN=CH0000000,OU=users,DC=chbdir,DC=org\", \"distinguishedName\": \"CN=CH0000000,OU=users,DC=chbdir,DC=org\", \"organizationUnits\": \"CN=CH0000000,OU=users,DC=chbdir,DC=org\", \"email\": \"foo@childrens.harvard.edu\", \"updated_at\": \"2018-10-04T18:28:23.371Z\", \"picture\": \"https://s.gravatar.com/avatar/blablablablablablablablablablablabla?s=480&r=pg&d=https%3A%2F%2Fcdn.auth0.com%2Favatars%2Fsp.png\", \"user_id\": \"ad|ldap-connector|blablablablablablablablablablablabla\", \"identities\": [ { \"user_id\": \"ldap-connector|blablablablablablablablablablablabla\", \"provider\": \"ad\", \"connection\": \"ldap-connector\", \"isSocial\": false } ], \"created_at\": \"2018-01-26T14:06:50.413Z\", \"username\": \"CH0000000\", \"app_metadata\": { \"roles\": [ \"ROLE_CITI_USER\" ] }, \"last_ip\": \"134.174.140.32\", \"last_login\": \"2018-10-04T18:28:23.091Z\", \"logins_count\": 399, \"blocked_for\": [], \"guardian_authenticators\": []}", + "github-access-token", "{ \"email\": \"blablabla@gmail.com\", \"name\": \"Some Girl\", \"picture\": \"https://avatars3.githubusercontent.com/u/0000000000?v=4\", \"nickname\": \"blablabla\", \"gravatar_id\": \"\", \"url\": \"https://api.github.com/users/blablabla\", \"html_url\": \"https://github.com/blablabla\", \"followers_url\": \"https://api.github.com/users/blablabla/followers\", \"following_url\": \"https://api.github.com/users/blablabla/following{/other_user}\", \"gists_url\": \"https://api.github.com/users/blablabla/gists{/gist_id}\", \"starred_url\": \"https://api.github.com/users/blablabla/starred{/owner}{/repo}\", \"subscriptions_url\": \"https://api.github.com/users/blablabla/subscriptions\", \"organizations_url\": \"https://api.github.com/users/blablabla/orgs\", \"repos_url\": \"https://api.github.com/users/blablabla/repos\", \"events_url\": \"https://api.github.com/users/blablabla/events{/privacy}\", \"received_events_url\": \"https://api.github.com/users/blablabla/received_events\", \"type\": \"User\", \"site_admin\": false, \"location\": \"Nowhere, USA\", \"hireable\": true, \"public_repos\": 8, \"public_gists\": \"0\", \"followers\": 3, \"following\": 1, \"updated_at\": \"2018-09-20T18:47:43.703Z\", \"emails\": [ { \"email\": \"blablabla@gmail.com\", \"primary\": true, \"verified\": true, \"visibility\": \"public\" }, { \"email\": \"blablabla@users.noreply.github.com\", \"primary\": false, \"verified\": true, \"visibility\": null } ], \"email_verified\": true, \"user_id\": \"github|0000000\", \"identities\": [ { \"provider\": \"github\", \"user_id\": \"000000000\", \"connection\": \"github\", \"isSocial\": true } ], \"created_at\": \"2016-10-22T22:38:20.437Z\", \"blog\": \"\", \"node_id\": \"blablabla=\", \"app_metadata\": { \"roles\": [ \"ROLE_CITI_USER\" ] }, \"last_ip\": \"134.174.140.198\", \"last_login\": \"2018-09-20T18:47:43.491Z\", \"logins_count\": 71, \"blocked_for\": [], \"guardian_authenticators\": []}", + "nih-gov-prod-access-token", "{ \"email\": \"NOBODY\", \"sessionIndex\": \"blablablabla\", \"UserPrincipalName\": \"\", \"Mail\": \"\", \"FirstName\": \"\", \"LastName\": \"\", \"MiddleName\": \"\", \"NEDID\": \"\", \"nameIdAttributes\": { \"value\": \"NOBODY\", \"Format\": \"urn:oasis:names:tc:SAML:2.0:nameid-format:persistent\" }, \"authenticationmethod\": \"urn:oasis:names:tc:SAML:2.0:ac:classes:Password\", \"issuer\": \"https://auth.nih.gov/IDP\", \"updated_at\": \"2018-07-23T19:32:51.505Z\", \"name\": \"\", \"picture\": \"https://cdn.auth0.com/avatars/default.png\", \"user_id\": \"samlp|NOBODY\", \"nickname\": \"\", \"identities\": [ { \"user_id\": \"NOBODY\", \"provider\": \"samlp\", \"connection\": \"nih-gov-prod\", \"isSocial\": false } ], \"created_at\": \"2018-04-02T13:10:25.654Z\", \"app_metadata\": { \"roles\": [ \"ROLE_CITI_USER\" ] }, \"last_ip\": \"134.174.140.195\", \"last_login\": \"2018-07-23T19:32:51.254Z\", \"logins_count\": 12, \"blocked_for\": [], \"guardian_authenticators\": []}", + "no-mapping-connection-token", "{ \"email\": \"foo@bar.com\", \"UserName\": \"foooo\", \"FirstName\": \"foo\", \"LastName\": \"oooo\",\"user_id\": \"samlp|fooBar\", \"identities\": [ { \"user_id\": \"fooBar\", \"provider\": \"samlp\", \"connection\": \"no-mapping-connection\", \"isSocial\": false } ]}", + "invalid-path-token", "{ \"email\": \"bar@foo.com\", \"UserName\": \"bahh\", \"user_id\": \"samlp|barFoo\", \"identities\": [ { \"user_id\": \"barFoo\", \"provider\": \"samlp\", \"connection\": \"invalid-path\", \"isSocial\": true } ]}", + "no-user-token", "{ \"email\": \"no@user.com\", \"UserName\": \"nooooooo\", \"user_id\": \"samlp|noUser\", \"identities\": [ { \"user_id\": \"noUser\", \"provider\": \"samlp\", \"connection\": \"no-user-connection\", \"isSocial\": false } ]}" + ); + String result = map.get(accessToken); + Map jsonMap = mapper.readValue(result, + new TypeReference>() { + }); + return mapper.valueToTree(jsonMap); + } + + public Optional mockConnection(String id) { + log.info("Mocking connection with id: {}", id); + return Optional.of(new Connection().setId(id)); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/AuthenticationServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/AuthenticationServiceTest.java new file mode 100644 index 000000000..b1d635b80 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/AuthenticationServiceTest.java @@ -0,0 +1,192 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import com.fasterxml.jackson.databind.JsonNode; +import edu.harvard.hms.dbmi.avillach.auth.entity.Connection; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import edu.harvard.hms.dbmi.avillach.auth.entity.UserClaims; +import edu.harvard.hms.dbmi.avillach.auth.exceptions.NotAuthorizedException; +import edu.harvard.hms.dbmi.avillach.auth.repository.ConnectionRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserRepository; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.authentication.Auth0AuthenticationService; +import edu.harvard.hms.dbmi.avillach.auth.utils.RestClientUtil; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockitoAnnotations; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.http.HttpHeaders; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.ContextConfiguration; + +import java.io.IOException; +import java.util.HashMap; +import java.util.Map; +import java.util.Optional; +import java.util.UUID; + +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertThrows; +import static org.mockito.ArgumentMatchers.*; +import static org.mockito.Mockito.*; + +@SpringBootTest +@ContextConfiguration(classes = {Auth0AuthenticationService.class}) +public class AuthenticationServiceTest { + + @MockBean + private OauthUserMatchingService matchingService; + @MockBean + private UserRepository userRepository; + @MockBean + private BasicMailService basicMailService; + @MockBean + private UserService userService; + @MockBean + private ConnectionRepository connectionRepository; + @MockBean + private RestClientUtil restClientUtil; + @MockBean + private CacheEvictionService cacheEvictionService; + + private Auth0AuthenticationService authenticationService; + + private final String accessToken = "dummyAccessToken"; + private final String redirectURI = "http://dummyRedirectUri.com"; + private final String userId = "user123"; + private final String connectionId = "conn123"; + private Map authRequest; + + @BeforeEach + public void setUp() { + MockitoAnnotations.openMocks(this); + authRequest = new HashMap<>(); + authRequest.put("access_token", accessToken); + authRequest.put("redirectURI", redirectURI); + + authenticationService = new Auth0AuthenticationService(matchingService, userRepository, basicMailService, userService, connectionRepository, restClientUtil, true, false, "localhost", cacheEvictionService); + } + + // Tests missing parameters in the authentication request + @Test + public void testGetToken_MissingParameters() throws IOException { + assertThrows(IllegalArgumentException.class, () -> { + authenticationService.authenticate(new HashMap<>(), "localhost"); // Empty map should trigger the exception + }); + } + + // Tests the failure in retrieving user information, expecting an IOException to be converted into a NotAuthorizedException + @Test + public void testGetToken_UserInfoRetrievalFails() throws IOException { + when(this.restClientUtil.retrieveGetResponseWithRequestConfiguration(anyString(), any(HttpHeaders.class), anyInt())) + .thenThrow(new NotAuthorizedException("Failed to retrieve user info")); + + assertThrows(NotAuthorizedException.class, () -> { + authenticationService.authenticate(authRequest, "localhost"); + }); + } + + // Tests the scenario where the user ID is not found in the user info retrieved + @Test + public void testGetToken_NoUserIdInUserInfo() throws IOException { + when(this.restClientUtil.retrieveGetResponseWithRequestConfiguration(anyString(), any(), anyInt())) + .thenReturn(new ResponseEntity<>("{}", HttpStatus.OK)); + + assertThrows(NotAuthorizedException.class, () -> { + authenticationService.authenticate(authRequest, "localhost"); + }); + } + + // Tests a successful token retrieval scenario + @Test + public void testGetToken_Successful() throws Exception { + setupSuccessfulTokenRetrievalScenario(); + + // return null for matching user + when(matchingService.matchTokenToUser(any())).thenReturn(null); + + HashMap token = authenticationService.authenticate(authRequest, "localhost"); + assertNotNull(token); + } + + // Additional test to handle retries in user info retrieval + @Test + public void testRetrieveUserInfo_WithRetries() throws Exception { + when(this.restClientUtil.retrieveGetResponseWithRequestConfiguration(anyString(), any(), anyInt())) + .thenThrow(new RuntimeException("Network error")) + .thenReturn(new ResponseEntity<>("{}", HttpStatus.OK)); + // Assuming retrieveUserInfo is accessible, or using reflection if it is private + JsonNode result = authenticationService.retrieveUserInfo(accessToken); + assertNotNull(result); + } + + // Tests matching a token to a user when no existing user is found and an attempt to create a user fails + @Test + public void testGetToken_NoUserMatchingAndCreationFails() throws Exception { + setupNoUserMatchScenario(); + + assertThrows(NotAuthorizedException.class, () -> { + authenticationService.authenticate(authRequest, "localhost"); + }); + } + + // Test scenario where denied access email is triggered + @Test + public void testGetToken_SendDeniedAccessEmail() throws Exception { + setupDeniedEmailScenario(); + this.authenticationService.setDeniedEmailEnabled(true); + try { + authenticationService.authenticate(authRequest, "localhost"); + } catch (Exception e) { + verify(basicMailService).sendDeniedAccessEmail(any()); + } + } + + private void setupSuccessfulTokenRetrievalScenario() throws IOException { + this.authenticationService.setDeniedEmailEnabled(false); + JsonNode mockUserInfo = mock(JsonNode.class); + when(mockUserInfo.get("user_id")).thenReturn(mock(JsonNode.class)); + when(mockUserInfo.get("user_id").asText()).thenReturn(userId); + when(mockUserInfo.get("identities")).thenReturn(mock(JsonNode.class)); + when(mockUserInfo.get("identities").get(0)).thenReturn(mock(JsonNode.class)); + when(mockUserInfo.get("identities").get(0).get("connection")).thenReturn(mock(JsonNode.class)); + when(mockUserInfo.get("identities").get(0).get("connection").asText()).thenReturn(connectionId); + + String validJson = "{" + + "\"user_id\": \"" + userId + "\"," + + "\"identities\": [" + + " {\"connection\": \"" + connectionId + "\"}" + + "]" + + "}"; + + when(restClientUtil.retrieveGetResponseWithRequestConfiguration(anyString(), any(HttpHeaders.class), anyInt())) + .thenReturn(new ResponseEntity<>(validJson, HttpStatus.OK)); + + // Create a test user + Connection connection = new Connection(); + connection.setId(connectionId); + + User user = new User(); + user.setSubject(userId); + user.setConnection(connection); + user.setUuid(UUID.randomUUID()); + + when(connectionRepository.findById(anyString())).thenReturn(Optional.of(connection)); + when(matchingService.matchTokenToUser(any())).thenReturn(user); + when(userRepository.findBySubjectAndConnection(anyString(), any(Connection.class))).thenReturn(user); + when(userService.getUserProfileResponse(any(UserClaims.class))).thenReturn(new HashMap<>()); + } + + private void setupNoUserMatchScenario() throws IOException { + setupSuccessfulTokenRetrievalScenario(); + + when(matchingService.matchTokenToUser(any())).thenReturn(null); + when(userRepository.findBySubjectAndConnection(anyString(), any(Connection.class))).thenReturn(null); + } + + private void setupDeniedEmailScenario() throws Exception { + setupNoUserMatchScenario(); + doThrow(new jakarta.mail.MessagingException("Failed sending email")).when(basicMailService).sendDeniedAccessEmail(any()); + } + +} \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/AuthorizationServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/AuthorizationServiceTest.java new file mode 100644 index 000000000..dcf1ed52b --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/AuthorizationServiceTest.java @@ -0,0 +1,426 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.hms.dbmi.avillach.auth.entity.*; + +import edu.harvard.hms.dbmi.avillach.auth.model.CustomUserDetails; +import edu.harvard.hms.dbmi.avillach.auth.repository.AccessRuleRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserConsentsRepository; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.authorization.AuthorizationService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.authorization.BdcConsentBasedAccessRuleEvaluator; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockitoAnnotations; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.security.authentication.UsernamePasswordAuthenticationToken; +import org.springframework.security.core.context.SecurityContext; +import org.springframework.security.core.context.SecurityContextHolder; +import org.springframework.test.context.ContextConfiguration; + +import java.util.*; + +import static org.junit.jupiter.api.Assertions.assertFalse; +import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.mockito.Mockito.when; + +@SpringBootTest +@ContextConfiguration(classes = {AuthorizationService.class, AccessRuleService.class}) +public class AuthorizationServiceTest { + + @MockBean + private SecurityContext securityContext; + + private AuthorizationService authorizationService; + private AccessRuleService accessRuleService; + + @MockBean + private SessionService sessionService; + + @MockBean + private AccessRuleRepository accessRuleRepository; + + @MockBean + private RoleService roleService; + + @MockBean + private BdcConsentBasedAccessRuleEvaluator bdcConsentBasedAccessRuleEvaluator; + + @MockBean + private UserConsentsRepository userConsentsRepository; + + @BeforeEach + public void setUp() { + MockitoAnnotations.openMocks(this); + SecurityContextHolder.setContext(securityContext); + + accessRuleService = new AccessRuleService(accessRuleRepository, "false", "false", "false", "false", "false", "false"); + authorizationService = new AuthorizationService( + accessRuleService, sessionService, roleService, bdcConsentBasedAccessRuleEvaluator, "fence,okta,open", userConsentsRepository + ); + } + + @Test + public void testIsAuthorized_AccessRulePassed() { + Application application = createTestApplication(); + User user = createTestUser(); + + // create access_rule for privilege + AccessRule accessRule = new AccessRule(); + accessRule.setUuid(UUID.randomUUID()); + accessRule.setRule("$.test"); + accessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + accessRule.setValue("value"); + + // set application and access_rule for all user privileges + for (Privilege privilege1 : user.getRoles().iterator().next().getPrivileges()) { + privilege1.setAccessRules(Collections.singleton(accessRule)); + privilege1.setApplication(application); + } + configureUserSecurityContext(user); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "value"); + requestBody.put("Target Service", "/query"); + + boolean result = authorizationService.isAuthorized(application, requestBody, user, false).result(); + + assertTrue(result); + } + + @Test + public void testIsAuthorized_AccessRuleFailed() { + Application application = createTestApplication(); + User user = createTestUser(); + configureUserSecurityContext(user); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "differentValue"); + + boolean result = authorizationService.isAuthorized(application, requestBody, user, false).result(); + + assertFalse(result); + } + + @Test + public void testEvaluateAccessRule_GatesPassed() { + AccessRule accessRule = new AccessRule(); + accessRule.setRule("$.test"); + accessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + accessRule.setValue("value"); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "value"); + + boolean result = accessRuleService.evaluateAccessRule(requestBody, accessRule); + + assertTrue(result); + } + + @Test + public void testEvaluateAccessRule_GatesFailed() { + AccessRule accessRule = new AccessRule(); + accessRule.setRule("$.test"); + accessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + accessRule.setValue("value"); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "differentValue"); + + boolean result = accessRuleService.evaluateAccessRule(requestBody, accessRule); + + assertFalse(result); + } + + @Test + public void testExtractAndCheckRule_Pass() { + AccessRule accessRule = new AccessRule(); + accessRule.setRule("$.test"); + accessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + accessRule.setValue("value"); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "value"); + + boolean result = accessRuleService.extractAndCheckRule(accessRule, requestBody); + + assertTrue(result); + } + + @Test + public void testExtractAndCheckRule_Fail() { + AccessRule accessRule = new AccessRule(); + accessRule.setRule("$.test"); + accessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + accessRule.setValue("value"); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "differentValue"); + + boolean result = accessRuleService.extractAndCheckRule(accessRule, requestBody); + + assertFalse(result); + } + + @Test + public void testDecisionMaker_Pass() { + AccessRule accessRule = new AccessRule(); + accessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + accessRule.setValue("value"); + + boolean result = accessRuleService.decisionMaker(accessRule, "value"); + + assertTrue(result); + } + + @Test + public void testDecisionMaker_Fail() { + AccessRule accessRule = new AccessRule(); + accessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + accessRule.setValue("value"); + + boolean result = accessRuleService.decisionMaker(accessRule, "differentValue"); + + assertFalse(result); + } + + @Test + public void testIsAuthorized_NoRequestBody() { + Application application = createTestApplication(); + User user = createTestUser(); + configureUserSecurityContext(user); + application.setPrivileges(user.getPrivilegesByApplication(application)); + + boolean result = authorizationService.isAuthorized(application, null, user, false).result(); + + assertTrue(result); + } + + @Test + public void testIsAuthorized_NoPrivileges() { + Application application = createTestApplication(); + User user = createTestUser(); + + user.getRoles().iterator().next().setPrivileges(Collections.emptySet()); + boolean result = authorizationService.isAuthorized(application, new HashMap<>(), user, false).result(); + + assertFalse(result); + } + + @Test + public void testEvaluateAccessRule_NoGates() { + AccessRule accessRule = new AccessRule(); + accessRule.setRule("$.test"); + accessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + accessRule.setValue("value"); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "value"); + + boolean result = accessRuleService.evaluateAccessRule(requestBody, accessRule); + + assertTrue(result); + } + + @Test + public void testEvaluateAccessRule_AllGatesPassed_AND() { + AccessRule gate1 = new AccessRule(); + gate1.setRule("$.test"); + gate1.setType(AccessRule.TypeNaming.ALL_EQUALS); + gate1.setValue("value"); + + AccessRule gate2 = new AccessRule(); + gate2.setRule("$.test2"); + gate2.setType(AccessRule.TypeNaming.ALL_EQUALS); + gate2.setValue("value2"); + + AccessRule accessRule = new AccessRule(); + accessRule.setGates(new HashSet<>(Arrays.asList(gate1, gate2))); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "value"); + requestBody.put("test2", "value2"); + + boolean result = accessRuleService.evaluateAccessRule(requestBody, accessRule); + + assertTrue(result); + } + + @Test + public void testEvaluateAccessRule_OneGateFails_AND() { + AccessRule gate1 = new AccessRule(); + gate1.setRule("$.test"); + gate1.setType(AccessRule.TypeNaming.ALL_EQUALS); + gate1.setValue("value"); + + AccessRule gate2 = new AccessRule(); + gate2.setRule("$.test2"); + gate2.setType(AccessRule.TypeNaming.ALL_EQUALS); + gate2.setValue("value2"); + + AccessRule accessRule = new AccessRule(); + accessRule.setGates(new HashSet<>(Arrays.asList(gate1, gate2))); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "value"); + requestBody.put("test2", "differentValue"); + + boolean result = accessRuleService.evaluateAccessRule(requestBody, accessRule); + + assertFalse(result); + } + + @Test + public void testEvaluateAccessRule_OneGatePassed_OR() { + AccessRule gate1 = new AccessRule(); + gate1.setRule("$.test"); + gate1.setType(AccessRule.TypeNaming.ALL_EQUALS); + gate1.setValue("value"); + + AccessRule gate2 = new AccessRule(); + gate2.setRule("$.test2"); + gate2.setType(AccessRule.TypeNaming.ALL_EQUALS); + gate2.setValue("value2"); + + AccessRule accessRule = new AccessRule(); + accessRule.setGates(new HashSet<>(Arrays.asList(gate1, gate2))); + accessRule.setGateAnyRelation(true); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "value"); + requestBody.put("test2", "differentValue"); + + boolean result = accessRuleService.evaluateAccessRule(requestBody, accessRule); + + assertTrue(result); + } + + @Test + public void testEvaluateAccessRule_AllGatesFail_OR() { + AccessRule gate1 = new AccessRule(); + gate1.setRule("$.test"); + gate1.setType(AccessRule.TypeNaming.ALL_EQUALS); + gate1.setValue("value"); + + AccessRule gate2 = new AccessRule(); + gate2.setRule("$.test2"); + gate2.setType(AccessRule.TypeNaming.ALL_EQUALS); + gate2.setValue("value2"); + + AccessRule accessRule = new AccessRule(); + accessRule.setGates(new HashSet<>(Arrays.asList(gate1, gate2))); + accessRule.setGateAnyRelation(true); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "differentValue"); + requestBody.put("test2", "differentValue"); + + boolean result = accessRuleService.evaluateAccessRule(requestBody, accessRule); + + assertFalse(result); + } + + @Test + public void testEvaluateAccessRule_EvaluateOnlyByGates() { + AccessRule gate1 = new AccessRule(); + gate1.setRule("$.test"); + gate1.setType(AccessRule.TypeNaming.ALL_EQUALS); + gate1.setValue("value"); + + AccessRule accessRule = new AccessRule(); + accessRule.setGates(new HashSet<>(Collections.singletonList(gate1))); + accessRule.setEvaluateOnlyByGates(true); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "value"); + + boolean result = accessRuleService.evaluateAccessRule(requestBody, accessRule); + + assertTrue(result); + } + + @Test + public void testEvaluateAccessRule_SubAccessRules() { + AccessRule subAccessRule = new AccessRule(); + subAccessRule.setRule("$.test2"); + subAccessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + subAccessRule.setValue("value2"); + + AccessRule accessRule = new AccessRule(); + accessRule.setRule("$.test"); + accessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + accessRule.setValue("value"); + accessRule.setSubAccessRule(new HashSet<>(Collections.singletonList(subAccessRule))); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "value"); + requestBody.put("test2", "value2"); + + boolean result = accessRuleService.evaluateAccessRule(requestBody, accessRule); + + assertTrue(result); + } + + private Role createTestRole() { + Role role = new Role(); + role.setName("TEST_ROLE"); + role.setUuid(UUID.randomUUID()); + role.setPrivileges(Collections.singleton(createTestPrivilege())); + return role; + } + + private Privilege createTestPrivilege() { + Privilege privilege = new Privilege(); + privilege.setName("TEST_PRIVILEGE"); + privilege.setUuid(UUID.randomUUID()); + return privilege; + } + + private void configureUserSecurityContext(User user) { + CustomUserDetails customUserDetails = new CustomUserDetails(user); + UsernamePasswordAuthenticationToken authentication = + new UsernamePasswordAuthenticationToken(customUserDetails, null, customUserDetails.getAuthorities()); + when(securityContext.getAuthentication()).thenReturn(authentication); + } + + private Role createSuperAdminRole() { + Role role = new Role(); + role.setName(AuthNaming.AuthRoleNaming.SUPER_ADMIN); + role.setUuid(UUID.randomUUID()); + role.setPrivileges(Collections.singleton(createSuperAdminPrivilege())); + return role; + } + + private Privilege createSuperAdminPrivilege() { + Privilege privilege = new Privilege(); + privilege.setName(AuthNaming.AuthRoleNaming.SUPER_ADMIN); + privilege.setUuid(UUID.randomUUID()); + return privilege; + } + + private User createTestUser() { + User user = new User(); + user.setUuid(UUID.randomUUID()); + user.setRoles(new HashSet<>(Collections.singleton(createTestRole()))); + user.setSubject("TEST_SUBJECT"); + user.setEmail("test@email.com"); + user.setAcceptedTOS(new Date()); + user.setActive(true); + user.setConnection(createTestConnection()); + return user; + } + + private Connection createTestConnection() { + Connection connection = new Connection(); + connection.setLabel("TEST_CONNECTION"); + return connection; + } + + private Application createTestApplication() { + Application application = new Application(); + application.setUuid(UUID.randomUUID()); + application.setName("TEST_APPLICATION"); + application.setPrivileges(new HashSet<>()); + return application; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/BasicMailServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/BasicMailServiceTest.java new file mode 100644 index 000000000..2eac91e59 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/BasicMailServiceTest.java @@ -0,0 +1,93 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import com.fasterxml.jackson.databind.JsonNode; +import com.github.mustachejava.Mustache; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import jakarta.mail.MessagingException; +import jakarta.mail.internet.MimeMessage; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockitoAnnotations; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.mail.javamail.JavaMailSender; +import org.springframework.test.context.ContextConfiguration; + +import static org.junit.jupiter.api.Assertions.assertNull; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.Mockito.*; + +@SpringBootTest +@ContextConfiguration(classes = {BasicMailService.class}) +public class BasicMailServiceTest { + + @MockBean + private JavaMailSender mailSender; + + @MockBean + private Mustache accessTemplate; + + @Autowired + private BasicMailService basicMailService; + + @Value("${application.template.path}") + private String templatePath = "src/test/resources/templates/"; + + @Value("${application.system.name}") + private String systemName = "TestSystem"; + + @Value("${application.access.grant.email.subject}") + private String accessGrantEmailSubject = "Access Granted"; + + @Value("${application.admin.users}") + private String adminUsers = "admin@test.com"; + + @BeforeEach + public void setUp() { + MockitoAnnotations.openMocks(this); + basicMailService = new BasicMailService(mailSender, templatePath, systemName, accessGrantEmailSubject, adminUsers); + } + + @Test + public void testCompileTemplate_FileNotFound() { + Mustache result = basicMailService.compileTemplate("nonExistent.mustache"); + assertNull(result); + } + + @Test + public void testSendUsersAccessEmail_NoTemplate() throws MessagingException { + User user = new User(); + user.setEmail("test@test.com"); + basicMailService.setAccessTemplate(null); + + basicMailService.sendUsersAccessEmail(user); + verify(mailSender, never()).send(any(MimeMessage.class)); + } + + @Test + public void testSendUsersAccessEmail_NoEmail() throws MessagingException { + User user = new User(); + user.setEmail(null); + + basicMailService.sendUsersAccessEmail(user); + verify(mailSender, never()).send(any(MimeMessage.class)); + } + + @Test + public void testSendDeniedAccessEmail_NoTemplate() throws MessagingException { + JsonNode userInfo = mock(JsonNode.class); + basicMailService.setDeniedTemplate(null); + + basicMailService.sendDeniedAccessEmail(userInfo); + verify(mailSender, never()).send(any(MimeMessage.class)); + } + + @Test + public void testSendEmail_EmptyParams() throws MessagingException { + basicMailService.sendEmail(accessTemplate, "", "", new Object()); + verify(mailSender, never()).send(any(MimeMessage.class)); + } + +} \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/CacheTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/CacheTest.java new file mode 100644 index 000000000..2a9c73b2f --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/CacheTest.java @@ -0,0 +1,251 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import com.fasterxml.jackson.core.JsonProcessingException; +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.hms.dbmi.avillach.auth.config.CustomKeyGenerator; +import edu.harvard.hms.dbmi.avillach.auth.entity.Application; +import edu.harvard.hms.dbmi.avillach.auth.entity.Privilege; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import edu.harvard.hms.dbmi.avillach.auth.repository.*; +import edu.harvard.hms.dbmi.avillach.auth.utils.FenceMappingUtility; +import edu.harvard.hms.dbmi.avillach.auth.utils.JWTUtil; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.*; +import org.mockito.junit.jupiter.MockitoExtension; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.cache.Cache; +import org.springframework.cache.CacheManager; +import org.springframework.cache.annotation.EnableCaching; +import org.springframework.cache.concurrent.ConcurrentMapCacheManager; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.context.annotation.Import; +import org.springframework.test.context.ContextConfiguration; + +import java.util.HashSet; +import java.util.Objects; +import java.util.Set; + +import static org.assertj.core.api.Assertions.*; +import static org.mockito.Mockito.*; + +@SpringBootTest +@ExtendWith(MockitoExtension.class) +@ContextConfiguration(classes = {UserService.class, AccessRuleService.class, CustomKeyGenerator.class, CacheEvictionService.class + +}) +@Import(CacheTest.TestCacheConfig.class) +public class CacheTest { + + @MockBean + private AccessRuleRepository accessRuleRepository; + + @MockBean + private BasicMailService basicMailService; + + @MockBean + private TOSService tosService; + + @MockBean + private UserRepository userRepository; + + @MockBean + private ConnectionRepository connectionRepository; + + @MockBean + private ApplicationRepository applicationRepository; + + @MockBean + private RoleService roleService; + + @MockBean + private JWTUtil jwtUtil; + + @MockBean + private SessionService sessionService; + + @MockBean + private UserConsentsRepository userConsentsRepository; + + @MockBean + private FenceMappingUtility fenceMappingUtility; + + @MockBean + private LoggingClient loggingClient; + + @Autowired + private AccessRuleService accessRuleService; + + @Autowired + private UserService userService; + + @Autowired + private CacheEvictionService cacheEvictionService; + + @Autowired + private CacheManager cacheManager; + + @Mock + private User mockUser; + + @Mock + private Application mockApplication; + + @BeforeEach + void setUp() { + MockitoAnnotations.openMocks(this); + Objects.requireNonNull(cacheManager.getCache("mergedRulesCache")).clear(); + Objects.requireNonNull(cacheManager.getCache("preProcessedAccessRules")).clear(); + Objects.requireNonNull(cacheManager.getCache("mergedTemplateCache")).clear(); + } + + @Test + public void testMergedRulesCache() throws JsonProcessingException { + Set mockPrivileges = new HashSet<>(); + when(mockUser.getSubject()).thenReturn("test_subject"); + when(mockUser.getPrivilegesByApplication(mockApplication)).thenReturn(mockPrivileges); + + // First call to the method - should execute the method logic and add the AccessRule set + accessRuleService.getAccessRulesForUserAndApp(mockUser, mockApplication); + verify(mockUser, times(1)).getPrivilegesByApplication(mockApplication); + + // Second call to the method with the same arguments - should hit the cache + accessRuleService.getAccessRulesForUserAndApp(mockUser, mockApplication); + verify(mockUser, times(1)).getPrivilegesByApplication(mockApplication); + } + + @Test + public void testMergedRulesCacheEvict() { + Cache cache = cacheManager.getCache("mergedRulesCache"); + + // Call the method to store the result in the cache + Set mockPrivileges = new HashSet<>(); + when(mockUser.getSubject()).thenReturn("test_subject"); + when(mockUser.getPrivilegesByApplication(mockApplication)).thenReturn(mockPrivileges); + + // First call to the method - should execute the method logic and add the AccessRule set + accessRuleService.getAccessRulesForUserAndApp(mockUser, mockApplication); + assertThat(cache.get("test_subject")).isNotNull(); + + // Evict the test_subject from the cache + accessRuleService.evictFromMergedAccessRuleCache("test_subject"); + assertThat(cache.get("test_subject")).isNull(); + } + + @Test + public void testCachedPreProcessAccessRules() { + when(mockUser.getSubject()).thenReturn("test_subject"); + Set mockedPrivileges = new HashSet<>(); + accessRuleService.cachedPreProcessAccessRules(mockUser, mockedPrivileges); + + Cache preProcessedAccessRules = cacheManager.getCache("preProcessedAccessRules"); + assertThat(preProcessedAccessRules).isNotNull(); + + // Verify the cache contains test_subject cache entry + assertThat(preProcessedAccessRules.get("test_subject")).isNotNull(); + } + + @Test + public void testCacheEvictPreProcessAccessRules() { + when(mockUser.getSubject()).thenReturn("test_subject"); + + Set mockedPrivileges = new HashSet<>(); + accessRuleService.cachedPreProcessAccessRules(mockUser, mockedPrivileges); + + Cache preProcessedAccessRules = cacheManager.getCache("preProcessedAccessRules"); + assertThat(preProcessedAccessRules).isNotNull(); + + // Verify the cache contains test_subject cache entry + assertThat(preProcessedAccessRules.get("test_subject")).isNotNull(); + + accessRuleService.evictFromPreProcessedAccessRules("test_subject"); + assertThat(preProcessedAccessRules.get("test_subject")).isNull(); + } + + @Test + public void testMergedTemplateCache() { + when(mockUser.getSubject()).thenReturn("test_subject"); + + Set mockPrivileges = new HashSet<>(); + when(mockUser.getPrivilegesByApplication(mockApplication)).thenReturn(mockPrivileges); + + // First call to the method - should execute the method logic and add the mergeTemplate + userService.mergeTemplate(mockUser, mockApplication); + verify(mockUser, times(1)).getPrivilegesByApplication(mockApplication); + + // Second call to the method - should be handled by the cache and getPrivilegesByApplication should not be called again + userService.mergeTemplate(mockUser, mockApplication); + verify(mockUser, times(1)).getPrivilegesByApplication(mockApplication); + } + + @Test + public void testCacheEvictMergedTemplateCache() { + when(mockUser.getSubject()).thenReturn("test_subject"); + + Set mockPrivileges = new HashSet<>(); + when(mockUser.getPrivilegesByApplication(mockApplication)).thenReturn(mockPrivileges); + + // First call to the method - should execute the method logic and add the mergeTemplate + userService.mergeTemplate(mockUser, mockApplication); + verify(mockUser, times(1)).getPrivilegesByApplication(mockApplication); + + Cache cache = cacheManager.getCache("mergedTemplateCache"); + assertThat(cache.get("test_subject")).isNotNull(); + + userService.evictFromCache("test_subject"); + assertThat(cache.get("test_subject")).isNull(); + } + + @Test + public void testCacheEvictionService() { + when(mockUser.getSubject()).thenReturn("test_subject"); + Set mockPrivileges = new HashSet<>(); + + when(mockUser.getPrivilegesByApplication(mockApplication)).thenReturn(mockPrivileges); + + // Initialize mergedTemplateCache + userService.mergeTemplate(mockUser, mockApplication); + + // Verify the cache contains mergedTemplateCache has test_subject + Cache mergedTemplateCache = cacheManager.getCache("mergedTemplateCache"); + assertThat(mergedTemplateCache.get("test_subject")).isNotNull(); + + // Initialize preProcessedAccessRules + when(mockUser.getSubject()).thenReturn("test_subject"); + accessRuleService.cachedPreProcessAccessRules(mockUser, mockPrivileges); + Cache preProcessedAccessRules = cacheManager.getCache("preProcessedAccessRules"); + + // Verify the cache contains test_subject cache entry + assertThat(preProcessedAccessRules).isNotNull(); + assertThat(preProcessedAccessRules.get("test_subject")).isNotNull(); + + when(mockUser.getSubject()).thenReturn("test_subject"); + when(mockUser.getPrivilegesByApplication(mockApplication)).thenReturn(mockPrivileges); + + // First call to the method - should execute the method logic and add the AccessRule set + accessRuleService.getAccessRulesForUserAndApp(mockUser, mockApplication); + Cache mergedRulesCache = cacheManager.getCache("mergedRulesCache"); + assertThat(mergedRulesCache).isNotNull(); + assertThat(mergedRulesCache.get("test_subject")).isNotNull(); + + cacheEvictionService.evictCache(mockUser); + assertThat(mergedRulesCache.get("test_subject")).isNull(); + assertThat(preProcessedAccessRules.get("test_subject")).isNull(); + assertThat(mergedTemplateCache.get("test_subject")).isNull(); + } + + @Configuration + @EnableCaching + public static class TestCacheConfig { + + @Bean + public CacheManager cacheManager() { + return new ConcurrentMapCacheManager("mergedRulesCache", "preProcessedAccessRules", "mergedTemplateCache"); + } + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/ConnectionWebServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/ConnectionWebServiceTest.java new file mode 100644 index 000000000..58f5daaa6 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/ConnectionWebServiceTest.java @@ -0,0 +1,134 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Connection; +import edu.harvard.hms.dbmi.avillach.auth.entity.UserMetadataMapping; +import edu.harvard.hms.dbmi.avillach.auth.repository.ConnectionRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserMetadataMappingRepository; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockitoAnnotations; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.test.context.ContextConfiguration; + +import java.util.*; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.ArgumentMatchers.anyList; +import static org.mockito.ArgumentMatchers.anyString; +import static org.mockito.ArgumentMatchers.argThat; +import static org.mockito.Mockito.*; + +@SpringBootTest +@ContextConfiguration(classes = {ConnectionWebService.class}) +public class ConnectionWebServiceTest { + + @MockBean + private ConnectionRepository connectionRepo; + + @MockBean + private UserMetadataMappingRepository userMetadataMappingRepo; + + @Autowired + private ConnectionWebService service; + + @BeforeEach + public void setUp() { + MockitoAnnotations.openMocks(this); + } + + private Connection createMockConnection(String id) { + Connection conn = new Connection(); + conn.setId(id); + conn.setLabel("Test Label"); + conn.setSubPrefix("Test SubPrefix"); + conn.setRequiredFields(String.valueOf(Arrays.asList("field1", "field2"))); + return conn; + } + + @Test + public void testAddConnection_Success() { + Connection conn = createMockConnection(UUID.randomUUID().toString()); + when(connectionRepo.findById(anyString())).thenReturn(Optional.empty()); + when(connectionRepo.saveAll(anyList())).thenReturn(Collections.singletonList(conn)); + + List result = service.addConnection(Collections.singletonList(conn)); + assertFalse(result.isEmpty()); + assertEquals(1, result.size()); + verify(connectionRepo, times(1)).saveAll(anyList()); + verify(userMetadataMappingRepo, times(1)).saveAll(argThat((List mappings) -> { + if (mappings.size() != 1) return false; + UserMetadataMapping m = mappings.get(0); + return "$.email".equals(m.getGeneralMetadataJsonPath()) + && "$.email".equals(m.getAuth0MetadataJsonPath()) + && conn.equals(m.getConnection()); + })); + } + + @Test + public void testAddConnection_FailureDueToNullFields() { + Connection conn = new Connection(); // missing required fields + assertThrows(IllegalArgumentException.class, () -> service.addConnection(Collections.singletonList(conn))); + verify(userMetadataMappingRepo, never()).saveAll(anyList()); + } + + @Test + public void testAddConnection_FailureDueToDuplicateId() { + Connection conn = createMockConnection("123"); + when(connectionRepo.findById("123")).thenReturn(Optional.of(conn)); + + assertThrows(IllegalArgumentException.class, () -> service.addConnection(Collections.singletonList(conn))); + verify(userMetadataMappingRepo, never()).saveAll(anyList()); + } + + @Test + public void testGetConnectionById_Success() { + Connection conn = createMockConnection("123"); + when(connectionRepo.findById("123")).thenReturn(Optional.of(conn)); + + Connection result = service.getConnectionById("123"); + assertNotNull(result); + assertEquals("123", result.getId()); + } + + @Test + public void testGetConnectionById_NotFound() { + when(connectionRepo.findById("123")).thenReturn(Optional.empty()); + assertThrows(IllegalArgumentException.class, () -> service.getConnectionById("123")); + } + + @Test + public void testGetAllConnections() { + Connection conn1 = createMockConnection("123"); + Connection conn2 = createMockConnection("124"); + when(connectionRepo.findAll()).thenReturn(Arrays.asList(conn1, conn2)); + + List results = service.getAllConnections(); + assertNotNull(results); + assertEquals(2, results.size()); + } + + @Test + public void testUpdateConnections() { + Connection conn1 = createMockConnection("123"); + when(connectionRepo.saveAll(anyList())).thenReturn(Collections.singletonList(conn1)); + + List results = service.updateConnections(Collections.singletonList(conn1)); + assertNotNull(results); + assertEquals(1, results.size()); + assertEquals("123", results.get(0).getId()); + } + + @Test + public void testRemoveConnectionById() { + doNothing().when(connectionRepo).deleteById("123"); + when(connectionRepo.findAll()).thenReturn(Collections.emptyList()); + + List results = service.removeConnectionById("123"); + assertTrue(results.isEmpty()); + verify(connectionRepo, times(1)).deleteById("123"); + verify(connectionRepo, times(1)).findAll(); + } + +} \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/CustomUserDetailServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/CustomUserDetailServiceTest.java new file mode 100644 index 000000000..ef2ab48e9 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/CustomUserDetailServiceTest.java @@ -0,0 +1,94 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Application; +import edu.harvard.hms.dbmi.avillach.auth.entity.Privilege; +import edu.harvard.hms.dbmi.avillach.auth.entity.Role; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; + +import edu.harvard.hms.dbmi.avillach.auth.model.CustomApplicationDetails; +import edu.harvard.hms.dbmi.avillach.auth.model.CustomUserDetails; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockitoAnnotations; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.security.core.userdetails.UserDetails; +import org.springframework.security.core.userdetails.UsernameNotFoundException; +import org.springframework.test.context.ContextConfiguration; + +import java.util.Optional; +import java.util.Set; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.when; + +@SpringBootTest +@ContextConfiguration(classes = {CustomUserDetailService.class}) +public class CustomUserDetailServiceTest { + + @MockBean + private UserService userService; + + @MockBean + private ApplicationService applicationService; + + @Autowired + private CustomUserDetailService customUserDetailService; + + @BeforeEach + public void setUp() { + MockitoAnnotations.openMocks(this); + } + + @Test + public void loadUserByUsername_withApplication_success() { + String applicationName = "testApp"; + Application application = new Application(); + application.setPrivileges(null); // Set the required fields as needed + when(applicationService.getApplicationByIdWithPrivileges(applicationName)).thenReturn(Optional.of(application)); + + UserDetails userDetails = customUserDetailService.loadUserByUsername("application:" + applicationName); + assertNotNull(userDetails); + assertInstanceOf(CustomApplicationDetails.class, userDetails); + } + + @Test + public void loadUserByUsername_withApplication_notFound() { + when(applicationService.getApplicationByIdWithPrivileges("invalidApp")).thenReturn(Optional.empty()); + + assertThrows(UsernameNotFoundException.class, () -> + customUserDetailService.loadUserByUsername("application:invalidApp")); + } + + @Test + public void loadUserByUsername_withUser_success() { + String username = "user@example.com"; + User user = new User(); + // Set roles for the user + Role role = new Role(); + role.setUuid(java.util.UUID.randomUUID()); + role.setName(AuthNaming.AuthRoleNaming.ADMIN); + user.setRoles(Set.of(role)); + + Privilege privilege = new Privilege(); + privilege.setUuid(java.util.UUID.randomUUID()); + privilege.setName("testPrivilege"); + role.setPrivileges(Set.of(privilege)); + + when(userService.findBySubject(username)).thenReturn(user); + + UserDetails userDetails = customUserDetailService.loadUserByUsername(username); + assertNotNull(userDetails); + assertInstanceOf(CustomUserDetails.class, userDetails); + } + + @Test + public void loadUserByUsername_withUser_notFound() { + when(userService.findBySubject("nonexistent@example.com")).thenReturn(null); + + assertThrows(UsernameNotFoundException.class, () -> + customUserDetailService.loadUserByUsername("nonexistent@example.com")); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/PrivilegeServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/PrivilegeServiceTest.java new file mode 100644 index 000000000..9c95e5e40 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/PrivilegeServiceTest.java @@ -0,0 +1,152 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Privilege; +import edu.harvard.hms.dbmi.avillach.auth.repository.PrivilegeRepository; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockitoAnnotations; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.security.core.Authentication; +import org.springframework.security.core.context.SecurityContext; +import org.springframework.security.core.context.SecurityContextHolder; +import org.springframework.test.context.ContextConfiguration; + +import java.util.Arrays; +import java.util.List; +import java.util.Optional; +import java.util.UUID; + +import static edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming.AuthRoleNaming.ADMIN; +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + +@SpringBootTest +@ContextConfiguration(classes = {PrivilegeService.class}) +public class PrivilegeServiceTest { + + @MockBean + private PrivilegeRepository privilegeRepository; + + @MockBean + private SecurityContext securityContext; + + @MockBean + private Authentication authentication; + + @MockBean + private ApplicationService applicationService; + + @MockBean + private AccessRuleService accessRuleService; + + @Autowired + private PrivilegeService privilegeService; + + @BeforeEach + public void setUp() { + MockitoAnnotations.openMocks(this); + SecurityContextHolder.setContext(securityContext); + when(securityContext.getAuthentication()).thenReturn(authentication); + } + + @Test + public void testDeletePrivilegeByPrivilegeId_Success() { + UUID privilegeId = UUID.randomUUID(); + Privilege privilege = new Privilege(); + privilege.setUuid(privilegeId); + privilege.setName("USER_PRIVILEGE"); + + when(privilegeRepository.findById(privilegeId)).thenReturn(Optional.of(privilege)); + when(authentication.getName()).thenReturn("testUser"); + + List privileges = Arrays.asList(new Privilege(), new Privilege()); + when(privilegeRepository.findAll()).thenReturn(privileges); + + List result = privilegeService.deletePrivilegeByPrivilegeId(privilegeId.toString()); + + assertEquals(privileges, result); + verify(privilegeRepository, times(1)).deleteById(privilegeId); + verify(privilegeRepository, times(2)).findAll(); + } + + @Test + public void testDeletePrivilegeByPrivilegeId_AdminPrivilege() { + UUID privilegeId = UUID.randomUUID(); + Privilege privilege = new Privilege(); + privilege.setUuid(privilegeId); + privilege.setName(ADMIN); + + when(privilegeRepository.findById(privilegeId)).thenReturn(Optional.of(privilege)); + when(authentication.getName()).thenReturn("testUser"); + + assertThrows(RuntimeException.class, () -> { + privilegeService.deletePrivilegeByPrivilegeId(privilegeId.toString()); + }); + } + + @Test + public void testUpdatePrivileges() { + List privileges = Arrays.asList(new Privilege(), new Privilege()); + + when(privilegeRepository.saveAll(privileges)).thenReturn(privileges); + when(privilegeRepository.findAll()).thenReturn(privileges); + + List result = privilegeService.updatePrivileges(privileges); + + assertEquals(privileges, result); + verify(privilegeRepository, times(1)).saveAll(privileges); + verify(privilegeRepository, times(1)).findAll(); + } + + @Test + public void testAddPrivileges() { + List privileges = Arrays.asList(new Privilege(), new Privilege()); + + when(privilegeRepository.saveAll(privileges)).thenReturn(privileges); + + List result = privilegeService.addPrivileges(privileges); + + assertEquals(privileges, result); + verify(privilegeRepository, times(1)).saveAll(privileges); + } + + @Test + public void testGetPrivilegesAll() { + List privileges = Arrays.asList(new Privilege(), new Privilege()); + + when(privilegeRepository.findAll()).thenReturn(privileges); + + List result = privilegeService.getPrivilegesAll(); + + assertEquals(privileges, result); + verify(privilegeRepository, times(1)).findAll(); + } + + @Test + public void testGetPrivilegeById_Found() { + UUID privilegeId = UUID.randomUUID(); + Privilege privilege = new Privilege(); + privilege.setUuid(privilegeId); + + when(privilegeRepository.findById(privilegeId)).thenReturn(Optional.of(privilege)); + + Privilege result = privilegeService.getPrivilegeById(privilegeId.toString()); + + assertEquals(privilege, result); + verify(privilegeRepository, times(1)).findById(privilegeId); + } + + @Test + public void testGetPrivilegeById_NotFound() { + UUID privilegeId = UUID.randomUUID(); + + when(privilegeRepository.findById(privilegeId)).thenReturn(Optional.empty()); + + Privilege result = privilegeService.getPrivilegeById(privilegeId.toString()); + + assertNull(result); + verify(privilegeRepository, times(1)).findById(privilegeId); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/RASPassPortServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/RASPassPortServiceTest.java new file mode 100644 index 000000000..7187a8085 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/RASPassPortServiceTest.java @@ -0,0 +1,282 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.hms.dbmi.avillach.auth.enums.PassportValidationResponse; +import edu.harvard.hms.dbmi.avillach.auth.model.ras.Ga4ghPassportV1; +import edu.harvard.hms.dbmi.avillach.auth.model.ras.Passport; +import edu.harvard.hms.dbmi.avillach.auth.model.ras.RasDbgapPermission; +import edu.harvard.hms.dbmi.avillach.auth.utils.JWTUtil; +import edu.harvard.hms.dbmi.avillach.auth.utils.RestClientUtil; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.ContextConfiguration; + +import java.time.Instant; +import java.util.*; +import java.util.concurrent.atomic.AtomicInteger; +import java.util.stream.Collectors; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.Mockito.when; + +@SpringBootTest +@ContextConfiguration(classes = {RASPassPortService.class}) +public class RASPassPortServiceTest { + + @MockBean + private RestClientUtil restClientUtil; + @MockBean + private CacheEvictionService cacheEvictionService; + @MockBean + private UserService userService; + @MockBean + private LoggingClient loggingClient; + + private RASPassPortService rasPassPortService; + + private String visa; + + @BeforeEach + public void setUp() throws Exception { + this.rasPassPortService = new RASPassPortService(restClientUtil, null, "https://test.com/", cacheEvictionService, null); + + // Parse the passport and get the visa so we can mock the validateVisa method + Optional passport = JWTUtil.parsePassportJWTV11(exampleRasPassport); + this.visa = passport.get().getGa4ghPassportV1().get(0); + + } + + private static final String exampleRasPassport = + "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6ImRlZmF1bHRfc3NsX2tleSJ9.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.sJwAZeR8cYyF-BCluC9fmiQAi14L7hC3DB4MoFQNNdoakUBujPZ-NlpfP2rBgJQ3CGcxsF95Vdczm6Yk4TKa68eXkKjkswjsSSQg0qErgFhN2jis9KMxnMfmfPNUfb0lioHtD-_oghRkd9239oUwLR06KB5Ux3mD4Pc0ZPbJxJcPmyP9DZ8WEHmAFIJpcoayHwJDr1jt-GbqUtaTCs1VQ9Habh8Z8fvwrlvQNj744m5eq6141bD0G15KgvbyYf9L4_PYNgMjTyUx9EGyetrxQ4XmOpDF_ZbFEhZliy80qfO2HGQzSId-dKXCvPI_SUWcCVeJqPwmXTirTt9qJ63ypw"; + + // Passport with two visas: LinkedIdentities (no ras_dbgap_permissions) + RAS dbGaP (with 2 permissions) + private static final String multiVisaPassportWithPermissions = "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6InRlc3Qta2V5In0" + + ".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" // gitleaks:allow + + ".fakesignature"; + + // Passport with two visas: LinkedIdentities (no ras_dbgap_permissions) + RAS dbGaP (empty permissions) + private static final String multiVisaPassportWithEmptyPermissions = "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6InRlc3Qta2V5In0" + + ".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" // gitleaks:allow + + ".fakesignature"; + + @Test + public void testGa4ghPassPortStudies_IsNull() { + Set permissions = rasPassPortService.ga4ghPassportToRasDbgapPermissions(null); + assertNull(permissions); + } + + @Test + public void testGa4gpPassportStudies_IsNotNull_And_ExpiredPermissionsExcluded() { + Optional passport = JWTUtil.parsePassportJWTV11(exampleRasPassport); + Set> ga4ghPassports = passport.get().getGa4ghPassportV1().stream().map(JWTUtil::parseGa4ghPassportV1) + .filter(Optional::isPresent).collect(Collectors.toSet()); + Set permissions = rasPassPortService.ga4ghPassportToRasDbgapPermissions(ga4ghPassports); + assertNotNull(permissions); + assertTrue(permissions.isEmpty()); + } + + @Test + public void testGa4gpPassportStudies_HasCorrectStudies() { + Optional passport = JWTUtil.parsePassportJWTV11(exampleRasPassport); + long futureDate = (Instant.now().toEpochMilli() / 1000) + 100000; + + // Update the expiry date of each permission in our test passport. All permissions in the example passport + // expired in 2022. + Set> ga4ghPassports = passport.get().getGa4ghPassportV1().stream().map(JWTUtil::parseGa4ghPassportV1) + .filter(Optional::isPresent).map(optionalPassport -> { + Ga4ghPassportV1 ga4ghPassportV1 = optionalPassport.get(); + List rasDbgapPermissions = ga4ghPassportV1.getRasDbgagPermissions(); + List newExpires = + rasDbgapPermissions.stream().peek(rasDbgapPermission -> rasDbgapPermission.setExpiration(futureDate)).toList(); + ga4ghPassportV1.setRasDbgapPermissions(newExpires); + return Optional.of(ga4ghPassportV1); + }).collect(Collectors.toSet()); + + Set permissions = rasPassPortService.ga4ghPassportToRasDbgapPermissions(ga4ghPassports); + + assertEquals(2, permissions.size()); + assertTrue(permissions.stream().anyMatch(p -> p.getPhsId().equals("phs000300"))); + assertTrue(permissions.stream().anyMatch(p -> p.getPhsId().equals("phs000006"))); + } + + @Test + public void testGa4gpPassportStudies_HalfAreExpired() { + Optional passport = JWTUtil.parsePassportJWTV11(exampleRasPassport); + long futureDate = (Instant.now().toEpochMilli() / 1000) + 100000; + long pastDate = (Instant.now().toEpochMilli() / 1000) - 100000; + + List expiredPHS = new ArrayList<>(); + List validPHS = new ArrayList<>(); + // Update the expiry date of each permission in our test passport. + // We alternate: even-indexed permissions become valid, odd-indexed ones remain (or become) invalid. + Set> ga4ghPassports = passport.get().getGa4ghPassportV1().stream().map(JWTUtil::parseGa4ghPassportV1) + .filter(Optional::isPresent).map(optionalPassport -> { + Ga4ghPassportV1 ga4ghPassportV1 = optionalPassport.get(); + List rasDbgapPermissions = ga4ghPassportV1.getRasDbgagPermissions(); + + AtomicInteger index = new AtomicInteger(); + List updatedPermissions = rasDbgapPermissions.stream().peek(permission -> { + if (index.getAndIncrement() % 2 == 0) { + // For even indices, use a valid future expiration. + permission.setExpiration(futureDate); + validPHS.add(permission.getPhsId()); + } else { + // For odd indices, use an expired (invalid) timestamp. + permission.setExpiration(pastDate); + expiredPHS.add(permission.getPhsId()); + } + }).collect(Collectors.toList()); + + ga4ghPassportV1.setRasDbgapPermissions(updatedPermissions); + return Optional.of(ga4ghPassportV1); + }).collect(Collectors.toSet()); + + // Convert the GA4GH passports to RAS DbGaP permissions. The underlying conversion + // should filter out the ones with invalid expiration dates. + Set permissions = rasPassPortService.ga4ghPassportToRasDbgapPermissions(ga4ghPassports); + + // We expect only the valid (future-dated) permissions to be returned. + assertEquals(validPHS.size(), permissions.size()); + + // verify only expected values are in permissions set + List finalPHS = permissions.stream().map(RasDbgapPermission::getPhsId).toList(); + assertEquals(finalPHS, validPHS, "The valid phs ids do not match the expected values."); + + // verify no expired permissions are in the passport. + expiredPHS + .forEach(phs -> assertFalse(finalPHS.contains(phs), "Expired phs id " + phs + " should not appear in the valid permissions.")); + } + + + @Test + public void testValidateVisa_Valid() { + when(restClientUtil.retrievePostResponse(any(String.class), any())).thenReturn(new ResponseEntity<>("Valid", HttpStatus.OK)); + Optional response = rasPassPortService.validateVisa(visa); + assertTrue(response.isPresent()); + assertEquals(PassportValidationResponse.VALID.getValue(), response.get()); + } + + @Test + public void testValidateVisa_Invalid() { + when(restClientUtil.retrievePostResponse(any(String.class), any())).thenReturn(new ResponseEntity<>("Invalid", HttpStatus.OK)); + Optional response = rasPassPortService.validateVisa(visa); + assertTrue(response.isPresent()); + assertEquals(PassportValidationResponse.INVALID.getValue(), response.get()); + } + + @Test + public void testValidateVisa_Missing() { + when(restClientUtil.retrievePostResponse(any(String.class), any())).thenReturn(new ResponseEntity<>("Missing", HttpStatus.OK)); + Optional response = rasPassPortService.validateVisa(visa); + assertTrue(response.isPresent()); + assertEquals(PassportValidationResponse.MISSING.getValue(), response.get()); + } + + @Test + public void testValidatePassport_InvalidVisa() { + when(restClientUtil.retrievePostResponse(any(String.class), any())) + .thenReturn(new ResponseEntity<>("Invalid Passport", HttpStatus.OK)); + Optional response = rasPassPortService.validateVisa(visa); + assertTrue(response.isPresent()); + assertEquals(PassportValidationResponse.INVALID_PASSPORT.getValue(), response.get()); + } + + @Test + public void testValidateVisa_VisaExpired() { + when(restClientUtil.retrievePostResponse(any(String.class), any())).thenReturn(new ResponseEntity<>("Visa Expired", HttpStatus.OK)); + Optional response = rasPassPortService.validateVisa(visa); + assertTrue(response.isPresent()); + assertEquals(PassportValidationResponse.VISA_EXPIRED.getValue(), response.get()); + } + + @Test + public void testValidateVisa_TxnError() { + when(restClientUtil.retrievePostResponse(any(String.class), any())).thenReturn(new ResponseEntity<>("Txn Error", HttpStatus.OK)); + Optional response = rasPassPortService.validateVisa(visa); + assertTrue(response.isPresent()); + assertEquals(PassportValidationResponse.TXN_ERROR.getValue(), response.get()); + } + + @Test + public void testValidateVisa_ExpirationError() { + when(restClientUtil.retrievePostResponse(any(String.class), any())) + .thenReturn(new ResponseEntity<>("Expiration Error", HttpStatus.OK)); + Optional response = rasPassPortService.validateVisa(visa); + assertTrue(response.isPresent()); + assertEquals(PassportValidationResponse.EXPIRATION_ERROR.getValue(), response.get()); + } + + @Test + public void testValidateVisa_ValidationError() { + when(restClientUtil.retrievePostResponse(any(String.class), any())) + .thenReturn(new ResponseEntity<>("Validation Error", HttpStatus.OK)); + Optional response = rasPassPortService.validateVisa(visa); + assertTrue(response.isPresent()); + assertEquals(PassportValidationResponse.VALIDATION_ERROR.getValue(), response.get()); + } + + @Test + public void testValidateVisa_ExpiredPolling() { + when(restClientUtil.retrievePostResponse(any(String.class), any())) + .thenReturn(new ResponseEntity<>("Expired Polling", HttpStatus.OK)); + Optional response = rasPassPortService.validateVisa(visa); + assertTrue(response.isPresent()); + assertEquals(PassportValidationResponse.EXPIRED_POLLING.getValue(), response.get()); + } + + @Test + public void testValidateVisa_PermissionUpdate() { + when(restClientUtil.retrievePostResponse(any(String.class), any())) + .thenReturn(new ResponseEntity<>("Permission Update", HttpStatus.OK)); + Optional response = rasPassPortService.validateVisa(visa); + assertTrue(response.isPresent()); + assertEquals(PassportValidationResponse.PERMISSION_UPDATE.getValue(), response.get()); + } + + @Test + public void testMultiVisaPassport_LinkedIdentitiesVisaHasNoPermissions_DoesNotThrowNPE() { + Optional passport = JWTUtil.parsePassportJWTV11(multiVisaPassportWithEmptyPermissions); + assertTrue(passport.isPresent()); + assertEquals(2, passport.get().getGa4ghPassportV1().size()); + + Set> ga4ghPassports = passport.get().getGa4ghPassportV1().stream().map(JWTUtil::parseGa4ghPassportV1) + .filter(Optional::isPresent).collect(Collectors.toSet()); + + // Should not throw NPE even though LinkedIdentities visa has no ras_dbgap_permissions + Set permissions = rasPassPortService.ga4ghPassportToRasDbgapPermissions(ga4ghPassports); + assertNotNull(permissions); + assertTrue(permissions.isEmpty()); + } + + @Test + public void testMultiVisaPassport_WithPermissions_ReturnsCorrectStudies() { + Optional passport = JWTUtil.parsePassportJWTV11(multiVisaPassportWithPermissions); + assertTrue(passport.isPresent()); + assertEquals(2, passport.get().getGa4ghPassportV1().size()); + + long futureDate = (Instant.now().toEpochMilli() / 1000) + 100000; + + Set> ga4ghPassports = passport.get().getGa4ghPassportV1().stream().map(JWTUtil::parseGa4ghPassportV1) + .filter(Optional::isPresent).map(optionalPassport -> { + Ga4ghPassportV1 ga4ghPassportV1 = optionalPassport.get(); + List rasDbgapPermissions = ga4ghPassportV1.getRasDbgagPermissions(); + List newExpires = + rasDbgapPermissions.stream().peek(rasDbgapPermission -> rasDbgapPermission.setExpiration(futureDate)).toList(); + ga4ghPassportV1.setRasDbgapPermissions(newExpires); + return Optional.of(ga4ghPassportV1); + }).collect(Collectors.toSet()); + + Set permissions = rasPassPortService.ga4ghPassportToRasDbgapPermissions(ga4ghPassports); + + // Only the dbGaP visa has permissions - LinkedIdentities visa has none + assertEquals(2, permissions.size()); + assertTrue(permissions.stream().anyMatch(p -> p.getPhsId().equals("phs000007"))); + assertTrue(permissions.stream().anyMatch(p -> p.getPhsId().equals("phs000179"))); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/RoleServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/RoleServiceTest.java new file mode 100644 index 000000000..d35b1b64f --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/RoleServiceTest.java @@ -0,0 +1,269 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.hms.dbmi.avillach.auth.entity.Privilege; +import edu.harvard.hms.dbmi.avillach.auth.entity.Role; + +import edu.harvard.hms.dbmi.avillach.auth.model.ras.RasDbgapPermission; +import edu.harvard.hms.dbmi.avillach.auth.repository.PrivilegeRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.RoleRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserRepository; +import edu.harvard.hms.dbmi.avillach.auth.utils.FenceMappingUtility; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockitoAnnotations; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.security.core.Authentication; +import org.springframework.security.core.context.SecurityContext; +import org.springframework.security.core.context.SecurityContextHolder; +import org.springframework.test.context.ContextConfiguration; + +import java.util.*; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.Mockito.*; + +@SpringBootTest +@ContextConfiguration(classes = {RoleService.class, PrivilegeService.class, UserRepository.class}) +public class RoleServiceTest { + + @MockBean + private UserRepository userRepository; + + @MockBean + private ApplicationService applicationService; + + @MockBean + private AccessRuleService accessRuleService; + + @MockBean + private RoleRepository roleRepository; + + @MockBean + private PrivilegeRepository privilegeRepo; + + @MockBean + private SecurityContext securityContext; + + @MockBean + private Authentication authentication; + + @MockBean + private FenceMappingUtility fenceMappingUtility; + + @MockBean + private LoggingClient loggingClient; + + @Autowired + private RoleService roleService; + + @Autowired + private PrivilegeService privilegeService; + + @BeforeEach + public void setUp() { + MockitoAnnotations.openMocks(this); + SecurityContextHolder.setContext(securityContext); + when(securityContext.getAuthentication()).thenReturn(authentication); + } + + @Test + public void testGetRoleById_String() { + UUID roleId = UUID.randomUUID(); + Role role = new Role(); + role.setUuid(roleId); + + when(roleRepository.findById(roleId)).thenReturn(Optional.of(role)); + + Optional result = roleService.getRoleById(roleId.toString()); + + assertTrue(result.isPresent()); + assertEquals(role, result.get()); + verify(roleRepository, times(1)).findById(roleId); + } + + @Test + public void testGetRoleById_UUID() { + UUID roleId = UUID.randomUUID(); + Role role = new Role(); + role.setUuid(roleId); + + when(roleRepository.findById(roleId)).thenReturn(Optional.of(role)); + + Optional result = roleService.getRoleById(roleId); + + assertTrue(result.isPresent()); + assertEquals(role, result.get()); + verify(roleRepository, times(1)).findById(roleId); + } + + @Test + public void testGetAllRoles() { + List roles = Arrays.asList(new Role(), new Role()); + + when(roleRepository.findAll()).thenReturn(roles); + + List result = roleService.getAllRoles(); + + assertEquals(roles, result); + verify(roleRepository, times(1)).findAll(); + } + + @Test + public void testAddRoles() { + List roles = Arrays.asList(new Role(), new Role()); + + when(roleRepository.saveAll(roles)).thenReturn(roles); + + List result = roleService.addRoles(roles); + + assertEquals(roles, result); + verify(roleRepository, times(1)).saveAll(roles); + } + + @Test + public void testAddRoles_PrivilegeNotFound() { + Role role = new Role(); + Privilege privilege = new Privilege(); + privilege.setUuid(UUID.randomUUID()); + role.setPrivileges(new HashSet<>(Collections.singletonList(privilege))); + + when(privilegeRepo.findById(privilege.getUuid())).thenReturn(Optional.empty()); + + assertThrows(RuntimeException.class, () -> { + roleService.addRoles(Collections.singletonList(role)); + }); + } + + @Test + public void testUpdateRoles() { + List roles = Arrays.asList(new Role(), new Role()); + + when(roleRepository.saveAll(roles)).thenReturn(roles); + + List result = roleService.updateRoles(roles); + + assertEquals(roles, result); + verify(roleRepository, times(1)).saveAll(roles); + } + + @Test + public void testUpdateRoles_PrivilegeNotFound() { + Role role = new Role(); + Privilege privilege = new Privilege(); + privilege.setUuid(UUID.randomUUID()); + role.setPrivileges(new HashSet<>(Collections.singletonList(privilege))); + + when(privilegeRepo.findById(privilege.getUuid())).thenReturn(Optional.empty()); + + assertThrows(RuntimeException.class, () -> { + roleService.updateRoles(Collections.singletonList(role)); + }); + } + + @Test + public void testRemoveRoleById_Success() { + Role role = new Role(); + UUID roleId = UUID.randomUUID(); + role.setUuid(roleId); + role.setName("Test Role"); + role.setDescription("Test Description"); + + when(roleRepository.findById(roleId)).thenReturn(Optional.of(role)); + when(roleRepository.findAll()).thenReturn(Collections.singletonList(role)); + + Optional> result = roleService.removeRoleById(roleId.toString()); + + assertTrue(result.isPresent()); + assertEquals(1, result.get().size()); + verify(roleRepository, times(1)).deleteById(roleId); + verify(roleRepository, times(1)).findAll(); + } + + @Test + public void testRemoveRoleById_RoleNotFound() { + UUID roleId = UUID.randomUUID(); + + when(roleRepository.findById(roleId)).thenReturn(Optional.empty()); + + Optional> result = roleService.removeRoleById(roleId.toString()); + + assertFalse(result.isPresent()); + verify(roleRepository, never()).deleteById(any()); + } + + @Test + public void testAddObjectToSet_RoleExists() { + Set roles = new HashSet<>(); + Role role = new Role(); + role.setUuid(UUID.randomUUID()); + + when(roleRepository.findById(role.getUuid())).thenReturn(Optional.of(role)); + + roleService.addObjectToSet(roles, role); + + assertTrue(roles.contains(role)); + } + + @Test + public void testAddObjectToSet_RoleNotFound() { + Set roles = new HashSet<>(); + Role role = new Role(); + role.setUuid(UUID.randomUUID()); + + when(roleRepository.findById(role.getUuid())).thenReturn(Optional.empty()); + assertThrows(RuntimeException.class, () -> { + roleService.addObjectToSet(roles, role); + }); + } + + @Test + public void getRoleNamesForDbgapPermissions_PermissionsAreNull() { + Set rolesForDbgapPermissions = roleService.getRoleNamesForDbgapPermissions(null); + assertNotNull(rolesForDbgapPermissions); + assertTrue(rolesForDbgapPermissions.isEmpty()); + } + + @Test + public void getRoleNamesForDbgapPermissions_PermissionsEmpty() { + Set rasDbgapPermissions = new HashSet<>(); + Set rolesForDbgapPermissions = roleService.getRoleNamesForDbgapPermissions(rasDbgapPermissions); + assertNotNull(rolesForDbgapPermissions); + assertTrue(rolesForDbgapPermissions.isEmpty()); + } + + @Test + public void getRoleNamesForDbgapPermissions() { + // {consentName='General Research Use', phsId='phs000006', version='v1', participantSet='p1', consentGroup='c1', role='pi', expiration=1641013200}, + // RasDbgapPermission{consentName='Exchange Area', phsId='phs000300', version='v1', participantSet='p1', consentGroup='c999', role='pi', expiration=1641013200} + RasDbgapPermission rasDbgapPermissionV1 = new RasDbgapPermission(); + rasDbgapPermissionV1.setRole("pi"); + rasDbgapPermissionV1.setConsentGroup("c1"); + rasDbgapPermissionV1.setConsentName("General Research Use"); + rasDbgapPermissionV1.setExpiration(1641013200); + rasDbgapPermissionV1.setParticipantSet("p1"); + rasDbgapPermissionV1.setPhsId("phs000006"); + rasDbgapPermissionV1.setVersion("v1"); + + RasDbgapPermission rasDbgapPermissionV2 = new RasDbgapPermission(); + rasDbgapPermissionV2.setRole("pi"); + rasDbgapPermissionV2.setConsentGroup("c1"); + rasDbgapPermissionV2.setConsentName("Exchange Area"); + rasDbgapPermissionV2.setExpiration(1641013200); + rasDbgapPermissionV2.setParticipantSet("p1"); + rasDbgapPermissionV2.setPhsId("phs000300"); + rasDbgapPermissionV2.setVersion("v1"); + + Set rasDbgapPermissions = new HashSet<>(); + rasDbgapPermissions.add(rasDbgapPermissionV1); + rasDbgapPermissions.add(rasDbgapPermissionV2); + + Set rolesForDbgapPermissions = roleService.getRoleNamesForDbgapPermissions(rasDbgapPermissions); + assertNotNull(rolesForDbgapPermissions); + System.out.println(rolesForDbgapPermissions); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/StudyAccessServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/StudyAccessServiceTest.java new file mode 100644 index 000000000..88cef9f84 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/StudyAccessServiceTest.java @@ -0,0 +1,71 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.hms.dbmi.avillach.auth.model.fenceMapping.StudyMetaData; +import edu.harvard.hms.dbmi.avillach.auth.utils.FenceMappingUtility; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockitoAnnotations; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.test.context.ContextConfiguration; + +import java.util.Map; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.mockito.Mockito.when; + +@SpringBootTest +@ContextConfiguration(classes = {StudyAccessService.class}) +public class StudyAccessServiceTest { + + @Autowired + private StudyAccessService studyAccessService; + + @MockBean + private RoleService roleService; + + @MockBean + private FenceMappingUtility fenceMappingUtility; + + @BeforeEach + public void init() { + MockitoAnnotations.openMocks(this); + } + + + @Test + public void testAddStudyAccessWithBlankIdentifier() { + String studyIdentifier = ""; + String status = studyAccessService.addStudyAccess(studyIdentifier); + assertEquals("Error: Study identifier cannot be blank", status); + } + + @Test + public void testAddStudyAccess() { + String studyIdentifier = "testStudy"; + StudyMetaData studyMetaData = new StudyMetaData(); + studyMetaData.setStudyIdentifier(studyIdentifier); + studyMetaData.setConsentGroupCode(""); + + when(fenceMappingUtility.getFENCEMapping()).thenReturn(Map.of(studyIdentifier, studyMetaData)); + when(roleService.upsertRole(null, "MANUAL_testStudy", "MANUAL_ role MANUAL_testStudy")).thenReturn(true); + + String status = studyAccessService.addStudyAccess(studyIdentifier); + assertEquals("Role 'MANUAL_testStudy' successfully created", status); + } + + @Test + public void testAddStudyAccessWithConsent() { + String studyIdentifier = "testStudy2.c2"; + StudyMetaData studyMetaData = new StudyMetaData(); + studyMetaData.setStudyIdentifier("testStudy2"); + studyMetaData.setConsentGroupCode("c2"); + + when(fenceMappingUtility.getFENCEMapping()).thenReturn(Map.of(studyIdentifier, studyMetaData)); + when(roleService.upsertRole(null, "MANUAL_testStudy2_c2", "MANUAL_ role MANUAL_testStudy2_c2")).thenReturn(true); + + String status = studyAccessService.addStudyAccess(studyIdentifier); + assertEquals("Role 'MANUAL_testStudy2_c2' successfully created", status); + } +} \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/TOSServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/TOSServiceTest.java new file mode 100644 index 000000000..1b7a08f72 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/TOSServiceTest.java @@ -0,0 +1,206 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.hms.dbmi.avillach.auth.entity.TermsOfService; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import edu.harvard.hms.dbmi.avillach.auth.repository.TermsOfServiceRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserRepository; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockitoAnnotations; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.test.context.ContextConfiguration; + +import java.util.Date; +import java.util.Optional; +import java.util.UUID; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.ArgumentMatchers.anyString; +import static org.mockito.Mockito.when; + +@SpringBootTest +@ContextConfiguration(classes = {TOSService.class}) +public class TOSServiceTest { + + @MockBean + private TermsOfServiceRepository termsOfServiceRepo; + + @MockBean + private UserRepository userRepo; + + private TOSService tosService; + + @BeforeEach + public void setUp() { + MockitoAnnotations.openMocks(this); + tosService = new TOSService(termsOfServiceRepo, userRepo, true); + } + + @Test + public void testHasUserAcceptedLatest_TOSDisabled() { + TOSService service = new TOSService(termsOfServiceRepo, userRepo, false); + + boolean result = service.hasUserAcceptedLatest("user-id"); + assertTrue(result); + } + + @Test + public void testHasUserAcceptedLatest_NoTOSFound() { + when(termsOfServiceRepo.findTopByOrderByDateUpdatedDesc()).thenReturn(Optional.empty()); + + boolean result = tosService.hasUserAcceptedLatest("user-id"); + assertTrue(result); + } + + @Test + public void testHasUserAcceptedLatest_UserNotAcceptedLatestTOS() { + User user = new User(); + user.setAcceptedTOS(new Date(0)); // Set an old date + + TermsOfService latestTOS = new TermsOfService(); + latestTOS.setDateUpdated(new Date()); + latestTOS.setContent("Latest TOS content"); + + when(userRepo.findById(any(UUID.class))).thenReturn(Optional.of(user)); + when(termsOfServiceRepo.findTopByOrderByDateUpdatedDesc()).thenReturn(Optional.of(latestTOS)); + + boolean result = tosService.hasUserAcceptedLatest(UUID.randomUUID().toString()); + assertFalse(result); + } + + @Test + public void testHasUserAcceptedLatest_UserAcceptedLatestTOS() { + User user = new User(); + user.setAcceptedTOS(new Date()); + + TermsOfService latestTOS = new TermsOfService(); + latestTOS.setDateUpdated(new Date(0)); // Set an old date + + when(userRepo.findBySubject(any(String.class))).thenReturn(user); + when(termsOfServiceRepo.findTopByOrderByDateUpdatedDesc()).thenReturn(Optional.of(latestTOS)); + + boolean result = tosService.hasUserAcceptedLatest(UUID.randomUUID().toString()); + assertTrue(result); + } + + @Test + public void testUpdateTermsOfService() { + String html = "

    New TOS content

    "; + + TermsOfService updatedTOS = new TermsOfService(); + updatedTOS.setContent(html); + when(termsOfServiceRepo.save(any(TermsOfService.class))).thenReturn(updatedTOS); + when(termsOfServiceRepo.findTopByOrderByDateUpdatedDesc()).thenReturn(Optional.of(updatedTOS)); + + Optional result = tosService.updateTermsOfService(html); + assertTrue(result.isPresent()); + assertEquals(html, result.get().getContent()); + } + + @Test + public void testGetLatest_TOSFound() { + String content = "

    Latest TOS content

    "; + + TermsOfService tos = new TermsOfService(); + tos.setContent(content); + when(termsOfServiceRepo.findTopByOrderByDateUpdatedDesc()).thenReturn(Optional.of(tos)); + + String result = tosService.getLatest(); + assertEquals(content, result); + } + + @Test + public void testGetLatest_NoTOSFound() { + when(termsOfServiceRepo.findTopByOrderByDateUpdatedDesc()).thenReturn(Optional.empty()); + + String result = tosService.getLatest(); + assertNull(result); + } + + @Test + public void testAcceptTermsOfService_UserExists() { + User user = new User(); + user.setSubject("user-id"); + + TermsOfService tos = new TermsOfService(); + tos.setDateUpdated(new Date()); + + when(userRepo.findBySubject(anyString())).thenReturn(user); + when(termsOfServiceRepo.findTopByOrderByDateUpdatedDesc()).thenReturn(Optional.of(tos)); + + User result = tosService.acceptTermsOfService("user-id"); + + assertNotNull(result); + assertNotNull(result.getAcceptedTOS()); + } + + @Test + public void testAcceptTermsOfService_UserDoesNotExist() { + when(userRepo.findBySubject(anyString())).thenReturn(null); + + assertThrows(RuntimeException.class, ()->{ + tosService.acceptTermsOfService("user-id"); + }); + } + + @Test + public void testAcceptTermsOfService_NoTOSInDatabase() { + User user = new User(); + user.setSubject("user-id"); + + when(userRepo.findBySubject(anyString())).thenReturn(user); + when(termsOfServiceRepo.findTopByOrderByDateUpdatedDesc()).thenReturn(Optional.empty()); + + assertThrows(RuntimeException.class, () -> { + tosService.acceptTermsOfService("user-id"); + }); + } + + @Test + public void testCheckAgainstTOSDate_UserAcceptedLatestTOS() { + User user = new User(); + user.setAcceptedTOS(new Date()); + + TermsOfService tos = new TermsOfService(); + tos.setDateUpdated(new Date(0)); // Set an old date + + when(userRepo.findById(any(UUID.class))).thenReturn(Optional.of(user)); + when(termsOfServiceRepo.findTopByOrderByDateUpdatedDesc()).thenReturn(Optional.of(tos)); + + boolean result = tosService.hasUserAcceptedLatest(UUID.randomUUID().toString()); + assertTrue(result); + } + + @Test + public void testCheckAgainstTOSDate_UserNotAcceptedLatestTOS() { + User user = new User(); + user.setAcceptedTOS(new Date(0)); + + TermsOfService tos = new TermsOfService(); + tos.setDateUpdated(new Date()); + tos.setContent("Latest TOS content"); + + when(userRepo.findById(any(UUID.class))).thenReturn(Optional.of(user)); + when(termsOfServiceRepo.findTopByOrderByDateUpdatedDesc()).thenReturn(Optional.of(tos)); + + boolean result = tosService.hasUserAcceptedLatest(UUID.randomUUID().toString()); + assertFalse(result); + } + + @Test + public void testCheckAgainstTOSDate_UserNotFound() { + when(userRepo.findById(any(UUID.class))).thenReturn(Optional.empty()); + + TermsOfService tos = new TermsOfService(); + tos.setDateUpdated(new Date()); + tos.setContent("Latest TOS content"); + + when(termsOfServiceRepo.findTopByOrderByDateUpdatedDesc()).thenReturn(Optional.of(tos)); + + boolean result = tosService.hasUserAcceptedLatest(UUID.randomUUID().toString()); + assertFalse(result); + } + +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/TokenServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/TokenServiceTest.java new file mode 100644 index 000000000..dfa858d20 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/TokenServiceTest.java @@ -0,0 +1,540 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Application; +import edu.harvard.hms.dbmi.avillach.auth.entity.Privilege; +import edu.harvard.hms.dbmi.avillach.auth.entity.Role; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; + +import edu.harvard.hms.dbmi.avillach.auth.model.*; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserRepository; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.authorization.AuthorizationService; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming; +import edu.harvard.hms.dbmi.avillach.auth.utils.JWTUtil; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockitoAnnotations; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.security.authentication.UsernamePasswordAuthenticationToken; +import org.springframework.security.core.Authentication; +import org.springframework.security.core.context.SecurityContext; +import org.springframework.security.core.context.SecurityContextHolder; +import org.springframework.security.web.authentication.WebAuthenticationDetailsSource; +import org.springframework.test.context.ContextConfiguration; + +import java.security.SecureRandom; +import java.util.*; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.when; + +@SpringBootTest +@ContextConfiguration(classes = {TokenService.class, JWTUtil.class}) +public class TokenServiceTest { + + @MockBean + private AuthorizationService authorizationService; + + @MockBean + private UserRepository userRepository; + + @MockBean + private SessionService sessionService; + + @MockBean + private UserService userService; + + private JWTUtil jwtUtil; + + @MockBean + private SecurityContext securityContext; + + private TokenService tokenService; + + private static final long testTokenExpiration = 1000L * 60 * 60; + + @BeforeEach + public void setUp() { + MockitoAnnotations.openMocks(this); + Authentication authentication = mock(Authentication.class); + + SecurityContextHolder.setContext(securityContext); + when(securityContext.getAuthentication()).thenReturn(authentication); + when(sessionService.isSessionExpired(any(String.class))).thenReturn(false); + jwtUtil = new JWTUtil(generate256Base64Secret(), true); + tokenService = new TokenService(authorizationService, userRepository, 1000L * 60 * 60, jwtUtil, sessionService, userService); + } + + @Test + public void testInspectToken_withValidToken() { + Application application = createTestApplication(); + configureApplicationSecurityContext(application); + + User user = createTestUser(); + Map claims = new HashMap<>(); + claims.put("sub", user.getSubject()); + + Map inputMap = new HashMap<>(); + String token = jwtUtil.createJwtToken( + "whatever", + "edu.harvard.hms.dbmi.psama", + claims, + claims.get("sub").toString(), + testTokenExpiration + ); + System.out.println(token); + inputMap.put("token", token); + + when(userRepository.findBySubject(user.getSubject())).thenReturn(user); + + Map response = tokenService.inspectToken(inputMap); + assertNull(response.get("message")); + assertTrue((Boolean) response.get("active")); + assertEquals(user.getSubject(), response.get("sub")); + assertEquals(user.getPrivilegeNameSet(), response.get("privileges")); + } + + @Test + public void testInspectToken_withNullToken() { + Map inputMap = new HashMap<>(); + inputMap.put("token", null); + + Map response = tokenService.inspectToken(inputMap); + assertEquals("Token not found", response.get("message")); + } + + @Test + public void testInspectToken_withEmptyToken() { + Map inputMap = new HashMap<>(); + inputMap.put("token", ""); + + Map response = tokenService.inspectToken(inputMap); + assertEquals("Token not found", response.get("message")); + } + + @Test + public void testInspectToken_withUserPrincipal() { + User user = createTestUser(); + Map claims = new HashMap<>(); + claims.put("sub", user.getSubject()); + + Map inputMap = new HashMap<>(); + String token = jwtUtil.createJwtToken( + "whatever", + "edu.harvard.hms.dbmi.psama", + claims, + claims.get("sub").toString(), + testTokenExpiration + ); + inputMap.put("token", token); + + configureUserSecurityContext(user); + + assertThrows(RuntimeException.class, () -> { + Map tokenInspection = tokenService.inspectToken(inputMap); + assertNotNull(tokenInspection.get("message")); + }); + } + + + @Test + public void testInspectToken_withValidToken_withNoAssociatedUser() { + Application application = createTestApplication(); + configureApplicationSecurityContext(application); + + User user = createTestUser(); + Map claims = new HashMap<>(); + claims.put("sub", user.getSubject()); + + Map inputMap = new HashMap<>(); + String token = jwtUtil.createJwtToken( + "whatever", + "edu.harvard.hms.dbmi.psama", + claims, + claims.get("sub").toString(), + testTokenExpiration + ); + System.out.println(token); + inputMap.put("token", token); + + when(userRepository.findBySubject(user.getSubject())).thenReturn(null); + + Map response = tokenService.inspectToken(inputMap); + assertEquals("user doesn't exist", response.get("message")); + } + + @Test + public void testInspectToken_withNoApplicationInSecurityContext() { + configureApplicationSecurityContext(null); + + User user = createTestUser(); + Map claims = new HashMap<>(); + claims.put("sub", user.getSubject()); + + Map inputMap = new HashMap<>(); + String token = jwtUtil.createJwtToken( + "whatever", + "edu.harvard.hms.dbmi.psama", + claims, + claims.get("sub").toString(), + testTokenExpiration + ); + System.out.println(token); + inputMap.put("token", token); + + when(userRepository.findBySubject(user.getSubject())).thenReturn(null); + assertThrows(NullPointerException.class, ()->{ + tokenService.inspectToken(inputMap); + }); + } + + /* + TODO: Investigate if this is a scenario we should be stopping. This test is successful, but the user has + no token associated with it. The code should at least verify hat the user has the token associated with it + that is being sent + */ + @Test + public void testLongTermInspectToken() { + Application application = createTestApplication(); + configureApplicationSecurityContext(application); + + User user = createTestUser(); + user.setSubject(user.getSubject()); + Map claims = new HashMap<>(); + claims.put("sub", user.getSubject()); + + Map inputMap = new HashMap<>(); + String token = jwtUtil.createJwtToken( + "whatever", + "edu.harvard.hms.dbmi.psama", + claims, + AuthNaming.LONG_TERM_TOKEN_PREFIX + "|" + claims.get("sub").toString(), + testTokenExpiration + ); + + inputMap.put("token", token); + when(userRepository.findBySubject(user.getSubject())).thenReturn(user); + + Map response = tokenService.inspectToken(inputMap); + assertNull(response.get("message")); + assertTrue((Boolean) response.get("active")); + assertEquals(AuthNaming.LONG_TERM_TOKEN_PREFIX + "|" + claims.get("sub").toString(), response.get("sub")); + assertEquals(user.getPrivilegeNameSet(), response.get("privileges")); + } + + @Test + public void testLongTermInspectToken_withUserTokenCompromised() { + Application application = createTestApplication(); + configureApplicationSecurityContext(application); + + User user = createTestUser(); + user.setSubject(user.getSubject()); + Map claims = new HashMap<>(); + claims.put("sub", user.getSubject()); + + Map inputMap = new HashMap<>(); + // Application Long term token + String token = jwtUtil.createJwtToken( + "whatever", + "edu.harvard.hms.dbmi.psama", + claims, + AuthNaming.LONG_TERM_TOKEN_PREFIX + "|" + claims.get("sub").toString(), + testTokenExpiration + ); + + String userToken = jwtUtil.createJwtToken( + "whatever1", // Different id + "edu.harvard.hms.dbmi.psama", + claims, + AuthNaming.LONG_TERM_TOKEN_PREFIX + "|" + claims.get("sub").toString(), + testTokenExpiration + ); + user.setToken(userToken); + + // User privileges should be a subset of the application's privileges + application.setPrivileges(user.getTotalPrivilege()); + inputMap.put("token", token); + when(userRepository.findBySubject(user.getSubject())).thenReturn(user); + + Map response = tokenService.inspectToken(inputMap); + assertEquals("Cannot find matched long term token, your token might have been refreshed.", response.get("message")); + } + + @Test + public void testLongTermInspectToken_withUserRolesNull() { + Application application = createTestApplication(); + configureApplicationSecurityContext(application); + + User user = createTestUser(); + user.setSubject(user.getSubject()); + Map claims = new HashMap<>(); + claims.put("sub", user.getSubject()); + + Map inputMap = new HashMap<>(); + // Application Long term token + String token = jwtUtil.createJwtToken( + "whatever", + "edu.harvard.hms.dbmi.psama", + claims, + AuthNaming.LONG_TERM_TOKEN_PREFIX + "|" + claims.get("sub").toString(), + testTokenExpiration + ); + user.setToken(token); + + // User privileges should be a subset of the application's privileges + application.setPrivileges(user.getTotalPrivilege()); + user.setRoles(null); + inputMap.put("token", token); + when(userRepository.findBySubject(user.getSubject())).thenReturn(user); + + Map response = tokenService.inspectToken(inputMap); + assertEquals("User doesn't have enough privileges.", response.get("message")); + } + + @Test + public void testLongTermInspectToken_withUserTokenCompromised_() { + Application application = createTestApplication(); + configureApplicationSecurityContext(application); + + User user = createTestUser(); + user.setSubject(user.getSubject()); + Map claims = new HashMap<>(); + claims.put("sub", user.getSubject()); + + Map inputMap = new HashMap<>(); + // Application Long term token + String token = jwtUtil.createJwtToken( + "whatever", + "edu.harvard.hms.dbmi.psama", + claims, + AuthNaming.LONG_TERM_TOKEN_PREFIX + "|" + claims.get("sub").toString(), + testTokenExpiration + ); + + user.setToken(token); + + // User privileges should be a subset of the application's privileges + application.setPrivileges(user.getTotalPrivilege()); + user.setRoles(null); + inputMap.put("token", token); + when(userRepository.findBySubject(user.getSubject())).thenReturn(user); + + Map response = tokenService.inspectToken(inputMap); + assertEquals("User doesn't have enough privileges.", response.get("message")); + } + + @Test + public void testRefreshToken_isExpired() throws InterruptedException { + User user = createTestUser(); + configureUserSecurityContext(user); + user.setSubject(user.getSubject()); + Map claims = new HashMap<>(); + claims.put("sub", user.getSubject()); + + // Application Long term token + String token = jwtUtil.createJwtToken( + "whatever", + "edu.harvard.hms.dbmi.psama", + claims, + claims.get("sub").toString(), + 1 + ); + + // Ensure the token expires so the unit test never fails. + Thread.sleep(1); + + // User privileges should be a subset of the application's privileges + when(userRepository.findBySubject(user.getSubject())).thenReturn(user); + when(userRepository.findById(user.getUuid())).thenReturn(Optional.of(user)); + + String authorizationHeader = "Bearer " + token; + RefreshToken response = tokenService.refreshToken(authorizationHeader); + assertTrue(response instanceof InvalidRefreshToken); + assertEquals("Cannot parse original token.", ((InvalidRefreshToken) response).error()); + } + + @Test + public void testRefreshToken() throws InterruptedException { + User user = createTestUser(); + configureUserSecurityContext(user); + user.setSubject(user.getSubject()); + Map claims = new HashMap<>(); + claims.put("sub", user.getSubject()); + + // Application Long term token + String token = jwtUtil.createJwtToken( + "whatever", + "edu.harvard.hms.dbmi.psama", + claims, + claims.get("sub").toString(), + testTokenExpiration + ); + + // User privileges should be a subset of the application's privileges + when(userRepository.findBySubject(user.getSubject())).thenReturn(user); + when(userRepository.findById(user.getUuid())).thenReturn(Optional.of(user)); + + String authorizationHeader = "Bearer " + token; + RefreshToken response = tokenService.refreshToken(authorizationHeader); + assertTrue(response instanceof ValidRefreshToken); + assertNotNull(((ValidRefreshToken) response).token()); + assertNotNull(((ValidRefreshToken) response).expirationDate()); + } + + @Test + public void testRefreshToken_whereUserNotExists() { + User user = createTestUser(); + configureUserSecurityContext(user); + user.setSubject(user.getSubject()); + Map claims = new HashMap<>(); + claims.put("sub", user.getSubject()); + + // Application Long term token + String token = jwtUtil.createJwtToken( + "whatever", + "edu.harvard.hms.dbmi.psama", + claims, + claims.get("sub").toString(), + testTokenExpiration + ); + + when(userRepository.findBySubject(user.getSubject())).thenReturn(null); + when(userRepository.findById(user.getUuid())).thenReturn(Optional.empty()); + + String authorizationHeader = "Bearer " + token; + RefreshToken refreshToken = tokenService.refreshToken(authorizationHeader); + assertTrue(refreshToken instanceof InvalidRefreshToken); + assertEquals("User doesn't exist anymore.", ((InvalidRefreshToken) refreshToken).error()); + } + + @Test + public void testRefreshToken_whereUserNotActive() { + User user = createTestUser(); + user.setActive(false); + configureUserSecurityContext(user); + user.setSubject(user.getSubject()); + Map claims = new HashMap<>(); + claims.put("sub", user.getSubject()); + + // Application Long term token + String token = jwtUtil.createJwtToken( + "whatever", + "edu.harvard.hms.dbmi.psama", + claims, + claims.get("sub").toString(), + testTokenExpiration + ); + + // User privileges should be a subset of the application's privileges + when(userRepository.findBySubject(user.getSubject())).thenReturn(user); + when(userRepository.findById(user.getUuid())).thenReturn(Optional.of(user)); + + String authorizationHeader = "Bearer " + token; + RefreshToken refreshToken = tokenService.refreshToken(authorizationHeader); + assertTrue(refreshToken instanceof InvalidRefreshToken); + assertEquals("User has been deactivated.", ((InvalidRefreshToken) refreshToken).error()); + } + + @Test + public void testRefreshToken_whereUserSubjectHasChanged() { + User user = createTestUser(); + configureUserSecurityContext(user); + user.setSubject(user.getSubject()); + Map claims = new HashMap<>(); + claims.put("sub", user.getSubject()); + + // Application Long term token + String token = jwtUtil.createJwtToken( + "whatever", + "edu.harvard.hms.dbmi.psama", + claims, + claims.get("sub").toString(), + testTokenExpiration + ); + user.setSubject("CHANGED_SUBJECT"); + + // User privileges should be a subset of the application's privileges + when(userRepository.findBySubject(user.getSubject())).thenReturn(user); + when(userRepository.findById(user.getUuid())).thenReturn(Optional.of(user)); + + String authorizationHeader = "Bearer " + token; + RefreshToken refreshToken = tokenService.refreshToken(authorizationHeader); + assertTrue(refreshToken instanceof InvalidRefreshToken); + assertEquals("User doesn't exist anymore.", ((InvalidRefreshToken) refreshToken).error()); + } + + private User createTestUser() { + User user = new User(); + user.setUuid(UUID.randomUUID()); + user.setRoles(Collections.singleton(createTestRole())); + user.setSubject("TEST_SUBJECT"); + user.setEmail("test@email.com"); + user.setAcceptedTOS(new Date()); + user.setActive(true); + + return user; + } + + private Role createTestRole() { + Role role = new Role(); + role.setName(AuthNaming.AuthRoleNaming.ADMIN); + role.setUuid(UUID.randomUUID()); + role.setPrivileges(Collections.singleton(createTestPrivilege())); + return role; + } + + private Privilege createTestPrivilege() { + Privilege privilege = new Privilege(); + privilege.setName("TEST_PRIVILEGE"); + privilege.setUuid(UUID.randomUUID()); + return privilege; + } + + private Application createTestApplication() { + Application application = new Application(); + application.setUuid(UUID.randomUUID()); + application.setName("TEST_APPLICATION"); + application.setToken(createValidApplicationTestToken(application)); + application.setPrivileges(new HashSet<>()); + return application; + } + + private void configureUserSecurityContext(User user) { + CustomUserDetails customUserDetails = new CustomUserDetails(user); + // configure security context + UsernamePasswordAuthenticationToken authentication = new UsernamePasswordAuthenticationToken(customUserDetails, null, customUserDetails.getAuthorities()); + when(securityContext.getAuthentication()).thenReturn(authentication); + } + + private void configureApplicationSecurityContext(Application application) { + CustomApplicationDetails customApplicationDetails = new CustomApplicationDetails(application); + UsernamePasswordAuthenticationToken authentication = new UsernamePasswordAuthenticationToken(customApplicationDetails, null, customApplicationDetails.getAuthorities()); + authentication.setDetails(new WebAuthenticationDetailsSource().buildDetails(mock(jakarta.servlet.http.HttpServletRequest.class))); + when(securityContext.getAuthentication()).thenReturn(authentication); + } + + private String createValidApplicationTestToken(Application application) { + return this.jwtUtil.createJwtToken( + null, null, + new HashMap<>( + Map.of( + "user_id", AuthNaming.PSAMA_APPLICATION_TOKEN_PREFIX + "|" + application.getName() + ) + ), + AuthNaming.PSAMA_APPLICATION_TOKEN_PREFIX + "|" + application.getUuid().toString(), 365L * 1000 * 60 * 60 * 24); + } + + /** + * Do not use this method in production code. This is only for testing purposes. + * + * @return a 256-bit base64 encoded secret + */ + private String generate256Base64Secret() { + SecureRandom random = new SecureRandom(); + byte[] secret = new byte[32]; + random.nextBytes(secret); + return Base64.getEncoder().encodeToString(secret); + } +} \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/UserMetadataMappingServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/UserMetadataMappingServiceTest.java new file mode 100644 index 000000000..b9611e8d5 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/UserMetadataMappingServiceTest.java @@ -0,0 +1,155 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.hms.dbmi.avillach.auth.entity.Connection; +import edu.harvard.hms.dbmi.avillach.auth.entity.UserMetadataMapping; +import edu.harvard.hms.dbmi.avillach.auth.repository.ConnectionRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserMetadataMappingRepository; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockitoAnnotations; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.test.context.ContextConfiguration; + +import java.util.Arrays; +import java.util.List; +import java.util.Optional; +import java.util.UUID; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertThrows; +import static org.mockito.Mockito.*; + +@SpringBootTest +@ContextConfiguration(classes = {UserMetadataMappingService.class}) +public class UserMetadataMappingServiceTest { + + @MockBean + private UserMetadataMappingRepository userMetadataMappingRepo; + + @MockBean + private ConnectionRepository connectionRepo; + + @Autowired + private UserMetadataMappingService userMetadataMappingService; + + @BeforeEach + public void setUp() { + MockitoAnnotations.openMocks(this); + } + + @Test + public void testGetAllMappingsForConnection() { + Connection connection = new Connection(); + connection.setId("testConnectionId"); + List mappings = Arrays.asList(new UserMetadataMapping(), new UserMetadataMapping()); + + when(userMetadataMappingRepo.findByConnection(connection)).thenReturn(mappings); + + List result = userMetadataMappingService.getAllMappingsForConnection(connection); + + assertEquals(mappings, result); + verify(userMetadataMappingRepo, times(1)).findByConnection(connection); + } + + @Test + public void testAddMappings_Success() { + Connection connection = new Connection(); + connection.setId("testConnectionId"); + + UserMetadataMapping mapping1 = new UserMetadataMapping(); + mapping1.setConnection(connection); + UserMetadataMapping mapping2 = new UserMetadataMapping(); + mapping2.setConnection(connection); + + List mappings = Arrays.asList(mapping1, mapping2); + + when(connectionRepo.findById("testConnectionId")).thenReturn(Optional.of(connection)); + when(userMetadataMappingRepo.saveAll(mappings)).thenReturn(mappings); + + List result = userMetadataMappingService.addMappings(mappings); + + assertEquals(mappings, result); + verify(connectionRepo, times(2)).findById("testConnectionId"); + verify(userMetadataMappingRepo, times(1)).saveAll(mappings); + } + + @Test + public void testAddMappings_ConnectionNotFound() { + Connection connection = new Connection(); + connection.setId("invalidConnectionId"); + + UserMetadataMapping mapping = new UserMetadataMapping(); + mapping.setConnection(connection); + + List mappings = List.of(mapping); + + when(connectionRepo.findById("invalidConnectionId")).thenReturn(Optional.empty()); + + assertThrows(IllegalArgumentException.class, () -> { + userMetadataMappingService.addMappings(mappings); + }); + } + + @Test + public void testGetAllMappings() { + List mappings = Arrays.asList(new UserMetadataMapping(), new UserMetadataMapping()); + + when(userMetadataMappingRepo.findAll()).thenReturn(mappings); + + List result = userMetadataMappingService.getAllMappings(); + + assertEquals(mappings, result); + verify(userMetadataMappingRepo, times(1)).findAll(); + } + + @Test + public void testGetAllMappingsForConnectionById_Success() { + Connection connection = new Connection(); + connection.setId("testConnectionId"); + + when(connectionRepo.findById("testConnectionId")).thenReturn(Optional.of(connection)); + + Connection result = userMetadataMappingService.getAllMappingsForConnection("testConnectionId"); + + assertEquals(connection, result); + verify(connectionRepo, times(1)).findById("testConnectionId"); + } + + @Test + public void testGetAllMappingsForConnectionById_NotFound() { + when(connectionRepo.findById("invalidConnectionId")).thenReturn(Optional.empty()); + + assertThrows(IllegalArgumentException.class, () -> { + userMetadataMappingService.getAllMappingsForConnection("invalidConnectionId"); + }); + } + + @Test + public void testUpdateUserMetadataMappings() { + List mappings = Arrays.asList(new UserMetadataMapping(), new UserMetadataMapping()); + + when(userMetadataMappingRepo.saveAll(mappings)).thenReturn(mappings); + + List result = userMetadataMappingService.updateUserMetadataMappings(mappings); + + assertEquals(mappings, result); + verify(userMetadataMappingRepo, times(1)).saveAll(mappings); + } + + @Test + public void testRemoveMetadataMappingByIdAndRetrieveAll() { + UUID mappingId = UUID.randomUUID(); + List mappings = Arrays.asList(new UserMetadataMapping(), new UserMetadataMapping()); + + doNothing().when(userMetadataMappingRepo).deleteById(mappingId); + when(userMetadataMappingRepo.findAll()).thenReturn(mappings); + + List result = userMetadataMappingService.removeMetadataMappingByIdAndRetrieveAll(mappingId.toString()); + + assertEquals(mappings, result); + verify(userMetadataMappingRepo, times(1)).deleteById(mappingId); + verify(userMetadataMappingRepo, times(1)).findAll(); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/UserServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/UserServiceTest.java new file mode 100644 index 000000000..3eaa4f34e --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/UserServiceTest.java @@ -0,0 +1,710 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.hms.dbmi.avillach.auth.entity.*; + +import edu.harvard.hms.dbmi.avillach.auth.model.CustomUserDetails; +import edu.harvard.hms.dbmi.avillach.auth.model.fenceMapping.StudyMetaData; +import edu.harvard.hms.dbmi.avillach.auth.repository.ApplicationRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.ConnectionRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserConsentsRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserRepository; +import edu.harvard.hms.dbmi.avillach.auth.utils.AuthNaming; +import edu.harvard.hms.dbmi.avillach.auth.utils.FenceMappingUtility; +import edu.harvard.hms.dbmi.avillach.auth.utils.JWTUtil; +import io.jsonwebtoken.Claims; +import io.jsonwebtoken.Jws; +import jakarta.mail.MessagingException; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.ArgumentCaptor; +import org.mockito.MockitoAnnotations; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.http.HttpHeaders; +import org.springframework.security.authentication.UsernamePasswordAuthenticationToken; +import org.springframework.security.core.Authentication; +import org.springframework.security.core.context.SecurityContext; +import org.springframework.security.core.context.SecurityContextHolder; +import org.springframework.test.context.ContextConfiguration; + +import java.security.SecureRandom; +import java.util.*; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + +@SpringBootTest +@ContextConfiguration(classes = {JWTUtil.class, UserService.class}) +public class UserServiceTest { + + @MockBean + private SecurityContext securityContext; + @MockBean + private BasicMailService basicMailService; + @MockBean + private TOSService tosService; + @MockBean + private UserRepository userRepository; + @MockBean + private ConnectionRepository connectionRepository; + @MockBean + private ApplicationRepository applicationRepository; + @MockBean + private RoleService roleService; + @MockBean + private JWTUtil mockJwtUtil; + @MockBean + private LoggingClient loggingClient; + private JWTUtil jwtUtil; + + private static final long defaultTokenExpirationTime = 1000L * 60 * 60; // 1 hour + private final long longTermTokenExpirationTime = 2592000000L; + + private UserService userService; + @MockBean + private UserConsentsRepository userConsentsRepository; + @MockBean + private FenceMappingUtility fenceMappingUtility; + + @BeforeEach + public void setUp() { + MockitoAnnotations.openMocks(this); + + Authentication authentication = mock(Authentication.class); + SecurityContextHolder.setContext(securityContext); + when(securityContext.getAuthentication()).thenReturn(authentication); + + jwtUtil = new JWTUtil(generate256Base64Secret(), true); + String applicationUUID = UUID.randomUUID().toString(); + userService = new UserService( + basicMailService, + tosService, + userRepository, + connectionRepository, + applicationRepository, + roleService, + userConsentsRepository, + fenceMappingUtility, + defaultTokenExpirationTime, + applicationUUID, + longTermTokenExpirationTime, + mockJwtUtil, + false, + "ADMIN,SUPER_ADMIN", + null); + } + + @Test + public void testGetUserProfileResponse() { + User user = createTestUser(); + when(userRepository.findByEmail(user.getEmail())).thenReturn(user); + + UserClaims userClaims = buildTestUserClaims(user); + HashMap result = userService.getUserProfileResponse(userClaims); + assertNotNull(result); + } + + @Test + public void testGetUserById_found() { + UUID testId = UUID.randomUUID(); + User user = createTestUser(); + user.setUuid(testId); + + when(userRepository.findById(testId)).thenReturn(Optional.of(user)); + + User result = userService.getUserById(testId.toString()); + assertNotNull(result); + assertEquals(testId, result.getUuid()); + } + + @Test + public void testGetUserById_notFound() { + UUID testId = UUID.randomUUID(); + when(userRepository.findById(testId)).thenReturn(Optional.empty()); + + assertThrows(IllegalArgumentException.class, ()-> { + userService.getUserById(testId.toString()); + }); + } + + @Test + public void testGetAllUsers() { + User user = createTestUser(); + when(userRepository.findAll()).thenReturn(List.of(user)); + + Iterable result = userService.getAllUsers(); + assertNotNull(result); + assertTrue(result.iterator().hasNext()); + } + + @Test + public void testAddUser() { + User user = createTestUser(); + when(userRepository.saveAll(List.of(user))).thenReturn(List.of(user)); + + List result = userService.addUser(List.of(user)); + assertNotNull(result); + } + + @Test + public void testAddUsers() { + User user = createTestUser(); + configureUserSecurityContext(user); + when(userRepository.saveAll(List.of(user))).thenReturn(List.of(user)); + + doAnswer(invocation -> new HashSet<>(user.getRoles())).when(roleService).getRolesByIds(anySet()); + + List result = userService.addUsers(List.of(user)); + System.out.println(result); + assertNotNull(result); + assertEquals(1, result.size()); + assertEquals(user, result.getFirst()); + } + + @Test + public void testAddUsers_SuperAdminRole() { + User user = createTestUser(); + user.getRoles().add(createSuperAdminRole()); + configureUserSecurityContext(user); + when(userRepository.saveAll(List.of(user))).thenReturn(List.of(user)); + + doAnswer(invocation -> new HashSet<>(user.getRoles())).when(roleService).getRolesByIds(anySet()); + + List result = userService.addUsers(List.of(user)); + assertNotNull(result); + assertEquals(1, result.size()); + assertEquals(user, result.getFirst()); + } + + @Test + public void testAddUsers_SuperAdminRole_withoutNecessaryPrivileges() { + User user = createTestUser(); + Set roles = user.getRoles(); + roles.add(createSuperAdminRole()); + user.setRoles(roles); + + doAnswer(invocation -> new HashSet<>(user.getRoles())).when(roleService).getRolesByIds(anySet()); + + System.out.println(user.getRoles()); + User loggedInUser = createTestUser(); + configureUserSecurityContext(loggedInUser); + when(userRepository.saveAll(List.of(user))).thenReturn(List.of(user)); + + assertThrows(IllegalArgumentException.class, () -> { + userService.addUsers(List.of(user)); + }); + + } + + @Test + public void testAddUsers_UserRoleNotExisting() { + User user = createTestUser(); + configureUserSecurityContext(user); + when(userRepository.saveAll(List.of(user))).thenReturn(List.of(user)); + + assertThrows(RuntimeException.class, () -> { + List result = userService.addUsers(List.of(user)); + assertNotNull(result); + assertEquals(1, result.size()); + assertEquals(user, result.getFirst()); + }); + } + + @Test + public void testAddUsers_UserEmailNull_AndBadMetadata() { + User user = createTestUser(); + configureUserSecurityContext(user); + + // set email to null + user.setEmail(null); + // set bad metadata + user.setGeneralMetadata("bad metadata"); + + when(userRepository.saveAll(List.of(user))).thenReturn(List.of(user)); + doAnswer(invocation -> new HashSet<>(user.getRoles())).when(roleService).getRolesByIds(anySet()); + + userService.addUsers(List.of(user)); + } + + @Test + public void testAddUsers_UserEmailNull_AndValidMetadata() { + User user = createTestUser(); + configureUserSecurityContext(user); + + // set email to null + user.setEmail(null); + // set bad metadata + user.setGeneralMetadata("{\"email\":\" " + user.getEmail() + "\"}"); + + when(userRepository.saveAll(List.of(user))).thenReturn(List.of(user)); + + doAnswer(invocation -> new HashSet<>(user.getRoles())).when(roleService).getRolesByIds(anySet()); + + userService.addUsers(List.of(user)); + } + + @Test + public void testUpdateUser() { + User user = createTestUser(); + configureUserSecurityContext(user); + when(userRepository.saveAll(List.of(user))).thenReturn(List.of(user)); + + doAnswer(invocation -> new HashSet<>(user.getRoles())).when(roleService).getRolesByIds(anySet()); + + when(userRepository.findById(user.getUuid())).thenReturn(Optional.of(user)); + + List result = userService.updateUser(List.of(user)); + assertNotNull(result); + } + + @Test + public void testUpdateUser_SuperAdminRole() { + User user = createTestUser(); + user.getRoles().add(createSuperAdminRole()); + configureUserSecurityContext(user); + when(userRepository.saveAll(List.of(user))).thenReturn(List.of(user)); + + doAnswer(invocation -> new HashSet<>(user.getRoles())).when(roleService).getRolesByIds(anySet()); + + when(userRepository.findById(user.getUuid())).thenReturn(Optional.of(user)); + + List result = userService.updateUser(List.of(user)); + assertNotNull(result); + } + + @Test + public void testUpdateUser_SuperAdminRole_withoutNecessaryPrivileges() { + User user = createTestUser(); + Set roles = user.getRoles(); + roles.add(createSuperAdminRole()); + user.setRoles(roles); + + doAnswer(invocation -> new HashSet<>(user.getRoles())).when(roleService).getRolesByIds(anySet()); + + User loggedInUser = createTestUser(); + configureUserSecurityContext(loggedInUser); + when(userRepository.saveAll(List.of(user))).thenReturn(List.of(user)); + + User userToFindByID = new User(); + userToFindByID.setUuid(user.getUuid()); + userToFindByID.setRoles(new HashSet<>()); + when(userRepository.findById(user.getUuid())).thenReturn(Optional.of(userToFindByID)); + + assertThrows(IllegalArgumentException.class, ()-> { + userService.updateUser(List.of(user)); + }); + } + + @Test + public void testGetUserProfileResponse_missingClaims() { + UserClaims userClaims = new UserClaims(); + userClaims.setEmail("test@example.com"); + // Missing "sub" - should return null since subject is required + HashMap result = userService.getUserProfileResponse(userClaims); + assertNull(result); + } + + @Test + public void testGetUserById_invalidUUID() { + assertThrows(IllegalArgumentException.class, () -> { + userService.getUserById("not-a-real-uuid"); + }); + } + + @Test + public void testSendUserUpdateEmails_success() throws MessagingException { + User user = createTestUser(); + List users = List.of(user); + when(userRepository.saveAll(users)).thenReturn(users); + configureUserSecurityContext(user); + + try { + userService.sendUserUpdateEmailsFromResponse(users); + } catch (Exception e) { + fail("Should not throw an exception when sending emails"); + } + + verify(basicMailService).sendUsersAccessEmail(user); + } + + @Test + public void testGetCurrentUser() { + User user = createTestUser(); + + + Map claims = new HashMap<>(); + claims.put("sub", user.getSubject()); + + // Application Long term token + String token = jwtUtil.createJwtToken( + "whatever", + "edu.harvard.hms.dbmi.psama", + claims, + claims.get("sub").toString(), + longTermTokenExpirationTime + ); + user.setToken(token); + configureUserSecurityContext(user); + + Jws claimsJws = this.jwtUtil.parseToken(token); + System.out.println(claimsJws); + + when(mockJwtUtil.parseToken(anyString())).thenReturn(claimsJws); + when(tosService.hasUserAcceptedLatest(any())).thenReturn(true); + User.UserForDisplay currentUser = userService.getCurrentUser("Bearer " + token, true); + assertNotNull(currentUser); + assertEquals(user.getToken(), currentUser.getToken()); + } + + @Test + public void testGetCurrentUser_withNoToken() { + User user = createTestUser(); + configureUserSecurityContext(user); + + Map claims = new HashMap<>(); + claims.put("sub", user.getSubject()); + + // Application Long term token + String token = jwtUtil.createJwtToken( + "whatever", + "edu.harvard.hms.dbmi.psama", + claims, + claims.get("sub").toString(), + longTermTokenExpirationTime + ); + + Jws claimsJws = this.jwtUtil.parseToken(token); + System.out.println(claimsJws); + when(mockJwtUtil.parseToken(anyString())).thenReturn(claimsJws); + when(tosService.hasUserAcceptedLatest(any())).thenReturn(true); + User.UserForDisplay currentUser = userService.getCurrentUser("Bearer " + token, true); + assertNotNull(currentUser); + assertEquals(user.getToken(), currentUser.getToken()); + } + + @Test + public void testGetCurrentUser_noUserInContext() { + when(securityContext.getAuthentication()).thenReturn(null); + + CustomUserDetails customUserDetails = new CustomUserDetails(null); + // configure security context + UsernamePasswordAuthenticationToken authentication = new UsernamePasswordAuthenticationToken(customUserDetails, null, customUserDetails.getAuthorities()); + when(securityContext.getAuthentication()).thenReturn(authentication); + + assertNull(userService.getCurrentUser("Bearer some-token", true)); + } + + @Test + public void testGetCurrentUser_withNoPrivileges() { + User user = createTestUser(); + user.setRoles(new HashSet<>()); + configureUserSecurityContext(user); + + Map claims = new HashMap<>(); + claims.put("sub", user.getSubject()); + + // Application Long term token + String token = jwtUtil.createJwtToken( + "whatever", + "edu.harvard.hms.dbmi.psama", + claims, + claims.get("sub").toString(), + longTermTokenExpirationTime + ); + + Jws claimsJws = this.jwtUtil.parseToken(token); + + when(mockJwtUtil.parseToken(anyString())).thenReturn(claimsJws); + user.setToken(token); + when(tosService.hasUserAcceptedLatest(any())).thenReturn(true); + User.UserForDisplay currentUser = userService.getCurrentUser("Bearer " + token, true); + assertNotNull(currentUser); + assertEquals(user.getToken(), currentUser.getToken()); + } + + @Test + public void testGetQueryTemplate_invalidApplicationId() { + assertThrows(IllegalArgumentException.class, ()->{ + userService.getQueryTemplate(null); + }); + } + + @Test + public void testGetUserProfileResponse_withoutAcceptedTOS() { + User user = createTestUser(); + when(tosService.hasUserAcceptedLatest(anyString())).thenReturn(false); + + UserClaims userClaims = buildTestUserClaims(user); + HashMap result = userService.getUserProfileResponse(userClaims); + assertEquals("false", result.get("acceptedTOS")); + } + + @Test + public void testGetUserProfileResponse_withAcceptedTOS() { + User user = createTestUser(); + when(tosService.hasUserAcceptedLatest(anyString())).thenReturn(true); + + UserClaims userClaims = buildTestUserClaims(user); + HashMap result = userService.getUserProfileResponse(userClaims); + assertEquals("true", result.get("acceptedTOS")); + } + + @Test + public void testGetQueryTemplate_validApplicationId() { + User user = createTestUser(); + configureUserSecurityContext(user); + Application application = createTestApplication(); + + + when(applicationRepository.findById(any(UUID.class))).thenReturn(Optional.of(application)); + when(applicationRepository.findById(application.getUuid())).thenReturn(Optional.of(application)); + + Optional result = userService.getQueryTemplate(application.getUuid().toString()); + assertTrue(result.isPresent()); + } + + @Test + public void testGetDefaultQueryTemplate() { + User user = createTestUser(); + configureUserSecurityContext(user); + Application application = createTestApplication(); + + when(applicationRepository.findById(any(UUID.class))).thenReturn(Optional.of(application)); + when(applicationRepository.findById(application.getUuid())).thenReturn(Optional.of(application)); + + Map result = userService.getDefaultQueryTemplate(); + assertTrue(result.containsKey("queryTemplate")); + assertNotNull(result.get("queryTemplate")); + } + + @Test + public void testAddUsers_withUserHavingEmptyRoleSet() { + User user = createTestUser(); + user.setRoles(null); + + configureUserSecurityContext(user); + when(userRepository.saveAll(List.of(user))).thenReturn(List.of(user)); + + assertThrows(IllegalArgumentException.class, () -> { + List result = userService.addUsers(List.of(user)); + assertNull(result.getFirst().getRoles()); + }); + } + + @Test + public void testUpdateUser_withNoChanges() { + User user = createTestUser(); + configureUserSecurityContext(user); + when(userRepository.findById(user.getUuid())).thenReturn(Optional.of(user)); + when(userRepository.saveAll(List.of(user))).thenReturn(List.of(user)); + + doAnswer(invocation -> new HashSet<>(user.getRoles())).when(roleService).getRolesByIds(anySet()); + + List result = userService.updateUser(List.of(user)); + assertEquals(user, result.getFirst()); + } + + @Test + public void testRefreshUserToken() { + User user = createTestUser(); + configureUserSecurityContext(user); + when(userRepository.saveAll(List.of(user))).thenReturn(List.of(user)); + + Map claims = new HashMap<>(); + claims.put("sub", user.getSubject()); + + // Application Long term token + String token = jwtUtil.createJwtToken( + "whatever", + "edu.harvard.hms.dbmi.psama", + claims, + claims.get("sub").toString(), + longTermTokenExpirationTime + ); + + String authorizationHeader = "Bearer " + token; + HttpHeaders headers = new HttpHeaders(); + headers.add("Authorization", authorizationHeader); + + Jws claimsJws = this.jwtUtil.parseToken(token); + when(mockJwtUtil.parseToken(anyString())).thenReturn(claimsJws); + when(mockJwtUtil.createJwtToken(anyString(), anyString(), anyMap(), anyString(), anyLong())).thenReturn(token); + + Map result = userService.refreshUserToken(headers); + assertNotNull(result); + assertEquals(token, result.get("userLongTermToken")); + } + + @Test + public void testChangeRole() { + User user = createTestUser(); + configureUserSecurityContext(user); + when(userRepository.save(user)).thenReturn(user); + + // new roles + Role role = createTestRole(); + role.setName("NEW_ROLE"); + + Set newRoles = new HashSet<>(); + newRoles.add(role); + + User user1 = userService.changeRole(user, newRoles); + assertNotNull(user1); + + assertEquals(newRoles, user1.getRoles()); + } + + @Test + public void testFindUserBySubject() { + User user = createTestUser(); + when(userRepository.findBySubject(user.getSubject())).thenReturn(user); + + User result = userService.findBySubject(user.getSubject()); + assertNotNull(result); + assertEquals(user, result); + } + + @Test + public void testSaveUser() { + User user = createTestUser(); + when(userRepository.save(user)).thenReturn(user); + + User result = userService.save(user); + assertNotNull(result); + assertEquals(user, result); + } + + @Test + public void updateUserConsents_newUser() { + when(fenceMappingUtility.getFENCEMapping()).thenReturn(Map.of("phs1234.c1", new StudyMetaData().setHarmonized(false).setDataType("P"))); + when(userConsentsRepository.findByUserId(any(UUID.class))).thenReturn(null); + User user = createTestUser(); + + userService.updateUserConsents(user, Set.of("phs1234.c1")); + + ArgumentCaptor userConsentsCaptor = ArgumentCaptor.forClass(UserConsents.class); + verify(userConsentsRepository).save(userConsentsCaptor.capture()); + assertEquals(Map.of("\\_consents\\", Set.of("phs1234.c1")), userConsentsCaptor.getValue().getConsents()); + } + + + @Test + public void updateUserConsents_existingUser() { + when(fenceMappingUtility.getFENCEMapping()).thenReturn(Map.of("phs1234.c1", new StudyMetaData().setHarmonized(false).setDataType("P"))); + when(userConsentsRepository.findByUserId(any(UUID.class))).thenReturn(new UserConsents().setConsents(Map.of("_consents", Set.of("phs345.c2")))); + User user = createTestUser(); + + userService.updateUserConsents(user, Set.of("phs1234.c1")); + + ArgumentCaptor userConsentsCaptor = ArgumentCaptor.forClass(UserConsents.class); + verify(userConsentsRepository).save(userConsentsCaptor.capture()); + assertEquals(Map.of("\\_consents\\", Set.of("phs1234.c1")), userConsentsCaptor.getValue().getConsents()); + } + + private UserClaims buildTestUserClaims(User user) { + UserClaims userClaims = new UserClaims(); + userClaims.setUuid(user.getUuid().toString()); + userClaims.setSub(user.getSubject()); + userClaims.setEmail(user.getEmail()); + userClaims.setName(user.getName()); + return userClaims; + } + + private User createTestUser() { + User user = new User(); + user.setUuid(UUID.randomUUID()); + user.setRoles(new HashSet<>(Collections.singleton(createTestRole()))); + user.setSubject("TEST_SUBJECT"); + user.setEmail("test@email.com"); + user.setAcceptedTOS(new Date()); + user.setActive(true); + + return user; + } + + private Application createTestApplication() { + Application application = new Application(); + application.setUuid(UUID.randomUUID()); + application.setName("TEST_APPLICATION"); + application.setToken(createValidApplicationTestToken(application)); + application.setPrivileges(new HashSet<>()); + return application; + } + + private String createValidApplicationTestToken(Application application) { + return this.jwtUtil.createJwtToken( + null, null, + new HashMap<>( + Map.of( + "user_id", AuthNaming.PSAMA_APPLICATION_TOKEN_PREFIX + "|" + application.getName() + ) + ), + AuthNaming.PSAMA_APPLICATION_TOKEN_PREFIX + "|" + application.getUuid().toString(), 365L * 1000 * 60 * 60 * 24); + } + + private Role createTestRole() { + Role role = new Role(); + role.setName("TEST_ROLE"); + role.setUuid(UUID.randomUUID()); + role.setPrivileges(Collections.singleton(createTestPrivilege())); + return role; + } + + private Privilege createTestPrivilege() { + Privilege privilege = new Privilege(); + privilege.setName("TEST_PRIVILEGE"); + privilege.setUuid(UUID.randomUUID()); + privilege.setQueryTemplate(createQueryTemplate("consent_concept_path_"+privilege.getUuid(), "project_name_"+privilege.getUuid(), "consent_group_"+privilege.getUuid())); + + return privilege; + } + + private void configureUserSecurityContext(User user) { + CustomUserDetails customUserDetails = new CustomUserDetails(user); + // configure security context + UsernamePasswordAuthenticationToken authentication = new UsernamePasswordAuthenticationToken(customUserDetails, null, customUserDetails.getAuthorities()); + when(securityContext.getAuthentication()).thenReturn(authentication); + } + + private Role createSuperAdminRole() { + Role role = new Role(); + role.setName(AuthNaming.AuthRoleNaming.SUPER_ADMIN); + role.setUuid(UUID.randomUUID()); + role.setPrivileges(Collections.singleton(createSuperAdminPrivilege())); + return role; + } + + private Privilege createSuperAdminPrivilege() { + Privilege privilege = new Privilege(); + privilege.setName(AuthNaming.AuthRoleNaming.SUPER_ADMIN); + privilege.setUuid(UUID.randomUUID()); + return privilege; + } + + /** + * Do not use this method in production code. This is only for testing purposes. + * + * @return a 256-bit base64 encoded secret + */ + private String generate256Base64Secret() { + SecureRandom random = new SecureRandom(); + byte[] secret = new byte[32]; + random.nextBytes(secret); + return Base64.getEncoder().encodeToString(secret); + } + + private String createQueryTemplate(String consent_concept_path, String project_name, String consent_group) { + return "{\"categoryFilters\": {\"" + + consent_concept_path + + "\":\"" + + project_name + "." + consent_group + + "\"}," + + "\"numericFilters\":{},\"requiredFields\":[]," + + "\"variantInfoFilters\":[{\"categoryVariantInfoFilters\":{},\"numericVariantInfoFilters\":{}}]," + + "\"expectedResultType\": \"COUNT\"" + + "}"; + } + +} \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/AuthenticationServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/AuthenticationServiceTest.java new file mode 100644 index 000000000..d3ce7490b --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/AuthenticationServiceTest.java @@ -0,0 +1,197 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl.authentication; + +import com.fasterxml.jackson.databind.JsonNode; +import edu.harvard.hms.dbmi.avillach.auth.entity.Connection; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import edu.harvard.hms.dbmi.avillach.auth.entity.UserClaims; +import edu.harvard.hms.dbmi.avillach.auth.exceptions.NotAuthorizedException; +import edu.harvard.hms.dbmi.avillach.auth.repository.ConnectionRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserRepository; +import edu.harvard.hms.dbmi.avillach.auth.service.AuthenticationService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.BasicMailService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.CacheEvictionService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.OauthUserMatchingService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.UserService; +import edu.harvard.hms.dbmi.avillach.auth.utils.RestClientUtil; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockitoAnnotations; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.http.HttpHeaders; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.ContextConfiguration; + +import java.io.IOException; +import java.util.HashMap; +import java.util.Map; +import java.util.Optional; +import java.util.UUID; + +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertThrows; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.ArgumentMatchers.anyInt; +import static org.mockito.ArgumentMatchers.anyString; +import static org.mockito.Mockito.*; + +@SpringBootTest +@ContextConfiguration(classes = {AuthenticationService.class}) +public class AuthenticationServiceTest { + + @MockBean + private OauthUserMatchingService matchingService; + @MockBean + private UserRepository userRepository; + @MockBean + private BasicMailService basicMailService; + @MockBean + private UserService userService; + @MockBean + private ConnectionRepository connectionRepository; + @MockBean + private RestClientUtil restClientUtil; + @MockBean + private CacheEvictionService cacheEvictionService; + + private Auth0AuthenticationService authenticationService; + + private final String accessToken = "dummyAccessToken"; + private Map authRequest; + + @BeforeEach + public void setUp() { + MockitoAnnotations.openMocks(this); + authRequest = new HashMap<>(); + authRequest.put("access_token", accessToken); + String redirectURI = "http://dummyRedirectUri.com"; + authRequest.put("redirectURI", redirectURI); + + authenticationService = new Auth0AuthenticationService(matchingService, userRepository, basicMailService, userService, connectionRepository, restClientUtil, true, false, "localhost", cacheEvictionService); + } + + // Tests missing parameters in the authentication request + @Test + public void testGetToken_MissingParameters() throws IOException { + assertThrows(IllegalArgumentException.class, () -> { + authenticationService.authenticate(new HashMap<>(), "localhost"); // Empty map should trigger the exception + }); + } + + // Tests the failure in retrieving user information, expecting an IOException to be converted into a NotAuthorizedException + @Test + public void testGetToken_UserInfoRetrievalFails() throws IOException { + when(this.restClientUtil.retrieveGetResponseWithRequestConfiguration(anyString(), any(HttpHeaders.class), anyInt())) + .thenThrow(new NotAuthorizedException("Failed to retrieve user info")); + + assertThrows(NotAuthorizedException.class, () -> { + authenticationService.authenticate(authRequest, "localhost"); + }); + } + + // Tests the scenario where the user ID is not found in the user info retrieved + @Test + public void testGetToken_NoUserIdInUserInfo() throws IOException { + when(this.restClientUtil.retrieveGetResponseWithRequestConfiguration(anyString(), any(), anyInt())) + .thenReturn(new ResponseEntity<>("{}", HttpStatus.OK)); + + assertThrows(NotAuthorizedException.class, () -> { + authenticationService.authenticate(authRequest, "localhost"); + }); + } + + // Tests a successful token retrieval scenario + @Test + public void testGetToken_Successful() throws Exception { + setupSuccessfulTokenRetrievalScenario(); + + // return null for matching user + when(matchingService.matchTokenToUser(any())).thenReturn(null); + + HashMap token = authenticationService.authenticate(authRequest, "localhost"); + assertNotNull(token); + } + + // Additional test to handle retries in user info retrieval + @Test + public void testRetrieveUserInfo_WithRetries() throws Exception { + when(this.restClientUtil.retrieveGetResponseWithRequestConfiguration(anyString(), any(), anyInt())) + .thenThrow(new RuntimeException("Network error")) + .thenReturn(new ResponseEntity<>("{}", HttpStatus.OK)); + // Assuming retrieveUserInfo is accessible, or using reflection if it is private + JsonNode result = authenticationService.retrieveUserInfo(accessToken); + assertNotNull(result); + } + + // Tests matching a token to a user when no existing user is found and an attempt to create a user fails + @Test + public void testGetToken_NoUserMatchingAndCreationFails() throws Exception { + setupNoUserMatchScenario(); + assertThrows(NotAuthorizedException.class, () -> { + authenticationService.authenticate(authRequest, "localhost"); + }); + } + + // Test scenario where denied access email is triggered + @Test + public void testGetToken_SendDeniedAccessEmail() throws Exception { + setupDeniedEmailScenario(); + this.authenticationService.setDeniedEmailEnabled(true); + try { + authenticationService.authenticate(authRequest, "localhost"); + } catch (Exception e) { + verify(basicMailService).sendDeniedAccessEmail(any()); + } + } + + private void setupSuccessfulTokenRetrievalScenario() throws IOException { + this.authenticationService.setDeniedEmailEnabled(false); + JsonNode mockUserInfo = mock(JsonNode.class); + when(mockUserInfo.get("user_id")).thenReturn(mock(JsonNode.class)); + String userId = "user123"; + when(mockUserInfo.get("user_id").asText()).thenReturn(userId); + when(mockUserInfo.get("identities")).thenReturn(mock(JsonNode.class)); + when(mockUserInfo.get("identities").get(0)).thenReturn(mock(JsonNode.class)); + when(mockUserInfo.get("identities").get(0).get("connection")).thenReturn(mock(JsonNode.class)); + String connectionId = "conn123"; + when(mockUserInfo.get("identities").get(0).get("connection").asText()).thenReturn(connectionId); + + String validJson = "{" + + "\"user_id\": \"" + userId + "\"," + + "\"identities\": [" + + " {\"connection\": \"" + connectionId + "\"}" + + "]" + + "}"; + + when(restClientUtil.retrieveGetResponseWithRequestConfiguration(anyString(), any(HttpHeaders.class), anyInt())) + .thenReturn(new ResponseEntity<>(validJson, HttpStatus.OK)); + + // Create a test user + Connection connection = new Connection(); + connection.setId(connectionId); + + User user = new User(); + user.setSubject(userId); + user.setConnection(connection); + user.setUuid(UUID.randomUUID()); + + when(connectionRepository.findById(anyString())).thenReturn(Optional.of(connection)); + when(matchingService.matchTokenToUser(any())).thenReturn(user); + when(userRepository.findBySubjectAndConnection(anyString(), any(Connection.class))).thenReturn(user); + when(userService.getUserProfileResponse(any(UserClaims.class))).thenReturn(new HashMap<>()); + } + + private void setupNoUserMatchScenario() throws IOException { + setupSuccessfulTokenRetrievalScenario(); + + when(matchingService.matchTokenToUser(any())).thenReturn(null); + when(userRepository.findBySubjectAndConnection(anyString(), any(Connection.class))).thenReturn(null); + } + + private void setupDeniedEmailScenario() throws Exception { + setupNoUserMatchScenario(); + doThrow(new jakarta.mail.MessagingException("Failed sending email")).when(basicMailService).sendDeniedAccessEmail(any()); + } + +} \ No newline at end of file diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/RASAuthenticationServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/RASAuthenticationServiceTest.java new file mode 100644 index 000000000..282de8a2e --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/RASAuthenticationServiceTest.java @@ -0,0 +1,202 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl.authentication; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.hms.dbmi.avillach.auth.entity.Connection; +import edu.harvard.hms.dbmi.avillach.auth.entity.Privilege; +import edu.harvard.hms.dbmi.avillach.auth.entity.Role; +import edu.harvard.hms.dbmi.avillach.auth.entity.User; +import edu.harvard.hms.dbmi.avillach.auth.entity.UserClaims; +import edu.harvard.hms.dbmi.avillach.auth.model.ras.Passport; +import edu.harvard.hms.dbmi.avillach.auth.model.ras.RasDbgapPermission; +import edu.harvard.hms.dbmi.avillach.auth.repository.RoleRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserRepository; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.*; +import edu.harvard.hms.dbmi.avillach.auth.utils.FenceMappingUtility; +import edu.harvard.hms.dbmi.avillach.auth.utils.RestClientUtil; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockitoAnnotations; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.context.ApplicationContext; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.ContextConfiguration; + +import java.util.*; + +import org.mockito.ArgumentCaptor; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + +@SpringBootTest +@ContextConfiguration(classes = {RASPassPortService.class, RASAuthenticationService.class, ApplicationContext.class}) +public class RASAuthenticationServiceTest { + + @MockBean + private UserService userService; + @MockBean + private RestClientUtil restClientUtil; + @MockBean + private ConnectionWebService connectionService; + @MockBean + private CacheEvictionService cacheEvictionService; + @MockBean + private RoleService roleService; + @MockBean + private UserRepository userRepository; + @MockBean + private ApplicationContext applicationContext; + @MockBean + private LoggingClient loggingClient; + + private RASPassPortService rasPassPortService; + private RASAuthenticationService rasAuthenticationService; + + private final String testAccessToken = "someRandomAccessToken"; + private final String code = "123123123"; + private final String testDomain = "https://testdomain.com"; + private Map authRequest; + private final String exampleRasPassport = "eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsImtpZCI6ImRlZmF1bHRfc3NsX2tleSJ9.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.sJwAZeR8cYyF-BCluC9fmiQAi14L7hC3DB4MoFQNNdoakUBujPZ-NlpfP2rBgJQ3CGcxsF95Vdczm6Yk4TKa68eXkKjkswjsSSQg0qErgFhN2jis9KMxnMfmfPNUfb0lioHtD-_oghRkd9239oUwLR06KB5Ux3mD4Pc0ZPbJxJcPmyP9DZ8WEHmAFIJpcoayHwJDr1jt-GbqUtaTCs1VQ9Habh8Z8fvwrlvQNj744m5eq6141bD0G15KgvbyYf9L4_PYNgMjTyUx9EGyetrxQ4XmOpDF_ZbFEhZliy80qfO2HGQzSId-dKXCvPI_SUWcCVeJqPwmXTirTt9qJ63ypw"; + + @BeforeEach + public void setUp() throws Exception { + MockitoAnnotations.openMocks(this); + RoleService roleService = new RoleService(mock(UserRepository.class), mock(RoleRepository.class), mock(PrivilegeService.class), mock(FenceMappingUtility.class), mock(ApplicationContext.class), null); + this.rasPassPortService = spy(new RASPassPortService(restClientUtil, userService, "", cacheEvictionService, null)); + doReturn(false).when(rasPassPortService).isExpired(any()); + + rasAuthenticationService = new RASAuthenticationService( + userService, + restClientUtil, + true, + "test.com", + "", + "", + "", + "https://stsstg.nih.gov", + roleService, + rasPassPortService, + connectionService, + cacheEvictionService + ); + + Connection rasConnection = new Connection(); + rasConnection.setSubPrefix("okta-ras|"); + rasConnection.setUuid(UUID.randomUUID()); + rasConnection.setId("okta-ras"); + rasConnection.setLabel("RAS"); + rasAuthenticationService.setRasConnection(rasConnection); + + authRequest = new HashMap<>(); + authRequest.put("code", code); + authRequest.put("redirectURI", testDomain); + } + + @Test + public void testAuthorizationCodeFlow_Successful() { + String data = "{\"access_token\":\"" + testAccessToken + "\", \"active\":true, \"id_token\":\"SomeRandomToken\"}"; + String payload = "token_type_hint=access_token&token=" + testAccessToken; + String redirectUri = "https://" + testDomain + "/login/loading"; + String queryString = "grant_type=authorization_code" + "&code=" + code + "&redirect_uri=" + redirectUri; + String introspectionResponse = + "{\"active\":true,\"sub\":\"example_email@test.com\",\"client_id\":\"test_client_id\"," + + "\"userid\":\"test_userid\",\"preferred_username\":\"testuser\"," + + "\"email\":\"okta_email@test.com\",\"firstName\":\"Test\",\"lastName\":\"User\"," + + "\"passport_jwt_v11\":\""+ exampleRasPassport +"\"}"; + + // token exchange + when(restClientUtil.retrievePostResponse(anyString(), any(), eq(queryString))).thenReturn(ResponseEntity.ok(data)); + // introspect + when(restClientUtil.retrievePostResponse(anyString(), any(), eq(payload))).thenReturn(ResponseEntity.ok(introspectionResponse)); + + doNothing().when(cacheEvictionService).evictCache(any(User.class)); + + User user = createTestUser(); + user.setSubject("okta-ras|adfadfaf"); + when(userService.createRasUser(any(), any())).thenReturn(Optional.of(user)); + when(userService.updateUserRoles(any(), any())).thenReturn(user); + when(userService.updateUserConsents(any(), any())).thenReturn(user); + + ArgumentCaptor claimsCaptor = ArgumentCaptor.forClass(UserClaims.class); + when(userService.getUserProfileResponse(claimsCaptor.capture())).thenReturn(new HashMap<>()); + + HashMap authenticate = rasAuthenticationService.authenticate(authRequest, testDomain); + assertNotNull(authenticate); + + UserClaims capturedClaims = claimsCaptor.getValue(); + assertEquals("test_userid", capturedClaims.getUserid()); + assertEquals("testuser", capturedClaims.getPreferred_username()); + assertEquals("test@email.com", capturedClaims.getEmail()); + assertEquals("RAS", capturedClaims.getIdp()); + assertEquals("https://ncbi.nlm.nih.gov/gap", capturedClaims.getUser_permission_group()); + } + + @Test + public void testUpdateUserRoles_withEmptyDBGapPermissions() throws JsonProcessingException { + String introspectionResponse = + "{\"active\":true,\"sub\":\"example_email@test.com\",\"client_id\":\"test_client_id\",\"passport_jwt_v11\":\""+ exampleRasPassport +"\"}"; + JsonNode introspectionResponseParsed = new ObjectMapper().readTree(introspectionResponse); + User user = createTestUser(); + Optional passport = this.rasPassPortService.extractPassport(introspectionResponseParsed); + assertTrue(passport.isPresent()); + + Set dbgapPermissions = new HashSet<>(); + Set dbgapRoleNames = new HashSet<>(); + + when(rasPassPortService.ga4ghPassportToRasDbgapPermissions(any())).thenReturn(dbgapPermissions); + when(roleService.getRoleNamesForDbgapPermissions(any())).thenReturn(dbgapRoleNames); + when(userService.updateUserRoles(any(), any())).thenReturn(user); + when(userService.updateUserConsents(any(), any())).thenReturn(user); + + user = this.rasAuthenticationService.updateRasUserRoles(code, user, passport.get()); + assertNotNull(user); + + // We are verifying that we attempt to update a users roles even if no dbgap roles are present. + verify(userService, times(1)).updateUserRoles(user, dbgapRoleNames); + } + + private User createTestUser() { + User user = new User(); + user.setUuid(UUID.randomUUID()); + user.setRoles(new HashSet<>(Collections.singleton(createTestRole()))); + user.setSubject("TEST_SUBJECT"); + user.setEmail("test@email.com"); + user.setAcceptedTOS(new Date()); + user.setActive(true); + + return user; + } + + private Role createTestRole() { + Role role = new Role(); + role.setName("TEST_ROLE"); + role.setUuid(UUID.randomUUID()); + role.setPrivileges(Collections.singleton(createTestPrivilege())); + return role; + } + + private Privilege createTestPrivilege() { + Privilege privilege = new Privilege(); + privilege.setName("TEST_PRIVILEGE"); + privilege.setUuid(UUID.randomUUID()); + privilege.setQueryTemplate(createQueryTemplate("consent_concept_path_"+privilege.getUuid(), "project_name_"+privilege.getUuid(), "consent_group_"+privilege.getUuid())); + + return privilege; + } + + private String createQueryTemplate(String consent_concept_path, String project_name, String consent_group) { + return "{\"categoryFilters\": {\"" + + consent_concept_path + + "\":\"" + + project_name + "." + consent_group + + "\"}," + + "\"numericFilters\":{},\"requiredFields\":[]," + + "\"variantInfoFilters\":[{\"categoryVariantInfoFilters\":{},\"numericVariantInfoFilters\":{}}]," + + "\"expectedResultType\": \"COUNT\"" + + "}"; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/AuthorizationServiceByUseCasesTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/AuthorizationServiceByUseCasesTest.java new file mode 100644 index 000000000..4d35b900b --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/AuthorizationServiceByUseCasesTest.java @@ -0,0 +1,785 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl.authorization; + +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.hms.dbmi.avillach.auth.entity.AccessRule; +import edu.harvard.hms.dbmi.avillach.auth.repository.AccessRuleRepository; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.AccessRuleService; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.Mockito; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.test.context.ContextConfiguration; + +import java.io.IOException; +import java.util.HashSet; +import java.util.Map; +import java.util.Set; +import java.util.UUID; + +import static org.junit.jupiter.api.Assertions.assertFalse; +import static org.junit.jupiter.api.Assertions.assertTrue; + +/** + *

    This is a test class from the view of high level use cases (user input aspect)

    + *
    + *

    This class should contain the following use cases:

    + *
      + *
    • A: Level 1 users must not include DATAFRAME as expectedResultType + *
      This is for the more general level 1 and level 2 abstractions we already have in other projects.
      • + *
    • B: A user has access to \\demographics\\ but not to \\laboratory\\ + *
      Basic study-level access control
      • + *
    • C: A user has access to everything for COUNT expectedResultType, but only \\demographics\\ for DATAFRAME + *
      This is level 1 for everything except level 2 for demographics Also emulates study level access where a user is level 1 for all studies and level 2 for a specific study + *
      Also emulates study level access where a user is level 1 for all studies and level 2 for a specific study + *
      • + *
    • D: A user has access to everything for COUNT and CROSS_COUNT expectedResultTypes but only has DATAFRAME access if they include \\demographics\\SEX\\male as a filter + *
      In this case male is being used to emulate a consent group based access control
      • + *
    • E: A user has access to \\laboratory\\ if they have included \\demographics\\SEX\\male as a filter, and has access to \\examination\\ if they have included \\demographics\\SEX\\female as a filter + *
      This is a more complex consent group based access control use-case, male is consent group A, female is consent group B
      • + *
    • F: A user has access to run queries with variantInfoFilters and specific variant category filters only. The user cannot include any other filters or select any fields and can only do COUNT queries. + *
      This is the authentication only variant search functionality.
      • + *
    + * + * We also have a class testing from the aspect of design, which means each test case is just testing one feature. + * @see AuthorizationServiceTest + */ +@SpringBootTest +@ContextConfiguration(classes = {AccessRuleService.class}) +public class AuthorizationServiceByUseCasesTest { + + @MockBean + private AccessRuleRepository accessRuleRepository; + + @Autowired + private AccessRuleService accessRuleService; + + private final ObjectMapper mapper = new ObjectMapper(); + + private static AccessRule rule_caseA; + private static AccessRule rule_caseB; + private static AccessRule rule_caseC; + private static AccessRule rule_caseD; + private static AccessRule rule_caseE; + private static AccessRule rule_caseE_2; + private static AccessRule rule_caseF; + private static AccessRule rule_caseG; + + private static AccessRule AR_CategoryFilter_String_contains; + private static AccessRule AR_CategoryFilter_Array_Contains; + private static AccessRule AR_ExpectedResultType_String_contains; + + + public static String sample_caseAB_pass = "{\n" + + " \"query\": {\n" + + " \"categoryFilters\": {\n" + + " \"\\\\demographics\\\\SEX\\\\\": [\n" + + " \"male\"\n" + + " ]\n" + + " },\n" + + " \"numericFilters\": {},\n" + + " \"requiredFields\": [\n" + + " \"\\\\demographics\\\\AGE\\\\\"\n" + + " ],\n" + + " \"expectedResultType\": \"COUNT\",\n" + + " \"fields\": [\n" + + " \"\\\\demographics\\\\SEX\\\\\",\n" + + " \"\\\\demographics\\\\AGE\\\\\"\n" + + " ]\n" + + " },\n" + + " \"resourceUUID\": \"8e8c7ed0-87ea-4342-b8da-f939e46bac26\",\n" + + " \"resourceCredentials\": {}\n" + + "}"; + + public static String sample_caseAB_fail = "{\n" + + " \"query\": {\n" + + " \"categoryFilters\": {\n" + + " \"\\\\laboratory\\\\SEX\\\\\": [\n" + + " \"male\"\n" + + " ]\n" + + " },\n" + + " \"numericFilters\": {},\n" + + " \"requiredFields\": [\n" + + " \"\\\\demographics\\\\AGE\\\\\"\n" + + " ],\n" + + " \"expectedResultType\": \"DATAFRAME\",\n" + + " \"fields\": [\n" + + " \"\\\\demographics\\\\SEX\\\\\",\n" + + " \"\\\\demographics\\\\AGE\\\\\"\n" + + " ]\n" + + " },\n" + + " \"resourceUUID\": \"8e8c7ed0-87ea-4342-b8da-f939e46bac26\",\n" + + " \"resourceCredentials\": {}\n" + + "}"; + + public static String sample_caseCD_pass = "{\n" + + " \"query\": {\n" + + " \"categoryFilters\": {\n" + + " \"\\\\demographics\\\\SEX\\\\\": [\n" + + " \"male\"\n" + + " ]\n" + + " },\n" + + " \"numericFilters\": {},\n" + + " \"requiredFields\": [\n" + + " \"\\\\demographics\\\\AGE\\\\\"\n" + + " ],\n" + + " \"expectedResultType\": \"dataframe\",\n" + + " \"fields\": [\n" + + " \"\\\\demographics\\\\SEX\\\\\",\n" + + " \"\\\\demographics\\\\AGE\\\\\"\n" + + " ]\n" + + " },\n" + + " \"resourceUUID\": \"8e8c7ed0-87ea-4342-b8da-f939e46bac26\",\n" + + " \"resourceCredentials\": {}\n" + + "}"; + + public static String sample_caseCD_fail = "{\n" + + " \"query\": {\n" + + " \"categoryFilters\": {\n" + + " \"\\\\demographics\\\\SEX\\\\\": [\n" + + " \"male\",\n" + + " \"female\"\n" + + " ]\n" + + " },\n" + + " \"numericFilters\": {},\n" + + " \"requiredFields\": [\n" + + " \"\\\\demographics\\\\AGE\\\\\"\n" + + " ],\n" + + " \"expectedResultType\": \"dataframe\",\n" + + " \"fields\": [\n" + + " \"\\\\demographics\\\\SEX\\\\\",\n" + + " \"\\\\demographics\\\\AGE\\\\\",\n" + + " \"\\\\laboratory\\\\AGE\\\\\"\n" + + " ]\n" + + " },\n" + + " \"resourceUUID\": \"8e8c7ed0-87ea-4342-b8da-f939e46bac26\",\n" + + " \"resourceCredentials\": {}\n" + + "}"; + + public static String sample_caseCD_fail_2 = "{\n" + + " \"query\": {\n" + + " \"categoryFilters\": {\n" + + " \"\\\\laboratory\\\\SEX\\\\\": [\n" + + " \"male\"\n" + + " ]\n" + + " },\n" + + " \"numericFilters\": {},\n" + + " \"requiredFields\": [\n" + + " \"\\\\demographics\\\\AGE\\\\\"\n" + + " ],\n" + + " \"expectedResultType\": \"dataframe\",\n" + + " \"fields\": [\n" + + " \"\\\\demographics\\\\SEX\\\\\",\n" + + " \"\\\\demographics\\\\AGE\\\\\"\n" + + " ]\n" + + " },\n" + + " \"resourceUUID\": \"8e8c7ed0-87ea-4342-b8da-f939e46bac26\",\n" + + " \"resourceCredentials\": {}\n" + + "}"; + + public static String sample_caseE_pass = "{\n" + + " \"query\": {\n" + + " \"categoryFilters\": {\n" + + " \"\\\\demographics\\\\SEX\\\\\": [\n" + + " \"male\"\n" + + " ]\n" + + " },\n" + + " \"numericFilters\": {},\n" + + " \"requiredFields\": [\n" + + " \"\\\\demographics\\\\AGE\\\\\"\n" + + " ],\n" + + " \"expectedResultType\": \"dataframe\",\n" + + " \"fields\": [\n" + + " \"\\\\demographics\\\\SEX\\\\\",\n" + + " \"\\\\laboratory\\\\AGE\\\\\"\n" + + " ]\n" + + " },\n" + + " \"resourceUUID\": \"8e8c7ed0-87ea-4342-b8da-f939e46bac26\",\n" + + " \"resourceCredentials\": {}\n" + + "}"; + + public static String sample_caseE_2_pass = "{\n" + + " \"query\": {\n" + + " \"categoryFilters\": {\n" + + " \"\\\\demographics\\\\SEX\\\\\": [\n" + + " \"female\"\n" + + " ]\n" + + " },\n" + + " \"numericFilters\": {},\n" + + " \"requiredFields\": [\n" + + " \"\\\\demographics\\\\AGE\\\\\"\n" + + " ],\n" + + " \"expectedResultType\": \"dataframe\",\n" + + " \"fields\": [\n" + + " \"\\\\demographics\\\\SEX\\\\\",\n" + + " \"\\\\examination\\\\AGE\\\\\"\n" + + " ]\n" + + " },\n" + + " \"resourceUUID\": \"8e8c7ed0-87ea-4342-b8da-f939e46bac26\",\n" + + " \"resourceCredentials\": {}\n" + + "}"; + + public static String sample_caseE_fail = "{\n" + + " \"query\": {\n" + + " \"categoryFilters\": {\n" + + " \"\\\\demographics\\\\SEX\\\\\": [\n" + + " \"nothing\"\n" + + " ]\n" + + " },\n" + + " \"numericFilters\": {},\n" + + " \"requiredFields\": [\n" + + " \"\\\\demographics\\\\AGE\\\\\"\n" + + " ],\n" + + " \"expectedResultType\": \"dataframe\",\n" + + " \"fields\": [\n" + + " \"\\\\demographics\\\\SEX\\\\\",\n" + + " \"\\\\examination\\\\AGE\\\\\",\n" + + " \"\\\\laboratory\\\\AGE\\\\\"\n" + + " ]\n" + + " },\n" + + " \"resourceUUID\": \"8e8c7ed0-87ea-4342-b8da-f939e46bac26\",\n" + + " \"resourceCredentials\": {}\n" + + "}"; + + public static String sample_caseE_2_fail = "{\n" + + " \"query\": {\n" + + " \"categoryFilters\": {\n" + + " \"\\\\demographics\\\\SEX\\\\\": [\n" + + " \"nothing\"\n" + + " ],\n" + + " \"\\\\laboratory\\\\SEX\\\\\": [\n" + + " \"male\"\n" + + " ]\n" + + " },\n" + + " \"numericFilters\": {},\n" + + " \"requiredFields\": [\n" + + " \"\\\\demographics\\\\AGE\\\\\"\n" + + " ],\n" + + " \"expectedResultType\": \"dataframe\",\n" + + " \"fields\": [\n" + + " \"\\\\demographics\\\\SEX\\\\\",\n" + + " \"\\\\examination\\\\AGE\\\\\"\n" + + " ]\n" + + " },\n" + + " \"resourceUUID\": \"8e8c7ed0-87ea-4342-b8da-f939e46bac26\",\n" + + " \"resourceCredentials\": {}\n" + + "}"; + + public static String sample_caseF_pass = "{\n" + + " \"resourceUUID\": \"8e8c7ed0-87ea-4342-b8da-f939e46bac26\",\n" + + " \"query\": {\n" + + " \"categoryFilters\": {\n" + + " \"3,112222,112222,C,T\": [\n" + + " \"1/1\"\n" + + " ]\n" + + " },\n" + + " \"numericFilters\": {},\n" + + " \"requiredFields\": [\n" + + " ],\n" + + " \"variantInfoFilters\": [\n" + + " {\n" + + " \"categoryVariantInfoFilters\": {\n" + + " \"HD\": [\n" + + " \"\\\"Asthma,_severe\\\"\"\n" + + " ]\n" + + " },\n" + + " \"numericVariantInfoFilters\": {}\n" + + " }\n" + + " ],\n" + + " \"expectedResultType\": \"COUNT\"\n" + + " },\n" + + " \"resourceCredentials\": {}\n" + + "}"; + + public static String sample_caseF_fail = "{\n" + + " \"resourceUUID\": \"8e8c7ed0-87ea-4342-b8da-f939e46bac26\",\n" + + " \"query\": {\n" + + " \"categoryFilters\": {\n" + + " \"3,112222,112222,C,T\": [\n" + + " \"1/1\"\n" + + " ],\n" + + " \"\\\\demographics\\\\SEX\\\\\": [\n" + + " \"male\"\n" + + " ]\n" + + " },\n" + + " \"numericFilters\": {},\n" + + " \"requiredFields\": [\n" + + " ],\n" + + " \"variantInfoFilters\": [\n" + + " {\n" + + " \"categoryVariantInfoFilters\": {\n" + + " \"HD\": [\n" + + " \"\\\"Asthma,_severe\\\"\"\n" + + " ]\n" + + " },\n" + + " \"numericVariantInfoFilters\": {}\n" + + " }\n" + + " ],\n" + + " \"expectedResultType\": \"COUNT\"\n" + + " },\n" + + " \"resourceCredentials\": {}\n" + + "}"; + + public static String sample_caseF_fail_2 = "{\n" + + " \"resourceUUID\": \"8e8c7ed0-87ea-4342-b8da-f939e46bac26\",\n" + + " \"query\": {\n" + + " \"categoryFilters\": {\n" + + " \"3,112222,112222,C,T\": [\n" + + " \"1/1\"\n" + + " ]\n" + + " },\n" + + " \"numericFilters\": {},\n" + + " \"requiredFields\": [\n" + + " ],\n" + + " \"expectedResultType\": \"COUNT\"\n" + + " },\n" + + " \"resourceCredentials\": {}\n" + + "}"; + + public static String sample_caseF_fail_3 = "{\n" + + " \"resourceUUID\": \"8e8c7ed0-87ea-4342-b8da-f939e46bac26\",\n" + + " \"query\": {\n" + + " \"categoryFilters\": {\n" + + " \"3,112222,112222,C,T\": [\n" + + " \"1/1\"\n" + + " ]\n" + + " },\n" + + " \"numericFilters\": {},\n" + + " \"requiredFields\": [\n" + + " ],\n" + + " \"variantInfoFilters\": [\n" + + " {\n" + + " \"categoryVariantInfoFilters\": {\n" + + " \"HD\": [\n" + + " \"\\\"Asthma,_severe\\\"\"\n" + + " ]\n" + + " },\n" + + " \"numericVariantInfoFilters\": {}\n" + + " }\n" + + " ],\n" + + " \"expectedResultType\": \"CROSS_COUNT\"\n" + + " },\n" + + " \"resourceCredentials\": {}\n" + + "}"; + + public static String sample_caseF_fail_4 = "{\n" + + " \"resourceUUID\": \"8e8c7ed0-87ea-4342-b8da-f939e46bac26\",\n" + + " \"query\": {\n" + + " \"categoryFilters\": {\n" + + " \"3,112222,112222,C,T\": [\n" + + " \"1/1\"\n" + + " ]\n" + + " },\n" + + " \"numericFilters\": {},\n" + + " \"requiredFields\": [\n" + + " \"\\\\000_UDN ID\\\\\"\n" + + " ],\n" + + " \"variantInfoFilters\": [\n" + + " {\n" + + " \"categoryVariantInfoFilters\": {\n" + + " \"HD\": [\n" + + " \"\\\"Asthma,_severe\\\"\"\n" + + " ]\n" + + " },\n" + + " \"numericVariantInfoFilters\": {}\n" + + " }\n" + + " ],\n" + + " \"expectedResultType\": \"COUNT\"\n" + + " },\n" + + " \"resourceCredentials\": {}\n" + + "}"; + + public static String sample_caseF_fail_5 = "{\n" + + " \"resourceUUID\": \"8e8c7ed0-87ea-4342-b8da-f939e46bac26\",\n" + + " \"query\": {\n" + + " \"categoryFilters\": {\n" + + " \"3,112222,112222,C,T\": [\n" + + " \"1/1\"\n" + + " ]\n" + + " },\n" + + " \"numericFilters\": {\"nothing\":null},\n" + + " \"requiredFields\": [\n" + + " ],\n" + + " \"variantInfoFilters\": [\n" + + " {\n" + + " \"categoryVariantInfoFilters\": {\n" + + " \"HD\": [\n" + + " \"\\\"Asthma,_severe\\\"\"\n" + + " ]\n" + + " },\n" + + " \"numericVariantInfoFilters\": {}\n" + + " }\n" + + " ],\n" + + " \"expectedResultType\": \"COUNT\"\n" + + " },\n" + + " \"resourceCredentials\": {}\n" + + "}"; + + // Sample for anyRecordOf test case (Case G) + public static String sample_caseG_pass = "{\n" + + " \"query\": {\n" + + " \"categoryFilters\": {\n" + + " },\n" + + " \"numericFilters\": {},\n" + + " \"requiredFields\": [],\n" + + " \"anyRecordOf\": [\n" + + " \"\\\\phs001001\\\\pht005655\\\\phv00354560\\\\age\\\\\"\n" + + " ],\n" + + " \"fields\": [\n" + + " \"\\\\_Topmed Study Accession with Subject ID\\\\\",\n" + + " \"\\\\_Parent Study Accession with Subject ID\\\\\"\n" + + " ],\n" + + " \"variantInfoFilters\": [\n" + + " {\n" + + " \"categoryVariantInfoFilters\": {},\n" + + " \"numericVariantInfoFilters\": {}\n" + + " }\n" + + " ],\n" + + " \"expectedResultType\": \"COUNT\"\n" + + " },\n" + + " \"resourceUUID\": \"02e23f52-f354-4e8b-992c-d37c8b9ba140\"\n" + + "}"; + + public static String sample_caseG_fail = "{\n" + + " \"query\": {\n" + + " \"categoryFilters\": {\n" + + " \"\\\\_consents\\\\\": [\n" + + " \"phs000956.c2\",\"phs001189.c1\",\"tutorial-biolincc_digitalis\",\"phs001143.c1\",\"phs001032.c1\",\"phs001013.c1\",\"phs001013.c2\",\"phs000280.c1\",\"phs000284.c1\",\"phs000200.c1\",\"phs000280.c2\",\"phs001040.c1\",\"phs000951.c1\",\"phs000974.c1\",\"tutorial-biolincc_camp\",\"phs000997.c1\",\"phs000200.c2\",\"phs000007.c2\",\"phs000974.c2\",\"phs000007.c1\",\"phs000993.c1\",\"phs000179.c1\",\"phs000993.c2\",\"phs001062.c1\",\"phs000964.c3\",\"phs000964.c4\",\"phs000285.c2\",\"phs000285.c1\",\"tutorial-biolincc_framingham\",\"phs000964.c1\",\"phs000964.c2\",\"phs000287.c1\",\"phs001211.c2\",\"phs001211.c1\",\"phs000287.c2\",\"phs000287.c3\",\"phs000287.c4\",\"open_access-1000Genomes\",\"phs001024.c1\",\"phs000209.c1\",\"phs000209.c2\"\n" + + " ]\n" + + " },\n" + + " \"numericFilters\": {\"age\": {\"min\": 20, \"max\": 80}},\n" + + " \"requiredFields\": [\"\\\\demographics\\\\AGE\\\\\"],\n" + + " \"anyRecordOf\": [\n" + + " \"\\\\different_path\\\\different_value\\\\\"\n" + + " ],\n" + + " \"fields\": [\n" + + " \"\\\\_Topmed Study Accession with Subject ID\\\\\",\n" + + " \"\\\\_Parent Study Accession with Subject ID\\\\\"\n" + + " ],\n" + + " \"variantInfoFilters\": [\n" + + " {\n" + + " \"categoryVariantInfoFilters\": {},\n" + + " \"numericVariantInfoFilters\": {}\n" + + " }\n" + + " ],\n" + + " \"expectedResultType\": \"DATAFRAME\"\n" + + " },\n" + + " \"resourceUUID\": \"02e23f52-f354-4e8b-992c-d37c8b9ba140\"\n" + + "}"; + + @BeforeAll + public static void init() { + initialTestCaseA(); + initialTestCaseB(); + initialTestCaseC(); + initialTestCaseD(); + initialTestCaseE(); + initialTestCaseF(); + initialTestCaseG(); + } + + @BeforeEach + public void setUp() { + AccessRuleRepository accessRuleRepository = Mockito.mock(AccessRuleRepository.class); + accessRuleService = new AccessRuleService(accessRuleRepository, "false", "false", "false", "false","false", "false"); + } + + @Test + public void testCaseA() throws IOException { + assertTrue(accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseAB_pass, Map.class), rule_caseA)); + assertFalse(accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseAB_fail, Map.class), rule_caseA)); + } + + private static void initialTestCaseA(){ + rule_caseA = new AccessRule(); + rule_caseA.setUuid(UUID.randomUUID()); + rule_caseA.setType(AccessRule.TypeNaming.NOT_CONTAINS_IGNORE_CASE); + rule_caseA.setName("rule_caseA"); + rule_caseA.setRule("$..expectedResultType"); +// rule_caseA.setRule("$..\\laboratory\\*"); + rule_caseA.setValue("DATAFRAME"); + } + + @Test + public void testCaseB() throws IOException { + assertTrue(accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseAB_pass, Map.class), rule_caseB)); + assertFalse(accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseAB_fail, Map.class), rule_caseB)); + } + + private static void initialTestCaseB(){ + rule_caseB = new AccessRule(); + rule_caseB.setUuid(UUID.randomUUID()); + rule_caseB.setName("rule_caseB"); + rule_caseB.setRule("$..*"); + rule_caseB.setType(AccessRule.TypeNaming.ANY_CONTAINS); + rule_caseB.setValue("\\demographics\\"); + + AccessRule rule_caseB_sub = new AccessRule(); + rule_caseB_sub.setUuid(UUID.randomUUID()); + rule_caseB_sub.setName("rule_caseB_sub"); + rule_caseB_sub.setRule("$..*"); + rule_caseB_sub.setType(AccessRule.TypeNaming.NOT_CONTAINS_IGNORE_CASE); + rule_caseB_sub.setCheckMapNode(true); + rule_caseB_sub.setValue("\\laboratory\\"); + Set accessRuleSubSet = new HashSet<>(); + accessRuleSubSet.add(rule_caseB_sub); + rule_caseB.setSubAccessRule(accessRuleSubSet); + } + + @Test + public void testCaseC() throws IOException { + assertTrue(accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseCD_pass, Map.class), rule_caseC)); + assertFalse(accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseCD_fail, Map.class), rule_caseC)); + assertFalse(accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseCD_fail_2, Map.class), rule_caseC)); + } + + private static void initialTestCaseC(){ + rule_caseC = new AccessRule(); + rule_caseC.setUuid(UUID.randomUUID()); + rule_caseC.setName("rule_caseC"); + + AccessRule rule_caseC_gate2 = new AccessRule(); + rule_caseC_gate2.setUuid(UUID.randomUUID()); + rule_caseC_gate2.setName("rule_caseC_gate2"); + rule_caseC_gate2.setRule("$.query.expectedResultType"); + rule_caseC_gate2.setType(AccessRule.TypeNaming.ALL_EQUALS_IGNORE_CASE); + rule_caseC_gate2.setValue("DATAFRAME"); + + Set rule_caseC_gates = new HashSet<>(); + rule_caseC_gates.add(rule_caseC_gate2); + rule_caseC.setGates(rule_caseC_gates); + + AccessRule rule_caseC_subRule = new AccessRule(); + rule_caseC_subRule.setUuid(UUID.randomUUID()); + rule_caseC_subRule.setName("rule_caseC_subRule"); + rule_caseC_subRule.setRule("$.query.categoryFilters"); + rule_caseC_subRule.setCheckMapNode(true); + rule_caseC_subRule.setCheckMapKeyOnly(true); + rule_caseC_subRule.setType(AccessRule.TypeNaming.ALL_CONTAINS); + rule_caseC_subRule.setValue("\\demographics\\"); + Set rule_caseC_subRules = new HashSet<>(); + rule_caseC_subRules.add(rule_caseC_subRule); + rule_caseC.setSubAccessRule(rule_caseC_subRules); + + AccessRule rule_caseC_subRule2 = new AccessRule(); + rule_caseC_subRule2.setUuid(UUID.randomUUID()); + rule_caseC_subRule2.setName("rule_caseC_subRule"); + rule_caseC_subRule2.setRule("$.query.requiredFields"); + rule_caseC_subRule2.setCheckMapNode(true); + rule_caseC_subRule2.setCheckMapKeyOnly(true); + rule_caseC_subRule2.setType(AccessRule.TypeNaming.ALL_CONTAINS); + rule_caseC_subRule2.setValue("\\demographics\\"); + rule_caseC_subRules.add(rule_caseC_subRule2); + + AccessRule rule_caseC_subRule3 = new AccessRule(); + rule_caseC_subRule3.setUuid(UUID.randomUUID()); + rule_caseC_subRule3.setName("rule_caseC_subRule"); + rule_caseC_subRule3.setRule("$.query.fields"); + rule_caseC_subRule3.setCheckMapNode(true); + rule_caseC_subRule3.setCheckMapKeyOnly(true); + rule_caseC_subRule3.setType(AccessRule.TypeNaming.ALL_CONTAINS); + rule_caseC_subRule3.setValue("\\demographics\\"); + rule_caseC_subRules.add(rule_caseC_subRule3); + } + + @Test + public void testCaseD() throws IOException { + assertTrue(accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseCD_pass, Map.class), rule_caseD)); + assertFalse(accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseCD_fail, Map.class), rule_caseD)); + assertFalse(accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseCD_fail_2, Map.class), rule_caseD)); + } + + private static void initialTestCaseD(){ + rule_caseD = new AccessRule(); + rule_caseD.setUuid(UUID.randomUUID()); + rule_caseD.setName("rule_caseD"); + rule_caseD.setRule("$.query.categoryFilters.\\demographics\\SEX\\"); + rule_caseD.setType(AccessRule.TypeNaming.ALL_EQUALS); + rule_caseD.setValue("male"); + + AccessRule rule_caseD_gate = new AccessRule(); + rule_caseD_gate.setUuid(UUID.randomUUID()); + rule_caseD_gate.setName("rule_caseD_gate"); + rule_caseD_gate.setRule("$.query.expectedResultType"); + rule_caseD_gate.setType(AccessRule.TypeNaming.ALL_EQUALS_IGNORE_CASE); + rule_caseD_gate.setValue("dataframe"); + Set rule_caseD_gates = new HashSet<>(); + rule_caseD_gates.add(rule_caseD_gate); + rule_caseD.setGates(rule_caseD_gates); + } + + @Test + public void testCaseE() throws IOException { + assertTrue( + accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseE_pass, Map.class), rule_caseE) + || accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseE_pass, Map.class), rule_caseE_2) + ); + + assertTrue( + accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseE_2_pass, Map.class), rule_caseE) + || accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseE_2_pass, Map.class), rule_caseE_2) + ); + + assertFalse( + accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseE_fail, Map.class), rule_caseE) + || accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseE_fail, Map.class), rule_caseE_2) + ); + + assertFalse( + accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseE_2_fail, Map.class), rule_caseE) + || accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseE_2_fail, Map.class), rule_caseE_2) + ); + + } + + private static void initialTestCaseE(){ + rule_caseE = new AccessRule(); + rule_caseE.setUuid(UUID.randomUUID()); + rule_caseE.setName("rule_caseE"); + rule_caseE.setRule("$.query.categoryFilters.\\demographics\\SEX\\"); + rule_caseE.setType(AccessRule.TypeNaming.ALL_EQUALS); + rule_caseE.setValue("male"); + + AccessRule rule_caseE_gate = new AccessRule(); + rule_caseE_gate.setUuid(UUID.randomUUID()); + rule_caseE_gate.setName("rule_caseE_gate"); + rule_caseE_gate.setRule("$..*"); + rule_caseE_gate.setType(AccessRule.TypeNaming.ANY_CONTAINS); + rule_caseE_gate.setValue("\\laboratory\\"); + rule_caseE_gate.setCheckMapNode(true); + Set rule_caseE_gates = new HashSet<>(); + rule_caseE_gates.add(rule_caseE_gate); + rule_caseE.setGates(rule_caseE_gates); + + rule_caseE_2 = new AccessRule(); + rule_caseE_2.setUuid(UUID.randomUUID()); + rule_caseE_2.setName("rule_caseE_2"); + rule_caseE_2.setRule("$.query.categoryFilters.\\demographics\\SEX\\"); + rule_caseE_2.setType(AccessRule.TypeNaming.ALL_EQUALS); + rule_caseE_2.setValue("female"); + + AccessRule rule_caseE_2_gate = new AccessRule(); + rule_caseE_2_gate.setUuid(UUID.randomUUID()); + rule_caseE_2_gate.setName("rule_caseE_2_gate"); + rule_caseE_2_gate.setRule("$..*"); + rule_caseE_2_gate.setType(AccessRule.TypeNaming.ANY_CONTAINS); + rule_caseE_2_gate.setValue("\\examination\\"); + rule_caseE_2_gate.setCheckMapNode(true); + Set rule_caseE_2_gates = new HashSet<>(); + rule_caseE_2_gates.add(rule_caseE_2_gate); + rule_caseE_2.setGates(rule_caseE_2_gates); + } + + + @Test + public void testCaseF() throws IOException { + assertTrue(accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseF_pass, Map.class), rule_caseF)); + assertFalse(accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseF_fail, Map.class), rule_caseF)); + assertFalse(accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseF_fail_2, Map.class), rule_caseF)); + assertFalse(accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseF_fail_3, Map.class), rule_caseF)); + assertFalse(accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseF_fail_4, Map.class), rule_caseF)); + assertFalse(accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseF_fail_5, Map.class), rule_caseF)); + } + + private static void initialTestCaseF(){ + rule_caseF = new AccessRule(); + rule_caseF.setUuid(UUID.randomUUID()); + rule_caseF.setName("rule_caseF"); + rule_caseF.setRule("$.query"); + rule_caseF.setType(AccessRule.TypeNaming.ANY_CONTAINS); + rule_caseF.setValue("variantInfoFilters"); + rule_caseF.setCheckMapNode(true); + rule_caseF.setCheckMapKeyOnly(true); + Set rule_caseF_subRules = new HashSet<>(); + rule_caseF.setSubAccessRule(rule_caseF_subRules); + + AccessRule rule_caseF_subRule = new AccessRule(); + rule_caseF_subRule.setUuid(UUID.randomUUID()); + rule_caseF_subRule.setName("rule_caseF_subRule"); + rule_caseF_subRule.setRule("$.query.categoryFilters"); + rule_caseF_subRule.setCheckMapNode(true); + rule_caseF_subRule.setCheckMapKeyOnly(true); + rule_caseF_subRule.setType(AccessRule.TypeNaming.ALL_REG_MATCH); + rule_caseF_subRule.setValue("^[0-9]*,[0-9]*,[0-9]*,[ATCG],[ATCG]$"); + rule_caseF_subRules.add(rule_caseF_subRule); + + + AccessRule rule_caseF_subRule_2 = new AccessRule(); + rule_caseF_subRule_2.setUuid(UUID.randomUUID()); + rule_caseF_subRule_2.setName("rule_caseF_subRule_2"); + rule_caseF_subRule_2.setRule("$.query.expectedResultType"); + rule_caseF_subRule_2.setType(AccessRule.TypeNaming.ALL_EQUALS_IGNORE_CASE); + rule_caseF_subRule_2.setValue("COUNT"); + rule_caseF_subRules.add(rule_caseF_subRule_2); + + AccessRule rule_caseF_subRule_3 = new AccessRule(); + rule_caseF_subRule_3.setUuid(UUID.randomUUID()); + rule_caseF_subRule_3.setName("rule_caseF_subRule_3"); + rule_caseF_subRule_3.setRule("$.query.numericFilters"); + rule_caseF_subRule_3.setType(AccessRule.TypeNaming.IS_EMPTY); + rule_caseF_subRules.add(rule_caseF_subRule_3); + + AccessRule rule_caseF_subRule_4 = new AccessRule(); + rule_caseF_subRule_4.setUuid(UUID.randomUUID()); + rule_caseF_subRule_4.setName("rule_caseF_subRule_4"); + rule_caseF_subRule_4.setRule("$.query.requiredFields"); + rule_caseF_subRule_4.setType(AccessRule.TypeNaming.IS_EMPTY); + rule_caseF_subRules.add(rule_caseF_subRule_4); + } + + @Test + public void testCaseG() throws IOException { + assertTrue(accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseG_pass, Map.class), rule_caseG)); + assertFalse(accessRuleService.evaluateAccessRule(mapper.readValue(sample_caseG_fail, Map.class), rule_caseG)); + } + + private static void initialTestCaseG(){ + rule_caseG = new AccessRule(); + rule_caseG.setUuid(UUID.randomUUID()); + rule_caseG.setName("rule_caseG"); + rule_caseG.setRule("$.query"); + rule_caseG.setType(AccessRule.TypeNaming.ANY_CONTAINS); + rule_caseG.setValue("anyRecordOf"); + rule_caseG.setCheckMapNode(true); + rule_caseG.setCheckMapKeyOnly(true); + + Set subRules = new HashSet<>(); + rule_caseG.setSubAccessRule(subRules); + + // Sub-rule 1: Check that expectedResultType is COUNT + AccessRule subRule1 = new AccessRule(); + subRule1.setUuid(UUID.randomUUID()); + subRule1.setName("rule_caseG_subRule1"); + subRule1.setRule("$.query.expectedResultType"); + subRule1.setType(AccessRule.TypeNaming.ALL_EQUALS_IGNORE_CASE); + subRule1.setValue("COUNT"); + subRules.add(subRule1); + + // Sub-rule 2: Check that numericFilters is empty + AccessRule subRule2 = new AccessRule(); + subRule2.setUuid(UUID.randomUUID()); + subRule2.setName("rule_caseG_subRule2"); + subRule2.setRule("$.query.numericFilters"); + subRule2.setType(AccessRule.TypeNaming.IS_EMPTY); + subRules.add(subRule2); + + // Sub-rule 3: Check that requiredFields is empty + AccessRule subRule3 = new AccessRule(); + subRule3.setUuid(UUID.randomUUID()); + subRule3.setName("rule_caseG_subRule3"); + subRule3.setRule("$.query.requiredFields"); + subRule3.setType(AccessRule.TypeNaming.IS_EMPTY); + subRules.add(subRule3); + + // Sub-rule 4: Check that anyRecordOf contains a specific path + AccessRule subRule4 = new AccessRule(); + subRule4.setUuid(UUID.randomUUID()); + subRule4.setName("rule_caseG_subRule4"); + subRule4.setRule("$.query.anyRecordOf[0]"); + subRule4.setType(AccessRule.TypeNaming.ALL_EQUALS); + subRule4.setValue("\\phs001001\\pht005655\\phv00354560\\age\\"); + subRules.add(subRule4); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/AuthorizationServiceHpdsV3TargetServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/AuthorizationServiceHpdsV3TargetServiceTest.java new file mode 100644 index 000000000..ac74e683b --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/AuthorizationServiceHpdsV3TargetServiceTest.java @@ -0,0 +1,67 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl.authorization; + +import org.junit.jupiter.api.Test; +import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.ValueSource; + +import static org.junit.jupiter.api.Assertions.assertFalse; +import static org.junit.jupiter.api.Assertions.assertTrue; + +/** + * Unit tests for {@link AuthorizationService#isHpdsV3TargetService(String)}.

    This helper controls when the HPDS-v3 consent-based access + * rule check is skipped, so it must match clean HPDS-v3 target service paths precisely (segment-aware), without being fooled by substrings + * like "v30", "v3ish", or paths where "hpds"/"v3" appear in the wrong position. + */ +class AuthorizationServiceHpdsV3TargetServiceTest { + + @ParameterizedTest + @ValueSource(strings = {"/hpds/auth/v3", "/hpds/auth/v3/query", "/hpds/auth/v3/query/abc/result", "/hpds/auth/v3/"}) + void returnsTrueForCleanHpdsV3Paths(String targetService) { + assertTrue(AuthorizationService.isHpdsV3TargetService(targetService)); + } + + @ParameterizedTest + @ValueSource( + strings = {"/dictionary/v3/hpds", "/hpds/auth/v30/query", "/hpds/auth/v3ish/query", "/hpds/v3/query", "/foo/hpds/auth/v3/query", + "/hpds/auth/v3-query", + // open-access requests are authorized via a separate endpoint and never reach this method + "/hpds/open/v3", "/hpds/open/v3/query/abc/result", "/v3/query"} + ) + void returnsFalseForNonMatchingPaths(String targetService) { + assertFalse(AuthorizationService.isHpdsV3TargetService(targetService)); + } + + @Test + void returnsFalseForNull() { + assertFalse(AuthorizationService.isHpdsV3TargetService(null)); + } + + @Test + void legacyV3PrefixIsNotMatchedByHelperButIsHandledSeparatelyByStartsWith() { + // isHpdsV3TargetService is intentionally narrow; the legacy "/v3" prefix continues to be + // handled by the separate startsWith("/v3") check in passesAccessRuleEvaluation until Phase 7. + assertFalse(AuthorizationService.isHpdsV3TargetService("/v3/query")); + } + + @Test + void combinedSkipPredicate_legacyV3PathSkips() { + assertTrue(skipsConsentCheck("/v3/query")); + } + + @Test + void combinedSkipPredicate_cleanHpdsV3PathSkips() { + assertTrue(skipsConsentCheck("/hpds/auth/v3/query")); + } + + @Test + void combinedSkipPredicate_unrelatedPathDoesNotSkip() { + assertFalse(skipsConsentCheck("/dictionary/x")); + } + + /** + * Mirrors the skip condition used in {@link AuthorizationService#passesAccessRuleEvaluation}. + */ + private static boolean skipsConsentCheck(String targetService) { + return targetService != null && (targetService.startsWith("/v3") || AuthorizationService.isHpdsV3TargetService(targetService)); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/AuthorizationServiceTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/AuthorizationServiceTest.java new file mode 100644 index 000000000..aadd6e85a --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/AuthorizationServiceTest.java @@ -0,0 +1,824 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl.authorization; + +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.hms.dbmi.avillach.auth.entity.*; +import edu.harvard.hms.dbmi.avillach.auth.model.CustomUserDetails; +import edu.harvard.hms.dbmi.avillach.auth.repository.AccessRuleRepository; +import edu.harvard.hms.dbmi.avillach.auth.repository.UserConsentsRepository; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.AccessRuleService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.RoleService; +import edu.harvard.hms.dbmi.avillach.auth.service.impl.SessionService; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockitoAnnotations; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.security.authentication.UsernamePasswordAuthenticationToken; +import org.springframework.security.core.context.SecurityContext; +import org.springframework.security.core.context.SecurityContextHolder; +import org.springframework.test.context.ContextConfiguration; + +import java.io.IOException; +import java.util.*; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + +@SpringBootTest +@ContextConfiguration(classes = {AuthorizationService.class, AccessRuleService.class}) +public class AuthorizationServiceTest { + + @MockBean + private SecurityContext securityContext; + + private AuthorizationService authorizationService; + + private AccessRuleService accessRuleService; + + @MockBean + private SessionService sessionService; + + @MockBean + private AccessRuleRepository accessRuleRepository; + + @MockBean + private RoleService roleService; + + @MockBean + private BdcConsentBasedAccessRuleEvaluator bdcConsentBasedAccessRuleEvaluator; + + @MockBean + private UserConsentsRepository userConsentsRepository; + + private final ObjectMapper mapper = new ObjectMapper(); + + private static AccessRule GATE_resouceUUID; + private static AccessRule GATE_has_expectedResultType; + private static AccessRule GATE_has_categoryFilters; + private static AccessRule GATE_has_requiredFields; + + private static AccessRule AR_CategoryFilter_String_contains; + private static AccessRule AR_CategoryFilter_Any_Contains; + private static AccessRule AR_Fields_ALL_SEX; + private static AccessRule AR_Fields_ALL_AGE; + private static AccessRule AR_Fields_IS_EMPTY; + private static AccessRule AR_Fields_IS_NOT_EMPTY; + private static AccessRule AR_ExpectedResultType_String_contains; + + private static String sample_matchGate = + "{\"queries\":[{\"resourceUUID\":\"8694e3d4-5cb4-410f-8431-993445e6d3f6\",\"query\":{\"expectedResultType\":\"DATAFRAME\"}}]}"; + + private static String sample_gates_all_any = + "{\"queries\":" + "[" + "{\"resourceUUID\":\"8694e3d4-5cb4-410f-8431-993445e6d3f6\"" + "}]}"; + + private static String sample_nestedGates = "{\"queries\":[{\n" + " \"query\": {\n" + " \"categoryFilters\": {\n" + + " \"\\\\demographics\\\\SEX\\\\\": [\n" + " \"male\"\n" + " ]\n" + " },\n" + " \"numericFilters\": {},\n" + + " \"expectedResultType\": \"DATAFRAME\",\n" + " \"fields\": [\n" + " \"\\\\demographics\\\\SEX\\\\\",\n" + + " \"\\\\demographics\\\\AGE\\\\\"\n" + " ]\n" + " },\n" + + " \"resourceUUID\": \"8694e3d4-5cb4-410f-8431-993445e6d3f6\",\n" + " \"resourceCredentials\": {}\n" + "}]\n" + "}"; + + private static String getSample_passGate_passCheck_array_contains = "{\"queries\":[{\n" + " \"query\": {\n" + + " \"categoryFilters\": {\n" + " \"\\\\demographics\\\\SEX\\\\\": [\n" + " \"male\"\n" + " ]\n" + " },\n" + + " \"numericFilters\": {},\n" + " \"requiredFields\": [\n" + " \"\\\\demographics\\\\AGE\\\\\"\n" + " ],\n" + + " \"expectedResultType\": \"DATAFRAME\",\n" + " \"fields\": [\n" + " \"\\\\demographics\\\\SEX\\\\\",\n" + + " \"\\\\demographics\\\\AGE\\\\\"\n" + " ]\n" + " },\n" + + " \"resourceUUID\": \"8694e3d4-5cb4-410f-8431-993445e6d3f6\",\n" + " \"resourceCredentials\": {}\n" + "}]\n" + "}"; + + private static String sample_passGate_passCheck_string_contains = "{\"queries\":[{\n" + " \"query\": {\n" + + " \"categoryFilters\": {\n" + " \"\\\\demographics\\\\SEX\\\\\": [\n" + " \"male\"\n" + " ]\n" + " },\n" + + " \"numericFilters\": {},\n" + " \"requiredFields\": [\n" + " \"\\\\demographics\\\\AGE\\\\\"\n" + " ],\n" + + " \"expectedResultType\": \"DATAFRAME\",\n" + " \"fields\": [\n" + " \"\\\\demographics\\\\SEX\\\\\"\n" + " ]\n" + + " },\n" + " \"resourceUUID\": \"8694e3d4-5cb4-410f-8431-993445e6d3f6\",\n" + " \"resourceCredentials\": {}\n" + "}]\n" + "}"; + + private static String sample_no_pass_gate = "{\"queries\":[{\n" + " \"query\": {\n" + " \"categoryFilters\": {\n" + + " \"\\\\demographics\\\\SEX\\\\\": [\n" + " \"male\"\n" + " ]\n" + " },\n" + " \"numericFilters\": {},\n" + + " \"requiredFields\": [\n" + " \"\\\\demographics\\\\AGE\\\\\"\n" + " ],\n" + + " \"expectedResultType\": \"DATAFRAME\",\n" + " \"fields\": [\n" + " \"\\\\demographics\\\\SEX\\\\\",\n" + + " \"\\\\demographics\\\\AGE\\\\\"\n" + " ]\n" + " },\n" + + " \"resourceUUID\": \"8694e3d4-5cb4-410f-8431-993445e6d3fd\",\n" + " \"resourceCredentials\": {}\n" + "}]\n" + "}"; + + private static String sample_UUID_8694e3d4_withFields_SEX_And_AGE = "{\"queries\":[{\n" + " \"query\": {\n" + + " \"categoryFilters\": {\n" + " \"\\\\demographics\\\\SEX\\\\\": [\n" + " \"male\"\n" + " ]\n" + " },\n" + + " \"numericFilters\": {},\n" + " \"requiredFields\": [\n" + " \"\\\\demographics\\\\AGE\\\\\"\n" + " ],\n" + + " \"expectedResultType\": \"DATAFRAME\",\n" + " \"fields\": [\n" + " \"\\\\demographics\\\\SEX\\\\\",\n" + + " \"\\\\demographics\\\\AGE\\\\\"\n" + " ]\n" + " },\n" + + " \"resourceUUID\": \"8694e3d4-5cb4-410f-8431-993445e6d3f6\",\n" + " \"resourceCredentials\": {}\n" + "}]\n" + "}"; + + private static String sample_UUID_8694e3d4_withFields_and_SEE_AGE_SEX = "{\"queries\":[{\n" + " \"query\": {\n" + + " \"categoryFilters\": {\n" + " \"\\\\demographics\\\\SEX\\\\\": [\n" + " \"male\"\n" + " ]\n" + " },\n" + + " \"numericFilters\": {},\n" + " \"requiredFields\": [\n" + " \"\\\\demographics\\\\AGE\\\\\"\n" + " ],\n" + + " \"expectedResultType\": \"DATAFRAME\",\n" + " \"fields\": [\n" + " \"\\\\demographics\\\\SEE\\\\\",\n" + + " \"\\\\demographics\\\\AGE\\\\\",\n" + " \"\\\\demographics\\\\SEX\\\\\"\n" + " ]\n" + " },\n" + + " \"resourceUUID\": \"8694e3d4-5cb4-410f-8431-993445e6d3f6\",\n" + " \"resourceCredentials\": {}\n" + "}]\n" + "}"; + + private static String sample_UUID_8694e3d4_withEmptyFields = "{\"queries\":[{\n" + " \"query\": {\n" + " \"categoryFilters\": {\n" + + " \"\\\\demographics\\\\SEX\\\\\": [\n" + " \"male\"\n" + " ]\n" + " },\n" + " \"numericFilters\": {},\n" + + " \"requiredFields\": [\n" + " \"\\\\demographics\\\\AGE\\\\\"\n" + " ],\n" + + " \"expectedResultType\": \"DATAFRAME\",\n" + " \"fields\": [\n" + " ]\n" + " },\n" + + " \"resourceUUID\": \"8694e3d4-5cb4-410f-8431-993445e6d3f6\",\n" + " \"resourceCredentials\": {}\n" + "}]\n" + "}"; + + private static String sample_UUID_8694e3d4_withNoFieldsNode = + "{\"queries\":[{\n" + " \"query\": {\n" + " \"categoryFilters\": {\n" + " \"\\\\demographics\\\\SEX\\\\\": [\n" + + " \"male\"\n" + " ]\n" + " },\n" + " \"numericFilters\": {},\n" + " \"requiredFields\": [\n" + + " \"\\\\demographics\\\\AGE\\\\\"\n" + " ],\n" + " \"expectedResultType\": \"DATAFRAME\"\n" + " },\n" + + " \"resourceUUID\": \"8694e3d4-5cb4-410f-8431-993445e6d3f6\",\n" + " \"resourceCredentials\": {}\n" + "}]\n" + "}"; + + @BeforeAll + public static void init() { + GATE_resouceUUID = new AccessRule(); + GATE_resouceUUID.setUuid(UUID.randomUUID()); + GATE_resouceUUID.setType(AccessRule.TypeNaming.ALL_EQUALS); + GATE_resouceUUID.setName("Gate_resoruceUUID"); + GATE_resouceUUID.setRule("$.queries..resourceUUID"); + GATE_resouceUUID.setValue("8694e3d4-5cb4-410f-8431-993445e6d3f6"); + + GATE_has_expectedResultType = new AccessRule(); + GATE_has_expectedResultType.setUuid(UUID.randomUUID()); + GATE_has_expectedResultType.setType(AccessRule.TypeNaming.ANY_CONTAINS); + GATE_has_expectedResultType.setName("GATE_has_expectedResultType"); + GATE_has_expectedResultType.setRule("$.queries..query"); + GATE_has_expectedResultType.setValue("expectedResultType"); + GATE_has_expectedResultType.setCheckMapNode(true); + GATE_has_expectedResultType.setCheckMapKeyOnly(true); + + GATE_has_categoryFilters = new AccessRule(); + GATE_has_categoryFilters.setUuid(UUID.randomUUID()); + GATE_has_categoryFilters.setType(AccessRule.TypeNaming.ANY_CONTAINS); + GATE_has_categoryFilters.setName("GATE_has_categoryFilters"); + GATE_has_categoryFilters.setRule("$.queries..query"); + GATE_has_categoryFilters.setValue("categoryFilters"); + GATE_has_categoryFilters.setCheckMapNode(true); + GATE_has_categoryFilters.setCheckMapKeyOnly(true); + + GATE_has_requiredFields = new AccessRule(); + GATE_has_requiredFields.setUuid(UUID.randomUUID()); + GATE_has_requiredFields.setType(AccessRule.TypeNaming.ANY_CONTAINS); + GATE_has_requiredFields.setName("GATE_has_requiredFields"); + GATE_has_requiredFields.setRule("$.queries..query"); + GATE_has_requiredFields.setValue("requiredFields"); + GATE_has_requiredFields.setCheckMapNode(true); + GATE_has_requiredFields.setCheckMapKeyOnly(true); + + AR_CategoryFilter_String_contains = new AccessRule(); + AR_CategoryFilter_String_contains.setUuid(UUID.randomUUID()); + AR_CategoryFilter_String_contains.setName("AR_CategoryFilter"); + AR_CategoryFilter_String_contains.setRule("$.queries..fields.*"); + AR_CategoryFilter_String_contains.setType(AccessRule.TypeNaming.ALL_CONTAINS); + AR_CategoryFilter_String_contains.setValue("\\demographics\\SEX\\"); + + AR_CategoryFilter_Any_Contains = new AccessRule(); + AR_CategoryFilter_Any_Contains.setName("AR_CategoryFilter"); + AR_CategoryFilter_Any_Contains.setRule("$.queries..fields.*"); + AR_CategoryFilter_Any_Contains.setType(AccessRule.TypeNaming.ANY_CONTAINS); + AR_CategoryFilter_Any_Contains.setValue("\\demographics\\SEX\\"); + + AR_Fields_ALL_SEX = new AccessRule(); + AR_Fields_ALL_SEX.setUuid(UUID.randomUUID()); + AR_Fields_ALL_SEX.setName("AR_CategoryFilter"); + AR_Fields_ALL_SEX.setRule("$.queries..fields.*"); + AR_Fields_ALL_SEX.setType(AccessRule.TypeNaming.ALL_CONTAINS); + AR_Fields_ALL_SEX.setValue("\\demographics\\SEX\\"); + Set gates = new HashSet<>(); + gates.add(GATE_resouceUUID); + AR_Fields_ALL_SEX.setGates(gates); + + + AR_Fields_ALL_AGE = new AccessRule(); + AR_Fields_ALL_AGE.setUuid(UUID.randomUUID()); + AR_Fields_ALL_AGE.setName("AR_CategoryFilter"); + AR_Fields_ALL_AGE.setRule("$.queries..fields.*"); + AR_Fields_ALL_AGE.setType(AccessRule.TypeNaming.ALL_CONTAINS); + AR_Fields_ALL_AGE.setValue("\\demographics\\AGE\\"); + Set gates_2 = new HashSet<>(); + gates_2.add(GATE_resouceUUID); + AR_Fields_ALL_AGE.setGates(gates_2); + + AR_Fields_IS_EMPTY = new AccessRule(); + AR_Fields_IS_EMPTY.setUuid(UUID.randomUUID()); + AR_Fields_IS_EMPTY.setName("AR_Fields_IS_EMPTY"); + AR_Fields_IS_EMPTY.setRule("$.queries..fields.*"); + AR_Fields_IS_EMPTY.setType(AccessRule.TypeNaming.IS_EMPTY); + + AR_Fields_IS_NOT_EMPTY = new AccessRule(); + AR_Fields_IS_NOT_EMPTY.setUuid(UUID.randomUUID()); + AR_Fields_IS_NOT_EMPTY.setName("AR_Fields_IS_EMPTY"); + AR_Fields_IS_NOT_EMPTY.setRule("$.queries..fields.*"); + AR_Fields_IS_NOT_EMPTY.setType(AccessRule.TypeNaming.IS_NOT_EMPTY); + } + + @BeforeEach + public void setUp() { + MockitoAnnotations.openMocks(this); + SecurityContextHolder.setContext(securityContext); + + when(sessionService.isSessionExpired(any(String.class))).thenReturn(false); + accessRuleService = new AccessRuleService(accessRuleRepository, "false", "false", "false", "false", "false", "false"); + authorizationService = new AuthorizationService( + accessRuleService, sessionService, roleService, bdcConsentBasedAccessRuleEvaluator, "fence,okta", userConsentsRepository + ); + } + + @Test + public void testIsAuthorized_AccessRulePassed() { + Application application = createTestApplication(); + User user = createTestUser(); + + // create access_rule for privilege + AccessRule accessRule = new AccessRule(); + accessRule.setUuid(UUID.randomUUID()); + accessRule.setRule("$.test"); + accessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + accessRule.setValue("value"); + + + // set application and access_rule for all user privileges + for (Privilege privilege1 : user.getRoles().iterator().next().getPrivileges()) { + privilege1.setAccessRules(Collections.singleton(accessRule)); + privilege1.setApplication(application); + } + configureUserSecurityContext(user); + user.setConnection(createFenceTestConnection()); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "value"); + requestBody.put("Target Service", "/query"); + + boolean result = authorizationService.isAuthorized(application, requestBody, user, false).result(); + + assertTrue(result); + } + + @Test + public void testIsAuthorized_AccessRuleFailed() { + Application application = createTestApplication(); + User user = createTestUser(); + configureUserSecurityContext(user); + user.setConnection(createFenceTestConnection()); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "differentValue"); + + boolean result = authorizationService.isAuthorized(application, requestBody, user, false).result(); + + assertFalse(result); + } + + @Test + public void testIsAuthorized_AccessRuleFailed_strict() { + Application application = createTestApplication(); + User user = createTestUser(); + configureUserSecurityContext(user); + user.setConnection(createFenceTestConnection()); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "differentValue"); + + boolean result = authorizationService.isAuthorized(application, requestBody, user, false).result(); + + assertFalse(result); + } + + private Connection createFenceTestConnection() { + Connection connection = new Connection(); + connection.setUuid(UUID.randomUUID()); + connection.setLabel("FENCE"); + connection.setSubPrefix("fence|"); + return connection; + } + + @Test + public void testEvaluateAccessRule_GatesPassed() { + AccessRule accessRule = new AccessRule(); + accessRule.setRule("$.test"); + accessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + accessRule.setValue("value"); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "value"); + + boolean result = accessRuleService.evaluateAccessRule(requestBody, accessRule); + + assertTrue(result); + } + + @Test + public void testEvaluateAccessRule_GatesFailed() { + AccessRule accessRule = new AccessRule(); + accessRule.setRule("$.test"); + accessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + accessRule.setValue("value"); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "differentValue"); + + boolean result = accessRuleService.evaluateAccessRule(requestBody, accessRule); + + assertFalse(result); + } + + @Test + public void testExtractAndCheckRule_Pass() { + AccessRule accessRule = new AccessRule(); + accessRule.setRule("$.test"); + accessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + accessRule.setValue("value"); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "value"); + + boolean result = accessRuleService.extractAndCheckRule(accessRule, requestBody); + + assertTrue(result); + } + + @Test + public void testExtractAndCheckRule_Fail() { + AccessRule accessRule = new AccessRule(); + accessRule.setRule("$.test"); + accessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + accessRule.setValue("value"); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "differentValue"); + + boolean result = accessRuleService.extractAndCheckRule(accessRule, requestBody); + + assertFalse(result); + } + + @Test + public void testDecisionMaker_Pass() { + AccessRule accessRule = new AccessRule(); + accessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + accessRule.setValue("value"); + + boolean result = accessRuleService.decisionMaker(accessRule, "value"); + + assertTrue(result); + } + + @Test + public void testDecisionMaker_Fail() { + AccessRule accessRule = new AccessRule(); + accessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + accessRule.setValue("value"); + + boolean result = accessRuleService.decisionMaker(accessRule, "differentValue"); + + assertFalse(result); + } + + @Test + public void testIsAuthorized_NoRequestBody() { + Application application = createTestApplication(); + User user = createTestUser(); + configureUserSecurityContext(user); + application.setPrivileges(user.getPrivilegesByApplication(application)); + + boolean result = authorizationService.isAuthorized(application, null, user, false).result(); + + assertTrue(result); + } + + @Test + public void testIsAuthorized_NoPrivileges() { + Application application = createTestApplication(); + User user = createTestUser(); + user.setConnection(createFenceTestConnection()); + + user.getRoles().iterator().next().setPrivileges(Collections.emptySet()); + boolean result = authorizationService.isAuthorized(application, new HashMap<>(), user, false).result(); + + assertFalse(result); + } + + @Test + public void testEvaluateAccessRule_NoGates() { + AccessRule accessRule = new AccessRule(); + accessRule.setRule("$.test"); + accessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + accessRule.setValue("value"); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "value"); + + boolean result = accessRuleService.evaluateAccessRule(requestBody, accessRule); + + assertTrue(result); + } + + @Test + public void testEvaluateAccessRule_AllGatesPassed_AND() { + AccessRule gate1 = new AccessRule(); + gate1.setRule("$.test"); + gate1.setType(AccessRule.TypeNaming.ALL_EQUALS); + gate1.setValue("value"); + + AccessRule gate2 = new AccessRule(); + gate2.setRule("$.test2"); + gate2.setType(AccessRule.TypeNaming.ALL_EQUALS); + gate2.setValue("value2"); + + AccessRule accessRule = new AccessRule(); + accessRule.setGates(new HashSet<>(Arrays.asList(gate1, gate2))); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "value"); + requestBody.put("test2", "value2"); + + boolean result = accessRuleService.evaluateAccessRule(requestBody, accessRule); + + assertTrue(result); + } + + @Test + public void testEvaluateAccessRule_OneGateFails_AND() { + AccessRule gate1 = new AccessRule(); + gate1.setRule("$.test"); + gate1.setType(AccessRule.TypeNaming.ALL_EQUALS); + gate1.setValue("value"); + + AccessRule gate2 = new AccessRule(); + gate2.setRule("$.test2"); + gate2.setType(AccessRule.TypeNaming.ALL_EQUALS); + gate2.setValue("value2"); + + AccessRule accessRule = new AccessRule(); + accessRule.setGates(new HashSet<>(Arrays.asList(gate1, gate2))); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "value"); + requestBody.put("test2", "differentValue"); + + boolean result = accessRuleService.evaluateAccessRule(requestBody, accessRule); + + assertFalse(result); + } + + @Test + public void testEvaluateAccessRule_OneGatePassed_OR() { + AccessRule gate1 = new AccessRule(); + gate1.setRule("$.test"); + gate1.setType(AccessRule.TypeNaming.ALL_EQUALS); + gate1.setValue("value"); + + AccessRule gate2 = new AccessRule(); + gate2.setRule("$.test2"); + gate2.setType(AccessRule.TypeNaming.ALL_EQUALS); + gate2.setValue("value2"); + + AccessRule accessRule = new AccessRule(); + accessRule.setGates(new HashSet<>(Arrays.asList(gate1, gate2))); + accessRule.setGateAnyRelation(true); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "value"); + requestBody.put("test2", "differentValue"); + + boolean result = accessRuleService.evaluateAccessRule(requestBody, accessRule); + + assertTrue(result); + } + + @Test + public void testEvaluateAccessRule_AllGatesFail_OR() { + AccessRule gate1 = new AccessRule(); + gate1.setRule("$.test"); + gate1.setType(AccessRule.TypeNaming.ALL_EQUALS); + gate1.setValue("value"); + + AccessRule gate2 = new AccessRule(); + gate2.setRule("$.test2"); + gate2.setType(AccessRule.TypeNaming.ALL_EQUALS); + gate2.setValue("value2"); + + AccessRule accessRule = new AccessRule(); + accessRule.setGates(new HashSet<>(Arrays.asList(gate1, gate2))); + accessRule.setGateAnyRelation(true); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "differentValue"); + requestBody.put("test2", "differentValue"); + + boolean result = accessRuleService.evaluateAccessRule(requestBody, accessRule); + + assertFalse(result); + } + + @Test + public void testEvaluateAccessRule_EvaluateOnlyByGates() { + AccessRule gate1 = new AccessRule(); + gate1.setRule("$.test"); + gate1.setType(AccessRule.TypeNaming.ALL_EQUALS); + gate1.setValue("value"); + + AccessRule accessRule = new AccessRule(); + accessRule.setGates(new HashSet<>(Collections.singletonList(gate1))); + accessRule.setEvaluateOnlyByGates(true); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "value"); + + boolean result = accessRuleService.evaluateAccessRule(requestBody, accessRule); + + assertTrue(result); + } + + @Test + public void testEvaluateAccessRule_SubAccessRules() { + AccessRule subAccessRule = new AccessRule(); + subAccessRule.setRule("$.test2"); + subAccessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + subAccessRule.setValue("value2"); + + AccessRule accessRule = new AccessRule(); + accessRule.setRule("$.test"); + accessRule.setType(AccessRule.TypeNaming.ALL_EQUALS); + accessRule.setValue("value"); + accessRule.setSubAccessRule(new HashSet<>(Collections.singletonList(subAccessRule))); + + Map requestBody = new HashMap<>(); + requestBody.put("test", "value"); + requestBody.put("test2", "value2"); + + boolean result = accessRuleService.evaluateAccessRule(requestBody, accessRule); + + assertTrue(result); + } + + @Test + public void testGates() throws IOException { + + assertTrue(accessRuleService.evaluateAccessRule(mapper.readValue(sample_matchGate, Map.class), GATE_resouceUUID)); + assertTrue(accessRuleService.evaluateAccessRule(mapper.readValue(sample_matchGate, Map.class), GATE_has_expectedResultType)); + + } + + @Test + public void testWithGate_passGate_passCheck_all_string_contains() throws IOException { + + Set gates = new HashSet<>(); + gates.add(GATE_resouceUUID); + AR_CategoryFilter_String_contains.setGates(gates); + assertTrue( + accessRuleService.evaluateAccessRule( + mapper.readValue(sample_passGate_passCheck_string_contains, Map.class), AR_CategoryFilter_String_contains + ) + ); + } + + @Test + public void testWithGate_passGate_notPassCheck_string_contains() throws IOException { + + Set gates = new HashSet<>(); + gates.add(GATE_resouceUUID); + AR_CategoryFilter_String_contains.setGates(gates); + assertFalse( + accessRuleService.evaluateAccessRule( + mapper.readValue(getSample_passGate_passCheck_array_contains, Map.class), AR_CategoryFilter_String_contains + ) + ); + } + + @Test + public void testWithGate_passGate_passCheck_Array_contains() throws IOException { + + Set gates = new HashSet<>(); + gates.add(GATE_resouceUUID); + AR_CategoryFilter_Any_Contains.setGates(gates); + assertTrue( + accessRuleService.evaluateAccessRule( + mapper.readValue(getSample_passGate_passCheck_array_contains, Map.class), AR_CategoryFilter_Any_Contains + ) + ); + } + + @Test + public void testWithGate_passGate_notPassCheck() throws IOException { + + Set gates = new HashSet<>(); + gates.add(GATE_resouceUUID); + AR_CategoryFilter_String_contains.setGates(gates); + assertFalse( + accessRuleService.evaluateAccessRule( + mapper.readValue(getSample_passGate_passCheck_array_contains, Map.class), AR_CategoryFilter_String_contains + ) + ); + } + + @Test + public void testWithGate_notPassGate() throws IOException { + Set gates = new HashSet<>(); + gates.add(GATE_resouceUUID); + AR_CategoryFilter_String_contains.setGates(gates); + assertFalse( + accessRuleService.evaluateAccessRule(mapper.readValue(sample_no_pass_gate, Map.class), AR_CategoryFilter_String_contains) + ); + } + + /** + * Testing merging functionality, empty nodes, and no such node + * + * @throws IOException + */ + @Test + public void testMerging_emptyNodes_noSuchNode() throws IOException { + Set inputAccessRules = new HashSet<>(); + inputAccessRules.add(AR_Fields_ALL_AGE); + inputAccessRules.add(AR_Fields_ALL_SEX); + + Set mergedAccessRules = accessRuleService.preProcessARBySortedKeys(inputAccessRules); + + assertEquals(1, mergedAccessRules.size()); + + assertTrue( + accessRuleService.evaluateAccessRule( + mapper.readValue(sample_UUID_8694e3d4_withFields_SEX_And_AGE, Map.class), mergedAccessRules.stream().findFirst().get() + ) + ); + + assertFalse( + accessRuleService.evaluateAccessRule( + mapper.readValue(sample_UUID_8694e3d4_withFields_and_SEE_AGE_SEX, Map.class), mergedAccessRules.stream().findFirst().get() + ) + ); + + assertFalse( + accessRuleService.evaluateAccessRule( + mapper.readValue(sample_UUID_8694e3d4_withEmptyFields, Map.class), mergedAccessRules.stream().findFirst().get() + ) + ); + + assertFalse( + accessRuleService.evaluateAccessRule( + mapper.readValue(sample_UUID_8694e3d4_withNoFieldsNode, Map.class), mergedAccessRules.stream().findFirst().get() + ) + ); + } + + /** + * AccessRule rule isEmpty and isNotEmpty are special cases, we should have a test case especially for it + * + * @throws IOException + */ + @Test + public void testRuleIsEmpty_IsNotEmpty() throws IOException { + assertTrue( + accessRuleService.evaluateAccessRule(mapper.readValue(sample_UUID_8694e3d4_withEmptyFields, Map.class), AR_Fields_IS_EMPTY) + ); + assertFalse( + accessRuleService.evaluateAccessRule(mapper.readValue(sample_UUID_8694e3d4_withEmptyFields, Map.class), AR_Fields_IS_NOT_EMPTY) + ); + } + + /** + * Test that anyRecordOf is evaluated correctly + * @throws IOException + */ + @Test + public void testAnyRecordOfEvaluation() throws IOException { + // Create an access rule for anyRecordOf with ANY_CONTAINS type + AccessRule anyRecordOfRuleAny = new AccessRule(); + anyRecordOfRuleAny.setUuid(UUID.randomUUID()); + anyRecordOfRuleAny.setRule("$.query.query.anyRecordOf.[*]"); + anyRecordOfRuleAny.setType(AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY); + anyRecordOfRuleAny.setValue("test_concept"); + + // Create a request body with anyRecordOf containing the test concept + String requestWithAnyRecordOf = "{\"query\":{\"query\":{\"anyRecordOf\":[\"test_concept\",\"other_concept\"]}}}"; + Map requestBodyWithAnyRecordOf = mapper.readValue(requestWithAnyRecordOf, Map.class); + + // Create a request body with anyRecordOf not containing the test concept + String requestWithoutAnyRecordOf = "{\"query\":{\"query\":{\"anyRecordOf\":[\"different_concept\",\"other_concept\"]}}}"; + Map requestBodyWithoutAnyRecordOf = mapper.readValue(requestWithoutAnyRecordOf, Map.class); + + // Create a request body with empty anyRecordOf + String requestWithEmptyAnyRecordOf = "{\"query\":{\"query\":{\"anyRecordOf\":[]}}}"; + Map requestBodyWithEmptyAnyRecordOf = mapper.readValue(requestWithEmptyAnyRecordOf, Map.class); + + // Create a request body with only test_concept + String requestWithTestConceptAnyRecordOf = "{\"query\":{\"query\":{\"anyRecordOf\":[\"test_concept\"]}}}"; + Map requestBodyWithTestConceptAnyRecordOf = mapper.readValue(requestWithTestConceptAnyRecordOf, Map.class); + + // Print debug information + + // Test that the rule fails when anyRecordOf contains more than just the test_concept + boolean result = accessRuleService.evaluateAccessRule(requestBodyWithAnyRecordOf, anyRecordOfRuleAny); + assertFalse(result); + + // Test that the rule fails when anyRecordOf does not contain the test concept + boolean result2 = accessRuleService.evaluateAccessRule(requestBodyWithoutAnyRecordOf, anyRecordOfRuleAny); + assertFalse(result2); + + // Test that the rule passes when anyRecordOf is empty + boolean result3 = accessRuleService.evaluateAccessRule(requestBodyWithEmptyAnyRecordOf, anyRecordOfRuleAny); + assertTrue(result3); + + // Test that the rule passes when anyRecordOf contains only test_concept + boolean result4 = accessRuleService.evaluateAccessRule(requestBodyWithTestConceptAnyRecordOf, anyRecordOfRuleAny); + assertTrue(result4); + } + + /** + * testing gates combination either all or any + * @throws IOException + */ + @Test + public void testGatesAllorAny() throws IOException { + AccessRule accessRuleGatesAllAny = new AccessRule(); + accessRuleGatesAllAny.setUuid(UUID.randomUUID()); + accessRuleGatesAllAny.setRule("$.queries..query.categoryFilter"); + accessRuleGatesAllAny.setType(AccessRule.TypeNaming.IS_NOT_EMPTY); + Set gates = new HashSet<>(); + gates.add(GATE_resouceUUID); + gates.add(GATE_has_expectedResultType); + accessRuleGatesAllAny.setGates(gates); + + // default is false, for testing, we explicitly set it here just for fluently reading code + accessRuleGatesAllAny.setGateAnyRelation(false); + // No gates applied, return false. + assertFalse(accessRuleService.evaluateAccessRule(mapper.readValue(sample_gates_all_any, Map.class), accessRuleGatesAllAny)); + + // the rules will deny the access, but since we set only evaluate gates with OR relationship, + // while the gates passes, it will return true. + // Here we test any relationship and evaluate only by gates. + accessRuleGatesAllAny.setGateAnyRelation(true); + accessRuleGatesAllAny.setEvaluateOnlyByGates(true); + assertTrue(accessRuleService.evaluateAccessRule(mapper.readValue(sample_gates_all_any, Map.class), accessRuleGatesAllAny)); + + } + + /** + * testing gates combination nested all and any + * @throws IOException + */ + @Test + public void testGateNestedAllorAny() throws IOException { + AccessRule accessRuleGatesAllandAny = new AccessRule(); + accessRuleGatesAllandAny.setUuid(UUID.randomUUID()); + accessRuleGatesAllandAny.setRule("$.queries..query.numericFilters.*"); + accessRuleGatesAllandAny.setType(AccessRule.TypeNaming.IS_NOT_EMPTY); + + // the relationship of the nestedGate here is + // GATE_resouceUUID && GATE_has_expectedResultType && (GATE_has_categoryFilters || GATE_has_requiredFields) + AccessRule orGate = new AccessRule(); + orGate.setUuid(UUID.randomUUID()); + orGate.setGateAnyRelation(true); + orGate.setName("Gate_OR_for_GATE_has_categoryFilters_GATE_has_requiredFields"); + Set gates = new HashSet<>(); + gates.add(GATE_has_requiredFields); + gates.add(GATE_has_categoryFilters); + orGate.setGates(gates); + orGate.setEvaluateOnlyByGates(true); + + Set gates2 = new HashSet<>(); + gates2.add(orGate); + gates2.add(GATE_resouceUUID); + gates2.add(GATE_has_expectedResultType); + accessRuleGatesAllandAny.setGates(gates2); + + assertFalse(accessRuleService.evaluateAccessRule(mapper.readValue(sample_nestedGates, Map.class), accessRuleGatesAllandAny)); + } + + private Role createTestRole() { + Role role = new Role(); + role.setName("TEST_ROLE"); + role.setUuid(UUID.randomUUID()); + role.setPrivileges(Collections.singleton(createTestPrivilege())); + return role; + } + + private Privilege createTestPrivilege() { + Privilege privilege = new Privilege(); + privilege.setName("TEST_PRIVILEGE"); + privilege.setUuid(UUID.randomUUID()); + return privilege; + } + + private void configureUserSecurityContext(User user) { + CustomUserDetails customUserDetails = new CustomUserDetails(user); + UsernamePasswordAuthenticationToken authentication = + new UsernamePasswordAuthenticationToken(customUserDetails, null, customUserDetails.getAuthorities()); + when(securityContext.getAuthentication()).thenReturn(authentication); + } + + private User createTestUser() { + User user = new User(); + user.setUuid(UUID.randomUUID()); + user.setRoles(new HashSet<>(Collections.singleton(createTestRole()))); + user.setSubject("TEST_SUBJECT"); + user.setEmail("test@email.com"); + user.setAcceptedTOS(new Date()); + user.setActive(true); + return user; + } + + private Application createTestApplication() { + Application application = new Application(); + application.setUuid(UUID.randomUUID()); + application.setName("TEST_APPLICATION"); + application.setPrivileges(new HashSet<>()); + return application; + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/BdcConsentBasedAccessRuleEvaluatorTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/BdcConsentBasedAccessRuleEvaluatorTest.java new file mode 100644 index 000000000..ff724eef6 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/BdcConsentBasedAccessRuleEvaluatorTest.java @@ -0,0 +1,258 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl.authorization; + +import edu.harvard.hms.dbmi.avillach.auth.entity.UserConsents; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.*; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +import java.util.List; +import java.util.Map; +import java.util.Set; + +import static org.junit.jupiter.api.Assertions.*; + +class BdcConsentBasedAccessRuleEvaluatorTest { + + + private BdcConsentBasedAccessRuleEvaluator bdcConsentBasedAccessRuleEvaluator; + + @BeforeEach + public void setup() { + bdcConsentBasedAccessRuleEvaluator = new BdcConsentBasedAccessRuleEvaluator(); + } + + @Test + public void evaluateAccessRule_validPhenotypicFilters_accept() { + UserConsents userConsents = new UserConsents().setConsents(Map.of("\\_consents\\", Set.of("phs123.c1", "phs456.c2"))); + Query query = new Query( + List.of(), List.of(), + new PhenotypicSubquery( + null, + List.of( + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs123\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs456\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs123\\data\\sex\\", Set.of("male", "female"), null, null, null) + ), Operator.AND + ), null, ResultType.COUNT, null, null + ); + + boolean result = bdcConsentBasedAccessRuleEvaluator.evaluateAccessRule(query, null, userConsents); + assertTrue(result); + } + + @Test + public void evaluateAccessRule_phenotypicFiltersOneWrongConsent_reject() { + UserConsents userConsents = new UserConsents().setConsents(Map.of("\\_consents\\", Set.of("phs123.c1", "phs456.c2"))); + Query query = new Query( + List.of(), List.of(), + new PhenotypicSubquery( + null, + List.of( + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs123\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs456\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs789\\data\\sex\\", Set.of("male", "female"), null, null, null) + ), Operator.AND + ), null, ResultType.COUNT, null, null + ); + + boolean result = bdcConsentBasedAccessRuleEvaluator.evaluateAccessRule(query, null, userConsents); + assertFalse(result); + } + + @Test + public void evaluateAccessRule_nestedInvalidPhenotypicFiltersConsent_reject() { + UserConsents userConsents = new UserConsents().setConsents(Map.of("\\_consents\\", Set.of("phs123.c1", "phs456.c2"))); + Query query = new Query( + List.of(), List.of(), + new PhenotypicSubquery( + null, + List.of( + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs123\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs456\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicSubquery(false, List.of(new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs789\\data\\sex\\", Set.of("male", "female"), null, null, null)), Operator.AND) + ), Operator.AND + ), null, ResultType.COUNT, null, null + ); + + boolean result = bdcConsentBasedAccessRuleEvaluator.evaluateAccessRule(query, null, userConsents); + assertFalse(result); + } + + + @Test + public void evaluateAccessRule_userNoConsents_reject() { + UserConsents userConsents = new UserConsents().setConsents(Map.of()); + Query query = new Query( + List.of(), List.of(), + new PhenotypicSubquery( + null, + List.of( + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs123\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs456\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs123\\data\\sex\\", Set.of("male", "female"), null, null, null) + ), Operator.AND + ), null, ResultType.COUNT, null, null + ); + + boolean result = bdcConsentBasedAccessRuleEvaluator.evaluateAccessRule(query, null, userConsents); + assertFalse(result); + } + + @Test + public void evaluateAccessRule_genomicFiltersValidTopmedConsents_accept() { + Map> consents = + Map.of("\\_consents\\", Set.of("phs123.c1", "phs456.c2"), "\\_topmed_consents\\", Set.of("phs123.c1", "phs456.c2")); + UserConsents userConsents = new UserConsents().setConsents(consents); + Query query = new Query( + List.of(), List.of(), + new PhenotypicSubquery( + null, + List.of( + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs123\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs456\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs123\\data\\sex\\", Set.of("male", "female"), null, null, null) + ), Operator.AND + ), List.of(new GenomicFilter("Gene_with_variant", List.of("CDH8"), null, null)), ResultType.COUNT, null, null + ); + + boolean result = bdcConsentBasedAccessRuleEvaluator.evaluateAccessRule(query, null, userConsents); + assertTrue(result); + } + + + @Test + public void evaluateAccessRule_genomicFiltersNoTopmedConsents_reject() { + UserConsents userConsents = new UserConsents().setConsents(Map.of("\\_consents\\", Set.of("phs123.c1", "phs456.c2"))); + Query query = new Query( + List.of(), List.of(), + new PhenotypicSubquery( + null, + List.of( + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs123\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs456\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs123\\data\\sex\\", Set.of("male", "female"), null, null, null) + ), Operator.AND + ), List.of(new GenomicFilter("Gene_with_variant", List.of("CDH8"), null, null)), ResultType.COUNT, null, null + ); + + boolean result = bdcConsentBasedAccessRuleEvaluator.evaluateAccessRule(query, null, userConsents); + assertFalse(result); + } + + + @Test + public void evaluateAccessRule_validHarmonizedPhenotypicFilters_accept() { + UserConsents userConsents = new UserConsents().setConsents(Map.of("\\_consents\\", Set.of("phs123.c1", "phs456.c2"), "\\_harmonized_consent\\", Set.of("phs789.c1", "phs789.c2"))); + Query query = new Query( + List.of(), List.of(), + new PhenotypicSubquery( + null, + List.of( + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs123\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\DCC Harmonized data set\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicSubquery(false, List.of(new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\DCC Harmonized data set\\data\\sex\\", Set.of("male", "female"), null, null, null)), Operator.AND) + ), Operator.AND + ), null, ResultType.COUNT, null, null + ); + + boolean result = bdcConsentBasedAccessRuleEvaluator.evaluateAccessRule(query, null, userConsents); + assertTrue(result); + } + + @Test + public void evaluateAccessRule_invalidNestedHarmonizedPhenotypicFilters_reject() { + UserConsents userConsents = new UserConsents().setConsents(Map.of("\\_consents\\", Set.of("phs123.c1", "phs456.c2"))); + Query query = new Query( + List.of(), List.of(), + new PhenotypicSubquery( + null, + List.of( + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs123\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs456\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicSubquery(false, List.of(new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\DCC Harmonized data set\\data\\sex\\", Set.of("male", "female"), null, null, null)), Operator.AND) + ), Operator.AND + ), null, ResultType.COUNT, null, null + ); + + boolean result = bdcConsentBasedAccessRuleEvaluator.evaluateAccessRule(query, null, userConsents); + assertFalse(result); + } + + @Test + public void evaluateAccessRule_harmonizedPhenotypicFiltersEmptyUserConsent_reject() { + UserConsents userConsents = new UserConsents().setConsents(Map.of("\\_consents\\", Set.of("phs123.c1", "phs456.c2"), "\\_harmonized_consent\\", Set.of())); + Query query = new Query( + List.of(), List.of(), + new PhenotypicSubquery( + null, + List.of( + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs123\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs456\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\DCC Harmonized data set\\data\\sex\\", Set.of("male", "female"), null, null, null) + ), Operator.AND + ), null, ResultType.COUNT, null, null + ); + + boolean result = bdcConsentBasedAccessRuleEvaluator.evaluateAccessRule(query, null, userConsents); + assertFalse(result); + } + + @Test + public void setAuthorizationFiltersForQuery_normalConsents_addOnlyConsents() { + UserConsents userConsents = new UserConsents().setConsents(Map.of("\\_consents\\", Set.of("phs123.c1", "phs456.c2"), "\\_harmonized_consent\\", Set.of("phs789.c1", "phs789.c2"))); + Query query = new Query( + List.of(), List.of(), + new PhenotypicSubquery( + null, + List.of( + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs123\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs456\\data\\age\\", null, 30.0, 40.0, null) + ), Operator.AND + ), null, ResultType.COUNT, null, null + ); + + Query queryWithConsents = bdcConsentBasedAccessRuleEvaluator.setAuthorizationFiltersForQuery(userConsents, query); + assertEquals(1, queryWithConsents.authorizationFilters().size()); + assertEquals(new AuthorizationFilter("\\_consents\\", Set.of("phs123.c1", "phs456.c2")), queryWithConsents.authorizationFilters().get(0)); + } + + @Test + public void evaluateAccessRule_filterIncludesTopmedAndParentStudyId_accept() { + UserConsents userConsents = new UserConsents().setConsents(Map.of("\\_consents\\", Set.of("phs123.c1", "phs456.c2"))); + Query query = new Query( + List.of(), List.of(), + new PhenotypicSubquery( + null, + List.of( + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs123\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs456\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\_Topmed Study Accession with Subject ID\\", Set.of("phs789"), null, null, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\_Parent Study Accession with Subject ID\\", Set.of("phs999"), null, null, null) + ), Operator.AND + ), null, ResultType.COUNT, null, null + ); + + boolean result = bdcConsentBasedAccessRuleEvaluator.evaluateAccessRule(query, null, userConsents); + assertTrue(result); + } + + @Test + public void evaluateAccessRule_selectIncludesTopmedAndParentStudyId_accept() { + UserConsents userConsents = new UserConsents().setConsents(Map.of("\\_consents\\", Set.of("phs123.c1", "phs456.c2"))); + Query query = new Query( + List.of("\\_Topmed Study Accession with Subject ID\\", "\\_Parent Study Accession with Subject ID\\", "\\_consents\\", "\\_harmonized_consent\\", "\\_topmed_consents\\"), List.of(), + new PhenotypicSubquery( + null, + List.of( + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs123\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs456\\data\\age\\", null, 30.0, 40.0, null), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\phs123\\data\\sex\\", Set.of("male", "female"), null, null, null) + ), Operator.AND + ), null, ResultType.COUNT, null, null + ); + + boolean result = bdcConsentBasedAccessRuleEvaluator.evaluateAccessRule(query, null, userConsents); + assertTrue(result); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/BdcConsentsBuilderTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/BdcConsentsBuilderTest.java new file mode 100644 index 000000000..7a63b8bbc --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authorization/BdcConsentsBuilderTest.java @@ -0,0 +1,169 @@ +package edu.harvard.hms.dbmi.avillach.auth.service.impl.authorization; + + +import edu.harvard.hms.dbmi.avillach.auth.model.fenceMapping.StudyMetaData; +import edu.harvard.hms.dbmi.avillach.auth.model.ras.RasDbgapPermission; +import org.junit.jupiter.api.Test; + +import java.util.HashMap; +import java.util.Map; +import java.util.Set; + +import static org.junit.jupiter.api.Assertions.*; + +public class BdcConsentsBuilderTest { + + private static final Map DEFAULT_FENCE_MAPPING = Map.of( + "phs123.c1", new StudyMetaData().setHarmonized(false).setDataType("P"), "phs123.c2", + new StudyMetaData().setHarmonized(false).setDataType("P"), "phs456.c1", new StudyMetaData().setHarmonized(true).setDataType("P"), + "phs456.c2", new StudyMetaData().setHarmonized(true).setDataType("P"), "phs789.c1", + new StudyMetaData().setHarmonized(false).setDataType("G"), "phs789.c2", new StudyMetaData().setHarmonized(false).setDataType("G"), + "phs999.c1", new StudyMetaData().setHarmonized(true).setDataType("G"), "phs999.c2", + new StudyMetaData().setHarmonized(true).setDataType("G"), "open_access-1000Genomes", + new StudyMetaData().setHarmonized(false).setDataType("P").setStudyType("public"), "tutorial-biolincc_framingham", + new StudyMetaData().setHarmonized(false).setDataType("P").setStudyType("public") + ); + + @Test + public void createConsents_noConsents_addPublic() { + Set userStudies = Set.of(); + Map> consents = new BdcConsentsBuilder(DEFAULT_FENCE_MAPPING, userStudies).createConsents(); + assertEquals(Set.of(BdcConsentsBuilder.CONSENTS_KEY), consents.keySet()); + assertEquals(consents.get(BdcConsentsBuilder.CONSENTS_KEY), Set.of("open_access-1000Genomes", "tutorial-biolincc_framingham")); + } + + @Test + public void createConsents_noConsentsNoPublic_throwException() { + Set userStudies = Set.of(); + assertThrows( + IllegalStateException.class, + () -> new BdcConsentsBuilder(Map.of("phs123.c1", new StudyMetaData().setHarmonized(false).setDataType("P")), userStudies) + .createConsents() + ); + } + + @Test + public void createConsents_oneNormalConsent() { + Set userStudies = Set.of("phs123.c1"); + Map> consents = new BdcConsentsBuilder(DEFAULT_FENCE_MAPPING, userStudies).createConsents(); + assertEquals(Set.of(BdcConsentsBuilder.CONSENTS_KEY), consents.keySet()); + assertEquals( + Set.of("phs123.c1", "open_access-1000Genomes", "tutorial-biolincc_framingham"), consents.get(BdcConsentsBuilder.CONSENTS_KEY) + ); + } + + @Test + public void createConsents_multipleNormalConsent() { + Set userStudies = Set.of("phs123.c1","phs123.c2"); + Map> consents = new BdcConsentsBuilder(DEFAULT_FENCE_MAPPING, userStudies).createConsents(); + assertEquals(Set.of(BdcConsentsBuilder.CONSENTS_KEY), consents.keySet()); + assertEquals( + Set.of("phs123.c1", "phs123.c2", "open_access-1000Genomes", "tutorial-biolincc_framingham"), + consents.get(BdcConsentsBuilder.CONSENTS_KEY) + ); + } + + @Test + public void createConsents_oneNormalConsentOneMissingConsent_ignoreMissingConsent() { + Set userStudies = Set.of("phs123.c1","phs321.c1"); + Map> consents = new BdcConsentsBuilder(DEFAULT_FENCE_MAPPING, userStudies).createConsents(); + assertEquals(Set.of(BdcConsentsBuilder.CONSENTS_KEY), consents.keySet()); + assertEquals( + Set.of("phs123.c1", "open_access-1000Genomes", "tutorial-biolincc_framingham"), consents.get(BdcConsentsBuilder.CONSENTS_KEY) + ); + } + + + @Test + public void createConsents_harmonizedConsentsOnly() { + Set userStudies = Set.of("phs456.c1","phs456.c2"); + Map> consents = new BdcConsentsBuilder(DEFAULT_FENCE_MAPPING, userStudies).createConsents(); + assertEquals(Set.of(BdcConsentsBuilder.CONSENTS_KEY, BdcConsentsBuilder.HARMONIZED_CONSENTS_KEY), consents.keySet()); + assertEquals( + Set.of("phs456.c1", "phs456.c2", "open_access-1000Genomes", "tutorial-biolincc_framingham"), + consents.get(BdcConsentsBuilder.CONSENTS_KEY) + ); + assertEquals(Set.of("phs456.c1", "phs456.c2"), consents.get(BdcConsentsBuilder.HARMONIZED_CONSENTS_KEY)); + } + + @Test + public void createConsents_multipleNormalAndHarmonizedConsents() { + Set userStudies = Set.of("phs123.c1","phs123.c2","phs456.c1"); + Map> consents = new BdcConsentsBuilder(DEFAULT_FENCE_MAPPING, userStudies).createConsents(); + assertEquals(Set.of(BdcConsentsBuilder.CONSENTS_KEY, BdcConsentsBuilder.HARMONIZED_CONSENTS_KEY), consents.keySet()); + assertEquals( + Set.of("phs123.c1", "phs123.c2", "phs456.c1", "open_access-1000Genomes", "tutorial-biolincc_framingham"), + consents.get(BdcConsentsBuilder.CONSENTS_KEY) + ); + assertEquals(Set.of("phs456.c1"), consents.get(BdcConsentsBuilder.HARMONIZED_CONSENTS_KEY)); + } + + + @Test + public void createConsents_genomicConsentsOnly() { + Set userStudies = Set.of("phs789.c1","phs789.c2"); + Map> consents = new BdcConsentsBuilder(DEFAULT_FENCE_MAPPING, userStudies).createConsents(); + assertEquals(Set.of(BdcConsentsBuilder.CONSENTS_KEY, BdcConsentsBuilder.TOPMED_CONSENTS_KEY), consents.keySet()); + assertEquals( + Set.of("phs789.c1", "phs789.c2", "open_access-1000Genomes", "tutorial-biolincc_framingham"), + consents.get(BdcConsentsBuilder.CONSENTS_KEY) + ); + assertEquals(Set.of("phs789.c1", "phs789.c2"), consents.get(BdcConsentsBuilder.TOPMED_CONSENTS_KEY)); + } + + @Test + public void createConsents_multipleNormalAndGenomicConsents() { + Set userStudies = Set.of("phs123.c1","phs123.c2","phs789.c1"); + Map> consents = new BdcConsentsBuilder(DEFAULT_FENCE_MAPPING, userStudies).createConsents(); + assertEquals(Set.of(BdcConsentsBuilder.CONSENTS_KEY, BdcConsentsBuilder.TOPMED_CONSENTS_KEY), consents.keySet()); + assertEquals( + Set.of("phs123.c1", "phs123.c2", "phs789.c1", "open_access-1000Genomes", "tutorial-biolincc_framingham"), + consents.get(BdcConsentsBuilder.CONSENTS_KEY) + ); + assertEquals(Set.of("phs789.c1"), consents.get(BdcConsentsBuilder.TOPMED_CONSENTS_KEY)); + } + + @Test + public void createConsents_harmonizedGenomicConsentsOnly() { + Set userStudies = Set.of("phs999.c1","phs999.c2"); + Map> consents = new BdcConsentsBuilder(DEFAULT_FENCE_MAPPING, userStudies).createConsents(); + assertEquals( + Set.of(BdcConsentsBuilder.CONSENTS_KEY, BdcConsentsBuilder.TOPMED_CONSENTS_KEY, BdcConsentsBuilder.HARMONIZED_CONSENTS_KEY), + consents.keySet() + ); + assertEquals( + Set.of("phs999.c1", "phs999.c2", "open_access-1000Genomes", "tutorial-biolincc_framingham"), + consents.get(BdcConsentsBuilder.CONSENTS_KEY) + ); + assertEquals(Set.of("phs999.c1", "phs999.c2"), consents.get(BdcConsentsBuilder.TOPMED_CONSENTS_KEY)); + assertEquals(Set.of("phs999.c1", "phs999.c2"), consents.get(BdcConsentsBuilder.HARMONIZED_CONSENTS_KEY)); + } + + @Test + public void createConsents_multipleNormalAndHarmonizedGenomicConsents() { + Set userStudies = Set.of("phs123.c1","phs123.c2","phs999.c1"); + Map> consents = new BdcConsentsBuilder(DEFAULT_FENCE_MAPPING, userStudies).createConsents(); + assertEquals( + Set.of(BdcConsentsBuilder.CONSENTS_KEY, BdcConsentsBuilder.TOPMED_CONSENTS_KEY, BdcConsentsBuilder.HARMONIZED_CONSENTS_KEY), + consents.keySet() + ); + assertEquals( + Set.of("phs123.c1", "phs123.c2", "phs999.c1", "open_access-1000Genomes", "tutorial-biolincc_framingham"), + consents.get(BdcConsentsBuilder.CONSENTS_KEY) + ); + assertEquals(Set.of("phs999.c1"), consents.get(BdcConsentsBuilder.TOPMED_CONSENTS_KEY)); + assertEquals(Set.of("phs999.c1"), consents.get(BdcConsentsBuilder.HARMONIZED_CONSENTS_KEY)); + } + + @Test + public void createConsents_publicGenomicStudy_shouldBeAddedToTopmedConsents() { + HashMap studyMetaData= new HashMap<>(DEFAULT_FENCE_MAPPING); + studyMetaData.put("open_access-1000Genomes", + new StudyMetaData().setHarmonized(false).setDataType("P/G").setStudyType("public")); + Set userStudies = Set.of(); + Map> consents = new BdcConsentsBuilder(studyMetaData, userStudies).createConsents(); + assertEquals(Set.of(BdcConsentsBuilder.CONSENTS_KEY, BdcConsentsBuilder.TOPMED_CONSENTS_KEY), consents.keySet()); + assertEquals(consents.get(BdcConsentsBuilder.CONSENTS_KEY), Set.of("open_access-1000Genomes", "tutorial-biolincc_framingham")); + assertEquals(consents.get(BdcConsentsBuilder.TOPMED_CONSENTS_KEY), Set.of("open_access-1000Genomes")); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/utils/AuditAttributesTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/utils/AuditAttributesTest.java new file mode 100644 index 000000000..b49173014 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/utils/AuditAttributesTest.java @@ -0,0 +1,51 @@ +package edu.harvard.hms.dbmi.avillach.auth.utils; + +import org.junit.jupiter.api.Test; +import org.springframework.mock.web.MockHttpServletRequest; + +import java.util.Map; + +import static org.junit.jupiter.api.Assertions.*; + +class AuditAttributesTest { + + @Test + void shouldPutAndRetrieveMetadata() { + MockHttpServletRequest request = new MockHttpServletRequest(); + AuditAttributes.putMetadata(request, "key1", "value1"); + AuditAttributes.putMetadata(request, "key2", 42); + + Map all = AuditAttributes.getMetadata(request); + assertEquals("value1", all.get("key1")); + assertEquals(42, all.get("key2")); + assertEquals(2, all.size()); + } + + @Test + void shouldIgnoreNullKeyOrValue() { + MockHttpServletRequest request = new MockHttpServletRequest(); + AuditAttributes.putMetadata(request, null, "value"); + AuditAttributes.putMetadata(request, "key", null); + + Map all = AuditAttributes.getMetadata(request); + assertTrue(all.isEmpty()); + } + + @Test + void shouldIgnoreNullRequest() { + AuditAttributes.putMetadata(null, "key", "value"); + Map all = AuditAttributes.getMetadata(null); + assertTrue(all.isEmpty()); + } + + @Test + void shouldNotIncludeNonAuditAttributes() { + MockHttpServletRequest request = new MockHttpServletRequest(); + request.setAttribute("some.other.attr", "not-audit"); + AuditAttributes.putMetadata(request, "audit_key", "audit_value"); + + Map all = AuditAttributes.getMetadata(request); + assertEquals(1, all.size()); + assertEquals("audit_value", all.get("audit_key")); + } +} diff --git a/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/utils/JsonUtilsTest.java b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/utils/JsonUtilsTest.java new file mode 100644 index 000000000..1d8e47368 --- /dev/null +++ b/services/pic-sure-auth-microapp/pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/auth/utils/JsonUtilsTest.java @@ -0,0 +1,251 @@ +package edu.harvard.hms.dbmi.avillach.auth.utils; + +import java.io.IOException; +import java.util.Collection; +import java.util.Map; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import com.fasterxml.jackson.core.JsonParseException; +import com.fasterxml.jackson.databind.JsonMappingException; +import org.junit.jupiter.api.Test; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.ContextConfiguration; + +import static org.junit.jupiter.api.Assertions.*; + +@SpringBootTest +@ContextConfiguration(classes = {JsonUtils.class}) +public class JsonUtilsTest { + + + /** + * {"queryTemplate":"{ + * \"categoryFilters\":{\"\\\\demographics\\\\SEX\\\\\":[\"male\"]}, + * \"numericFilters\":{\"\\\\demographics\\\\AGE\\\\\":{\"max\":\"50\"}}, + * \"requiredFields\":[\"\\\\_Study Accession with Patient ID\\\\\"], + * \"anyRecordOf\":[], + * \"variantInfoFilters\":[ + * {\"categoryVariantInfoFilters\":{}, + * \"numericVariantInfoFilters\":{}}], + * \"expectedResultType\":[\"COUNT\"]}" + * } + */ + + @Test + public void testmergeTemplateMap() throws IOException { + ObjectMapper objectMapper = new ObjectMapper(); + //template with one category filter and one required field + String template1Str = "{\"numericFilters\":{},\"categoryFilters\":{\"\\\\demographics\\\\SEX\\\\\":[\"male\"]},\"requiredFields\":[\"\\\\_Study Accession with Patient ID\\\\\"],\"anyRecordOf\":[],\"variantInfoFilters\":[{\"categoryVariantInfoFilters\":{},\"numericVariantInfoFilters\":{}}],\"expectedResultType\":\"COUNT\"}"; + Map template1 = objectMapper.readValue(template1Str, Map.class); + + //template with one numeric filter and one required field + String template2Str = "{\"categoryFilters\":{},\"numericFilters\":{\"\\\\demographics\\\\AGE\\\\\":{\"max\":\"50\"}},\"requiredFields\":[\"\\\\_Study Accession with Patient ID\\\\\"],\"anyRecordOf\":[],\"variantInfoFilters\":[{\"categoryVariantInfoFilters\":{},\"numericVariantInfoFilters\":{}}],\"expectedResultType\":\"COUNT\"}"; + Map template2 = objectMapper.readValue(template2Str, Map.class); + + Map mergedTemplate = JsonUtils.mergeTemplateMap(template1, template2); + + assertNotNull(mergedTemplate.get("categoryFilters")); + + assertNotNull(mergedTemplate.get("numericFilters")); + + assertNotNull(mergedTemplate.get("anyRecordOf")); + + assertNotNull(mergedTemplate.get("requiredFields")); + + //both required fields (same) should have been merged + assertInstanceOf(Collection.class, mergedTemplate.get("requiredFields")); + assertEquals(1, ((Collection)mergedTemplate.get("requiredFields")).size()); + + assertNotNull(mergedTemplate.get("variantInfoFilters")); + + assertNotNull(mergedTemplate.get("expectedResultType")); + } + + /** + * Make sure we don't fail is one parameter is empty + * @throws JsonParseException + * @throws JsonMappingException + * @throws IOException + */ + @Test + public void testmergeTemplateMapEmptyMap() throws IOException { + ObjectMapper objectMapper = new ObjectMapper(); + //template with one category filter and one required field + String template1Str = "{\"numericFilters\":{},\"categoryFilters\":{\"\\\\demographics\\\\SEX\\\\\":[\"male\"]},\"requiredFields\":[\"\\\\_Study Accession with Patient ID\\\\\"],\"anyRecordOf\":[],\"variantInfoFilters\":[{\"categoryVariantInfoFilters\":{},\"numericVariantInfoFilters\":{}}],\"expectedResultType\":\"COUNT\"}"; + Map template1 = objectMapper.readValue(template1Str, Map.class); + + //template with one numeric filter and one required field + String template2Str = "{}"; + Map template2 = objectMapper.readValue(template2Str, Map.class); + + Map mergedTemplate = JsonUtils.mergeTemplateMap(template1, template2); + + assertNotNull(mergedTemplate.get("categoryFilters")); + + assertNotNull(mergedTemplate.get("numericFilters")); + + assertNotNull(mergedTemplate.get("anyRecordOf")); + + assertNotNull(mergedTemplate.get("requiredFields")); + + //both required fields (same) should have been merged + assertInstanceOf(Collection.class, mergedTemplate.get("requiredFields")); + assertEquals(1, ((Collection)mergedTemplate.get("requiredFields")).size()); + + assertNotNull(mergedTemplate.get("variantInfoFilters")); + + assertNotNull(mergedTemplate.get("expectedResultType")); + } + + /** + * Make sure we don't fail is one parameter is empty + * @throws JsonParseException + * @throws JsonMappingException + * @throws IOException + */ + @Test + public void testmergeTemplateMapEmptyMapInverse() throws IOException { + ObjectMapper objectMapper = new ObjectMapper(); + //template with one category filter and one required field + String template1Str = "{\"numericFilters\":{},\"categoryFilters\":{\"\\\\demographics\\\\SEX\\\\\":[\"male\"]},\"requiredFields\":[\"\\\\_Study Accession with Patient ID\\\\\"],\"anyRecordOf\":[],\"variantInfoFilters\":[{\"categoryVariantInfoFilters\":{},\"numericVariantInfoFilters\":{}}],\"expectedResultType\":\"COUNT\"}"; + Map template1 = objectMapper.readValue(template1Str, Map.class); + + //empty object + String template2Str = "{}"; + Map template2 = objectMapper.readValue(template2Str, Map.class); + + //Make sure this works for both parameters + Map mergedTemplate = JsonUtils.mergeTemplateMap(template2, template1); + + assertNotNull(mergedTemplate.get("categoryFilters")); + + assertNotNull(mergedTemplate.get("numericFilters")); + + assertNotNull(mergedTemplate.get("anyRecordOf")); + + assertNotNull(mergedTemplate.get("requiredFields")); + + //both required fields (same) should have been merged + assertInstanceOf(Collection.class, mergedTemplate.get("requiredFields")); + assertEquals(1, ((Collection)mergedTemplate.get("requiredFields")).size()); + + assertNotNull(mergedTemplate.get("variantInfoFilters")); + + assertNotNull(mergedTemplate.get("expectedResultType")); + } + + @Test + public void testmergeTemplateMapMergeFilters() throws IOException{ + ObjectMapper objectMapper = new ObjectMapper(); + //template with one category filter and one required field + String template1Str = "{\"numericFilters\":{},\"categoryFilters\":{\"\\\\demographics\\\\SEX\\\\\":[\"male\"]},\"requiredFields\":[\"\\\\_Study Accession with Patient ID\\\\\"],\"anyRecordOf\":[],\"variantInfoFilters\":[{\"categoryVariantInfoFilters\":{},\"numericVariantInfoFilters\":{}}],\"expectedResultType\":\"COUNT\"}"; + Map template1 = objectMapper.readValue(template1Str, Map.class); + + //template with one category filter (different value) and one required field + String template2Str = "{\"numericFilters\":{},\"categoryFilters\":{\"\\\\demographics\\\\SEX\\\\\":[\"female\"]},\"requiredFields\":[\"\\\\_Study Accession with Patient ID\\\\\"],\"anyRecordOf\":[],\"variantInfoFilters\":[{\"categoryVariantInfoFilters\":{},\"numericVariantInfoFilters\":{}}],\"expectedResultType\":\"COUNT\"}"; + Map template2 = objectMapper.readValue(template2Str, Map.class); + + Map mergedTemplate = JsonUtils.mergeTemplateMap(template1, template2); + + //validate that the same category filters are merged + assertNotNull(mergedTemplate.get("categoryFilters")); + assertInstanceOf(Map.class, mergedTemplate.get("categoryFilters")); + Map categoryFilters = (Map)mergedTemplate.get("categoryFilters"); + assertEquals(1, categoryFilters.size()); + + //less escaping needed here for some reason + assertNotNull(categoryFilters.get("\\demographics\\SEX\\")); + assertTrue(categoryFilters.get("\\demographics\\SEX\\") instanceof Collection); + assertEquals(2, ((Collection)categoryFilters.get("\\demographics\\SEX\\")).size()); + + assertNotNull(mergedTemplate.get("numericFilters")); + + assertNotNull(mergedTemplate.get("anyRecordOf")); + + assertNotNull(mergedTemplate.get("requiredFields")); + + //both required fields (same) should have been merged + assertTrue(mergedTemplate.get("requiredFields") instanceof Collection); + assertEquals(1, ((Collection)mergedTemplate.get("requiredFields")).size()); + + assertNotNull(mergedTemplate.get("variantInfoFilters")); + + assertNotNull(mergedTemplate.get("expectedResultType")); + } + + @Test + public void testmergeTemplateMapMultipleNumericFilters() throws IOException{ + ObjectMapper objectMapper = new ObjectMapper(); + //template with one category filter and one required field + String template1Str = "{\"categoryFilters\":{},\"numericFilters\":{\"\\\\demographics\\\\AGE\\\\\":{\"min\":\"20\"}},\"requiredFields\":[\"\\\\_Study Accession with Patient ID\\\\\"],\"anyRecordOf\":[],\"variantInfoFilters\":[{\"categoryVariantInfoFilters\":{},\"numericVariantInfoFilters\":{}}],\"expectedResultType\":\"COUNT\"}"; + Map template1 = objectMapper.readValue(template1Str, Map.class); + + //template with one numeric filter and one required field + String template2Str = "{\"categoryFilters\":{},\"numericFilters\":{\"\\\\demographics\\\\AGE\\\\\":{\"max\":\"50\"}},\"requiredFields\":[\"\\\\_Study Accession with Patient ID\\\\\"],\"anyRecordOf\":[],\"variantInfoFilters\":[{\"categoryVariantInfoFilters\":{},\"numericVariantInfoFilters\":{}}],\"expectedResultType\":\"COUNT\"}"; + Map template2 = objectMapper.readValue(template2Str, Map.class); + + Map mergedTemplate = JsonUtils.mergeTemplateMap(template1, template2); + + assertNotNull(mergedTemplate.get("categoryFilters")); + + assertNotNull(mergedTemplate.get("numericFilters")); + assertTrue(mergedTemplate.get("numericFilters") instanceof Map); + Map categoryFilters = (Map)mergedTemplate.get("numericFilters"); + assertEquals(1, categoryFilters.size()); + + //less escaping needed here for some reason + assertNotNull(categoryFilters.get("\\demographics\\AGE\\")); + assertTrue(categoryFilters.get("\\demographics\\AGE\\") instanceof Map); + assertEquals(2, ((Map)categoryFilters.get("\\demographics\\AGE\\")).size()); + //values are all stored as strings, since json/js doesn't care + assertEquals("50", ((Map)categoryFilters.get("\\demographics\\AGE\\")).get("max")); + assertEquals("20", ((Map)categoryFilters.get("\\demographics\\AGE\\")).get("min")); + + + assertNotNull(mergedTemplate.get("anyRecordOf")); + + assertNotNull(mergedTemplate.get("requiredFields")); + + //both required fields (same) should have been merged + assertTrue(mergedTemplate.get("requiredFields") instanceof Collection); + assertEquals(1, ((Collection)mergedTemplate.get("requiredFields")).size()); + + assertNotNull(mergedTemplate.get("variantInfoFilters")); + + assertNotNull(mergedTemplate.get("expectedResultType")); + } + + + @Test + public void testmergeTemplateMapVariantInfo() throws IOException{ + ObjectMapper objectMapper = new ObjectMapper(); + //template with one category filter and one required field + String template1Str = "{\"numericFilters\":{},\"categoryFilters\":{},\"requiredFields\":[],\"anyRecordOf\":[],\"variantInfoFilters\":[{\"categoryVariantInfoFilters\":{\"variant_severity\":[\"HIGH\"]},\"numericVariantInfoFilters\":{}}],\"expectedResultType\":\"COUNT\"}"; + Map template1 = objectMapper.readValue(template1Str, Map.class); + + //template with one numeric filter and one required field + String template2Str = "{\"categoryFilters\":{},\"numericFilters\":{},\"requiredFields\":[],\"anyRecordOf\":[],\"variantInfoFilters\":[{\"categoryVariantInfoFilters\":{\"variant_severity\":[\"LOW\"]},\"numericVariantInfoFilters\":{}}],\"expectedResultType\":\"COUNT\"}"; + Map template2 = objectMapper.readValue(template2Str, Map.class); + + Map mergedTemplate = JsonUtils.mergeTemplateMap(template1, template2); + + assertNotNull(mergedTemplate.get("categoryFilters")); + + assertNotNull(mergedTemplate.get("numericFilters")); + + assertNotNull(mergedTemplate.get("anyRecordOf")); + + assertNotNull(mergedTemplate.get("requiredFields")); + + //NO required fields in this test + assertTrue(mergedTemplate.get("requiredFields") instanceof Collection); + assertEquals(0, ((Collection)mergedTemplate.get("requiredFields")).size()); + + assertNotNull(mergedTemplate.get("variantInfoFilters")); + assertTrue(mergedTemplate.get("variantInfoFilters") instanceof Collection); + Collection variantInfoFilters = (Collection)mergedTemplate.get("variantInfoFilters"); + + assertNotNull(mergedTemplate.get("expectedResultType")); + } +} diff --git a/services/pic-sure-auth-microapp/pom.xml b/services/pic-sure-auth-microapp/pom.xml new file mode 100644 index 000000000..2546aa38b --- /dev/null +++ b/services/pic-sure-auth-microapp/pom.xml @@ -0,0 +1,18 @@ + + + 4.0.0 + + edu.harvard.hms.dbmi.avillach + pic-sure-api + ${revision} + ../../pom.xml + + edu.harvard.hms.dbmi.avillach.picsure.auth.microapp + pic-sure-auth-microapp + pom + pic-sure-auth-microapp + + pic-sure-auth-services + + diff --git a/services/pic-sure-gateway/Dockerfile b/services/pic-sure-gateway/Dockerfile new file mode 100644 index 000000000..fc3369baf --- /dev/null +++ b/services/pic-sure-gateway/Dockerfile @@ -0,0 +1,5 @@ +FROM amazoncorretto:25 +WORKDIR /app +COPY target/pic-sure-gateway-*.jar /app/app.jar +EXPOSE 8080 +ENTRYPOINT ["sh", "-c", "java ${JAVA_OPTS} -jar /app/app.jar --spring.profiles.active=${SPRING_PROFILE:-aio}"] diff --git a/services/pic-sure-gateway/README.md b/services/pic-sure-gateway/README.md new file mode 100644 index 000000000..a984f3ca8 --- /dev/null +++ b/services/pic-sure-gateway/README.md @@ -0,0 +1,32 @@ +# pic-sure-gateway + +Spring Cloud Gateway MVC (servlet) front door for PIC-SURE. Static, per-service routes forward to `logging`, `dictionary`, `uploader`, +`visualization`, `hpds` (query-service), `configuration`, and `dataset` (operations-service) — see `application.yml` for the full route +table. The gateway owns query-read authorization end to end: it authenticates via PSAMA introspection, audits requests, and buffers/dispatches +as needed. There is no catch-all route; any path that doesn't match a configured route 404s. + +## Build & test + +```bash +# from the repo root (JDK 25 — enforced) +mvn -pl services/pic-sure-gateway -am verify +``` + +`NoRegistryRouteTest` and `RouteOwnedPrefixDriftTest` bind `spring.cloud.gateway.server.webmvc.routes` straight from the Spring +environment (Spring Cloud 2025.0.x property prefix) and assert every configured route is gateway-owned, catching route-table drift at +build time. + +## Run + +```bash +# local jar +java -jar target/pic-sure-gateway-*.jar --spring.profiles.active=local + +# container on the AIO `picsure` network +cp env.example .env # adjust if needed +docker compose up --build +``` + +Config: `HPDS_QUERY_SERVICE_URL`, `OPERATIONS_SERVICE_URL`, `TOKEN_INTROSPECTION_URL` (PSAMA), `SPRING_PROFILE` (`aio` default | `local`). +Observability: `/actuator/health`, `/actuator/prometheus`, `/actuator/metrics` (off by default; enabled via `PICSURE_ACTUATOR_EXPOSURE`); +every response carries `X-Request-Id` (generated if absent) and logs carry it as MDC `requestId`. diff --git a/services/pic-sure-gateway/docker-compose.yml b/services/pic-sure-gateway/docker-compose.yml new file mode 100644 index 000000000..9a7766f73 --- /dev/null +++ b/services/pic-sure-gateway/docker-compose.yml @@ -0,0 +1,14 @@ +services: + gateway: + build: . + image: pic-sure-gateway:local + environment: + - SPRING_PROFILE=${SPRING_PROFILE:-aio} + ports: + - "8090:8080" + networks: + - picsure + +networks: + picsure: + external: true diff --git a/services/pic-sure-gateway/env.example b/services/pic-sure-gateway/env.example new file mode 100644 index 000000000..b06631fae --- /dev/null +++ b/services/pic-sure-gateway/env.example @@ -0,0 +1,3 @@ +# Copy to .env for local docker-compose runs (gitignored). +# Spring profile: aio (Docker DNS) or local. +SPRING_PROFILE=aio diff --git a/services/pic-sure-gateway/pom.xml b/services/pic-sure-gateway/pom.xml new file mode 100644 index 000000000..f7eed1608 --- /dev/null +++ b/services/pic-sure-gateway/pom.xml @@ -0,0 +1,93 @@ + + + 4.0.0 + + edu.harvard.hms.dbmi.avillach + pic-sure-api + ${revision} + ../../pom.xml + + pic-sure-gateway + jar + pic-sure-gateway + Spring Cloud Gateway MVC front door for PIC-SURE + + + + + org.springframework.cloud + spring-cloud-starter-gateway-server-webmvc + + + org.springframework.boot + spring-boot-starter-actuator + + + io.micrometer + micrometer-registry-prometheus + + + org.springframework.boot + spring-boot-starter-security + + + com.fasterxml.jackson.core + jackson-databind + + + + edu.harvard.hms.dbmi.avillach + pic-sure-spring-commons + + + + edu.harvard.dbmi.avillach + pic-sure-logging-client + + + org.springframework.boot + spring-boot-starter-test + test + + + org.wiremock + wiremock-standalone + test + + + + + + + org.springframework.boot + spring-boot-maven-plugin + + + + repackage + + + + + + + org.apache.maven.plugins + maven-surefire-plugin + + + **/Test*.java + **/*Test.java + **/*Tests.java + **/*TestCase.java + **/*IT.java + + + + + + diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/GatewayApplication.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/GatewayApplication.java new file mode 100644 index 000000000..937fab7b3 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/GatewayApplication.java @@ -0,0 +1,12 @@ +package edu.harvard.hms.dbmi.avillach.gateway; + +import org.springframework.boot.SpringApplication; +import org.springframework.boot.autoconfigure.SpringBootApplication; + +@SpringBootApplication +public class GatewayApplication { + + static void main(String[] args) { + SpringApplication.run(GatewayApplication.class, args); + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/auth/BufferedRequestWrapper.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/auth/BufferedRequestWrapper.java new file mode 100644 index 000000000..1b6d1bd15 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/auth/BufferedRequestWrapper.java @@ -0,0 +1,74 @@ +package edu.harvard.hms.dbmi.avillach.gateway.auth; + +import java.io.BufferedReader; +import java.io.ByteArrayInputStream; +import java.io.IOException; +import java.io.InputStreamReader; +import java.nio.charset.StandardCharsets; + +import jakarta.servlet.ReadListener; +import jakarta.servlet.ServletInputStream; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletRequestWrapper; + +/** + * Wraps an {@link HttpServletRequest} around an already-buffered {@code byte[]} body so downstream auth filters (introspection, consent + * body swap) can read — and, via {@link #setBody}, replace — the request body, and so the body can be re-read (each + * {@link #getInputStream()} call yields a fresh stream over the current bytes). + */ +public class BufferedRequestWrapper extends HttpServletRequestWrapper { + + private byte[] body; + + public BufferedRequestWrapper(HttpServletRequest request, byte[] initialBody) { + super(request); + this.body = initialBody == null ? new byte[0] : initialBody; + } + + public byte[] getBody() { + return body; + } + + public void setBody(byte[] newBody) { + this.body = newBody == null ? new byte[0] : newBody; + } + + @Override + public ServletInputStream getInputStream() { + ByteArrayInputStream bais = new ByteArrayInputStream(body); + return new ServletInputStream() { + @Override + public int read() { + return bais.read(); + } + + @Override + public boolean isFinished() { + return bais.available() == 0; + } + + @Override + public boolean isReady() { + return true; + } + + @Override + public void setReadListener(ReadListener listener) {} + }; + } + + @Override + public BufferedReader getReader() throws IOException { + return new BufferedReader(new InputStreamReader(getInputStream(), StandardCharsets.UTF_8)); + } + + @Override + public int getContentLength() { + return body.length; + } + + @Override + public long getContentLengthLong() { + return body.length; + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/auth/IntrospectionRequest.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/auth/IntrospectionRequest.java new file mode 100644 index 000000000..88115a0fb --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/auth/IntrospectionRequest.java @@ -0,0 +1,9 @@ +package edu.harvard.hms.dbmi.avillach.gateway.auth; + +import com.fasterxml.jackson.annotation.JsonInclude; + +import java.util.Map; + +@JsonInclude(JsonInclude.Include.NON_NULL) +public record IntrospectionRequest(String token, Map request) { +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/auth/IntrospectionResponse.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/auth/IntrospectionResponse.java new file mode 100644 index 000000000..ca6fdb73c --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/auth/IntrospectionResponse.java @@ -0,0 +1,17 @@ +package edu.harvard.hms.dbmi.avillach.gateway.auth; + +import com.fasterxml.jackson.annotation.JsonAlias; +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; + +import java.util.List; + +@JsonIgnoreProperties(ignoreUnknown = true) +public record IntrospectionResponse( + boolean active, + // PSAMA's inspect response carries the user UUID as "uuid" (UserService#responseMap / UserClaims#toMap); it never + // sends a "userId" field. Without this alias X-User-Id is never propagated and the query/operations services' + // header-based authn rejects every request. + @JsonAlias("uuid") String userId, String sub, String email, String roles, List privileges, Boolean tokenRefreshed, String token, + String query +) { +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/auth/PsamaClient.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/auth/PsamaClient.java new file mode 100644 index 000000000..eecf1f5b3 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/auth/PsamaClient.java @@ -0,0 +1,38 @@ +package edu.harvard.hms.dbmi.avillach.gateway.auth; + +import java.util.Map; + +import org.springframework.http.MediaType; +import org.springframework.web.client.RestClient; + +import com.fasterxml.jackson.databind.JsonNode; + +/** + * HTTP client for the PSAMA authentication microapp's token introspection and open-access validation endpoints. + */ +public class PsamaClient { + + private final RestClient http; + private final String introspectionUrl; + private final String openAccessValidateUrl; + private final String serviceToken; + + public PsamaClient(RestClient http, String introspectionUrl, String openAccessValidateUrl, String serviceToken) { + this.http = http; + this.introspectionUrl = introspectionUrl; + this.openAccessValidateUrl = openAccessValidateUrl; + this.serviceToken = serviceToken; + } + + public IntrospectionResponse introspect(String userToken, Map requestMeta) { + IntrospectionRequest body = new IntrospectionRequest(userToken, requestMeta); + return http.post().uri(introspectionUrl).header("Authorization", "Bearer " + serviceToken).contentType(MediaType.APPLICATION_JSON) + .body(body).retrieve().body(IntrospectionResponse.class); + } + + public boolean validateOpenAccess(Map requestBody) { + JsonNode resp = http.post().uri(openAccessValidateUrl).header("Authorization", "Bearer " + serviceToken) + .contentType(MediaType.APPLICATION_JSON).body(requestBody).retrieve().body(JsonNode.class); + return resp != null && resp.isBoolean() && resp.asBoolean(); + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/auth/QueryAuthFetcher.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/auth/QueryAuthFetcher.java new file mode 100644 index 000000000..7780e2dd5 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/auth/QueryAuthFetcher.java @@ -0,0 +1,78 @@ +package edu.harvard.hms.dbmi.avillach.gateway.auth; + +import java.util.Optional; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +import org.springframework.http.HttpStatus; +import org.springframework.web.client.ResourceAccessException; +import org.springframework.web.client.RestClient; +import org.springframework.web.client.RestClientException; +import org.springframework.web.client.RestClientResponseException; + +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; + +/** + * Fetches the stored query JSON for (/v3)?/query/{id}/(result|signed-url) paths from operations-service's gateway-only + * {@code /operations/internal/queries/{id}/dispatch} endpoint, so PSAMA can authorize these bodyless reads using the original query shape — + * NO database access from the gateway itself. Sends the mandatory internal dispatch token (X-PIC-SURE-INTERNAL-TOKEN). Fail-closed: ANY + * error (incl. 403) denies the request. + */ +public class QueryAuthFetcher { + + static final String INTERNAL_TOKEN_HEADER = "X-PIC-SURE-INTERNAL-TOKEN"; + + private static final Pattern RESULT_OR_SIGNED_URL = Pattern.compile(".*/query/([^/]+)/(?:result|signed-url)/?$"); + + private final RestClient http; + private final String queryServiceBaseUrl; // HPDS_QUERY_SERVICE_URL + private final String internalToken; // QUERY_SERVICE_INTERNAL_TOKEN + + public QueryAuthFetcher(RestClient http, String queryServiceBaseUrl, String internalToken) { + this.http = http; + this.queryServiceBaseUrl = queryServiceBaseUrl; + this.internalToken = internalToken; + } + + public Optional queryJsonForPath(String path) { + if (path == null) { + return Optional.empty(); + } + Matcher m = RESULT_OR_SIGNED_URL.matcher(path); + if (!m.matches()) { + return Optional.empty(); + } + return Optional.of(fetchDispatch(m.group(1))); + } + + private String fetchDispatch(String picsureId) { + DispatchResponse resp; + try { + resp = http.get().uri(queryServiceBaseUrl + "/operations/internal/queries/{id}/dispatch", picsureId) + .header(INTERNAL_TOKEN_HEADER, internalToken).retrieve().body(DispatchResponse.class); + } catch (RestClientResponseException e) { + int status = e.getStatusCode().value(); + // honest status + fail-closed: + if (status == 404) { + throw new PicsureException(HttpStatus.NOT_FOUND, "query_not_found", "No stored query for id " + picsureId); + } + if (status == 403) { + // missing/wrong internal token: a config error must NEVER serve a result. + throw new PicsureException(HttpStatus.BAD_GATEWAY, "dispatch_forbidden", "Query dispatch rejected the internal token"); + } + throw new PicsureException(HttpStatus.BAD_GATEWAY, "dispatch_failed", "Query dispatch returned " + e.getStatusCode()); + } catch (ResourceAccessException e) { + throw new PicsureException(HttpStatus.GATEWAY_TIMEOUT, "dispatch_unreachable", "Query service unreachable for dispatch"); + } catch (RestClientException e) { + // malformed/undeserializable response — fail closed + throw new PicsureException(HttpStatus.BAD_GATEWAY, "dispatch_malformed", "Query dispatch returned an unreadable response"); + } + if (resp == null || resp.queryJson() == null || resp.queryJson().isBlank()) { + throw new PicsureException(HttpStatus.BAD_GATEWAY, "dispatch_empty", "Dispatch returned no query for id " + picsureId); + } + return resp.queryJson(); + } + + record DispatchResponse(String queryJson) { + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/ActuatorSecurityConfig.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/ActuatorSecurityConfig.java new file mode 100644 index 000000000..ac5ba2ddd --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/ActuatorSecurityConfig.java @@ -0,0 +1,28 @@ +package edu.harvard.hms.dbmi.avillach.gateway.config; + +import org.springframework.boot.context.properties.EnableConfigurationProperties; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.core.annotation.Order; +import org.springframework.security.config.annotation.web.builders.HttpSecurity; +import org.springframework.security.web.SecurityFilterChain; + +import edu.harvard.hms.dbmi.avillach.commons.security.ActuatorSecurityHelper; +import edu.harvard.hms.dbmi.avillach.commons.security.ActuatorTokenProperties; + +/** + * Gates {@code /actuator/**} (all three services) behind {@code X-Application-Token} via the shared {@link ActuatorSecurityHelper}. + * Registered at {@code @Order(0)} so it wins over the gateway's permit-all main chain ({@link SecurityConfig}, tagged {@code @Order(10)}) + * for actuator paths -- the two chains never compete because {@code EndpointRequest.toAnyEndpoint()} scopes this chain to + * {@code /actuator/**} only. + */ +@Configuration +@EnableConfigurationProperties(ActuatorTokenProperties.class) +public class ActuatorSecurityConfig { + + @Bean + @Order(0) + SecurityFilterChain actuatorChain(HttpSecurity http, ActuatorTokenProperties props) throws Exception { + return ActuatorSecurityHelper.actuatorChain(http, props); + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/GatewaySecurityProperties.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/GatewaySecurityProperties.java new file mode 100644 index 000000000..0b72ff8fc --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/GatewaySecurityProperties.java @@ -0,0 +1,34 @@ +package edu.harvard.hms.dbmi.avillach.gateway.config; + +import java.util.List; + +import org.springframework.boot.context.properties.ConfigurationProperties; + +/** + * DB-free auth-chain configuration, bound from {@code picsure.gateway.security.*}. Backs {@link SecurityConfig}'s filter/bean wiring; see + * each field's referenced env var for the operational knob it maps to. + */ +@ConfigurationProperties(prefix = "picsure.gateway.security") +public record GatewaySecurityProperties( + List allowListPrefixes, boolean openAccessEnabled, String userIdClaim, + // GATEWAY_AUTH_MAX_BODY_BYTES -- auth-buffering cap; 413 over it + int maxBodyBytes, String introspectionUrl, String openAccessValidateUrl, String serviceToken, + // HPDS_QUERY_SERVICE_URL -- no longer read by QueryAuthFetcher (dispatch now points at operationsServiceUrl + // below), kept because the same env var also feeds the /hpds/** route and query-service health entry. + String queryServiceUrl, + // OPERATIONS_SERVICE_URL -- for QueryAuthFetcher dispatch (dispatch lives on operations-service, + // the sole DB owner) + String operationsServiceUrl, + // QUERY_SERVICE_INTERNAL_TOKEN -- X-PIC-SURE-INTERNAL-TOKEN, same value sent to operations-service now + String queryServiceInternalToken +) { + public GatewaySecurityProperties { + allowListPrefixes = allowListPrefixes == null ? List.of() : List.copyOf(allowListPrefixes); + if (userIdClaim == null) { + userIdClaim = "userId"; + } + if (maxBodyBytes <= 0) { + maxBodyBytes = 10_485_760; // 10 MiB default (GATEWAY_AUTH_MAX_BODY_BYTES) + } + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/HealthConfig.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/HealthConfig.java new file mode 100644 index 000000000..2c19df8c1 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/HealthConfig.java @@ -0,0 +1,68 @@ +package edu.harvard.hms.dbmi.avillach.gateway.config; + +import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.context.properties.EnableConfigurationProperties; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.core.Ordered; +import org.springframework.core.annotation.Order; +import org.springframework.http.MediaType; +import org.springframework.web.servlet.function.RequestPredicates; +import org.springframework.web.servlet.function.RouterFunction; +import org.springframework.web.servlet.function.RouterFunctions; +import org.springframework.web.servlet.function.ServerResponse; + +import edu.harvard.hms.dbmi.avillach.gateway.health.DownstreamHealthProperties; +import edu.harvard.hms.dbmi.avillach.gateway.health.SystemHealthService; +import edu.harvard.hms.dbmi.avillach.gateway.health.SystemStatusController; + +/** + * Registers the deep-health pieces as Spring beans so the {@code /system/status} legacy text controller and the {@code /actuator/health} + * composite can consume them. + */ +@Configuration +@EnableConfigurationProperties(DownstreamHealthProperties.class) +public class HealthConfig { + + @Bean + public SystemHealthService systemHealthService(DownstreamHealthProperties props) { + return new SystemHealthService(props); + } + + @Bean + public SystemStatusController systemStatusController( + SystemHealthService systemHealthService, @Value("${picsure.gateway.health.status-window-ms:60000}") long statusWindowMs + ) { + return new SystemStatusController(systemHealthService, statusWindowMs); + } + + /** + * Exposes {@code GET /system/status} at highest precedence. The gateway's own composite {@code RouterFunction} bean carries no explicit + * {@code @Order} (so it defaults to {@code Ordered.LOWEST_PRECEDENCE}); ordering this bean at {@code HIGHEST_PRECEDENCE} guarantees it + * is tried first within {@code RouterFunctionMapping}. See {@link SystemStatusController}'s class Javadoc for the full precedence + * chain. + */ + @Bean + @Order(Ordered.HIGHEST_PRECEDENCE) + public RouterFunction systemStatusRoute(SystemStatusController controller) { + return RouterFunctions.route( + RequestPredicates.GET("/system/status"), + request -> ServerResponse.ok().contentType(MediaType.TEXT_PLAIN).body(controller.status()) + ); + } + + /** + * Returns a clean 404 for {@code /actuator/**} when actuator is disabled (the default: no {@code PICSURE_ACTUATOR_EXPOSURE} set). + * Actuator endpoints are served by {@code WebMvcEndpointHandlerMapping} (order -100, ahead of {@code RouterFunctionMapping}), so + * whenever an endpoint IS exposed this route is never consulted for it; but an UNexposed {@code /actuator/*} path would otherwise fall + * through unhandled. Ordering at {@code HIGHEST_PRECEDENCE} ensures this guard is reached first, so unexposed actuator endpoints are + * never reachable unless explicitly enabled. + */ + @Bean + @Order(Ordered.HIGHEST_PRECEDENCE) + public RouterFunction actuatorCatchAllGuard() { + return RouterFunctions.route( + RequestPredicates.path("/actuator").or(RequestPredicates.path("/actuator/**")), request -> ServerResponse.notFound().build() + ); + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/ObservabilityConfig.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/ObservabilityConfig.java new file mode 100644 index 000000000..a7f697ce5 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/ObservabilityConfig.java @@ -0,0 +1,42 @@ +package edu.harvard.hms.dbmi.avillach.gateway.config; + +import org.springframework.boot.web.servlet.FilterRegistrationBean; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.core.Ordered; + +import edu.harvard.hms.dbmi.avillach.commons.request.RequestIdFilter; +import edu.harvard.hms.dbmi.avillach.gateway.request.AccessLogFilter; +import edu.harvard.hms.dbmi.avillach.gateway.request.InboundIdentityHeaderSanitizingFilter; + +@Configuration +public class ObservabilityConfig { + + @Bean + public FilterRegistrationBean requestIdFilter() { + FilterRegistrationBean registration = new FilterRegistrationBean<>(new RequestIdFilter()); + registration.setOrder(Ordered.HIGHEST_PRECEDENCE); + return registration; + } + + @Bean + public FilterRegistrationBean accessLogFilter() { + // One order below RequestIdFilter so every access line carries MDC[requestId]. + FilterRegistrationBean registration = new FilterRegistrationBean<>(new AccessLogFilter()); + registration.setOrder(Ordered.HIGHEST_PRECEDENCE + 1); + return registration; + } + + /** + * Registered UNCONDITIONALLY, as an independent trust boundary alongside the always-on DB-free auth chain in {@code SecurityConfig}: a + * client must never be able to inject the gateway-owned {@code X-User-*} identity headers. See + * {@link InboundIdentityHeaderSanitizingFilter}'s Javadoc for the trust-boundary rationale. + */ + @Bean + public FilterRegistrationBean inboundIdentityHeaderSanitizingFilter() { + FilterRegistrationBean registration = + new FilterRegistrationBean<>(new InboundIdentityHeaderSanitizingFilter()); + registration.setOrder(Ordered.HIGHEST_PRECEDENCE + 2); + return registration; + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/RouteSurfaceProperties.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/RouteSurfaceProperties.java new file mode 100644 index 000000000..de4666d7d --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/RouteSurfaceProperties.java @@ -0,0 +1,28 @@ +package edu.harvard.hms.dbmi.avillach.gateway.config; + +import java.util.List; + +import org.springframework.boot.context.properties.ConfigurationProperties; + +/** + * Binds {@code picsure.gateway.security.owned-prefixes}: the list of gateway-owned route surfaces (the routes in {@code application.yml}: + * {@code /logging}, {@code /dictionary}, {@code /uploader}, {@code /visualization}, {@code /hpds}, {@code /operations}). These paths are + * served directly by their backends. Everything else is unowned -- unmatched, and so 404s. + * + *

    Deliberately a small, separate {@code @ConfigurationProperties} record on the SAME prefix as {@link GatewaySecurityProperties} (Spring + * binds several properties classes to overlapping prefixes as long as the component names they claim don't collide, and + * {@code owned-prefixes} is new -- see also {@code ActuatorTokenProperties} elsewhere in the app for another example of this pattern). The + * {@link #DEFAULT_OWNED_PREFIXES default list} matches the owned route paths in {@code application.yml}; a drift-guard test asserts every + * configured route is covered, so adding a route without extending this list fails the build. + */ +@ConfigurationProperties(prefix = "picsure.gateway.security") +public record RouteSurfaceProperties(List ownedPrefixes) { + + /** Default gateway-owned prefixes — must stay in lock-step with the routes in {@code application.yml}. */ + public static final List DEFAULT_OWNED_PREFIXES = + List.of("/logging", "/dictionary", "/uploader", "/visualization", "/hpds", "/operations"); + + public RouteSurfaceProperties { + ownedPrefixes = (ownedPrefixes == null || ownedPrefixes.isEmpty()) ? DEFAULT_OWNED_PREFIXES : List.copyOf(ownedPrefixes); + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/RouteSurfaces.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/RouteSurfaces.java new file mode 100644 index 000000000..2341b2a5c --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/RouteSurfaces.java @@ -0,0 +1,54 @@ +package edu.harvard.hms.dbmi.avillach.gateway.config; + +import java.util.List; + +/** + * Classifies a request path as a gateway-OWNED route surface (a direct route to a backend) or unowned (unmatched, and so 404s -- there is + * no catch-all route). Used by the route drift-guard test to assert every configured route is covered by the default owned prefixes. + * + *

    Matching is SEGMENT-SAFE: a prefix matches only on an exact equal or a following {@code /} boundary ({@code equals(prefix)} or + * {@code startsWith(prefix + "/")}) — never a bare {@code startsWith}. So {@code /logging} covers {@code /logging} and {@code /logging/x} + * but NOT {@code /loggingAdmin/x}, which is a different route. + * + *

    Raw-requestURI safety. Callers match on the raw {@code getRequestURI()} (not a decoded/normalized path). That is safe against + * matrix-parameter (e.g. {@code /hpds;x=y}), encoded-slash ({@code %2F}) and double-slash ({@code //}) evasion ONLY because Spring + * Security's default {@link org.springframework.security.web.firewall.StrictHttpFirewall} rejects those requests BEFORE the auth filters + * run — so a path that reaches this matcher has already been normalized/blocked upstream. A future custom {@code HttpFirewall} that relaxes + * those defaults would reopen the seam (a request could then present a raw URI that this segment-safe match reads as unowned/owned + * differently than the backend resolves it); revisit this matching if the firewall is ever relaxed. + */ +public final class RouteSurfaces { + + private final List ownedPrefixes; + + public RouteSurfaces(List ownedPrefixes) { + this.ownedPrefixes = List.copyOf(ownedPrefixes); + } + + /** A {@code RouteSurfaces} over {@link RouteSurfaceProperties#DEFAULT_OWNED_PREFIXES} — for tests and non-Spring callers. */ + public static RouteSurfaces withDefaults() { + return new RouteSurfaces(RouteSurfaceProperties.DEFAULT_OWNED_PREFIXES); + } + + /** True iff {@code path} is on a gateway-owned route surface (segment-safe prefix match). Null/blank → not owned. */ + public boolean isOwned(String path) { + if (path == null || path.isEmpty()) { + return false; + } + for (String prefix : ownedPrefixes) { + if (path.equals(prefix) || path.startsWith(prefix + "/")) { + return true; + } + } + return false; + } + + /** True iff {@code path} is unowned (everything not on a gateway-owned route surface -- unmatched paths 404). */ + public boolean isCatchAll(String path) { + return !isOwned(path); + } + + List ownedPrefixes() { + return ownedPrefixes; + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/SecurityConfig.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/SecurityConfig.java new file mode 100644 index 000000000..8544d3167 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/config/SecurityConfig.java @@ -0,0 +1,148 @@ +package edu.harvard.hms.dbmi.avillach.gateway.config; + +import java.time.Duration; + +import org.springframework.boot.context.properties.EnableConfigurationProperties; +import org.springframework.boot.http.client.ClientHttpRequestFactoryBuilder; +import org.springframework.boot.http.client.ClientHttpRequestFactorySettings; +import org.springframework.boot.web.servlet.FilterRegistrationBean; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.core.annotation.Order; +import org.springframework.security.config.annotation.web.builders.HttpSecurity; +import org.springframework.security.web.SecurityFilterChain; +import org.springframework.web.client.RestClient; +import org.springframework.web.context.annotation.RequestScope; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import edu.harvard.hms.dbmi.avillach.commons.audit.AuditContext; +import edu.harvard.hms.dbmi.avillach.gateway.auth.PsamaClient; +import edu.harvard.hms.dbmi.avillach.gateway.auth.QueryAuthFetcher; +import edu.harvard.hms.dbmi.avillach.gateway.filter.BodyMutationFilter; +import edu.harvard.hms.dbmi.avillach.gateway.filter.BufferingFilter; +import edu.harvard.hms.dbmi.avillach.gateway.filter.IdentityPropagationFilter; +import edu.harvard.hms.dbmi.avillach.gateway.filter.OpenAccessFilter; +import edu.harvard.hms.dbmi.avillach.gateway.filter.PsamaIntrospectionFilter; +import edu.harvard.hms.dbmi.avillach.gateway.filter.TokenRefreshResponseFilter; +import io.micrometer.core.instrument.MeterRegistry; + +/** + * Wires the DB-free auth filter chain: {@code BufferingFilter}(10) -> {@code OpenAccessFilter}(20) -> + * {@code PsamaIntrospectionFilter}(30) -> {@code BodyMutationFilter}(35) -> {@code TokenRefreshResponseFilter}(40) -> + * {@code IdentityPropagationFilter}(50). The audit filter (60) is wired in {@code AuditFilterConfig}. No datasource, no JPA -- + * {@link PsamaClient} and {@link QueryAuthFetcher} talk to PSAMA / the query service over HTTP only.

    Spring Security itself stays + * permit-all: the introspection filter above is the real auth boundary, matching the WAR's JWTFilter model rather than Spring Security's + * authentication machinery. + * + *

    Always enforced: all SEVEN filters register unconditionally and enforce every route -- there is no mode switch or + * pass-through/transparent path. + */ +@Configuration +@EnableConfigurationProperties(GatewaySecurityProperties.class) +public class SecurityConfig { + + // Auth-boundary HTTP clients (PSAMA introspection, query-service dispatch) run synchronously inside the request path; a + // hung upstream must not tie up a Tomcat worker indefinitely, so both get bounded connect/read timeouts. + static final Duration AUTH_CONNECT_TIMEOUT = Duration.ofSeconds(2); + static final Duration AUTH_READ_TIMEOUT = Duration.ofSeconds(10); + + static final ClientHttpRequestFactorySettings AUTH_REQUEST_FACTORY_SETTINGS = + ClientHttpRequestFactorySettings.defaults().withConnectTimeout(AUTH_CONNECT_TIMEOUT).withReadTimeout(AUTH_READ_TIMEOUT); + + private static RestClient.Builder timeoutBoundedRestClientBuilder() { + return RestClient.builder().requestFactory(ClientHttpRequestFactoryBuilder.detect().build(AUTH_REQUEST_FACTORY_SETTINGS)); + } + + @Bean + @Order(10) // Yields /actuator/** to ActuatorSecurityConfig's @Order(0) chain. + SecurityFilterChain http(HttpSecurity http) throws Exception { + // Gateway permits all at the Security layer; the introspection filter is the real auth boundary. + return http.csrf(csrf -> csrf.disable()).authorizeHttpRequests(a -> a.anyRequest().permitAll()).build(); + } + + @Bean + ObjectMapper objectMapper() { + return new ObjectMapper(); + } + + /** + * Per-request audit metadata holder. Request-scoped (rather than a shared singleton) so concurrent requests never leak metadata into + * each other; singleton filters hold a TARGET_CLASS scoped proxy that resolves to the current request's instance. + */ + @Bean + @RequestScope + AuditContext auditContext() { + return new AuditContext(); + } + + @Bean + PsamaClient psamaClient(GatewaySecurityProperties props) { + return new PsamaClient( + timeoutBoundedRestClientBuilder().build(), props.introspectionUrl(), props.openAccessValidateUrl(), props.serviceToken() + ); + } + + @Bean + QueryAuthFetcher queryAuthFetcher(GatewaySecurityProperties props) { + // The dispatch endpoint (/operations/internal/queries/{id}/dispatch) lives on operations-service, the + // sole DB owner -- not the DB-free query-service. + return new QueryAuthFetcher( + timeoutBoundedRestClientBuilder().build(), props.operationsServiceUrl(), props.queryServiceInternalToken() + ); + } + + @Bean + FilterRegistrationBean bufferingFilter(GatewaySecurityProperties props, MeterRegistry meterRegistry) { + var r = new FilterRegistrationBean<>(new BufferingFilter(props.maxBodyBytes(), meterRegistry)); + r.setOrder(10); + r.addUrlPatterns("/*"); + return r; + } + + @Bean + FilterRegistrationBean openAccessFilter( + PsamaClient client, AuditContext audit, ObjectMapper json, GatewaySecurityProperties props + ) { + var r = new FilterRegistrationBean<>(new OpenAccessFilter(client, audit, json, props.openAccessEnabled())); + r.setOrder(20); + r.addUrlPatterns("/*"); + return r; + } + + @Bean + FilterRegistrationBean introspectionFilter( + PsamaClient client, AuditContext audit, ObjectMapper json, QueryAuthFetcher fetcher, GatewaySecurityProperties props + ) { + var r = new FilterRegistrationBean<>( + new PsamaIntrospectionFilter(client, audit, json, fetcher, props.allowListPrefixes(), props.userIdClaim()) + ); + r.setOrder(30); + r.addUrlPatterns("/*"); + return r; + } + + @Bean + FilterRegistrationBean bodyMutationFilter(ObjectMapper json) { + var r = new FilterRegistrationBean<>(new BodyMutationFilter(json)); + r.setOrder(35); + r.addUrlPatterns("/*"); + return r; + } + + @Bean + FilterRegistrationBean tokenRefreshFilter() { + var r = new FilterRegistrationBean<>(new TokenRefreshResponseFilter()); + r.setOrder(40); + r.addUrlPatterns("/*"); + return r; + } + + @Bean + FilterRegistrationBean identityFilter() { + var r = new FilterRegistrationBean<>(new IdentityPropagationFilter()); + r.setOrder(50); + r.addUrlPatterns("/*"); + return r; + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/error/GatewayErrors.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/error/GatewayErrors.java new file mode 100644 index 000000000..c11bb197c --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/error/GatewayErrors.java @@ -0,0 +1,32 @@ +package edu.harvard.hms.dbmi.avillach.gateway.error; + +import java.io.IOException; + +import org.slf4j.MDC; +import org.springframework.http.HttpStatus; + +import jakarta.servlet.http.HttpServletResponse; + +/** + * Writes the commons additive error-body shape ({@code {errorType, message, requestId}}, matching + * {@code edu.harvard.hms.dbmi.avillach.commons.error.GatewayExceptionAdvice}) directly to a servlet response, for filters that run before + * Spring MVC's exception-handling machinery is reachable (e.g. {@code BufferingFilter}'s 413 short-circuit). {@code requestId} comes from + * {@code MDC[requestId]}, set by {@code edu.harvard.hms.dbmi.avillach.commons.request.RequestIdFilter}. + */ +public final class GatewayErrors { + + private GatewayErrors() {} + + public static void write(HttpServletResponse resp, HttpStatus status, String errorType, String message) throws IOException { + resp.setStatus(status.value()); + resp.setContentType("application/json"); + String requestId = MDC.get("requestId"); + String body = "{\"errorType\":\"" + escape(errorType) + "\",\"message\":\"" + escape(message) + "\",\"requestId\":" + + (requestId == null ? "null" : "\"" + escape(requestId) + "\"") + "}"; + resp.getWriter().write(body); + } + + private static String escape(String value) { + return value.replace("\\", "\\\\").replace("\"", "\\\""); + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/AuditFilterConfig.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/AuditFilterConfig.java new file mode 100644 index 000000000..8f25bc570 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/AuditFilterConfig.java @@ -0,0 +1,64 @@ +package edu.harvard.hms.dbmi.avillach.gateway.filter; + +import java.util.List; +import java.util.regex.Pattern; + +import org.springframework.boot.web.servlet.FilterRegistrationBean; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; + +import edu.harvard.hms.dbmi.avillach.commons.audit.AuditContext; +import edu.harvard.hms.dbmi.avillach.commons.audit.AuditLoggingFilter; +import edu.harvard.hms.dbmi.avillach.commons.audit.AuditRoute; +import edu.harvard.hms.dbmi.avillach.commons.audit.AuditRouteTable; +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingClientFactory; + +/** + * Wires the audit-emission filter: {@link LoggingClient} (env-driven, no-op when unconfigured), the verified route table (mirrors the + * legacy WAR {@code AuditLoggingFilter.java:55-65}, minus the removed {@code PROXY} row -- there is no {@code /proxy} prefix in the new + * per-service scheme), and the {@link AuditLoggingFilter} registration itself at order 60, the outermost emitter on the way out of the + * chain (after {@code IdentityPropagationFilter} at 50 in {@code SecurityConfig}). + */ +@Configuration +public class AuditFilterConfig { + + // Leading service prefix(es) + optional /v3, e.g. "/query", "/hpds/auth/v3/query". + private static final String PFX = "^(?:/[a-z0-9-]+)+?(?:/v3)?"; + + @Bean + public LoggingClient loggingClient() { + return LoggingClientFactory.create("gateway"); + } + + @Bean + public AuditRouteTable auditRouteTable() { + // First match wins (query/sync before query). Mirrors WAR AuditLoggingFilter.java:55-65 minus PROXY. + return new AuditRouteTable( + List.of( + new AuditRoute(Pattern.compile(PFX + "/query/sync/?$"), "POST", "QUERY", "query.sync"), + new AuditRoute(Pattern.compile(PFX + "/query/?$"), "POST", "QUERY", "query.submitted"), + new AuditRoute(Pattern.compile(PFX + "/query/[^/]+/status/?$"), null, "QUERY", "query.status"), + new AuditRoute(Pattern.compile(PFX + "/query/[^/]+/result/?$"), null, "DATA_ACCESS", "query.result"), + new AuditRoute(Pattern.compile(PFX + "/query/[^/]+/signed-url/?$"), null, "DATA_ACCESS", "query.signed_url"), + new AuditRoute(Pattern.compile(PFX + "/query/[^/]+/metadata/?$"), null, "QUERY", "query.metadata"), + new AuditRoute(Pattern.compile(PFX + "/search/[^/]+/?$"), "POST", "SEARCH", "search.execute"), + new AuditRoute(Pattern.compile(PFX + "/search/[^/]+/values/"), null, "SEARCH", "search.values", true) + ) + ); + } + + @Bean + public FilterRegistrationBean auditLoggingFilter(LoggingClient client, AuditRouteTable routes, AuditContext audit) { + // VERIFIED skip-list (AuditLoggingFilter.java:122-127): ends-with /system/status, /openapi.json (base + // class); contains /info/, /bin/continuous, /logging (was /proxy/pic-sure-logging/ -- no /proxy prefix in + // the new scheme). Gateway-local /actuator, /openapi, /swagger-ui added on top (net-new concerns). + AuditLoggingFilter filter = new AuditLoggingFilter( + client, routes, audit, List.of("/info/", "/bin/continuous", "/logging", "/actuator", "/openapi", "/swagger-ui") + ); + var registration = new FilterRegistrationBean<>(filter); + registration.setOrder(60); // outermost emitter on the way out + registration.addUrlPatterns("/*"); + return registration; + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/BodyMutationFilter.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/BodyMutationFilter.java new file mode 100644 index 000000000..6647de9a1 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/BodyMutationFilter.java @@ -0,0 +1,84 @@ +package edu.harvard.hms.dbmi.avillach.gateway.filter; + +import java.io.IOException; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.http.HttpStatus; +import org.springframework.web.filter.OncePerRequestFilter; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.node.ObjectNode; + +import edu.harvard.hms.dbmi.avillach.gateway.auth.BufferedRequestWrapper; +import edu.harvard.hms.dbmi.avillach.gateway.error.GatewayErrors; +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +/** + * SECURITY-CRITICAL: when PSAMA injected consent filters (ATTR_MUTATED_QUERY), rewrite the buffered body's top-level "query" before + * forwarding (mirrors the WAR's JWTFilter:304-308). Best-effort on a non-JSON body. Forwarding the un-swapped body would leak unauthorized + * data, so this swap must never be skipped when the attribute is present. FAIL CLOSED: if a mutation is required (ATTR_MUTATED_QUERY + * present) and building the mutated body throws, the request is rejected with a 500 rather than forwarded with the original, un-swapped + * body. + */ +public class BodyMutationFilter extends OncePerRequestFilter { + + public static final String ATTR_MUTATED_QUERY = "mutatedQuery"; + private static final Logger log = LoggerFactory.getLogger(BodyMutationFilter.class); + + private final ObjectMapper json; + + public BodyMutationFilter(ObjectMapper json) { + this.json = json; + } + + @Override + protected void doFilterInternal(HttpServletRequest req, HttpServletResponse resp, FilterChain chain) + throws ServletException, IOException { + Object mutated = req.getAttribute(ATTR_MUTATED_QUERY); + if (mutated instanceof String mutatedQueryJson && req instanceof BufferedRequestWrapper buffered) { + try { + buffered.setBody(mergeQueryIntoBody(buffered.getBody(), mutatedQueryJson)); + } catch (IOException e) { + // FAIL CLOSED: a mutation was required (consent filters were injected) but could not be applied. + // Forwarding the original body here would leak unauthorized data, so reject instead of proceeding. + log.error("Could not merge mutated query; rejecting request instead of forwarding original body. {}", e.getMessage()); + GatewayErrors.write( + resp, HttpStatus.INTERNAL_SERVER_ERROR, "body_mutation_failed", + "Unable to apply required consent filtering to the request body." + ); + return; + } + } + chain.doFilter(req, resp); + } + + private byte[] mergeQueryIntoBody(byte[] originalBody, String mutatedQueryJson) throws IOException { + ObjectNode root; + if (originalBody != null && originalBody.length > 0) { + // Best-effort: a non-JSON original body must not abort the swap (that would forward the + // un-swapped, potentially unauthorized body) -- fall back to a fresh object wrapping the query. + JsonNode parsed; + try { + parsed = json.readTree(originalBody); + } catch (IOException notJson) { + parsed = null; + } + root = (parsed != null && parsed.isObject()) ? (ObjectNode) parsed : json.createObjectNode(); + } else { + root = json.createObjectNode(); + } + JsonNode mutatedNode; + try { + mutatedNode = json.readTree(mutatedQueryJson); + } catch (IOException notJson) { + mutatedNode = json.getNodeFactory().textNode(mutatedQueryJson); + } + root.set("query", mutatedNode); + return json.writeValueAsBytes(root); + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/BufferingFilter.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/BufferingFilter.java new file mode 100644 index 000000000..6d23e5406 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/BufferingFilter.java @@ -0,0 +1,71 @@ +package edu.harvard.hms.dbmi.avillach.gateway.filter; + +import java.io.ByteArrayOutputStream; +import java.io.IOException; +import java.io.InputStream; + +import org.springframework.http.HttpStatus; +import org.springframework.web.filter.OncePerRequestFilter; + +import edu.harvard.hms.dbmi.avillach.gateway.auth.BufferedRequestWrapper; +import edu.harvard.hms.dbmi.avillach.gateway.error.GatewayErrors; +import io.micrometer.core.instrument.MeterRegistry; +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +/** + * Buffers the request body (so downstream auth filters can read/mutate it), capped at GATEWAY_AUTH_MAX_BODY_BYTES. Over-cap → HTTP 413 with + * the additive error body {errorType:REQUEST_BODY_TOO_LARGE,...} returned BEFORE PSAMA is ever called; body content is NEVER logged; a + * body-too-large metric is emitted. + */ +public class BufferingFilter extends OncePerRequestFilter { + + static final String BODY_TOO_LARGE_METRIC = "gateway.auth.body_too_large"; + + private final int maxBytes; + private final MeterRegistry meterRegistry; + + public BufferingFilter(int maxBytes, MeterRegistry meterRegistry) { + this.maxBytes = maxBytes; + this.meterRegistry = meterRegistry; + } + + @Override + protected void doFilterInternal(HttpServletRequest req, HttpServletResponse resp, FilterChain chain) + throws ServletException, IOException { + byte[] body; + try { + body = readBody(req); + } catch (BodyTooLargeException e) { + // Do NOT log body content. Emit metric, return 413 with the additive error body, never call PSAMA. + meterRegistry.counter(BODY_TOO_LARGE_METRIC).increment(); + GatewayErrors.write( + resp, HttpStatus.PAYLOAD_TOO_LARGE, "REQUEST_BODY_TOO_LARGE", + "Request body exceeds the maximum size allowed for authorization processing." + ); + return; + } + chain.doFilter(new BufferedRequestWrapper(req, body), resp); + } + + private byte[] readBody(HttpServletRequest req) throws IOException { + ByteArrayOutputStream out = new ByteArrayOutputStream(Math.max(0, (int) req.getContentLengthLong())); + try (InputStream in = req.getInputStream()) { + byte[] buf = new byte[8192]; + int read, total = 0; + while ((read = in.read(buf)) > 0) { + total += read; + if (total > maxBytes) { + throw new BodyTooLargeException(); + } + out.write(buf, 0, read); + } + } + return out.toByteArray(); + } + + private static final class BodyTooLargeException extends RuntimeException { + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/IdentityPropagationFilter.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/IdentityPropagationFilter.java new file mode 100644 index 000000000..8ecceac47 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/IdentityPropagationFilter.java @@ -0,0 +1,135 @@ +package edu.harvard.hms.dbmi.avillach.gateway.filter; + +import java.io.IOException; +import java.util.Collections; +import java.util.Enumeration; +import java.util.LinkedHashMap; +import java.util.LinkedHashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.UUID; + +import org.slf4j.MDC; +import org.springframework.web.filter.OncePerRequestFilter; + +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import edu.harvard.hms.dbmi.avillach.commons.request.RequestIdFilter; +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletRequestWrapper; +import jakarta.servlet.http.HttpServletResponse; + +/** + * SCG MVC forwards via a {@code HandlerFunction}; request attributes don't become outbound headers automatically. This filter wraps the + * request and adds the {@code X-User-*} headers from the attributes the introspection/open-access filters set — including + * {@code X-User-Privileges} — plus {@code X-Request-Id} (propagate the incoming one, reuse the commons {@link RequestIdFilter}'s MDC value, + * or generate). Downstream maps {@code X-User-Privileges} to {@code GrantedAuthority}s for {@code @RolesAllowed}-equivalent checks.

    The + * five {@code X-User-*} headers ({@link GatewayUserResolver#HEADER_USER_ID}, {@code _SUBJECT}, {@code _EMAIL}, {@code _ROLES}, + * {@code _PRIVILEGES}) are gateway-owned: the wrapper NEVER falls through to the raw client request for them. Whatever the gateway resolved + * (possibly nothing) is authoritative -- a client cannot spoof these by sending its own values, even where the gateway resolved an + * empty/null value (e.g. open-access requests, users with no privileges). + */ +public class IdentityPropagationFilter extends OncePerRequestFilter { + + static final String HEADER_REQUEST_ID = "X-Request-Id"; // commons RequestIdFilter owns generation + + public IdentityPropagationFilter() {} + + @Override + protected void doFilterInternal(HttpServletRequest req, HttpServletResponse resp, FilterChain chain) + throws ServletException, IOException { + chain.doFilter(new IdentityHeadersRequest(req), resp); + } + + static class IdentityHeadersRequest extends HttpServletRequestWrapper { + + /** Gateway-owned identity headers: never sourced from the raw client request, regardless of name casing. */ + private static final Set GATEWAY_OWNED_HEADERS = Set.of( + GatewayUserResolver.HEADER_USER_ID, GatewayUserResolver.HEADER_USER_SUBJECT, GatewayUserResolver.HEADER_USER_EMAIL, + GatewayUserResolver.HEADER_USER_ROLES, GatewayUserResolver.HEADER_USER_PRIVILEGES + ); + + private final Map overrides = new LinkedHashMap<>(); + + IdentityHeadersRequest(HttpServletRequest req) { + super(req); + put(GatewayUserResolver.HEADER_USER_ID, attr(req, GatewayUserResolver.HEADER_USER_ID)); + put(GatewayUserResolver.HEADER_USER_SUBJECT, attr(req, GatewayUserResolver.HEADER_USER_SUBJECT)); + put(GatewayUserResolver.HEADER_USER_EMAIL, attr(req, GatewayUserResolver.HEADER_USER_EMAIL)); + put(GatewayUserResolver.HEADER_USER_ROLES, attr(req, GatewayUserResolver.HEADER_USER_ROLES)); + put(GatewayUserResolver.HEADER_USER_PRIVILEGES, attr(req, GatewayUserResolver.HEADER_USER_PRIVILEGES)); + put(HEADER_REQUEST_ID, resolveRequestId(req)); + } + + private static String resolveRequestId(HttpServletRequest req) { + String requestId = req.getHeader(HEADER_REQUEST_ID); + if (requestId != null && !requestId.isEmpty()) { + return requestId; + } + // No inbound header: reuse the id the commons RequestIdFilter (runs earlier, highest precedence) already put in + // MDC so response headers, access logs, downstream headers, and audit records all correlate under one id. + String mdcRequestId = MDC.get(RequestIdFilter.MDC_KEY); + if (mdcRequestId != null && !mdcRequestId.isEmpty()) { + return mdcRequestId; + } + return UUID.randomUUID().toString(); + } + + private static String attr(HttpServletRequest r, String key) { + Object v = r.getAttribute(key); + return v == null ? null : v.toString(); + } + + private void put(String k, String v) { + if (v != null && !v.isEmpty()) overrides.put(k, v); + } + + /** Returns the canonical gateway-owned header name matching {@code name} case-insensitively, or {@code null} if not owned. */ + private static String ownedCanonicalName(String name) { + for (String owned : GATEWAY_OWNED_HEADERS) { + if (owned.equalsIgnoreCase(name)) return owned; + } + return null; + } + + @Override + public String getHeader(String name) { + String owned = ownedCanonicalName(name); + if (owned != null) { + // Gateway-owned: authoritative even when unresolved (null) -- never fall through to the client's request. + return overrides.get(owned); + } + String v = overrides.get(name); + return v != null ? v : super.getHeader(name); + } + + @Override + public Enumeration getHeaderNames() { + Set names = new LinkedHashSet<>(); + Enumeration superNames = super.getHeaderNames(); + while (superNames != null && superNames.hasMoreElements()) { + String n = superNames.nextElement(); + if (ownedCanonicalName(n) == null) { + // Drop any client-supplied gateway-owned header name; only the resolved value (added below, if any) may appear. + names.add(n); + } + } + names.addAll(overrides.keySet()); + return Collections.enumeration(names); + } + + @Override + public Enumeration getHeaders(String name) { + String owned = ownedCanonicalName(name); + if (owned != null) { + String v = overrides.get(owned); + return v != null ? Collections.enumeration(List.of(v)) : Collections.emptyEnumeration(); + } + String v = overrides.get(name); + if (v != null) return Collections.enumeration(List.of(v)); + return super.getHeaders(name); + } + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/OpenAccessFilter.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/OpenAccessFilter.java new file mode 100644 index 000000000..acbe152fd --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/OpenAccessFilter.java @@ -0,0 +1,107 @@ +package edu.harvard.hms.dbmi.avillach.gateway.filter; + +import java.io.IOException; +import java.util.HashMap; +import java.util.Map; + +import org.springframework.http.HttpStatus; +import org.springframework.web.filter.OncePerRequestFilter; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.node.ObjectNode; + +import edu.harvard.hms.dbmi.avillach.commons.audit.AuditContext; +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import edu.harvard.hms.dbmi.avillach.gateway.auth.BufferedRequestWrapper; +import edu.harvard.hms.dbmi.avillach.gateway.auth.PsamaClient; +import edu.harvard.hms.dbmi.avillach.gateway.error.GatewayErrors; +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +/** + * Handles no-bearer requests when open access is enabled, short-circuiting before {@code PsamaIntrospectionFilter} runs. Triggers when open + * access is enabled AND {@code Authorization} is blank or ≤ 7 chars ({@code JWTFilter.java:154-157}). The open-access payload is a + * different shape than introspection ({@code JWTFilter.java:389-394}): {@code { "request": { "Target Service": "", "query": + * }, "ipAddress": "OPEN_ACCESS:" }} — no {@code token} field, adds {@code ipAddress}. PSAMA returns + * a bare boolean: {@code true} grants with username {@code OPEN_ACCESS:}; {@code false} denies with a 401. A real bearer token, or + * open access disabled, passes through untouched. + */ +public class OpenAccessFilter extends OncePerRequestFilter { + + private final PsamaClient psama; + private final AuditContext audit; + private final ObjectMapper json; + private final boolean openAccessEnabled; + + public OpenAccessFilter(PsamaClient psama, AuditContext audit, ObjectMapper json, boolean openAccessEnabled) { + this.psama = psama; + this.audit = audit; + this.json = json; + this.openAccessEnabled = openAccessEnabled; + } + + @Override + protected void doFilterInternal(HttpServletRequest req, HttpServletResponse resp, FilterChain chain) + throws ServletException, IOException { + String authz = req.getHeader("Authorization"); + boolean noToken = authz == null || authz.isBlank() || authz.length() <= 7; // JWTFilter.java:154-157 + + if (!openAccessEnabled || !noToken) { + chain.doFilter(req, resp); + return; + } + + Map queryMap = buildOpenAccessRequest(req); + Map body = new HashMap<>(); + body.put("request", queryMap); + String hostMarker = openAccessIpAddress(req); + body.put("ipAddress", hostMarker); // NO token field (JWTFilter.java:389-394) + + if (!psama.validateOpenAccess(body)) { + audit.put("auth_result", "failure"); + audit.put("auth_action", "open_access.denied"); + GatewayErrors.write(resp, HttpStatus.UNAUTHORIZED, "unauthorized", "User is not authorized."); + return; + } + req.setAttribute(GatewayUserResolver.HEADER_USER_ID, hostMarker); + audit.put("auth_result", "success"); + audit.put("auth_action", "open_access.granted"); + chain.doFilter(req, resp); + } + + /** {@code "OPEN_ACCESS:"} marker sent as {@code ipAddress} to PSAMA's open-access validate endpoint (JWTFilter.java:389-394). */ + private static String openAccessIpAddress(HttpServletRequest req) { + return "OPEN_ACCESS:" + (req.getServerName() == null ? "unknown" : req.getServerName()); + } + + /** Builds the inner {@code { "Target Service", "query" }} request map sent to PSAMA's open-access validate endpoint. */ + private Map buildOpenAccessRequest(HttpServletRequest req) { + Map queryMap = new HashMap<>(); + queryMap.put("Target Service", req.getRequestURI()); // real path + if (req instanceof BufferedRequestWrapper buffered && buffered.getBody().length > 0) { + try { + JsonNode parsed = json.readTree(buffered.getBody()); + stripResourceCredentials(parsed); + queryMap.put("query", parsed); + } catch (IOException ignored) { + // best-effort, mirrors the WAR + } + } + return queryMap; + } + + private void stripResourceCredentials(JsonNode node) { + if (node == null) { + return; + } + if (node.isObject()) { + ((ObjectNode) node).remove("resourceCredentials"); + node.fields().forEachRemaining(e -> stripResourceCredentials(e.getValue())); + } else if (node.isArray()) { + node.forEach(this::stripResourceCredentials); + } + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/PsamaIntrospectionFilter.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/PsamaIntrospectionFilter.java new file mode 100644 index 000000000..66215a466 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/PsamaIntrospectionFilter.java @@ -0,0 +1,243 @@ +package edu.harvard.hms.dbmi.avillach.gateway.filter; + +import java.io.IOException; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Optional; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.http.HttpStatus; +import org.springframework.web.filter.OncePerRequestFilter; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.node.ObjectNode; + +import edu.harvard.hms.dbmi.avillach.commons.audit.AuditContext; +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import edu.harvard.hms.dbmi.avillach.gateway.auth.BufferedRequestWrapper; +import edu.harvard.hms.dbmi.avillach.gateway.auth.IntrospectionResponse; +import edu.harvard.hms.dbmi.avillach.gateway.auth.PsamaClient; +import edu.harvard.hms.dbmi.avillach.gateway.auth.QueryAuthFetcher; +import edu.harvard.hms.dbmi.avillach.gateway.error.GatewayErrors; +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +/** + * Ports the bulk of the WAR's {@code JWTFilter}: per-request PSAMA token introspection. Runs after {@code OpenAccessFilter} (no-bearer + * short-circuit) and {@code BufferingFilter} (body buffering). Allow-lists {@code GET /system/status} (audited as {@code SYSTEM_MONITOR}), + * any path ending in {@code /openapi.json}, and any configured prefix — none of these call PSAMA. Every other request must carry a real + * {@code Bearer} token (open access is handled entirely upstream by {@code OpenAccessFilter}); the introspection request sends the REAL + * request path as the root-level {@code "Target Service"} (no canonical-mapping table) and the buffered body (or, for the result/signed-url + * paths once the gateway owns query-read auth, the {@link QueryAuthFetcher} dispatch result) as {@code "query"}, with + * {@code resourceCredentials} stripped and NEVER a {@code formattedQuery} field (PSAMA only ever uses it for logging, never authorization). + * If the body is not valid JSON, {@code "query"} is omitted entirely rather than forwarding the raw, unstripped bytes (which could still + * textually contain {@code resourceCredentials}). On success this filter stashes {@code X-User-*} request attributes — including + * privileges, the real {@code @RolesAllowed} signal — for {@code IdentityPropagationFilter} to turn into outbound headers; on + * {@code tokenRefreshed} it stashes {@link #ATTR_REFRESHED_TOKEN} for {@code TokenRefreshResponseFilter}; on a returned {@code query} it + * stashes {@code BodyMutationFilter.ATTR_MUTATED_QUERY} for {@code BodyMutationFilter} to apply — this filter does NOT mutate the body + * itself. {@code active:false} denies with a 401 additive error body. {@link QueryAuthFetcher}/introspection infrastructure failures + * ({@link PicsureException}, or any introspection transport error) are fail-closed: the mapped status/error body is written and the request + * is never forwarded. + */ +public class PsamaIntrospectionFilter extends OncePerRequestFilter { + + private static final Logger log = LoggerFactory.getLogger(PsamaIntrospectionFilter.class); + + public static final String ATTR_REFRESHED_TOKEN = "refreshedToken"; + + // Mirrors operations-service's own public-GET security rule — the configuration list (root) and a + // single {id} read are public, EXCEPT anything under /operations/configuration/admin/**. Matches at most one path + // segment after /operations/configuration/, with an optional trailing slash: /operations/configuration/{id} or + // /operations/configuration/{id}/. + private static final Pattern CONFIGURATION_ID_READ = Pattern.compile("^/operations/configuration/([^/]+)/?$"); + + private final PsamaClient psama; + private final AuditContext audit; + private final ObjectMapper json; + private final QueryAuthFetcher queryAuthFetcher; + private final List allowListPrefixes; + private final String userIdClaim; + + public PsamaIntrospectionFilter( + PsamaClient psama, AuditContext audit, ObjectMapper json, QueryAuthFetcher queryAuthFetcher, List allowListPrefixes, + String userIdClaim + ) { + this.psama = psama; + this.audit = audit; + this.json = json; + this.queryAuthFetcher = queryAuthFetcher; + this.allowListPrefixes = List.copyOf(allowListPrefixes); + this.userIdClaim = userIdClaim; + } + + @Override + protected boolean shouldNotFilter(HttpServletRequest req) { + return isPublicConfigurationRead(req.getMethod(), req.getRequestURI()); + } + + /** + * Config-GET bypass carried over from the operations-service split: {@code GET /operations/configuration(/)?} (the list) and {@code GET + * /operations/configuration/{id}(/)?} (a single read) are public reads on operations-service itself, so the gateway must not demand a + * Bearer token for them either. Both slash forms are accepted even though the controller serves only the slash-less one -- the bypass + * errs open on shape so the backend, not the auth layer, owns the 404. Method-AND-path precise: any other method, and all of + * {@code /operations/configuration/admin/**} (including bare {@code /operations/configuration/admin}), stay introspected. + */ + private boolean isPublicConfigurationRead(String method, String path) { + if (!"GET".equals(method) || path == null) { + return false; + } + if (path.equals("/operations/configuration") || path.equals("/operations/configuration/")) { + return true; + } + Matcher m = CONFIGURATION_ID_READ.matcher(path); + return m.matches() && !"admin".equals(m.group(1)); + } + + @Override + protected void doFilterInternal(HttpServletRequest req, HttpServletResponse resp, FilterChain chain) + throws ServletException, IOException { + + String path = req.getRequestURI() == null ? "" : req.getRequestURI(); + String method = req.getMethod(); + + if ("GET".equals(method) && (path.equals("/system/status") || path.equals("/v3/system/status"))) { + audit.put("username", "SYSTEM_MONITOR"); + chain.doFilter(req, resp); + return; + } + if (path.endsWith("/openapi.json")) { + chain.doFilter(req, resp); + return; + } + for (String prefix : allowListPrefixes) { + if (path.equals(prefix) || path.startsWith(prefix + "/")) { + chain.doFilter(req, resp); + return; + } + } + + String authz = req.getHeader("Authorization"); + if (authz == null || authz.isBlank()) { + denied(resp, "missing_token", "No authorization header found."); + return; + } + if (!authz.startsWith("Bearer ")) { + denied(resp, "malformed_token", "Authorization header is not a Bearer token."); + return; + } + String token = authz.substring(7).trim(); + if (token.isEmpty()) { + denied(resp, "empty_token", "No token found in authorization header."); + return; + } + + Map requestMeta; + try { + requestMeta = buildIntrospectionRequest(req, path); + } catch (PicsureException e) { + // QueryAuthFetcher fail-closed: honest status + additive error body. + mapPicsureException(resp, e); + return; + } + + IntrospectionResponse intro; + try { + intro = psama.introspect(token, requestMeta); + } catch (PicsureException e) { + // Preserve the existing PicsureException mapping (status/errorType from the exception) rather than + // flattening it into a generic 502 below. + mapPicsureException(resp, e); + return; + } catch (Exception e) { + log.error("PSAMA introspection failed", e); + audit.put("auth_result", "failure"); + audit.put("auth_failure_reason", "introspection_unreachable"); + GatewayErrors.write(resp, HttpStatus.BAD_GATEWAY, "introspection_unreachable", "Token introspection failed."); + return; + } + + if (intro == null || !intro.active()) { + denied(resp, "invalid_token", "Token invalid or expired."); + return; + } + + req.setAttribute(GatewayUserResolver.HEADER_USER_ID, intro.userId()); + req.setAttribute(GatewayUserResolver.HEADER_USER_SUBJECT, intro.sub()); + req.setAttribute(GatewayUserResolver.HEADER_USER_EMAIL, intro.email()); + req.setAttribute(GatewayUserResolver.HEADER_USER_ROLES, intro.roles() == null ? "" : intro.roles()); + // privileges are the real @RolesAllowed signal — propagate them. + req.setAttribute( + GatewayUserResolver.HEADER_USER_PRIVILEGES, intro.privileges() == null ? "" : String.join(",", intro.privileges()) + ); + audit.put("auth_result", "success"); + + if (Boolean.TRUE.equals(intro.tokenRefreshed()) && intro.token() != null) { + req.setAttribute(ATTR_REFRESHED_TOKEN, intro.token()); + } + if (intro.query() != null) { + req.setAttribute(BodyMutationFilter.ATTR_MUTATED_QUERY, intro.query()); + } + + chain.doFilter(req, resp); + } + + private void denied(HttpServletResponse resp, String reason, String message) throws IOException { + audit.put("auth_result", "failure"); + audit.put("auth_failure_reason", reason); + GatewayErrors.write(resp, HttpStatus.UNAUTHORIZED, "unauthorized", message); + } + + private void mapPicsureException(HttpServletResponse resp, PicsureException e) throws IOException { + audit.put("auth_result", "failure"); + audit.put("auth_failure_reason", "dispatch_error"); + GatewayErrors.write(resp, e.getStatus(), e.getErrorType(), e.getMessage()); + } + + private Map buildIntrospectionRequest(HttpServletRequest req, String path) { + Map requestMeta = new HashMap<>(); + // Send the REAL request path verbatim, root-level. No canonical-mapping table. + requestMeta.put("Target Service", path); + + // result/signed-url: fetch the stored query over HTTP (DB-free) so PSAMA can authorize these + // bodyless reads using the original query shape. + Optional storedQuery = queryAuthFetcher.queryJsonForPath(path); // may throw PicsureException (fail-closed) + try { + if (storedQuery.isPresent()) { + JsonNode stored = json.readTree(storedQuery.get()); + stripResourceCredentials(stored); + requestMeta.put("query", stored); + } else if (req instanceof BufferedRequestWrapper buffered && buffered.getBody().length > 0) { + JsonNode body = json.readTree(buffered.getBody()); + stripResourceCredentials(body); + requestMeta.put("query", body); + } + } catch (IOException e) { + // Do NOT forward the raw, unstripped body: a malformed body may still textually contain + // resourceCredentials secrets, and we have no parsed JSON to strip them from. Omit "query" + // entirely rather than risk leaking it to PSAMA. Never log body content here. + log.debug("request body was not valid JSON; omitting query from introspection payload"); + } + // NO formattedQuery: PSAMA uses it only for access-log strings, never for authorization. + return requestMeta; + } + + private void stripResourceCredentials(JsonNode node) { + if (node == null) { + return; + } + if (node.isObject()) { + ((ObjectNode) node).remove("resourceCredentials"); + node.fields().forEachRemaining(e -> stripResourceCredentials(e.getValue())); + } else if (node.isArray()) { + node.forEach(this::stripResourceCredentials); + } + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/TokenRefreshResponseFilter.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/TokenRefreshResponseFilter.java new file mode 100644 index 000000000..9175689a5 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/filter/TokenRefreshResponseFilter.java @@ -0,0 +1,23 @@ +package edu.harvard.hms.dbmi.avillach.gateway.filter; + +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; +import org.springframework.http.HttpHeaders; +import org.springframework.web.filter.OncePerRequestFilter; + +import java.io.IOException; + +public class TokenRefreshResponseFilter extends OncePerRequestFilter { + + @Override + protected void doFilterInternal(HttpServletRequest req, HttpServletResponse resp, FilterChain chain) + throws ServletException, IOException { + chain.doFilter(req, resp); + Object refreshed = req.getAttribute(PsamaIntrospectionFilter.ATTR_REFRESHED_TOKEN); + if (refreshed != null) { + resp.setHeader(HttpHeaders.AUTHORIZATION, "Bearer " + refreshed); + } + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/AggregateHealth.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/AggregateHealth.java new file mode 100644 index 000000000..280c577ba --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/AggregateHealth.java @@ -0,0 +1,11 @@ +package edu.harvard.hms.dbmi.avillach.gateway.health; + +import java.util.List; + +/** Rollup over all probed downstreams. */ +public record AggregateHealth(boolean running, List components) { + public static AggregateHealth from(List components) { + boolean running = components.stream().allMatch(DownstreamHealth::up); + return new AggregateHealth(running, components); + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/DownstreamHealth.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/DownstreamHealth.java new file mode 100644 index 000000000..042aa25b4 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/DownstreamHealth.java @@ -0,0 +1,5 @@ +package edu.harvard.hms.dbmi.avillach.gateway.health; + +/** Result of probing a single downstream. */ +public record DownstreamHealth(String name, String resolvedUrl, boolean up, String detail) { +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/DownstreamHealthContributor.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/DownstreamHealthContributor.java new file mode 100644 index 000000000..36ddf02f3 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/DownstreamHealthContributor.java @@ -0,0 +1,49 @@ +package edu.harvard.hms.dbmi.avillach.gateway.health; + +import java.util.Iterator; +import java.util.LinkedHashMap; +import java.util.Map; + +import org.springframework.boot.actuate.health.CompositeHealthContributor; +import org.springframework.boot.actuate.health.Health; +import org.springframework.boot.actuate.health.HealthContributor; +import org.springframework.boot.actuate.health.HealthIndicator; +import org.springframework.boot.actuate.health.NamedContributor; +import org.springframework.stereotype.Component; + +/** + * Surfaces each monitored downstream as a component under {@code /actuator/health}. One aggregate probe per scrape (the + * {@code /system/status} throttle does not apply here; Actuator's scrape interval governs frequency). Unaffected by the gateway's + * route-backed {@code RouterFunction} beans: Actuator's own {@code WebMvcEndpointHandlerMapping} is order -100, ahead of + * {@code RouterFunctionMapping} (order -1). + */ +@Component("downstreams") +public class DownstreamHealthContributor implements CompositeHealthContributor { + + private final SystemHealthService health; + + public DownstreamHealthContributor(SystemHealthService health) { + this.health = health; + } + + private Map snapshot() { + Map map = new LinkedHashMap<>(); + for (DownstreamHealth c : health.check().components()) { + HealthIndicator indicator = + () -> (c.up() ? Health.up() : Health.down()).withDetail("url", c.resolvedUrl()).withDetail("detail", c.detail()).build(); + map.put(c.name(), indicator); + } + return map; + } + + @Override + public HealthContributor getContributor(String name) { + return snapshot().get(name); + } + + @Override + public Iterator> iterator() { + Map map = snapshot(); + return map.entrySet().stream().map(e -> NamedContributor.of(e.getKey(), e.getValue())).iterator(); + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/DownstreamHealthProperties.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/DownstreamHealthProperties.java new file mode 100644 index 000000000..98bcb4521 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/DownstreamHealthProperties.java @@ -0,0 +1,24 @@ +package edu.harvard.hms.dbmi.avillach.gateway.health; + +import java.util.List; + +import org.springframework.boot.context.properties.ConfigurationProperties; + +/** + * Config-driven list of downstreams the gateway's deep-health composer probes, bound from {@code picsure.gateway.health.*}. Backs + * {@link SystemHealthService}. + */ +@ConfigurationProperties(prefix = "picsure.gateway.health") +public record DownstreamHealthProperties( + List downstreams, Integer connectTimeoutMs, Integer readTimeoutMs, String applicationToken +) { + public DownstreamHealthProperties { + downstreams = downstreams == null ? List.of() : List.copyOf(downstreams); + if (connectTimeoutMs == null) { + connectTimeoutMs = 1000; + } + if (readTimeoutMs == null) { + readTimeoutMs = 2000; + } + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/MonitoredDownstream.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/MonitoredDownstream.java new file mode 100644 index 000000000..e5689dda9 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/MonitoredDownstream.java @@ -0,0 +1,37 @@ +package edu.harvard.hms.dbmi.avillach.gateway.health; + +/** + * One monitored downstream. + * + * @param name component name surfaced in /actuator/health and logs + * @param baseUrl base URL (reuse the routing env-var URL) + * @param healthPath path appended to baseUrl; default "/actuator/health", overridable (logging -> "/health"; an interim non-Actuator + * service -> "/info") + * @param method HTTP method for the probe ("GET" or "POST"); default GET + * @param requestBody body sent for POST probes (e.g. "{}" for a PSAMA introspection fallback) + * @param sendAppToken whether to send the application/service bearer on the probe + * @param successStatus expected HTTP status for "up" (default 200) + * @param requireStatusUp if true, also require an Actuator body of {"status":"UP"} + */ +public record MonitoredDownstream( + String name, String baseUrl, String healthPath, String method, String requestBody, boolean sendAppToken, Integer successStatus, + boolean requireStatusUp +) { + public MonitoredDownstream { + if (healthPath == null || healthPath.isBlank()) { + healthPath = "/actuator/health"; + } + if (method == null || method.isBlank()) { + method = "GET"; + } + if (successStatus == null) { + successStatus = 200; + } + } + + public String resolvedUrl() { + String base = baseUrl.endsWith("/") ? baseUrl.substring(0, baseUrl.length() - 1) : baseUrl; + String path = healthPath.startsWith("/") ? healthPath : "/" + healthPath; + return base + path; + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/SystemHealthService.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/SystemHealthService.java new file mode 100644 index 000000000..dbc03b6da --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/SystemHealthService.java @@ -0,0 +1,103 @@ +package edu.harvard.hms.dbmi.avillach.gateway.health; + +import java.time.Duration; +import java.util.ArrayList; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.concurrent.CompletableFuture; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.boot.http.client.ClientHttpRequestFactoryBuilder; +import org.springframework.boot.http.client.ClientHttpRequestFactorySettings; +import org.springframework.http.HttpMethod; +import org.springframework.http.MediaType; +import org.springframework.web.client.RestClient; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; + +/** + * Pings each configured downstream in parallel, dedups by resolved URL, and rolls the results up into an aggregate RUNNING/DEGRADED + * verdict. One ping per service (no cascade): each service's own deep {@code /actuator/health} already covers its dependencies, so the + * gateway does not double-probe a backend another service fronts. Downstreams that resolve to the same URL (e.g. hpds-open / hpds-auth + * collapsing onto a single HPDS instance in an AIO deployment) are probed once and the result is fanned back out to every name sharing that + * URL. + */ +public class SystemHealthService { + + private static final Logger log = LoggerFactory.getLogger(SystemHealthService.class); + + private final DownstreamHealthProperties props; + private final RestClient http; + private final ObjectMapper json = new ObjectMapper(); + + public SystemHealthService(DownstreamHealthProperties props) { + this.props = props; + // Health probes run off the request path (a background composer), but a slow/hanging downstream must still + // not tie up the aggregator indefinitely -- short, bounded connect/read timeouts, same pattern as + // SecurityConfig's auth-boundary clients. + ClientHttpRequestFactorySettings settings = ClientHttpRequestFactorySettings.defaults() + .withConnectTimeout(Duration.ofMillis(props.connectTimeoutMs())).withReadTimeout(Duration.ofMillis(props.readTimeoutMs())); + this.http = RestClient.builder().requestFactory(ClientHttpRequestFactoryBuilder.detect().build(settings)).build(); + } + + public AggregateHealth check() { + // Group entries by resolved URL so a shared backend is probed once. + Map> byUrl = new LinkedHashMap<>(); + for (MonitoredDownstream d : props.downstreams()) { + byUrl.computeIfAbsent(d.resolvedUrl(), k -> new ArrayList<>()).add(d); + } + + List>> futures = new ArrayList<>(); + for (Map.Entry> e : byUrl.entrySet()) { + List sharing = e.getValue(); + MonitoredDownstream representative = sharing.get(0); + futures.add(CompletableFuture.supplyAsync(() -> { + boolean up = probe(representative); + String detail = up ? "up" : "unreachable"; + List results = new ArrayList<>(); + for (MonitoredDownstream d : sharing) { + results.add(new DownstreamHealth(d.name(), d.resolvedUrl(), up, detail)); + } + return results; + })); + } + + List components = new ArrayList<>(); + for (CompletableFuture> f : futures) { + components.addAll(f.join()); + } + return AggregateHealth.from(components); + } + + /** Probe a single downstream. Returns true iff it is considered up. Overridable for unit tests. */ + protected boolean probe(MonitoredDownstream d) { + try { + RestClient.RequestBodySpec spec = http.method(HttpMethod.valueOf(d.method())).uri(d.resolvedUrl()); + if (d.sendAppToken() && props.applicationToken() != null) { + spec = spec.header("Authorization", "Bearer " + props.applicationToken()); + } + if ("POST".equalsIgnoreCase(d.method())) { + spec = spec.contentType(MediaType.APPLICATION_JSON).body(d.requestBody() == null ? "{}" : d.requestBody()); + } + var response = spec.retrieve().toEntity(String.class); + if (response.getStatusCode().value() != d.successStatus()) { + return false; + } + if (d.requireStatusUp()) { + String body = response.getBody(); + if (body == null) { + return false; + } + JsonNode node = json.readTree(body); + return node.hasNonNull("status") && "UP".equalsIgnoreCase(node.get("status").asText()); + } + return true; + } catch (Exception ex) { + log.warn("Health probe failed for {} ({}): {}", d.name(), d.resolvedUrl(), ex.getMessage()); + return false; + } + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/SystemStatusController.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/SystemStatusController.java new file mode 100644 index 000000000..638049913 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/health/SystemStatusController.java @@ -0,0 +1,53 @@ +package edu.harvard.hms.dbmi.avillach.gateway.health; + +/** + * Backward-compatible replacement for the WAR's SystemService {@code /system/status}. Plain-text, unauthenticated (on the introspection + * allow-list), throttled to one real deep check per window with a cached last result to avoid a DoS via the deep probes. + * + *

    Deliberately not a {@code @RestController}/{@code @GetMapping}: the gateway's route-backed {@code RouterFunction} beans are + * registered via {@code RouterFunctionMapping}, which Spring wires at order -1 -- ahead of {@code RequestMappingHandlerMapping} (order 0). + * An annotated controller mapping here would be silently overridden by any same-path {@code RouterFunction}. See + * {@link edu.harvard.hms.dbmi.avillach.gateway.config.HealthConfig} for the higher-precedence {@code RouterFunction} that actually exposes + * this at {@code GET /system/status}. (Actuator's own endpoints are unaffected: {@code WebMvcEndpointHandlerMapping} is order -100, ahead + * of {@code RouterFunctionMapping}.) + */ +public class SystemStatusController { + + static final String RUNNING = "RUNNING"; + static final String DEGRADED = "ONE OR MORE COMPONENTS DEGRADED"; + + private final SystemHealthService health; + private final long windowMs; + + private volatile String lastStatus = "UNTESTED"; + private volatile long lastCheck = 0L; + + public SystemStatusController(SystemHealthService health, long windowMs) { + this.health = health; + this.windowMs = windowMs; + } + + public String status() { + long now = System.currentTimeMillis(); + if (now - lastCheck < windowMs && lastCheck != 0L) { + return lastStatus; + } + synchronized (this) { + if (now - lastCheck < windowMs && lastCheck != 0L) { + return lastStatus; + } + lastCheck = now; + try { + lastStatus = health.check().running() ? RUNNING : DEGRADED; + } catch (Exception e) { + lastStatus = DEGRADED; + } + return lastStatus; + } + } + + /** Test hook: reset the throttle window so the next call re-checks. */ + void expireCacheForTest() { + this.lastCheck = 0L; + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/request/AccessLogFilter.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/request/AccessLogFilter.java new file mode 100644 index 000000000..445505283 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/request/AccessLogFilter.java @@ -0,0 +1,39 @@ +package edu.harvard.hms.dbmi.avillach.gateway.request; + +import java.io.IOException; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.web.filter.OncePerRequestFilter; + +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +/** + * Emits one INFO line per request — method, path, status, duration — so the container log stream shows live traffic (ALS-12238). Runs + * inside {@link RequestIdFilter}, so the JSON encoder decorates every line with {@code MDC[requestId]}. Actuator endpoints are skipped: + * health probes and Prometheus scrapes would otherwise dominate the stream. + */ +public class AccessLogFilter extends OncePerRequestFilter { + + private static final Logger LOG = LoggerFactory.getLogger("gateway.access"); + + @Override + protected boolean shouldNotFilter(HttpServletRequest request) { + return request.getRequestURI().startsWith("/actuator"); + } + + @Override + protected void doFilterInternal(HttpServletRequest request, HttpServletResponse response, FilterChain filterChain) + throws ServletException, IOException { + long start = System.nanoTime(); + try { + filterChain.doFilter(request, response); + } finally { + long durationMs = (System.nanoTime() - start) / 1_000_000; + LOG.info("{} {} {} {}ms", request.getMethod(), request.getRequestURI(), response.getStatus(), durationMs); + } + } +} diff --git a/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/request/InboundIdentityHeaderSanitizingFilter.java b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/request/InboundIdentityHeaderSanitizingFilter.java new file mode 100644 index 000000000..0efe69483 --- /dev/null +++ b/services/pic-sure-gateway/src/main/java/edu/harvard/hms/dbmi/avillach/gateway/request/InboundIdentityHeaderSanitizingFilter.java @@ -0,0 +1,83 @@ +package edu.harvard.hms.dbmi.avillach.gateway.request; + +import java.io.IOException; +import java.util.Collections; +import java.util.Enumeration; +import java.util.LinkedHashSet; +import java.util.Set; + +import org.springframework.web.filter.OncePerRequestFilter; + +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletRequestWrapper; +import jakarta.servlet.http.HttpServletResponse; + +/** + * Defense-in-depth, registered UNCONDITIONALLY (see {@code ObservabilityConfig}): strips the five gateway-owned {@code X-User-*} identity + * headers ({@link GatewayUserResolver#HEADER_USER_ID}, {@code _SUBJECT}, {@code _EMAIL}, {@code _ROLES}, {@code _PRIVILEGES}) from every + * inbound CLIENT request before anything downstream -- routing, the auth chain, or the WildFly proxy -- can ever see a client-supplied + * value.

    {@link edu.harvard.hms.dbmi.avillach.gateway.filter.IdentityPropagationFilter} already hides these headers from the client, + * but this filter exists as an independent trust boundary: even if the DB-free auth chain were ever bypassed, misconfigured, or WildFly is + * nonetheless configured to trust these headers directly from the gateway (its {@code GatewayHeaderFilter}), a client's own + * {@code X-User-Id}/{@code X-User-Privileges}/etc. must never pass through untouched -- that would be an identity/privilege-spoofing hole. + * This filter closes that hole unconditionally, independent of anything the auth chain does.

    Runs at + * {@link org.springframework.core.Ordered#HIGHEST_PRECEDENCE} {@code + 2}: right after the commons {@code RequestIdFilter} (+0) and + * {@code AccessLogFilter} (+1), and before the DB-free auth chain (order 10+). + * {@link edu.harvard.hms.dbmi.avillach.gateway.filter.IdentityPropagationFilter} (order 50) still runs afterward and sets the + * gateway-resolved values on its own wrapper, which never falls through to the (already-sanitized) client request for these names -- so + * normal propagation of resolved identity is unaffected by this filter running first. + */ +public class InboundIdentityHeaderSanitizingFilter extends OncePerRequestFilter { + + @Override + protected void doFilterInternal(HttpServletRequest request, HttpServletResponse response, FilterChain filterChain) + throws ServletException, IOException { + filterChain.doFilter(new SanitizedIdentityHeadersRequest(request), response); + } + + static class SanitizedIdentityHeadersRequest extends HttpServletRequestWrapper { + + /** Gateway-owned identity headers: always hidden from the raw client request, regardless of name casing. */ + private static final Set STRIPPED_HEADERS = Set.of( + GatewayUserResolver.HEADER_USER_ID, GatewayUserResolver.HEADER_USER_SUBJECT, GatewayUserResolver.HEADER_USER_EMAIL, + GatewayUserResolver.HEADER_USER_ROLES, GatewayUserResolver.HEADER_USER_PRIVILEGES + ); + + SanitizedIdentityHeadersRequest(HttpServletRequest request) { + super(request); + } + + private static boolean isStripped(String name) { + for (String stripped : STRIPPED_HEADERS) { + if (stripped.equalsIgnoreCase(name)) return true; + } + return false; + } + + @Override + public String getHeader(String name) { + return isStripped(name) ? null : super.getHeader(name); + } + + @Override + public Enumeration getHeaders(String name) { + return isStripped(name) ? Collections.emptyEnumeration() : super.getHeaders(name); + } + + @Override + public Enumeration getHeaderNames() { + Set names = new LinkedHashSet<>(); + Enumeration superNames = super.getHeaderNames(); + while (superNames != null && superNames.hasMoreElements()) { + String n = superNames.nextElement(); + if (!isStripped(n)) { + names.add(n); + } + } + return Collections.enumeration(names); + } + } +} diff --git a/services/pic-sure-gateway/src/main/resources/application-aio.yml b/services/pic-sure-gateway/src/main/resources/application-aio.yml new file mode 100644 index 000000000..88436e06a --- /dev/null +++ b/services/pic-sure-gateway/src/main/resources/application-aio.yml @@ -0,0 +1,54 @@ +# AIO profile: query-service, operations-service, and PSAMA are reachable by Docker DNS +# on the shared `picsure` network. HPDS_QUERY_SERVICE_URL and OPERATIONS_SERVICE_URL may +# still override (see application.yml for defaults). + +# PSAMA is reachable by Docker DNS on the `picsure` network. These match WildFly's +# java:global/token_introspection_url and openAccessValidateUrl in standalone.xml. +# Env vars still override (BDC sets its own). The service token stays env-only. +picsure: + gateway: + security: + introspection-url: ${TOKEN_INTROSPECTION_URL:http://psama:8090/auth/token/inspect} + open-access-validate-url: ${OPEN_ACCESS_VALIDATE_URL:http://psama:8090/auth/open/validate} + # Deep-health downstream list the gateway aggregates into + # /system/status and /actuator/health. AIO service DNS on the picsure network. + # PSAMA uses the transitional introspection-ping (active:false = reachable) until + # its Actuator lands; HPDS/dictionary report DOWN until their Actuator arrives. + # visualization + logging already expose health today. + health: + connect-timeout-ms: 2000 + read-timeout-ms: 3000 + application-token: ${TOKEN_INTROSPECTION_TOKEN:} + downstreams: + - name: psama + # PSAMA now ships Actuator; use its real deep /auth/actuator/health + # (db indicator). context-path is /auth. The transitional introspection-ping + # (POST /auth/token/inspect, {}, app token) is retained in git history as the + # fallback if a PSAMA deploy ever lags the actuator rollout. + base-url: ${PSAMA_URL:http://psama:8090} + health-path: /auth/actuator/health + require-status-up: true + - name: visualization + base-url: ${VISUALIZATION_URL:http://visualization} + health-path: /actuator/health + require-status-up: true + - name: logging + base-url: ${LOGGING_HEALTH_URL:http://pic-sure-logging} + health-path: /health + require-status-up: false + - name: hpds + base-url: ${HPDS_URL:http://hpds:8080} + health-path: /actuator/health + require-status-up: true + - name: dictionary + base-url: ${DICTIONARY_URL:http://dictionary-api} + health-path: /actuator/health + require-status-up: true + - name: operations-service + base-url: ${OPERATIONS_SERVICE_URL:http://pic-sure-operations-service:8080} + health-path: /operations/actuator/health + require-status-up: true + - name: query-service + base-url: ${HPDS_QUERY_SERVICE_URL:http://pic-sure-hpds-query-service:8080} + health-path: /actuator/health + require-status-up: true diff --git a/services/pic-sure-gateway/src/main/resources/application-local.yml b/services/pic-sure-gateway/src/main/resources/application-local.yml new file mode 100644 index 000000000..58fcdf73f --- /dev/null +++ b/services/pic-sure-gateway/src/main/resources/application-local.yml @@ -0,0 +1,2 @@ +# Local profile: point HPDS_QUERY_SERVICE_URL at a locally reachable query-service, e.g. +# HPDS_QUERY_SERVICE_URL=http://localhost:8081 java -jar target/pic-sure-gateway-*.jar --spring.profiles.active=local diff --git a/services/pic-sure-gateway/src/main/resources/application.yml b/services/pic-sure-gateway/src/main/resources/application.yml new file mode 100644 index 000000000..0f0f71d7f --- /dev/null +++ b/services/pic-sure-gateway/src/main/resources/application.yml @@ -0,0 +1,137 @@ +spring: + application: + name: pic-sure-gateway + cloud: + gateway: + server: + webmvc: + routes: + # Explicit clean-prefix route for the logging service, replacing the + # legacy /proxy/pic-sure-logging relay. StripPrefix=1 drops the leading /logging segment + # because the logging service (Javalin) serves its API at root (/audit, + # /health, /info) — mirroring the old /proxy relay's prefix strip. /logging is + # on the introspection allow-list, so it is not authenticated. + # /dictionary, /uploader, and /visualization are AUTHENTICATED (not on the + # allow-list): the introspection filter runs on the pre-strip public path + # (Target Service = /dictionary/x), which the PSAMA access-rule + # migrations now authorize (^/dictionary(/.*)?$ / ^/uploader(/.*)?$ / + # ^/visualization(/.*)?$). Same StripPrefix=1 as /logging (dictionary-api, + # uploader, and the visualization container all serve their APIs at root). + # /hpds is handled separately below (query-service ingress). + - id: logging + uri: ${LOGGING_URL:http://pic-sure-logging} + order: 100 + predicates: + - Path=/logging/** + filters: + - StripPrefix=1 + - id: dictionary + uri: ${DICTIONARY_URL:http://dictionary-api} + order: 100 + predicates: + - Path=/dictionary/** + filters: + - StripPrefix=1 + - id: uploader + uri: ${UPLOADER_URL:http://uploader:8080} + order: 100 + predicates: + - Path=/uploader/** + filters: + - StripPrefix=1 + - id: visualization + uri: ${VISUALIZATION_URL:http://visualization} + order: 100 + predicates: + - Path=/visualization/** + filters: + - StripPrefix=1 + # Query-service and operations-service ingress. Unlike the routes + # above, these serve at the VERBATIM public path — NO StripPrefix. /hpds/{auth,open}[/v3]/query|search + # is served entirely by the DB-free query-service, which selects auth/open from the path itself. + # /operations/** is served by operations-service, the sole DB owner (also home to + # the internal query dispatch API PsamaIntrospectionFilter/QueryAuthFetcher calls for result/signed-url + # auth). /operations/configuration/** carries a public-GET carve-out for the introspection filter itself + # (see PsamaIntrospectionFilter#isPublicConfigurationRead) — everything else (POST/PATCH/DELETE, all + # /operations/configuration/admin/**, and all of /operations/dataset/**) is introspected as usual by the + # always-on auth chain. + - id: hpds + uri: ${HPDS_QUERY_SERVICE_URL:http://pic-sure-hpds-query-service:8080} + order: 100 + predicates: + - Path=/hpds/** + - id: operations + uri: ${OPERATIONS_SERVICE_URL:http://pic-sure-operations-service:8080} + order: 100 + predicates: + - Path=/operations/** + +management: + endpoints: + web: + exposure: + # OFF BY DEFAULT: the default 'none' is a sentinel that matches no endpoint, so nothing under /actuator/** + # is reachable (404). (An EMPTY include is NOT off -- Spring Boot then falls back to its built-in default of + # exposing health.) AIO's gateway.env sets PICSURE_ACTUATOR_EXPOSURE=health,info to turn it on; the public + # /system/status check (a RouterFunction, not an actuator endpoint) stays available regardless. + # prometheus/metrics are added via this same env var when the monitoring (M2) rollout lands -- no code change. + include: ${PICSURE_ACTUATOR_EXPOSURE:none} + endpoint: + health: + show-details: ${PICSURE_ACTUATOR_DETAILS:never} # default never; when_authorized (set in AIO) gates detail behind the X-Application-Token + probes: + enabled: true # /actuator/health/liveness stays shallow-open + group: + liveness: + include: livenessState # pin liveness to the app's own state; downstreams + # (registered as the "downstreams" top-level contributor) must never flip + # this probe DOWN -- deploy/container healthchecks poll this endpoint. + health: + defaults: + enabled: true + metrics: + distribution: + # Publish client-observable latency percentiles per route for the pass-through + # baseline and ongoing comparison (visible at /actuator/prometheus and + # /actuator/metrics/http.server.requests). + percentiles: + http.server.requests: 0.5, 0.95, 0.99 + percentiles-histogram: + http.server.requests: true + prometheus: + metrics: + export: + enabled: true + +server: + port: 8080 + +# DB-free auth/audit chain -- always enforced; every request goes through PSAMA introspection. +# Secrets come from the environment (gateway.env); non-secret defaults are here. +picsure: + # The shared X-Application-Token gate for THIS service's own /actuator/** endpoints (see + # ActuatorSecurityConfig / the shared ActuatorSecurityHelper in pic-sure-spring-commons). Distinct from + # picsure.gateway.health.application-token below, which is the Bearer token the gateway sends OUTBOUND when + # probing downstreams' deep health -- same env-driven pattern, deliberately separate secrets/purposes. + actuator: + require-token: ${PICSURE_ACTUATOR_REQUIRE_TOKEN:true} + token: ${PICSURE_APPLICATION_TOKEN:} + header-name: X-Application-Token + gateway: + security: + open-access-enabled: ${GATEWAY_OPEN_ACCESS_ENABLED:false} + user-id-claim: sub + max-body-bytes: ${GATEWAY_AUTH_MAX_BODY_BYTES:10485760} + introspection-url: ${TOKEN_INTROSPECTION_URL:} + open-access-validate-url: ${OPEN_ACCESS_VALIDATE_URL:} + service-token: ${TOKEN_INTROSPECTION_TOKEN:} + query-service-url: ${HPDS_QUERY_SERVICE_URL:} + operations-service-url: ${OPERATIONS_SERVICE_URL:} + query-service-internal-token: ${QUERY_SERVICE_INTERNAL_TOKEN:} + # Allowed list of prefixes that do not require authentication. The logging service has its own access key + # for security. The other paths are publicly available. + allow-list-prefixes: + - /logging + - /actuator + - /openapi + - /swagger-ui diff --git a/services/pic-sure-gateway/src/main/resources/logback-spring.xml b/services/pic-sure-gateway/src/main/resources/logback-spring.xml new file mode 100644 index 000000000..98be0a5ed --- /dev/null +++ b/services/pic-sure-gateway/src/main/resources/logback-spring.xml @@ -0,0 +1,24 @@ + + + + + + + %d{HH:mm:ss.SSS} %-5level [%X{requestId}] %logger{36} - %msg%n + + + + + + + + + + + + + + + + + diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/GatewayApplicationTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/GatewayApplicationTest.java new file mode 100644 index 000000000..70cbf6427 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/GatewayApplicationTest.java @@ -0,0 +1,20 @@ +package edu.harvard.hms.dbmi.avillach.gateway; + +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.context.ApplicationContext; + +@SpringBootTest +class GatewayApplicationTest { + + @Autowired + private ApplicationContext context; + + @Test + void contextLoads() { + assertThat(context).isNotNull(); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/auth/PsamaClientTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/auth/PsamaClientTest.java new file mode 100644 index 000000000..86f6d6669 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/auth/PsamaClientTest.java @@ -0,0 +1,85 @@ +package edu.harvard.hms.dbmi.avillach.gateway.auth; + +import static com.github.tomakehurst.wiremock.client.WireMock.equalTo; +import static com.github.tomakehurst.wiremock.client.WireMock.okJson; +import static com.github.tomakehurst.wiremock.client.WireMock.post; +import static com.github.tomakehurst.wiremock.client.WireMock.postRequestedFor; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.Map; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.springframework.web.client.RestClient; + +import com.github.tomakehurst.wiremock.WireMockServer; + +class PsamaClientTest { + + static WireMockServer psama; + + @BeforeAll + static void start() { + // http2PlainDisabled avoids a known JDK HttpClient <-> WireMock(Jetty) h2c upgrade bug that manifests as + // "RST_STREAM: Stream cancelled" when RestClient's default JDK-backed request factory is used. + psama = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + psama.start(); + } + + @AfterAll + static void stop() { + psama.stop(); + } + + private PsamaClient client() { + return new PsamaClient( + RestClient.builder().build(), "http://127.0.0.1:" + psama.port() + "/token/introspect", + "http://127.0.0.1:" + psama.port() + "/open/validate", "service-token" + ); + } + + @Test + void postsIntrospectionWithServiceBearerAndParsesPrivileges() { + psama.stubFor( + post(urlEqualTo("/token/introspect")).willReturn( + okJson( + "{\"active\":true,\"userId\":\"u-1\",\"email\":\"a@b\",\"sub\":\"s-1\",\"roles\":\"ADMIN\",\"privileges\":[\"SUPER_ADMIN\"]}" + ) + ) + ); + + IntrospectionResponse resp = client().introspect("user-token", Map.of("Target Service", "/info")); + assertThat(resp.active()).isTrue(); + assertThat(resp.userId()).isEqualTo("u-1"); + assertThat(resp.privileges()).containsExactly("SUPER_ADMIN"); + + psama.verify(postRequestedFor(urlEqualTo("/token/introspect")).withHeader("Authorization", equalTo("Bearer service-token"))); + } + + @Test + void bindsUserIdFromPsamaUuidField() { + // The REAL PSAMA inspect response carries the user UUID as "uuid" (UserService/UserClaims) -- there is no + // "userId" field. X-User-Id propagation (and thus query/operations-service authn) depends on this binding. + psama.stubFor( + post(urlEqualTo("/token/introspect")).willReturn( + okJson( + "{\"active\":true,\"uuid\":\"7c5e0618-0000-0000-0000-000000000000\",\"email\":\"a@b\"," + + "\"sub\":\"LONG_TERM_TOKEN|s-1\",\"roles\":\"ADMIN\",\"privileges\":[\"SUPER_ADMIN\"]}" + ) + ) + ); + + IntrospectionResponse resp = client().introspect("user-token", Map.of("Target Service", "/hpds/auth/query/sync")); + assertThat(resp.active()).isTrue(); + assertThat(resp.userId()).isEqualTo("7c5e0618-0000-0000-0000-000000000000"); + } + + @Test + void openValidateReturnsBareBoolean() { + psama.stubFor(post(urlEqualTo("/open/validate")).willReturn(okJson("true"))); + assertThat(client().validateOpenAccess(Map.of("ipAddress", "OPEN_ACCESS:host"))).isTrue(); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/auth/QueryAuthFetcherTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/auth/QueryAuthFetcherTest.java new file mode 100644 index 000000000..aecda0961 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/auth/QueryAuthFetcherTest.java @@ -0,0 +1,97 @@ +package edu.harvard.hms.dbmi.avillach.gateway.auth; + +import static com.github.tomakehurst.wiremock.client.WireMock.equalTo; +import static com.github.tomakehurst.wiremock.client.WireMock.forbidden; +import static com.github.tomakehurst.wiremock.client.WireMock.get; +import static com.github.tomakehurst.wiremock.client.WireMock.getRequestedFor; +import static com.github.tomakehurst.wiremock.client.WireMock.notFound; +import static com.github.tomakehurst.wiremock.client.WireMock.okJson; +import static com.github.tomakehurst.wiremock.client.WireMock.serverError; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.assertj.core.api.Assertions.assertThat; +import static org.assertj.core.api.Assertions.assertThatThrownBy; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.springframework.http.HttpStatus; +import org.springframework.web.client.RestClient; + +import com.github.tomakehurst.wiremock.WireMockServer; + +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; + +class QueryAuthFetcherTest { + + static WireMockServer qs; + + @BeforeAll + static void start() { + // http2PlainDisabled avoids a known JDK HttpClient <-> WireMock(Jetty) h2c upgrade bug that manifests as + // "RST_STREAM: Stream cancelled" when RestClient's default JDK-backed request factory is used. + qs = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + qs.start(); + } + + @AfterAll + static void stop() { + qs.stop(); + } + + private QueryAuthFetcher fetcher() { + return new QueryAuthFetcher(RestClient.builder().build(), "http://127.0.0.1:" + qs.port(), "internal-secret"); + } + + @Test + void fetchesStoredQueryForResultPathAndSendsInternalToken() { + qs.stubFor( + get(urlEqualTo("/operations/internal/queries/abc-123/dispatch")).willReturn(okJson("{\"queryJson\":\"{\\\"stored\\\":true}\"}")) + ); + assertThat(fetcher().queryJsonForPath("/query/abc-123/result")).contains("{\"stored\":true}"); + qs.verify( + getRequestedFor(urlEqualTo("/operations/internal/queries/abc-123/dispatch")) + .withHeader("X-PIC-SURE-INTERNAL-TOKEN", equalTo("internal-secret")) + ); + } + + @Test + void failsClosedOn403AsForbiddenDeny() { + qs.stubFor(get(urlEqualTo("/operations/internal/queries/forbidden/dispatch")).willReturn(forbidden())); + assertThatThrownBy(() -> fetcher().queryJsonForPath("/query/forbidden/result")).isInstanceOf(PicsureException.class) + .extracting(e -> ((PicsureException) e).getStatus()).isEqualTo(HttpStatus.BAD_GATEWAY); + } + + @Test + void fetchesStoredQueryForV3SignedUrlPath() { + qs.stubFor(get(urlEqualTo("/operations/internal/queries/q9/dispatch")).willReturn(okJson("{\"queryJson\":\"{\\\"v3\\\":1}\"}"))); + assertThat(fetcher().queryJsonForPath("/v3/query/q9/signed-url")).contains("{\"v3\":1}"); + } + + @Test + void returnsEmptyForNonStoredQueryPaths() { + assertThat(fetcher().queryJsonForPath("/query")).isEmpty(); + assertThat(fetcher().queryJsonForPath("/query/abc/status")).isEmpty(); + } + + @Test + void failsClosedOn404AsNotFound() { + qs.stubFor(get(urlEqualTo("/operations/internal/queries/missing/dispatch")).willReturn(notFound())); + assertThatThrownBy(() -> fetcher().queryJsonForPath("/query/missing/result")).isInstanceOf(PicsureException.class) + .extracting(e -> ((PicsureException) e).getStatus()).isEqualTo(HttpStatus.NOT_FOUND); + } + + @Test + void failsClosedOnUpstream500AsBadGateway() { + qs.stubFor(get(urlEqualTo("/operations/internal/queries/boom/dispatch")).willReturn(serverError())); + assertThatThrownBy(() -> fetcher().queryJsonForPath("/query/boom/result")).isInstanceOf(PicsureException.class) + .extracting(e -> ((PicsureException) e).getStatus()).isEqualTo(HttpStatus.BAD_GATEWAY); + } + + @Test + void failsClosedOnEmptyBodyAsBadGateway() { + qs.stubFor(get(urlEqualTo("/operations/internal/queries/empty/dispatch")).willReturn(okJson("{\"queryJson\":\"\"}"))); + assertThatThrownBy(() -> fetcher().queryJsonForPath("/query/empty/result")).isInstanceOf(PicsureException.class) + .extracting(e -> ((PicsureException) e).getStatus()).isEqualTo(HttpStatus.BAD_GATEWAY); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/config/DownstreamHealthPropertiesAioBindingTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/config/DownstreamHealthPropertiesAioBindingTest.java new file mode 100644 index 000000000..2bd097b7a --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/config/DownstreamHealthPropertiesAioBindingTest.java @@ -0,0 +1,46 @@ +package edu.harvard.hms.dbmi.avillach.gateway.config; + +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.Optional; + +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.ActiveProfiles; + +import edu.harvard.hms.dbmi.avillach.gateway.health.DownstreamHealthProperties; +import edu.harvard.hms.dbmi.avillach.gateway.health.MonitoredDownstream; + +/** + * Under the {@code aio} profile, the deep-health downstream list must aggregate the two new services -- operations-service (the sole DB + * owner) and query-service (DB-free {@code /hpds/**}) -- alongside the existing entries, mirroring their shape (Actuator health, + * {@code require-status-up: true}). + */ +@SpringBootTest +@ActiveProfiles("aio") +class DownstreamHealthPropertiesAioBindingTest { + + @Autowired + private DownstreamHealthProperties props; + + private Optional byName(String name) { + return props.downstreams().stream().filter(d -> d.name().equals(name)).findFirst(); + } + + @Test + void operationsServiceIsAggregatedWithActuatorHealthAndRequiresStatusUp() { + MonitoredDownstream d = byName("operations-service").orElseThrow(); + assertThat(d.baseUrl()).isEqualTo("http://pic-sure-operations-service:8080"); + assertThat(d.healthPath()).isEqualTo("/operations/actuator/health"); + assertThat(d.requireStatusUp()).isTrue(); + } + + @Test + void queryServiceIsAggregatedWithActuatorHealthAndRequiresStatusUp() { + MonitoredDownstream d = byName("query-service").orElseThrow(); + assertThat(d.baseUrl()).isEqualTo("http://pic-sure-hpds-query-service:8080"); + assertThat(d.healthPath()).isEqualTo("/actuator/health"); + assertThat(d.requireStatusUp()).isTrue(); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/config/GatewaySecurityPropertiesAioBindingTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/config/GatewaySecurityPropertiesAioBindingTest.java new file mode 100644 index 000000000..a5340f057 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/config/GatewaySecurityPropertiesAioBindingTest.java @@ -0,0 +1,30 @@ +package edu.harvard.hms.dbmi.avillach.gateway.config; + +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.ActiveProfiles; + +/** + * Pins the AIO profile override: under the {@code aio} profile, PSAMA URLs resolve to the AIO Docker-network DNS names rather than the + * empty base defaults. + */ +@SpringBootTest +@ActiveProfiles("aio") +class GatewaySecurityPropertiesAioBindingTest { + + @Autowired + private GatewaySecurityProperties props; + + @Test + void introspectionUrlResolvesToAioPsamaDns() { + assertThat(props.introspectionUrl()).isEqualTo("http://psama:8090/auth/token/inspect"); + } + + @Test + void openAccessValidateUrlResolvesToAioPsamaDns() { + assertThat(props.openAccessValidateUrl()).isEqualTo("http://psama:8090/auth/open/validate"); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/config/HealthConfigTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/config/HealthConfigTest.java new file mode 100644 index 000000000..232a65f48 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/config/HealthConfigTest.java @@ -0,0 +1,27 @@ +package edu.harvard.hms.dbmi.avillach.gateway.config; + +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; + +import edu.harvard.hms.dbmi.avillach.gateway.health.DownstreamHealthProperties; +import edu.harvard.hms.dbmi.avillach.gateway.health.SystemHealthService; + +/** Proves HealthConfig registers the deep-health beans so the /system/status controller and the actuator composite can consume them. */ +@SpringBootTest +class HealthConfigTest { + + @Autowired + private SystemHealthService systemHealthService; + + @Autowired + private DownstreamHealthProperties downstreamHealthProperties; + + @Test + void registersHealthBeans() { + assertThat(systemHealthService).isNotNull(); + assertThat(downstreamHealthProperties).isNotNull(); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/config/QueryAuthFetcherDispatchWiringTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/config/QueryAuthFetcherDispatchWiringTest.java new file mode 100644 index 000000000..0b8bb6249 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/config/QueryAuthFetcherDispatchWiringTest.java @@ -0,0 +1,118 @@ +package edu.harvard.hms.dbmi.avillach.gateway.config; + +import static com.github.tomakehurst.wiremock.client.WireMock.anyRequestedFor; +import static com.github.tomakehurst.wiremock.client.WireMock.anyUrl; +import static com.github.tomakehurst.wiremock.client.WireMock.equalTo; +import static com.github.tomakehurst.wiremock.client.WireMock.get; +import static com.github.tomakehurst.wiremock.client.WireMock.getRequestedFor; +import static com.github.tomakehurst.wiremock.client.WireMock.okJson; +import static com.github.tomakehurst.wiremock.client.WireMock.post; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.web.server.LocalServerPort; +import org.springframework.boot.test.web.client.TestRestTemplate; +import org.springframework.http.HttpEntity; +import org.springframework.http.HttpHeaders; +import org.springframework.http.HttpMethod; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.springframework.test.context.TestPropertySource; + +import com.github.tomakehurst.wiremock.WireMockServer; + +/** + * The internal query dispatch that {@code QueryAuthFetcher} fetches (for PSAMA introspection of {@code result}/{@code signed-url} paths) + * lives on operations-service (the sole DB owner), NOT the query-service. Proves the wiring end-to-end through the real filter chain: a + * {@code GET /query/{id}/result} request must fetch the dispatch from {@code OPERATIONS_SERVICE_URL}, then 404 (no route owns + * {@code /query/**} — there is no catch-all to forward to). The query-service stub is wired to fail loudly (500) so an accidental dispatch + * call there surfaces as a test failure rather than a silent pass. + */ +@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT) +@TestPropertySource(properties = {"picsure.gateway.security.query-service-internal-token=internal-secret"}) +class QueryAuthFetcherDispatchWiringTest { + + static WireMockServer operationsStub; + static WireMockServer queryServiceStub; + static WireMockServer psamaStub; + + @DynamicPropertySource + static void urls(DynamicPropertyRegistry registry) { + operationsStub = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + operationsStub.start(); + registry.add("OPERATIONS_SERVICE_URL", operationsStub::baseUrl); + + // Dispatch must NOT land here anymore -- if it does, this stub answers with 500 and the introspection call + // (hence the whole request) fails. + queryServiceStub = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + queryServiceStub.start(); + registry.add("HPDS_QUERY_SERVICE_URL", queryServiceStub::baseUrl); + + psamaStub = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + psamaStub.start(); + registry.add("TOKEN_INTROSPECTION_URL", () -> psamaStub.baseUrl() + "/auth/token/inspect"); + } + + @AfterAll + static void stopStubs() { + operationsStub.stop(); + queryServiceStub.stop(); + psamaStub.stop(); + } + + @BeforeEach + void resetStubs() { + operationsStub.resetAll(); + operationsStub.stubFor( + get(urlEqualTo("/operations/internal/queries/abc-123/dispatch")) + .withHeader("X-PIC-SURE-INTERNAL-TOKEN", equalTo("internal-secret")) + .willReturn(okJson("{\"queryJson\":\"{\\\"stored\\\":true}\"}")) + ); + + queryServiceStub.resetAll(); + + psamaStub.resetAll(); + psamaStub.stubFor( + post(urlEqualTo("/auth/token/inspect")) + .willReturn(okJson("{\"active\":true,\"userId\":\"u-1\",\"sub\":\"s-1\",\"email\":\"a@b\",\"role\":\"USER\"}")) + ); + } + + @Autowired + private TestRestTemplate rest; + + + @LocalServerPort + int port; + + /** + * Dial the loopback ADDRESS, never the name. {@code localhost} resolves to {@code ::1} before {@code 127.0.0.1} on macOS, while these + * test servers bind the IPv4 wildcard -- so an unrelated local process holding the same port number on {@code [::]} can answer instead, + * and the test fails with a bewildering status from a server it never meant to contact. Relative {@code TestRestTemplate} URLs go + * through {@code LocalHostUriTemplateHandler}, which hardcodes the name {@code localhost}; absolute URLs bypass it entirely. + */ + private String url(String path) { + return "http://127.0.0.1:" + port + path; + } + + @Test + void dispatchForResultPathIsFetchedFromOperationsServiceNotQueryService() { + HttpHeaders headers = new HttpHeaders(); + headers.set("Authorization", "Bearer user-token"); + ResponseEntity response = + rest.exchange(url("/query/abc-123/result"), HttpMethod.GET, new HttpEntity<>(headers), String.class); + + // The dispatch succeeded via operations-service, so PSAMA introspection ran (active:true). No route owns + // /query/**, so the request 404s -- there is no catch-all left to forward it to. + assertThat(response.getStatusCode().value()).isEqualTo(404); + operationsStub.verify(1, getRequestedFor(urlEqualTo("/operations/internal/queries/abc-123/dispatch"))); + queryServiceStub.verify(0, anyRequestedFor(anyUrl())); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/config/RouteSurfacesTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/config/RouteSurfacesTest.java new file mode 100644 index 000000000..b8d48a41a --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/config/RouteSurfacesTest.java @@ -0,0 +1,51 @@ +package edu.harvard.hms.dbmi.avillach.gateway.config; + +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.List; + +import org.junit.jupiter.api.Test; + +/** + * Segment-safe route-surface classification. A prefix matches only on an exact equal or a following {@code /} boundary -- never a bare + * {@code startsWith} -- so a sibling route whose path merely shares a text prefix ({@code /loggingAdmin} vs {@code /logging}) is NOT + * misclassified as owned. + */ +class RouteSurfacesTest { + + private final RouteSurfaces surfaces = RouteSurfaces.withDefaults(); + + @Test + void ownsEachDefaultPrefixExactlyAndUnderASegmentBoundary() { + for (String prefix : RouteSurfaceProperties.DEFAULT_OWNED_PREFIXES) { + assertThat(surfaces.isOwned(prefix)).as("exact %s", prefix).isTrue(); + assertThat(surfaces.isOwned(prefix + "/")).as("%s/", prefix).isTrue(); + assertThat(surfaces.isOwned(prefix + "/deep/path")).as("%s/deep/path", prefix).isTrue(); + } + } + + @Test + void doesNotMatchSiblingPathSharingATextPrefix() { + // /loggingAdmin must NOT match owned prefix /logging + assertThat(surfaces.isOwned("/loggingAdmin")).isFalse(); + assertThat(surfaces.isOwned("/loggingAdmin/x")).isFalse(); + assertThat(surfaces.isOwned("/operationsx")).isFalse(); // vs /operations + assertThat(surfaces.isOwned("/hpdsx")).isFalse(); // vs /hpds + } + + @Test + void unownedIsEverythingNotOwned() { + assertThat(surfaces.isCatchAll("/picsure/query/sync")).isTrue(); + assertThat(surfaces.isCatchAll("/v3/search/abc")).isTrue(); + assertThat(surfaces.isCatchAll("/hpds/auth/v3/query/sync")).isFalse(); + assertThat(surfaces.isOwned(null)).isFalse(); + assertThat(surfaces.isCatchAll(null)).isTrue(); + } + + @Test + void honorsAConfiguredOverrideList() { + RouteSurfaces custom = new RouteSurfaces(List.of("/only")); + assertThat(custom.isOwned("/only/x")).isTrue(); + assertThat(custom.isOwned("/hpds/x")).isFalse(); // default prefixes no longer owned under the override + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/config/SecurityConfigTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/config/SecurityConfigTest.java new file mode 100644 index 000000000..d79213a03 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/config/SecurityConfigTest.java @@ -0,0 +1,39 @@ +package edu.harvard.hms.dbmi.avillach.gateway.config; + +import static org.assertj.core.api.Assertions.assertThat; + +import java.time.Duration; +import java.util.List; + +import org.junit.jupiter.api.Test; + +import edu.harvard.hms.dbmi.avillach.gateway.auth.PsamaClient; +import edu.harvard.hms.dbmi.avillach.gateway.auth.QueryAuthFetcher; + +/** + * Pins FIX 2: the auth-boundary RestClients ({@link PsamaClient}, {@link QueryAuthFetcher}) must never be built with unbounded connect/read + * timeouts -- a hung PSAMA or query-service response must not stall the synchronous auth filter chain / a Tomcat worker indefinitely. + */ +class SecurityConfigTest { + + @Test + void authRequestFactorySettingsHaveBoundedConnectAndReadTimeouts() { + assertThat(SecurityConfig.AUTH_REQUEST_FACTORY_SETTINGS.connectTimeout()).isEqualTo(Duration.ofSeconds(2)); + assertThat(SecurityConfig.AUTH_REQUEST_FACTORY_SETTINGS.readTimeout()).isEqualTo(Duration.ofSeconds(10)); + // Both must be non-zero/non-null -- a zero or absent timeout means "wait forever" for the underlying HTTP client. + assertThat(SecurityConfig.AUTH_CONNECT_TIMEOUT).isPositive(); + assertThat(SecurityConfig.AUTH_READ_TIMEOUT).isPositive(); + } + + @Test + void psamaClientAndQueryAuthFetcherBeansBuildSuccessfullyWithTimeoutBoundedClients() { + SecurityConfig config = new SecurityConfig(); + GatewaySecurityProperties props = new GatewaySecurityProperties( + List.of(), false, "userId", 1024, "http://psama.local/introspect", "http://psama.local/open-access", "svc-token", + "http://query.local", "http://operations.local", "internal-token" + ); + + assertThat(config.psamaClient(props)).isNotNull(); + assertThat(config.queryAuthFetcher(props)).isNotNull(); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/error/GatewayErrorsTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/error/GatewayErrorsTest.java new file mode 100644 index 000000000..a7117504b --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/error/GatewayErrorsTest.java @@ -0,0 +1,40 @@ +package edu.harvard.hms.dbmi.avillach.gateway.error; + +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.Test; +import org.slf4j.MDC; +import org.springframework.http.HttpStatus; +import org.springframework.mock.web.MockHttpServletResponse; + +class GatewayErrorsTest { + + @AfterEach + void clearMdc() { + MDC.clear(); + } + + @Test + void writesStatusContentTypeAndEscapedBodyWithNullRequestIdWhenMdcEmpty() throws Exception { + MockHttpServletResponse resp = new MockHttpServletResponse(); + + GatewayErrors + .write(resp, HttpStatus.PAYLOAD_TOO_LARGE, "REQUEST_BODY_TOO_LARGE", "Request body exceeds the \"max\" size \\ allowed."); + + assertThat(resp.getStatus()).isEqualTo(413); + assertThat(resp.getContentType()).isEqualTo("application/json"); + assertThat(resp.getContentAsString()).contains("\"errorType\":\"REQUEST_BODY_TOO_LARGE\"") + .contains("\"message\":\"Request body exceeds the \\\"max\\\" size \\\\ allowed.\"").contains("\"requestId\":null"); + } + + @Test + void includesQuotedRequestIdWhenMdcSet() throws Exception { + MockHttpServletResponse resp = new MockHttpServletResponse(); + MDC.put("requestId", "r-1"); + + GatewayErrors.write(resp, HttpStatus.BAD_REQUEST, "SOME_ERROR", "plain message"); + + assertThat(resp.getContentAsString()).contains("\"requestId\":\"r-1\""); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/AggregateAuditRouteTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/AggregateAuditRouteTest.java new file mode 100644 index 000000000..fd9de2fb3 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/AggregateAuditRouteTest.java @@ -0,0 +1,41 @@ +package edu.harvard.hms.dbmi.avillach.gateway.filter; + +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.Optional; + +import org.junit.jupiter.api.Test; + +import edu.harvard.hms.dbmi.avillach.commons.audit.AuditRoute; + +/** + * Reconciles the pic-sure-hpds-query-service aggregate open path against the gateway's audit route table: the legacy WAR's v1 + * {@code AggregateDataSharingResourceRS} emitted a bespoke inline {@code aggregate.query_sync} audit event, while its v3 sibling emitted + * NONE at all (the missing-audit gap). Neither is ported -- the query-service performs no audit emission of its own; instead, both + * {@code /hpds/open/query/sync} (v1) and {@code /hpds/open/v3/query/sync} (v3) are audited identically, at this single gateway chokepoint, + * as {@code QUERY}/{@code query.sync}. This closes the v3 gap and unifies the action name (accepted, documented deviation from the WAR's + * {@code aggregate.query_sync}), at the cost of the WAR's per-event {@code resource_id} metadata field (the gateway audit schema is uniform + * across all query traffic, see {@link AuditFilterConfig}). + */ +class AggregateAuditRouteTest { + + private final AuditFilterConfig config = new AuditFilterConfig(); + + @Test + void openV1QuerySyncMapsToQuerySync() { + Optional r = config.auditRouteTable().match("/hpds/open/query/sync", "POST"); + + assertThat(r).isPresent(); + assertThat(r.get().getEventType()).isEqualTo("QUERY"); + assertThat(r.get().getAction()).isEqualTo("query.sync"); + } + + @Test + void openV3QuerySyncMapsToQuerySync() { + Optional r = config.auditRouteTable().match("/hpds/open/v3/query/sync", "POST"); + + assertThat(r).isPresent(); + assertThat(r.get().getEventType()).isEqualTo("QUERY"); + assertThat(r.get().getAction()).isEqualTo("query.sync"); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/BodyMutationFilterTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/BodyMutationFilterTest.java new file mode 100644 index 000000000..c34c069ce --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/BodyMutationFilterTest.java @@ -0,0 +1,119 @@ +package edu.harvard.hms.dbmi.avillach.gateway.filter; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.Mockito.doThrow; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.never; +import static org.mockito.Mockito.spy; +import static org.mockito.Mockito.verify; + +import org.junit.jupiter.api.Test; +import org.springframework.mock.web.MockHttpServletRequest; +import org.springframework.mock.web.MockHttpServletResponse; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; + +import edu.harvard.hms.dbmi.avillach.gateway.auth.BufferedRequestWrapper; +import jakarta.servlet.FilterChain; +import jakarta.servlet.http.HttpServletResponse; + +class BodyMutationFilterTest { + + @Test + void swapsTopLevelQueryWhenAttributePresent() throws Exception { + // BufferedRequestWrapper delegates setAttribute/getAttribute to the wrapped request, so it must be + // backed by a real attribute store (MockHttpServletRequest) rather than a bare Mockito mock, which + // would silently drop the attribute set below and make this security-critical test pass vacuously. + BufferedRequestWrapper req = + new BufferedRequestWrapper(new MockHttpServletRequest(), "{\"query\":\"original\",\"resourceUUID\":\"r-1\"}".getBytes()); + req.setAttribute(BodyMutationFilter.ATTR_MUTATED_QUERY, "{\"_topmed_consents\":[\"phs1\"]}"); + HttpServletResponse resp = mock(HttpServletResponse.class); + FilterChain chain = mock(FilterChain.class); + + new BodyMutationFilter(new ObjectMapper()).doFilter(req, resp, chain); + + verify(chain).doFilter(req, resp); + String newBody = new String(req.getBody()); + assertThat(newBody).contains("_topmed_consents"); + assertThat(newBody).contains("\"resourceUUID\":\"r-1\""); + } + + @Test + void noAttributeLeavesBodyUntouched() throws Exception { + BufferedRequestWrapper req = new BufferedRequestWrapper(new MockHttpServletRequest(), "{\"query\":\"original\"}".getBytes()); + HttpServletResponse resp = mock(HttpServletResponse.class); + FilterChain chain = mock(FilterChain.class); + + new BodyMutationFilter(new ObjectMapper()).doFilter(req, resp, chain); + + verify(chain).doFilter(req, resp); + assertThat(new String(req.getBody())).isEqualTo("{\"query\":\"original\"}"); + } + + @Test + void wrapsMutatedQueryWhenOriginalBodyIsNotJson() throws Exception { + BufferedRequestWrapper req = new BufferedRequestWrapper(new MockHttpServletRequest(), "not json at all".getBytes()); + req.setAttribute(BodyMutationFilter.ATTR_MUTATED_QUERY, "{\"_topmed_consents\":[\"phs1\"]}"); + HttpServletResponse resp = mock(HttpServletResponse.class); + FilterChain chain = mock(FilterChain.class); + + new BodyMutationFilter(new ObjectMapper()).doFilter(req, resp, chain); + + verify(chain).doFilter(req, resp); + String newBody = new String(req.getBody()); + assertThat(newBody).contains("_topmed_consents").contains("\"query\":"); + } + + @Test + void storesNonJsonMutatedQueryAsTextNode() throws Exception { + BufferedRequestWrapper req = + new BufferedRequestWrapper(new MockHttpServletRequest(), "{\"query\":\"original\",\"resourceUUID\":\"r-1\"}".getBytes()); + req.setAttribute(BodyMutationFilter.ATTR_MUTATED_QUERY, "not json at all"); + HttpServletResponse resp = mock(HttpServletResponse.class); + FilterChain chain = mock(FilterChain.class); + + new BodyMutationFilter(new ObjectMapper()).doFilter(req, resp, chain); + + verify(chain).doFilter(req, resp); + String newBody = new String(req.getBody()); + assertThat(newBody).isEqualTo("{\"query\":\"not json at all\",\"resourceUUID\":\"r-1\"}"); + } + + @Test + void wrapsMutatedQueryWhenOriginalBodyIsEmpty() throws Exception { + BufferedRequestWrapper req = new BufferedRequestWrapper(new MockHttpServletRequest(), new byte[0]); + req.setAttribute(BodyMutationFilter.ATTR_MUTATED_QUERY, "{\"_topmed_consents\":[\"phs1\"]}"); + HttpServletResponse resp = mock(HttpServletResponse.class); + FilterChain chain = mock(FilterChain.class); + + new BodyMutationFilter(new ObjectMapper()).doFilter(req, resp, chain); + + verify(chain).doFilter(req, resp); + String newBody = new String(req.getBody()); + assertThat(newBody).isEqualTo("{\"query\":{\"_topmed_consents\":[\"phs1\"]}}"); + } + + @Test + void failsClosedAndSkipsChainWhenMutationRequiredButBuildingBodyThrows() throws Exception { + // Force the guarded failure inside mergeQueryIntoBody: writeValueAsBytes is the only call in that + // method not already wrapped in a try/catch that swallows IOException, so spying on it lets us + // simulate a future fallible step throwing without changing production code. + ObjectMapper mapper = spy(new ObjectMapper()); + doThrow(new JsonProcessingException("boom") {}).when(mapper).writeValueAsBytes(any()); + + BufferedRequestWrapper req = new BufferedRequestWrapper(new MockHttpServletRequest(), "{\"query\":\"original\"}".getBytes()); + req.setAttribute(BodyMutationFilter.ATTR_MUTATED_QUERY, "{\"_topmed_consents\":[\"phs1\"]}"); + MockHttpServletResponse resp = new MockHttpServletResponse(); + FilterChain chain = mock(FilterChain.class); + + new BodyMutationFilter(mapper).doFilter(req, resp, chain); + + verify(chain, never()).doFilter(any(), any()); + assertThat(resp.getStatus()).isEqualTo(500); + assertThat(resp.getContentAsString()).contains("body_mutation_failed"); + // The original, un-swapped body must never be forwarded. + assertThat(new String(req.getBody())).isEqualTo("{\"query\":\"original\"}"); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/BufferingFilterTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/BufferingFilterTest.java new file mode 100644 index 000000000..ac55bc031 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/BufferingFilterTest.java @@ -0,0 +1,87 @@ +package edu.harvard.hms.dbmi.avillach.gateway.filter; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.mockito.Mockito.any; +import static org.mockito.Mockito.eq; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.never; +import static org.mockito.Mockito.verify; +import static org.mockito.Mockito.when; + +import java.io.ByteArrayInputStream; + +import org.junit.jupiter.api.Test; +import org.mockito.ArgumentCaptor; +import org.springframework.mock.web.MockHttpServletResponse; + +import edu.harvard.hms.dbmi.avillach.gateway.auth.BufferedRequestWrapper; +import io.micrometer.core.instrument.simple.SimpleMeterRegistry; +import jakarta.servlet.FilterChain; +import jakarta.servlet.ReadListener; +import jakarta.servlet.ServletInputStream; +import jakarta.servlet.ServletRequest; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +class BufferingFilterTest { + + private static ServletInputStream stream(String s) { + ByteArrayInputStream bais = new ByteArrayInputStream(s.getBytes()); + return new ServletInputStream() { + @Override + public int read() { + return bais.read(); + } + + @Override + public boolean isFinished() { + return bais.available() == 0; + } + + @Override + public boolean isReady() { + return true; + } + + @Override + public void setReadListener(ReadListener l) {} + }; + } + + @Test + void wrapsRequestSoBodyCanBeReadTwice() throws Exception { + HttpServletRequest req = mock(HttpServletRequest.class); + HttpServletResponse resp = mock(HttpServletResponse.class); + FilterChain chain = mock(FilterChain.class); + when(req.getRequestURI()).thenReturn("/query"); + when(req.getInputStream()).thenReturn(stream("hello")); + when(req.getContentLengthLong()).thenReturn(5L); + + new BufferingFilter(64 * 1024, new SimpleMeterRegistry()).doFilter(req, resp, chain); + + ArgumentCaptor captor = ArgumentCaptor.forClass(ServletRequest.class); + verify(chain).doFilter(captor.capture(), eq(resp)); + BufferedRequestWrapper wrapped = (BufferedRequestWrapper) captor.getValue(); + assertThat(new String(wrapped.getBody())).isEqualTo("hello"); + } + + @Test + void overCapReturns413WithErrorBodyBeforeChainAndIncrementsMetric() throws Exception { + SimpleMeterRegistry metrics = new SimpleMeterRegistry(); + BufferingFilter f = new BufferingFilter(8, metrics); // tiny cap + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getRequestURI()).thenReturn("/query"); + when(req.getContentLengthLong()).thenReturn(100L); + when(req.getInputStream()).thenReturn(stream("this body is well over the tiny cap")); + MockHttpServletResponse resp = new MockHttpServletResponse(); + FilterChain chain = mock(FilterChain.class); + + f.doFilter(req, resp, chain); + + assertThat(resp.getStatus()).isEqualTo(413); + assertThat(resp.getContentAsString()).contains("\"errorType\":\"REQUEST_BODY_TOO_LARGE\"") + .contains("Request body exceeds the maximum size allowed for authorization processing."); + verify(chain, never()).doFilter(any(), any()); // PSAMA never reached + assertThat(metrics.counter("gateway.auth.body_too_large").count()).isEqualTo(1.0); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/IdentityPropagationFilterTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/IdentityPropagationFilterTest.java new file mode 100644 index 000000000..396989aca --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/IdentityPropagationFilterTest.java @@ -0,0 +1,174 @@ +package edu.harvard.hms.dbmi.avillach.gateway.filter; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.mockito.Mockito.eq; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.verify; +import static org.mockito.Mockito.when; + +import java.util.Collections; +import java.util.List; + +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.Test; +import org.mockito.ArgumentCaptor; +import org.slf4j.MDC; + +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import edu.harvard.hms.dbmi.avillach.commons.request.RequestIdFilter; +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletRequest; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +class IdentityPropagationFilterTest { + + @AfterEach + void clearMdc() { + MDC.clear(); + } + + @Test + void copiesAttributesToHeadersIncludingPrivilegesAndRequestId() throws Exception { + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getAttribute(GatewayUserResolver.HEADER_USER_ID)).thenReturn("u-1"); + when(req.getAttribute(GatewayUserResolver.HEADER_USER_EMAIL)).thenReturn("a@b"); + when(req.getAttribute(GatewayUserResolver.HEADER_USER_PRIVILEGES)).thenReturn("SUPER_ADMIN"); + when(req.getHeader("X-Request-Id")).thenReturn("req-42"); + when(req.getHeaderNames()).thenReturn(Collections.emptyEnumeration()); + + HttpServletResponse resp = mock(HttpServletResponse.class); + FilterChain chain = mock(FilterChain.class); + new IdentityPropagationFilter().doFilter(req, resp, chain); + + ArgumentCaptor cap = ArgumentCaptor.forClass(ServletRequest.class); + verify(chain).doFilter(cap.capture(), eq(resp)); + HttpServletRequest wrapped = (HttpServletRequest) cap.getValue(); + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_ID)).isEqualTo("u-1"); + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_PRIVILEGES)).isEqualTo("SUPER_ADMIN"); + assertThat(wrapped.getHeader("X-Request-Id")).isEqualTo("req-42"); + } + + @Test + void generatesRequestIdWhenAbsent() throws Exception { + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getHeaderNames()).thenReturn(Collections.emptyEnumeration()); + HttpServletResponse resp = mock(HttpServletResponse.class); + FilterChain chain = mock(FilterChain.class); + new IdentityPropagationFilter().doFilter(req, resp, chain); + + ArgumentCaptor cap = ArgumentCaptor.forClass(ServletRequest.class); + verify(chain).doFilter(cap.capture(), eq(resp)); + assertThat(((HttpServletRequest) cap.getValue()).getHeader("X-Request-Id")).isNotBlank(); + } + + // ---- FIX 1: gateway-owned X-User-* headers must never fall through to a client-supplied value ---- + + @Test + void clientSpoofedPrivilegesAreNotVisibleWhenGatewayResolvedNone() throws Exception { + // Gateway resolved a user id but no privileges (e.g. a user with an empty privilege set); the client tries to + // inject its own elevated privileges via the raw request header. + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getAttribute(GatewayUserResolver.HEADER_USER_ID)).thenReturn("u-1"); + when(req.getHeader(GatewayUserResolver.HEADER_USER_PRIVILEGES)).thenReturn("SYSTEM,ADMIN"); + when(req.getHeaders(GatewayUserResolver.HEADER_USER_PRIVILEGES)).thenReturn(Collections.enumeration(List.of("SYSTEM,ADMIN"))); + when(req.getHeaderNames()).thenReturn(Collections.enumeration(List.of(GatewayUserResolver.HEADER_USER_PRIVILEGES))); + + HttpServletResponse resp = mock(HttpServletResponse.class); + FilterChain chain = mock(FilterChain.class); + new IdentityPropagationFilter().doFilter(req, resp, chain); + + ArgumentCaptor cap = ArgumentCaptor.forClass(ServletRequest.class); + verify(chain).doFilter(cap.capture(), eq(resp)); + HttpServletRequest wrapped = (HttpServletRequest) cap.getValue(); + + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_PRIVILEGES)).isNull(); + assertThat(wrapped.getHeaders(GatewayUserResolver.HEADER_USER_PRIVILEGES).hasMoreElements()).isFalse(); + assertThat(Collections.list(wrapped.getHeaderNames())).doesNotContain(GatewayUserResolver.HEADER_USER_PRIVILEGES); + } + + @Test + void openAccessRequestStripsClientSuppliedRolesSubjectAndEmail() throws Exception { + // Open-access path: only X-User-Id is resolved by the gateway. The client sends its own Roles/Subject/Email + // trying to impersonate an authenticated, privileged user. + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getAttribute(GatewayUserResolver.HEADER_USER_ID)).thenReturn("open-access"); + when(req.getHeader(GatewayUserResolver.HEADER_USER_ROLES)).thenReturn("ADMIN"); + when(req.getHeader(GatewayUserResolver.HEADER_USER_SUBJECT)).thenReturn("spoofed-subject"); + when(req.getHeader(GatewayUserResolver.HEADER_USER_EMAIL)).thenReturn("spoofed@example.com"); + when(req.getHeaderNames()).thenReturn( + Collections.enumeration( + List.of( + GatewayUserResolver.HEADER_USER_ROLES, GatewayUserResolver.HEADER_USER_SUBJECT, GatewayUserResolver.HEADER_USER_EMAIL + ) + ) + ); + + HttpServletResponse resp = mock(HttpServletResponse.class); + FilterChain chain = mock(FilterChain.class); + new IdentityPropagationFilter().doFilter(req, resp, chain); + + ArgumentCaptor cap = ArgumentCaptor.forClass(ServletRequest.class); + verify(chain).doFilter(cap.capture(), eq(resp)); + HttpServletRequest wrapped = (HttpServletRequest) cap.getValue(); + + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_ID)).isEqualTo("open-access"); + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_ROLES)).isNull(); + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_SUBJECT)).isNull(); + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_EMAIL)).isNull(); + List names = Collections.list(wrapped.getHeaderNames()); + assertThat(names).doesNotContain( + GatewayUserResolver.HEADER_USER_ROLES, GatewayUserResolver.HEADER_USER_SUBJECT, GatewayUserResolver.HEADER_USER_EMAIL + ); + } + + @Test + void gatewayResolvedIdentityHeadersStillPropagateNormally() throws Exception { + // Sanity check: when the gateway *does* resolve all five headers, they still flow through -- FIX 1 must not + // break the normal authenticated path. + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getAttribute(GatewayUserResolver.HEADER_USER_ID)).thenReturn("u-1"); + when(req.getAttribute(GatewayUserResolver.HEADER_USER_SUBJECT)).thenReturn("sub-1"); + when(req.getAttribute(GatewayUserResolver.HEADER_USER_EMAIL)).thenReturn("a@b"); + when(req.getAttribute(GatewayUserResolver.HEADER_USER_ROLES)).thenReturn("USER"); + when(req.getAttribute(GatewayUserResolver.HEADER_USER_PRIVILEGES)).thenReturn("VIEW_DATA"); + when(req.getHeaderNames()).thenReturn(Collections.emptyEnumeration()); + + HttpServletResponse resp = mock(HttpServletResponse.class); + FilterChain chain = mock(FilterChain.class); + new IdentityPropagationFilter().doFilter(req, resp, chain); + + ArgumentCaptor cap = ArgumentCaptor.forClass(ServletRequest.class); + verify(chain).doFilter(cap.capture(), eq(resp)); + HttpServletRequest wrapped = (HttpServletRequest) cap.getValue(); + + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_ID)).isEqualTo("u-1"); + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_SUBJECT)).isEqualTo("sub-1"); + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_EMAIL)).isEqualTo("a@b"); + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_ROLES)).isEqualTo("USER"); + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_PRIVILEGES)).isEqualTo("VIEW_DATA"); + List names = Collections.list(wrapped.getHeaderNames()); + assertThat(names).contains( + GatewayUserResolver.HEADER_USER_ID, GatewayUserResolver.HEADER_USER_SUBJECT, GatewayUserResolver.HEADER_USER_EMAIL, + GatewayUserResolver.HEADER_USER_ROLES, GatewayUserResolver.HEADER_USER_PRIVILEGES + ); + } + + // ---- FIX 3: request-id correlation must unify with the commons RequestIdFilter's MDC value ---- + + @Test + void reusesMdcRequestIdWhenNoInboundHeaderPresent() throws Exception { + // Simulates the commons RequestIdFilter (highest precedence, runs earlier) having already generated an id + // and bound it to MDC, without an inbound X-Request-Id header on the raw client request. + MDC.put(RequestIdFilter.MDC_KEY, "rid-1"); + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getHeaderNames()).thenReturn(Collections.emptyEnumeration()); + HttpServletResponse resp = mock(HttpServletResponse.class); + FilterChain chain = mock(FilterChain.class); + new IdentityPropagationFilter().doFilter(req, resp, chain); + + ArgumentCaptor cap = ArgumentCaptor.forClass(ServletRequest.class); + verify(chain).doFilter(cap.capture(), eq(resp)); + assertThat(((HttpServletRequest) cap.getValue()).getHeader("X-Request-Id")).isEqualTo("rid-1"); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/OpenAccessFilterTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/OpenAccessFilterTest.java new file mode 100644 index 000000000..ff730d622 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/OpenAccessFilterTest.java @@ -0,0 +1,105 @@ +package edu.harvard.hms.dbmi.avillach.gateway.filter; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.Mockito.eq; +import static org.mockito.Mockito.lenient; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.never; +import static org.mockito.Mockito.verify; +import static org.mockito.Mockito.verifyNoInteractions; +import static org.mockito.Mockito.when; + +import java.io.PrintWriter; +import java.io.StringWriter; +import java.util.HashMap; +import java.util.Map; + +import org.junit.jupiter.api.Test; +import org.mockito.ArgumentCaptor; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import edu.harvard.hms.dbmi.avillach.commons.audit.AuditContext; +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import edu.harvard.hms.dbmi.avillach.gateway.auth.BufferedRequestWrapper; +import edu.harvard.hms.dbmi.avillach.gateway.auth.PsamaClient; +import jakarta.servlet.FilterChain; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +class OpenAccessFilterTest { + + private OpenAccessFilter filter(PsamaClient client, AuditContext ctx, boolean enabled) { + return new OpenAccessFilter(client, ctx, new ObjectMapper(), enabled); + } + + @Test + void enabledOpenAccessWithRealBearerPassesThroughToIntrospection() throws Exception { + PsamaClient client = mock(PsamaClient.class); + OpenAccessFilter f = filter(client, new AuditContext(), true); + BufferedRequestWrapper req = wrap("Bearer real-token"); + FilterChain chain = mock(FilterChain.class); + f.doFilter(req, mock(HttpServletResponse.class), chain); + verify(chain).doFilter(eq(req), any()); + verifyNoInteractions(client); + } + + @Test + void enabledOpenAccessNoBearerSendsRealPathShapeAndGrants() throws Exception { + PsamaClient client = mock(PsamaClient.class); + when(client.validateOpenAccess(any())).thenReturn(true); + AuditContext ctx = new AuditContext(); + OpenAccessFilter f = filter(client, ctx, true); + + BufferedRequestWrapper req = wrap(null); // URI is /v3/search/abc + f.doFilter(req, mock(HttpServletResponse.class), mock(FilterChain.class)); + + assertThat(req.getAttribute(GatewayUserResolver.HEADER_USER_ID).toString()).startsWith("OPEN_ACCESS:"); + assertThat(ctx.getMetadata()).containsEntry("auth_action", "open_access.granted"); + + ArgumentCaptor> cap = ArgumentCaptor.forClass(Map.class); + verify(client).validateOpenAccess(cap.capture()); + Map body = cap.getValue(); + assertThat(body).doesNotContainKey("token"); + assertThat(body.get("ipAddress").toString()).startsWith("OPEN_ACCESS:"); + @SuppressWarnings("unchecked") + Map request = (Map) body.get("request"); + assertThat(request.get("Target Service")).isEqualTo("/v3/search/abc"); // real path verbatim + } + + @Test + void enabledOpenAccessFalseValidationReturns401() throws Exception { + PsamaClient client = mock(PsamaClient.class); + when(client.validateOpenAccess(any())).thenReturn(false); + AuditContext ctx = new AuditContext(); + OpenAccessFilter f = filter(client, ctx, true); + + HttpServletResponse resp = mock(HttpServletResponse.class); + lenient().when(resp.getWriter()).thenReturn(new PrintWriter(new StringWriter())); + FilterChain chain = mock(FilterChain.class); + f.doFilter(wrap(null), resp, chain); + + verify(resp).setStatus(401); + verify(chain, never()).doFilter(any(), any()); + assertThat(ctx.getMetadata()).containsEntry("auth_action", "open_access.denied"); + } + + private static BufferedRequestWrapper wrap(String authHeader) { + HttpServletRequest base = mock(HttpServletRequest.class); + when(base.getRequestURI()).thenReturn("/v3/search/abc"); + lenient().when(base.getMethod()).thenReturn("POST"); + if (authHeader != null) when(base.getHeader("Authorization")).thenReturn(authHeader); + lenient().when(base.getServerName()).thenReturn("aio.local"); + // Bare Mockito mocks don't retain state across calls; BufferedRequestWrapper delegates + // setAttribute/getAttribute to the wrapped request (HttpServletRequestWrapper default), so back + // them with a real map here to exercise that delegation faithfully. + Map attributes = new HashMap<>(); + lenient().doAnswer(inv -> { + attributes.put(inv.getArgument(0), inv.getArgument(1)); + return null; + }).when(base).setAttribute(any(), any()); + lenient().when(base.getAttribute(any())).thenAnswer(inv -> attributes.get(inv.getArgument(0))); + return new BufferedRequestWrapper(base, new byte[0]); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/PsamaIntrospectionFilterTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/PsamaIntrospectionFilterTest.java new file mode 100644 index 000000000..f91ee9094 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/PsamaIntrospectionFilterTest.java @@ -0,0 +1,366 @@ +package edu.harvard.hms.dbmi.avillach.gateway.filter; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.ArgumentMatchers.eq; +import static org.mockito.Mockito.lenient; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.never; +import static org.mockito.Mockito.verify; +import static org.mockito.Mockito.verifyNoInteractions; +import static org.mockito.Mockito.when; + +import java.io.PrintWriter; +import java.io.StringWriter; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Optional; + +import org.junit.jupiter.api.Test; +import org.mockito.ArgumentCaptor; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import edu.harvard.hms.dbmi.avillach.commons.audit.AuditContext; +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import edu.harvard.hms.dbmi.avillach.gateway.auth.BufferedRequestWrapper; +import edu.harvard.hms.dbmi.avillach.gateway.auth.IntrospectionResponse; +import edu.harvard.hms.dbmi.avillach.gateway.auth.PsamaClient; +import edu.harvard.hms.dbmi.avillach.gateway.auth.QueryAuthFetcher; +import jakarta.servlet.FilterChain; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +class PsamaIntrospectionFilterTest { + + private PsamaIntrospectionFilter filter(PsamaClient client, AuditContext ctx, QueryAuthFetcher fetcher) { + return new PsamaIntrospectionFilter( + client, ctx, new ObjectMapper(), fetcher, List.of("/actuator", "/openapi", "/swagger-ui", "/logging"), "userId" + ); + } + + @Test + void rejectsMissingAuthorizationHeader() throws Exception { + PsamaClient client = mock(PsamaClient.class); + QueryAuthFetcher fetcher = mock(QueryAuthFetcher.class); + AuditContext ctx = new AuditContext(); + PsamaIntrospectionFilter f = filter(client, ctx, fetcher); + + BufferedRequestWrapper req = wrap(null, new byte[0], "/query"); + HttpServletResponse resp = mock(HttpServletResponse.class); + lenient().when(resp.getWriter()).thenReturn(new PrintWriter(new StringWriter())); + FilterChain chain = mock(FilterChain.class); + + f.doFilter(req, resp, chain); + + verify(resp).setStatus(401); + verify(chain, never()).doFilter(any(), any()); + assertThat(ctx.getMetadata()).containsEntry("auth_failure_reason", "missing_token"); + } + + @Test + void onActiveTokenStoresClaimsIncludingPrivilegesAndForwards() throws Exception { + PsamaClient client = mock(PsamaClient.class); + QueryAuthFetcher fetcher = mock(QueryAuthFetcher.class); + when(fetcher.queryJsonForPath(any())).thenReturn(Optional.empty()); + when(client.introspect(eq("user-token"), any())).thenReturn( + new IntrospectionResponse(true, "u-1", "s-1", "alice@example.com", "ADMIN", List.of("SUPER_ADMIN"), false, null, null) + ); + AuditContext ctx = new AuditContext(); + PsamaIntrospectionFilter f = filter(client, ctx, fetcher); + + BufferedRequestWrapper req = wrap("Bearer user-token", "{}".getBytes(), "/query"); + HttpServletResponse resp = mock(HttpServletResponse.class); + lenient().when(resp.getWriter()).thenReturn(new PrintWriter(new StringWriter())); + FilterChain chain = mock(FilterChain.class); + f.doFilter(req, resp, chain); + + assertThat(req.getAttribute(GatewayUserResolver.HEADER_USER_ID)).isEqualTo("u-1"); + assertThat(req.getAttribute(GatewayUserResolver.HEADER_USER_EMAIL)).isEqualTo("alice@example.com"); + assertThat(req.getAttribute(GatewayUserResolver.HEADER_USER_PRIVILEGES)).isEqualTo("SUPER_ADMIN"); + assertThat(ctx.getMetadata()).containsEntry("auth_result", "success"); + verify(chain).doFilter(req, resp); + } + + @Test + void onActiveTokenWithMultiplePrivilegesJoinsThemWithComma() throws Exception { + PsamaClient client = mock(PsamaClient.class); + QueryAuthFetcher fetcher = mock(QueryAuthFetcher.class); + when(fetcher.queryJsonForPath(any())).thenReturn(Optional.empty()); + when(client.introspect(eq("user-token"), any())).thenReturn( + new IntrospectionResponse( + true, "u-1", "s-1", "alice@example.com", "ADMIN", List.of("SUPER_ADMIN", "DATA_ADMIN", "USER"), false, null, null + ) + ); + AuditContext ctx = new AuditContext(); + PsamaIntrospectionFilter f = filter(client, ctx, fetcher); + + BufferedRequestWrapper req = wrap("Bearer user-token", "{}".getBytes(), "/query"); + HttpServletResponse resp = mock(HttpServletResponse.class); + lenient().when(resp.getWriter()).thenReturn(new PrintWriter(new StringWriter())); + FilterChain chain = mock(FilterChain.class); + f.doFilter(req, resp, chain); + + assertThat(req.getAttribute(GatewayUserResolver.HEADER_USER_PRIVILEGES)).isEqualTo("SUPER_ADMIN,DATA_ADMIN,USER"); + verify(chain).doFilter(req, resp); + } + + @Test + void sendsRealPathAsTargetServiceAndStripsResourceCredentials() throws Exception { + PsamaClient client = mock(PsamaClient.class); + QueryAuthFetcher fetcher = mock(QueryAuthFetcher.class); + when(fetcher.queryJsonForPath(any())).thenReturn(Optional.empty()); + when(client.introspect(eq("user-token"), any())) + .thenReturn(new IntrospectionResponse(true, "u-1", "s-1", "a@b", "ADMIN", List.of(), false, null, null)); + PsamaIntrospectionFilter f = filter(client, new AuditContext(), fetcher); + + byte[] body = "{\"resourceCredentials\":{\"BEARER_TOKEN\":\"secret\"},\"query\":{\"a\":1}}".getBytes(); + // real path is sent verbatim: no /v3 rewriting, no canonical mapping + BufferedRequestWrapper req = wrap("Bearer user-token", body, "/v3/query"); + HttpServletResponse resp = mock(HttpServletResponse.class); + lenient().when(resp.getWriter()).thenReturn(new PrintWriter(new StringWriter())); + f.doFilter(req, resp, mock(FilterChain.class)); + + @SuppressWarnings("unchecked") + ArgumentCaptor> meta = ArgumentCaptor.forClass(Map.class); + verify(client).introspect(eq("user-token"), meta.capture()); + assertThat(meta.getValue().get("Target Service")).isEqualTo("/v3/query"); + assertThat(meta.getValue().toString()).doesNotContain("resourceCredentials"); + assertThat(meta.getValue().toString()).doesNotContain("formattedQuery"); + } + + @Test + void malformedJsonBodyOmitsQueryAndDoesNotLeakSecrets() throws Exception { + PsamaClient client = mock(PsamaClient.class); + QueryAuthFetcher fetcher = mock(QueryAuthFetcher.class); + when(fetcher.queryJsonForPath(any())).thenReturn(Optional.empty()); + when(client.introspect(eq("user-token"), any())) + .thenReturn(new IntrospectionResponse(true, "u-1", "s-1", "a@b", "ADMIN", List.of(), false, null, null)); + PsamaIntrospectionFilter f = filter(client, new AuditContext(), fetcher); + + // Truncated/invalid JSON that still textually contains a resourceCredentials secret. + byte[] malformed = "{\"resourceCredentials\":{\"BEARER_TOKEN\":\"super-secret-value\"".getBytes(); + BufferedRequestWrapper req = wrap("Bearer user-token", malformed, "/query"); + HttpServletResponse resp = mock(HttpServletResponse.class); + lenient().when(resp.getWriter()).thenReturn(new PrintWriter(new StringWriter())); + f.doFilter(req, resp, mock(FilterChain.class)); + + @SuppressWarnings("unchecked") + ArgumentCaptor> meta = ArgumentCaptor.forClass(Map.class); + verify(client).introspect(eq("user-token"), meta.capture()); + assertThat(meta.getValue()).doesNotContainKey("query"); + assertThat(meta.getValue().toString()).doesNotContain("super-secret-value"); + } + + @Test + void invalidTokenReturns401() throws Exception { + PsamaClient client = mock(PsamaClient.class); + QueryAuthFetcher fetcher = mock(QueryAuthFetcher.class); + when(fetcher.queryJsonForPath(any())).thenReturn(Optional.empty()); + when(client.introspect(any(), any())).thenReturn(new IntrospectionResponse(false, null, null, null, null, null, null, null, null)); + PsamaIntrospectionFilter f = filter(client, new AuditContext(), fetcher); + + BufferedRequestWrapper req = wrap("Bearer user-token", "{}".getBytes(), "/query"); + HttpServletResponse resp = mock(HttpServletResponse.class); + lenient().when(resp.getWriter()).thenReturn(new PrintWriter(new StringWriter())); + FilterChain chain = mock(FilterChain.class); + f.doFilter(req, resp, chain); + + verify(resp).setStatus(401); + verify(chain, never()).doFilter(any(), any()); + } + + @Test + void stashesRefreshedTokenAndMutatedQueryAttributes() throws Exception { + PsamaClient client = mock(PsamaClient.class); + QueryAuthFetcher fetcher = mock(QueryAuthFetcher.class); + when(fetcher.queryJsonForPath(any())).thenReturn(Optional.empty()); + when(client.introspect(any(), any())) + .thenReturn(new IntrospectionResponse(true, "u-1", "s-1", "a@b", "ADMIN", List.of(), true, "new-token", "{\"new\":1}")); + PsamaIntrospectionFilter f = filter(client, new AuditContext(), fetcher); + + BufferedRequestWrapper req = wrap("Bearer user-token", "{}".getBytes(), "/query"); + HttpServletResponse resp = mock(HttpServletResponse.class); + lenient().when(resp.getWriter()).thenReturn(new PrintWriter(new StringWriter())); + f.doFilter(req, resp, mock(FilterChain.class)); + + assertThat(req.getAttribute(PsamaIntrospectionFilter.ATTR_REFRESHED_TOKEN)).isEqualTo("new-token"); + assertThat(req.getAttribute(BodyMutationFilter.ATTR_MUTATED_QUERY)).isEqualTo("{\"new\":1}"); + } + + @Test + void systemStatusGetIsAllowListedAsSystemMonitor() throws Exception { + PsamaClient client = mock(PsamaClient.class); + AuditContext ctx = new AuditContext(); + PsamaIntrospectionFilter f = filter(client, ctx, mock(QueryAuthFetcher.class)); + + BufferedRequestWrapper req = wrap(null, new byte[0], "/system/status", "GET"); + FilterChain chain = mock(FilterChain.class); + f.doFilter(req, mock(HttpServletResponse.class), chain); + + verifyNoInteractions(client); + verify(chain).doFilter(eq(req), any()); + assertThat(ctx.getMetadata()).containsEntry("username", "SYSTEM_MONITOR"); + } + + @Test + void prefixAllowListSkipsIntrospection() throws Exception { + PsamaClient client = mock(PsamaClient.class); + PsamaIntrospectionFilter f = filter(client, new AuditContext(), mock(QueryAuthFetcher.class)); + + BufferedRequestWrapper req = wrap(null, new byte[0], "/logging/event"); + FilterChain chain = mock(FilterChain.class); + f.doFilter(req, mock(HttpServletResponse.class), chain); + + verifyNoInteractions(client); + verify(chain).doFilter(eq(req), any()); + } + + @Test + void nestedSystemStatusPathIsNotAllowListed() throws Exception { + PsamaClient client = mock(PsamaClient.class); + AuditContext ctx = new AuditContext(); + PsamaIntrospectionFilter f = filter(client, ctx, mock(QueryAuthFetcher.class)); + + BufferedRequestWrapper req = wrap(null, new byte[0], "/foo/system/status", "GET"); + HttpServletResponse resp = mock(HttpServletResponse.class); + lenient().when(resp.getWriter()).thenReturn(new PrintWriter(new StringWriter())); + FilterChain chain = mock(FilterChain.class); + f.doFilter(req, resp, chain); + + verifyNoInteractions(client); + verify(chain, never()).doFilter(any(), any()); + verify(resp).setStatus(401); + assertThat(ctx.getMetadata()).doesNotContainEntry("username", "SYSTEM_MONITOR"); + } + + @Test + void prefixAllowListDoesNotMatchSiblingPathWithSamePrefixText() throws Exception { + PsamaClient client = mock(PsamaClient.class); + PsamaIntrospectionFilter f = filter(client, new AuditContext(), mock(QueryAuthFetcher.class)); + + // Allow-listed prefix is "/logging"; "/loggingAdmin/x" must NOT match it. + BufferedRequestWrapper req = wrap(null, new byte[0], "/loggingAdmin/x"); + HttpServletResponse resp = mock(HttpServletResponse.class); + lenient().when(resp.getWriter()).thenReturn(new PrintWriter(new StringWriter())); + FilterChain chain = mock(FilterChain.class); + f.doFilter(req, resp, chain); + + verifyNoInteractions(client); + verify(chain, never()).doFilter(any(), any()); + verify(resp).setStatus(401); + } + + @Test + void publicConfigurationRootGetIsNotIntrospected() throws Exception { + PsamaIntrospectionFilter f = filter(mock(PsamaClient.class), new AuditContext(), mock(QueryAuthFetcher.class)); + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getRequestURI()).thenReturn("/operations/configuration/"); + when(req.getMethod()).thenReturn("GET"); + assertThat(f.shouldNotFilter(req)).isTrue(); + } + + @Test + void publicConfigurationRootGetWithoutTrailingSlashIsNotIntrospected() throws Exception { + // The slash-less form is what the controller actually serves (Spring 6 has no lenient slash matching). + PsamaIntrospectionFilter f = filter(mock(PsamaClient.class), new AuditContext(), mock(QueryAuthFetcher.class)); + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getRequestURI()).thenReturn("/operations/configuration"); + when(req.getMethod()).thenReturn("GET"); + assertThat(f.shouldNotFilter(req)).isTrue(); + } + + @Test + void publicConfigurationIdReadGetIsNotIntrospected() throws Exception { + PsamaIntrospectionFilter f = filter(mock(PsamaClient.class), new AuditContext(), mock(QueryAuthFetcher.class)); + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getRequestURI()).thenReturn("/operations/configuration/3f2c8e1a-uuid/"); + when(req.getMethod()).thenReturn("GET"); + assertThat(f.shouldNotFilter(req)).isTrue(); + } + + @Test + void publicConfigurationIdReadGetWithoutTrailingSlashIsNotIntrospected() throws Exception { + PsamaIntrospectionFilter f = filter(mock(PsamaClient.class), new AuditContext(), mock(QueryAuthFetcher.class)); + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getRequestURI()).thenReturn("/operations/configuration/3f2c8e1a-uuid"); + when(req.getMethod()).thenReturn("GET"); + assertThat(f.shouldNotFilter(req)).isTrue(); + } + + @Test + void configurationAdminGetIsIntrospected() throws Exception { + PsamaIntrospectionFilter f = filter(mock(PsamaClient.class), new AuditContext(), mock(QueryAuthFetcher.class)); + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getRequestURI()).thenReturn("/operations/configuration/admin/x"); + when(req.getMethod()).thenReturn("GET"); + assertThat(f.shouldNotFilter(req)).isFalse(); + } + + @Test + void configurationAdminRootGetIsIntrospected() throws Exception { + PsamaIntrospectionFilter f = filter(mock(PsamaClient.class), new AuditContext(), mock(QueryAuthFetcher.class)); + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getRequestURI()).thenReturn("/operations/configuration/admin"); + when(req.getMethod()).thenReturn("GET"); + assertThat(f.shouldNotFilter(req)).isFalse(); + } + + @Test + void configurationAdminPostIsIntrospected() throws Exception { + PsamaIntrospectionFilter f = filter(mock(PsamaClient.class), new AuditContext(), mock(QueryAuthFetcher.class)); + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getRequestURI()).thenReturn("/operations/configuration/admin/x"); + when(req.getMethod()).thenReturn("POST"); + assertThat(f.shouldNotFilter(req)).isFalse(); + } + + @Test + void configurationRootPostIsIntrospected() throws Exception { + PsamaIntrospectionFilter f = filter(mock(PsamaClient.class), new AuditContext(), mock(QueryAuthFetcher.class)); + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getRequestURI()).thenReturn("/operations/configuration/"); + when(req.getMethod()).thenReturn("POST"); + assertThat(f.shouldNotFilter(req)).isFalse(); + } + + @Test + void configurationIdReadPostIsIntrospected() throws Exception { + PsamaIntrospectionFilter f = filter(mock(PsamaClient.class), new AuditContext(), mock(QueryAuthFetcher.class)); + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getRequestURI()).thenReturn("/operations/configuration/abc-123/"); + when(req.getMethod()).thenReturn("POST"); + assertThat(f.shouldNotFilter(req)).isFalse(); + } + + @Test + void datasetPathIsIntrospected() throws Exception { + PsamaIntrospectionFilter f = filter(mock(PsamaClient.class), new AuditContext(), mock(QueryAuthFetcher.class)); + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getRequestURI()).thenReturn("/operations/dataset/named/abc-123"); + when(req.getMethod()).thenReturn("GET"); + assertThat(f.shouldNotFilter(req)).isFalse(); + } + + private static BufferedRequestWrapper wrap(String authHeader, byte[] body, String uri) { + return wrap(authHeader, body, uri, "POST"); + } + + private static BufferedRequestWrapper wrap(String authHeader, byte[] body, String uri, String method) { + HttpServletRequest base = mock(HttpServletRequest.class); + if (authHeader != null) when(base.getHeader("Authorization")).thenReturn(authHeader); + when(base.getRequestURI()).thenReturn(uri); + lenient().when(base.getMethod()).thenReturn(method); + // Bare Mockito mocks don't retain state across calls; BufferedRequestWrapper delegates + // setAttribute/getAttribute to the wrapped request (HttpServletRequestWrapper default), so back + // them with a real map here to exercise that delegation faithfully. + Map attributes = new HashMap<>(); + lenient().doAnswer(inv -> { + attributes.put(inv.getArgument(0), inv.getArgument(1)); + return null; + }).when(base).setAttribute(any(), any()); + lenient().when(base.getAttribute(any())).thenAnswer(inv -> attributes.get(inv.getArgument(0))); + return new BufferedRequestWrapper(base, body); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/TokenRefreshResponseFilterTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/TokenRefreshResponseFilterTest.java new file mode 100644 index 000000000..ae2fd6484 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/filter/TokenRefreshResponseFilterTest.java @@ -0,0 +1,33 @@ +package edu.harvard.hms.dbmi.avillach.gateway.filter; + +import jakarta.servlet.FilterChain; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; +import org.junit.jupiter.api.Test; + +import static org.mockito.Mockito.*; + +class TokenRefreshResponseFilterTest { + + @Test + void copiesRefreshedTokenToAuthorizationHeaderAsBearer() throws Exception { + HttpServletRequest req = mock(HttpServletRequest.class); + HttpServletResponse resp = mock(HttpServletResponse.class); + FilterChain chain = mock(FilterChain.class); + when(req.getAttribute(PsamaIntrospectionFilter.ATTR_REFRESHED_TOKEN)).thenReturn("new-token"); + + new TokenRefreshResponseFilter().doFilter(req, resp, chain); + + verify(chain).doFilter(req, resp); + verify(resp).setHeader("Authorization", "Bearer new-token"); + } + + @Test + void noHeaderWhenNoRefresh() throws Exception { + HttpServletRequest req = mock(HttpServletRequest.class); + HttpServletResponse resp = mock(HttpServletResponse.class); + FilterChain chain = mock(FilterChain.class); + new TokenRefreshResponseFilter().doFilter(req, resp, chain); + verify(resp, never()).setHeader(eq("Authorization"), anyString()); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/ActuatorHealthEndpointIT.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/ActuatorHealthEndpointIT.java new file mode 100644 index 000000000..7df352a42 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/ActuatorHealthEndpointIT.java @@ -0,0 +1,102 @@ +package edu.harvard.hms.dbmi.avillach.gateway.health; + +import static com.github.tomakehurst.wiremock.client.WireMock.aResponse; +import static com.github.tomakehurst.wiremock.client.WireMock.get; +import static com.github.tomakehurst.wiremock.client.WireMock.okJson; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.web.server.LocalServerPort; +import org.springframework.boot.test.context.SpringBootTest.WebEnvironment; +import org.springframework.boot.test.web.client.TestRestTemplate; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.springframework.test.context.TestPropertySource; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.github.tomakehurst.wiremock.WireMockServer; + +/** + * End-to-end: hits the real {@code GET /actuator/health} HTTP endpoint (not just the {@link DownstreamHealthContributor} bean directly, as + * {@link ActuatorHealthIT} does) and asserts the JSON composite shows the "hpds" component DOWN. Actuator is OFF BY DEFAULT (empty exposure + * in application.yml), so this test context explicitly exposes {@code health} and forces {@code show-details} to {@code always} -- + * production exposes/gates via PICSURE_ACTUATOR_EXPOSURE / PICSURE_ACTUATOR_DETAILS (see application.yml). + */ +@SpringBootTest(webEnvironment = WebEnvironment.RANDOM_PORT) +@TestPropertySource(properties = {"management.endpoints.web.exposure.include=health", "management.endpoint.health.show-details=always"}) +class ActuatorHealthEndpointIT { + + static WireMockServer hpds; + + @Autowired + private TestRestTemplate rest; + + + @LocalServerPort + int port; + + /** + * Dial the loopback ADDRESS, never the name. {@code localhost} resolves to {@code ::1} before {@code 127.0.0.1} on macOS, while these + * test servers bind the IPv4 wildcard -- so an unrelated local process holding the same port number on {@code [::]} can answer instead, + * and the test fails with a bewildering status from a server it never meant to contact. Relative {@code TestRestTemplate} URLs go + * through {@code LocalHostUriTemplateHandler}, which hardcodes the name {@code localhost}; absolute URLs bypass it entirely. + */ + private String url(String path) { + return "http://127.0.0.1:" + port + path; + } + + @BeforeAll + static void start() { + hpds = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + hpds.start(); + hpds.stubFor(get(urlEqualTo("/actuator/health")).willReturn(aResponse().withStatus(503))); + } + + @AfterAll + static void stop() { + hpds.stop(); + } + + @DynamicPropertySource + static void props(DynamicPropertyRegistry r) { + r.add("picsure.gateway.health.downstreams[0].name", () -> "hpds"); + r.add("picsure.gateway.health.downstreams[0].base-url", () -> "http://127.0.0.1:" + hpds.port()); + r.add("picsure.gateway.health.downstreams[0].require-status-up", () -> "true"); + } + + @Test + void actuatorHealthShowsDownDownstreamAsDown() throws Exception { + ResponseEntity response = rest.getForEntity(url("/actuator/health"), String.class); + + JsonNode body = new ObjectMapper().readTree(response.getBody()); + JsonNode hpdsComponent = body.path("components").path("downstreams").path("components").path("hpds"); + + assertThat(hpdsComponent.path("status").asText()).isEqualTo("DOWN"); + assertThat(body.path("status").asText()).isEqualTo("DOWN"); + } + + /** + * Pins the operational invariant this class exists to guard: {@code downstreams} is a top-level composite contributor, so a single DOWN + * sibling flips the ROOT {@code /actuator/health} to DOWN (asserted above) -- but {@code /actuator/health/liveness} is pinned via + * {@code management.endpoint.health.group.liveness.include: livenessState} (application.yml) and must stay UP regardless. Deploy + * smoke-polls and container healthchecks must probe this shallow endpoint, not the aggregate root, or a degraded/restarting downstream + * (e.g. HPDS) would fail the gateway's own healthcheck and could kill the container. + */ + @Test + void livenessStaysUpWhenDownstreamIsDown() throws Exception { + ResponseEntity response = rest.getForEntity(url("/actuator/health/liveness"), String.class); + + assertThat(response.getStatusCode().value()).isEqualTo(200); + + JsonNode body = new ObjectMapper().readTree(response.getBody()); + assertThat(body.path("status").asText()).isEqualTo("UP"); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/ActuatorHealthIT.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/ActuatorHealthIT.java new file mode 100644 index 000000000..73a7935d0 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/ActuatorHealthIT.java @@ -0,0 +1,74 @@ +package edu.harvard.hms.dbmi.avillach.gateway.health; + +import static com.github.tomakehurst.wiremock.client.WireMock.aResponse; +import static com.github.tomakehurst.wiremock.client.WireMock.get; +import static com.github.tomakehurst.wiremock.client.WireMock.okJson; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.actuate.health.HealthContributor; +import org.springframework.boot.actuate.health.HealthIndicator; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; + +import com.github.tomakehurst.wiremock.WireMockServer; + +/** + * Proves {@link DownstreamHealthContributor} surfaces each monitored downstream as its own health component, driven by real HTTP probes + * (via WireMock) through the real Spring context -- an up downstream reports UP, a down downstream reports DOWN. + */ +@SpringBootTest +class ActuatorHealthIT { + + static WireMockServer hpds; + static WireMockServer psama; + + @Autowired + DownstreamHealthContributor contributor; + + @BeforeAll + static void start() { + hpds = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + psama = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + hpds.start(); + psama.start(); + hpds.stubFor(get(urlEqualTo("/actuator/health")).willReturn(okJson("{\"status\":\"UP\"}"))); + psama.stubFor(get(urlEqualTo("/actuator/health")).willReturn(aResponse().withStatus(503))); + } + + @AfterAll + static void stop() { + hpds.stop(); + psama.stop(); + } + + @DynamicPropertySource + static void props(DynamicPropertyRegistry r) { + r.add("picsure.gateway.health.downstreams[0].name", () -> "hpds"); + r.add("picsure.gateway.health.downstreams[0].base-url", () -> "http://127.0.0.1:" + hpds.port()); + r.add("picsure.gateway.health.downstreams[0].require-status-up", () -> "true"); + r.add("picsure.gateway.health.downstreams[1].name", () -> "psama"); + r.add("picsure.gateway.health.downstreams[1].base-url", () -> "http://127.0.0.1:" + psama.port()); + r.add("picsure.gateway.health.downstreams[1].require-status-up", () -> "true"); + } + + @Test + void exposesDownstreamAsHealthComponent() { + HealthContributor c = contributor.getContributor("hpds"); + assertThat(c).isInstanceOf(HealthIndicator.class); + assertThat(((HealthIndicator) c).health().getStatus().getCode()).isEqualTo("UP"); + } + + @Test + void exposesDownDownstreamAsDown() { + HealthContributor c = contributor.getContributor("psama"); + assertThat(c).isInstanceOf(HealthIndicator.class); + assertThat(((HealthIndicator) c).health().getStatus().getCode()).isEqualTo("DOWN"); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/RecordingSystemHealthService.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/RecordingSystemHealthService.java new file mode 100644 index 000000000..353ed828a --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/RecordingSystemHealthService.java @@ -0,0 +1,70 @@ +package edu.harvard.hms.dbmi.avillach.gateway.health; + +import java.util.Collections; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.concurrent.ConcurrentHashMap; +import java.util.concurrent.CopyOnWriteArrayList; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; + +/** + * Test-only {@link SystemHealthService} subclass that overrides the protected {@code probe} override point so unit tests can exercise dedup + * / rollup semantics without any real HTTP traffic. The real HTTP path is covered by {@link SystemHealthServiceIT} via WireMock. + */ +class RecordingSystemHealthService extends SystemHealthService { + + private static final ObjectMapper MAPPER = new ObjectMapper(); + + private final List probedUrls = new CopyOnWriteArrayList<>(); + private final Set downUrls = ConcurrentHashMap.newKeySet(); + private final Map stubs = new ConcurrentHashMap<>(); + + RecordingSystemHealthService(DownstreamHealthProperties props) { + super(props); + } + + List probedUrls() { + return Collections.unmodifiableList(probedUrls); + } + + void markDown(String resolvedUrl) { + downUrls.add(resolvedUrl); + } + + void stub(String resolvedUrl, int status, String body) { + stubs.put(resolvedUrl, new Stub(status, body)); + } + + @Override + protected boolean probe(MonitoredDownstream d) { + String url = d.resolvedUrl(); + probedUrls.add(url); + + if (downUrls.contains(url)) { + return false; + } + + Stub stub = stubs.get(url); + if (stub == null) { + return true; + } + if (stub.status() != d.successStatus()) { + return false; + } + if (d.requireStatusUp()) { + try { + JsonNode node = MAPPER.readTree(stub.body()); + return node.hasNonNull("status") && "UP".equalsIgnoreCase(node.get("status").asText()); + } catch (Exception ex) { + return false; + } + } + return true; + } + + private record Stub(int status, String body) { + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/SystemHealthServiceIT.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/SystemHealthServiceIT.java new file mode 100644 index 000000000..fa9cf6e8e --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/SystemHealthServiceIT.java @@ -0,0 +1,68 @@ +package edu.harvard.hms.dbmi.avillach.gateway.health; + +import static com.github.tomakehurst.wiremock.client.WireMock.aResponse; +import static com.github.tomakehurst.wiremock.client.WireMock.get; +import static com.github.tomakehurst.wiremock.client.WireMock.okJson; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.List; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; + +import com.github.tomakehurst.wiremock.WireMockServer; + +/** + * Exercises the real HTTP path (unlike {@link SystemHealthServiceTest}, which stubs {@code probe} directly): a Spring Boot Actuator-style + * sibling ({@code {"status":"UP"}}), a Javalin-logging-style {@code /health} (200 with a differently-shaped body, no status predicate), and + * a downstream that is down. + */ +class SystemHealthServiceIT { + + static WireMockServer actuatorUp; // Spring Boot sibling: {"status":"UP"} + static WireMockServer loggingUp; // Javalin /health: 200 {"status":"healthy"} + static WireMockServer down; + + @BeforeAll + static void start() { + // http2PlainDisabled avoids a known JDK HttpClient <-> WireMock(Jetty) h2c upgrade bug that manifests as + // "RST_STREAM: Stream cancelled" when RestClient's default JDK-backed request factory is used. + actuatorUp = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + loggingUp = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + down = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + actuatorUp.start(); + loggingUp.start(); + down.start(); + actuatorUp.stubFor(get(urlEqualTo("/actuator/health")).willReturn(okJson("{\"status\":\"UP\"}"))); + loggingUp.stubFor(get(urlEqualTo("/health")).willReturn(okJson("{\"status\":\"healthy\"}"))); + down.stubFor(get(urlEqualTo("/actuator/health")).willReturn(aResponse().withStatus(503))); + } + + @AfterAll + static void stop() { + actuatorUp.stop(); + loggingUp.stop(); + down.stop(); + } + + @Test + void aggregatesDeepActuatorAndJavalinHealthAndOneDownDegradesIt() { + DownstreamHealthProperties props = new DownstreamHealthProperties( + List.of( + new MonitoredDownstream("psama", "http://127.0.0.1:" + actuatorUp.port(), null, null, null, false, 200, true), + new MonitoredDownstream("logging", "http://127.0.0.1:" + loggingUp.port(), "/health", null, null, false, 200, false), + new MonitoredDownstream("hpds", "http://127.0.0.1:" + down.port(), null, null, null, false, 200, true) + ), 500, 1000, null + ); + + AggregateHealth agg = new SystemHealthService(props).check(); + + assertThat(agg.running()).isFalse(); // hpds down -> DEGRADED + assertThat(agg.components()).filteredOn(c -> c.name().equals("psama")).allMatch(DownstreamHealth::up); + assertThat(agg.components()).filteredOn(c -> c.name().equals("logging")).allMatch(DownstreamHealth::up); + assertThat(agg.components()).filteredOn(c -> c.name().equals("hpds")).noneMatch(DownstreamHealth::up); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/SystemHealthServiceTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/SystemHealthServiceTest.java new file mode 100644 index 000000000..4b9389ff0 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/SystemHealthServiceTest.java @@ -0,0 +1,52 @@ +package edu.harvard.hms.dbmi.avillach.gateway.health; + +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.List; + +import org.junit.jupiter.api.Test; + +class SystemHealthServiceTest { + + private MonitoredDownstream up(String name, String url) { + return new MonitoredDownstream(name, url, "/actuator/health", "GET", null, false, 200, false); + } + + @Test + void dedupsByResolvedUrl() { + // In single-HPDS envs the open and auth HPDS collapse onto one URL. + DownstreamHealthProperties props = new DownstreamHealthProperties( + List.of(up("hpds-open", "http://hpds:8080"), up("hpds-auth", "http://hpds:8080")), 1000, 2000, null + ); + RecordingSystemHealthService svc = new RecordingSystemHealthService(props); + AggregateHealth agg = svc.check(); + assertThat(svc.probedUrls()).containsExactly("http://hpds:8080/actuator/health"); + assertThat(agg.components()).extracting(DownstreamHealth::name).containsExactlyInAnyOrder("hpds-open", "hpds-auth"); + assertThat(agg.running()).isTrue(); + } + + @Test + void oneDownMakesAggregateDegraded() { + DownstreamHealthProperties props = + new DownstreamHealthProperties(List.of(up("a", "http://a:8080"), up("b", "http://b:8080")), 1000, 2000, null); + RecordingSystemHealthService svc = new RecordingSystemHealthService(props); + svc.markDown("http://b:8080/actuator/health"); + AggregateHealth agg = svc.check(); + assertThat(agg.running()).isFalse(); + assertThat(agg.components()).anySatisfy(c -> { + assertThat(c.name()).isEqualTo("b"); + assertThat(c.up()).isFalse(); + }); + } + + @Test + void successPredicateRequiresStatusUpBody() { + MonitoredDownstream strict = new MonitoredDownstream("dict", "http://dict:8080", "/actuator/health", "GET", null, false, 200, true); + RecordingSystemHealthService svc = + new RecordingSystemHealthService(new DownstreamHealthProperties(List.of(strict), 1000, 2000, null)); + svc.stub("http://dict:8080/actuator/health", 200, "{\"status\":\"DOWN\"}"); + assertThat(svc.check().running()).isFalse(); + svc.stub("http://dict:8080/actuator/health", 200, "{\"status\":\"UP\"}"); + assertThat(svc.check().running()).isTrue(); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/SystemStatusControllerTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/SystemStatusControllerTest.java new file mode 100644 index 000000000..139e28629 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/SystemStatusControllerTest.java @@ -0,0 +1,52 @@ +package edu.harvard.hms.dbmi.avillach.gateway.health; + +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.List; +import java.util.concurrent.atomic.AtomicInteger; + +import org.junit.jupiter.api.Test; + +class SystemStatusControllerTest { + + /** Counts how many times the underlying aggregate check runs, to prove throttling. */ + static class CountingHealthService extends SystemHealthService { + final AtomicInteger calls = new AtomicInteger(); + volatile boolean running = true; + + CountingHealthService() { + super(new DownstreamHealthProperties(List.of(), 1000, 2000, null)); + } + + @Override + public AggregateHealth check() { + calls.incrementAndGet(); + return new AggregateHealth(running, List.of()); + } + } + + @Test + void mapsRunningAndDegradedStrings() { + CountingHealthService svc = new CountingHealthService(); + SystemStatusController controller = new SystemStatusController(svc, 60_000L); + + svc.running = true; + assertThat(controller.status()).isEqualTo("RUNNING"); + + controller.expireCacheForTest(); + svc.running = false; + assertThat(controller.status()).isEqualTo("ONE OR MORE COMPONENTS DEGRADED"); + } + + @Test + void throttlesRepeatedCallsToOnePerWindow() { + CountingHealthService svc = new CountingHealthService(); + SystemStatusController controller = new SystemStatusController(svc, 60_000L); + + controller.status(); + controller.status(); + controller.status(); + + assertThat(svc.calls.get()).isEqualTo(1); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/SystemStatusEndpointIT.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/SystemStatusEndpointIT.java new file mode 100644 index 000000000..7adab09f8 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/health/SystemStatusEndpointIT.java @@ -0,0 +1,79 @@ +package edu.harvard.hms.dbmi.avillach.gateway.health; + +import static com.github.tomakehurst.wiremock.client.WireMock.aResponse; +import static com.github.tomakehurst.wiremock.client.WireMock.get; +import static com.github.tomakehurst.wiremock.client.WireMock.okJson; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.web.server.LocalServerPort; +import org.springframework.boot.test.context.SpringBootTest.WebEnvironment; +import org.springframework.boot.test.web.client.TestRestTemplate; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; + +import com.github.tomakehurst.wiremock.WireMockServer; + +/** + * End-to-end wiring check over real HTTP: {@code /system/status} composed through the real Spring context (HealthConfig bean -> + * SystemHealthService -> SystemStatusController), against a WireMock downstream that is down, proving the legacy plain-text DEGRADED + * contract survives the full stack, not just the unit-level fake in {@link SystemStatusControllerTest}. + */ +@SpringBootTest(webEnvironment = WebEnvironment.RANDOM_PORT) +class SystemStatusEndpointIT { + + static WireMockServer down; + + @Autowired + private TestRestTemplate rest; + + + @LocalServerPort + int port; + + /** + * Dial the loopback ADDRESS, never the name. {@code localhost} resolves to {@code ::1} before {@code 127.0.0.1} on macOS, while these + * test servers bind the IPv4 wildcard -- so an unrelated local process holding the same port number on {@code [::]} can answer instead, + * and the test fails with a bewildering status from a server it never meant to contact. Relative {@code TestRestTemplate} URLs go + * through {@code LocalHostUriTemplateHandler}, which hardcodes the name {@code localhost}; absolute URLs bypass it entirely. + */ + private String url(String path) { + return "http://127.0.0.1:" + port + path; + } + + @BeforeAll + static void start() { + down = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + down.start(); + down.stubFor(get(urlEqualTo("/actuator/health")).willReturn(aResponse().withStatus(503))); + } + + @AfterAll + static void stop() { + down.stop(); + } + + @DynamicPropertySource + static void props(DynamicPropertyRegistry r) { + r.add("picsure.gateway.health.downstreams[0].name", () -> "hpds"); + r.add("picsure.gateway.health.downstreams[0].base-url", () -> "http://127.0.0.1:" + down.port()); + r.add("picsure.gateway.health.downstreams[0].require-status-up", () -> "true"); + } + + @Test + void reportsDegradedTextOverHttpWhenADownstreamIsDown() { + ResponseEntity response = rest.getForEntity(url("/system/status"), String.class); + + assertThat(response.getStatusCode().is2xxSuccessful()).isTrue(); + assertThat(response.getHeaders().getContentType()).isNotNull().matches(t -> t.isCompatibleWith(MediaType.TEXT_PLAIN)); + assertThat(response.getBody()).isEqualTo("ONE OR MORE COMPONENTS DEGRADED"); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/request/AccessLogFilterTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/request/AccessLogFilterTest.java new file mode 100644 index 000000000..cba5ff56b --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/request/AccessLogFilterTest.java @@ -0,0 +1,73 @@ +package edu.harvard.hms.dbmi.avillach.gateway.request; + +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.slf4j.LoggerFactory; +import org.springframework.mock.web.MockFilterChain; +import org.springframework.mock.web.MockHttpServletRequest; +import org.springframework.mock.web.MockHttpServletResponse; + +import ch.qos.logback.classic.Logger; +import ch.qos.logback.classic.spi.ILoggingEvent; +import ch.qos.logback.core.read.ListAppender; + +class AccessLogFilterTest { + + private final AccessLogFilter filter = new AccessLogFilter(); + private final ListAppender appender = new ListAppender<>(); + private final Logger accessLogger = (Logger) LoggerFactory.getLogger("gateway.access"); + + @BeforeEach + void attachAppender() { + appender.start(); + accessLogger.addAppender(appender); + } + + @AfterEach + void detachAppender() { + accessLogger.detachAppender(appender); + } + + @Test + void logsOneLinePerRequestWithMethodPathStatusAndDuration() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/query/sync"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + assertThat(appender.list).hasSize(1); + String line = appender.list.get(0).getFormattedMessage(); + assertThat(line).startsWith("POST /query/sync 200 ").endsWith("ms"); + } + + @Test + void skipsActuatorEndpointsSoProbesAndScrapesDoNotFloodTheLog() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/actuator/health"); + + filter.doFilter(request, new MockHttpServletResponse(), new MockFilterChain()); + + assertThat(appender.list).isEmpty(); + } + + @Test + void logsEvenWhenTheChainThrows() { + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/query/boom"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(500); + + try { + filter.doFilter(request, response, (req, resp) -> { + throw new RuntimeException("upstream exploded"); + }); + } catch (Exception expected) { + // the filter must re-throw; the access line must still be written + } + + assertThat(appender.list).hasSize(1); + assertThat(appender.list.get(0).getFormattedMessage()).startsWith("GET /query/boom 500 "); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/request/InboundIdentityHeaderSanitizingFilterTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/request/InboundIdentityHeaderSanitizingFilterTest.java new file mode 100644 index 000000000..896a2b0a2 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/request/InboundIdentityHeaderSanitizingFilterTest.java @@ -0,0 +1,88 @@ +package edu.harvard.hms.dbmi.avillach.gateway.request; + +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.Collections; +import java.util.List; +import java.util.concurrent.atomic.AtomicReference; + +import org.junit.jupiter.api.Test; +import org.springframework.mock.web.MockHttpServletRequest; +import org.springframework.mock.web.MockHttpServletResponse; + +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import jakarta.servlet.http.HttpServletRequest; + +/** + * FIX 1 (critical, defense-in-depth): {@link InboundIdentityHeaderSanitizingFilter} is registered UNCONDITIONALLY in + * {@code ObservabilityConfig} as an independent trust boundary, separate from {@code IdentityPropagationFilter} in the always-on DB-free + * auth chain. These tests exercise the filter standalone: even if the auth chain were ever bypassed or misconfigured, or WildFly is + * nonetheless configured to trust these headers directly from the gateway, this filter must still strip them. + */ +class InboundIdentityHeaderSanitizingFilterTest { + + private final InboundIdentityHeaderSanitizingFilter filter = new InboundIdentityHeaderSanitizingFilter(); + + @Test + void stripsAllFiveClientSuppliedIdentityHeadersUnconditionally() throws Exception { + // The dangerous case: a client tries to spoof an elevated identity directly, with no other filter in front of + // this one to stop it. + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/query/sync"); + request.addHeader(GatewayUserResolver.HEADER_USER_ID, "spoofed-id"); + request.addHeader(GatewayUserResolver.HEADER_USER_SUBJECT, "spoofed-subject"); + request.addHeader(GatewayUserResolver.HEADER_USER_EMAIL, "spoofed@example.com"); + request.addHeader(GatewayUserResolver.HEADER_USER_ROLES, "ADMIN"); + request.addHeader(GatewayUserResolver.HEADER_USER_PRIVILEGES, "SYSTEM,ADMIN"); + request.addHeader("X-Other-Header", "kept"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + AtomicReference captured = new AtomicReference<>(); + filter.doFilter(request, response, (req, resp) -> captured.set((HttpServletRequest) req)); + + HttpServletRequest wrapped = captured.get(); + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_ID)).isNull(); + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_SUBJECT)).isNull(); + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_EMAIL)).isNull(); + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_ROLES)).isNull(); + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_PRIVILEGES)).isNull(); + assertThat(wrapped.getHeader("X-Other-Header")).isEqualTo("kept"); + + assertThat(wrapped.getHeaders(GatewayUserResolver.HEADER_USER_PRIVILEGES).hasMoreElements()).isFalse(); + assertThat(wrapped.getHeaders(GatewayUserResolver.HEADER_USER_ID).hasMoreElements()).isFalse(); + + List names = Collections.list(wrapped.getHeaderNames()); + assertThat(names).doesNotContain( + GatewayUserResolver.HEADER_USER_ID, GatewayUserResolver.HEADER_USER_SUBJECT, GatewayUserResolver.HEADER_USER_EMAIL, + GatewayUserResolver.HEADER_USER_ROLES, GatewayUserResolver.HEADER_USER_PRIVILEGES + ); + assertThat(names).contains("X-Other-Header"); + } + + @Test + void headerStrippingIsCaseInsensitive() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/query/sync"); + request.addHeader("x-user-privileges", "SYSTEM,ADMIN"); + request.addHeader("X-USER-ID", "spoofed-id"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + AtomicReference captured = new AtomicReference<>(); + filter.doFilter(request, response, (req, resp) -> captured.set((HttpServletRequest) req)); + + HttpServletRequest wrapped = captured.get(); + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_PRIVILEGES)).isNull(); + assertThat(wrapped.getHeader(GatewayUserResolver.HEADER_USER_ID)).isNull(); + assertThat(Collections.list(wrapped.getHeaderNames())).doesNotContain("x-user-privileges", "X-USER-ID"); + } + + @Test + void nonIdentityHeadersPassThroughUnchangedWhenNoSpoofAttempted() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/query/sync"); + request.addHeader("Authorization", "Bearer abc"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + AtomicReference captured = new AtomicReference<>(); + filter.doFilter(request, response, (req, resp) -> captured.set((HttpServletRequest) req)); + + assertThat(captured.get().getHeader("Authorization")).isEqualTo("Bearer abc"); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/routing/ConfigurationRouteTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/routing/ConfigurationRouteTest.java new file mode 100644 index 000000000..8d58d2212 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/routing/ConfigurationRouteTest.java @@ -0,0 +1,124 @@ +package edu.harvard.hms.dbmi.avillach.gateway.routing; + +import static com.github.tomakehurst.wiremock.client.WireMock.aResponse; +import static com.github.tomakehurst.wiremock.client.WireMock.any; +import static com.github.tomakehurst.wiremock.client.WireMock.anyRequestedFor; +import static com.github.tomakehurst.wiremock.client.WireMock.anyUrl; +import static com.github.tomakehurst.wiremock.client.WireMock.get; +import static com.github.tomakehurst.wiremock.client.WireMock.getRequestedFor; +import static com.github.tomakehurst.wiremock.client.WireMock.serverError; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.web.server.LocalServerPort; +import org.springframework.boot.test.web.client.TestRestTemplate; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; + +import com.github.tomakehurst.wiremock.WireMockServer; + +/** + * The single {@code /operations/**} route forwards VERBATIM (no prefix strip) to operations-service. The auth/audit chain always enforces, + * specifically proving the public config-GET bypass ({@code PsamaIntrospectionFilter#isPublicConfigurationRead}): + * {@code GET /operations/configuration/} and {@code GET /operations/configuration/{id}/} must reach operations-service WITHOUT a Bearer + * token and WITHOUT ever calling PSAMA — the introspection stub is wired to fail loudly (500) so any accidental introspection call surfaces + * as a test failure rather than a silent pass. + */ +@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT) +class ConfigurationRouteTest { + + static WireMockServer operationsStub; + static WireMockServer psamaStub; + + @DynamicPropertySource + static void urls(DynamicPropertyRegistry registry) { + operationsStub = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + operationsStub.start(); + registry.add("OPERATIONS_SERVICE_URL", operationsStub::baseUrl); + + psamaStub = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + psamaStub.start(); + registry.add("TOKEN_INTROSPECTION_URL", () -> psamaStub.baseUrl() + "/auth/token/inspect"); + } + + @AfterAll + static void stopStubs() { + operationsStub.stop(); + psamaStub.stop(); + } + + @BeforeEach + void resetStubs() { + operationsStub.resetAll(); + operationsStub + .stubFor(get(urlEqualTo("/operations/configuration/")).willReturn(aResponse().withStatus(200).withBody("config-list-ok"))); + operationsStub.stubFor( + get(urlEqualTo("/operations/configuration")).willReturn(aResponse().withStatus(200).withBody("config-list-slashless-ok")) + ); + operationsStub.stubFor( + get(urlEqualTo("/operations/configuration/abc-123/")).willReturn(aResponse().withStatus(200).withBody("config-read-ok")) + ); + + psamaStub.resetAll(); + // If the bypass ever regressed and introspection were called for these paths, fail loudly (500) instead of + // silently succeeding — a passing test here must mean PSAMA was never reached. + psamaStub.stubFor(any(anyUrl()).willReturn(serverError())); + } + + @Autowired + private TestRestTemplate rest; + + + @LocalServerPort + int port; + + /** + * Dial the loopback ADDRESS, never the name. {@code localhost} resolves to {@code ::1} before {@code 127.0.0.1} on macOS, while these + * test servers bind the IPv4 wildcard -- so an unrelated local process holding the same port number on {@code [::]} can answer instead, + * and the test fails with a bewildering status from a server it never meant to contact. Relative {@code TestRestTemplate} URLs go + * through {@code LocalHostUriTemplateHandler}, which hardcodes the name {@code localhost}; absolute URLs bypass it entirely. + */ + private String url(String path) { + return "http://127.0.0.1:" + port + path; + } + + @Test + void forwardsConfigurationRootGetWithoutBearerTokenAndSkipsIntrospection() { + ResponseEntity response = rest.getForEntity(url("/operations/configuration/"), String.class); + + assertThat(response.getStatusCode().value()).isEqualTo(200); + assertThat(response.getBody()).isEqualTo("config-list-ok"); + // No prefix strip: operations-service saw the exact inbound path, /operations/configuration/. + operationsStub.verify(getRequestedFor(urlEqualTo("/operations/configuration/"))); + psamaStub.verify(0, anyRequestedFor(anyUrl())); + } + + @Test + void forwardsSlashlessConfigurationRootGetWithoutBearerTokenAndSkipsIntrospection() { + // The slash-less list is the form the operations-service controller actually serves; the bypass + // must not demand a Bearer for it either. + ResponseEntity response = rest.getForEntity(url("/operations/configuration"), String.class); + + assertThat(response.getStatusCode().value()).isEqualTo(200); + assertThat(response.getBody()).isEqualTo("config-list-slashless-ok"); + operationsStub.verify(getRequestedFor(urlEqualTo("/operations/configuration"))); + psamaStub.verify(0, anyRequestedFor(anyUrl())); + } + + @Test + void forwardsConfigurationIdReadGetWithoutBearerTokenAndSkipsIntrospection() { + ResponseEntity response = rest.getForEntity(url("/operations/configuration/abc-123/"), String.class); + + assertThat(response.getStatusCode().value()).isEqualTo(200); + assertThat(response.getBody()).isEqualTo("config-read-ok"); + operationsStub.verify(getRequestedFor(urlEqualTo("/operations/configuration/abc-123/"))); + psamaStub.verify(0, anyRequestedFor(anyUrl())); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/routing/DatasetRouteTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/routing/DatasetRouteTest.java new file mode 100644 index 000000000..99a6f2983 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/routing/DatasetRouteTest.java @@ -0,0 +1,99 @@ +package edu.harvard.hms.dbmi.avillach.gateway.routing; + +import static com.github.tomakehurst.wiremock.client.WireMock.aResponse; +import static com.github.tomakehurst.wiremock.client.WireMock.get; +import static com.github.tomakehurst.wiremock.client.WireMock.getRequestedFor; +import static com.github.tomakehurst.wiremock.client.WireMock.okJson; +import static com.github.tomakehurst.wiremock.client.WireMock.post; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.web.server.LocalServerPort; +import org.springframework.boot.test.web.client.TestRestTemplate; +import org.springframework.http.HttpEntity; +import org.springframework.http.HttpHeaders; +import org.springframework.http.HttpMethod; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; + +import com.github.tomakehurst.wiremock.WireMockServer; + +/** + * The single {@code /operations/**} route forwards VERBATIM (no prefix strip) to operations-service, the sole DB owner, for the + * {@code /operations/dataset/**} sub-path too. Proves the higher-priority route (order 100) matches; there is no catch-all fallback. + * {@code /operations} is not allow-listed, so under the always-on auth/audit chain the request needs a valid bearer plus an active PSAMA + * introspection stub. + */ +@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT) +class DatasetRouteTest { + + static WireMockServer operationsStub; + static WireMockServer psamaStub; + + @DynamicPropertySource + static void urls(DynamicPropertyRegistry registry) { + operationsStub = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + operationsStub.start(); + registry.add("OPERATIONS_SERVICE_URL", operationsStub::baseUrl); + + psamaStub = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + psamaStub.start(); + registry.add("TOKEN_INTROSPECTION_URL", () -> psamaStub.baseUrl() + "/auth/token/inspect"); + } + + @AfterAll + static void stopStubs() { + operationsStub.stop(); + psamaStub.stop(); + } + + @BeforeEach + void resetStubs() { + operationsStub.resetAll(); + operationsStub + .stubFor(get(urlEqualTo("/operations/dataset/named/abc-123")).willReturn(aResponse().withStatus(200).withBody("dataset-ok"))); + + psamaStub.resetAll(); + psamaStub.stubFor( + post(urlEqualTo("/auth/token/inspect")) + .willReturn(okJson("{\"active\":true,\"userId\":\"u-1\",\"sub\":\"s-1\",\"email\":\"a@b\",\"role\":\"USER\"}")) + ); + } + + @Autowired + private TestRestTemplate rest; + + + @LocalServerPort + int port; + + /** + * Dial the loopback ADDRESS, never the name. {@code localhost} resolves to {@code ::1} before {@code 127.0.0.1} on macOS, while these + * test servers bind the IPv4 wildcard -- so an unrelated local process holding the same port number on {@code [::]} can answer instead, + * and the test fails with a bewildering status from a server it never meant to contact. Relative {@code TestRestTemplate} URLs go + * through {@code LocalHostUriTemplateHandler}, which hardcodes the name {@code localhost}; absolute URLs bypass it entirely. + */ + private String url(String path) { + return "http://127.0.0.1:" + port + path; + } + + @Test + void forwardsDatasetPathToOperationsServiceVerbatim() { + HttpHeaders headers = new HttpHeaders(); + headers.set("Authorization", "Bearer user-token"); + ResponseEntity response = + rest.exchange(url("/operations/dataset/named/abc-123"), HttpMethod.GET, new HttpEntity<>(headers), String.class); + + assertThat(response.getStatusCode().value()).isEqualTo(200); + assertThat(response.getBody()).isEqualTo("dataset-ok"); + // No prefix strip: operations-service saw the exact inbound path, /operations/dataset/named/abc-123. + operationsStub.verify(getRequestedFor(urlEqualTo("/operations/dataset/named/abc-123"))); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/routing/HpdsRouteTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/routing/HpdsRouteTest.java new file mode 100644 index 000000000..88248aa68 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/routing/HpdsRouteTest.java @@ -0,0 +1,98 @@ +package edu.harvard.hms.dbmi.avillach.gateway.routing; + +import static com.github.tomakehurst.wiremock.client.WireMock.aResponse; +import static com.github.tomakehurst.wiremock.client.WireMock.get; +import static com.github.tomakehurst.wiremock.client.WireMock.getRequestedFor; +import static com.github.tomakehurst.wiremock.client.WireMock.okJson; +import static com.github.tomakehurst.wiremock.client.WireMock.post; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.web.server.LocalServerPort; +import org.springframework.boot.test.web.client.TestRestTemplate; +import org.springframework.http.HttpEntity; +import org.springframework.http.HttpHeaders; +import org.springframework.http.HttpMethod; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; + +import com.github.tomakehurst.wiremock.WireMockServer; + +/** + * The explicit {@code /hpds/**} route forwards VERBATIM (no prefix strip) to the DB-free query-service — the query-service itself selects + * auth vs. open (and v3 vs. legacy) from the path, so the gateway must not rewrite it. Proves the higher-priority route (order 100) matches + * (no catch-all fallback exists), and that the backend sees the exact inbound path. {@code /hpds} is not allow-listed, so under the + * always-on auth/audit chain the request needs a valid bearer plus an active PSAMA introspection stub. + */ +@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT) +class HpdsRouteTest { + + static WireMockServer hpdsStub; + static WireMockServer psamaStub; + + @DynamicPropertySource + static void urls(DynamicPropertyRegistry registry) { + hpdsStub = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + hpdsStub.start(); + registry.add("HPDS_QUERY_SERVICE_URL", hpdsStub::baseUrl); + + psamaStub = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + psamaStub.start(); + registry.add("TOKEN_INTROSPECTION_URL", () -> psamaStub.baseUrl() + "/auth/token/inspect"); + } + + @AfterAll + static void stopStubs() { + hpdsStub.stop(); + psamaStub.stop(); + } + + @BeforeEach + void resetStubs() { + hpdsStub.resetAll(); + hpdsStub.stubFor(get(urlEqualTo("/hpds/auth/v3/query/abc-123/status")).willReturn(aResponse().withStatus(200).withBody("hpds-ok"))); + + psamaStub.resetAll(); + psamaStub.stubFor( + post(urlEqualTo("/auth/token/inspect")) + .willReturn(okJson("{\"active\":true,\"userId\":\"u-1\",\"sub\":\"s-1\",\"email\":\"a@b\",\"role\":\"USER\"}")) + ); + } + + @Autowired + private TestRestTemplate rest; + + + @LocalServerPort + int port; + + /** + * Dial the loopback ADDRESS, never the name. {@code localhost} resolves to {@code ::1} before {@code 127.0.0.1} on macOS, while these + * test servers bind the IPv4 wildcard -- so an unrelated local process holding the same port number on {@code [::]} can answer instead, + * and the test fails with a bewildering status from a server it never meant to contact. Relative {@code TestRestTemplate} URLs go + * through {@code LocalHostUriTemplateHandler}, which hardcodes the name {@code localhost}; absolute URLs bypass it entirely. + */ + private String url(String path) { + return "http://127.0.0.1:" + port + path; + } + + @Test + void forwardsHpdsPathToQueryServiceVerbatim() { + HttpHeaders headers = new HttpHeaders(); + headers.set("Authorization", "Bearer user-token"); + ResponseEntity response = + rest.exchange(url("/hpds/auth/v3/query/abc-123/status"), HttpMethod.GET, new HttpEntity<>(headers), String.class); + + assertThat(response.getStatusCode().value()).isEqualTo(200); + assertThat(response.getBody()).isEqualTo("hpds-ok"); + // No prefix strip: the query-service saw the exact inbound path, /hpds/auth/v3/query/abc-123/status. + hpdsStub.verify(getRequestedFor(urlEqualTo("/hpds/auth/v3/query/abc-123/status"))); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/routing/LoggingRouteTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/routing/LoggingRouteTest.java new file mode 100644 index 000000000..5cc3a719c --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/routing/LoggingRouteTest.java @@ -0,0 +1,79 @@ +package edu.harvard.hms.dbmi.avillach.gateway.routing; + +import static com.github.tomakehurst.wiremock.client.WireMock.aResponse; +import static com.github.tomakehurst.wiremock.client.WireMock.get; +import static com.github.tomakehurst.wiremock.client.WireMock.getRequestedFor; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.client.WireMock.urlPathEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.web.server.LocalServerPort; +import org.springframework.boot.test.web.client.TestRestTemplate; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; + +import com.github.tomakehurst.wiremock.WireMockServer; + +/** + * The explicit {@code /logging/**} route forwards to the logging service with the leading {@code /logging} segment stripped (the logging + * service serves its API at root — {@code /audit}, {@code /health}). This replaces the legacy {@code /proxy/pic-sure-logging} relay. The + * request must reach the logging stub via the explicit route (order 100); there is no catch-all fallback. + */ +@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT) +class LoggingRouteTest { + + static WireMockServer loggingStub; + + @DynamicPropertySource + static void loggingUrl(DynamicPropertyRegistry registry) { + loggingStub = new WireMockServer(options().bindAddress("127.0.0.1").dynamicPort().http2PlainDisabled(true)); + loggingStub.start(); + registry.add("LOGGING_URL", loggingStub::baseUrl); + } + + @AfterAll + static void stopStub() { + loggingStub.stop(); + } + + @BeforeEach + void resetStub() { + loggingStub.resetAll(); + // The logging service serves at root, so after StripPrefix the gateway forwards to /audit. + loggingStub.stubFor(get(urlPathEqualTo("/audit")).willReturn(aResponse().withStatus(200).withBody("logging-ok"))); + } + + @Autowired + private TestRestTemplate rest; + + + @LocalServerPort + int port; + + /** + * Dial the loopback ADDRESS, never the name. {@code localhost} resolves to {@code ::1} before {@code 127.0.0.1} on macOS, while these + * test servers bind the IPv4 wildcard -- so an unrelated local process holding the same port number on {@code [::]} can answer instead, + * and the test fails with a bewildering status from a server it never meant to contact. Relative {@code TestRestTemplate} URLs go + * through {@code LocalHostUriTemplateHandler}, which hardcodes the name {@code localhost}; absolute URLs bypass it entirely. + */ + private String url(String path) { + return "http://127.0.0.1:" + port + path; + } + + @Test + void forwardsLoggingPathToLoggingServiceWithPrefixStripped() { + ResponseEntity response = rest.getForEntity(url("/logging/audit"), String.class); + + assertThat(response.getStatusCode().value()).isEqualTo(200); + assertThat(response.getBody()).isEqualTo("logging-ok"); + // The /logging prefix was stripped: the logging service saw /audit, never /logging/audit. + loggingStub.verify(getRequestedFor(urlEqualTo("/audit"))); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/routing/NoRegistryRouteTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/routing/NoRegistryRouteTest.java new file mode 100644 index 000000000..c18f7f365 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/routing/NoRegistryRouteTest.java @@ -0,0 +1,47 @@ +package edu.harvard.hms.dbmi.avillach.gateway.routing; + +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.stream.Collectors; + +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.context.properties.bind.Bindable; +import org.springframework.boot.context.properties.bind.Binder; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.core.env.Environment; + +/** + * The resource registry is removed. Assert on the configured route IDS (behavior-pinning, not a weak bean-name check) — the gateway exposes + * NO {@code /info/resources} or {@code /resource} route. Those paths are unmatched and 404. + * + *

    Configured routes: {@code logging}, {@code dictionary}, {@code uploader}, {@code visualization}, plus {@code hpds}, {@code operations} + * — verbatim routes to the query-service / operations-service. The load-bearing assertion is that no registry id ever appears. + */ +@SpringBootTest +class NoRegistryRouteTest { + + @Autowired + Environment env; + + @SuppressWarnings("unchecked") + private Set configuredRouteIds() { + List> routes = Binder.get(env) + .bind("spring.cloud.gateway.server.webmvc.routes", Bindable.listOf((Class>) (Class) Map.class)) + .orElse(List.of()); + return routes.stream().map(r -> String.valueOf(r.get("id"))).collect(Collectors.toSet()); + } + + @Test + void exposesOnlyTheExpectedRouteIdsAndNoRegistryRoute() { + Set ids = configuredRouteIds(); + assertThat(ids).containsExactlyInAnyOrder("logging", "dictionary", "uploader", "visualization", "hpds", "operations"); + assertThat(ids).noneMatch(id -> { + String lower = id.toLowerCase(); + return lower.contains("resource") || lower.contains("info-resources"); + }); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/routing/RouteOwnedPrefixDriftTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/routing/RouteOwnedPrefixDriftTest.java new file mode 100644 index 000000000..4b245b903 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/routing/RouteOwnedPrefixDriftTest.java @@ -0,0 +1,86 @@ +package edu.harvard.hms.dbmi.avillach.gateway.routing; + +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.Collection; +import java.util.List; +import java.util.Map; + +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.context.properties.bind.Bindable; +import org.springframework.boot.context.properties.bind.Binder; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.core.env.Environment; + +import edu.harvard.hms.dbmi.avillach.gateway.config.RouteSurfaces; + +/** + * Drift guard: every configured route must be covered by the default gateway-owned prefixes + * ({@code RouteSurfaceProperties.DEFAULT_OWNED_PREFIXES}, via {@link RouteSurfaces#withDefaults()}), and no route may declare an unowned, + * bare wildcard (catch-all) predicate. Binds {@code spring.cloud.gateway.server.webmvc.routes} straight from the environment (same Binder + * technique as {@code NoRegistryRouteTest}) so that adding a route to {@code application.yml} without extending the owned-prefixes default + * fails THIS test -- the route table can never silently drift out of sync with what the gateway owns. + */ +@SpringBootTest +class RouteOwnedPrefixDriftTest { + + @Autowired + Environment env; + + private final RouteSurfaces surfaces = RouteSurfaces.withDefaults(); + + @SuppressWarnings("unchecked") + private List> configuredRoutes() { + return Binder.get(env) + .bind("spring.cloud.gateway.server.webmvc.routes", Bindable.listOf((Class>) (Class) Map.class)) + .orElse(List.of()); + } + + @Test + void everyRouteIsCoveredByDefaultOwnedPrefixes() { + List> routes = configuredRoutes(); + assertThat(routes).as("routes must be bound from application.yml").isNotEmpty(); + + for (Map route : routes) { + String base = ownedBaseOf(route); + assertThat(base).as("no route may declare an unowned, bare wildcard catch-all (id=%s)", route.get("id")).isNotEmpty(); + assertThat(surfaces.isOwned(base)).as("owned prefix covers route path %s (id=%s)", base, route.get("id")).isTrue(); + assertThat(surfaces.isOwned(base + "/sub/path")).as("owned prefix covers under %s (id=%s)", base, route.get("id")).isTrue(); + } + } + + /** The route's Path predicate stripped of its trailing {@code /**} (or {@code /*}); empty string for a {@code /**} catch-all. */ + private static String ownedBaseOf(Map route) { + String path = pathPredicate(route); + assertThat(path).as("route %s must declare a Path predicate", route.get("id")).isNotNull(); + if (path.endsWith("/**")) { + return path.substring(0, path.length() - "/**".length()); + } + if (path.endsWith("/*")) { + return path.substring(0, path.length() - "/*".length()); + } + return path; + } + + private static String pathPredicate(Map route) { + // Binding the shortcut predicate list from application.yml yields either a List or an index-keyed Map + // (e.g. {0=Path=/logging/**}); handle both by scanning every value for the Path predicate. + Object predicates = route.get("predicates"); + Collection entries = switch (predicates) { + case List list -> list; + case Map map -> map.values(); + case null, default -> List.of(); + }; + for (Object predicate : entries) { + String s = String.valueOf(predicate); + int idx = s.indexOf("Path="); + if (idx >= 0) { + String value = s.substring(idx + "Path=".length()); + int comma = value.indexOf(','); + return (comma >= 0 ? value.substring(0, comma) : value).trim(); + } + } + return null; + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/security/ActuatorDisabledByDefaultTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/security/ActuatorDisabledByDefaultTest.java new file mode 100644 index 000000000..9ec158262 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/security/ActuatorDisabledByDefaultTest.java @@ -0,0 +1,61 @@ +package edu.harvard.hms.dbmi.avillach.gateway.security; + +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.web.server.LocalServerPort; +import org.springframework.http.ResponseEntity; +import org.springframework.http.client.ClientHttpResponse; +import org.springframework.test.context.ActiveProfiles; +import org.springframework.web.client.ResponseErrorHandler; +import org.springframework.web.client.RestTemplate; + +/** + * Locks in the security posture the whole actuator change rests on: with NO {@code PICSURE_ACTUATOR_EXPOSURE} set, + * {@code management.endpoints.web.exposure.include} resolves to empty (see application.yml), so every {@code /actuator/**} endpoint is + * unmapped (404) -- nothing is exposed to the world by default. The public {@code /system/status} basic health check is a + * {@code RouterFunction}, not an actuator endpoint, so it stays available regardless. AIO opts back in via gateway.env; the + * enabled-and-gated behavior is proven by {@link ActuatorSecurityIntegrationTest}. + */ +@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT) +@ActiveProfiles("local") +class ActuatorDisabledByDefaultTest { + + @LocalServerPort + int port; + private final RestTemplate rest = new RestTemplate(); + + @BeforeEach + void noThrow() { + rest.setErrorHandler(new ResponseErrorHandler() { + @Override + public boolean hasError(ClientHttpResponse r) { + return false; + } + + @Override + public void handleError(ClientHttpResponse r) {} + }); + } + + private String url(String path) { + return "http://127.0.0.1:" + port + path; + } + + @Test + void actuatorEndpointsAreUnmappedByDefault() { + assertThat(rest.getForEntity(url("/actuator/health"), String.class).getStatusCode().value()).isEqualTo(404); + assertThat(rest.getForEntity(url("/actuator/health/liveness"), String.class).getStatusCode().value()).isEqualTo(404); + assertThat(rest.getForEntity(url("/actuator/info"), String.class).getStatusCode().value()).isEqualTo(404); + assertThat(rest.getForEntity(url("/actuator/prometheus"), String.class).getStatusCode().value()).isEqualTo(404); + } + + @Test + void systemStatusBasicHealthCheckStaysAvailable() { + ResponseEntity r = rest.getForEntity(url("/system/status"), String.class); + assertThat(r.getStatusCode().value()).isEqualTo(200); + assertThat(r.getBody()).isEqualTo("RUNNING"); + } +} diff --git a/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/security/ActuatorSecurityIntegrationTest.java b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/security/ActuatorSecurityIntegrationTest.java new file mode 100644 index 000000000..d03e10a23 --- /dev/null +++ b/services/pic-sure-gateway/src/test/java/edu/harvard/hms/dbmi/avillach/gateway/security/ActuatorSecurityIntegrationTest.java @@ -0,0 +1,109 @@ +package edu.harvard.hms.dbmi.avillach.gateway.security; + +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.boot.test.autoconfigure.actuate.observability.AutoConfigureObservability; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.web.server.LocalServerPort; +import org.springframework.http.HttpEntity; +import org.springframework.http.HttpHeaders; +import org.springframework.http.HttpMethod; +import org.springframework.http.ResponseEntity; +import org.springframework.http.client.ClientHttpResponse; +import org.springframework.test.context.ActiveProfiles; +import org.springframework.test.context.TestPropertySource; +import org.springframework.web.client.ResponseErrorHandler; +import org.springframework.web.client.RestTemplate; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; + +/** + * Full-context proof that the token-gated actuator chain (order 0) and the gateway's permit-all main chain (order 10) coexist end-to-end -- + * health stays open (never 401) and shallow without a token, component detail and {@code /actuator/prometheus} are gated by + * {@code X-Application-Token}. Deep health indicators may report UP or DOWN in this isolated context (no live PSAMA/downstreams are + * configured on the {@code local} profile) -- what matters is that the status code is never 401 and detail visibility tracks the token. + */ +@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT) +@AutoConfigureObservability // prometheus export is disabled by default in @SpringBootTest contexts +@ActiveProfiles("local") +// Actuator is OFF BY DEFAULT (empty exposure in application.yml); this test exercises the security gating, so it +// explicitly enables the endpoints and the when_authorized detail behavior the AIO deployment turns on. +@TestPropertySource( + properties = {"management.endpoints.web.exposure.include=health,info,prometheus,metrics", + "management.endpoint.health.show-details=when_authorized", "picsure.actuator.require-token=true", + "picsure.actuator.token=secret-xyz"} +) +class ActuatorSecurityIntegrationTest { + + @LocalServerPort + int port; + private final RestTemplate rest = new RestTemplate(); + private final ObjectMapper json = new ObjectMapper(); + + @BeforeEach + void noThrow() { + rest.setErrorHandler(new ResponseErrorHandler() { + @Override + public boolean hasError(ClientHttpResponse r) { + return false; + } + + @Override + public void handleError(ClientHttpResponse r) {} + }); + } + + private String url(String path) { + return "http://127.0.0.1:" + port + path; + } + + @Test + void healthIsOpenAndShallowWithoutToken() throws Exception { + ResponseEntity r = rest.getForEntity(url("/actuator/health"), String.class); + assertThat(r.getStatusCode().value()).isNotEqualTo(401); // open to the load balancer + JsonNode body = json.readTree(r.getBody()); + assertThat(body.has("status")).isTrue(); + assertThat(body.has("components")).isFalse(); // no detail leaks to anonymous callers + } + + @Test + void livenessIsOpenWithoutToken() { + ResponseEntity r = rest.getForEntity(url("/actuator/health/liveness"), String.class); + assertThat(r.getStatusCode().value()).isEqualTo(200); + } + + @Test + void healthRevealsDetailWithToken() throws Exception { + HttpHeaders h = new HttpHeaders(); + h.set("X-Application-Token", "secret-xyz"); + ResponseEntity r = rest.exchange(url("/actuator/health"), HttpMethod.GET, new HttpEntity<>(h), String.class); + JsonNode body = json.readTree(r.getBody()); + assertThat(body.has("components")).isTrue(); // DETAIL revealed by valid token + } + + @Test + void prometheusRejectedWithoutToken() { + ResponseEntity r = rest.getForEntity(url("/actuator/prometheus"), String.class); + assertThat(r.getStatusCode().value()).isEqualTo(401); + } + + @Test + void prometheusOkWithToken() { + HttpHeaders h = new HttpHeaders(); + h.set("X-Application-Token", "secret-xyz"); + ResponseEntity r = rest.exchange(url("/actuator/prometheus"), HttpMethod.GET, new HttpEntity<>(h), String.class); + assertThat(r.getStatusCode().value()).isEqualTo(200); + } + + /** + * Coexistence: a non-actuator, non-gated endpoint must remain reachable -- the actuator securityMatcher scopes to /actuator/** only. + */ + @Test + void systemStatusRemainsReachableWithoutToken() { + ResponseEntity r = rest.getForEntity(url("/system/status"), String.class); + assertThat(r.getStatusCode().value()).isNotEqualTo(401); + } +} diff --git a/services/pic-sure-hpds-query-service/Dockerfile b/services/pic-sure-hpds-query-service/Dockerfile new file mode 100644 index 000000000..32d1e9c67 --- /dev/null +++ b/services/pic-sure-hpds-query-service/Dockerfile @@ -0,0 +1,5 @@ +FROM amazoncorretto:25 +WORKDIR /app +COPY target/pic-sure-hpds-query-service-*.jar /app/app.jar +EXPOSE 8080 +ENTRYPOINT ["sh", "-c", "java ${JAVA_OPTS} -jar /app/app.jar"] diff --git a/services/pic-sure-hpds-query-service/README.md b/services/pic-sure-hpds-query-service/README.md new file mode 100644 index 000000000..ce1c24e03 --- /dev/null +++ b/services/pic-sure-hpds-query-service/README.md @@ -0,0 +1,10 @@ +# pic-sure-hpds-query-service + +DB-free single HPDS ingress (Phase 4) + open-path aggregate obfuscation (Phase 5). + +## Rollback (aggregate fold — Phase 5) +The legacy `pic-sure-aggregate-data-sharing-resource` WAR remains deployed on WildFly through Phase 6 and is +removed only in Phase 7. The open-path obfuscation now runs here (`/hpds/open[/v3]/query/sync`). To revert to +the WAR (BDC/prod only — the AIO does not deploy the aggregate WAR): repoint the gateway's `/hpds/open/**` +route back to WildFly's aggregate WAR context and redeploy. This service's aggregate endpoints keep running +but receive no traffic. (In single-HPDS AIO there is nothing to roll back to.) diff --git a/services/pic-sure-hpds-query-service/pom.xml b/services/pic-sure-hpds-query-service/pom.xml new file mode 100644 index 000000000..91db64597 --- /dev/null +++ b/services/pic-sure-hpds-query-service/pom.xml @@ -0,0 +1,104 @@ + + + 4.0.0 + + + edu.harvard.hms.dbmi.avillach + pic-sure-api + ${revision} + ../../pom.xml + + + pic-sure-hpds-query-service + ${revision} + jar + + pic-sure-hpds-query-service + The single HPDS ingress: executes queries + concept search against HPDS. DB-FREE -- persists/loads + queries by calling pic-sure-operations-service's internal query API over HTTP instead of owning any database. + Trusts the gateway's X-User-* headers; performs no JWT validation locally. + + + + org.springframework.boot + spring-boot-starter-web + + + org.springframework.boot + spring-boot-starter-actuator + + + + io.micrometer + micrometer-registry-prometheus + + + org.springframework.boot + spring-boot-starter-security + + + org.springframework.boot + spring-boot-starter-validation + + + + + edu.harvard.hms.dbmi.avillach + pic-sure-spring-commons + + + + edu.harvard.hms.dbmi.avillach + pic-sure-api-model + + + + edu.harvard.hms.dbmi.avillach.hpds + pic-sure-hpds-model + + + + + org.apache.httpcomponents.client5 + httpclient5 + + + + org.springframework.boot + spring-boot-starter-test + test + + + org.wiremock + wiremock-standalone + test + + + + + + + org.springframework.boot + spring-boot-maven-plugin + + + + repackage + + + + + + + + + + github + GitHub HMS-DBMI Apache Maven Packages + https://maven.pkg.github.com/hms-dbmi/pic-sure + + + diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/QueryServiceApplication.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/QueryServiceApplication.java new file mode 100644 index 000000000..7a995ceaf --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/QueryServiceApplication.java @@ -0,0 +1,24 @@ +package edu.harvard.hms.dbmi.avillach.query; + +import org.springframework.boot.SpringApplication; +import org.springframework.boot.autoconfigure.SpringBootApplication; +import org.springframework.context.annotation.Import; + +import edu.harvard.hms.dbmi.avillach.commons.error.GatewayExceptionAdvice; + +/** + * Entry point for pic-sure-hpds-query-service: the single HPDS ingress. DB-FREE -- this service owns no database of its own; it + * persists/loads queries by calling pic-sure-operations-service's internal query API over HTTP (see + * {@link edu.harvard.hms.dbmi.avillach.query.operations.OperationsClient}). + * + *

    {@link GatewayExceptionAdvice} (from {@code pic-sure-spring-commons}) is imported explicitly because it lives outside this + * application's base package, so component scanning alone would not pick it up. + */ +@SpringBootApplication +@Import(GatewayExceptionAdvice.class) +public class QueryServiceApplication { + + public static void main(String[] args) { + SpringApplication.run(QueryServiceApplication.class, args); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateBackendClient.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateBackendClient.java new file mode 100644 index 000000000..a5c4b5847 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateBackendClient.java @@ -0,0 +1,123 @@ +package edu.harvard.hms.dbmi.avillach.query.aggregate; + +import java.util.UUID; + +import org.springframework.beans.factory.annotation.Qualifier; +import org.springframework.http.HttpHeaders; +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Component; +import org.springframework.web.client.RestClient; +import org.springframework.web.client.RestClientException; + +import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest; +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import edu.harvard.dbmi.avillach.domain.SearchResults; +import edu.harvard.hms.dbmi.avillach.query.config.AggregateProperties; +import edu.harvard.hms.dbmi.avillach.query.hpds.HpdsCommunicationException; +import edu.harvard.hms.dbmi.avillach.query.hpds.ResourceWebClient; + +/** + * Pooled client to the open HPDS backend (+ visualization service) that the aggregate/obfuscation surface talks to. Direct port of + * {@code AggregateDataSharingResourceRS}'s {@code postRequest}/{@code getHttpResponse} plumbing: every downstream call carries + * {@code Authorization: Bearer } (the WAR's {@code Bearer } -- no regression), and every call + * builds a fresh chained request body that carries the inbound query/credentials/resourceUUID but overrides the resourceUUID with the + * configured {@code targetResourceId} when one is set (WAR's {@code createChainRequest}/info-request inline chaining). + * + *

    Only the calls the obfuscation surface actually makes are exposed here: {@link #search} (used to fetch the study-consents allow-list), + * {@link #querySync} (the obfuscated sync path + the internal CROSS_COUNT lookup) and {@link #binContinuous} (visualization binning). The + * async query-lifecycle calls ({@code /query}, {@code /query/{id}/status}, {@code /query/{id}/result}, {@code /query/format}, + * {@code /info}) are NOT proxied through this client: the open async submit is routed through {@code QueryService} (DB-free persistence + + * dispatch, see {@link AggregateService#query}), and every subsequent read op is served by the v3 read ingress + * ({@code /hpds/{backend}/v3/...}, {@link edu.harvard.hms.dbmi.avillach.query.query.HpdsQueryV3Controller}) off the stored (already + * consent-scoped) query. + * + *

    Non-2xx responses and I/O failures surface as {@link HpdsCommunicationException} (mapped to 502 by + * {@code edu.harvard.hms.dbmi.avillach.query.error.GlobalExceptionHandler}), mirroring {@code ResourceWebClient}'s error-handling + * convention for the sibling HPDS client in this module. + */ +@Component +public class AggregateBackendClient { + + /** + * The HPDS response header carrying the query/result metadata (e.g. the result id). Sourced from the module's own + * {@link ResourceWebClient#QUERY_METADATA_FIELD} so the aggregate sync path reads AND re-emits the SAME header name + * ({@code "queryMetadata"}) that the legacy WAR's {@code ResourceWebClient} and both aggregate resources + * ({@code AggregateDataSharingResourceRS}/{@code RSV3}) used -- never a divergent literal that would silently drop the header. + */ + public static final String QUERY_METADATA_FIELD = ResourceWebClient.QUERY_METADATA_FIELD; + + private final RestClient http; + private final AggregateProperties props; + + public AggregateBackendClient(@Qualifier("aggregateRestClient") RestClient http, AggregateProperties props) { + this.http = http; + this.props = props; + } + + public SearchResults search(QueryRequest req) { + return postJson(openUrl("/search"), chain(req), SearchResults.class); + } + + /** Raw body + propagated queryMetadata header. The chained body carries the FULL request (resourceUUID injected). */ + public ResponseEntity querySync(QueryRequest req, AggregateVariant variant) { + String uri = openUrl(variant.downstreamVersionPrefix + "/query/sync"); + try { + return post(uri, chain(req)).retrieve().toEntity(String.class); + } catch (RestClientException e) { + throw new HpdsCommunicationException("Aggregate query/sync call failed: " + uri, e); + } + } + + /** Visualization /bin/continuous (v3 prepends /v3). vizRequest already carries the viz resourceUUID. */ + public String binContinuous(QueryRequest vizRequest, AggregateVariant variant) { + String uri = props.getVisualizationUrl() + variant.downstreamVersionPrefix + "/bin/continuous"; + try { + return withAuth(http.post().uri(uri).contentType(MediaType.APPLICATION_JSON)).body(vizRequest).retrieve().body(String.class); + } catch (RestClientException e) { + throw new HpdsCommunicationException("Aggregate bin/continuous call failed: " + uri, e); + } + } + + // ---- internals ---- + + /** Inject the configured resourceUUID (was target.resource.id) + carry inbound query/credentials. */ + private QueryRequest chain(QueryRequest in) { + QueryRequest out = new GeneralQueryRequest(); + if (in != null) { + out.setQuery(in.getQuery()); + out.setResourceCredentials(in.getResourceCredentials()); + out.setResourceUUID(in.getResourceUUID()); + } + String targetId = props.getTargetResourceId(); + if (targetId != null && !targetId.isEmpty()) { + out.setResourceUUID(UUID.fromString(targetId)); + } + return out; + } + + private String openUrl(String path) { + return props.getHpdsOpenUrl() + path; + } + + private RestClient.RequestBodySpec post(String absoluteUrl, QueryRequest body) { + return withAuth(http.post().uri(absoluteUrl).contentType(MediaType.APPLICATION_JSON)).body(body); + } + + private T postJson(String uri, QueryRequest body, Class type) { + try { + return post(uri, body).retrieve().body(type); + } catch (RestClientException e) { + throw new HpdsCommunicationException("Aggregate backend call failed: " + uri, e); + } + } + + /** Inject the configured open-backend service token (HPDS_OPEN_TOKEN) when present. */ + private RestClient.RequestBodySpec withAuth(RestClient.RequestBodySpec spec) { + String token = props.getHpdsOpenToken(); + if (token != null && !token.isBlank()) { + spec = spec.header(HttpHeaders.AUTHORIZATION, "Bearer " + token); + } + return spec; + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateController.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateController.java new file mode 100644 index 000000000..79de883b3 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateController.java @@ -0,0 +1,55 @@ +package edu.harvard.hms.dbmi.avillach.query.aggregate; + +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import org.springframework.web.bind.annotation.PostMapping; +import org.springframework.web.bind.annotation.RequestBody; +import org.springframework.web.bind.annotation.RequestMapping; +import org.springframework.web.bind.annotation.RestController; + +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import edu.harvard.dbmi.avillach.domain.QueryStatus; +import io.swagger.v3.oas.annotations.tags.Tag; + +/** + * The v1 aggregate/obfuscation ingress: {@code POST /hpds/open/query/sync} and {@code POST /hpds/open/query}. Direct port of + * {@code AggregateDataSharingResourceRS}'s {@code querySync}/{@code query} entry points (no inline audit -- the gateway audits this path, + * see {@code AuditRouteTable}). Open-access: no {@link edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUser} guard here -- + * {@code WebSecurityConfig} already requires an authenticated caller for all of {@code /hpds/**} (the "open"/"auth" distinction is about + * which HPDS backend answers the query and whether its data is public, not about API-level authentication). + * + *

    {@code /hpds/open/query[/sync]} routing: the generic v1 ingress ({@code /hpds/{backend}/query[/sync]} for any backend) was + * removed, so {@code /hpds/auth/query[/sync]} no longer exists at all. {@code /hpds/open/query} and {@code /hpds/open/query/sync} are + * served ONLY by this controller's literal mappings (consent-scoped / obfuscated). The remaining open-path read endpoints + * ({@code /hpds/open/v3/query/{id}/status}, {@code /result}, {@code /signed-url}, {@code /metadata}) flow through + * {@link edu.harvard.hms.dbmi.avillach.query.query.HpdsQueryV3Controller} (the generic v3 ingress) instead. + * + *

    Two open submissions are intercepted: {@code query/sync} (the only endpoint the WAR ever obfuscated -- see {@link AggregateService}'s + * Javadoc) and {@code query} (the async submit, which the WAR consent-scoped via {@code changeQueryToOpenCrossCount} for CROSS_COUNT before + * dispatch -- finding I6). The async submit delegates persistence + dispatch to {@code QueryService}, so the STORED query is the rewritten, + * consent-scoped one; the subsequent read endpoints therefore stay on the generic controller and operate on the safe stored query. This + * controller deliberately does NOT re-implement {@code /info}, {@code /search}, {@code /query/{id}/status}, {@code /query/{id}/result}, or + * {@code /query/format} under the literal {@code /hpds/open} prefix -- doing so would shadow them away from the generic controller for no + * benefit (they were never obfuscated in the WAR, and the read ops already operate on the consent-scoped stored query). + */ +@RestController +@RequestMapping("/hpds/open") +@Tag(name = "aggregate-data-sharing (open)") +public class AggregateController { + + private final AggregateService service; + + public AggregateController(AggregateService service) { + this.service = service; + } + + @PostMapping(value = "/query/sync", produces = MediaType.APPLICATION_JSON_VALUE) + public ResponseEntity querySync(@RequestBody QueryRequest req) { + return service.querySync(req, AggregateVariant.V1); + } + + @PostMapping("/query") + public QueryStatus query(@RequestBody QueryRequest req) { + return service.query(req, AggregateVariant.V1); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateService.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateService.java new file mode 100644 index 000000000..028ba5495 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateService.java @@ -0,0 +1,248 @@ +package edu.harvard.hms.dbmi.avillach.query.aggregate; + +import java.io.IOException; +import java.io.UncheckedIOException; +import java.util.LinkedHashMap; +import java.util.Map; +import java.util.Set; +import java.util.UUID; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.http.HttpStatus; +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Service; + +import com.fasterxml.jackson.core.type.TypeReference; +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.node.ArrayNode; +import com.fasterxml.jackson.databind.node.ObjectNode; + +import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest; +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import edu.harvard.dbmi.avillach.domain.QueryStatus; +import edu.harvard.dbmi.avillach.domain.SearchResults; +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; +import edu.harvard.hms.dbmi.avillach.query.config.AggregateProperties; +import edu.harvard.hms.dbmi.avillach.query.hpds.HpdsBackendSelector; +import edu.harvard.hms.dbmi.avillach.query.query.QueryService; + +/** + * Direct port of {@code AggregateDataSharingResourceRS}/{@code AggregateDataSharingResourceRSV3}'s orchestration -- the querySync + * obfuscation dispatch, the {@code CROSS_COUNT} query alteration ({@code changeQueryToOpenCrossCount}), and the continuous-suppression + * rule. Stores no {@code Query} rows itself (this module is DB-free); the async open submit ({@link #query}) delegates persistence and HPDS + * dispatch to {@link QueryService} (which persists over HTTP via operations-service), and does not implement {@code RequestScopedHeader} + * (dead code in the WAR -- dropped) or perform inline audit logging (handled in the gateway). + * + *

    PRIVACY-CRITICAL: {@link #ALLOWED_RESULT_TYPES} is the exact 10-type allow-list from the WAR; a type not on it is rejected with + * a 400 rather than silently forwarded. The per-type dispatch in {@link #getExpectedResponse} determines which types get threshold/variance + * obfuscation (COUNT, CROSS_COUNT, CATEGORICAL_CROSS_COUNT, CONTINUOUS_CROSS_COUNT) versus a raw pass-through (INFO_COLUMN_LISTING, + * OBSERVATION_COUNT, OBSERVATION_CROSS_COUNT, VARIANT_COUNT_FOR_QUERY, AGGREGATE_VCF_EXCERPT, VCF_EXCERPT -- none of these were obfuscated + * in the WAR either). Any divergence here is a privacy regression. + */ +@Service +public class AggregateService { + + private static final String STUDIES_CONSENTS_PATH = "\\_studies_consents\\"; + + /** Exact port of the WAR's {@code querySync} allow-list (identical in v1 and v3). */ + private static final Set ALLOWED_RESULT_TYPES = Set.of( + "COUNT", "CROSS_COUNT", "INFO_COLUMN_LISTING", "OBSERVATION_COUNT", "OBSERVATION_CROSS_COUNT", "CATEGORICAL_CROSS_COUNT", + "CONTINUOUS_CROSS_COUNT", "VARIANT_COUNT_FOR_QUERY", "AGGREGATE_VCF_EXCERPT", "VCF_EXCERPT" + ); + + private final Logger logger = LoggerFactory.getLogger(getClass()); + private final ObjectMapper objectMapper = new ObjectMapper(); + + private final AggregateBackendClient backend; + private final ObfuscationService obfuscation; + private final AggregateProperties props; + private final QueryService queryService; + + public AggregateService( + AggregateBackendClient backend, ObfuscationService obfuscation, AggregateProperties props, QueryService queryService + ) { + this.backend = backend; + this.obfuscation = obfuscation; + this.props = props; + this.queryService = queryService; + } + + // ---- async open submit ---- + + /** + * Async open-channel submit. Direct port of the WAR aggregate resources' {@code query()} entry point + * ({@code AggregateDataSharingResourceRS.query} / {@code RSV3.query}): validate the request and -- only for a {@code CROSS_COUNT} + * submission -- rewrite it via {@link #changeQueryToOpenCrossCount} (force {@code CROSS_COUNT} + inject the full study-consents + * allow-list under the variant's consents field) BEFORE it is persisted and dispatched. Non-{@code CROSS_COUNT} types are forwarded + * unchanged, exactly as the WAR's async {@code query()} did (it had no allow-list; that guard existed only on {@code querySync}). + * + *

    Consent-scoping fix (I6): persistence + HPDS dispatch are delegated to {@link QueryService} (the module's DB-free create + * flow), so the STORED query is the REWRITTEN one. Every later status/result/signed-url/metadata call -- served by the v3 read ingress + * ({@code /hpds/{backend}/v3/...}, {@link edu.harvard.hms.dbmi.avillach.query.query.HpdsQueryV3Controller}) off the stored query -- + * therefore operates on the safe, consent-scoped query rather than the raw submission. This closes the gap where an unwired open async + * path dispatched the raw query with no consent-scoping. + */ + public QueryStatus query(QueryRequest req, AggregateVariant variant) { + checkQuery(req); + JsonNode node = objectMapper.valueToTree(req.getQuery()); + req.setQuery(node); + requireExpectedResultType(node); + if ("CROSS_COUNT".equalsIgnoreCase(node.get("expectedResultType").asText())) { + changeQueryToOpenCrossCount(req, variant); + } + return variant == AggregateVariant.V3 ? queryService.queryV3(HpdsBackendSelector.OPEN, req) + : queryService.query(HpdsBackendSelector.OPEN, req); + } + + // ---- the obfuscation core ---- + + public ResponseEntity querySync(QueryRequest req, AggregateVariant variant) { + checkQuery(req); + JsonNode node = objectMapper.valueToTree(req.getQuery()); + req.setQuery(node); + requireExpectedResultType(node); + + String expectedResultType = node.get("expectedResultType").asText(); + if (!ALLOWED_RESULT_TYPES.contains(expectedResultType)) { + logger.warn("Incorrect Result Type: {}", expectedResultType); + throw new PicsureException(HttpStatus.BAD_REQUEST, "bad_request", "Incorrect result type: " + expectedResultType); + } + + if ("CROSS_COUNT".equalsIgnoreCase(expectedResultType)) { + changeQueryToOpenCrossCount(req, variant); + } + + ResponseEntity backendResp = backend.querySync(req, variant); + String entityString = backendResp.getBody(); + String responseString = getExpectedResponse(expectedResultType, entityString, req, variant); + + ResponseEntity.BodyBuilder out = ResponseEntity.ok().contentType(MediaType.APPLICATION_JSON); + String metadata = backendResp.getHeaders().getFirst(AggregateBackendClient.QUERY_METADATA_FIELD); + if (metadata != null) { + out.header(AggregateBackendClient.QUERY_METADATA_FIELD, metadata); + } + return out.body(responseString); + } + + /** + * Dispatches on {@code expectedResultType} to the matching obfuscation path. Types allow-listed but not obfuscated in the WAR + * (INFO_COLUMN_LISTING, OBSERVATION_COUNT, OBSERVATION_CROSS_COUNT, VARIANT_COUNT_FOR_QUERY, AGGREGATE_VCF_EXCERPT, VCF_EXCERPT) fall + * through unmodified. + */ + private String getExpectedResponse(String expectedResultType, String entityString, QueryRequest req, AggregateVariant variant) { + try { + switch (expectedResultType) { + case "COUNT": + return obfuscation.obfuscateCount(entityString); + case "CROSS_COUNT": + return objectMapper.writeValueAsString(obfuscation.processCrossCounts(entityString)); + case "CATEGORICAL_CROSS_COUNT": + return obfuscation.processCategoricalCrossCounts(entityString, getCrossCountForQuery(req, variant)); + case "CONTINUOUS_CROSS_COUNT": + return processContinuousCrossCounts(entityString, getCrossCountForQuery(req, variant), req, variant); + default: + return entityString; + } + } catch (IOException e) { + throw new UncheckedIOException("Error processing aggregate response", e); + } + } + + /** No matter the type, fetch the CROSS_COUNT incl. ALL study consents (used for variance + suppression). */ + private String getCrossCountForQuery(QueryRequest req, AggregateVariant variant) { + changeQueryToOpenCrossCount(req, variant); + return backend.querySync(req, variant).getBody(); + } + + private String processContinuousCrossCounts(String continuousJson, String crossCountJson, QueryRequest req, AggregateVariant variant) + throws IOException { + if (continuousJson == null || crossCountJson == null) { + return null; + } + Map crossCounts = objectMapper.readValue(crossCountJson, new TypeReference<>() {}); + int generatedVariance = obfuscation.generateVarianceWithCrossCounts(crossCounts); + + if (obfuscation.canShowContinuousCrossCounts(crossCounts)) { + // NOTE: despite the name, this signals SUPPRESSION -- ported verbatim from ObfuscationService/the WAR. + return null; + } + + if (props.hasVisualization()) { + Map> continuous = objectMapper.readValue(continuousJson, new TypeReference<>() {}); + Map> binned = getBinnedContinuousCrossCount(req, continuous, variant); + return objectMapper.writeValueAsString(obfuscation.obfuscateCrossCount(generatedVariance, binned)); + } else { + Map> continuous = objectMapper.readValue(continuousJson, new TypeReference<>() {}); + return objectMapper.writeValueAsString(obfuscation.obfuscateCrossCount(generatedVariance, continuous)); + } + } + + /** Replaces the WAR's {@code ResourceRepository.getById(visualizationResourceId)} with the configured viz URL (DB-free). */ + private Map> getBinnedContinuousCrossCount( + QueryRequest req, Map> continuous, AggregateVariant variant + ) throws IOException { + QueryRequest vizRequest = new GeneralQueryRequest(); + vizRequest.setQuery(continuous); + vizRequest.setResourceCredentials(req.getResourceCredentials()); + String vizId = props.getVisualizationResourceId(); + if (vizId != null && !vizId.isBlank()) { + vizRequest.setResourceUUID(UUID.fromString(vizId)); + } + String binResponse = backend.binContinuous(vizRequest, variant); + return objectMapper.readValue(binResponse, new TypeReference<>() {}); + } + + // ---- query mutation (variant-aware) ---- + + /** Sets expectedResultType to CROSS_COUNT and injects the full study-consents allow-list under the variant's consents field. */ + private QueryRequest changeQueryToOpenCrossCount(QueryRequest req, AggregateVariant variant) { + JsonNode node = objectMapper.valueToTree(req.getQuery()); + JsonNode withCrossCount = setExpectedResultTypeToCrossCount(node); + JsonNode withConsents = addStudyConsentsToQuery(withCrossCount, variant); + req.setQuery(withConsents); + return req; + } + + private JsonNode setExpectedResultTypeToCrossCount(JsonNode jsonNode) { + for (JsonNode parent : jsonNode.findParents("expectedResultType")) { + ((ObjectNode) parent).put("expectedResultType", "CROSS_COUNT"); + } + return jsonNode; + } + + private JsonNode addStudyConsentsToQuery(JsonNode jsonNode, AggregateVariant variant) { + SearchResults consentResults = getAllStudyConsents(); + LinkedHashMap resultsMap = objectMapper.convertValue(consentResults.getResults(), new TypeReference<>() {}); + LinkedHashMap phenotypes = objectMapper.convertValue(resultsMap.get("phenotypes"), new TypeReference<>() {}); + + ArrayNode arrayNode = objectMapper.createArrayNode(); + for (String key : phenotypes.keySet()) { + arrayNode.add(key); + } + ((ObjectNode) jsonNode).set(variant.consentsField, arrayNode); // v1: crossCountFields, v3: select + return jsonNode; + } + + private SearchResults getAllStudyConsents() { + QueryRequest studiesConsents = new GeneralQueryRequest(); + studiesConsents.setQuery(STUDIES_CONSENTS_PATH); + return backend.search(studiesConsents); // /search -- NO /v3 prefix in either variant + } + + // ---- guards ---- + + private static void checkQuery(QueryRequest req) { + if (req == null || req.getQuery() == null) { + throw new PicsureException(HttpStatus.BAD_REQUEST, "bad_request", "Missing query data"); + } + } + + private static void requireExpectedResultType(JsonNode node) { + if (!node.has("expectedResultType")) { + throw new PicsureException(HttpStatus.BAD_REQUEST, "bad_request", "Missing query data"); + } + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateV3Controller.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateV3Controller.java new file mode 100644 index 000000000..e094a6080 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateV3Controller.java @@ -0,0 +1,47 @@ +package edu.harvard.hms.dbmi.avillach.query.aggregate; + +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import org.springframework.web.bind.annotation.PostMapping; +import org.springframework.web.bind.annotation.RequestBody; +import org.springframework.web.bind.annotation.RequestMapping; +import org.springframework.web.bind.annotation.RestController; + +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import edu.harvard.dbmi.avillach.domain.QueryStatus; +import io.swagger.v3.oas.annotations.tags.Tag; + +/** + * The v3 aggregate/obfuscation ingress: {@code POST /hpds/open/v3/query/sync} and {@code POST /hpds/open/v3/query}. Same delegation as + * {@link AggregateController} except it passes {@link AggregateVariant#V3} to {@link AggregateService}, which yields the {@code select} + * consents field (not {@code crossCountFields}) and the {@code /v3} downstream HPDS prefix. No inline audit here either -- the gateway + * audits both variants identically, closing the WAR's v3 missing-audit gap. Both v3 aggregate resources + * ({@code AggregateDataSharingResourceRSV3}) supported the async {@code query} submit, so it is mirrored here. + * + *

    Coexistence with {@code HpdsQueryV3Controller}: that controller maps the generic, path-variable + * {@code /hpds/{backend}/v3/query} and {@code /hpds/{backend}/v3/query/sync}. This controller maps the LITERAL {@code /hpds/open/v3/query} + * and {@code /hpds/open/v3/query/sync}, which Spring MVC prefers, so {@code /hpds/auth/v3/query[/sync]} still flows through the generic + * controller. As with the v1 controller, only the two open submissions ({@code query/sync}, {@code query}) are intercepted -- the open-path + * v3 read endpoints are deliberately left to the generic controller (see {@link AggregateController}'s Javadoc for the full rationale). + */ +@RestController +@RequestMapping("/hpds/open/v3") +@Tag(name = "aggregate-data-sharing (open, v3)") +public class AggregateV3Controller { + + private final AggregateService service; + + public AggregateV3Controller(AggregateService service) { + this.service = service; + } + + @PostMapping(value = "/query/sync", produces = MediaType.APPLICATION_JSON_VALUE) + public ResponseEntity querySync(@RequestBody QueryRequest req) { + return service.querySync(req, AggregateVariant.V3); + } + + @PostMapping("/query") + public QueryStatus query(@RequestBody QueryRequest req) { + return service.query(req, AggregateVariant.V3); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateVariant.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateVariant.java new file mode 100644 index 000000000..2bf638291 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateVariant.java @@ -0,0 +1,23 @@ +package edu.harvard.hms.dbmi.avillach.query.aggregate; + +/** + * Captures the only two ways the v1 ({@code /aggregate-data-sharing}) and v3 ({@code /v3/aggregate-data-sharing}) WAR resources diverged: + * the query field name used to carry the study-consents allow-list injected by {@code changeQueryToOpenCrossCount} + * ({@code crossCountFields} for v1, {@code select} for v3), and the downstream path prefix applied ONLY to the {@code query/sync} and + * {@code bin/continuous} calls (the v3 WAR's {@code getHttpResponse} hardcoded a {@code "/v3"} prefix; every other downstream call -- + * {@code /info}, {@code /search}, {@code /query}, {@code /query/{id}/status}, {@code /query/{id}/result}, {@code /query/format} -- stayed + * unprefixed in both variants). + */ +public enum AggregateVariant { + V1("crossCountFields", ""), V3("select", "/v3"); + + public final String consentsField; + + /** Prepended to the downstream path for query/sync + bin/continuous ONLY. */ + public final String downstreamVersionPrefix; + + AggregateVariant(String consentsField, String downstreamVersionPrefix) { + this.consentsField = consentsField; + this.downstreamVersionPrefix = downstreamVersionPrefix; + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/ObfuscatedCount.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/ObfuscatedCount.java new file mode 100644 index 000000000..c6222ed85 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/ObfuscatedCount.java @@ -0,0 +1,69 @@ +package edu.harvard.hms.dbmi.avillach.query.aggregate; + +import java.util.Objects; + +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; + +/** + * Direct port of {@code edu.harvard.hms.dbmi.avillach.ObfuscatedCount} from the WAR's pic-sure-aggregate-data-sharing-resource -- an + * immutable {count, display, variance} carrier serialized to JSON. + */ +public final class ObfuscatedCount { + + @JsonProperty("count") + private final int count; + + @JsonProperty("display") + private final String display; + + /** + * Half-width of the uncertainty band around {@link #count}, or null when the value is exact (authorized path). Consumers render the + * band as [max(0, count - variance), count + variance]. + */ + @JsonProperty("variance") + private final Integer variance; + + @JsonCreator + public ObfuscatedCount( + @JsonProperty("count") int count, @JsonProperty("display") String display, @JsonProperty("variance") Integer variance + ) { + this.count = count; + this.display = display; + this.variance = variance; + } + + /** Wraps a plain (non-obfuscated) integer count; display is the stringified number, variance null. */ + public static ObfuscatedCount ofInt(int count) { + return new ObfuscatedCount(count, Integer.toString(count), null); + } + + public int count() { + return count; + } + + public String display() { + return display; + } + + public Integer variance() { + return variance; + } + + @Override + public boolean equals(Object other) { + if (this == other) return true; + if (!(other instanceof ObfuscatedCount that)) return false; + return count == that.count && Objects.equals(display, that.display) && Objects.equals(variance, that.variance); + } + + @Override + public int hashCode() { + return Objects.hash(count, display, variance); + } + + @Override + public String toString() { + return "ObfuscatedCount{count=" + count + ", display='" + display + "', variance=" + variance + "}"; + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/ObfuscationService.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/ObfuscationService.java new file mode 100644 index 000000000..349104e78 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/ObfuscationService.java @@ -0,0 +1,188 @@ +package edu.harvard.hms.dbmi.avillach.query.aggregate; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.core.type.TypeReference; +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.hms.dbmi.avillach.query.config.AggregateProperties; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.stereotype.Service; + +import java.util.ArrayList; +import java.util.HashSet; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.Optional; +import java.util.Set; +import java.util.UUID; + +/** + * Pure obfuscation math ported from {@code edu.harvard.hms.dbmi.avillach.AggregateDataSharingResourceRS} (identical across the WAR's V1 and + * V3 variants). This is the privacy-critical surface: the threshold/variance/salt math, the randomize() logic, and the "< threshold" + * suppression rule must match the WAR EXACTLY -- any divergence changes what counts get suppressed/perturbed, which is a privacy + * regression. + */ +@Service +public class ObfuscationService { + + private static final String STUDIES_CONSENTS_KEY = "\\_studies_consents\\"; + + private final Logger logger = LoggerFactory.getLogger(getClass()); + private final ObjectMapper objectMapper = new ObjectMapper(); + private final VisualizationFormatter visualizationFormatter; + + private final int threshold; + private final int variance; + private final String randomSalt; + + public ObfuscationService(AggregateProperties props, VisualizationFormatter visualizationFormatter) { + this.visualizationFormatter = visualizationFormatter; + this.threshold = props.getObfuscation().getThreshold(); + this.variance = props.getObfuscation().getVariance(); + String salt = props.getObfuscation().getSalt(); + this.randomSalt = (salt == null || salt.isBlank()) ? UUID.randomUUID().toString() : salt; + } + + public int getThreshold() { + return threshold; + } + + /** + * Generates a random variance for the request based on the passed entityString. The variance is between -variance and +variance: the + * salt is appended to the entityString, hashed, and the hashcode is taken mod (variance * 2 + 1), shifted down by variance. Ported + * verbatim from the WAR's generateRequestVariance(). + */ + int generateRequestVariance(String entityString) { + return Math.abs((entityString + randomSalt).hashCode()) % (variance * 2 + 1) - variance; + } + + ObfuscatedCount randomize(int crossCount, int requestVariance) { + int randomized = Math.max(crossCount + requestVariance, threshold); + return new ObfuscatedCount(randomized, randomized + " ±" + variance, variance); + } + + /** + * Core privacy floor: small (potentially identifiable) cohorts get hidden behind a "< threshold" display. The value is encoded as + * count 0 with variance threshold-1, so consumers rendering the uncertainty band [max(0, count - variance), count + variance] draw + * 0..threshold-1 -- the true count lies somewhere in that band but we don't disclose where. + * + *

    Returns empty when the value is at or above the threshold (caller should then call {@link #randomize}). + */ + Optional applyThresholdFloor(int actualCount) { + if (actualCount < threshold) { + return Optional.of(new ObfuscatedCount(0, "< " + threshold, threshold - 1)); + } + return Optional.empty(); + } + + /** + * String overload for callers (COUNT / CROSS_COUNT) that hold the value as a JSON string. Logs and returns empty on parse failure so + * the caller can fall through to its untouched-value path. + */ + Optional applyThresholdFloor(String actualCount) { + try { + return applyThresholdFloor(Integer.parseInt(actualCount)); + } catch (NumberFormatException nfe) { + logger.warn("Count was not a number! {}", actualCount); + return Optional.empty(); + } + } + + /** COUNT case: floor if below threshold, else variance-randomize; non-numeric passes through unchanged. */ + public String obfuscateCount(String entityString) { + try { + int count = Integer.parseInt(entityString); + int requestVariance = generateRequestVariance(entityString); + return applyThresholdFloor(count).map(ObfuscatedCount::display).orElseGet(() -> randomize(count, requestVariance).display()); + } catch (NumberFormatException nfe) { + logger.warn("COUNT response was not a number! {}", entityString); + return entityString; + } + } + + /** CROSS_COUNT case: floor-then-randomize each entry with one deterministic per-query variance. */ + public Map processCrossCounts(String entityString) throws JsonProcessingException { + Map crossCounts = objectMapper.readValue(entityString, new TypeReference<>() {}); + int requestVariance = generateVarianceWithCrossCounts(crossCounts); + return obfuscateCrossCounts(crossCounts, requestVariance); + } + + private Map obfuscateCrossCounts(Map crossCounts, int requestVariance) { + Set obfuscatedKeys = new HashSet<>(); + if (crossCounts != null) { + crossCounts.keySet().forEach(key -> { + String crossCount = crossCounts.get(key); + Optional floored = applyThresholdFloor(crossCount); + floored.ifPresent(x -> obfuscatedKeys.add(key)); + crossCounts.put(key, floored.map(ObfuscatedCount::display).orElse(crossCount)); + }); + crossCounts.keySet().forEach(key -> { + String crossCount = crossCounts.get(key); + if (!obfuscatedKeys.contains(key)) { + crossCounts.put(key, randomize(Integer.parseInt(crossCount), requestVariance).display()); + } + }); + } + return crossCounts; + } + + /** Deterministic per-query variance from the sorted key:value\n join (so reruns match). */ + public int generateVarianceWithCrossCounts(Map crossCounts) { + List> entryList = new ArrayList<>(crossCounts.entrySet()); + entryList.sort(Map.Entry.comparingByKey()); + StringBuilder crossCountsString = new StringBuilder(); + entryList.forEach(e -> crossCountsString.append(e.getKey()).append(":").append(e.getValue()).append("\n")); + return generateRequestVariance(crossCountsString.toString()); + } + + /** Suppress continuous when the study-consents cross-count is below threshold or zero. */ + public boolean canShowContinuousCrossCounts(Map crossCounts) { + String lessThanThresholdStr = "< " + this.threshold; + String v = crossCounts.get(STUDIES_CONSENTS_KEY); + return v.contains(lessThanThresholdStr) || v.equals("0"); + } + + /** CATEGORICAL case: bucket via the formatter, then obfuscate. Null inputs short-circuit to null. */ + public String processCategoricalCrossCounts(String categoricalEntityString, String crossCountEntityString) + throws JsonProcessingException { + if (categoricalEntityString == null || crossCountEntityString == null) { + return null; + } + Map crossCounts = objectMapper.readValue(crossCountEntityString, new TypeReference<>() {}); + int generatedVariance = generateVarianceWithCrossCounts(crossCounts); + + Map> categorical = objectMapper.readValue(categoricalEntityString, new TypeReference<>() {}); + if (categorical == null) { + return categoricalEntityString; + } + for (Map.Entry> entry : categorical.entrySet()) { + if (visualizationFormatter.skipKey(entry.getKey())) continue; + categorical.put(entry.getKey(), visualizationFormatter.processResults(entry.getValue())); + } + return objectMapper.writeValueAsString(obfuscateCrossCount(generatedVariance, categorical)); + } + + /** Obfuscate every value of a nested cross-count map. */ + public Map> obfuscateCrossCount( + int generatedVariance, Map> crossCount + ) { + Map> result = new LinkedHashMap<>(); + crossCount.forEach((key, value) -> { + Map obfuscated = new LinkedHashMap<>(); + value.forEach((innerKey, innerValue) -> { + int count = toInt(innerValue); + obfuscated.put(innerKey, applyThresholdFloor(count).orElseGet(() -> randomize(count, generatedVariance))); + }); + result.put(key, obfuscated); + }); + return result; + } + + /** Jackson hands Object-typed counts (Integer/Long/Double/String); narrow to int, preserving the WAR's breadth. */ + static int toInt(Object value) { + if (value instanceof Number n) return n.intValue(); + if (value instanceof String s) return Integer.parseInt(s); + throw new IllegalArgumentException("Cross-count value was neither Number nor numeric String: " + value); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/VisualizationFormatter.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/VisualizationFormatter.java new file mode 100644 index 000000000..b4b7e1350 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/aggregate/VisualizationFormatter.java @@ -0,0 +1,99 @@ +package edu.harvard.hms.dbmi.avillach.query.aggregate; + +import org.springframework.stereotype.Component; + +import java.util.Collections; +import java.util.HashMap; +import java.util.HashSet; +import java.util.LinkedHashMap; +import java.util.Map; +import java.util.function.Supplier; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +/** + * Ported from {@code edu.harvard.dbmi.avillach.util.VisualizationUtil} (pic-sure-util) -- only the methods the aggregate obfuscation path + * uses ({@code skipKey}, {@code processResults} + its private helpers). Self-contained so the query service does not depend on the + * WildFly-era pic-sure-util. Logic is an unmodified, instance-method port of the static original. + */ +@Component +public class VisualizationFormatter { + + private static final String CONSENTS_KEY = "\\_consents\\"; + private static final String HARMONIZED_CONSENT_KEY = "\\_harmonized_consent\\"; + private static final String TOPMED_CONSENTS_KEY = "\\_topmed_consents\\"; + private static final String PARENT_CONSENTS_KEY = "\\_parent_consents\\"; + private static final int MAX_X_LABEL_LINE_LENGTH = 45; + private static final boolean LIMITED = true; + private static final int LIMIT_SIZE = 7; + + public boolean skipKey(String key) { + return key.equals(CONSENTS_KEY) || key.equals(HARMONIZED_CONSENT_KEY) || key.equals(TOPMED_CONSENTS_KEY) + || key.equals(PARENT_CONSENTS_KEY); + } + + public Map processResults(Map axisMap) { + Map converted = new HashMap<>(); + for (Map.Entry entry : axisMap.entrySet()) { + if (entry.getValue() instanceof Integer i) { + converted.put(entry.getKey(), i); + } + } + return new HashMap<>(doProcessResults(converted)); + } + + private Map doProcessResults(Map axisMap) { + Map finalAxisMap = axisMap; + if (LIMITED && axisMap.size() > (LIMIT_SIZE + 1)) { + Supplier>> stream = + () -> finalAxisMap.entrySet().stream().sorted(Collections.reverseOrder(Map.Entry.comparingByValue())); + Integer otherSum = stream.get().skip(LIMIT_SIZE).mapToInt(Map.Entry::getValue).sum(); + axisMap = stream.get().limit(LIMIT_SIZE) + .collect(Collectors.toMap(Map.Entry::getKey, Map.Entry::getValue, (e1, e2) -> e2, LinkedHashMap::new)); + axisMap = limitKeySize(axisMap).entrySet().stream().sorted(Collections.reverseOrder(Map.Entry.comparingByValue())) + .collect(Collectors.toMap(Map.Entry::getKey, Map.Entry::getValue, (e1, e2) -> e2, LinkedHashMap::new)); + axisMap.put("Other", otherSum); + } else { + axisMap = limitKeySize(finalAxisMap).entrySet().stream().sorted(Collections.reverseOrder(Map.Entry.comparingByValue())) + .collect(Collectors.toMap(Map.Entry::getKey, Map.Entry::getValue, (e1, e2) -> e2, LinkedHashMap::new)); + } + return axisMap; + } + + private Map limitKeySize(Map axisMap) { + if (axisMap == null) throw new IllegalArgumentException("axisMap cannot be null"); + Map newAxisMap = new HashMap<>(); + HashSet keys = new HashSet<>(); + axisMap.forEach((key, value) -> { + String adjustedKey = key.length() < MAX_X_LABEL_LINE_LENGTH ? key : createAdjustedKey(axisMap, keys, key); + newAxisMap.put(adjustedKey, value); + keys.add(adjustedKey); + }); + return newAxisMap; + } + + private String createAdjustedKey(Map axisMap, HashSet keys, String key) { + String keyPrefix = key.substring(0, MAX_X_LABEL_LINE_LENGTH); + return isKeyPrefixInAxisMap(axisMap, keyPrefix) ? generateUniqueKey(keys, key) : appendEllipsis(keyPrefix); + } + + private boolean isKeyPrefixInAxisMap(Map axisMap, String keyPrefix) { + return axisMap.keySet().stream().anyMatch(k -> k.startsWith(keyPrefix)); + } + + private String generateUniqueKey(HashSet keys, String key) { + int countFromEnd = 6; + String proposedKey; + do { + proposedKey = String.format( + "%s...%s", key.substring(0, MAX_X_LABEL_LINE_LENGTH - 3 - countFromEnd), key.substring(key.length() - countFromEnd) + ); + countFromEnd++; + } while (keys.contains(proposedKey)); + return proposedKey; + } + + private String appendEllipsis(String keyPrefixAdjusted) { + return String.format("%s...", keyPrefixAdjusted); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/ActuatorSecurityConfig.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/ActuatorSecurityConfig.java new file mode 100644 index 000000000..2cfe8e1cc --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/ActuatorSecurityConfig.java @@ -0,0 +1,28 @@ +package edu.harvard.hms.dbmi.avillach.query.config; + +import org.springframework.boot.context.properties.EnableConfigurationProperties; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.core.annotation.Order; +import org.springframework.security.config.annotation.web.builders.HttpSecurity; +import org.springframework.security.web.SecurityFilterChain; + +import edu.harvard.hms.dbmi.avillach.commons.security.ActuatorSecurityHelper; +import edu.harvard.hms.dbmi.avillach.commons.security.ActuatorTokenProperties; + +/** + * Gates {@code /actuator/**} behind {@code X-Application-Token} via the shared {@link ActuatorSecurityHelper}. Registered at + * {@code @Order(0)} so it wins over {@link WebSecurityConfig}'s gateway-header-trust main chain ({@code @Order(10)}) for actuator paths -- + * the two chains never compete because {@code EndpointRequest.toAnyEndpoint()} scopes this chain to {@code /actuator/**} only, leaving + * {@code /hpds/**}, {@code /query/**}, {@code /search/**} governed exactly as {@link WebSecurityConfig} defines. + */ +@Configuration +@EnableConfigurationProperties(ActuatorTokenProperties.class) +public class ActuatorSecurityConfig { + + @Bean + @Order(0) + SecurityFilterChain actuatorChain(HttpSecurity http, ActuatorTokenProperties props) throws Exception { + return ActuatorSecurityHelper.actuatorChain(http, props); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/AggregateConfig.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/AggregateConfig.java new file mode 100644 index 000000000..7af02a2b3 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/AggregateConfig.java @@ -0,0 +1,15 @@ +package edu.harvard.hms.dbmi.avillach.query.config; + +import org.springframework.boot.context.properties.EnableConfigurationProperties; +import org.springframework.context.annotation.Configuration; + +/** + * Registers {@link AggregateProperties} as a bean, mirroring how {@link HpdsClientConfig} enables {@link HpdsProperties}. + * {@code ObfuscationService} (query.aggregate) is a component-scanned {@code @Service} that depends on {@link AggregateProperties} being + * bound from config, so this wiring has to exist even though the HTTP orchestration around it (visualization RestClient, controllers) is a + * later unit. + */ +@Configuration +@EnableConfigurationProperties(AggregateProperties.class) +public class AggregateConfig { +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/AggregateHttpClientConfig.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/AggregateHttpClientConfig.java new file mode 100644 index 000000000..d8c536271 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/AggregateHttpClientConfig.java @@ -0,0 +1,38 @@ +package edu.harvard.hms.dbmi.avillach.query.config; + +import java.util.concurrent.TimeUnit; + +import org.apache.hc.client5.http.config.ConnectionConfig; +import org.apache.hc.client5.http.impl.classic.CloseableHttpClient; +import org.apache.hc.client5.http.impl.classic.HttpClients; +import org.apache.hc.client5.http.impl.io.PoolingHttpClientConnectionManager; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.http.client.HttpComponentsClientHttpRequestFactory; +import org.springframework.web.client.RestClient; + +/** + * A single pooled {@link RestClient} (Apache HttpComponents 5, maxTotal 100 / 20-per-route -- matching the legacy WAR's + * {@code PoolingHttpClientConnectionManager}, see {@code AggregateHttpClientConfig}'s counterpart {@link HpdsClientConfig}) for talking to + * the open HPDS backend and the visualization service. It has NO base URL and NO default Authorization header: absolute per-request URLs + * and the {@code Authorization: Bearer } header are supplied per-call by {@code AggregateBackendClient}. The + * {@link AggregateProperties} bean itself is already registered by {@code AggregateConfig} (Unit 5a) via + * {@code @EnableConfigurationProperties} -- this class only adds the HTTP client bean. + */ +@Configuration +public class AggregateHttpClientConfig { + + @Bean("aggregateRestClient") + RestClient aggregateRestClient(AggregateProperties props) { + PoolingHttpClientConnectionManager cm = new PoolingHttpClientConnectionManager(); + cm.setMaxTotal(100); // matches the WAR's PoolingHttpClientConnectionManager + cm.setDefaultMaxPerRoute(20); + cm.setDefaultConnectionConfig( + ConnectionConfig.custom().setConnectTimeout(props.getConnectTimeoutSec(), TimeUnit.SECONDS) + .setSocketTimeout(props.getReadTimeoutSec(), TimeUnit.SECONDS).build() + ); + CloseableHttpClient httpClient = HttpClients.custom().setConnectionManager(cm).build(); + HttpComponentsClientHttpRequestFactory rf = new HttpComponentsClientHttpRequestFactory(httpClient); + return RestClient.builder().requestFactory(rf).build(); // no base URL -- absolute per call + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/AggregateProperties.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/AggregateProperties.java new file mode 100644 index 000000000..44501a893 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/AggregateProperties.java @@ -0,0 +1,125 @@ +package edu.harvard.hms.dbmi.avillach.query.config; + +import org.springframework.boot.context.properties.ConfigurationProperties; + +/** + * Aggregate/obfuscation config (replaces the WAR's {@code resource.properties} + DB resource lookup). The {@code @ConfigurationProperties} + * bean is declared/enabled in the aggregate wiring config (a later task); this class is a plain bindable POJO so it can also be constructed + * directly in tests. + */ +@ConfigurationProperties(prefix = "aggregate") +public class AggregateProperties { + + /** Open HPDS backend; same value as HPDS_OPEN_URL (the query service's open backend). */ + private String hpdsOpenUrl; + /** Bearer token for the open HPDS backend (+ visualization); same value as HPDS_OPEN_TOKEN. Was target.picsure.token. */ + private String hpdsOpenToken; + /** + * Visualization service base URL; replaces the DB ResourceRepository.getById(visualizationResourceId). Blank = no binning (raw + * fallback). + */ + private String visualizationUrl; + /** Optional resourceUUID injected into the visualization /bin/continuous request body (parity with the WAR). */ + private String visualizationResourceId; + /** Optional resourceUUID injected into every downstream HPDS request body (was target.resource.id). */ + private String targetResourceId; + private int connectTimeoutSec = 10; + private int readTimeoutSec = 60; + + private final Obfuscation obfuscation = new Obfuscation(); + + public static class Obfuscation { + private int threshold = 10; // ApplicationProperties.DEFAULT_OBFUSCATION_THRESHOLD + private int variance = 3; // ApplicationProperties.DEFAULT_OBFUSCATION_VARIANCE + private String salt; // null/blank => random UUID at startup (ObfuscationService) + + public int getThreshold() { + return threshold; + } + + public void setThreshold(int t) { + this.threshold = t; + } + + public int getVariance() { + return variance; + } + + public void setVariance(int v) { + this.variance = v; + } + + public String getSalt() { + return salt; + } + + public void setSalt(String s) { + this.salt = s; + } + } + + public String getHpdsOpenUrl() { + return hpdsOpenUrl; + } + + public void setHpdsOpenUrl(String u) { + this.hpdsOpenUrl = u; + } + + public String getHpdsOpenToken() { + return hpdsOpenToken; + } + + public void setHpdsOpenToken(String t) { + this.hpdsOpenToken = t; + } + + public String getVisualizationUrl() { + return visualizationUrl; + } + + public void setVisualizationUrl(String u) { + this.visualizationUrl = u; + } + + public String getVisualizationResourceId() { + return visualizationResourceId; + } + + public void setVisualizationResourceId(String id) { + this.visualizationResourceId = id; + } + + public String getTargetResourceId() { + return targetResourceId; + } + + public void setTargetResourceId(String id) { + this.targetResourceId = id; + } + + public int getConnectTimeoutSec() { + return connectTimeoutSec; + } + + public void setConnectTimeoutSec(int s) { + this.connectTimeoutSec = s; + } + + public int getReadTimeoutSec() { + return readTimeoutSec; + } + + public void setReadTimeoutSec(int s) { + this.readTimeoutSec = s; + } + + public Obfuscation getObfuscation() { + return obfuscation; + } + + /** True when a visualization service is configured (gate for continuous binning). */ + public boolean hasVisualization() { + return visualizationUrl != null && !visualizationUrl.isBlank(); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/GatewayPrivilegesFilter.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/GatewayPrivilegesFilter.java new file mode 100644 index 000000000..7d7e7830f --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/GatewayPrivilegesFilter.java @@ -0,0 +1,40 @@ +package edu.harvard.hms.dbmi.avillach.query.config; + +import java.io.IOException; +import java.util.List; + +import org.springframework.security.authentication.UsernamePasswordAuthenticationToken; +import org.springframework.security.core.authority.SimpleGrantedAuthority; +import org.springframework.security.core.context.SecurityContextHolder; +import org.springframework.web.filter.OncePerRequestFilter; + +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUser; +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +/** + * Rebuilds a {@code SecurityContext} from the gateway's {@code X-User-*} headers purely so {@link WebSecurityConfig}'s path rules can be + * expressed declaratively (e.g. {@code /hpds/**} requiring an authenticated caller). The gateway is the sole PSAMA client and has already + * authorized the request; this service performs no JWT validation of its own and trusts the headers (network ACLs prevent direct access). + * + *

    Delegates to {@link GatewayUserResolver#resolve(HttpServletRequest)}: when {@code X-User-Id} is absent, {@code resolve} yields + * {@link java.util.Optional#empty()} and this filter leaves the {@code SecurityContext} untouched -- the request stays anonymous. + */ +public class GatewayPrivilegesFilter extends OncePerRequestFilter { + + @Override + protected void doFilterInternal(HttpServletRequest request, HttpServletResponse response, FilterChain filterChain) + throws ServletException, IOException { + GatewayUserResolver.resolve(request).ifPresent(this::authenticate); + filterChain.doFilter(request, response); + } + + private void authenticate(GatewayUser user) { + List authorities = user.getPrivileges().stream().map(SimpleGrantedAuthority::new).toList(); + var authentication = new UsernamePasswordAuthenticationToken(user.getUserId(), "N/A", authorities); + SecurityContextHolder.getContext().setAuthentication(authentication); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/GatewayUserArgumentResolver.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/GatewayUserArgumentResolver.java new file mode 100644 index 000000000..dc2cb0e0c --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/GatewayUserArgumentResolver.java @@ -0,0 +1,32 @@ +package edu.harvard.hms.dbmi.avillach.query.config; + +import org.springframework.core.MethodParameter; +import org.springframework.web.bind.support.WebDataBinderFactory; +import org.springframework.web.context.request.NativeWebRequest; +import org.springframework.web.method.support.HandlerMethodArgumentResolver; +import org.springframework.web.method.support.ModelAndViewContainer; + +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUser; +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import jakarta.servlet.http.HttpServletRequest; + +/** + * Resolves a {@link GatewayUser} controller argument by re-deriving it from the gateway's {@code X-User-*} headers via + * {@link GatewayUserResolver#resolve(HttpServletRequest)}. Yields {@code null} when the gateway supplied no identity (no {@code X-User-Id} + * header) -- controllers that require an identity must null-check and reject accordingly. + */ +public class GatewayUserArgumentResolver implements HandlerMethodArgumentResolver { + + @Override + public boolean supportsParameter(MethodParameter parameter) { + return GatewayUser.class.equals(parameter.getParameterType()); + } + + @Override + public Object resolveArgument( + MethodParameter parameter, ModelAndViewContainer mavContainer, NativeWebRequest webRequest, WebDataBinderFactory binderFactory + ) { + HttpServletRequest request = (HttpServletRequest) webRequest.getNativeRequest(); + return GatewayUserResolver.resolve(request).orElse(null); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/HpdsClientConfig.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/HpdsClientConfig.java new file mode 100644 index 000000000..eae4c11d6 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/HpdsClientConfig.java @@ -0,0 +1,39 @@ +package edu.harvard.hms.dbmi.avillach.query.config; + +import java.util.concurrent.TimeUnit; + +import org.apache.hc.client5.http.config.ConnectionConfig; +import org.apache.hc.client5.http.impl.classic.CloseableHttpClient; +import org.apache.hc.client5.http.impl.classic.HttpClients; +import org.apache.hc.client5.http.impl.io.PoolingHttpClientConnectionManager; +import org.springframework.boot.context.properties.EnableConfigurationProperties; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.http.client.HttpComponentsClientHttpRequestFactory; +import org.springframework.web.client.RestClient; + +/** + * A single pooled {@link RestClient} (Apache HttpComponents 5, maxTotal 100 / 20-per-route -- matching the legacy WAR's + * {@code PoolingHttpClientConnectionManager}) for talking to HPDS. It has NO base URL and NO default Authorization header: + * {@link edu.harvard.hms.dbmi.avillach.query.hpds.HpdsBackendSelector} resolves the target backend's absolute base + service token, and the + * per-backend token is applied per-call on the injecting endpoints (a later task) so that non-injecting search/values calls stay + * token-free. + */ +@Configuration +@EnableConfigurationProperties(HpdsProperties.class) +public class HpdsClientConfig { + + @Bean + RestClient hpdsClient(HpdsProperties props) { + PoolingHttpClientConnectionManager cm = new PoolingHttpClientConnectionManager(); + cm.setMaxTotal(100); + cm.setDefaultMaxPerRoute(20); + cm.setDefaultConnectionConfig( + ConnectionConfig.custom().setConnectTimeout(props.getConnectTimeoutSec(), TimeUnit.SECONDS) + .setSocketTimeout(props.getReadTimeoutSec(), TimeUnit.SECONDS).build() + ); + CloseableHttpClient httpClient = HttpClients.custom().setConnectionManager(cm).build(); + HttpComponentsClientHttpRequestFactory rf = new HttpComponentsClientHttpRequestFactory(httpClient); + return RestClient.builder().requestFactory(rf).build(); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/HpdsProperties.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/HpdsProperties.java new file mode 100644 index 000000000..ebb9b8557 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/HpdsProperties.java @@ -0,0 +1,81 @@ +package edu.harvard.hms.dbmi.avillach.query.config; + +import org.springframework.boot.context.properties.ConfigurationProperties; + +/** + * Per-backend HPDS connection settings. There is a single pooled {@link org.springframework.web.client.RestClient} (see + * {@link HpdsClientConfig}) with no base URL of its own -- callers select the target backend's absolute base + service token via + * {@link edu.harvard.hms.dbmi.avillach.query.hpds.HpdsBackendSelector} and pass it per-call. + */ +@ConfigurationProperties(prefix = "hpds") +public class HpdsProperties { + + /** HPDS_AUTH_URL -- the auth (non-obfuscated) backend base, e.g. http://hpds:8080/PIC-SURE */ + private String authUrl; + /** HPDS_AUTH_TOKEN -- the service Bearer token for the auth backend. SECRET. */ + private String authToken; + /** HPDS_OPEN_URL -- the open (aggregate/obfuscated) backend base. In AIO both equal authUrl. */ + private String openUrl; + /** HPDS_OPEN_TOKEN -- the service Bearer token for the open backend. SECRET. (May be blank if not needed.) */ + private String openToken; + /** Health probe path appended to each backend base. */ + private String healthPath = "/actuator/health"; + private int connectTimeoutSec = 10; + private int readTimeoutSec = 300; + + public String getAuthUrl() { + return authUrl; + } + + public void setAuthUrl(String authUrl) { + this.authUrl = authUrl; + } + + public String getAuthToken() { + return authToken; + } + + public void setAuthToken(String authToken) { + this.authToken = authToken; + } + + public String getOpenUrl() { + return openUrl; + } + + public void setOpenUrl(String openUrl) { + this.openUrl = openUrl; + } + + public String getOpenToken() { + return openToken; + } + + public void setOpenToken(String openToken) { + this.openToken = openToken; + } + + public String getHealthPath() { + return healthPath; + } + + public void setHealthPath(String healthPath) { + this.healthPath = healthPath; + } + + public int getConnectTimeoutSec() { + return connectTimeoutSec; + } + + public void setConnectTimeoutSec(int connectTimeoutSec) { + this.connectTimeoutSec = connectTimeoutSec; + } + + public int getReadTimeoutSec() { + return readTimeoutSec; + } + + public void setReadTimeoutSec(int readTimeoutSec) { + this.readTimeoutSec = readTimeoutSec; + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/OperationsClientConfig.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/OperationsClientConfig.java new file mode 100644 index 000000000..35e3af297 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/OperationsClientConfig.java @@ -0,0 +1,47 @@ +package edu.harvard.hms.dbmi.avillach.query.config; + +import java.util.concurrent.TimeUnit; + +import org.apache.hc.client5.http.config.ConnectionConfig; +import org.apache.hc.client5.http.impl.classic.CloseableHttpClient; +import org.apache.hc.client5.http.impl.classic.HttpClients; +import org.apache.hc.client5.http.impl.io.PoolingHttpClientConnectionManager; +import org.springframework.beans.factory.annotation.Qualifier; +import org.springframework.boot.context.properties.EnableConfigurationProperties; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.http.client.HttpComponentsClientHttpRequestFactory; +import org.springframework.web.client.RestClient; + +import edu.harvard.hms.dbmi.avillach.query.operations.OperationsClient; + +/** + * The pooled {@link RestClient} backing {@link OperationsClient}. Unlike {@link HpdsClientConfig}'s HPDS client (which serves two backends + * with different tokens and therefore carries no default Authorization header), this client talks to exactly one target -- + * operations-service -- so its base URL and the {@code X-PIC-SURE-INTERNAL-TOKEN} shared secret are set once as defaults and apply to every + * call. + */ +@Configuration +@EnableConfigurationProperties(OperationsProperties.class) +public class OperationsClientConfig { + + @Bean + RestClient operationsRestClient(OperationsProperties props) { + PoolingHttpClientConnectionManager cm = new PoolingHttpClientConnectionManager(); + cm.setMaxTotal(50); + cm.setDefaultMaxPerRoute(20); + cm.setDefaultConnectionConfig( + ConnectionConfig.custom().setConnectTimeout(props.getConnectTimeoutSec(), TimeUnit.SECONDS) + .setSocketTimeout(props.getReadTimeoutSec(), TimeUnit.SECONDS).build() + ); + CloseableHttpClient httpClient = HttpClients.custom().setConnectionManager(cm).build(); + HttpComponentsClientHttpRequestFactory rf = new HttpComponentsClientHttpRequestFactory(httpClient); + return RestClient.builder().baseUrl(props.getBaseUrl()).defaultHeader("X-PIC-SURE-INTERNAL-TOKEN", props.getInternalToken()) + .requestFactory(rf).build(); + } + + @Bean + OperationsClient operationsClient(@Qualifier("operationsRestClient") RestClient operationsRestClient) { + return new OperationsClient(operationsRestClient); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/OperationsProperties.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/OperationsProperties.java new file mode 100644 index 000000000..56efeca27 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/OperationsProperties.java @@ -0,0 +1,53 @@ +package edu.harvard.hms.dbmi.avillach.query.config; + +import org.springframework.boot.context.properties.ConfigurationProperties; + +/** + * Connection settings for {@link edu.harvard.hms.dbmi.avillach.query.operations.OperationsClient}, the DB-free persistence path to + * pic-sure-operations-service's internal query API. + */ +@ConfigurationProperties(prefix = "picsure.query.operations") +public class OperationsProperties { + + /** OPERATIONS_SERVICE_URL -- base URL of pic-sure-operations-service, e.g. http://operations-service:8080 */ + private String baseUrl; + /** + * QUERY_SERVICE_INTERNAL_TOKEN -- shared secret sent as {@code X-PIC-SURE-INTERNAL-TOKEN} on every call, checked by + * operations-service's {@code InternalTokenFilter} against its own {@code picsure.operations.internal-token}. SECRET. + */ + private String internalToken; + private int connectTimeoutSec = 10; + private int readTimeoutSec = 60; + + public String getBaseUrl() { + return baseUrl; + } + + public void setBaseUrl(String baseUrl) { + this.baseUrl = baseUrl; + } + + public String getInternalToken() { + return internalToken; + } + + public void setInternalToken(String internalToken) { + this.internalToken = internalToken; + } + + public int getConnectTimeoutSec() { + return connectTimeoutSec; + } + + public void setConnectTimeoutSec(int connectTimeoutSec) { + this.connectTimeoutSec = connectTimeoutSec; + } + + public int getReadTimeoutSec() { + return readTimeoutSec; + } + + public void setReadTimeoutSec(int readTimeoutSec) { + this.readTimeoutSec = readTimeoutSec; + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/WebMvcConfig.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/WebMvcConfig.java new file mode 100644 index 000000000..14e206420 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/WebMvcConfig.java @@ -0,0 +1,20 @@ +package edu.harvard.hms.dbmi.avillach.query.config; + +import java.util.List; + +import org.springframework.context.annotation.Configuration; +import org.springframework.web.method.support.HandlerMethodArgumentResolver; +import org.springframework.web.servlet.config.annotation.WebMvcConfigurer; + +/** + * Registers {@link GatewayUserArgumentResolver} so later controllers can declare a {@code GatewayUser} method parameter and receive the + * caller's identity, re-derived from the gateway's {@code X-User-*} headers. + */ +@Configuration +public class WebMvcConfig implements WebMvcConfigurer { + + @Override + public void addArgumentResolvers(List resolvers) { + resolvers.add(new GatewayUserArgumentResolver()); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/WebSecurityConfig.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/WebSecurityConfig.java new file mode 100644 index 000000000..7ee9431d2 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/config/WebSecurityConfig.java @@ -0,0 +1,44 @@ +package edu.harvard.hms.dbmi.avillach.query.config; + +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.core.annotation.Order; +import org.springframework.security.config.annotation.web.builders.HttpSecurity; +import org.springframework.security.config.http.SessionCreationPolicy; +import org.springframework.security.web.SecurityFilterChain; +import org.springframework.security.web.access.intercept.AuthorizationFilter; + +/** + * Security posture for the single HPDS ingress. This service performs NO JWT validation of its own -- the gateway is the sole PSAMA client + * and has already authorized the request; {@link GatewayPrivilegesFilter} rebuilds a {@code SecurityContext} from the gateway's + * {@code X-User-*} headers purely so the rules below can be expressed declaratively. Network ACLs (not this filter chain) are what actually + * stop a client from reaching this service directly and forging the headers. + * + *

    Path rules, in the order they are declared (first match wins):

    1. {@code /actuator/health}, {@code /actuator/info}, + * {@code /openapi/**}, {@code /swagger-ui/**}, {@code /v3/api-docs/**} -- unauthenticated (ops/tooling surfaces, never gated behind caller + * identity).
    2. {@code /hpds/**} -- requires an authenticated caller, i.e. the gateway supplied {@code X-User-Id}. Spring Security's + * {@code authenticated()} already excludes the default anonymous principal (see {@code AuthenticatedAuthorizationManager}), so a request + * with no identity is correctly rejected rather than silently treated as authenticated.
    3. Everything else is permitted at this + * layer; the controllers built in later tasks enforce any remaining per-endpoint rules themselves. There is deliberately NO + * {@code /internal/**} endpoint on this service -- dispatch/persistence lives on pic-sure-operations-service, reached via + * {@link edu.harvard.hms.dbmi.avillach.query.operations.OperationsClient}.
    + * + *

    CSRF is disabled and sessions are stateless: every request carries its own trust via headers, there is no browser session to protect + * and nothing is stored server-side between requests. + */ +@Configuration +public class WebSecurityConfig { + + @Bean + @Order(10) // yields /actuator/** to ActuatorSecurityConfig's @Order(0) chain. + SecurityFilterChain filterChain(HttpSecurity http) throws Exception { + return http.csrf(csrf -> csrf.disable()) + .sessionManagement(session -> session.sessionCreationPolicy(SessionCreationPolicy.STATELESS)) + // Populate the SecurityContext from X-User-Privileges BEFORE authorization runs. + .addFilterBefore(new GatewayPrivilegesFilter(), AuthorizationFilter.class) + .authorizeHttpRequests( + auth -> auth.requestMatchers("/actuator/health", "/actuator/info", "/openapi/**", "/swagger-ui/**", "/v3/api-docs/**") + .permitAll().requestMatchers("/hpds/**").authenticated().anyRequest().permitAll() + ).build(); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/error/GlobalExceptionHandler.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/error/GlobalExceptionHandler.java new file mode 100644 index 000000000..55903254d --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/error/GlobalExceptionHandler.java @@ -0,0 +1,68 @@ +package edu.harvard.hms.dbmi.avillach.query.error; + +import java.util.LinkedHashMap; +import java.util.Map; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.slf4j.MDC; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.web.bind.annotation.ExceptionHandler; +import org.springframework.web.bind.annotation.RestControllerAdvice; +import org.springframework.web.servlet.resource.NoResourceFoundException; + +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; +import edu.harvard.hms.dbmi.avillach.query.hpds.HpdsCommunicationException; + +/** + * This service's own exception-to-HTTP mapping. {@code pic-sure-spring-commons}' {@code GatewayExceptionAdvice} already maps + * {@link PicsureException} to its carried status with the {@code {errorType,message,requestId}} body shape -- that handler is duplicated + * here (identical behavior) rather than relied upon exclusively, because Spring's {@code ExceptionHandlerExceptionResolver} picks the FIRST + * {@code @ControllerAdvice} bean (in an unspecified-by-us order) that has ANY matching handler for a given exception, not the most-specific + * match across all beans. Keeping a self-contained {@link PicsureException} handler in this same class guarantees this advice always + * resolves the most specific handler for its own {@link #unknown} catch-all, regardless of whichever advice bean Spring happens to consult + * first -- {@code GatewayExceptionAdvice}'s equivalent handler (if consulted first) produces the identical response. + * + *

    Adds three mappings the commons base does not have: {@link HpdsCommunicationException} -> 502 (HPDS is upstream infrastructure; the + * legacy WAR returned 500 for this case, which was never an honest status), {@link NoResourceFoundException} -> 404 (route absence for + * removed v1 generic ingress), and any other unmapped exception -> 500, all sharing the same commons error body shape. + */ +@RestControllerAdvice +public class GlobalExceptionHandler { + + private static final Logger logger = LoggerFactory.getLogger(GlobalExceptionHandler.class); + + @ExceptionHandler(PicsureException.class) + public ResponseEntity> handlePicsureException(PicsureException e) { + return body(e.getStatus(), e.getErrorType(), e.getMessage()); + } + + @ExceptionHandler(HpdsCommunicationException.class) + public ResponseEntity> hpdsUnavailable(HpdsCommunicationException e) { + return body(HttpStatus.BAD_GATEWAY, "upstream_unavailable", e.getMessage()); + } + + /** + * Route absence must surface as an honest 404, not fall into the {@link #unknown} 500 catch-all. This matters since the legacy v1 query + * ingress ({@code /hpds/{backend}/query/**}) was removed: callers still submitting to those routes must see "gone", not "server error". + */ + @ExceptionHandler(NoResourceFoundException.class) + public ResponseEntity> noRoute(NoResourceFoundException e) { + return body(HttpStatus.NOT_FOUND, "not_found", "No such resource: " + e.getResourcePath()); + } + + @ExceptionHandler(Exception.class) + public ResponseEntity> unknown(Exception e) { + logger.error("Unhandled exception", e); + return body(HttpStatus.INTERNAL_SERVER_ERROR, "internal_error", "An unexpected error occurred"); + } + + private static ResponseEntity> body(HttpStatus status, String errorType, String message) { + Map b = new LinkedHashMap<>(); + b.put("errorType", errorType); + b.put("message", message); + b.put("requestId", MDC.get("requestId")); + return ResponseEntity.status(status).body(b); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/health/HpdsHealthIndicator.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/health/HpdsHealthIndicator.java new file mode 100644 index 000000000..2a388e987 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/health/HpdsHealthIndicator.java @@ -0,0 +1,113 @@ +package edu.harvard.hms.dbmi.avillach.query.health; + +import java.util.LinkedHashSet; +import java.util.Set; +import java.util.concurrent.TimeUnit; + +import org.apache.hc.client5.http.config.ConnectionConfig; +import org.apache.hc.client5.http.impl.classic.CloseableHttpClient; +import org.apache.hc.client5.http.impl.classic.HttpClients; +import org.apache.hc.client5.http.impl.io.PoolingHttpClientConnectionManager; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.actuate.health.Health; +import org.springframework.boot.actuate.health.HealthIndicator; +import org.springframework.boot.actuate.health.Status; +import org.springframework.http.client.HttpComponentsClientHttpRequestFactory; +import org.springframework.stereotype.Component; +import org.springframework.web.client.RestClient; + +import edu.harvard.hms.dbmi.avillach.query.config.HpdsProperties; + +/** + * Deep health for this DB-free service: there is no {@code DataSource} to probe (this module owns no database at all -- see the class + * javadoc on {@code QueryService}), so the only real dependency worth reporting on is HPDS reachability. Probes each DISTINCT configured + * backend base (auth/open -- in AIO they're typically the same URL and collapse to a single probe) with a short GET to + * {@code {origin(base)}{healthPath}} -- HPDS exposes Actuator at the host root, not under the {@code /PIC-SURE} query context, so the probe + * uses the base URL's origin ({@code scheme://authority}), not the full query base; {@code UP} only when every distinct base responds with + * a 2xx. The gateway composes this service's own deep health into its aggregate view -- this indicator does not cascade into probing + * anything beyond HPDS itself. + * + *

    The probe client uses its OWN short, health-check-specific connect/read timeouts ({@link #HEALTH_CONNECT_TIMEOUT_SEC}/ + * {@link #HEALTH_READ_TIMEOUT_SEC}) rather than {@link HpdsProperties#getConnectTimeoutSec()}/{@link HpdsProperties#getReadTimeoutSec()} -- + * those are sized for real query traffic (default 300s read) and would let a black-holed HPDS hang {@code /actuator/health} (which the + * gateway aggregates) for minutes. A health probe must fail fast and report {@code DOWN}, never hang. + */ +@Component("hpds") +public class HpdsHealthIndicator implements HealthIndicator { + + private static final int HEALTH_CONNECT_TIMEOUT_SEC = 2; + private static final int HEALTH_READ_TIMEOUT_SEC = 3; + + private final HpdsProperties props; + private final RestClient probe; + + @Autowired + public HpdsHealthIndicator(HpdsProperties props, RestClient.Builder builder) { + this.props = props; + this.probe = builder.requestFactory(timeoutBoundRequestFactory()).build(); + } + + HpdsHealthIndicator(HpdsProperties props, RestClient probe) { // test constructor + this.props = props; + this.probe = probe; + } + + /** + * Mirrors {@code HpdsClientConfig}'s pooled-client timeout setup, but with short, health-specific values baked into the pooled + * {@link CloseableHttpClient} itself (a {@link org.apache.hc.client5.http.io.HttpClientConnectionManager}'s + * {@code defaultConnectionConfig} is where Apache HttpComponents 5 timeouts actually live -- the per-request setters on + * {@link HttpComponentsClientHttpRequestFactory} are no-ops once a preconfigured {@code CloseableHttpClient} is supplied). + */ + private static HttpComponentsClientHttpRequestFactory timeoutBoundRequestFactory() { + PoolingHttpClientConnectionManager cm = new PoolingHttpClientConnectionManager(); + cm.setDefaultConnectionConfig( + ConnectionConfig.custom().setConnectTimeout(HEALTH_CONNECT_TIMEOUT_SEC, TimeUnit.SECONDS) + .setSocketTimeout(HEALTH_READ_TIMEOUT_SEC, TimeUnit.SECONDS).build() + ); + CloseableHttpClient httpClient = HttpClients.custom().setConnectionManager(cm).build(); + return new HttpComponentsClientHttpRequestFactory(httpClient); + } + + @Override + public Health health() { + Set bases = new LinkedHashSet<>(); // dedup auth/open (collapse in AIO) + if (props.getAuthUrl() != null) { + bases.add(props.getAuthUrl()); + } + if (props.getOpenUrl() != null) { + bases.add(props.getOpenUrl()); + } + + Health.Builder result = Health.up(); + boolean down = false; + for (String base : bases) { + String url = originOf(base) + props.getHealthPath(); + try { + probe.get().uri(url).retrieve().toBodilessEntity(); // 2xx -> reachable + result.withDetail(base, "UP"); + } catch (Exception e) { + down = true; + result.withDetail(base, "DOWN: " + e.getMessage()); + } + } + return down ? result.status(Status.DOWN).build() : result.build(); + } + + /** + * HPDS serves its Actuator health at the host ROOT (e.g. {@code http://hpds:8080/actuator/health}), while the query API base carries + * the {@code /PIC-SURE} context (e.g. {@code http://hpds:8080/PIC-SURE}). So the health probe targets the URL's ORIGIN + * ({@code scheme://authority}) + {@code healthPath}, not the query base + {@code healthPath} (which would 404). Falls back to the raw + * base if it can't be parsed as an absolute URL. + */ + static String originOf(String base) { + try { + java.net.URI u = java.net.URI.create(base.trim()); + if (u.getScheme() != null && u.getAuthority() != null) { + return u.getScheme() + "://" + u.getAuthority(); + } + } catch (RuntimeException ignored) { + // fall through to raw base + } + return base; + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/hpds/HpdsBackendSelector.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/hpds/HpdsBackendSelector.java new file mode 100644 index 000000000..b009c2bd3 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/hpds/HpdsBackendSelector.java @@ -0,0 +1,54 @@ +package edu.harvard.hms.dbmi.avillach.query.hpds; + +import org.springframework.http.HttpStatus; +import org.springframework.stereotype.Component; + +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; +import edu.harvard.hms.dbmi.avillach.query.config.HpdsProperties; + +/** + * Maps the ingress {@code {backend}} path segment ("auth" or "open") to the HPDS call target: the backend's absolute base URL and its + * service token. v3 endpoints compose the base by appending {@code /v3} (preserving the legacy WAR's {@code resourceRSPath + "/v3/"} + * convention). Query-lifecycle calls use {@code target.token()} (Bearer auth); search/values calls use only {@code target.baseUrl()} -- no + * token. + */ +@Component +public class HpdsBackendSelector { + + public static final String AUTH = "auth"; + public static final String OPEN = "open"; + + private final HpdsProperties props; + + public HpdsBackendSelector(HpdsProperties props) { + this.props = props; + } + + /** The HPDS call target: the base URL (with {@code /v3} appended for v3) and the per-backend service token. */ + public record HpdsTarget(String baseUrl, String token) { + } + + /** + * @param backend the ingress segment: "auth" or "open" + * @param v3 whether the target endpoint is v3 (append "/v3" to the base) + * @return the HPDS target (URL + service token) for that backend + */ + public HpdsTarget select(String backend, boolean v3) { + String base; + String token; + switch (backend == null ? "" : backend) { + case AUTH -> { + base = props.getAuthUrl(); + token = props.getAuthToken(); + } + case OPEN -> { + base = props.getOpenUrl(); + token = props.getOpenToken(); + } + default -> throw new PicsureException( + HttpStatus.BAD_REQUEST, "bad_request", "Unknown HPDS backend '" + backend + "' (expected 'auth' or 'open')" + ); + } + return new HpdsTarget(v3 ? base + "/v3" : base, token); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/hpds/HpdsCommunicationException.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/hpds/HpdsCommunicationException.java new file mode 100644 index 000000000..2dad6cd52 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/hpds/HpdsCommunicationException.java @@ -0,0 +1,13 @@ +package edu.harvard.hms.dbmi.avillach.query.hpds; + +/** Thrown when the HPDS backend is unreachable or returns a non-2xx status. Mapped to 502. */ +public class HpdsCommunicationException extends RuntimeException { + + public HpdsCommunicationException(String message) { + super(message); + } + + public HpdsCommunicationException(String message, Throwable cause) { + super(message, cause); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/hpds/ResourceWebClient.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/hpds/ResourceWebClient.java new file mode 100644 index 000000000..91cc705e4 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/hpds/ResourceWebClient.java @@ -0,0 +1,128 @@ +package edu.harvard.hms.dbmi.avillach.query.hpds; + +import java.net.URI; +import java.util.Optional; + +import org.springframework.beans.factory.annotation.Qualifier; +import org.springframework.http.HttpHeaders; +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Component; +import org.springframework.web.client.RestClient; +import org.springframework.web.client.RestClientException; +import org.springframework.web.util.UriComponentsBuilder; + +import edu.harvard.dbmi.avillach.domain.PaginatedSearchResult; +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import edu.harvard.dbmi.avillach.domain.QueryStatus; +import edu.harvard.dbmi.avillach.domain.SearchResults; +import edu.harvard.hms.dbmi.avillach.query.hpds.HpdsBackendSelector.HpdsTarget; + +/** + * RestClient port of the legacy {@code ResourceWebClient} (pic-sure-resource-api). Query-lifecycle calls ({@link #query}, + * {@link #queryStatus}, {@link #queryResult}, {@link #queryResultSignedUrl}, {@link #querySync}) inject + * {@code Authorization: Bearer } -- parity with the WAR's {@code createHeaders(...BEARER_TOKEN...)} after + * {@code PicsureQueryService} put {@code resource.getToken()} into the credentials. {@link #search} and {@link #searchConceptValues} inject + * NO service token -- parity with {@code PicsureSearchService}, which never set {@code BEARER_TOKEN}. HPDS non-2xx / IO errors surface as + * {@link HpdsCommunicationException} (mapped to 502 upstream). + */ +@Component +public class ResourceWebClient { + + /** Verified field name on the legacy ResourceWebClient (ResourceWebClient.java:43). */ + public static final String QUERY_METADATA_FIELD = "queryMetadata"; + + private final RestClient http; + + public ResourceWebClient(@Qualifier("hpdsClient") RestClient hpdsClient) { + this.http = hpdsClient; + } + + public record QuerySyncResult(byte[] body, String queryMetadata) { + } + + // --- query lifecycle: inject the per-backend service token (parity with the WAR's resource.getToken()) --- + + public QueryStatus query(HpdsTarget target, QueryRequest req) { + return postJson(target, target.baseUrl() + "/query", req, QueryStatus.class); + } + + public QueryStatus queryStatus(HpdsTarget target, String resourceResultId, QueryRequest req) { + return postJson(target, target.baseUrl() + "/query/" + resourceResultId + "/status", req, QueryStatus.class); + } + + /** Octet-stream, FULLY BUFFERED -- parity with ResourceWebClient.queryResult/readBytesFromResponse. */ + public ResponseEntity queryResult(HpdsTarget target, String resourceResultId, QueryRequest req) { + try { + return http.post().uri(target.baseUrl() + "/query/" + resourceResultId + "/result").headers(h -> authorize(h, target)) + .contentType(MediaType.APPLICATION_JSON).body(req).retrieve().toEntity(byte[].class); + } catch (RestClientException e) { + throw new HpdsCommunicationException("HPDS result call failed: " + target.baseUrl(), e); + } + } + + /** JSON string, FULLY BUFFERED -- parity with ResourceWebClient.queryResultSignedUrl. */ + public ResponseEntity queryResultSignedUrl(HpdsTarget target, String resourceResultId, QueryRequest req) { + try { + return http.post().uri(target.baseUrl() + "/query/" + resourceResultId + "/signed-url").headers(h -> authorize(h, target)) + .contentType(MediaType.APPLICATION_JSON).body(req).retrieve().toEntity(String.class); + } catch (RestClientException e) { + throw new HpdsCommunicationException("HPDS signed-url call failed: " + target.baseUrl(), e); + } + } + + /** Body bytes + optional queryMetadata response header + optional request-source request header. */ + public QuerySyncResult querySync(HpdsTarget target, QueryRequest req, String requestSource) { + try { + ResponseEntity down = + http.post().uri(target.baseUrl() + "/query/sync").contentType(MediaType.APPLICATION_JSON).headers(h -> { + authorize(h, target); + if (requestSource != null) { + h.add("request-source", requestSource); + } + }).body(req).retrieve().toEntity(byte[].class); + return new QuerySyncResult(down.getBody(), down.getHeaders().getFirst(QUERY_METADATA_FIELD)); + } catch (RestClientException e) { + throw new HpdsCommunicationException("HPDS sync call failed: " + target.baseUrl(), e); + } + } + + // --- search: NO service token (parity with PicsureSearchService, which never set BEARER_TOKEN) --- + + public SearchResults search(String base, QueryRequest req) { + try { + return http.post().uri(base + "/search").contentType(MediaType.APPLICATION_JSON).body(req).retrieve().body(SearchResults.class); + } catch (RestClientException e) { + throw new HpdsCommunicationException("HPDS search call failed: " + base, e); + } + } + + public PaginatedSearchResult searchConceptValues( + String base, QueryRequest req, String conceptPath, String query, Integer page, Integer size + ) { + try { + URI uri = UriComponentsBuilder.fromUriString(base + "/search/values/").queryParam("genomicConceptPath", conceptPath) + .queryParam("query", query).queryParamIfPresent("page", Optional.ofNullable(page)) + .queryParamIfPresent("size", Optional.ofNullable(size)).encode().build().toUri(); + return http.get().uri(uri).retrieve().body(PaginatedSearchResult.class); + } catch (RestClientException e) { + throw new HpdsCommunicationException("HPDS search/values call failed: " + base, e); + } + } + + /** Adds Authorization: Bearer when the backend has one configured. */ + private static void authorize(HttpHeaders h, HpdsTarget target) { + if (target.token() != null && !target.token().isBlank()) { + h.add(HttpHeaders.AUTHORIZATION, "Bearer " + target.token()); + } + } + + private T postJson(HpdsTarget target, String uri, QueryRequest req, Class type) { + try { + return http.post().uri(uri).headers(h -> authorize(h, target)).contentType(MediaType.APPLICATION_JSON).body(req).retrieve() + .body(type); + } catch (RestClientException e) { + throw new HpdsCommunicationException("HPDS call failed: " + uri, e); + } + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/operations/OperationsClient.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/operations/OperationsClient.java new file mode 100644 index 000000000..245afb5cb --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/operations/OperationsClient.java @@ -0,0 +1,97 @@ +package edu.harvard.hms.dbmi.avillach.query.operations; + +import java.util.UUID; + +import org.springframework.http.HttpStatus; +import org.springframework.web.client.HttpClientErrorException; +import org.springframework.web.client.ResourceAccessException; +import org.springframework.web.client.RestClient; +import org.springframework.web.client.RestClientException; + +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; + +/** + * The DB-free persistence path: this service owns no database, so every read/write of a stored query goes over HTTP to + * pic-sure-operations-service's internal query API. The wrapped {@link RestClient} is pre-configured (base URL + the + * {@code X-PIC-SURE-INTERNAL-TOKEN} shared secret, see {@code OperationsClientConfig}) so every call made through this class automatically + * authenticates to operations-service's {@code InternalTokenFilter}. + * + *

    Method/endpoint contracts are FIXED by operations-service (see + * {@code edu.harvard.hms.dbmi.avillach.operations.query.InternalQueryController}); the DTOs here are client-side copies of that service's + * request/response shapes, matched byte-for-byte since this module cannot depend on operations-service's classes without pulling in its + * JPA/entity graph. + * + *

    A persistence failure must never be swallowed: any 5xx, timeout, or malformed response from operations-service is surfaced as a + * {@link PicsureException} (BAD_GATEWAY or GATEWAY_TIMEOUT) rather than returning a null/partial result. Only {@link #get(UUID)} has a + * documented 404 contract (NOT_FOUND); a 404 from {@link #update(UUID, UpdateQueryRequest)} falls into the generic bad-gateway handling + * below, since no NOT_FOUND semantics are specified for that call yet. + * + *

    NOT a {@code @Component}: it is registered exactly once, by {@code OperationsClientConfig}, wired to the specific + * {@code operationsRestClient} bean -- the context also contains a second, differently-configured {@code RestClient} bean for HPDS (see + * {@code HpdsClientConfig}), so relying on by-type autowiring here would be ambiguous. + */ +public class OperationsClient { + + private static final String QUERIES_PATH = "/operations/internal/queries"; + + private final RestClient http; + + public OperationsClient(RestClient http) { + this.http = http; + } + + /** {@code POST /operations/internal/queries} -> 201 {@code { "picsureId": "" } }. */ + public UUID save(SaveQueryRequest request) { + SaveQueryResponse response = + execute(() -> http.post().uri(QUERIES_PATH).body(request).retrieve().body(SaveQueryResponse.class), "save"); + if (response == null || response.picsureId() == null) { + throw badGateway("save", "operations-service returned no picsureId"); + } + return response.picsureId(); + } + + /** {@code GET /operations/internal/queries/{id}} -> 200 {@link StoredQuery}; 404 -> {@link PicsureException} NOT_FOUND. */ + public StoredQuery get(UUID picsureId) { + try { + return http.get().uri(QUERIES_PATH + "/{id}", picsureId).retrieve().body(StoredQuery.class); + } catch (HttpClientErrorException.NotFound e) { + throw new PicsureException(HttpStatus.NOT_FOUND, "not_found", "No stored query for picsureId " + picsureId); + } catch (ResourceAccessException e) { + throw gatewayTimeout("get", e); + } catch (RestClientException e) { + throw badGateway("get", e.getMessage()); + } + } + + /** {@code PATCH /operations/internal/queries/{id}}; null fields on {@code request} mean "leave unchanged". */ + public void update(UUID picsureId, UpdateQueryRequest request) { + execute(() -> { + http.patch().uri(QUERIES_PATH + "/{id}", picsureId).body(request).retrieve().toBodilessEntity(); + return null; + }, "update"); + } + + private T execute(java.util.function.Supplier call, String operation) { + try { + return call.get(); + } catch (ResourceAccessException e) { + throw gatewayTimeout(operation, e); + } catch (RestClientException e) { + throw badGateway(operation, e.getMessage()); + } + } + + private PicsureException badGateway(String operation, String detail) { + return new PicsureException(HttpStatus.BAD_GATEWAY, "bad_gateway", "operations-service " + operation + " failed: " + detail); + } + + private PicsureException gatewayTimeout(String operation, Exception cause) { + return new PicsureException( + HttpStatus.GATEWAY_TIMEOUT, "gateway_timeout", "operations-service " + operation + " timed out: " + cause.getMessage() + ); + } + + /** Shape of the {@code POST /operations/internal/queries} response body: {@code { "picsureId": "" } }. */ + private record SaveQueryResponse(UUID picsureId) { + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/operations/SaveQueryRequest.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/operations/SaveQueryRequest.java new file mode 100644 index 000000000..52abe2953 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/operations/SaveQueryRequest.java @@ -0,0 +1,11 @@ +package edu.harvard.hms.dbmi.avillach.query.operations; + +/** + * Request body for {@code POST /internal/queries} on pic-sure-operations-service. Mirrors + * {@code edu.harvard.hms.dbmi.avillach.operations.query.SaveQueryRequest} byte-for-byte -- this service is DB-free and reaches its + * persistence store solely through {@link OperationsClient}, so this is a client-side copy of the operations-service DTO, not a shared + * dependency. {@code status} is the {@code edu.harvard.dbmi.avillach.domain.PicSureStatus} enum NAME (e.g. {@code "QUEUED"}), kept as a + * plain string on the wire. {@code metadata} is base64-encoded bytes, or {@code null} when there is none. + */ +public record SaveQueryRequest(String query, String resourceResultId, String status, String version, String metadata) { +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/operations/StoredQuery.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/operations/StoredQuery.java new file mode 100644 index 000000000..3d7d32b52 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/operations/StoredQuery.java @@ -0,0 +1,12 @@ +package edu.harvard.hms.dbmi.avillach.query.operations; + +import java.util.UUID; + +/** + * Public JSON shape returned by {@code GET /internal/queries/{picsureId}} on pic-sure-operations-service. Mirrors + * {@code edu.harvard.hms.dbmi.avillach.operations.query.StoredQuery} byte-for-byte. {@code status} is the + * {@code edu.harvard.dbmi.avillach.domain.PicSureStatus} enum NAME (or {@code null} if unset). {@code metadata} is base64-encoded bytes (or + * {@code null} if unset). + */ +public record StoredQuery(UUID picsureId, String query, String resourceResultId, String status, String version, String metadata) { +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/operations/UpdateQueryRequest.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/operations/UpdateQueryRequest.java new file mode 100644 index 000000000..52448d333 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/operations/UpdateQueryRequest.java @@ -0,0 +1,9 @@ +package edu.harvard.hms.dbmi.avillach.query.operations; + +/** + * Request body for {@code PATCH /internal/queries/{picsureId}} on pic-sure-operations-service. Mirrors + * {@code edu.harvard.hms.dbmi.avillach.operations.query.UpdateQueryRequest} byte-for-byte: every field is nullable and means "leave + * unchanged" when absent. + */ +public record UpdateQueryRequest(String status, String resourceResultId, String metadata) { +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/query/HpdsQueryV3Controller.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/query/HpdsQueryV3Controller.java new file mode 100644 index 000000000..0f8ad025c --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/query/HpdsQueryV3Controller.java @@ -0,0 +1,102 @@ +package edu.harvard.hms.dbmi.avillach.query.query; + +import java.util.UUID; + +import org.springframework.http.HttpStatus; +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import org.springframework.web.bind.annotation.GetMapping; +import org.springframework.web.bind.annotation.PathVariable; +import org.springframework.web.bind.annotation.PostMapping; +import org.springframework.web.bind.annotation.RequestBody; +import org.springframework.web.bind.annotation.RequestHeader; +import org.springframework.web.bind.annotation.RequestMapping; +import org.springframework.web.bind.annotation.RequestParam; +import org.springframework.web.bind.annotation.RestController; + +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import edu.harvard.dbmi.avillach.domain.QueryStatus; +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; + +/** + * The sole HPDS query lifecycle ingress: {@code /hpds/{backend}/v3/query/**}. {@code {backend}} is {@code auth} or {@code open} (validated + * downstream by {@link QueryService} via {@code HpdsBackendSelector}). The legacy v1 ingress ({@code /hpds/{backend}/query/**}) was + * removed; new queries are always stored as version {@code "3"}. Read ops still dispatch HPDS-side on the STORED query's version, so + * previously stored v1 rows remain retrievable via their v1 routes. + */ +@RestController +@RequestMapping("/hpds/{backend}/v3") +public class HpdsQueryV3Controller { + + private final QueryService service; + + public HpdsQueryV3Controller(QueryService service) { + this.service = service; + } + + @PostMapping("/query") + public QueryStatus query( + @PathVariable("backend") String backend, @RequestBody QueryRequest req, + @RequestParam(name = "isInstitute", required = false) Boolean isInstitute + ) { + rejectInstitutionalQuery(isInstitute); + return service.queryV3(backend, req); + } + + @PostMapping("/query/sync") + public ResponseEntity querySync( + @PathVariable("backend") String backend, @RequestBody QueryRequest req, + @RequestHeader(name = "request-source", required = false) String requestSource + ) { + return syncResponse(service.querySync(backend, req, requestSource)); + } + + @PostMapping("/query/{id}/status") + public QueryStatus status(@PathVariable("backend") String backend, @PathVariable("id") UUID id, @RequestBody QueryRequest req) { + return service.queryStatus(backend, id, req); + } + + @PostMapping(value = "/query/{id}/result", produces = MediaType.APPLICATION_OCTET_STREAM_VALUE) + public ResponseEntity result( + @PathVariable("backend") String backend, @PathVariable("id") UUID id, @RequestBody QueryRequest req + ) { + return service.queryResult(backend, id, req); + } + + @PostMapping(value = "/query/{id}/signed-url", produces = MediaType.APPLICATION_JSON_VALUE) + public ResponseEntity signedUrl( + @PathVariable("backend") String backend, @PathVariable("id") UUID id, @RequestBody QueryRequest req + ) { + return service.queryResultSignedUrl(backend, id, req); + } + + @GetMapping("/query/{id}/metadata") + public QueryStatus metadata(@PathVariable("backend") String backend, @PathVariable("id") UUID id) { + return service.queryMetadata(id); // DB-only, backend irrelevant + } + + /** + * Federated/GIC queries were removed. The parameter stays bound on purpose: {@code QueryRequest}'s {@code defaultImpl} silently + * reinterprets a {@code "@type":"FederatedQueryRequest"} body as a {@code GeneralQueryRequest}, so this flag is the only surviving + * signal of federated intent. Accepting it would return 200 for a query whose federation had been quietly discarded. + */ + static void rejectInstitutionalQuery(Boolean isInstitute) { + if (Boolean.TRUE.equals(isInstitute)) { + throw new PicsureException(HttpStatus.GONE, "gone", "Institutional (federated) queries are no longer supported"); + } + } + + /** + * Re-emits the {@code queryMetadata} response header like the WAR's querySync, as application/json. WAR fidelity: PicsureRSv3 declares + * class-level {@code @Produces("application/json")} and querySync has NO method-level override -- only {@code /query/{id}/result} is + * octet-stream. Labeling sync octet-stream breaks the frontend, whose api layer intentionally treats octet-stream responses as binary + * downloads (ArrayBuffer), swallowing count results. + */ + static ResponseEntity syncResponse(QueryService.QuerySyncResponse r) { + ResponseEntity.BodyBuilder b = ResponseEntity.ok().contentType(MediaType.APPLICATION_JSON); + if (r.queryMetadata() != null) { + b.header("queryMetadata", r.queryMetadata()); + } + return b.body(r.body()); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/query/QueryService.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/query/QueryService.java new file mode 100644 index 000000000..0e361e8b9 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/query/QueryService.java @@ -0,0 +1,291 @@ +package edu.harvard.hms.dbmi.avillach.query.query; + +import java.nio.charset.StandardCharsets; +import java.util.Base64; +import java.util.HashMap; +import java.util.Map; +import java.util.UUID; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Service; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.json.JsonMapper; +import com.fasterxml.jackson.databind.node.ObjectNode; + +import edu.harvard.dbmi.avillach.domain.PicSureStatus; +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import edu.harvard.dbmi.avillach.domain.QueryStatus; +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.translation.QueryTranslator; +import edu.harvard.hms.dbmi.avillach.query.hpds.HpdsBackendSelector; +import edu.harvard.hms.dbmi.avillach.query.hpds.HpdsBackendSelector.HpdsTarget; +import edu.harvard.hms.dbmi.avillach.query.hpds.ResourceWebClient; +import edu.harvard.hms.dbmi.avillach.query.operations.OperationsClient; +import edu.harvard.hms.dbmi.avillach.query.operations.SaveQueryRequest; +import edu.harvard.hms.dbmi.avillach.query.operations.StoredQuery; +import edu.harvard.hms.dbmi.avillach.query.operations.UpdateQueryRequest; + +/** + * Ports the legacy WAR's {@code PicsureQueryService} (create/sync/status/result/signed-url/metadata) into a DB-free service: every place + * the legacy code read/wrote a local {@code Query} JPA entity, this class instead calls {@link OperationsClient} over HTTP. There is no + * local UUID generation and no local {@code Query} entity anywhere in this module -- operations-service is the sole source of the {@code + * picsureId} and the sole persistence store. + * + *

    Decision 9 (the signed-url bug fix): {@link #queryStatus}, {@link #queryResult}, and {@link #queryResultSignedUrl} all dispatch + * to HPDS using the backend implied by the ingress {@code {backend}} path segment (auth/open) AND the v3-ness of the STORED query's {@code + * version} field (never a value passed in on the request). The legacy WAR applied this "stored version decides v1 vs v3" rule to status and + * result, but not to signed-url ({@code PicsureQueryService.java:197+}) -- a v1-path signed-url request for a v3-stored query never reached + * HPDS's {@code /v3} routes. Here all three read ops share the same {@link #isV3(StoredQuery)} check, closing that gap. + */ +@Service +public class QueryService { + + private static final Logger logger = LoggerFactory.getLogger(QueryService.class); + private static final ObjectMapper MAPPER = new ObjectMapper(); + /** + * Lenient mapper used ONLY to deserialize a stored v1 {@code query} node in {@link #tryTranslate}: unknown fields on a stored row that + * predate the current v1 {@code Query} model must not abort translation, so this mapper (unlike {@link #MAPPER}) does not fail on + * unknown properties. Never used for anything else in this class. + */ + private static final ObjectMapper V1_QUERY_MAPPER = + JsonMapper.builder().disable(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES).build(); + private static final String CURRENT_VERSION = "3"; + + private final OperationsClient operationsClient; + private final ResourceWebClient hpds; + private final HpdsBackendSelector selector; + + public QueryService(OperationsClient operationsClient, ResourceWebClient hpds, HpdsBackendSelector selector) { + this.operationsClient = operationsClient; + this.hpds = hpds; + this.selector = selector; + } + + public record QuerySyncResponse(byte[] body, String queryMetadata) { + } + + // --- create / sync --- + + public QueryStatus query(String backend, QueryRequest req) { + return create(backend, req, false); + } + + public QueryStatus queryV3(String backend, QueryRequest req) { + return create(backend, req, true); + } + + private QueryStatus create(String backend, QueryRequest req, boolean v3) { + if (req == null) { + throw new PicsureException(HttpStatus.BAD_REQUEST, "bad_request", "Missing query data"); + } + HpdsTarget target = selector.select(backend, v3); // URL + service token + + QueryStatus results = hpds.query(target, req); // HPDS call first (parity: query() calls HPDS then persists) + String version = v3 ? CURRENT_VERSION : null; + String metadataBase64 = buildMetadataBase64(results); + + UUID picsureId = operationsClient.save( + new SaveQueryRequest( + serializeQuery(req), results.getResourceResultId(), statusName(results.getStatus()), version, metadataBase64 + ) + ); + results.setPicsureResultId(picsureId); + + if (results.getResourceResultId() == null) { // create-time fallback (PRESERVE) + String fallbackId = picsureId.toString(); + results.setResourceResultId(fallbackId); + operationsClient.update(picsureId, new UpdateQueryRequest(null, fallbackId, null)); + } + results.setResourceID(req.getResourceUUID()); // echo (no Resource entity) + return results; + } + + public QuerySyncResponse querySync(String backend, QueryRequest req, String requestSource) { + if (req == null) { + throw new PicsureException(HttpStatus.BAD_REQUEST, "bad_request", "Missing query data"); + } + HpdsTarget target = selector.select(backend, true); // sync's only remaining caller is the v3 ingress + String version = CURRENT_VERSION; + + // persist FIRST (parity: sync persists then calls HPDS) + UUID picsureId = operationsClient.save(new SaveQueryRequest(serializeQuery(req), null, null, version, null)); + + ResourceWebClient.QuerySyncResult down = hpds.querySync(target, req, requestSource); + String resourceResultId = down.queryMetadata() != null ? down.queryMetadata() : picsureId.toString(); + operationsClient.update(picsureId, new UpdateQueryRequest(null, resourceResultId, null)); + + return new QuerySyncResponse(down.body(), down.queryMetadata()); + } + + /** Port of copyQuery's metadata assembly (PicsureQueryService.java:380-419) minus Resource + AuditContext. */ + private String buildMetadataBase64(QueryStatus response) { + Map meta = response.getResultMetadata(); + if (meta == null) { + meta = new HashMap<>(); + } + response.setResultMetadata(meta); + if (meta.isEmpty()) { + return null; + } + try { + byte[] raw = MAPPER.writeValueAsString(meta).getBytes(StandardCharsets.UTF_8); // raw UTF-8 bytes (NOT gzip) + return Base64.getEncoder().encodeToString(raw); + } catch (JsonProcessingException e) { + logger.warn("Unable to serialize query metadata", e); + return null; + } + } + + /** null query → null blob; else the serialized full QueryRequest (including resourceCredentials -- stripped only at dispatch time). */ + private String serializeQuery(QueryRequest req) { + if (req.getQuery() == null) { + return null; + } + try { + return MAPPER.writeValueAsString(req); + } catch (JsonProcessingException e) { + throw new PicsureException(HttpStatus.BAD_REQUEST, "bad_request", "Incorrectly formatted request"); + } + } + + private static String statusName(PicSureStatus status) { + return status == null ? null : status.name(); + } + + // --- read ops with uniform stored-version dispatch --- + + public QueryStatus queryStatus(String backend, UUID picsureId, QueryRequest req) { + StoredQuery stored = load(picsureId); + HpdsTarget target = selector.select(backend, isV3(stored)); // backend from path, version from the stored row + QueryStatus status = hpds.queryStatus(target, stored.resourceResultId(), req); + status.setPicsureResultId(picsureId); + operationsClient.update(picsureId, new UpdateQueryRequest(statusName(status.getStatus()), null, null)); + status.setResourceID(resourceUuidFromStored(stored)); + return status; + } + + public ResponseEntity queryResult(String backend, UUID picsureId, QueryRequest req) { + StoredQuery stored = load(picsureId); + return hpds.queryResult(selector.select(backend, isV3(stored)), stored.resourceResultId(), req); + } + + public ResponseEntity queryResultSignedUrl(String backend, UUID picsureId, QueryRequest req) { + StoredQuery stored = load(picsureId); + // DECISION 9 FIX: dispatch on STORED version for signed-url too (the legacy WAR omitted this). + return hpds.queryResultSignedUrl(selector.select(backend, isV3(stored)), stored.resourceResultId(), req); + } + + private StoredQuery load(UUID picsureId) { + if (picsureId == null) { + throw new PicsureException(HttpStatus.BAD_REQUEST, "bad_request", "Missing query id"); + } + return operationsClient.get(picsureId); // throws PicsureException(NOT_FOUND) on an unknown id + } + + /** Preserves PicsureQueryService.isV3Query: version major == "3" (null-safe). */ + static boolean isV3(StoredQuery query) { + String v = query.version(); + return v != null && v.split("\\.")[0].equals(CURRENT_VERSION); + } + + /** resourceID echo without a Resource entity: parse the resourceUUID out of the stored query JSON. */ + private UUID resourceUuidFromStored(StoredQuery query) { + try { + String json = query.query(); + if (json == null || json.isBlank()) { + return null; + } + JsonNode node = MAPPER.readTree(json).get("resourceUUID"); + return (node == null || node.isNull()) ? null : UUID.fromString(node.asText()); + } catch (Exception e) { + return null; + } + } + + // --- metadata (DB-only, no HPDS) --- + + public QueryStatus queryMetadata(UUID id) { + if (id == null) { + throw new PicsureException(HttpStatus.BAD_REQUEST, "bad_request", "Missing query id"); + } + StoredQuery stored = load(id); + + QueryStatus response = new QueryStatus(); + response.setPicsureResultId(stored.picsureId()); + response.setResourceID(resourceUuidFromStored(stored)); + response.setStatus(stored.status() == null ? null : PicSureStatus.valueOf(stored.status())); + response.setResourceResultId(stored.resourceResultId()); + + Map metadata = new HashMap<>(); + try { + metadata.put("queryJson", buildQueryJson(stored)); + metadata.put("queryResultMetadata", decodeMetadata(stored.metadata())); + } catch (JsonProcessingException e) { + logger.warn("Unable to read stored query/metadata for {}", id, e); + } + response.setResultMetadata(metadata); + return response; + } + + private static String decodeMetadata(String base64Metadata) { + if (base64Metadata == null) { + return null; + } + return new String(Base64.getDecoder().decode(base64Metadata), StandardCharsets.UTF_8); + } + + /** + * The stored-query body for the {@code /metadata} response. For a v3 row (or a null body) this is the raw parsed JSON, byte-for-byte as + * before. For a v1 row it is the same {@code QueryRequest} wrapper with its nested {@code query} translated to the v3 shape, so clients + * see one shape regardless of when the query was stored. Any translation failure falls back to the untranslated body (never an error); + * a genuinely unparseable body still propagates {@link JsonProcessingException} to preserve the prior "queryJson absent" behavior. + */ + Object buildQueryJson(StoredQuery stored) throws JsonProcessingException { + String json = stored.query(); + if (json == null) { + return null; + } + if (!isV3(stored)) { + JsonNode translated = tryTranslate(json); + if (translated != null) { + // Normalize to the same Map shape the v3/raw path returns, so queryJson has one type regardless of stored version. + return MAPPER.convertValue(translated, Object.class); + } + } + return MAPPER.readValue(json, Object.class); + } + + /** + * Attempts to translate a stored v1 {@code QueryRequest} wrapper: parse it, deserialize its {@code query} node as a v1 {@code Query}, + * translate to v3, and re-embed. Returns {@code null} (caller falls back to the raw body) when the body is not a wrapper object, has no + * object-valued {@code query} node, or cannot be translated + * ({@link edu.harvard.hms.dbmi.avillach.hpds.data.query.translation.UntranslatableQueryException} or any Jackson error). Never throws. + */ + JsonNode tryTranslate(String json) { + try { + JsonNode root = MAPPER.readTree(json); + if (!(root instanceof ObjectNode wrapper)) { + return null; + } + JsonNode queryNode = wrapper.get("query"); + if (queryNode == null || !queryNode.isObject()) { + return null; + } + edu.harvard.hms.dbmi.avillach.hpds.data.query.Query v1 = + V1_QUERY_MAPPER.treeToValue(queryNode, edu.harvard.hms.dbmi.avillach.hpds.data.query.Query.class); + edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query v3 = QueryTranslator.translate(v1); + wrapper.set("query", MAPPER.valueToTree(v3)); + return wrapper; + } catch (Exception e) { + logger.warn("Unable to translate stored v1 query to v3; returning it untranslated", e); + return null; + } + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/search/HpdsSearchController.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/search/HpdsSearchController.java new file mode 100644 index 000000000..e90bf4d23 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/search/HpdsSearchController.java @@ -0,0 +1,48 @@ +package edu.harvard.hms.dbmi.avillach.query.search; + +import java.util.UUID; + +import org.springframework.web.bind.annotation.GetMapping; +import org.springframework.web.bind.annotation.PathVariable; +import org.springframework.web.bind.annotation.PostMapping; +import org.springframework.web.bind.annotation.RequestBody; +import org.springframework.web.bind.annotation.RequestParam; +import org.springframework.web.bind.annotation.RestController; + +import edu.harvard.dbmi.avillach.domain.PaginatedSearchResult; +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import edu.harvard.dbmi.avillach.domain.SearchResults; + +/** + * Ports the legacy WAR's {@code PicsureRS}/{@code PicsureRSv3} search endpoints. Mapped under BOTH the v1 and v3 ingress prefixes for a + * given {@code {backend}} (multi-path {@code @RequestMapping} arrays) because search behaves identically either way -- unlike the query + * lifecycle, {@link SearchService} always resolves the backend's non-versioned base (see its class javadoc): search is never versioned + * downstream on HPDS. The {@code resourceId} path variable is retained for ingress contract parity (an HPDS-internal identifier) but is not + * used for routing here -- it is forwarded inside the request body, not read off the path. + */ +@RestController +public class HpdsSearchController { + + private final SearchService service; + + public HpdsSearchController(SearchService service) { + this.service = service; + } + + @PostMapping({"/hpds/{backend}/search/{resourceId}", "/hpds/{backend}/v3/search/{resourceId}"}) + public SearchResults search( + @PathVariable("backend") String backend, @PathVariable("resourceId") UUID resourceId, @RequestBody QueryRequest req + ) { + return service.search(backend, req); + } + + @GetMapping(value = {"/hpds/{backend}/search/{resourceId}/values/", "/hpds/{backend}/v3/search/{resourceId}/values/"}, consumes = "*/*") + public PaginatedSearchResult values( + @PathVariable("backend") String backend, @PathVariable("resourceId") UUID resourceId, + @RequestBody(required = false) QueryRequest req, @RequestParam(name = "genomicConceptPath", required = false) String conceptPath, + @RequestParam(name = "query", required = false) String query, @RequestParam(name = "page", required = false) Integer page, + @RequestParam(name = "size", required = false) Integer size + ) { + return service.searchConceptValues(backend, req, conceptPath, query, page, size); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/search/SearchService.java b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/search/SearchService.java new file mode 100644 index 000000000..1fb95c1a1 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/java/edu/harvard/hms/dbmi/avillach/query/search/SearchService.java @@ -0,0 +1,51 @@ +package edu.harvard.hms.dbmi.avillach.query.search; + +import org.springframework.http.HttpStatus; +import org.springframework.stereotype.Service; + +import edu.harvard.dbmi.avillach.domain.PaginatedSearchResult; +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import edu.harvard.dbmi.avillach.domain.SearchResults; +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; +import edu.harvard.hms.dbmi.avillach.query.hpds.HpdsBackendSelector; +import edu.harvard.hms.dbmi.avillach.query.hpds.ResourceWebClient; + +/** + * Ports the legacy WAR's {@code PicsureSearchService.search}/{@code searchGenomicConceptValues} (:46-109) minus Resource + AuditContext. + * Backend (auth/open) comes from the ingress {@code {backend}} path segment via {@link HpdsBackendSelector}, mirroring + * {@link edu.harvard.hms.dbmi.avillach.query.query.QueryService}. + * + *

    Search is NOT versioned downstream: unlike the query-lifecycle calls, the legacy WAR's {@code PicsureSearchService} always hit + * HPDS at the backend's base path with no {@code /v3} suffix, even though the controller layer accepts both v1 and v3 ingress paths. This + * class always resolves the backend with {@code v3=false} to preserve that (search endpoints on HPDS are not versioned). + * + *

    Also preserves that search/values calls carry NO service token: {@link ResourceWebClient#search} and + * {@link ResourceWebClient#searchConceptValues} take a plain base URL string (not an {@code HpdsTarget}), so the per-backend service token + * resolved by {@link HpdsBackendSelector} is never attached -- parity with {@code PicsureSearchService}, which never set + * {@code BEARER_TOKEN} on these calls. + */ +@Service +public class SearchService { + + private final ResourceWebClient hpds; + private final HpdsBackendSelector selector; + + public SearchService(ResourceWebClient hpds, HpdsBackendSelector selector) { + this.hpds = hpds; + this.selector = selector; + } + + public SearchResults search(String backend, QueryRequest req) { + if (req == null) { + throw new PicsureException(HttpStatus.BAD_REQUEST, "bad_request", "Missing search data"); + } + // Non-versioned downstream, no service token: only the resolved base URL is used. + return hpds.search(selector.select(backend, false).baseUrl(), req); + } + + public PaginatedSearchResult searchConceptValues( + String backend, QueryRequest req, String conceptPath, String query, Integer page, Integer size + ) { + return hpds.searchConceptValues(selector.select(backend, false).baseUrl(), req, conceptPath, query, page, size); + } +} diff --git a/services/pic-sure-hpds-query-service/src/main/resources/application.yml b/services/pic-sure-hpds-query-service/src/main/resources/application.yml new file mode 100644 index 000000000..beda46b4a --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/main/resources/application.yml @@ -0,0 +1,70 @@ +spring: + application: + name: pic-sure-hpds-query-service + +server: + port: ${SERVER_PORT:8080} + +hpds: + # HPDS_AUTH_URL / HPDS_AUTH_TOKEN: the auth (non-obfuscated) backend base + service Bearer token. + auth-url: ${HPDS_AUTH_URL:} + auth-token: ${HPDS_AUTH_TOKEN:} + # HPDS_OPEN_URL / HPDS_OPEN_TOKEN: the open (aggregate/obfuscated) backend base + service Bearer token. + # In AIO both HPDS_* URL vars point at the same HPDS instance. + open-url: ${HPDS_OPEN_URL:} + open-token: ${HPDS_OPEN_TOKEN:} + +picsure: + query: + operations: + # OPERATIONS_SERVICE_URL: base URL of pic-sure-operations-service (the sole pic-sure-DB owner). This service + # is DB-free -- every query read/write goes over HTTP through OperationsClient. + base-url: ${OPERATIONS_SERVICE_URL:} + # QUERY_SERVICE_INTERNAL_TOKEN: shared secret sent as X-PIC-SURE-INTERNAL-TOKEN on every operations-service + # call, checked by that service's InternalTokenFilter. Fail-closed on the operations-service side if unset. + internal-token: ${QUERY_SERVICE_INTERNAL_TOKEN:} + # The X-Application-Token gate for /actuator/** (ActuatorSecurityConfig + the shared + # ActuatorSecurityHelper in pic-sure-spring-commons). Shallow health/liveness/readiness stay open regardless. + actuator: + require-token: ${PICSURE_ACTUATOR_REQUIRE_TOKEN:true} + token: ${PICSURE_APPLICATION_TOKEN:} + header-name: X-Application-Token + +aggregate: + # HPDS_OPEN_URL / HPDS_OPEN_TOKEN: same open-backend values as hpds.open-url / hpds.open-token above, + # reused here so the aggregate obfuscation path talks to the same open HPDS backend. + hpds-open-url: ${HPDS_OPEN_URL:} + hpds-open-token: ${HPDS_OPEN_TOKEN:} + # VISUALIZATION_URL: base URL of the visualization service; replaces the WAR's DB ResourceRepository.getById() + # lookup. Blank = no binning configured (continuous cross-count obfuscation falls back to raw per-value counts). + visualization-url: ${VISUALIZATION_URL:} + visualization-resource-id: ${AGGREGATE_VISUALIZATION_RESOURCE_ID:} + target-resource-id: ${AGGREGATE_TARGET_RESOURCE_ID:} + connect-timeout-sec: 10 + read-timeout-sec: 60 + obfuscation: + threshold: ${AGGREGATE_OBFUSCATION_THRESHOLD:10} + variance: ${AGGREGATE_OBFUSCATION_VARIANCE:3} + salt: ${AGGREGATE_OBFUSCATION_SALT:} + +management: + endpoints: + web: + exposure: + # OFF BY DEFAULT: 'none' is a sentinel that matches no endpoint, so /actuator/** is 404. (An EMPTY include is + # NOT off -- Spring Boot then falls back to exposing health.) AIO enables it via PICSURE_ACTUATOR_EXPOSURE; + # prometheus/metrics are added via the same var in the monitoring (M2) rollout. + include: ${PICSURE_ACTUATOR_EXPOSURE:none} + endpoint: + health: + show-details: ${PICSURE_ACTUATOR_DETAILS:never} # default never; when_authorized (AIO) gates detail behind picsure.actuator.token + probes: + enabled: true # /actuator/health/liveness stays shallow-open + group: + # Explicit liveness group (mirrors the gateway's) -- pins /actuator/health/liveness to the app's + # own process state so it never depends on HPDS reachability or auto-registration nuances of probes.enabled. + liveness: + include: livenessState + health: + defaults: + enabled: true diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/QueryServiceApplicationTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/QueryServiceApplicationTest.java new file mode 100644 index 000000000..1bbbb0575 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/QueryServiceApplicationTest.java @@ -0,0 +1,63 @@ +package edu.harvard.hms.dbmi.avillach.query; + +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.context.ApplicationContext; +import org.springframework.web.client.RestClient; + +import edu.harvard.hms.dbmi.avillach.query.hpds.HpdsBackendSelector; +import edu.harvard.hms.dbmi.avillach.query.operations.OperationsClient; + +/** + * Context-load smoke test: the module must boot with the HPDS + operations-service URLs pointed at dummy values (see + * src/test/resources/application.yml) and the DB-free beans (HpdsBackendSelector, the pooled HPDS RestClient, OperationsClient, the pooled + * operations RestClient) must all be wired. No DB, no H2 -- this service owns none. + */ +@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.MOCK) +class QueryServiceApplicationTest { + + @Autowired + private ApplicationContext context; + + @Autowired + private HpdsBackendSelector hpdsBackendSelector; + + @Autowired + private OperationsClient operationsClient; + + @Autowired + @org.springframework.beans.factory.annotation.Qualifier("hpdsClient") + private RestClient hpdsClient; + + @Autowired + @org.springframework.beans.factory.annotation.Qualifier("operationsRestClient") + private RestClient operationsRestClient; + + @Test + void contextLoads() { + assertThat(context).isNotNull(); + } + + @Test + void hpdsBackendSelectorIsWired() { + assertThat(hpdsBackendSelector).isNotNull(); + var target = hpdsBackendSelector.select("auth", false); + assertThat(target.baseUrl()).isEqualTo("http://localhost:1/PIC-SURE"); + assertThat(target.token()).isEqualTo("test-auth-token"); + } + + @Test + void operationsClientIsWired() { + assertThat(operationsClient).isNotNull(); + } + + @Test + void restClientBeansAreDistinctAndWired() { + assertThat(hpdsClient).isNotNull(); + assertThat(operationsRestClient).isNotNull(); + assertThat(hpdsClient).isNotSameAs(operationsRestClient); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateAsyncOpenQueryTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateAsyncOpenQueryTest.java new file mode 100644 index 000000000..4d9b228b8 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateAsyncOpenQueryTest.java @@ -0,0 +1,166 @@ +package edu.harvard.hms.dbmi.avillach.query.aggregate; + +import static com.github.tomakehurst.wiremock.client.WireMock.matchingJsonPath; +import static com.github.tomakehurst.wiremock.client.WireMock.okJson; +import static com.github.tomakehurst.wiremock.client.WireMock.postRequestedFor; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.ArgumentMatchers.argThat; +import static org.mockito.Mockito.never; +import static org.mockito.Mockito.verify; +import static org.mockito.Mockito.when; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.jsonPath; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status; + +import java.util.UUID; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.MediaType; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.springframework.test.context.bean.override.mockito.MockitoBean; +import org.springframework.test.web.servlet.MockMvc; + +import com.github.tomakehurst.wiremock.WireMockServer; +import com.github.tomakehurst.wiremock.client.WireMock; + +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import edu.harvard.hms.dbmi.avillach.query.operations.OperationsClient; +import edu.harvard.hms.dbmi.avillach.query.operations.SaveQueryRequest; + +/** + * Full-context proof of finding I6 (async open path consent-scoping). Real {@link AggregateService} + + * {@link edu.harvard.hms.dbmi.avillach.query.query.QueryService} + HpdsBackendSelector/ResourceWebClient; WireMock stands in for the open + * HPDS backend (the {@code /search} study-consents lookup and the {@code /PIC-SURE/query} async submit), and a Mockito + * {@link OperationsClient} stands in for operations-service persistence (this module is DB-free). + * + *

    Asserts: (a) {@code POST /hpds/open/query} for a CROSS_COUNT submission is rewritten (force CROSS_COUNT + inject the study-consents + * allow-list) and the REWRITTEN query is what gets persisted AND dispatched -- so any later status/result read served off the stored query + * is already consent-scoped; (b) the generic authorized path {@code /hpds/auth/v3/query} is UNTOUCHED (no rewrite, no consent lookup); (c) + * a WAR-rejected shape (missing {@code expectedResultType}) is still a 400 before any backend/persistence call. + */ +@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.MOCK) +@AutoConfigureMockMvc +class AggregateAsyncOpenQueryTest { + + private static final String USER = "auth0|alice"; + + static WireMockServer hpds; + + @BeforeAll + static void start() { + hpds = new WireMockServer(options().dynamicPort().http2PlainDisabled(true)); + hpds.start(); + } + + @AfterAll + static void stop() { + hpds.stop(); + } + + @DynamicPropertySource + static void props(DynamicPropertyRegistry registry) { + registry.add("hpds.auth-url", () -> "http://localhost:" + hpds.port() + "/PIC-SURE"); + registry.add("hpds.open-url", () -> "http://localhost:" + hpds.port() + "/PIC-SURE"); + // AggregateBackendClient (study-consents lookup) posts to the open backend root + registry.add("aggregate.hpds-open-url", () -> "http://localhost:" + hpds.port()); + } + + @Autowired + private MockMvc mockMvc; + + @MockitoBean + private OperationsClient operationsClient; + + @BeforeEach + void reset() { + hpds.resetAll(); + } + + @Test + void openAsyncCrossCountIsRewrittenAndConsentScopedBeforePersistAndDispatch() throws Exception { + hpds.stubFor( + WireMock.post(urlEqualTo("/search")).willReturn(okJson("{\"results\":{\"phenotypes\":{\"consentA\":{},\"consentB\":{}}}}")) + ); + hpds.stubFor( + WireMock.post(urlEqualTo("/PIC-SURE/query")).willReturn(okJson("{\"resourceResultId\":\"rr-async\",\"status\":\"PENDING\"}")) + ); + when(operationsClient.save(any())).thenReturn(UUID.randomUUID()); + + mockMvc.perform( + post("/hpds/open/query").header(GatewayUserResolver.HEADER_USER_ID, USER).contentType(MediaType.APPLICATION_JSON) + .content("{\"query\":{\"expectedResultType\":\"CROSS_COUNT\"}}") + ).andExpect(status().isOk()).andExpect(jsonPath("$.resourceResultId").value("rr-async")); + + // The STORED query is the rewritten, consent-scoped one -- NOT the raw submission. + verify(operationsClient).save( + argThat((SaveQueryRequest r) -> r.query() != null && r.query().contains("crossCountFields") && r.query().contains("consentA")) + ); + // The consent lookup happened and the async submit dispatched the injected allow-list to HPDS. + hpds.verify(postRequestedFor(urlEqualTo("/search"))); + hpds.verify(postRequestedFor(urlEqualTo("/PIC-SURE/query")).withRequestBody(matchingJsonPath("$.query.crossCountFields"))); + } + + @Test + void openAsyncV3CrossCountUsesSelectAndHitsV3Base() throws Exception { + hpds.stubFor( + WireMock.post(urlEqualTo("/search")).willReturn(okJson("{\"results\":{\"phenotypes\":{\"consentA\":{},\"consentB\":{}}}}")) + ); + hpds.stubFor( + WireMock.post(urlEqualTo("/PIC-SURE/v3/query")) + .willReturn(okJson("{\"resourceResultId\":\"rr-async3\",\"status\":\"PENDING\"}")) + ); + when(operationsClient.save(any())).thenReturn(UUID.randomUUID()); + + mockMvc.perform( + post("/hpds/open/v3/query").header(GatewayUserResolver.HEADER_USER_ID, USER).contentType(MediaType.APPLICATION_JSON) + .content("{\"query\":{\"expectedResultType\":\"CROSS_COUNT\"}}") + ).andExpect(status().isOk()); + + verify(operationsClient) + .save(argThat((SaveQueryRequest r) -> "3".equals(r.version()) && r.query() != null && r.query().contains("select"))); + hpds.verify(postRequestedFor(urlEqualTo("/PIC-SURE/v3/query")).withRequestBody(matchingJsonPath("$.query.select"))); + } + + @Test + void authAsyncQueryIsNotRewritten() throws Exception { + hpds.stubFor( + WireMock.post(urlEqualTo("/PIC-SURE/v3/query")).willReturn(okJson("{\"resourceResultId\":\"rr-auth\",\"status\":\"PENDING\"}")) + ); + when(operationsClient.save(any())).thenReturn(UUID.randomUUID()); + + mockMvc.perform( + post("/hpds/auth/v3/query").header(GatewayUserResolver.HEADER_USER_ID, USER).contentType(MediaType.APPLICATION_JSON) + .content("{\"query\":{\"expectedResultType\":\"DATAFRAME\"}}") + ).andExpect(status().isOk()); + + // Generic authorized path: the raw DATAFRAME query is stored + dispatched unchanged; no consent lookup, no CROSS_COUNT rewrite. + verify(operationsClient).save( + argThat((SaveQueryRequest r) -> r.query() != null && r.query().contains("DATAFRAME") && !r.query().contains("crossCountFields")) + ); + hpds.verify(0, postRequestedFor(urlEqualTo("/search"))); + hpds.verify( + postRequestedFor(urlEqualTo("/PIC-SURE/v3/query")) + .withRequestBody(matchingJsonPath("$.query.expectedResultType", WireMock.equalTo("DATAFRAME"))) + ); + } + + @Test + void openAsyncQueryMissingExpectedResultTypeIsRejectedAs400() throws Exception { + mockMvc.perform( + post("/hpds/open/query").header(GatewayUserResolver.HEADER_USER_ID, USER).contentType(MediaType.APPLICATION_JSON) + .content("{\"query\":{\"foo\":\"bar\"}}") + ).andExpect(status().isBadRequest()).andExpect(jsonPath("$.errorType").value("bad_request")); + + verify(operationsClient, never()).save(any()); + hpds.verify(0, postRequestedFor(urlEqualTo("/search"))); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateBackendClientTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateBackendClientTest.java new file mode 100644 index 000000000..3933845e8 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateBackendClientTest.java @@ -0,0 +1,128 @@ +package edu.harvard.hms.dbmi.avillach.query.aggregate; + +import static com.github.tomakehurst.wiremock.client.WireMock.aResponse; +import static com.github.tomakehurst.wiremock.client.WireMock.matchingJsonPath; +import static com.github.tomakehurst.wiremock.client.WireMock.okJson; +import static com.github.tomakehurst.wiremock.client.WireMock.post; +import static com.github.tomakehurst.wiremock.client.WireMock.postRequestedFor; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static org.assertj.core.api.Assertions.assertThat; +import static org.assertj.core.api.Assertions.assertThatThrownBy; + +import java.util.UUID; + +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.http.ResponseEntity; +import org.springframework.web.client.RestClient; + +import com.github.tomakehurst.wiremock.WireMockServer; +import com.github.tomakehurst.wiremock.client.WireMock; + +import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest; +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import edu.harvard.hms.dbmi.avillach.query.config.AggregateProperties; +import edu.harvard.hms.dbmi.avillach.query.hpds.HpdsCommunicationException; + +class AggregateBackendClientTest { + + WireMockServer hpds; + + @BeforeEach + void start() { + hpds = new WireMockServer(0); + hpds.start(); + } + + @AfterEach + void stop() { + hpds.stop(); + } + + private AggregateProperties properties() { + AggregateProperties props = new AggregateProperties(); + props.setHpdsOpenUrl("http://localhost:" + hpds.port()); + props.setVisualizationUrl("http://localhost:" + hpds.port()); + props.setHpdsOpenToken("open-token"); + return props; + } + + private AggregateBackendClient client() { + return new AggregateBackendClient(RestClient.builder().build(), properties()); + } + + private QueryRequest req(Object query) { + return new GeneralQueryRequest().setQuery(query); + } + + @Test + void querySyncSendsBearerTokenAndPropagatesMetadata() { + // finding I5: HPDS emits the metadata under "queryMetadata" (the legacy WAR's ResourceWebClient.QUERY_METADATA_FIELD); the + // client must surface that exact header. Stubbing the real name here (not the constant) keeps this a genuine contract check. + hpds.stubFor( + post(urlEqualTo("/query/sync")).withHeader("Content-Type", WireMock.containing("application/json")) + .willReturn(aResponse().withStatus(200).withHeader("queryMetadata", "abc").withBody("42")) + ); + + ResponseEntity resp = client().querySync(req("{}"), AggregateVariant.V1); + + assertThat(resp.getBody()).isEqualTo("42"); + assertThat(resp.getHeaders().getFirst(AggregateBackendClient.QUERY_METADATA_FIELD)).isEqualTo("abc"); + assertThat(AggregateBackendClient.QUERY_METADATA_FIELD).isEqualTo("queryMetadata"); + hpds.verify(postRequestedFor(urlEqualTo("/query/sync")).withHeader("Authorization", WireMock.equalTo("Bearer open-token"))); + } + + @Test + void v3QuerySyncPrependsVersionPrefix() { + hpds.stubFor(post(urlEqualTo("/v3/query/sync")).willReturn(okJson("7"))); + ResponseEntity resp = client().querySync(req("{}"), AggregateVariant.V3); + assertThat(resp.getBody()).isEqualTo("7"); + hpds.verify(postRequestedFor(urlEqualTo("/v3/query/sync"))); + } + + @Test + void v1BinContinuousHasNoVersionPrefix() { + hpds.stubFor(post(urlEqualTo("/bin/continuous")).willReturn(okJson("{}"))); + client().binContinuous(req("{}"), AggregateVariant.V1); + hpds.verify(postRequestedFor(urlEqualTo("/bin/continuous"))); + } + + @Test + void v3BinContinuousPrependsVersionPrefix() { + hpds.stubFor(post(urlEqualTo("/v3/bin/continuous")).willReturn(okJson("{}"))); + client().binContinuous(req("{}"), AggregateVariant.V3); + hpds.verify(postRequestedFor(urlEqualTo("/v3/bin/continuous"))); + } + + @Test + void injectsConfiguredTargetResourceId() { + String id = UUID.randomUUID().toString(); + AggregateProperties props = properties(); + props.setTargetResourceId(id); + AggregateBackendClient c = new AggregateBackendClient(RestClient.builder().build(), props); + + hpds.stubFor(post(urlEqualTo("/search")).willReturn(okJson("{\"searchQuery\":\"q\",\"results\":{}}"))); + c.search(req("\\_studies_consents\\")); + + hpds.verify(postRequestedFor(urlEqualTo("/search")).withRequestBody(matchingJsonPath("$.resourceUUID", WireMock.equalTo(id)))); + } + + @Test + void nonTwoxxResponseThrowsHpdsCommunicationException() { + hpds.stubFor(post(urlEqualTo("/query/sync")).willReturn(aResponse().withStatus(500))); + assertThatThrownBy(() -> client().querySync(req("{}"), AggregateVariant.V1)).isInstanceOf(HpdsCommunicationException.class); + } + + @Test + void noTokenConfiguredOmitsAuthorizationHeader() { + AggregateProperties props = properties(); + props.setHpdsOpenToken(null); + AggregateBackendClient c = new AggregateBackendClient(RestClient.builder().build(), props); + + hpds.stubFor(post(urlEqualTo("/query/sync")).willReturn(okJson("1"))); + c.querySync(req("{}"), AggregateVariant.V1); + + hpds.verify(postRequestedFor(urlEqualTo("/query/sync")).withoutHeader("Authorization")); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateControllerTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateControllerTest.java new file mode 100644 index 000000000..88aee9158 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateControllerTest.java @@ -0,0 +1,130 @@ +package edu.harvard.hms.dbmi.avillach.query.aggregate; + +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.assertj.core.api.Assertions.assertThat; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.ArgumentMatchers.eq; +import static org.mockito.Mockito.verify; +import static org.mockito.Mockito.verifyNoInteractions; +import static org.mockito.Mockito.when; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.content; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.springframework.test.context.bean.override.mockito.MockitoBean; +import org.springframework.test.web.servlet.MockMvc; + +import com.github.tomakehurst.wiremock.WireMockServer; +import com.github.tomakehurst.wiremock.client.WireMock; + +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import edu.harvard.hms.dbmi.avillach.query.hpds.HpdsCommunicationException; +import edu.harvard.hms.dbmi.avillach.query.operations.OperationsClient; + +/** + * MockMvc coverage of {@link AggregateController} (the v1 obfuscation ingress at {@code /hpds/open/query/sync}), with + * {@link AggregateService} replaced by a Mockito mock (the obfuscation logic itself is exhaustively covered by + * {@link AggregateServiceTest}) -- this class exists to prove the CONTROLLER WIRING: a literal {@code /hpds/open/query/sync} request must + * be dispatched to this controller (and therefore through obfuscation). The generic v1 ingress was removed, so other backends' v1 routes + * ({@code /hpds/auth/query/sync}) no longer exist at all -- they 404 rather than falling through to any other controller. + */ +@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.MOCK) +@AutoConfigureMockMvc +class AggregateControllerTest { + + private static final String USER = "auth0|alice"; + + static WireMockServer hpds; + + @BeforeAll + static void start() { + hpds = new WireMockServer(options().dynamicPort().http2PlainDisabled(true)); + hpds.start(); + } + + @AfterAll + static void stop() { + hpds.stop(); + } + + @DynamicPropertySource + static void hpdsProps(DynamicPropertyRegistry registry) { + // Backs the QueryService/HpdsBackendSelector wiring the context needs to start; the AggregateService bean itself is mocked, so + // aggregate.* properties are irrelevant to this test class. + registry.add("hpds.auth-url", () -> "http://localhost:" + hpds.port() + "/PIC-SURE"); + registry.add("hpds.open-url", () -> "http://localhost:" + hpds.port() + "/PIC-SURE"); + } + + @Autowired + private MockMvc mockMvc; + + @MockitoBean + private AggregateService aggregateService; + + @MockitoBean + private OperationsClient operationsClient; + + @BeforeEach + void resetStubs() { + hpds.resetAll(); + } + + @Test + void openQuerySyncRoutesToAggregateServiceObfuscationAndReturnsResult() throws Exception { + when(aggregateService.querySync(any(QueryRequest.class), eq(AggregateVariant.V1))) + .thenReturn(ResponseEntity.ok().contentType(MediaType.APPLICATION_JSON).body("< 10")); + + mockMvc + .perform( + post("/hpds/open/query/sync").header(GatewayUserResolver.HEADER_USER_ID, USER).contentType(MediaType.APPLICATION_JSON) + .content("{\"query\":{\"expectedResultType\":\"COUNT\"}}") + ).andExpect(status().isOk()).andExpect(content().string("< 10")); + + verify(aggregateService).querySync(any(QueryRequest.class), eq(AggregateVariant.V1)); + verifyNoInteractions(operationsClient); // the aggregate path never touches operations-service persistence + hpds.verify(0, WireMock.postRequestedFor(urlEqualTo("/PIC-SURE/query/sync"))); // never reached the generic HPDS backend + } + + @Test + void authQuerySyncRouteIsGoneAndNeverHitsAggregateController() throws Exception { + mockMvc.perform( + post("/hpds/auth/query/sync").header(GatewayUserResolver.HEADER_USER_ID, USER).contentType(MediaType.APPLICATION_JSON) + .content("{\"query\":\"q\"}") + ).andExpect(status().isNotFound()); + + verifyNoInteractions(aggregateService); // aggregate controller maps /hpds/open only + } + + @Test + void openQuerySyncWithoutGatewayIdentityIsUnauthorized() throws Exception { + mockMvc.perform(post("/hpds/open/query/sync").contentType(MediaType.APPLICATION_JSON).content("{\"query\":\"q\"}")) + .andExpect(result -> assertThat(result.getResponse().getStatus()).isIn(401, 403)); + + verifyNoInteractions(aggregateService); + } + + @Test + void openQuerySyncUpstreamErrorSurfacesAs502() throws Exception { + when(aggregateService.querySync(any(QueryRequest.class), eq(AggregateVariant.V1))) + .thenThrow(new HpdsCommunicationException("Aggregate query/sync call failed", new RuntimeException("boom"))); + + mockMvc + .perform( + post("/hpds/open/query/sync").header(GatewayUserResolver.HEADER_USER_ID, USER).contentType(MediaType.APPLICATION_JSON) + .content("{\"query\":{\"expectedResultType\":\"COUNT\"}}") + ).andExpect(status().isBadGateway()); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateServiceTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateServiceTest.java new file mode 100644 index 000000000..27c991ed5 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateServiceTest.java @@ -0,0 +1,282 @@ +package edu.harvard.hms.dbmi.avillach.query.aggregate; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.assertj.core.api.Assertions.assertThatThrownBy; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.ArgumentMatchers.eq; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.never; +import static org.mockito.Mockito.verify; +import static org.mockito.Mockito.verifyNoInteractions; +import static org.mockito.Mockito.when; + +import java.util.LinkedHashMap; +import java.util.Map; + +import org.junit.jupiter.api.Test; +import org.mockito.ArgumentCaptor; +import org.springframework.http.ResponseEntity; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest; +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import edu.harvard.dbmi.avillach.domain.SearchResults; +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; +import edu.harvard.hms.dbmi.avillach.query.config.AggregateProperties; +import edu.harvard.hms.dbmi.avillach.query.query.QueryService; + +class AggregateServiceTest { + + private final ObjectMapper mapper = new ObjectMapper(); + + private ObfuscationService obfuscation() { + AggregateProperties p = new AggregateProperties(); + p.getObfuscation().setThreshold(10); + p.getObfuscation().setVariance(3); + p.getObfuscation().setSalt("fixed"); + return new ObfuscationService(p, new VisualizationFormatter()); + } + + /** obfuscation-path tests don't exercise persistence; a throwaway QueryService mock keeps their construction terse. */ + private AggregateService service(AggregateBackendClient backend, AggregateProperties props) { + return new AggregateService(backend, obfuscation(), props, mock(QueryService.class)); + } + + private QueryRequest sync(String expectedResultType) { + return new GeneralQueryRequest().setQuery(Map.of("expectedResultType", expectedResultType)); + } + + @Test + void rejectsDisallowedResultTypeWith400() { + AggregateBackendClient backend = mock(AggregateBackendClient.class); + AggregateService svc = service(backend, new AggregateProperties()); + assertThatThrownBy(() -> svc.querySync(sync("DATAFRAME"), AggregateVariant.V1)).isInstanceOf(PicsureException.class); + verify(backend, never()).querySync(any(), any()); + } + + @Test + void rejectsMissingExpectedResultTypeWith400() { + AggregateBackendClient backend = mock(AggregateBackendClient.class); + AggregateService svc = service(backend, new AggregateProperties()); + QueryRequest noErt = new GeneralQueryRequest().setQuery(Map.of("fields", "x")); + assertThatThrownBy(() -> svc.querySync(noErt, AggregateVariant.V1)).isInstanceOf(PicsureException.class); + } + + @Test + void rejectsNullQueryWith400() { + AggregateBackendClient backend = mock(AggregateBackendClient.class); + AggregateService svc = service(backend, new AggregateProperties()); + assertThatThrownBy(() -> svc.querySync(new GeneralQueryRequest(), AggregateVariant.V1)).isInstanceOf(PicsureException.class); + } + + @Test + void countBelowThresholdIsFloored() { + AggregateBackendClient backend = mock(AggregateBackendClient.class); + when(backend.querySync(any(), eq(AggregateVariant.V1))).thenReturn(ResponseEntity.ok("5")); + AggregateService svc = service(backend, new AggregateProperties()); + + ResponseEntity out = svc.querySync(sync("COUNT"), AggregateVariant.V1); + assertThat(out.getBody()).isEqualTo("< 10"); + } + + @Test + void countAtOrAboveThresholdIsVarianceRandomized() { + AggregateBackendClient backend = mock(AggregateBackendClient.class); + when(backend.querySync(any(), eq(AggregateVariant.V1))).thenReturn(ResponseEntity.ok("100")); + AggregateService svc = service(backend, new AggregateProperties()); + + ResponseEntity out = svc.querySync(sync("COUNT"), AggregateVariant.V1); + assertThat(out.getBody()).matches("\\d+ ±3"); + } + + @Test + void crossCountObfuscatesEachEntry() throws Exception { + AggregateBackendClient backend = mock(AggregateBackendClient.class); + // changeQueryToOpenCrossCount first searches consents, then the backend returns the cross counts + when(backend.search(any())).thenReturn(consentsSearch()); + when(backend.querySync(any(), eq(AggregateVariant.V1))) + .thenReturn(ResponseEntity.ok("{\"\\\\study\\\\a\\\\\":\"5\",\"\\\\study\\\\b\\\\\":\"100\"}")); + AggregateService svc = service(backend, new AggregateProperties()); + + ResponseEntity out = svc.querySync(sync("CROSS_COUNT"), AggregateVariant.V1); + Map body = mapper.readValue(out.getBody(), Map.class); + assertThat(body.get("\\study\\a\\")).isEqualTo("< 10"); + assertThat(body.get("\\study\\b\\")).matches("\\d+ ±3"); + } + + @Test + void crossCountUsesCrossCountFieldsForV1() { + AggregateBackendClient backend = mock(AggregateBackendClient.class); + when(backend.search(any())).thenReturn(consentsSearch()); + when(backend.querySync(any(), eq(AggregateVariant.V1))).thenReturn(ResponseEntity.ok("{}")); + AggregateService svc = service(backend, new AggregateProperties()); + + svc.querySync(sync("CROSS_COUNT"), AggregateVariant.V1); + + ArgumentCaptor cap = ArgumentCaptor.forClass(QueryRequest.class); + verify(backend).querySync(cap.capture(), eq(AggregateVariant.V1)); + @SuppressWarnings("unchecked") + Map query = mapper.convertValue(cap.getValue().getQuery(), Map.class); + assertThat(query).containsKey("crossCountFields").doesNotContainKey("select"); + } + + @Test + void crossCountUsesSelectFieldForV3() { + AggregateBackendClient backend = mock(AggregateBackendClient.class); + when(backend.search(any())).thenReturn(consentsSearch()); + when(backend.querySync(any(), eq(AggregateVariant.V3))).thenReturn(ResponseEntity.ok("{}")); + AggregateService svc = service(backend, new AggregateProperties()); + + svc.querySync(sync("CROSS_COUNT"), AggregateVariant.V3); + + // capture the mutated request sent to the backend; assert it carries `select`, not `crossCountFields` + ArgumentCaptor cap = ArgumentCaptor.forClass(QueryRequest.class); + verify(backend).querySync(cap.capture(), eq(AggregateVariant.V3)); + @SuppressWarnings("unchecked") + Map query = mapper.convertValue(cap.getValue().getQuery(), Map.class); + assertThat(query).containsKey("select").doesNotContainKey("crossCountFields"); + } + + @Test + void categoricalCrossCountObfuscatesViaCrossCountLookup() { + AggregateBackendClient backend = mock(AggregateBackendClient.class); + when(backend.search(any())).thenReturn(consentsSearch()); + // first querySync call returns the raw categorical payload; the CROSS_COUNT lookup (getCrossCountForQuery) + // is a second call to querySync with the mutated (CROSS_COUNT) request + when(backend.querySync(any(), eq(AggregateVariant.V1))) + .thenReturn(ResponseEntity.ok("{\"\\\\gender\\\\\":{\"male\":5,\"female\":100}}")) + .thenReturn(ResponseEntity.ok("{\"\\\\_studies_consents\\\\\":\"500\"}")); + AggregateService svc = service(backend, new AggregateProperties()); + + ResponseEntity out = svc.querySync(sync("CATEGORICAL_CROSS_COUNT"), AggregateVariant.V1); + assertThat(out.getBody()).contains("\"male\"").contains("< 10"); + } + + @Test + void continuousCrossCountSuppressedWhenStudyConsentsBelowThreshold() { + AggregateBackendClient backend = mock(AggregateBackendClient.class); + when(backend.search(any())).thenReturn(consentsSearch()); + when(backend.querySync(any(), eq(AggregateVariant.V1))).thenReturn(ResponseEntity.ok("{\"\\\\age\\\\\":{\"5\":1}}")) + .thenReturn(ResponseEntity.ok("{\"\\\\_studies_consents\\\\\":\"< 10\"}")); + AggregateService svc = service(backend, new AggregateProperties()); + + ResponseEntity out = svc.querySync(sync("CONTINUOUS_CROSS_COUNT"), AggregateVariant.V1); + assertThat(out.getBody()).isNull(); + } + + @Test + void continuousCrossCountObfuscatesRawWhenNoVisualizationConfigured() { + AggregateBackendClient backend = mock(AggregateBackendClient.class); + when(backend.search(any())).thenReturn(consentsSearch()); + when(backend.querySync(any(), eq(AggregateVariant.V1))).thenReturn(ResponseEntity.ok("{\"\\\\age\\\\\":{\"5\":100}}")) + .thenReturn(ResponseEntity.ok("{\"\\\\_studies_consents\\\\\":\"500\"}")); + AggregateService svc = service(backend, new AggregateProperties()); + + ResponseEntity out = svc.querySync(sync("CONTINUOUS_CROSS_COUNT"), AggregateVariant.V1); + assertThat(out.getBody()).contains("\"5\"").matches(s -> s.matches(".*±3.*")); + } + + @Test + void continuousCrossCountBinsViaVisualizationWhenConfigured() { + AggregateBackendClient backend = mock(AggregateBackendClient.class); + when(backend.search(any())).thenReturn(consentsSearch()); + when(backend.querySync(any(), eq(AggregateVariant.V1))).thenReturn(ResponseEntity.ok("{\"\\\\age\\\\\":{\"5\":100}}")) + .thenReturn(ResponseEntity.ok("{\"\\\\_studies_consents\\\\\":\"500\"}")); + when(backend.binContinuous(any(), eq(AggregateVariant.V1))).thenReturn("{\"\\\\age\\\\\":{\"0-10\":100}}"); + AggregateProperties props = new AggregateProperties(); + props.setVisualizationUrl("http://viz.example"); + AggregateService svc = service(backend, props); + + ResponseEntity out = svc.querySync(sync("CONTINUOUS_CROSS_COUNT"), AggregateVariant.V1); + assertThat(out.getBody()).contains("\"0-10\""); + verify(backend).binContinuous(any(), eq(AggregateVariant.V1)); + } + + // ---- async open submit (finding I6): CROSS_COUNT is consent-scoped, then persisted+dispatched via QueryService ---- + + @Test + void asyncOpenCrossCountIsRewrittenThenDispatchedViaQueryServiceV1() { + AggregateBackendClient backend = mock(AggregateBackendClient.class); + when(backend.search(any())).thenReturn(consentsSearch()); + QueryService queryService = mock(QueryService.class); + AggregateService svc = new AggregateService(backend, obfuscation(), new AggregateProperties(), queryService); + + svc.query(sync("CROSS_COUNT"), AggregateVariant.V1); + + // The query handed to QueryService for persistence+dispatch is the REWRITTEN cross-count query (consent-scoped), never the raw one. + ArgumentCaptor cap = ArgumentCaptor.forClass(QueryRequest.class); + verify(queryService).query(eq("open"), cap.capture()); + @SuppressWarnings("unchecked") + Map query = mapper.convertValue(cap.getValue().getQuery(), Map.class); + assertThat(query).containsKey("crossCountFields"); // full study-consents allow-list injected + assertThat(query.get("expectedResultType")).isEqualTo("CROSS_COUNT"); + } + + @Test + void asyncOpenCrossCountUsesSelectAndDispatchesViaQueryServiceV3() { + AggregateBackendClient backend = mock(AggregateBackendClient.class); + when(backend.search(any())).thenReturn(consentsSearch()); + QueryService queryService = mock(QueryService.class); + AggregateService svc = new AggregateService(backend, obfuscation(), new AggregateProperties(), queryService); + + svc.query(sync("CROSS_COUNT"), AggregateVariant.V3); + + ArgumentCaptor cap = ArgumentCaptor.forClass(QueryRequest.class); + verify(queryService).queryV3(eq("open"), cap.capture()); + @SuppressWarnings("unchecked") + Map query = mapper.convertValue(cap.getValue().getQuery(), Map.class); + assertThat(query).containsKey("select").doesNotContainKey("crossCountFields"); + } + + @Test + void asyncOpenNonCrossCountIsForwardedUnchanged() { + // WAR parity: the async query() only rewrites CROSS_COUNT; other types pass through unchanged (and fetch no consents). + AggregateBackendClient backend = mock(AggregateBackendClient.class); + QueryService queryService = mock(QueryService.class); + AggregateService svc = new AggregateService(backend, obfuscation(), new AggregateProperties(), queryService); + + svc.query(sync("COUNT"), AggregateVariant.V1); + + ArgumentCaptor cap = ArgumentCaptor.forClass(QueryRequest.class); + verify(queryService).query(eq("open"), cap.capture()); + @SuppressWarnings("unchecked") + Map query = mapper.convertValue(cap.getValue().getQuery(), Map.class); + assertThat(query.get("expectedResultType")).isEqualTo("COUNT"); + assertThat(query).doesNotContainKey("crossCountFields"); + verify(backend, never()).search(any()); + } + + @Test + void asyncOpenQueryRejectsMissingExpectedResultTypeWith400() { + // WAR parity: the async query() rejected a missing expectedResultType (MISSING_DATA) before touching the backend. + AggregateBackendClient backend = mock(AggregateBackendClient.class); + QueryService queryService = mock(QueryService.class); + AggregateService svc = new AggregateService(backend, obfuscation(), new AggregateProperties(), queryService); + + QueryRequest noErt = new GeneralQueryRequest().setQuery(Map.of("fields", "x")); + assertThatThrownBy(() -> svc.query(noErt, AggregateVariant.V1)).isInstanceOf(PicsureException.class); + verifyNoInteractions(queryService); + } + + @Test + void propagatesQueryMetadataHeaderUnderRealHpdsHeaderName() { + // NON-TAUTOLOGICAL (finding I5): the stub uses the REAL HPDS header literal "queryMetadata", NOT the constant. Under the old + // "resultMetadata" bug the service would read getFirst("resultMetadata") == null from this response and DROP the header, so this + // assertion would fail. It passes only when the constant resolves to the real name. + AggregateBackendClient backend = mock(AggregateBackendClient.class); + when(backend.querySync(any(), eq(AggregateVariant.V1))).thenReturn(ResponseEntity.ok().header("queryMetadata", "rid").body("12")); + AggregateService svc = service(backend, new AggregateProperties()); + + ResponseEntity out = svc.querySync(sync("COUNT"), AggregateVariant.V1); + assertThat(out.getHeaders().getFirst("queryMetadata")).isEqualTo("rid"); + assertThat(AggregateBackendClient.QUERY_METADATA_FIELD).isEqualTo("queryMetadata"); + } + + private SearchResults consentsSearch() { + Map phenotypes = new LinkedHashMap<>(); + phenotypes.put("\\study\\a\\consent\\", Map.of()); + phenotypes.put("\\study\\b\\consent\\", Map.of()); + return new SearchResults().setResults(Map.of("phenotypes", phenotypes)); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateV3ControllerTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateV3ControllerTest.java new file mode 100644 index 000000000..dde40d8e8 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/AggregateV3ControllerTest.java @@ -0,0 +1,134 @@ +package edu.harvard.hms.dbmi.avillach.query.aggregate; + +import static com.github.tomakehurst.wiremock.client.WireMock.aResponse; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.assertj.core.api.Assertions.assertThat; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.ArgumentMatchers.eq; +import static org.mockito.Mockito.verify; +import static org.mockito.Mockito.verifyNoInteractions; +import static org.mockito.Mockito.when; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.content; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.springframework.test.context.bean.override.mockito.MockitoBean; +import org.springframework.test.web.servlet.MockMvc; + +import com.github.tomakehurst.wiremock.WireMockServer; +import com.github.tomakehurst.wiremock.client.WireMock; + +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import edu.harvard.hms.dbmi.avillach.query.hpds.HpdsCommunicationException; +import edu.harvard.hms.dbmi.avillach.query.operations.OperationsClient; + +/** + * MockMvc coverage of {@link AggregateV3Controller} (the v3 obfuscation ingress at {@code /hpds/open/v3/query/sync}), mirroring + * {@link AggregateControllerTest}: {@link AggregateService} is mocked (obfuscation logic itself lives in {@link AggregateServiceTest}), and + * the point of this class is the routing/coexistence behavior with + * {@link edu.harvard.hms.dbmi.avillach.query.query.HpdsQueryV3Controller}'s generic {@code /hpds/{backend}/v3/query/sync} mapping. + */ +@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.MOCK) +@AutoConfigureMockMvc +class AggregateV3ControllerTest { + + private static final String USER = "auth0|alice"; + + static WireMockServer hpds; + + @BeforeAll + static void start() { + hpds = new WireMockServer(options().dynamicPort().http2PlainDisabled(true)); + hpds.start(); + } + + @AfterAll + static void stop() { + hpds.stop(); + } + + @DynamicPropertySource + static void hpdsProps(DynamicPropertyRegistry registry) { + registry.add("hpds.auth-url", () -> "http://localhost:" + hpds.port() + "/PIC-SURE"); + registry.add("hpds.open-url", () -> "http://localhost:" + hpds.port() + "/PIC-SURE"); + } + + @Autowired + private MockMvc mockMvc; + + @MockitoBean + private AggregateService aggregateService; + + @MockitoBean + private OperationsClient operationsClient; + + @BeforeEach + void resetStubs() { + hpds.resetAll(); + } + + @Test + void openV3QuerySyncRoutesToAggregateServiceV3AndReturnsResult() throws Exception { + when(aggregateService.querySync(any(QueryRequest.class), eq(AggregateVariant.V3))) + .thenReturn(ResponseEntity.ok().contentType(MediaType.APPLICATION_JSON).body("{}")); + + mockMvc + .perform( + post("/hpds/open/v3/query/sync").header(GatewayUserResolver.HEADER_USER_ID, USER) + .contentType(MediaType.APPLICATION_JSON).content("{\"query\":{\"expectedResultType\":\"CROSS_COUNT\"}}") + ).andExpect(status().isOk()).andExpect(content().string("{}")); + + verify(aggregateService).querySync(any(QueryRequest.class), eq(AggregateVariant.V3)); + verifyNoInteractions(operationsClient); + hpds.verify(0, WireMock.postRequestedFor(urlEqualTo("/PIC-SURE/v3/query/sync"))); + } + + @Test + void authV3QuerySyncIsNotInterceptedByAggregateV3Controller() throws Exception { + hpds.stubFor( + WireMock.post(urlEqualTo("/PIC-SURE/v3/query/sync")) + .willReturn(aResponse().withStatus(200).withHeader("queryMetadata", "rr-3").withBody("payload")) + ); + + mockMvc.perform( + post("/hpds/auth/v3/query/sync").header(GatewayUserResolver.HEADER_USER_ID, USER).contentType(MediaType.APPLICATION_JSON) + .content("{\"query\":\"q\"}") + ).andExpect(status().isOk()).andExpect(content().contentType(MediaType.APPLICATION_JSON)); + + verifyNoInteractions(aggregateService); + hpds.verify(WireMock.postRequestedFor(urlEqualTo("/PIC-SURE/v3/query/sync"))); + } + + @Test + void openV3QuerySyncWithoutGatewayIdentityIsUnauthorized() throws Exception { + mockMvc.perform(post("/hpds/open/v3/query/sync").contentType(MediaType.APPLICATION_JSON).content("{\"query\":\"q\"}")) + .andExpect(result -> assertThat(result.getResponse().getStatus()).isIn(401, 403)); + + verifyNoInteractions(aggregateService); + } + + @Test + void openV3QuerySyncUpstreamErrorSurfacesAs502() throws Exception { + when(aggregateService.querySync(any(QueryRequest.class), eq(AggregateVariant.V3))) + .thenThrow(new HpdsCommunicationException("Aggregate query/sync call failed", new RuntimeException("boom"))); + + mockMvc + .perform( + post("/hpds/open/v3/query/sync").header(GatewayUserResolver.HEADER_USER_ID, USER) + .contentType(MediaType.APPLICATION_JSON).content("{\"query\":{\"expectedResultType\":\"CROSS_COUNT\"}}") + ).andExpect(status().isBadGateway()); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/ObfuscatedCountShapeTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/ObfuscatedCountShapeTest.java new file mode 100644 index 000000000..911793e38 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/ObfuscatedCountShapeTest.java @@ -0,0 +1,132 @@ +package edu.harvard.hms.dbmi.avillach.query.aggregate; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.hms.dbmi.avillach.query.config.AggregateProperties; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +import java.util.Optional; + +import static org.assertj.core.api.Assertions.assertThat; + +/** + * Ported (JUnit 4 -> JUnit 5) from the WAR's {@code edu.harvard.hms.dbmi.avillach.ObfuscatedCountShapeTest}, which verified that the + * obfuscation methods produce the rich {@code {count, display, variance}} shape required by the visualization-resource for + * Plotly-compatible chart values. The WAR exercised both the V1 and V3 {@code AggregateDataSharingResourceRS} copies (identical math in + * both); here there is a single {@link ObfuscationService}, so this pins the same golden values against that one implementation. + */ +class ObfuscatedCountShapeTest { + + private ObfuscationService subject; + + @BeforeEach + void setup() { + AggregateProperties props = new AggregateProperties(); + props.getObfuscation().setThreshold(10); + props.getObfuscation().setVariance(3); + props.getObfuscation().setSalt("salt-for-test"); + subject = new ObfuscationService(props, new VisualizationFormatter()); + } + + @Test + void applyThresholdFloor_belowThreshold_returnsZeroCountWithThresholdBandAndLessThanDisplay() { + Optional result = subject.applyThresholdFloor(3); + + assertThat(result).isPresent(); + assertThat(result.get().count()).isZero(); + assertThat(result.get().display()).isEqualTo("< 10"); + assertThat(result.get().variance()).isEqualTo(9); + } + + @Test + void applyThresholdFloor_zero_returnsZeroCountWithThresholdBandAndLessThanDisplay() { + Optional result = subject.applyThresholdFloor(0); + + assertThat(result).isPresent(); + assertThat(result.get().count()).isZero(); + assertThat(result.get().display()).isEqualTo("< 10"); + assertThat(result.get().variance()).isEqualTo(9); + } + + @Test + void applyThresholdFloor_atOrAboveThreshold_returnsEmpty() { + assertThat(subject.applyThresholdFloor(10)).isEmpty(); + assertThat(subject.applyThresholdFloor(999)).isEmpty(); + } + + @Test + void applyThresholdFloor_stringOverload_nonNumeric_returnsEmpty() { + assertThat(subject.applyThresholdFloor("not-a-number")).isEmpty(); + } + + @Test + void randomize_appliesVariance_returnsNumericDisplayAndVariance() { + ObfuscatedCount result = subject.randomize(100, 2); + + assertThat(result.count()).isEqualTo(102); + assertThat(result.display()).isEqualTo("102 ±3"); + assertThat(result.variance()).isEqualTo(3); + } + + @Test + void randomize_floorsAtThreshold_whenVarianceTakesItBelow() { + ObfuscatedCount result = subject.randomize(10, -5); + + assertThat(result.count()).isEqualTo(10); + assertThat(result.display()).isEqualTo("10 ±3"); + assertThat(result.variance()).isEqualTo(3); + } + + @Test + void toInt_acceptsAllJacksonNumberRuntimeTypes() { + // Jackson deserializes JSON numbers into Integer when they fit, Long for larger magnitudes, Double when + // decimal. The replacement must accept all of these, matching the WAR's toInt() breadth. + assertThat(ObfuscationService.toInt(Integer.valueOf(42))).isEqualTo(42); + assertThat(ObfuscationService.toInt(Long.valueOf(42L))).isEqualTo(42); + assertThat(ObfuscationService.toInt(Double.valueOf(42.0))).isEqualTo(42); + assertThat(ObfuscationService.toInt(Short.valueOf((short) 42))).isEqualTo(42); + assertThat(ObfuscationService.toInt("42")).isEqualTo(42); + } + + @Test + void ofInt_factory_producesStringifiedDisplayAndNullVariance() { + ObfuscatedCount result = ObfuscatedCount.ofInt(45000); + + assertThat(result.count()).isEqualTo(45000); + assertThat(result.display()).isEqualTo("45000"); + assertThat(result.variance()).isNull(); + } + + /** + * Pins the JSON wire shape that visualization-resource (and any other consumer) deserializes against. If field names ever drift, this + * test fails BEFORE the cross-repo contract silently breaks in production. + */ + @Test + void jsonShape_serializesAsCountDisplayAndVarianceFields() throws JsonProcessingException { + ObjectMapper mapper = new ObjectMapper(); + ObfuscatedCount value = new ObfuscatedCount(222, "222 ±3", 3); + + String json = mapper.writeValueAsString(value); + + assertThat(json).isEqualTo("{\"count\":222,\"display\":\"222 ±3\",\"variance\":3}"); + + ObfuscatedCount roundTripped = mapper.readValue(json, ObfuscatedCount.class); + assertThat(roundTripped).isEqualTo(value); + } + + /** + * Exact (authorized) values serialize variance as an explicit null, and below-threshold values pin the {@code {count: 0, variance: + * threshold-1}} encoding the frontend's band rule depends on. + */ + @Test + void jsonShape_nullVarianceAndBelowThresholdEncoding() throws JsonProcessingException { + ObjectMapper mapper = new ObjectMapper(); + + assertThat(mapper.writeValueAsString(ObfuscatedCount.ofInt(45000))) + .isEqualTo("{\"count\":45000,\"display\":\"45000\",\"variance\":null}"); + + ObfuscatedCount belowThreshold = subject.applyThresholdFloor(3).orElseThrow(IllegalStateException::new); + assertThat(mapper.writeValueAsString(belowThreshold)).isEqualTo("{\"count\":0,\"display\":\"< 10\",\"variance\":9}"); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/ObfuscatedCountTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/ObfuscatedCountTest.java new file mode 100644 index 000000000..af6e88f44 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/ObfuscatedCountTest.java @@ -0,0 +1,32 @@ +package edu.harvard.hms.dbmi.avillach.query.aggregate; + +import com.fasterxml.jackson.databind.ObjectMapper; +import org.junit.jupiter.api.Test; + +import static org.assertj.core.api.Assertions.assertThat; + +class ObfuscatedCountTest { + + @Test + void carriesFieldsAndValueEquality() { + ObfuscatedCount a = new ObfuscatedCount(0, "< 10", 9); + ObfuscatedCount b = new ObfuscatedCount(0, "< 10", 9); + assertThat(a).isEqualTo(b); + assertThat(a.display()).isEqualTo("< 10"); + assertThat(a.count()).isZero(); + assertThat(a.variance()).isEqualTo(9); + } + + @Test + void ofIntHasNullVariance() { + ObfuscatedCount c = ObfuscatedCount.ofInt(42); + assertThat(c.display()).isEqualTo("42"); + assertThat(c.variance()).isNull(); + } + + @Test + void serializesCountDisplayVariance() throws Exception { + String json = new ObjectMapper().writeValueAsString(new ObfuscatedCount(13, "13 ±3", 3)); + assertThat(json).contains("\"count\":13").contains("\"display\":\"13 ±3\"").contains("\"variance\":3"); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/ObfuscationServiceTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/ObfuscationServiceTest.java new file mode 100644 index 000000000..fb9bae3f3 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/ObfuscationServiceTest.java @@ -0,0 +1,83 @@ +package edu.harvard.hms.dbmi.avillach.query.aggregate; + +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.hms.dbmi.avillach.query.config.AggregateProperties; +import org.junit.jupiter.api.Test; + +import java.util.LinkedHashMap; +import java.util.Map; + +import static org.assertj.core.api.Assertions.assertThat; + +class ObfuscationServiceTest { + + private final ObjectMapper mapper = new ObjectMapper(); + + private ObfuscationService svc(String salt) { + AggregateProperties props = new AggregateProperties(); + props.getObfuscation().setThreshold(10); + props.getObfuscation().setVariance(3); + props.getObfuscation().setSalt(salt); + return new ObfuscationService(props, new VisualizationFormatter()); + } + + @Test + void thresholdFloorBelowThreshold() { + assertThat(svc("s").applyThresholdFloor(5)).contains(new ObfuscatedCount(0, "< 10", 9)); + } + + @Test + void thresholdFloorAtOrAboveThresholdIsEmpty() { + assertThat(svc("s").applyThresholdFloor(10)).isEmpty(); + } + + @Test + void randomizeUsesConfiguredVarianceInDisplayAndFloorsAtThreshold() { + // count 100, requestVariance 0 => 100; display shows the CONFIGURED variance (3), not the request one + assertThat(svc("s").randomize(100, 0)).isEqualTo(new ObfuscatedCount(100, "100 ±3", 3)); + // count 8, requestVariance -5 => max(3,10) floored to threshold 10 + assertThat(svc("s").randomize(8, -5)).isEqualTo(new ObfuscatedCount(10, "10 ±3", 3)); + } + + @Test + void requestVarianceIsDeterministicAndInRange() { + ObfuscationService s = svc("fixed"); + int v1 = s.generateRequestVariance("payload"); + int v2 = s.generateRequestVariance("payload"); + assertThat(v1).isEqualTo(v2); // deterministic + assertThat(v1).isBetween(-3, 3); // [-variance, +variance] + } + + @Test + void countObfuscationFloorsSmallAndRandomizesLarge() { + ObfuscationService s = svc("fixed"); + assertThat(s.obfuscateCount("5")).isEqualTo("< 10"); + assertThat(s.obfuscateCount("100")).matches("\\d+ ±3"); + assertThat(s.obfuscateCount("not-a-number")).isEqualTo("not-a-number"); // NFE => passthrough + } + + @Test + void crossCountFloorsBelowThresholdAndRandomizesAbove() throws Exception { + String input = mapper.writeValueAsString(new LinkedHashMap<>(Map.of("\\study\\a\\", "5", "\\study\\b\\", "100"))); + Map out = svc("fixed").processCrossCounts(input); + assertThat(out.get("\\study\\a\\")).isEqualTo("< 10"); + assertThat(out.get("\\study\\b\\")).matches("\\d+ ±3"); + } + + @Test + void continuousSuppressedWhenStudyConsentsBelowThresholdOrZero() { + ObfuscationService s = svc("fixed"); + assertThat(s.canShowContinuousCrossCounts(Map.of("\\_studies_consents\\", "< 10"))).isTrue(); + assertThat(s.canShowContinuousCrossCounts(Map.of("\\_studies_consents\\", "0"))).isTrue(); + assertThat(s.canShowContinuousCrossCounts(Map.of("\\_studies_consents\\", "500"))).isFalse(); + } + + @Test + void obfuscateCrossCountFloorsAndRandomizesNested() { + Map> nested = new LinkedHashMap<>(); + nested.put("\\axis\\", new LinkedHashMap<>(Map.of("male", 5, "female", 100))); + var out = svc("fixed").obfuscateCrossCount(0, nested); + assertThat(out.get("\\axis\\").get("male")).isEqualTo(new ObfuscatedCount(0, "< 10", 9)); + assertThat(out.get("\\axis\\").get("female")).isEqualTo(new ObfuscatedCount(100, "100 ±3", 3)); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/VisualizationFormatterTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/VisualizationFormatterTest.java new file mode 100644 index 000000000..c8eed979e --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/aggregate/VisualizationFormatterTest.java @@ -0,0 +1,38 @@ +package edu.harvard.hms.dbmi.avillach.query.aggregate; + +import org.junit.jupiter.api.Test; + +import java.util.LinkedHashMap; +import java.util.Map; + +import static org.assertj.core.api.Assertions.assertThat; + +class VisualizationFormatterTest { + + private final VisualizationFormatter fmt = new VisualizationFormatter(); + + @Test + void skipsConsentAxisKeys() { + assertThat(fmt.skipKey("\\_consents\\")).isTrue(); + assertThat(fmt.skipKey("\\_harmonized_consent\\")).isTrue(); + assertThat(fmt.skipKey("\\_topmed_consents\\")).isTrue(); + assertThat(fmt.skipKey("\\_parent_consents\\")).isTrue(); + assertThat(fmt.skipKey("\\demographics\\SEX\\")).isFalse(); + } + + @Test + void collapsesBeyondSevenIntoOther() { + Map axis = new LinkedHashMap<>(); + for (int i = 0; i < 10; i++) axis.put("cat" + i, i + 1); // 10 categories, all Integer + Map out = fmt.processResults(axis); + assertThat(out).containsKey("Other"); + assertThat(out.size()).isEqualTo(8); // top 7 + Other + } + + @Test + void keepsSmallMapsIntact() { + Map axis = new LinkedHashMap<>(Map.of("a", 1, "b", 2)); + Map out = fmt.processResults(axis); + assertThat(out).containsOnlyKeys("a", "b"); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/config/ActuatorSecurityConfigTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/config/ActuatorSecurityConfigTest.java new file mode 100644 index 000000000..e45847c90 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/config/ActuatorSecurityConfigTest.java @@ -0,0 +1,92 @@ +package edu.harvard.hms.dbmi.avillach.query.config; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post; + +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.actuate.observability.AutoConfigureObservability; +import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.MediaType; +import org.springframework.test.context.TestPropertySource; +import org.springframework.test.web.servlet.MockMvc; +import org.springframework.test.web.servlet.MvcResult; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; + +/** + * Proves the {@code ActuatorSecurityConfig} chain (order 0) and the pre-existing {@link WebSecurityConfig} main chain (order 10) coexist on + * hpds-query-service: the actuator chain owns {@code /actuator/**} (shallow health open, detail/prometheus gated by + * {@code X-Application-Token}) while the main chain's {@code authenticated()} rule on {@code /hpds/**} is untouched. + * + *

    The test config points {@code hpds.auth-url}/{@code hpds.open-url} at an unreachable placeholder (see + * {@code src/test/resources/application.yml}), so the deep HPDS-reachability indicator legitimately reports DOWN here (503) -- what this + * test pins is that health is never 401 (open to the load balancer regardless of UP/DOWN) and that component detail visibility tracks the + * token, not the HTTP status. + * + *

    {@code src/test/resources/application.yml} is a self-contained test config that Spring Boot's classpath config loading resolves + * INSTEAD OF (not merged with) {@code src/main/resources/application.yml} -- test-classes precedes classes on the Surefire classpath, and + * {@code classpath:/application.yml} resolves to a single resource. The production {@code management.*}/{@code picsure.actuator.*} block + * therefore never reaches this test context, so this class supplies the equivalent settings itself via {@code @TestPropertySource} rather + * than relying on the (shadowed) main resource file. + */ +@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.MOCK) +@AutoConfigureMockMvc +@AutoConfigureObservability // prometheus export is disabled by default in @SpringBootTest contexts +@TestPropertySource( + properties = {"picsure.actuator.require-token=true", "picsure.actuator.token=query-secret", + "management.endpoints.web.exposure.include=health,info,prometheus,metrics", + "management.endpoint.health.show-details=when_authorized", "management.endpoint.health.probes.enabled=true", + "management.endpoint.health.group.liveness.include=livenessState"} +) +class ActuatorSecurityConfigTest { + + @Autowired + private MockMvc mockMvc; + + private final ObjectMapper json = new ObjectMapper(); + + @Test + void healthIsOpenAndShallowWithoutToken() throws Exception { + MvcResult res = mockMvc.perform(get("/actuator/health")).andReturn(); + assertThat(res.getResponse().getStatus()).isNotEqualTo(401); // open to the load balancer regardless of UP/DOWN + JsonNode body = json.readTree(res.getResponse().getContentAsString()); + assertThat(body.has("status")).isTrue(); + assertThat(body.has("components")).isFalse(); + } + + @Test + void livenessIsOpenWithoutToken() throws Exception { + MvcResult res = mockMvc.perform(get("/actuator/health/liveness")).andReturn(); + assertThat(res.getResponse().getStatus()).isNotEqualTo(401); + } + + @Test + void healthRevealsComponentDetailWithValidToken() throws Exception { + MvcResult res = mockMvc.perform(get("/actuator/health").header("X-Application-Token", "query-secret")).andReturn(); + JsonNode body = json.readTree(res.getResponse().getContentAsString()); + assertThat(body.has("components")).isTrue(); // DETAIL revealed regardless of UP/DOWN + } + + @Test + void prometheusRejectedWithoutToken() throws Exception { + MvcResult res = mockMvc.perform(get("/actuator/prometheus")).andReturn(); + assertThat(res.getResponse().getStatus()).isEqualTo(401); + } + + @Test + void prometheusOkWithToken() throws Exception { + MvcResult res = mockMvc.perform(get("/actuator/prometheus").header("X-Application-Token", "query-secret")).andReturn(); + assertThat(res.getResponse().getStatus()).isEqualTo(200); + } + + /** Coexistence: the main chain's authenticated() gate on /hpds/** must be unaffected by the actuator chain. */ + @Test + void hpdsEndpointStillRequiresAuthenticationAlongsideActuatorChain() throws Exception { + mockMvc.perform(post("/hpds/auth/query").contentType(MediaType.APPLICATION_JSON).content("{\"query\":\"q\"}")) + .andExpect(result -> assertThat(result.getResponse().getStatus()).isIn(401, 403)); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/config/AggregatePropertiesTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/config/AggregatePropertiesTest.java new file mode 100644 index 000000000..3612696bd --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/config/AggregatePropertiesTest.java @@ -0,0 +1,40 @@ +package edu.harvard.hms.dbmi.avillach.query.config; + +import org.junit.jupiter.api.Test; +import org.springframework.boot.context.properties.bind.Binder; +import org.springframework.boot.context.properties.source.MapConfigurationPropertySource; + +import java.util.Map; + +import static org.assertj.core.api.Assertions.assertThat; + +class AggregatePropertiesTest { + + @Test + void bindsNestedObfuscationAndUrls() { + var source = new MapConfigurationPropertySource( + Map.of( + "aggregate.hpds-open-url", "http://hpds-open:8080", "aggregate.hpds-open-token", "open-token", + "aggregate.visualization-url", "http://viz:8080", "aggregate.obfuscation.threshold", "10", "aggregate.obfuscation.variance", + "3", "aggregate.obfuscation.salt", "fixed-salt" + ) + ); + AggregateProperties props = new Binder(source).bind("aggregate", AggregateProperties.class).get(); + + assertThat(props.getHpdsOpenUrl()).isEqualTo("http://hpds-open:8080"); + assertThat(props.getHpdsOpenToken()).isEqualTo("open-token"); + assertThat(props.getVisualizationUrl()).isEqualTo("http://viz:8080"); + assertThat(props.getObfuscation().getThreshold()).isEqualTo(10); + assertThat(props.getObfuscation().getVariance()).isEqualTo(3); + assertThat(props.getObfuscation().getSalt()).isEqualTo("fixed-salt"); + } + + @Test + void appliesDefaults() { + AggregateProperties props = new AggregateProperties(); + assertThat(props.getObfuscation().getThreshold()).isEqualTo(10); + assertThat(props.getObfuscation().getVariance()).isEqualTo(3); + assertThat(props.getConnectTimeoutSec()).isEqualTo(10); + assertThat(props.getReadTimeoutSec()).isEqualTo(60); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/error/GlobalExceptionHandlerTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/error/GlobalExceptionHandlerTest.java new file mode 100644 index 000000000..e2a3f4e52 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/error/GlobalExceptionHandlerTest.java @@ -0,0 +1,47 @@ +package edu.harvard.hms.dbmi.avillach.query.error; + +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.Map; + +import org.junit.jupiter.api.Test; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; + +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; +import edu.harvard.hms.dbmi.avillach.query.hpds.HpdsCommunicationException; + +/** + * Unit tests for {@link GlobalExceptionHandler}: HPDS-upstream failures map to 502 (the WAR returned 500 for this case; HPDS is upstream + * infrastructure so 502 is the honest status), {@link PicsureException} maps to its own carried status, and any other unmapped exception + * maps to 500 -- all three sharing the commons {@code {errorType,message,requestId}} body shape. + */ +class GlobalExceptionHandlerTest { + + private final GlobalExceptionHandler handler = new GlobalExceptionHandler(); + + @Test + void mapsHpdsCommunicationTo502() { + ResponseEntity> resp = handler.hpdsUnavailable(new HpdsCommunicationException("down")); + + assertThat(resp.getStatusCode()).isEqualTo(HttpStatus.BAD_GATEWAY); + assertThat(resp.getBody()).containsEntry("errorType", "upstream_unavailable").containsEntry("message", "down"); + } + + @Test + void mapsPicsureExceptionToItsCarriedStatus() { + ResponseEntity> resp = + handler.handlePicsureException(new PicsureException(HttpStatus.BAD_REQUEST, "bad_request", "nope")); + + assertThat(resp.getStatusCode()).isEqualTo(HttpStatus.BAD_REQUEST); + assertThat(resp.getBody()).containsEntry("errorType", "bad_request").containsEntry("message", "nope"); + } + + @Test + void mapsUnknownExceptionTo500WithCommonsShape() { + ResponseEntity> resp = handler.unknown(new RuntimeException("boom")); + + assertThat(resp.getStatusCode()).isEqualTo(HttpStatus.INTERNAL_SERVER_ERROR); + assertThat(resp.getBody()).containsKey("errorType").containsKey("message").containsKey("requestId"); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/health/HpdsHealthIndicatorTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/health/HpdsHealthIndicatorTest.java new file mode 100644 index 000000000..cd7b711ac --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/health/HpdsHealthIndicatorTest.java @@ -0,0 +1,110 @@ +package edu.harvard.hms.dbmi.avillach.query.health; + +import static com.github.tomakehurst.wiremock.client.WireMock.aResponse; +import static com.github.tomakehurst.wiremock.client.WireMock.get; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.springframework.boot.actuate.health.Health; +import org.springframework.boot.actuate.health.Status; +import org.springframework.web.client.RestClient; + +import com.github.tomakehurst.wiremock.WireMockServer; + +import edu.harvard.hms.dbmi.avillach.query.config.HpdsProperties; + +/** + * DB-free deep health: this service owns no DataSource, so its only real dependency to probe is HPDS reachability. Both configured backends + * (auth/open) are probed via a short GET to {@code {origin(base)}{healthPath}} (HPDS Actuator is at the host root, not under /PIC-SURE); UP + * only when every distinct base responds 2xx. + */ +class HpdsHealthIndicatorTest { + + static WireMockServer hpds; + + @BeforeAll + static void start() { + hpds = new WireMockServer(options().dynamicPort().http2PlainDisabled(true)); + hpds.start(); + } + + @AfterAll + static void stop() { + hpds.stop(); + } + + private HpdsProperties props() { + HpdsProperties p = new HpdsProperties(); + String base = "http://localhost:" + hpds.port() + "/PIC-SURE"; + p.setAuthUrl(base); + p.setOpenUrl(base); + p.setHealthPath("/actuator/health"); + return p; + } + + @Test + void upWhenHpdsResponds() { + hpds.stubFor(get(urlEqualTo("/actuator/health")).willReturn(aResponse().withStatus(200))); + + Health h = new HpdsHealthIndicator(props(), RestClient.builder().build()).health(); + + assertThat(h.getStatus()).isEqualTo(Status.UP); + } + + @Test + void downWhenHpdsErrors() { + hpds.resetAll(); + hpds.stubFor(get(urlEqualTo("/actuator/health")).willReturn(aResponse().withStatus(503))); + + Health h = new HpdsHealthIndicator(props(), RestClient.builder().build()).health(); + + assertThat(h.getStatus()).isEqualTo(Status.DOWN); + } + + @Test + void downWhenHpdsUnreachable() { + HpdsProperties p = props(); // capture the (dynamic) port while the server is still up + hpds.stop(); // then simulate connection failure + + try { + Health h = new HpdsHealthIndicator(p, RestClient.builder().build()).health(); + assertThat(h.getStatus()).isEqualTo(Status.DOWN); + } finally { + hpds.start(); // restart unconditionally so sibling tests (shared static server) aren't left stranded + } + } + + @Test + void dedupesIdenticalAuthAndOpenBases() { + hpds.stubFor(get(urlEqualTo("/actuator/health")).willReturn(aResponse().withStatus(200))); + HpdsProperties p = props(); // authUrl == openUrl + + Health h = new HpdsHealthIndicator(p, RestClient.builder().build()).health(); + + assertThat(h.getStatus()).isEqualTo(Status.UP); + assertThat(h.getDetails()).hasSize(1); // one distinct base, not two + } + + /** + * The probe must fail fast rather than hang on a black-holed HPDS. Exercises the real {@code @Autowired}-visible constructor (which + * wires the short, health-specific read timeout onto the probe's {@code RestClient.Builder}) against a WireMock stub that delays its + * response far longer than that timeout. If the timeout were NOT applied (the pre-fix behavior), this call would block for the full + * stubbed delay instead of failing at the ~3s read-timeout mark. + */ + @Test + void probeFailsFastInsteadOfHangingOnASlowHpds() { + hpds.resetAll(); + hpds.stubFor(get(urlEqualTo("/actuator/health")).willReturn(aResponse().withStatus(200).withFixedDelay(15_000))); + + long start = System.nanoTime(); + Health h = new HpdsHealthIndicator(props(), RestClient.builder()).health(); // real ctor: builder gets timeout-bound requestFactory + long elapsedMs = (System.nanoTime() - start) / 1_000_000; + + assertThat(h.getStatus()).isEqualTo(Status.DOWN); + assertThat(elapsedMs).isLessThan(10_000); // well under the 15s stub delay -- the read timeout fired, the probe did not wait it out + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/hpds/HpdsBackendSelectorTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/hpds/HpdsBackendSelectorTest.java new file mode 100644 index 000000000..8fd28afe6 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/hpds/HpdsBackendSelectorTest.java @@ -0,0 +1,59 @@ +package edu.harvard.hms.dbmi.avillach.query.hpds; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.assertj.core.api.Assertions.assertThatThrownBy; + +import org.junit.jupiter.api.Test; + +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; +import edu.harvard.hms.dbmi.avillach.query.config.HpdsProperties; + +class HpdsBackendSelectorTest { + + private HpdsBackendSelector selector() { + HpdsProperties p = new HpdsProperties(); + p.setAuthUrl("http://hpds-auth:8080/PIC-SURE"); + p.setAuthToken("auth-secret"); + p.setOpenUrl("http://hpds-open:8080/PIC-SURE"); + p.setOpenToken("open-secret"); + return new HpdsBackendSelector(p); + } + + @Test + void authV1() { + var t = selector().select("auth", false); + assertThat(t.baseUrl()).isEqualTo("http://hpds-auth:8080/PIC-SURE"); + assertThat(t.token()).isEqualTo("auth-secret"); + } + + @Test + void openV1() { + var t = selector().select("open", false); + assertThat(t.baseUrl()).isEqualTo("http://hpds-open:8080/PIC-SURE"); + assertThat(t.token()).isEqualTo("open-secret"); + } + + @Test + void authV3AppendsV3KeepsToken() { + var t = selector().select("auth", true); + assertThat(t.baseUrl()).isEqualTo("http://hpds-auth:8080/PIC-SURE/v3"); + assertThat(t.token()).isEqualTo("auth-secret"); + } + + @Test + void openV3AppendsV3KeepsToken() { + var t = selector().select("open", true); + assertThat(t.baseUrl()).isEqualTo("http://hpds-open:8080/PIC-SURE/v3"); + assertThat(t.token()).isEqualTo("open-secret"); + } + + @Test + void unknownBackendThrows() { + assertThatThrownBy(() -> selector().select("bogus", false)).isInstanceOf(PicsureException.class); + } + + @Test + void nullBackendThrows() { + assertThatThrownBy(() -> selector().select(null, false)).isInstanceOf(PicsureException.class); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/hpds/ResourceWebClientTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/hpds/ResourceWebClientTest.java new file mode 100644 index 000000000..bc3398f82 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/hpds/ResourceWebClientTest.java @@ -0,0 +1,155 @@ +package edu.harvard.hms.dbmi.avillach.query.hpds; + +import static com.github.tomakehurst.wiremock.client.WireMock.absent; +import static com.github.tomakehurst.wiremock.client.WireMock.aResponse; +import static com.github.tomakehurst.wiremock.client.WireMock.equalTo; +import static com.github.tomakehurst.wiremock.client.WireMock.get; +import static com.github.tomakehurst.wiremock.client.WireMock.okJson; +import static com.github.tomakehurst.wiremock.client.WireMock.post; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.client.WireMock.urlPathEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.assertj.core.api.Assertions.assertThat; +import static org.assertj.core.api.Assertions.assertThatThrownBy; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.springframework.http.ResponseEntity; +import org.springframework.web.client.RestClient; + +import com.github.tomakehurst.wiremock.WireMockServer; + +import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest; +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import edu.harvard.hms.dbmi.avillach.query.hpds.HpdsBackendSelector.HpdsTarget; + +class ResourceWebClientTest { + + static WireMockServer hpds; + static final String TOKEN = "svc-token-123"; + + @BeforeAll + static void start() { + // http2PlainDisabled avoids a known JDK HttpClient <-> WireMock(Jetty) h2c upgrade bug (RST_STREAM) when + // RestClient's default JDK-backed request factory is used (see OperationsClientTest). + hpds = new WireMockServer(options().dynamicPort().http2PlainDisabled(true)); + hpds.start(); + } + + @AfterAll + static void stop() { + hpds.stop(); + } + + private ResourceWebClient client() { + return new ResourceWebClient(RestClient.builder().build()); + } + + private String base() { + return "http://localhost:" + hpds.port() + "/PIC-SURE"; + } + + private HpdsTarget target() { + return new HpdsTarget(base(), TOKEN); + } + + private QueryRequest req() { + GeneralQueryRequest r = new GeneralQueryRequest(); + r.setQuery("q"); + return r; + } + + @Test + void queryInjectsServiceBearerToken() { + hpds.stubFor( + post(urlEqualTo("/PIC-SURE/query")).withHeader("Authorization", equalTo("Bearer " + TOKEN)) // service token preserved + .willReturn(okJson("{\"resourceResultId\":\"rr-1\",\"status\":\"PENDING\"}")) + ); + + var status = client().query(target(), req()); + + assertThat(status.getResourceResultId()).isEqualTo("rr-1"); + } + + @Test + void resultBuffersOctetStreamWithToken() { + hpds.stubFor( + post(urlEqualTo("/PIC-SURE/query/rr-1/result")).withHeader("Authorization", equalTo("Bearer " + TOKEN)) + .willReturn(aResponse().withStatus(200).withBody(new byte[] {1, 2, 3})) + ); + + ResponseEntity resp = client().queryResult(target(), "rr-1", req()); + + assertThat(resp.getBody()).containsExactly(1, 2, 3); + } + + @Test + void signedUrlBuffersJsonStringWithToken() { + hpds.stubFor( + post(urlEqualTo("/PIC-SURE/query/rr-1/signed-url")).withHeader("Authorization", equalTo("Bearer " + TOKEN)) + .willReturn(okJson("{\"url\":\"https://s3/x\"}")) + ); + + ResponseEntity resp = client().queryResultSignedUrl(target(), "rr-1", req()); + + assertThat(resp.getBody()).contains("https://s3/x"); + } + + @Test + void querySyncInjectsTokenPropagatesMetadataHeaderAndSendsRequestSource() { + hpds.stubFor( + post(urlEqualTo("/PIC-SURE/query/sync")).withHeader("Authorization", equalTo("Bearer " + TOKEN)) + .withHeader("request-source", equalTo("UI")) + .willReturn(aResponse().withStatus(200).withHeader("queryMetadata", "rr-9").withBody("payload")) + ); + + var result = client().querySync(target(), req(), "UI"); + + assertThat(new String(result.body())).isEqualTo("payload"); + assertThat(result.queryMetadata()).isEqualTo("rr-9"); + } + + @Test + void statusInjectsToken() { + hpds.stubFor( + post(urlEqualTo("/PIC-SURE/query/rr-1/status")).withHeader("Authorization", equalTo("Bearer " + TOKEN)) + .willReturn(okJson("{\"resourceResultId\":\"rr-1\",\"status\":\"AVAILABLE\"}")) + ); + + var status = client().queryStatus(target(), "rr-1", req()); + + assertThat(status.getStatus().name()).isEqualTo("AVAILABLE"); + } + + @Test + void searchDoesNotInjectServiceToken() { // parity with PicsureSearchService (no BEARER_TOKEN) + hpds.stubFor( + post(urlEqualTo("/PIC-SURE/search")).withHeader("Authorization", absent()) + .willReturn(okJson("{\"searchQuery\":\"q\",\"results\":{}}")) + ); + + var result = client().search(base(), req()); // String base, not HpdsTarget -- no token path + + assertThat(result).isNotNull(); + } + + @Test + void searchValuesIsGetWithParamsAndNoServiceToken() { + hpds.stubFor( + get(urlPathEqualTo("/PIC-SURE/search/values/")).withHeader("Authorization", absent()) + .withQueryParam("genomicConceptPath", equalTo("\\gene\\")).withQueryParam("query", equalTo("BRCA")) + .withQueryParam("page", equalTo("1")).willReturn(okJson("{\"results\":[],\"page\":1,\"total\":0}")) + ); + + var result = client().searchConceptValues(base(), req(), "\\gene\\", "BRCA", 1, 10); + + assertThat(result).isNotNull(); + } + + @Test + void hpdsNon2xxThrowsCommunicationException() { + hpds.stubFor(post(urlEqualTo("/PIC-SURE/query")).willReturn(aResponse().withStatus(500))); + assertThatThrownBy(() -> client().query(target(), req())).isInstanceOf(HpdsCommunicationException.class); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/operations/OperationsClientTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/operations/OperationsClientTest.java new file mode 100644 index 000000000..c3b69e461 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/operations/OperationsClientTest.java @@ -0,0 +1,153 @@ +package edu.harvard.hms.dbmi.avillach.query.operations; + +import static com.github.tomakehurst.wiremock.client.WireMock.aResponse; +import static com.github.tomakehurst.wiremock.client.WireMock.equalTo; +import static com.github.tomakehurst.wiremock.client.WireMock.equalToJson; +import static com.github.tomakehurst.wiremock.client.WireMock.get; +import static com.github.tomakehurst.wiremock.client.WireMock.getRequestedFor; +import static com.github.tomakehurst.wiremock.client.WireMock.okJson; +import static com.github.tomakehurst.wiremock.client.WireMock.patch; +import static com.github.tomakehurst.wiremock.client.WireMock.patchRequestedFor; +import static com.github.tomakehurst.wiremock.client.WireMock.post; +import static com.github.tomakehurst.wiremock.client.WireMock.postRequestedFor; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.assertj.core.api.Assertions.assertThat; +import static org.assertj.core.api.Assertions.assertThatThrownBy; + +import java.util.UUID; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.springframework.http.HttpStatus; +import org.springframework.web.client.RestClient; + +import com.github.tomakehurst.wiremock.WireMockServer; + +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; + +class OperationsClientTest { + + static WireMockServer ops; + + @BeforeAll + static void start() { + // http2PlainDisabled avoids a known JDK HttpClient <-> WireMock(Jetty) h2c upgrade bug (RST_STREAM) when + // RestClient's default JDK-backed request factory is used. + ops = new WireMockServer(options().dynamicPort().http2PlainDisabled(true)); + ops.start(); + } + + @AfterAll + static void stop() { + ops.stop(); + } + + private OperationsClient client() { + RestClient http = + RestClient.builder().baseUrl("http://localhost:" + ops.port()).defaultHeader("X-PIC-SURE-INTERNAL-TOKEN", "test-token").build(); + return new OperationsClient(http); + } + + @Test + void savePostsToInternalQueriesAndReturnsPicsureId() { + UUID id = UUID.randomUUID(); + ops.stubFor( + post(urlEqualTo("/operations/internal/queries")).willReturn( + aResponse().withStatus(201).withHeader("Content-Type", "application/json").withBody("{\"picsureId\":\"" + id + "\"}") + ) + ); + + SaveQueryRequest req = new SaveQueryRequest("{}", null, "QUEUED", "v1", null); + UUID result = client().save(req); + + assertThat(result).isEqualTo(id); + ops.verify( + postRequestedFor(urlEqualTo("/operations/internal/queries")).withHeader("X-PIC-SURE-INTERNAL-TOKEN", equalTo("test-token")) + .withRequestBody( + equalToJson("{\"query\":\"{}\",\"resourceResultId\":null,\"status\":\"QUEUED\",\"version\":\"v1\",\"metadata\":null}") + ) + ); + } + + @Test + void saveMalformedResponseThrowsBadGateway() { + ops.stubFor( + post(urlEqualTo("/operations/internal/queries")) + .willReturn(aResponse().withStatus(201).withHeader("Content-Type", "application/json").withBody("{\"picsureId\":null}")) + ); + + assertThatThrownBy(() -> client().save(new SaveQueryRequest("{}", null, "QUEUED", "v1", null))) + .isInstanceOfSatisfying(PicsureException.class, e -> assertThat(e.getStatus()).isEqualTo(HttpStatus.BAD_GATEWAY)); + } + + @Test + void saveServerErrorThrowsBadGateway() { + ops.stubFor(post(urlEqualTo("/operations/internal/queries")).willReturn(aResponse().withStatus(500))); + + assertThatThrownBy(() -> client().save(new SaveQueryRequest("{}", null, "QUEUED", "v1", null))) + .isInstanceOfSatisfying(PicsureException.class, e -> assertThat(e.getStatus()).isEqualTo(HttpStatus.BAD_GATEWAY)); + } + + @Test + void getReturnsStoredQuery() { + UUID id = UUID.randomUUID(); + ops.stubFor( + get(urlEqualTo("/operations/internal/queries/" + id)).willReturn( + okJson( + "{\"picsureId\":\"" + id + + "\",\"query\":\"{}\",\"resourceResultId\":\"r-1\",\"status\":\"COMPLETE\",\"version\":\"v1\",\"metadata\":\"YWJj\"}" + ) + ) + ); + + StoredQuery result = client().get(id); + + assertThat(result).isEqualTo(new StoredQuery(id, "{}", "r-1", "COMPLETE", "v1", "YWJj")); + ops.verify( + getRequestedFor(urlEqualTo("/operations/internal/queries/" + id)).withHeader("X-PIC-SURE-INTERNAL-TOKEN", equalTo("test-token")) + ); + } + + @Test + void getNotFoundThrowsPicsureExceptionNotFound() { + UUID id = UUID.randomUUID(); + ops.stubFor(get(urlEqualTo("/operations/internal/queries/" + id)).willReturn(aResponse().withStatus(404))); + + assertThatThrownBy(() -> client().get(id)) + .isInstanceOfSatisfying(PicsureException.class, e -> assertThat(e.getStatus()).isEqualTo(HttpStatus.NOT_FOUND)); + } + + @Test + void getServerErrorThrowsBadGateway() { + UUID id = UUID.randomUUID(); + ops.stubFor(get(urlEqualTo("/operations/internal/queries/" + id)).willReturn(aResponse().withStatus(503))); + + assertThatThrownBy(() -> client().get(id)) + .isInstanceOfSatisfying(PicsureException.class, e -> assertThat(e.getStatus()).isEqualTo(HttpStatus.BAD_GATEWAY)); + } + + @Test + void updatePatchesInternalQueries() { + UUID id = UUID.randomUUID(); + ops.stubFor(patch(urlEqualTo("/operations/internal/queries/" + id)).willReturn(aResponse().withStatus(204))); + + client().update(id, new UpdateQueryRequest("COMPLETE", "r-1", null)); + + ops.verify( + patchRequestedFor(urlEqualTo("/operations/internal/queries/" + id)) + .withHeader("X-PIC-SURE-INTERNAL-TOKEN", equalTo("test-token")) + .withRequestBody(equalToJson("{\"status\":\"COMPLETE\",\"resourceResultId\":\"r-1\",\"metadata\":null}")) + ); + } + + @Test + void updateServerErrorThrowsBadGateway() { + UUID id = UUID.randomUUID(); + ops.stubFor(patch(urlEqualTo("/operations/internal/queries/" + id)).willReturn(aResponse().withStatus(500))); + + assertThatThrownBy(() -> client().update(id, new UpdateQueryRequest("COMPLETE", null, null))) + .isInstanceOfSatisfying(PicsureException.class, e -> assertThat(e.getStatus()).isEqualTo(HttpStatus.BAD_GATEWAY)); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/query/HpdsQueryControllerTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/query/HpdsQueryControllerTest.java new file mode 100644 index 000000000..d643b1d43 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/query/HpdsQueryControllerTest.java @@ -0,0 +1,173 @@ +package edu.harvard.hms.dbmi.avillach.query.query; + +import static com.github.tomakehurst.wiremock.client.WireMock.aResponse; +import static com.github.tomakehurst.wiremock.client.WireMock.okJson; +import static com.github.tomakehurst.wiremock.client.WireMock.postRequestedFor; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.assertj.core.api.Assertions.assertThat; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.ArgumentMatchers.argThat; +import static org.mockito.Mockito.verify; +import static org.mockito.Mockito.when; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.jsonPath; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status; + +import java.util.UUID; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.MediaType; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.springframework.test.context.bean.override.mockito.MockitoBean; +import org.springframework.test.web.servlet.MockMvc; + +import com.github.tomakehurst.wiremock.WireMockServer; +import com.github.tomakehurst.wiremock.client.WireMock; + +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import edu.harvard.hms.dbmi.avillach.query.operations.OperationsClient; +import edu.harvard.hms.dbmi.avillach.query.operations.SaveQueryRequest; +import edu.harvard.hms.dbmi.avillach.query.operations.StoredQuery; + +/** + * Full-context MockMvc coverage of the {@code /hpds/{backend}/v3/query/**} ingress: {@link HpdsQueryV3Controller} (the sole query lifecycle + * ingress -- the legacy v1 ingress was removed) against a real {@link edu.harvard.hms.dbmi.avillach.query.hpds.HpdsBackendSelector}/ + * {@link edu.harvard.hms.dbmi.avillach.query.hpds.ResourceWebClient} pair, WireMock standing in for HPDS, and a Mockito + * {@link OperationsClient} standing in for pic-sure-operations-service (this module is DB-free -- there is no embedded DB to run against). + * The real {@code WebSecurityConfig} filter chain is exercised too (no mocked security), so the auth-required assertion is a genuine + * end-to-end check. + */ +@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.MOCK) +@AutoConfigureMockMvc +class HpdsQueryControllerTest { + + private static final String USER = "auth0|alice"; + + static WireMockServer hpds; + + @BeforeAll + static void start() { + hpds = new WireMockServer(options().dynamicPort().http2PlainDisabled(true)); + hpds.start(); + } + + @AfterAll + static void stop() { + hpds.stop(); + } + + @DynamicPropertySource + static void hpdsProps(DynamicPropertyRegistry registry) { + registry.add("hpds.auth-url", () -> "http://localhost:" + hpds.port() + "/PIC-SURE"); + registry.add("hpds.open-url", () -> "http://localhost:" + hpds.port() + "/PIC-SURE"); + } + + @Autowired + private MockMvc mockMvc; + + @MockitoBean + private OperationsClient operationsClient; + + @BeforeEach + void resetStubs() { + hpds.resetAll(); + } + + // --- create: v3 stamps version "3" and hits the /v3 HPDS base --- + + @Test + void v3QueryCreatesWithVersion3AndHitsV3Base() throws Exception { + UUID picsureId = UUID.randomUUID(); + hpds.stubFor( + WireMock.post(urlEqualTo("/PIC-SURE/v3/query")).willReturn(okJson("{\"resourceResultId\":\"rr-3\",\"status\":\"PENDING\"}")) + ); + when(operationsClient.save(any())).thenReturn(picsureId); + + mockMvc.perform( + post("/hpds/auth/v3/query").header(GatewayUserResolver.HEADER_USER_ID, USER).contentType(MediaType.APPLICATION_JSON) + .content("{\"query\":\"q\"}") + ).andExpect(status().isOk()).andExpect(jsonPath("$.resourceResultId").value("rr-3")); + + verify(operationsClient).save(argThat((SaveQueryRequest r) -> "3".equals(r.version()))); + hpds.verify(postRequestedFor(urlEqualTo("/PIC-SURE/v3/query"))); + } + + // --- read ops dispatch on the STORED version, never the ingress path's version --- + + @Test + void resultViaV3PathAlsoDispatchesOnStoredVersionNotIngressVersion() throws Exception { + UUID id = UUID.randomUUID(); + StoredQuery stored = new StoredQuery(id, "{}", "rr-1", "PENDING", null, null); // v1-stored, requested via the v3 path + when(operationsClient.get(id)).thenReturn(stored); + hpds.stubFor( + WireMock.post(urlEqualTo("/PIC-SURE/query/rr-1/result")).willReturn(aResponse().withStatus(200).withBody(new byte[] {9})) + ); + + mockMvc.perform( + post("/hpds/auth/v3/query/{id}/result", id).header(GatewayUserResolver.HEADER_USER_ID, USER) + .contentType(MediaType.APPLICATION_JSON).content("{}") + ).andExpect(status().isOk()); + + hpds.verify(postRequestedFor(urlEqualTo("/PIC-SURE/query/rr-1/result"))); // NOT /v3 + } + + // --- upstream failures surface as 502, not 200/500 --- + + @Test + void hpds500SurfacesAs502() throws Exception { + hpds.stubFor(WireMock.post(urlEqualTo("/PIC-SURE/v3/query")).willReturn(aResponse().withStatus(500))); + + mockMvc.perform( + post("/hpds/auth/v3/query").header(GatewayUserResolver.HEADER_USER_ID, USER).contentType(MediaType.APPLICATION_JSON) + .content("{\"query\":\"q\"}") + ).andExpect(status().isBadGateway()).andExpect(jsonPath("$.errorType").value("upstream_unavailable")); + } + + // --- ?isInstitute=true is gone: federated/GIC queries are no longer supported --- + // + // The guard must stay until at least one release after removal. Jackson's defaultImpl silently + // reinterprets a {"@type":"FederatedQueryRequest"} body as a GeneralQueryRequest, so isInstitute + // is the ONLY remaining signal that a caller intended a federated submission. Without this guard + // such a caller gets a 200 for a query stripped of its federation. Do not delete as dead code. + + @Test + void isInstituteIsGoneOnV3Controller() throws Exception { + mockMvc.perform( + post("/hpds/auth/v3/query").param("isInstitute", "true").header(GatewayUserResolver.HEADER_USER_ID, USER) + .header(GatewayUserResolver.HEADER_USER_EMAIL, "alice@harvard.edu").contentType(MediaType.APPLICATION_JSON) + .content("{\"query\":\"q\"}") + ).andExpect(status().isGone()).andExpect(jsonPath("$.errorType").value("gone")); + } + + // --- /hpds/** requires an authenticated caller --- + + @Test + void queryWithoutGatewayIdentityIsRejected() throws Exception { + mockMvc.perform(post("/hpds/auth/v3/query").contentType(MediaType.APPLICATION_JSON).content("{\"query\":\"q\"}")) + .andExpect(result -> assertThat(result.getResponse().getStatus()).isIn(401, 403)); + } + + @Test + void resultWithoutGatewayIdentityIsRejected() throws Exception { + mockMvc.perform(post("/hpds/auth/v3/query/{id}/result", UUID.randomUUID()).contentType(MediaType.APPLICATION_JSON).content("{}")) + .andExpect(result -> assertThat(result.getResponse().getStatus()).isIn(401, 403)); + } + + // --- the legacy v1 ingress routes were removed --- + + @Test + void legacyV1QueryRouteIsGone() throws Exception { + mockMvc.perform( + post("/hpds/auth/query").header(GatewayUserResolver.HEADER_USER_ID, USER).contentType(MediaType.APPLICATION_JSON) + .content("{\"query\":\"q\"}") + ).andExpect(status().isNotFound()); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/query/QueryServiceTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/query/QueryServiceTest.java new file mode 100644 index 000000000..a626d4088 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/query/QueryServiceTest.java @@ -0,0 +1,337 @@ +package edu.harvard.hms.dbmi.avillach.query.query; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.assertj.core.api.Assertions.assertThatThrownBy; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.ArgumentMatchers.argThat; +import static org.mockito.ArgumentMatchers.eq; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.verify; +import static org.mockito.Mockito.verifyNoMoreInteractions; +import static org.mockito.Mockito.when; + +import java.util.Map; +import java.util.UUID; + +import org.junit.jupiter.api.Test; +import org.springframework.http.HttpStatus; + +import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest; +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import edu.harvard.dbmi.avillach.domain.QueryStatus; +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; +import edu.harvard.hms.dbmi.avillach.query.config.HpdsProperties; +import edu.harvard.hms.dbmi.avillach.query.hpds.HpdsBackendSelector; +import edu.harvard.hms.dbmi.avillach.query.hpds.HpdsBackendSelector.HpdsTarget; +import edu.harvard.hms.dbmi.avillach.query.hpds.ResourceWebClient; +import edu.harvard.hms.dbmi.avillach.query.operations.OperationsClient; +import edu.harvard.hms.dbmi.avillach.query.operations.SaveQueryRequest; +import edu.harvard.hms.dbmi.avillach.query.operations.StoredQuery; +import edu.harvard.hms.dbmi.avillach.query.operations.UpdateQueryRequest; +import edu.harvard.dbmi.avillach.domain.PicSureStatus; + +/** + * DB-free port of the legacy WAR's {@code PicsureQueryServiceTest}: every place the brief expected a local + * {@code QueryRepository}/{@code Query} entity now goes through {@link OperationsClient} instead (create/sync persist via + * {@code operationsClient.save}/{@code update}; read ops load via {@code operationsClient.get}). + */ +class QueryServiceTest { + + OperationsClient operationsClient = mock(OperationsClient.class); + ResourceWebClient hpds = mock(ResourceWebClient.class); + HpdsProperties props = props(); + HpdsBackendSelector selector = new HpdsBackendSelector(props); + QueryService service = new QueryService(operationsClient, hpds, selector); + + private static HpdsProperties props() { + HpdsProperties p = new HpdsProperties(); + p.setAuthUrl("http://hpds/PIC-SURE"); + p.setOpenUrl("http://hpds/PIC-SURE"); + return p; + } + + private QueryRequest req() { + GeneralQueryRequest r = new GeneralQueryRequest(); + r.setQuery("q"); + r.setResourceUUID(UUID.randomUUID()); + return r; + } + + private QueryStatus hpdsStatus(String rrid) { + QueryStatus s = new QueryStatus(); + s.setResourceResultId(rrid); + s.setStatus(PicSureStatus.PENDING); + return s; + } + + // --- create --- + + @Test + void createPersistsViaOperationsClientAndTranslatesIds() { + UUID picsureId = UUID.randomUUID(); + when(hpds.query(any(HpdsTarget.class), any())).thenReturn(hpdsStatus("rr-1")); + when(operationsClient.save(any())).thenReturn(picsureId); + + QueryStatus out = service.query("auth", req()); + + assertThat(out.getPicsureResultId()).isEqualTo(picsureId); + assertThat(out.getResourceResultId()).isEqualTo("rr-1"); + verify(operationsClient).save(argThat((SaveQueryRequest r) -> "rr-1".equals(r.resourceResultId()) && r.version() == null)); + verify(hpds).query(argThat((HpdsTarget t) -> "http://hpds/PIC-SURE".equals(t.baseUrl())), any()); // v1 base + } + + @Test + void createFallbackCopiesPicsureIdWhenHpdsHasNoResourceResultId() { + UUID picsureId = UUID.randomUUID(); + when(hpds.query(any(HpdsTarget.class), any())).thenReturn(hpdsStatus(null)); // HPDS returned no id + when(operationsClient.save(any())).thenReturn(picsureId); + + QueryStatus out = service.query("auth", req()); + + assertThat(out.getResourceResultId()).isEqualTo(out.getPicsureResultId().toString()); // fallback + verify(operationsClient) + .update(eq(picsureId), argThat((UpdateQueryRequest u) -> picsureId.toString().equals(u.resourceResultId()))); + } + + @Test + void createV3StampsVersion3() { + UUID picsureId = UUID.randomUUID(); + when(hpds.query(any(HpdsTarget.class), any())).thenReturn(hpdsStatus("rr-3")); + when(operationsClient.save(any())).thenReturn(picsureId); + + service.queryV3("auth", req()); + + verify(operationsClient).save(argThat((SaveQueryRequest r) -> "3".equals(r.version()))); + verify(hpds).query(argThat((HpdsTarget t) -> "http://hpds/PIC-SURE/v3".equals(t.baseUrl())), any()); // v3 base + } + + @Test + void createEchoesResourceUuidFromRequest() { + UUID picsureId = UUID.randomUUID(); + QueryRequest request = req(); + when(hpds.query(any(HpdsTarget.class), any())).thenReturn(hpdsStatus("rr-1")); + when(operationsClient.save(any())).thenReturn(picsureId); + + QueryStatus out = service.query("auth", request); + + assertThat(out.getResourceID()).isEqualTo(request.getResourceUUID()); + } + + // --- sync --- + + @Test + void syncFallsBackToPicsureIdWhenNoMetadataHeader() { + UUID picsureId = UUID.randomUUID(); + when(operationsClient.save(any())).thenReturn(picsureId); + when(hpds.querySync(any(HpdsTarget.class), any(), any())) + .thenReturn(new ResourceWebClient.QuerySyncResult("body".getBytes(), null)); + + var resp = service.querySync("auth", req(), "UI"); + + assertThat(new String(resp.body())).isEqualTo("body"); + // resourceResultId persisted = the picsureId when no header (maintain WAR behavior) + verify(operationsClient) + .update(eq(picsureId), argThat((UpdateQueryRequest u) -> picsureId.toString().equals(u.resourceResultId()))); + } + + @Test + void syncUsesMetadataHeaderAsResourceResultIdWhenPresent() { + UUID picsureId = UUID.randomUUID(); + when(operationsClient.save(any())).thenReturn(picsureId); + when(hpds.querySync(any(HpdsTarget.class), any(), any())) + .thenReturn(new ResourceWebClient.QuerySyncResult("body".getBytes(), "hpds-meta-id")); + + service.querySync("auth", req(), "UI"); + + verify(operationsClient).update(eq(picsureId), argThat((UpdateQueryRequest u) -> "hpds-meta-id".equals(u.resourceResultId()))); + } + + // --- read ops --- + + @Test + void unknownQueryIdThrowsNotFound() { + UUID id = UUID.randomUUID(); + when(operationsClient.get(id)).thenThrow( + new edu.harvard.hms.dbmi.avillach.commons.error.PicsureException( + org.springframework.http.HttpStatus.NOT_FOUND, "not_found", "Query not found: " + id + ) + ); + + org.junit.jupiter.api.Assertions + .assertThrows(edu.harvard.hms.dbmi.avillach.commons.error.PicsureException.class, () -> service.queryStatus("auth", id, req())); + } + + @Test + void signedUrlDispatchesV3WhenStoredVersionIs3() { // THE BUG FIX + UUID id = UUID.randomUUID(); + StoredQuery stored = new StoredQuery(id, "{}", "rr-1", "PENDING", "3", null); // v1-path request, v3-stored query + when(operationsClient.get(id)).thenReturn(stored); + when(hpds.queryResultSignedUrl(any(HpdsTarget.class), eq("rr-1"), any())) + .thenReturn(org.springframework.http.ResponseEntity.ok("{\"url\":\"x\"}")); + + service.queryResultSignedUrl("auth", id, req()); + + verify(hpds).queryResultSignedUrl(argThat((HpdsTarget t) -> "http://hpds/PIC-SURE/v3".equals(t.baseUrl())), eq("rr-1"), any()); // /v3 + // base, + // not + // v1 + } + + @Test + void resultDispatchesV1WhenStoredVersionIsNull() { + UUID id = UUID.randomUUID(); + StoredQuery stored = new StoredQuery(id, "{}", "rr-2", "PENDING", null, null); + when(operationsClient.get(id)).thenReturn(stored); + when(hpds.queryResult(any(HpdsTarget.class), eq("rr-2"), any())) + .thenReturn(org.springframework.http.ResponseEntity.ok(new byte[] {1})); + + service.queryResult("auth", id, req()); + + verify(hpds).queryResult(argThat((HpdsTarget t) -> "http://hpds/PIC-SURE".equals(t.baseUrl())), eq("rr-2"), any()); + } + + @Test + void statusUsesStoredResourceResultIdAndV1ForNullVersionAndPersistsNewStatus() { + UUID id = UUID.randomUUID(); + StoredQuery stored = new StoredQuery(id, "{\"resourceUUID\":\"" + UUID.randomUUID() + "\"}", "rr-7", "PENDING", null, null); + when(operationsClient.get(id)).thenReturn(stored); + QueryStatus s = hpdsStatus("rr-7"); + s.setStatus(PicSureStatus.AVAILABLE); + when(hpds.queryStatus(any(HpdsTarget.class), eq("rr-7"), any())).thenReturn(s); + + QueryStatus out = service.queryStatus("auth", id, req()); + + assertThat(out.getPicsureResultId()).isEqualTo(id); + verify(hpds).queryStatus(argThat((HpdsTarget t) -> "http://hpds/PIC-SURE".equals(t.baseUrl())), eq("rr-7"), any()); // v1 base + verify(operationsClient).update(eq(id), argThat((UpdateQueryRequest u) -> "AVAILABLE".equals(u.status()))); + } + + @Test + void statusEchoesResourceUuidParsedFromStoredQueryJson() { + UUID id = UUID.randomUUID(); + UUID resourceUuid = UUID.randomUUID(); + StoredQuery stored = new StoredQuery(id, "{\"resourceUUID\":\"" + resourceUuid + "\"}", "rr-7", "PENDING", null, null); + when(operationsClient.get(id)).thenReturn(stored); + when(hpds.queryStatus(any(HpdsTarget.class), eq("rr-7"), any())).thenReturn(hpdsStatus("rr-7")); + + QueryStatus out = service.queryStatus("auth", id, req()); + + assertThat(out.getResourceID()).isEqualTo(resourceUuid); + } + + // --- metadata --- + + @Test + void metadataBuildsResultMetadataShapeWithoutCallingHpds() { + UUID id = UUID.randomUUID(); + StoredQuery stored = new StoredQuery( + id, "{\"resourceUUID\":\"" + UUID.randomUUID() + "\",\"query\":\"q\"}", "rr-1", "AVAILABLE", null, + java.util.Base64.getEncoder().encodeToString("{\"commonAreaUUID\":\"x\"}".getBytes()) + ); + when(operationsClient.get(id)).thenReturn(stored); + + QueryStatus out = service.queryMetadata(id); + + assertThat(out.getResultMetadata()).containsKey("queryJson"); + assertThat(out.getResultMetadata()).containsKey("queryResultMetadata"); + assertThat((String) out.getResultMetadata().get("queryResultMetadata")).contains("commonAreaUUID"); + org.mockito.Mockito.verifyNoInteractions(hpds); + } + + @Test + void metadataUnknownIdThrowsNotFound() { + UUID id = UUID.randomUUID(); + when(operationsClient.get(id)).thenThrow(new PicsureException(HttpStatus.NOT_FOUND, "not_found", "nope")); + + assertThatThrownBy(() -> service.queryMetadata(id)) + .isInstanceOfSatisfying(PicsureException.class, e -> assertThat(e.getStatus()).isEqualTo(HttpStatus.NOT_FOUND)); + + verify(operationsClient).get(id); // the one lookup queryMetadata is allowed to make + verifyNoMoreInteractions(operationsClient); // pins that no second (e.g. common-area) lookup is attempted + } + + /** + * A row written before the federated removal stores a serialized FederatedQueryRequest. queryMetadata must still read it: it parses the + * stored blob into a plain {@code Map} via {@code MAPPER.readValue(..., Object.class)}, so {@code "@type"} is just another map key and + * any value — known, unknown, or garbage — parses fine. That's why this test would still pass if the blob's {@code "@type"} were + * replaced with a nonsense value: it pins the parse path, not the subtype registry. The subtype-registry fallback (via + * {@code QueryRequest}'s {@code defaultImpl}) is separately pinned by + * {@code QueryRequestTest.shouldDeserializeRemovedFederatedTypeAsGeneralQueryRequest} in pic-sure-api-model. + */ + @Test + @SuppressWarnings("unchecked") + void metadataReadsALegacyFederatedStoredRow() { + UUID id = UUID.randomUUID(); + String legacyBlob = + "{\"@type\":\"FederatedQueryRequest\"," + "\"query\":{\"expectedResultType\":\"COUNT\"}," + "\"commonAreaUUID\":\"" + + UUID.randomUUID() + "\"," + "\"institutionOfOrigin\":\"BCH\"," + "\"requesterEmail\":\"alice@harvard.edu\"}"; + when(operationsClient.get(id)).thenReturn(new StoredQuery(id, legacyBlob, "rr-legacy", "AVAILABLE", "3", null)); + + QueryStatus result = service.queryMetadata(id); + + Map resultMetadata = result.getResultMetadata(); + Map queryJson = (Map) resultMetadata.get("queryJson"); + assertThat(queryJson).isNotNull(); + assertThat(queryJson).containsKey("query"); + assertThat(result.getPicsureResultId()).isEqualTo(id); + } + + @Test + @SuppressWarnings("unchecked") + void metadataTranslatesStoredV1QueryToV3Shape() { + UUID id = UUID.randomUUID(); + String v1Blob = "{\"resourceUUID\":\"" + UUID.randomUUID() + "\",\"query\":{" + + "\"expectedResultType\":\"COUNT\",\"categoryFilters\":{\"\\\\sex\\\\\":[\"M\"]}}}"; + when(operationsClient.get(id)).thenReturn(new StoredQuery(id, v1Blob, "rr-1", "AVAILABLE", null, null)); + + QueryStatus out = service.queryMetadata(id); + + Map queryJson = (Map) out.getResultMetadata().get("queryJson"); + assertThat(queryJson).isNotNull(); + assertThat(queryJson).containsKey("resourceUUID"); // wrapper preserved + Map inner = (Map) queryJson.get("query"); + assertThat(inner).containsKey("phenotypicClause"); // v3 field present + assertThat(inner).doesNotContainKey("categoryFilters"); // v1 field gone + } + + @Test + @SuppressWarnings("unchecked") + void metadataFallsBackToUntranslatedOnUntranslatableV1Row() { + UUID id = UUID.randomUUID(); + // two non-empty variantInfoFilters groups -> UntranslatableQueryException -> fall back to raw + String v1Blob = + "{\"query\":{\"expectedResultType\":\"COUNT\",\"categoryFilters\":{\"\\\\sex\\\\\":[\"M\"]}," + "\"variantInfoFilters\":[" + + "{\"categoryVariantInfoFilters\":{\"Gene_with_variant\":[\"A\"]},\"numericVariantInfoFilters\":{}}," + + "{\"categoryVariantInfoFilters\":{\"Gene_with_variant\":[\"B\"]},\"numericVariantInfoFilters\":{}}]}}"; + when(operationsClient.get(id)).thenReturn(new StoredQuery(id, v1Blob, "rr-1", "AVAILABLE", null, null)); + + QueryStatus out = service.queryMetadata(id); + + Map queryJson = (Map) out.getResultMetadata().get("queryJson"); + Map inner = (Map) queryJson.get("query"); + assertThat(inner).containsKey("variantInfoFilters"); // untranslated v1 body preserved + assertThat(inner).containsKey("categoryFilters"); // raw v1 body returned in full, not partially translated + assertThat(inner).doesNotContainKey("phenotypicClause"); // no translation output leaked in + } + + @Test + @SuppressWarnings("unchecked") + void metadataLeavesV3StoredRowUntranslated() { + UUID id = UUID.randomUUID(); + String v3Blob = "{\"resourceUUID\":\"" + UUID.randomUUID() + "\",\"query\":{" + + "\"expectedResultType\":\"COUNT\",\"phenotypicClause\":{\"phenotypicFilterType\":\"REQUIRED\"," + + "\"conceptPath\":\"\\\\x\\\\\"},\"genomicFilters\":[]}}"; + when(operationsClient.get(id)).thenReturn(new StoredQuery(id, v3Blob, "rr-1", "AVAILABLE", "3", null)); + + QueryStatus out = service.queryMetadata(id); + + Map queryJson = (Map) out.getResultMetadata().get("queryJson"); + Map inner = (Map) queryJson.get("query"); + // non-null structural assertion: a wrongly-applied v1 translation would produce a different/empty clause, + // so asserting the exact conceptPath survives discriminates "left alone" from "translated". + assertThat(inner.get("phenotypicClause")).isNotNull(); + @SuppressWarnings("unchecked") + Map clause = (Map) inner.get("phenotypicClause"); + assertThat(clause.get("conceptPath")).isEqualTo("\\x\\"); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/search/HpdsSearchControllerTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/search/HpdsSearchControllerTest.java new file mode 100644 index 000000000..7e65a1d9e --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/search/HpdsSearchControllerTest.java @@ -0,0 +1,163 @@ +package edu.harvard.hms.dbmi.avillach.query.search; + +import static com.github.tomakehurst.wiremock.client.WireMock.aResponse; +import static com.github.tomakehurst.wiremock.client.WireMock.equalTo; +import static com.github.tomakehurst.wiremock.client.WireMock.getRequestedFor; +import static com.github.tomakehurst.wiremock.client.WireMock.okJson; +import static com.github.tomakehurst.wiremock.client.WireMock.postRequestedFor; +import static com.github.tomakehurst.wiremock.client.WireMock.urlEqualTo; +import static com.github.tomakehurst.wiremock.client.WireMock.urlPathEqualTo; +import static com.github.tomakehurst.wiremock.core.WireMockConfiguration.options; +import static org.assertj.core.api.Assertions.assertThat; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.jsonPath; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status; + +import java.util.UUID; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.MediaType; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.springframework.test.context.bean.override.mockito.MockitoBean; +import org.springframework.test.web.servlet.MockMvc; + +import com.github.tomakehurst.wiremock.WireMockServer; +import com.github.tomakehurst.wiremock.client.WireMock; + +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import edu.harvard.hms.dbmi.avillach.query.operations.OperationsClient; + +/** + * Full-context MockMvc coverage of {@code /hpds/{backend}[/v3]/search/**}. Search is NOT versioned downstream (matching the ported + * {@code PicsureSearchService}): both the v1 and v3 ingress paths for a given backend must land on the SAME non-{@code /v3} HPDS URL. + * {@code auth} and {@code open} are pointed at distinct paths on one WireMock instance so backend selection is verifiable without running + * two servers. + */ +@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.MOCK) +@AutoConfigureMockMvc +class HpdsSearchControllerTest { + + private static final String USER = "auth0|alice"; + + static WireMockServer hpds; + + @BeforeAll + static void start() { + hpds = new WireMockServer(options().dynamicPort().http2PlainDisabled(true)); + hpds.start(); + } + + @AfterAll + static void stop() { + hpds.stop(); + } + + @DynamicPropertySource + static void hpdsProps(DynamicPropertyRegistry registry) { + registry.add("hpds.auth-url", () -> "http://localhost:" + hpds.port() + "/AUTH"); + registry.add("hpds.open-url", () -> "http://localhost:" + hpds.port() + "/OPEN"); + } + + @Autowired + private MockMvc mockMvc; + + @MockitoBean + private OperationsClient operationsClient; // unused by search, present so the whole context (incl. query controllers) wires cleanly + + @BeforeEach + void resetStubs() { + hpds.resetAll(); + } + + @Test + void searchOnAuthBackendMapsToSameDownstreamUrlForV1AndV3() throws Exception { + UUID resourceId = UUID.randomUUID(); + hpds.stubFor(WireMock.post(urlEqualTo("/AUTH/search")).willReturn(okJson("{\"searchQuery\":\"q\",\"results\":{}}"))); + + mockMvc.perform( + post("/hpds/auth/search/{resourceId}", resourceId).header(GatewayUserResolver.HEADER_USER_ID, USER) + .contentType(MediaType.APPLICATION_JSON).content("{\"query\":\"q\"}") + ).andExpect(status().isOk()); + + mockMvc.perform( + post("/hpds/auth/v3/search/{resourceId}", resourceId).header(GatewayUserResolver.HEADER_USER_ID, USER) + .contentType(MediaType.APPLICATION_JSON).content("{\"query\":\"q\"}") + ).andExpect(status().isOk()); + + hpds.verify(2, postRequestedFor(urlEqualTo("/AUTH/search"))); // same non-versioned URL both times + } + + @Test + void searchOnOpenBackendResolvesToOpenUrl() throws Exception { + UUID resourceId = UUID.randomUUID(); + hpds.stubFor(WireMock.post(urlEqualTo("/OPEN/search")).willReturn(okJson("{\"searchQuery\":\"q\",\"results\":{}}"))); + + mockMvc.perform( + post("/hpds/open/search/{resourceId}", resourceId).header(GatewayUserResolver.HEADER_USER_ID, USER) + .contentType(MediaType.APPLICATION_JSON).content("{\"query\":\"q\"}") + ).andExpect(status().isOk()); + + hpds.verify(postRequestedFor(urlEqualTo("/OPEN/search"))); + } + + @Test + void searchViaV3PathNeverHitsAVersionedDownstreamUrl() throws Exception { + UUID resourceId = UUID.randomUUID(); + hpds.stubFor(WireMock.post(urlEqualTo("/AUTH/search")).willReturn(okJson("{\"searchQuery\":\"q\",\"results\":{}}"))); + + mockMvc.perform( + post("/hpds/auth/v3/search/{resourceId}", resourceId).header(GatewayUserResolver.HEADER_USER_ID, USER) + .contentType(MediaType.APPLICATION_JSON).content("{\"query\":\"q\"}") + ).andExpect(status().isOk()); + + hpds.verify(0, postRequestedFor(urlEqualTo("/AUTH/v3/search"))); // search is never versioned downstream + } + + @Test + void valuesEndpointMapsForBothV1AndV3OnAuthBackend() throws Exception { + UUID resourceId = UUID.randomUUID(); + hpds.stubFor( + WireMock.get(urlPathEqualTo("/AUTH/search/values/")).withQueryParam("genomicConceptPath", equalTo("\\gene\\")) + .withQueryParam("query", equalTo("BRCA")).willReturn(okJson("{\"results\":[],\"page\":1,\"total\":0}")) + ); + + mockMvc.perform( + get("/hpds/auth/search/{resourceId}/values/", resourceId).header(GatewayUserResolver.HEADER_USER_ID, USER) + .param("genomicConceptPath", "\\gene\\").param("query", "BRCA") + ).andExpect(status().isOk()).andExpect(jsonPath("$.total").value(0)); + + mockMvc.perform( + get("/hpds/auth/v3/search/{resourceId}/values/", resourceId).header(GatewayUserResolver.HEADER_USER_ID, USER) + .param("genomicConceptPath", "\\gene\\").param("query", "BRCA") + ).andExpect(status().isOk()).andExpect(jsonPath("$.total").value(0)); + + hpds.verify(2, getRequestedFor(urlPathEqualTo("/AUTH/search/values/"))); + } + + @Test + void hpdsFailureOnSearchSurfacesAs502() throws Exception { + UUID resourceId = UUID.randomUUID(); + hpds.stubFor(WireMock.post(urlEqualTo("/AUTH/search")).willReturn(aResponse().withStatus(500))); + + mockMvc.perform( + post("/hpds/auth/search/{resourceId}", resourceId).header(GatewayUserResolver.HEADER_USER_ID, USER) + .contentType(MediaType.APPLICATION_JSON).content("{\"query\":\"q\"}") + ).andExpect(status().isBadGateway()); + } + + @Test + void searchWithoutGatewayIdentityIsRejected() throws Exception { + UUID resourceId = UUID.randomUUID(); + mockMvc.perform( + post("/hpds/auth/search/{resourceId}", resourceId).contentType(MediaType.APPLICATION_JSON).content("{\"query\":\"q\"}") + ).andExpect(result -> assertThat(result.getResponse().getStatus()).isIn(401, 403)); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/search/SearchServiceTest.java b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/search/SearchServiceTest.java new file mode 100644 index 000000000..52980c4fe --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/java/edu/harvard/hms/dbmi/avillach/query/search/SearchServiceTest.java @@ -0,0 +1,105 @@ +package edu.harvard.hms.dbmi.avillach.query.search; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.ArgumentMatchers.eq; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.never; +import static org.mockito.Mockito.verify; +import static org.mockito.Mockito.when; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest; +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import edu.harvard.dbmi.avillach.domain.SearchResults; +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; +import edu.harvard.hms.dbmi.avillach.query.config.HpdsProperties; +import edu.harvard.hms.dbmi.avillach.query.hpds.HpdsBackendSelector; +import edu.harvard.hms.dbmi.avillach.query.hpds.HpdsCommunicationException; +import edu.harvard.hms.dbmi.avillach.query.hpds.ResourceWebClient; + +/** + * Ports the legacy WAR's {@code PicsureSearchServiceTest} coverage of {@code search}/{@code searchGenomicConceptValues} minus Resource + + * AuditContext: backend resolution comes from the ingress {@code {backend}} path segment via {@link HpdsBackendSelector}, and both calls go + * through {@link ResourceWebClient#search} / {@link ResourceWebClient#searchConceptValues}, which never receive an {@code Authorization} + * header (verified indirectly here by asserting only the non-versioned base URL string is passed -- the client itself is the thing that + * omits the token; see {@code ResourceWebClientTest} for that half of the parity guarantee). + */ +class SearchServiceTest { + + ResourceWebClient hpds = mock(ResourceWebClient.class); + HpdsProperties props = props(); + HpdsBackendSelector selector = new HpdsBackendSelector(props); + SearchService service = new SearchService(hpds, selector); + + private static HpdsProperties props() { + HpdsProperties p = new HpdsProperties(); + p.setAuthUrl("http://hpds/PIC-SURE"); + p.setOpenUrl("http://hpds/PIC-SURE"); + return p; + } + + private QueryRequest req() { + GeneralQueryRequest r = new GeneralQueryRequest(); + r.setQuery("BRCA"); + return r; + } + + @Test + void searchUsesNonVersionedBase() { + SearchResults sr = new SearchResults(); + when(hpds.search(eq("http://hpds/PIC-SURE"), any())).thenReturn(sr); + + assertThat(service.search("auth", req())).isSameAs(sr); + + verify(hpds).search(eq("http://hpds/PIC-SURE"), any()); // no /v3, no token param + } + + @Test + void searchResolvesOpenBackendSeparatelyFromAuth() { + props.setOpenUrl("http://hpds-open/PIC-SURE"); + SearchResults sr = new SearchResults(); + when(hpds.search(eq("http://hpds-open/PIC-SURE"), any())).thenReturn(sr); + + service.search("open", req()); + + verify(hpds).search(eq("http://hpds-open/PIC-SURE"), any()); + } + + @Test + void searchRejectsNullRequest() { + Assertions.assertThrows(PicsureException.class, () -> service.search("auth", null)); + } + + @Test + void searchPropagatesHpdsUpstreamError() { + when(hpds.search(any(), any())).thenThrow(new HpdsCommunicationException("boom")); + + Assertions.assertThrows(HpdsCommunicationException.class, () -> service.search("auth", req())); + } + + @Test + void valuesPassesParamsThroughOnNonVersionedBase() { + service.searchConceptValues("auth", req(), "\\gene\\", "BRCA", 1, 10); + + verify(hpds).searchConceptValues(eq("http://hpds/PIC-SURE"), any(), eq("\\gene\\"), eq("BRCA"), eq(1), eq(10)); + } + + @Test + void valuesPropagatesHpdsUpstreamError() { + when(hpds.searchConceptValues(any(), any(), any(), any(), any(), any())).thenThrow(new HpdsCommunicationException("boom")); + + Assertions.assertThrows( + HpdsCommunicationException.class, () -> service.searchConceptValues("auth", req(), "\\gene\\", "BRCA", 1, 10) + ); + } + + @Test + void unknownBackendIsRejectedBeforeReachingHpds() { + Assertions.assertThrows(PicsureException.class, () -> service.search("bogus", req())); + + verify(hpds, never()).search(any(), any()); + } +} diff --git a/services/pic-sure-hpds-query-service/src/test/resources/application.yml b/services/pic-sure-hpds-query-service/src/test/resources/application.yml new file mode 100644 index 000000000..1239ce8d1 --- /dev/null +++ b/services/pic-sure-hpds-query-service/src/test/resources/application.yml @@ -0,0 +1,11 @@ +hpds: + auth-url: http://localhost:1/PIC-SURE + auth-token: test-auth-token + open-url: http://localhost:1/PIC-SURE + open-token: test-open-token + +picsure: + query: + operations: + base-url: http://localhost:1 + internal-token: test diff --git a/services/pic-sure-hpds/.github/release.yml b/services/pic-sure-hpds/.github/release.yml new file mode 100644 index 000000000..0db6cd02d --- /dev/null +++ b/services/pic-sure-hpds/.github/release.yml @@ -0,0 +1,20 @@ +changelog: + exclude: + labels: + - ignore-for-release + categories: + - title: Breaking Changes + labels: + - breaking-change + - title: Features + labels: + - feature + - title: Enhancements + labels: + - enhancement + - title: Bug Fixes + labels: + - bug + - title: Other Changes + labels: + - "*" diff --git a/services/pic-sure-hpds/.github/workflows/github-actions-deploy-snapshots.yml b/services/pic-sure-hpds/.github/workflows/github-actions-deploy-snapshots.yml new file mode 100644 index 000000000..695f5c5f8 --- /dev/null +++ b/services/pic-sure-hpds/.github/workflows/github-actions-deploy-snapshots.yml @@ -0,0 +1,21 @@ +name: Maven Deploy Snapshots + +on: + push: + branches: [ main ] + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd #v6.0.2 + - name: Set up JDK 25 + uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 #v5.2.0 + with: + java-version: '25' + distribution: 'temurin' + - name: Build with Maven + run: mvn --update-snapshots deploy + env: + GITHUB_TOKEN: ${{ github.token }} diff --git a/services/pic-sure-hpds/.github/workflows/github-actions-test.yml b/services/pic-sure-hpds/.github/workflows/github-actions-test.yml new file mode 100644 index 000000000..2d656e7b0 --- /dev/null +++ b/services/pic-sure-hpds/.github/workflows/github-actions-test.yml @@ -0,0 +1,19 @@ +name: Maven Run Tests + +on: [ push ] + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd #v6.0.2 + - name: Set up JDK 25 + uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 #v5.2.0 + with: + java-version: '25' + distribution: 'temurin' + - name: Test with Maven + run: mvn --update-snapshots test + env: + GITHUB_TOKEN: ${{ github.token }} diff --git a/services/pic-sure-hpds/.github/workflows/label-checker.yml b/services/pic-sure-hpds/.github/workflows/label-checker.yml new file mode 100644 index 000000000..4806967a4 --- /dev/null +++ b/services/pic-sure-hpds/.github/workflows/label-checker.yml @@ -0,0 +1,21 @@ +name: Label Checker +on: + pull_request: + types: + - opened + - synchronize + - reopened + - labeled + - unlabeled + +jobs: + + check_labels: + name: Check labels + runs-on: ubuntu-latest + steps: + - uses: agilepathway/label-checker@c3d16ad512e7cea5961df85ff2486bb774caf3c5 # v1.6.65 + with: + one_of: breaking-change,enhancement,bug,documentation,ignore-for-release,dependencies + repo_token: ${{ secrets.GITHUB_TOKEN }} + diff --git a/services/pic-sure-hpds/.gitignore b/services/pic-sure-hpds/.gitignore new file mode 100644 index 000000000..d65523d6e --- /dev/null +++ b/services/pic-sure-hpds/.gitignore @@ -0,0 +1,33 @@ +docker/src/main/resources/gitCommit.properties + +target/ +pom.xml.tag +pom.xml.releaseBackup +pom.xml.versionsBackup +pom.xml.next +release.properties +dependency-reduced-pom.xml +buildNumber.properties +.mvn/timing.properties + +# Avoid ignoring Maven wrapper jar file (.jar files are usually ignored) +!/.mvn/wrapper/maven-wrapper.jar + +# Eclipse files +.classpath +.project +.settings/ + +*.jar +*.war + +war-exec.properties +war-exec.manifest +.extract/ + +.DS_Store + +*.iml +.idea/ + +.java-version \ No newline at end of file diff --git a/services/pic-sure-hpds/.sdkmanrc b/services/pic-sure-hpds/.sdkmanrc new file mode 100644 index 000000000..6217ebafd --- /dev/null +++ b/services/pic-sure-hpds/.sdkmanrc @@ -0,0 +1 @@ +java=24.0.2-tem diff --git a/services/pic-sure-hpds/CODE_OF_CONDUCT.md b/services/pic-sure-hpds/CODE_OF_CONDUCT.md new file mode 100644 index 000000000..e0cf97b8f --- /dev/null +++ b/services/pic-sure-hpds/CODE_OF_CONDUCT.md @@ -0,0 +1,128 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, religion, or sexual identity +and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the + overall community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or + advances of any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email + address, without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official e-mail address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +avillach_lab_developers@googlegroups.com. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series +of actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or +permanent ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within +the community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.0, available at +https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. + +Community Impact Guidelines were inspired by [Mozilla's code of conduct +enforcement ladder](https://github.com/mozilla/diversity). + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see the FAQ at +https://www.contributor-covenant.org/faq. Translations are available at +https://www.contributor-covenant.org/translations. diff --git a/services/pic-sure-hpds/LICENSE b/services/pic-sure-hpds/LICENSE new file mode 100644 index 000000000..261eeb9e9 --- /dev/null +++ b/services/pic-sure-hpds/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. 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As such, PIC-SURE-HPDS can manage arbitrarily large datasets with very little computing. + +For clinical data, datasets are stored as two files: metadata and data. The metadata file contains the internal data dictionary, high-level dataset-specific information, and file offsets for each variable's data within the data file. The data file contains data for three concepts: patient index, numerical index, and categorical index. [How to load phenotypic data into HPDS](https://github.com/hms-dbmi/pic-sure-hpds-phenotype-load-example/tree/master/nhanes-load-example) + +For genomic data, variants that are not represented in the database are not stored. Genomic sample data is stored separately from variant annotations in HPDS. Variant annotations are stored using the same Numerical Index, and Categorical Index described above, indexing variant IDs instead of patient IDs. [How to load genomic data into HPDS](https://github.com/hms-dbmi/pic-sure-hpds-genotype-load-example) + + +## Pre-requisites + +* Java 25 +* Before contributing code, please set up our git hook: + `cp code-formatting/pre-commit.sh .git/hooks/pre-commit` + * To skip formatting on a block of code, wrap in `spotless:off`, `spotless:on` comments diff --git a/services/pic-sure-hpds/code-formatting/eclipse-formatter.xml b/services/pic-sure-hpds/code-formatting/eclipse-formatter.xml new file mode 100644 index 000000000..e7cfababf --- /dev/null +++ b/services/pic-sure-hpds/code-formatting/eclipse-formatter.xml @@ -0,0 +1,402 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/services/pic-sure-hpds/code-formatting/pre-commit.sh b/services/pic-sure-hpds/code-formatting/pre-commit.sh new file mode 100755 index 000000000..ed051d182 --- /dev/null +++ b/services/pic-sure-hpds/code-formatting/pre-commit.sh @@ -0,0 +1,28 @@ +#!/bin/sh -e +CWD=$(pwd) +cd $(git rev-parse --show-toplevel) +format_cmd="" + +# skip if NO_VERIFY env var set +if [ "$NO_VERIFY" ]; then + echo 'code formatting skipped' 1>&2 + exit 0 +fi + +# I'm not great at bash, so this is a bit ugly, but I'll explain each pipe +# 1. Get all staged files +# 2. Reduce to just .java files +# 3. Replace newlines with commas (this was really hard to do in sed) +# 4. Replace commas with $,^.* +# 5. Crop off the last 4 chars +# This results in foo.java$,^.*bar.java$,^.*baz.java$ +# I then append ^.* to the beginning of that. +STAGED_JAVA_FILES_AS_REGEX=$(git diff --staged --name-only --diff-filter=ACMR | grep '.java$' | tr '\n' ',' | sed -e 's/,/$,^.*/g' | sed 's/.\{4\}$//') +FILES_TO_RESTAGE=$(git diff --staged --name-only --diff-filter=ACMR) +if [ -n "$STAGED_JAVA_FILES_AS_REGEX" ]; then + echo "Found the following staged java files to format: $STAGED_JAVA_FILES_AS_REGEX" + mvn spotless:apply -DspotlessFiles=^.*$STAGED_JAVA_FILES_AS_REGEX + git add $FILES_TO_RESTAGE +fi + +cd $CWD \ No newline at end of file diff --git a/services/pic-sure-hpds/common/pom.xml b/services/pic-sure-hpds/common/pom.xml new file mode 100644 index 000000000..5d08375bf --- /dev/null +++ b/services/pic-sure-hpds/common/pom.xml @@ -0,0 +1,29 @@ + + + 4.0.0 + + pic-sure-hpds + edu.harvard.hms.dbmi.avillach.hpds + ${revision} + + + common + + common + + + commons-io + commons-io + + + com.google.guava + guava + + + com.fasterxml.jackson.core + jackson-databind + + + diff --git a/services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/crypto/Crypto.java b/services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/crypto/Crypto.java new file mode 100644 index 000000000..a6d014519 --- /dev/null +++ b/services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/crypto/Crypto.java @@ -0,0 +1,120 @@ +package edu.harvard.hms.dbmi.avillach.hpds.crypto; + + +import java.io.FileInputStream; +import java.io.IOException; +import java.nio.ByteBuffer; +import java.nio.charset.Charset; +import java.security.InvalidAlgorithmParameterException; +import java.security.InvalidKeyException; +import java.security.NoSuchAlgorithmException; +import java.security.SecureRandom; +import java.util.HashMap; + +import javax.crypto.BadPaddingException; +import javax.crypto.Cipher; +import javax.crypto.IllegalBlockSizeException; +import javax.crypto.NoSuchPaddingException; +import javax.crypto.SecretKey; +import javax.crypto.ShortBufferException; +import javax.crypto.spec.GCMParameterSpec; +import javax.crypto.spec.SecretKeySpec; + +import org.apache.commons.io.IOUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +public class Crypto { + + public static final String DEFAULT_KEY_NAME = "DEFAULT"; + + // This needs to be set in a static initializer block to be overridable in tests. + private static final String DEFAULT_ENCRYPTION_KEY_PATH; + static { + DEFAULT_ENCRYPTION_KEY_PATH = "/opt/local/hpds/encryption_key"; + } + + private static final Logger LOGGER = LoggerFactory.getLogger(Crypto.class); + + private static final HashMap keys = new HashMap(); + + public static void loadDefaultKey() { + loadKey(DEFAULT_KEY_NAME, DEFAULT_ENCRYPTION_KEY_PATH); + } + + public static void loadKey(String keyName, String filePath) { + try { + setKey(keyName, IOUtils.toString(new FileInputStream(filePath), Charset.forName("UTF-8")).trim().getBytes()); + LOGGER.info("****LOADED CRYPTO KEY****"); + } catch (IOException e) { + LOGGER.error("****CRYPTO KEY NOT FOUND****", e); + } + } + + public static byte[] encryptData(byte[] plaintextBytes) { + return encryptData(DEFAULT_KEY_NAME, plaintextBytes); + } + + public static byte[] encryptData(String keyName, byte[] plaintextBytes) { + byte[] key = keys.get(keyName); + SecureRandom secureRandom = new SecureRandom(); + SecretKey secretKey = new SecretKeySpec(key, "AES"); + byte[] iv = new byte[12]; // NEVER REUSE THIS IV WITH SAME KEY + secureRandom.nextBytes(iv); + byte[] cipherText; + Cipher cipher; + try { + cipher = Cipher.getInstance("AES/GCM/NoPadding"); + GCMParameterSpec parameterSpec = new GCMParameterSpec(128, iv); // 128 bit auth tag length + cipher.init(Cipher.ENCRYPT_MODE, secretKey, parameterSpec); + cipherText = new byte[cipher.getOutputSize(plaintextBytes.length)]; + cipher.doFinal(plaintextBytes, 0, plaintextBytes.length, cipherText, 0); + LOGGER.debug("Length of cipherText : " + cipherText.length); + ByteBuffer byteBuffer = ByteBuffer.allocate(4 + iv.length + cipherText.length); + byteBuffer.putInt(iv.length); + byteBuffer.put(iv); + byteBuffer.put(cipherText); + byte[] cipherMessage = byteBuffer.array(); + return cipherMessage; + } catch ( + NoSuchAlgorithmException | NoSuchPaddingException | InvalidKeyException | InvalidAlgorithmParameterException + | ShortBufferException | IllegalBlockSizeException | BadPaddingException e + ) { + throw new RuntimeException("Exception while trying to encrypt data : ", e); + } + } + + public static byte[] decryptData(byte[] encrypted) { + return decryptData(DEFAULT_KEY_NAME, encrypted); + } + + public static byte[] decryptData(String keyName, byte[] encrypted) { + byte[] key = keys.get(keyName); + ByteBuffer byteBuffer = ByteBuffer.wrap(encrypted); + int ivLength = byteBuffer.getInt(); + byte[] iv = new byte[ivLength]; + byteBuffer.get(iv); + byte[] cipherText = new byte[byteBuffer.remaining()]; + byteBuffer.get(cipherText); + Cipher cipher; + try { + cipher = Cipher.getInstance("AES/GCM/NoPadding"); + cipher.init(Cipher.DECRYPT_MODE, new SecretKeySpec(key, "AES"), new GCMParameterSpec(128, iv)); + return cipher.doFinal(cipherText); + } catch ( + NoSuchAlgorithmException | NoSuchPaddingException | InvalidKeyException | InvalidAlgorithmParameterException + | IllegalBlockSizeException | BadPaddingException e + ) { + throw new RuntimeException("Exception caught trying to decrypt data : " + e, e); + } + } + + private static void setKey(String keyName, byte[] key) { + keys.put(keyName, key); + } + + public static boolean hasKey(String keyName) { + return keys.containsKey(keyName); + } + +} diff --git a/services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/exception/NotEnoughMemoryException.java b/services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/exception/NotEnoughMemoryException.java new file mode 100644 index 000000000..5cb595abb --- /dev/null +++ b/services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/exception/NotEnoughMemoryException.java @@ -0,0 +1,14 @@ +package edu.harvard.hms.dbmi.avillach.hpds.exception; + +public class NotEnoughMemoryException extends RuntimeException { + + private static final long serialVersionUID = 2592915631853567560L; + + public NotEnoughMemoryException() { + super( + "Not enough available heap space to allocate results array." + + "Please reduce ID_BATCH_SIZE or CACHE_SIZE system property or increase the heap available to this application. " + + "This query will be retried up to 3 times." + ); + } +} diff --git a/services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/exception/ResultSetTooLargeException.java b/services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/exception/ResultSetTooLargeException.java new file mode 100644 index 000000000..051b6f049 --- /dev/null +++ b/services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/exception/ResultSetTooLargeException.java @@ -0,0 +1,20 @@ +package edu.harvard.hms.dbmi.avillach.hpds.exception; + +public class ResultSetTooLargeException extends RuntimeException { + /** + * This exception is thrown when a result set would be larger in memory than Integer.MAX_INT bytes. This is a JVM limitation... but + * seriously people... + * + * You actually don't need that much data on the client side, work with us to implement whatever filtering you need. + * + * @param multiplesOfCapacity The number of pieces to split this result to actually have it work. + */ + public ResultSetTooLargeException(long multiplesOfCapacity) { + super( + "The result set is too large to handle in one request. " + "We have a plan to fix this limitation, but for now try " + + "splitting your selected fields array in " + multiplesOfCapacity + " equal pieces " + "and running " + multiplesOfCapacity + + " queries. Additionally, do you actually " + "need all this data? Do you have the compute resources " + + "to handle processing it?" + ); + } +} diff --git a/services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/storage/FileBackedByteIndexedStorage.java b/services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/storage/FileBackedByteIndexedStorage.java new file mode 100644 index 000000000..6c9ce95e2 --- /dev/null +++ b/services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/storage/FileBackedByteIndexedStorage.java @@ -0,0 +1,121 @@ +package edu.harvard.hms.dbmi.avillach.hpds.storage; + +import java.io.*; +import java.util.Set; +import java.util.concurrent.ConcurrentHashMap; +import java.util.function.Function; + +public abstract class FileBackedByteIndexedStorage implements Serializable { + private static final long serialVersionUID = -7297090745384302635L; + protected transient RandomAccessFile storage; + protected ConcurrentHashMap index; + protected File storageFile; + protected boolean completed = false; + + + public FileBackedByteIndexedStorage(Class keyClass, Class valueClass, File storageFile) throws FileNotFoundException { + this.index = new ConcurrentHashMap(); + this.storageFile = storageFile; + this.storage = new RandomAccessFile(this.storageFile, "rw"); + } + + public void updateStorageDirectory(File storageDirectory) { + if (!storageDirectory.isDirectory()) { + throw new IllegalArgumentException("storageDirectory is not a directory"); + } + String currentStoreageFilename = storageFile.getName(); + storageFile = new File(storageDirectory, currentStoreageFilename); + } + + public Set keys() { + return index.keySet(); + } + + public void put(K key, V value) { + if (completed) { + throw new RuntimeException("A completed FileBackedByteIndexedStorage cannot be modified."); + } + Long[] recordIndex; + try (ByteArrayOutputStream out = writeObject(value)) { + recordIndex = new Long[2]; + synchronized (storage) { + storage.seek(storage.length()); + recordIndex[0] = storage.getFilePointer(); + storage.write(out.toByteArray()); + recordIndex[1] = storage.getFilePointer() - recordIndex[0]; + } + } catch (IOException e) { + throw new UncheckedIOException(e); + } + index.put(key, recordIndex); + } + + public void load(Iterable values, Function mapper) { + // make sure we start fresh + if (this.storageFile.exists()) { + this.storageFile.delete(); + } + try (RandomAccessFile storage = new RandomAccessFile(storageFile, "rw");) { + this.storage = storage; + for (V value : values) { + put(mapper.apply(value), value); + } + complete(); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + } + + public void open() { + try { + this.storage = new RandomAccessFile(this.storageFile, "rwd"); + } catch (FileNotFoundException e) { + throw new UncheckedIOException(e); + } + } + + public void complete() { + this.completed = true; + } + + public V get(K key) { + try { + // todo: make this class immutable and remove this lock/check altogether + synchronized (this) { + if (this.storage == null) { + this.open(); + } + } + Long[] offsetsInStorage = index.get(key); + if (offsetsInStorage != null) { + Long offsetInStorage = index.get(key)[0]; + int offsetLength = index.get(key)[1].intValue(); + if (offsetInStorage != null && offsetLength > 0) { + byte[] buffer = new byte[offsetLength]; + synchronized (storage) { + storage.seek(offsetInStorage); + storage.readFully(buffer); + } + V readObject = readObject(buffer); + return readObject; + } else { + return null; + } + } else { + return null; + } + } catch (IOException e) { + throw new UncheckedIOException(e); + } + } + + protected abstract V readObject(byte[] buffer); + + protected abstract ByteArrayOutputStream writeObject(V value) throws IOException; + + public V getOrELse(K key, V defaultValue) { + V result = get(key); + return result == null ? defaultValue : result; + } + +} diff --git a/services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/storage/FileBackedJavaIndexedStorage.java b/services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/storage/FileBackedJavaIndexedStorage.java new file mode 100644 index 000000000..dc30ada05 --- /dev/null +++ b/services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/storage/FileBackedJavaIndexedStorage.java @@ -0,0 +1,34 @@ +package edu.harvard.hms.dbmi.avillach.hpds.storage; + +import java.io.*; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; + +public class FileBackedJavaIndexedStorage extends FileBackedByteIndexedStorage { + public FileBackedJavaIndexedStorage(Class keyClass, Class valueClass, File storageFile) throws FileNotFoundException { + super(keyClass, valueClass, storageFile); + } + + protected ByteArrayOutputStream writeObject(V value) throws IOException { + ByteArrayOutputStream out = new ByteArrayOutputStream(); + try ( + GZIPOutputStream gzipOutputStream = new GZIPOutputStream(out); ObjectOutputStream oos = new ObjectOutputStream(gzipOutputStream) + ) { + oos.writeObject(value); + oos.flush(); + } + return out; + } + + @Override + protected V readObject(byte[] buffer) { + try (ObjectInputStream in = new ObjectInputStream(new GZIPInputStream(new ByteArrayInputStream(buffer)));) { + V readObject = (V) in.readObject(); + return readObject; + } catch (IOException e) { + throw new UncheckedIOException(e); + } catch (ClassNotFoundException e) { + throw new RuntimeException(e); + } + } +} diff --git a/services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/storage/FileBackedJsonIndexStorage.java b/services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/storage/FileBackedJsonIndexStorage.java new file mode 100644 index 000000000..89e5133df --- /dev/null +++ b/services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/storage/FileBackedJsonIndexStorage.java @@ -0,0 +1,40 @@ +package edu.harvard.hms.dbmi.avillach.hpds.storage; + +import com.fasterxml.jackson.core.type.TypeReference; +import com.fasterxml.jackson.databind.ObjectMapper; + +import java.io.*; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; + +public abstract class FileBackedJsonIndexStorage extends FileBackedByteIndexedStorage { + private static final long serialVersionUID = -1086729119489479152L; + + protected transient ObjectMapper objectMapper = new ObjectMapper(); + + public FileBackedJsonIndexStorage(File storageFile) throws FileNotFoundException { + super(null, null, storageFile); + } + + protected ByteArrayOutputStream writeObject(V value) throws IOException { + ByteArrayOutputStream out = new ByteArrayOutputStream(); + objectMapper.writeValue(new GZIPOutputStream(out), value); + return out; + } + + protected V readObject(byte[] buffer) { + try (GZIPInputStream gzipInputStream = new GZIPInputStream(new ByteArrayInputStream(buffer))) { + return objectMapper.readValue(gzipInputStream, getTypeReference()); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + + // Required to populate the objectMapper on deserialization + private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException { + in.defaultReadObject(); + objectMapper = new ObjectMapper(); + } + + public abstract TypeReference getTypeReference(); +} diff --git a/services/pic-sure-hpds/common/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/crypto/CryptoDefaultKeyTest.java b/services/pic-sure-hpds/common/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/crypto/CryptoDefaultKeyTest.java new file mode 100644 index 000000000..d5f59fd73 --- /dev/null +++ b/services/pic-sure-hpds/common/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/crypto/CryptoDefaultKeyTest.java @@ -0,0 +1,49 @@ +package edu.harvard.hms.dbmi.avillach.hpds.crypto; + +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; +import org.springframework.test.context.event.annotation.BeforeTestClass; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import java.io.File; +import java.lang.reflect.Field; +import java.lang.reflect.Modifier; + +@Disabled // We should rewrite the crypto class to make it more testable, these tests don't work on certain JDKs +public class CryptoDefaultKeyTest { + + String TEST_MESSAGE = "This is a test."; + + @BeforeTestClass + public static void overrideDefaultKeyLocation() throws IllegalArgumentException, IllegalAccessException {} + + @Test + public void testCryptoLoadsKey() throws IllegalArgumentException, IllegalAccessException, NoSuchFieldException, SecurityException { + Field field = Crypto.class.getDeclaredField("DEFAULT_ENCRYPTION_KEY_PATH"); + field.setAccessible(true); + Field modifiersField = Field.class.getDeclaredField("modifiers"); + modifiersField.setAccessible(true); + modifiersField.setInt(field, field.getModifiers() & ~Modifier.FINAL); + field.set(Crypto.class, new File("src/test/resources/test_encryption_key").getAbsolutePath()); + Crypto.loadDefaultKey(); + assertTrue(Crypto.hasKey(Crypto.DEFAULT_KEY_NAME)); + } + + @Test + public void testEncryptDecrypt() throws IllegalArgumentException, IllegalAccessException, NoSuchFieldException, SecurityException { + Field field = Crypto.class.getDeclaredField("DEFAULT_ENCRYPTION_KEY_PATH"); + field.setAccessible(true); + Field modifiersField = Field.class.getDeclaredField("modifiers"); + modifiersField.setAccessible(true); + modifiersField.setInt(field, field.getModifiers() & ~Modifier.FINAL); + field.set(Crypto.class, new File("src/test/resources/test_encryption_key").getAbsolutePath()); + Crypto.loadDefaultKey(); + byte[] ciphertext = Crypto.encryptData(TEST_MESSAGE.getBytes()); + assertTrue(!new String(ciphertext).contentEquals(TEST_MESSAGE)); + String plaintext = new String(Crypto.decryptData(ciphertext)); + assertEquals(plaintext, TEST_MESSAGE); + } + +} diff --git a/services/pic-sure-hpds/common/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/crypto/CryptoNamedKeyTest.java b/services/pic-sure-hpds/common/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/crypto/CryptoNamedKeyTest.java new file mode 100644 index 000000000..d18d1495e --- /dev/null +++ b/services/pic-sure-hpds/common/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/crypto/CryptoNamedKeyTest.java @@ -0,0 +1,64 @@ +package edu.harvard.hms.dbmi.avillach.hpds.crypto; + +import java.io.File; +import java.lang.reflect.Field; +import java.lang.reflect.Modifier; + +import javax.crypto.AEADBadTagException; + +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; +import org.springframework.test.context.event.annotation.BeforeTestClass; + +import static org.junit.jupiter.api.Assertions.*; + +@Disabled // We should rewrite the crypto class to make it more testable, these tests don't work on certain JDKs +public class CryptoNamedKeyTest { + + private static final String TEST_NAMED_ENCRYPTIOON_KEY_PATH = "src/test/resources/test_named_encryption_key"; + + String TEST_MESSAGE = "This is a test."; + + String TEST_NAMED_KEY = "TEST_NAMED_KEY"; + + @BeforeTestClass + public static void overrideDefaultKeyLocation() + throws IllegalArgumentException, IllegalAccessException, NoSuchFieldException, SecurityException { + Field field = Crypto.class.getDeclaredField("DEFAULT_ENCRYPTION_KEY_PATH"); + field.setAccessible(true); + Field modifiersField = Field.class.getDeclaredField("modifiers"); + modifiersField.setAccessible(true); + modifiersField.setInt(field, field.getModifiers() & ~Modifier.FINAL); + field.set(Crypto.class, new File("src/test/resources/test_encryption_key").getAbsolutePath()); + Crypto.loadDefaultKey(); + } + + @Test + public void testNamedKeyEncryptDecrypt() { + Crypto.loadKey("TEST_NAMED_KEY", TEST_NAMED_ENCRYPTIOON_KEY_PATH); + byte[] ciphertext = Crypto.encryptData(TEST_MESSAGE.getBytes()); + assertTrue(!new String(ciphertext).contentEquals(TEST_MESSAGE)); + String plaintext = new String(Crypto.decryptData(ciphertext)); + assertEquals(plaintext, TEST_MESSAGE); + } + + @Test + public void testNamedKeyEncryptNotUsingDefaultKey() { + assertThrows(AEADBadTagException.class, () -> { + Crypto.loadKey(TEST_NAMED_KEY, TEST_NAMED_ENCRYPTIOON_KEY_PATH); + byte[] ciphertext = Crypto.encryptData(TEST_NAMED_KEY, TEST_MESSAGE.getBytes()); + assertFalse(new String(ciphertext).contentEquals(TEST_MESSAGE)); + Crypto.decryptData(ciphertext); + }); + } + + @Test + public void testNamedKeyDecryptNotUsingDefaultKey() { + assertThrows(AEADBadTagException.class, () -> { + Crypto.loadKey(TEST_NAMED_KEY, TEST_NAMED_ENCRYPTIOON_KEY_PATH); + byte[] ciphertext = Crypto.encryptData(TEST_MESSAGE.getBytes()); + assertTrue(!new String(ciphertext).contentEquals(TEST_MESSAGE)); + Crypto.decryptData(TEST_NAMED_KEY, ciphertext); + }); + } +} diff --git a/services/pic-sure-hpds/common/src/test/resources/test_encryption_key b/services/pic-sure-hpds/common/src/test/resources/test_encryption_key new file mode 100644 index 000000000..80bb1b63e --- /dev/null +++ b/services/pic-sure-hpds/common/src/test/resources/test_encryption_key @@ -0,0 +1 @@ +0000000000000000 \ No newline at end of file diff --git a/services/pic-sure-hpds/common/src/test/resources/test_named_encryption_key b/services/pic-sure-hpds/common/src/test/resources/test_named_encryption_key new file mode 100644 index 000000000..d3720b6d6 --- /dev/null +++ b/services/pic-sure-hpds/common/src/test/resources/test_named_encryption_key @@ -0,0 +1 @@ +1111111111111111 \ No newline at end of file diff --git a/services/pic-sure-hpds/data/pom.xml b/services/pic-sure-hpds/data/pom.xml new file mode 100644 index 000000000..abcff078a --- /dev/null +++ b/services/pic-sure-hpds/data/pom.xml @@ -0,0 +1,59 @@ + + + 4.0.0 + + pic-sure-hpds + edu.harvard.hms.dbmi.avillach.hpds + ${revision} + + + data + + data + + + + + + edu.harvard.hms.dbmi.avillach.hpds + common + + + com.google.guava + guava + + + org.apache.commons + commons-csv + + + com.fasterxml.jackson.core + jackson-databind + + + de.siegmar + fastcsv + + + com.oracle.database.jdbc + ojdbc10 + + + org.springframework + spring-jdbc + + + software.amazon.awssdk + s3 + + + + commons-logging + commons-logging + + + + + + diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/BucketIndexBySample.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/BucketIndexBySample.java new file mode 100644 index 000000000..afa68be0d --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/BucketIndexBySample.java @@ -0,0 +1,191 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; + +import java.io.*; +import java.math.BigInteger; +import java.util.*; +import java.util.concurrent.ConcurrentHashMap; +import java.util.stream.Collectors; + +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedJavaIndexedStorage; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedByteIndexedStorage; + +public class BucketIndexBySample implements Serializable { + private static final long serialVersionUID = -1230735595028630687L; + private static final String STORAGE_FILE_NAME = "BucketIndexBySampleStorage.javabin"; + + List patientIds; + ArrayList contigSet; + + transient Logger log = LoggerFactory.getLogger(BucketIndexBySample.class); + + /** + * Threadsafe Map of patientNum to a BigInteger which acts as a bitmask of the buckets in which each patient has a variant. The bits in + * the BigInteger are indexed by the bucketList. To find the offset of a bucket's bit in the mask use + * patientBucketMask.get(patientId).testBit(Collections + */ + private FileBackedByteIndexedStorage patientBucketMasks; + + /** + * ArrayList containing all bucket keys in the dataset used as an index for the patientBucketMask offsets. This list is in natural sort + * order so Collections.binarySearch should be used instead of indexOf when finding the offset of a given bucket. + */ + private ArrayList bucketList = new ArrayList(); + + public BucketIndexBySample(VariantStore variantStore, String storageDir) throws FileNotFoundException { + log.info("Creating new Bucket Index by Sample"); + final String storageFileStr = storageDir + STORAGE_FILE_NAME; + + contigSet = new ArrayList(variantStore.getVariantMaskStorage().keySet()); + + // Create a bucketList, containing keys for all buckets in the variantStore + for (String contig : contigSet) { + FileBackedByteIndexedStorage> contigStore = + variantStore.getVariantMaskStorage().get(contig); + if (contigStore != null && contigStore.keys() != null) { + bucketList.addAll(contigStore.keys().stream().map((Integer bucket) -> { + return contig + ":" + bucket; + }).collect(Collectors.toList())); + log.debug("Found " + contigStore.keys().size() + " buckets in contig " + contig); + } else { + log.debug("null entry for contig " + contig); + } + } + + // bucketList must be sorted so we can later use binarySearch to find offsets for specific buckets + // in the patientBucketMask records + Collections.sort(bucketList); + + log.debug("Found " + bucketList.size() + " total buckets"); + + // get all patientIds as Integers, eventually this should be fixed in variantStore so they are + // Integers to begin with, which would mean reloading all variant data everywhere so that will + // have to wait. + patientIds = Arrays.stream(variantStore.getPatientIds()).map(id -> { + return Integer.parseInt(id); + }).collect(Collectors.toList()); + + // create empty char arrays for each patient + char[][] patientBucketCharMasks = new char[patientIds.size()][bucketList.size()]; + for (int x = 0; x < patientBucketCharMasks.length; x++) { + patientBucketCharMasks[x] = emptyBucketMaskChar(); + } + contigSet.parallelStream().forEach((contig) -> { + FileBackedByteIndexedStorage> contigStore = + variantStore.getVariantMaskStorage().get(contig); + if (contigStore != null && contigStore.keys() != null) { + contigStore.keys().stream().forEach((Integer bucket) -> { + String bucketKey = contig + ":" + bucket; + + // Create a bitmask with 1 values for each patient who has any variant in this bucket + VariantMask[] patientMaskForBucket = {new VariantMaskSparseImpl(Set.of())}; + contigStore.get(bucket).values().forEach((VariableVariantMasks masks) -> { + if (masks.heterozygousMask != null) { + patientMaskForBucket[0] = patientMaskForBucket[0].union(masks.heterozygousMask); + } + // add hetreo no call bits to mask + if (masks.heterozygousNoCallMask != null) { + patientMaskForBucket[0] = patientMaskForBucket[0].union(masks.heterozygousNoCallMask); + } + if (masks.homozygousMask != null) { + patientMaskForBucket[0] = patientMaskForBucket[0].union(masks.homozygousMask); + } + }); + + // For each patient set the patientBucketCharMask entry to 0 or 1 if they have a variant in the bucket. + int indexOfBucket = Collections.binarySearch(bucketList, bucketKey) + 2; // patientBucketCharMasks has bookend bits + for (int x = 0; x < patientIds.size(); x++) { + if (patientMaskForBucket[0].testBit(x)) { + patientBucketCharMasks[x][indexOfBucket] = '1'; + } else { + patientBucketCharMasks[x][indexOfBucket] = '0'; + } + } + }); + } else { + log.info("null entry for contig " + contig); + } + log.info("completed contig " + contig); + }); + + // populate patientBucketMasks with bucketMasks for each patient + patientBucketMasks = new FileBackedJavaIndexedStorage(Integer.class, BigInteger.class, new File(storageFileStr)); + + int[] processedPatients = new int[1]; + patientIds.parallelStream().forEach((patientId) -> { + BigInteger patientMask = new BigInteger(new String(patientBucketCharMasks[patientIds.indexOf(patientId)]), 2); + patientBucketMasks.put(patientId, patientMask); + processedPatients[0] += 1; + int processedPatientsCount = processedPatients[0]; + if (processedPatientsCount % 1000 == 0) { + log.debug("wrote " + processedPatientsCount + " patient bucket masks"); + } + }); + patientBucketMasks.complete(); + log.info("Done creating patient bucket masks"); + } + + /** + * Given a set of variants and a set of patientNums, filter out variants which no patients in the patientSet have any variant in the + * bucket. This operation is extremely fast and cuts down on processing by excluding variants for queries where not all patients are + * included. + * + * @param variantSet + * @param patientSet + * @return + * @throws IOException + */ + public Set filterVariantSetForPatientSet(Set variantSet, Collection patientSet) throws IOException { + + BigInteger patientBucketMask = patientSet.stream().findFirst().map(id -> patientBucketMasks.get(id)) + .orElseGet(() -> new BigInteger(new String(emptyBucketMaskChar()), 2)); + + BigInteger _defaultMask = patientBucketMask; + List patientBucketmasksForSet = + patientSet.parallelStream().map((patientNum) -> patientBucketMasks.get(patientNum)).collect(Collectors.toList()); + for (BigInteger patientMask : patientBucketmasksForSet) { + patientBucketMask = patientMask.or(patientBucketMask); + } + + BigInteger _bucketMask = patientBucketMask; + int maxIndex = bucketList.size() - 1; // use to invert testBit index + return variantSet.parallelStream().filter((variantSpec) -> { + String bucketKey = variantSpec.split(",")[0] + ":" + (Integer.parseInt(variantSpec.split(",")[1]) / 1000); + + // testBit uses inverted indexes include +2 offset for bookends + int bucketKeyIndex = Collections.binarySearch(bucketList, bucketKey); + if (bucketKeyIndex < 0) { + return false; + } + return _bucketMask.testBit(maxIndex - bucketKeyIndex + 2); + }).collect(Collectors.toSet()); + } + + private char[] _emptyBucketMaskChar = null; + + /** + * Produce an empty patientBucketMask char[] by cloning a momoized empty patientBucketMask after the first has been created. + * + * @return + */ + private char[] emptyBucketMaskChar() { + if (_emptyBucketMaskChar == null) { + char[] bucketMaskChar = new char[bucketList.size() + 4]; + bucketMaskChar[0] = '1'; + bucketMaskChar[1] = '1'; + bucketMaskChar[bucketMaskChar.length - 1] = '1'; + bucketMaskChar[bucketMaskChar.length - 2] = '1'; + for (int x = 2; x < bucketMaskChar.length - 2; x++) { + bucketMaskChar[x] = '0'; + } + _emptyBucketMaskChar = bucketMaskChar; + } + return _emptyBucketMaskChar.clone(); + } + + public void updateStorageDirectory(File storageDirectory) { + patientBucketMasks.updateStorageDirectory(storageDirectory); + } +} diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/CompressedIndex.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/CompressedIndex.java new file mode 100644 index 000000000..224b9273b --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/CompressedIndex.java @@ -0,0 +1,180 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; + +import java.io.*; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Set; +import java.util.SortedMap; +import java.util.TreeMap; +import java.util.TreeSet; +import java.util.stream.Collectors; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; + +import org.apache.commons.io.output.ByteArrayOutputStream; + +import com.google.common.collect.Lists; +import com.google.common.collect.Range; + +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedByteIndexedStorage; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +public class CompressedIndex implements Serializable { + + /** + * + */ + private static final long serialVersionUID = 5089713203903957829L; + private static final Logger log = LoggerFactory.getLogger(CompressedIndex.class); + public Float min = Float.MAX_VALUE, max = Float.MIN_VALUE; + private HashMap, byte[]> compressedRangeMap; + private int valueCount; + + public TreeMap> buildContinuousValuesMap(FileBackedByteIndexedStorage allValues) { + TreeMap> continuousValueMap = new TreeMap<>(); + for (String key : allValues.keys()) { + try { + Float DoubleValue = Float.parseFloat(key.trim()); + TreeSet currentValues = continuousValueMap.get(DoubleValue); + if (currentValues == null) { + currentValues = new TreeSet<>(); + continuousValueMap.put(DoubleValue, currentValues); + } + currentValues.add(key); + continuousValueMap.put(DoubleValue, currentValues); + setMinAndMax(DoubleValue); + } catch (NumberFormatException e) { + String[] valuesInKey = key.split(","); + if (valuesInKey.length > 1) { + for (String value : valuesInKey) { + try { + Float DoubleValue = Float.parseFloat(value.trim()); + TreeSet currentValues = continuousValueMap.get(DoubleValue); + if (currentValues == null) { + currentValues = new TreeSet<>(); + continuousValueMap.put(DoubleValue, currentValues); + } + currentValues.add(key); + continuousValueMap.put(DoubleValue, currentValues); + setMinAndMax(DoubleValue); + } catch (NumberFormatException e3) { + log.info("Unable to parse value : " + value.trim()); + } + } + } + } + } + this.setValueCount(continuousValueMap.size()); + return continuousValueMap; + } + + private void setMinAndMax(Float DoubleValue) { + if (min > DoubleValue) { + min = DoubleValue; + } + if (max < DoubleValue) { + max = DoubleValue; + } + } + + public void buildIndex(TreeMap> continuousValueMap) { + Set continuousValuesMapKeys = new TreeSet(continuousValueMap.keySet()); + List> partitions = Lists.partition(new ArrayList(continuousValuesMapKeys), 1000); + HashMap, TreeMap>> rangeMap = new HashMap<>(); + List partition = partitions.get(0); + SortedMap> partitionMap = continuousValueMap.subMap(partition.get(0), partition.get(partition.size() - 1)); + rangeMap.put(Range.openClosed(partition.get(0), partition.get(partition.size() - 1)), new TreeMap<>(partitionMap)); + for (int x = 0; x < partitions.size() - 1; x++) { + partition = partitions.get(x); + partitionMap = continuousValueMap.subMap(partition.get(0), partition.get(partition.size() - 1)); + rangeMap.put(Range.openClosed(partition.get(0), partitions.get(x + 1).get(0)), new TreeMap<>(partitionMap)); + } + partition = partitions.get(partitions.size() - 1); + partitionMap = continuousValueMap.subMap(partition.get(0), partition.get(partition.size() - 1)); + rangeMap.put(Range.openClosed(partition.get(0), partition.get(partition.size() - 1)), new TreeMap<>(partitionMap)); + compressedRangeMap = new HashMap<>(rangeMap.entrySet().stream().collect(Collectors.toMap((key) -> { + return key.getKey(); + }, (part) -> { + byte[] compressed = null; + try ( + ByteArrayOutputStream baos = new ByteArrayOutputStream(); GZIPOutputStream gzos = + new GZIPOutputStream(baos); ObjectOutputStream out = new ObjectOutputStream(gzos); + ) { + out.writeObject(part.getValue()); + out.flush(); + out.close(); + gzos.flush(); + gzos.close(); + compressed = baos.toByteArray(); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + return compressed; + }))); + } + + public List getValuesInRange(Range targetRange) { + + log.debug("Getting valuesInRange : " + targetRange); + // Get a list of ranges that are connected to the target range + List connectedRanges = compressedRangeMap.keySet().stream().filter((range) -> { + return range.isConnected(targetRange); + }).collect(Collectors.toList()); + + // Get a list of ranges that enclose the target range completely + List enclosingRanges = connectedRanges.stream().filter((range) -> { + return targetRange.encloses(range); + }).collect(Collectors.toList()); + + List valuesInRange = new ArrayList<>(); + + // Add all variants from enclosing ranges + enclosingRanges.forEach(range -> { + TreeMap> continousValueMap = retrieveRangeMap(range); + continousValueMap.values().forEach(variantSet -> { + valuesInRange.addAll(variantSet); + }); + }); + + // We already added all variants in the enclosing ranges + connectedRanges.removeAll(enclosingRanges); + + connectedRanges.forEach(range -> { + TreeMap> continousValueMap = retrieveRangeMap(range); + log.debug("Searching within : " + range.lowerEndpoint() + " : " + range.upperEndpoint()); + continousValueMap.entrySet().stream().forEach(entry -> { + if (targetRange.contains(entry.getKey())) { + log.debug("Adding : " + entry.getValue().first() + " : " + entry.getValue().last()); + valuesInRange.addAll(entry.getValue()); + } + }); + }); + return valuesInRange; + } + + private TreeMap> retrieveRangeMap(Range range) { + TreeMap> continousValueMap = null; + try ( + ByteArrayInputStream bais = new ByteArrayInputStream(compressedRangeMap.get(range)); GZIPInputStream gzis = + new GZIPInputStream(bais); ObjectInputStream ois = new ObjectInputStream(gzis); + ) { + continousValueMap = (TreeMap>) ois.readObject(); + } catch (IOException e) { + throw new UncheckedIOException(e); + } catch (ClassNotFoundException e) { + throw new RuntimeException(e); + } + return continousValueMap; + } + + public int getValueCount() { + return valueCount; + } + + public void setValueCount(int valueCount) { + this.valueCount = valueCount; + } + +} diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/FileBackedByteIndexedInfoStore.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/FileBackedByteIndexedInfoStore.java new file mode 100644 index 000000000..35b6de942 --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/FileBackedByteIndexedInfoStore.java @@ -0,0 +1,156 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; + +import java.io.*; +import java.util.*; +import java.util.concurrent.ConcurrentHashMap; +import java.util.concurrent.ConcurrentSkipListSet; +import java.util.stream.Collectors; +import java.util.zip.GZIPOutputStream; + +import edu.harvard.hms.dbmi.avillach.hpds.data.storage.FileBackedStorageVariantIndexImpl; +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedByteIndexedStorage; +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedJavaIndexedStorage; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +public class FileBackedByteIndexedInfoStore implements Serializable { + + private static final long serialVersionUID = 6478256007934827195L; + private static final Logger log = LoggerFactory.getLogger(FileBackedByteIndexedInfoStore.class); + public final String column_key; + public final String description; + public boolean isContinuous; + public Float min = Float.MAX_VALUE, max = Float.MIN_VALUE; + + private FileBackedByteIndexedStorage allValues; + public TreeMap> continuousValueMap; + + public CompressedIndex continuousValueIndex; + + public FileBackedByteIndexedStorage getAllValues() { + return allValues; + } + + public List search(String term) { + if (isContinuous) { + return new ArrayList(); + } else { + return allValues.keys().stream().filter((value) -> { + String lowerTerm = term.toLowerCase(Locale.ENGLISH); + return value.toLowerCase(Locale.ENGLISH).contains(lowerTerm); + }).collect(Collectors.toList()); + } + } + + public void addEntry(String value, Integer[] variantIds) throws IOException { + allValues.put(value, variantIds); + } + + + public void complete() { + this.allValues.complete(); + } + + public FileBackedByteIndexedInfoStore(File storageFolder, InfoStore infoStore) throws IOException { + this.allValues = new FileBackedStorageVariantIndexImpl(new File(storageFolder, infoStore.column_key + "_infoStoreStorage.javabin")); + this.description = infoStore.description; + this.column_key = infoStore.column_key; + this.isContinuous = infoStore.isNumeric(); + this.allValues.open(); + if (isContinuous) { + normalizeNumericStore(infoStore); + } + TreeSet sortedKeys = new TreeSet(infoStore.allValues.keySet()); + log.debug(infoStore.column_key + " : " + sortedKeys.size() + " values"); + int x = 0; + for (String key : sortedKeys) { + if (key.contentEquals(".")) { + log.debug("Skipping . value for " + infoStore.column_key); + } else { + if (x % 10000 == 0) { + log.debug(infoStore.column_key + " " + ((((double) x) / sortedKeys.size()) * 100) + "% done"); + } + ConcurrentSkipListSet variantIds = infoStore.allValues.get(key); + addEntry(key, variantIds.toArray(new Integer[variantIds.size()])); + x++; + } + } + this.allValues.complete(); + if (isContinuous) { + log.debug(this.column_key + " is continuous, building continuousValueIndex and nulling continuousValueMap."); + this.continuousValueIndex = new CompressedIndex(); + TreeMap> continuousValueMap = this.continuousValueIndex.buildContinuousValuesMap(this.allValues); + this.continuousValueIndex.buildIndex(continuousValueMap); + this.continuousValueMap = null; + } + } + + private static void normalizeNumericStore(InfoStore store) { + TreeSet allKeys = new TreeSet(store.allValues.keySet()); + + ConcurrentHashMap> normalizedValues = new ConcurrentHashMap<>(); + for (String key : allKeys) { + String[] keys = key.split(","); + ConcurrentSkipListSet variantIds = store.allValues.get(key); + if (key.contentEquals(".")) { + // don't add it + } else if (keyHasMultipleValues(keys)) { + for (String value : keys) { + if (value.contentEquals(".")) { + + } else { + ConcurrentSkipListSet normalizedVariantIds = normalizedValues.get(value); + if (normalizedVariantIds == null) { + normalizedVariantIds = variantIds; + } else { + normalizedVariantIds.addAll(variantIds); + } + normalizedValues.put(value, normalizedVariantIds); + } + } + } else { + if (key.contentEquals(".")) { + + } else { + ConcurrentSkipListSet normalizedVariantIds = normalizedValues.get(key); + if (normalizedVariantIds == null) { + normalizedVariantIds = variantIds; + } else { + normalizedVariantIds.addAll(variantIds); + } + normalizedValues.put(key, normalizedVariantIds); + } + } + + } + store.allValues = normalizedValues; + } + + private static boolean keyHasMultipleValues(String[] keys) { + int x = 0; + for (String k : keys) { + if (k == null || k.isEmpty()) { + + } else { + x++; + } + } + return x > 1; + } + + public void updateStorageDirectory(File storageDirectory) { + allValues.updateStorageDirectory(storageDirectory); + } + + public void write(File outputFile) { + try ( + FileOutputStream fos = new FileOutputStream(outputFile); GZIPOutputStream gzos = + new GZIPOutputStream(fos); ObjectOutputStream oos = new ObjectOutputStream(gzos); + ) { + oos.writeObject(this); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + } +} + diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/InfoColumnMeta.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/InfoColumnMeta.java new file mode 100644 index 000000000..189a22be1 --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/InfoColumnMeta.java @@ -0,0 +1,5 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; + +public record InfoColumnMeta(String key, String description, boolean continuous, Float min, Float max) { + +} diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/InfoStore.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/InfoStore.java new file mode 100644 index 000000000..8669df967 --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/InfoStore.java @@ -0,0 +1,91 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.List; +import java.util.Locale; +import java.util.concurrent.ConcurrentHashMap; +import java.util.concurrent.ConcurrentHashMap.KeySetView; +import java.util.concurrent.ConcurrentSkipListSet; +import java.util.stream.Collectors; + +public class InfoStore implements Serializable { + + private static final long serialVersionUID = 6478256007934827195L; + private static final Logger log = LoggerFactory.getLogger(InfoStore.class); + public final String column_key; + public final String description; + + public ConcurrentHashMap> allValues = new ConcurrentHashMap<>(); + private String prefix; + + public List search(String term) { + if (isNumeric()) { + return new ArrayList(); + } else { + return allValues.keySet().stream().filter((value) -> { + String lowerTerm = term.toLowerCase(Locale.ENGLISH); + return value.toLowerCase(Locale.ENGLISH).contains(lowerTerm); + }).collect(Collectors.toList()); + } + } + + public InfoStore(String description, String delimiter, String key) { + this.prefix = key + "="; + this.description = description; + this.column_key = key; + } + + public boolean isNumeric() { + int nonNumericCount = 0; + int numericCount = 0; + log.debug("Testing for numeric : " + this.column_key + " : " + allValues.size() + " values"); + KeySetView> allKeys = allValues.keySet(); + for (String key : allKeys) { + try { + Double.parseDouble(key); + numericCount++; + } catch (NumberFormatException e) { + String[] keys = key.split(","); + for (String key2 : keys) { + try { + Double.parseDouble(key2); + numericCount++; + } catch (NumberFormatException e2) { + if (key.contentEquals(".")) { + nonNumericCount++; + } + } + } + } + if (nonNumericCount > 1) { + log.debug(this.column_key + " is not numeric"); + return false; + } + if (numericCount > 10000 || numericCount > (allKeys.size() / 2)) { + log.debug(this.column_key + " is numeric"); + return true; + } + } ; + log.debug(this.column_key + " is not numeric"); + return false; + } + + public void processRecord(Integer variantId, String[] infoValues) { + for (String value : infoValues) { + if (value.startsWith(prefix)) { + String valueWithoutkey = value.substring(prefix.length()); + ConcurrentSkipListSet entriesForValue = allValues.get(valueWithoutkey); + if (entriesForValue == null) { + entriesForValue = new ConcurrentSkipListSet<>(); + allValues.put(valueWithoutkey, entriesForValue); + } + entriesForValue.add(variantId); + } + } + } + +} diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariableVariantMasks.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariableVariantMasks.java new file mode 100644 index 000000000..cebb3fffd --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariableVariantMasks.java @@ -0,0 +1,263 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; + +import com.fasterxml.jackson.annotation.JsonInclude; +import com.fasterxml.jackson.annotation.JsonProperty; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.Serializable; +import java.math.BigInteger; +import java.util.*; +import java.util.concurrent.ConcurrentHashMap; +import java.util.stream.Collectors; + +public class VariableVariantMasks implements Serializable { + + private static Logger log = LoggerFactory.getLogger(VariableVariantMasks.class); + + private static final long serialVersionUID = 6225420483804601477L; + private static final String oneone = "11"; + private static final char one = '1'; + private static final char zero = '0'; + private static final String hetero = "0/1"; + private static final String heteroDel = "1/0"; + private static final String heteroPhased = "0|1"; + private static final String heteroPhased2 = "1|0"; + private static final String homo = "1/1"; + private static final String homoPhased = "1|1"; + private static final String homoNoCall = "./."; + private static final String heteroNoCall = "./1"; + + private static Map emptyBitmaskMap = new ConcurrentHashMap<>(); + + public static int SPARSE_VARIANT_THRESHOLD = 5; + + /* + * These indices result from the char values of the 3 characters in a VCF sample record summed as integers % 7 + * + * This allows us to not actually do string comparisons, instead we add 3 values, do one modulus operation, then use the result as the + * index into the result array. + */ + + // ./0 = (46 + 47 + 48) % 7 = 1 + // 0|. = (48 + 124 + 46) % 7 = 1 + // .|0 = (46 + 124 + 48) % 7 = 1 + public static final int HETERO_NOCALL_REF_CHAR_INDEX = 1; + + // ./1 = (46 + 47 + 49) % 7 = 2 + // 1|. = (49 + 124 + 46) % 7 = 2 + // .|1 = (46 + 124 + 49) % 7 = 2 + // ./1 = (46 + 47 + 49) % 7 = 2 + // 1|. = (49 + 124 + 46) % 7 = 2 + // .|1 = (46 + 124 + 49) % 7 = 2 + public static final int HETERO_NOCALL_VARIANT_CHAR_INDEX = 2; + + // 0/0 = (48 + 47 + 48) % 7 = 3 + // 0|0 = (48 + 124 + 48) % 7 = 3 + public static final int ZERO_ZERO_CHAR_INDEX = 3; + + // 0/1 = (48 + 47 + 49) % 7 = 4 + // 1|0 = (49 + 124 + 48) % 7 = 4 + // 0|1 = (48 + 124 + 49) % 7 = 4 + public static final int ZERO_ONE_CHAR_INDEX = 4; + + // 1/1 = (49 + 47 + 49) % 7 = 5 + // 1|1 = (49 + 124 + 49) % 7 = 5 + public static final int ONE_ONE_CHAR_INDEX = 5; + + // ./. = (46 + 47 + 46) % 7 = 6 + // .|. = (46 + 124 + 46) % 7 = 6 + public static final int HOMO_NOCALL_CHAR_INDEX = 6; + + public VariableVariantMasks(char[][] maskValues) { + String heteroMaskStringRaw = new String(maskValues[ZERO_ONE_CHAR_INDEX]); + String homoMaskStringRaw = new String(maskValues[ONE_ONE_CHAR_INDEX]); + String heteroNoCallMaskStringRaw = new String(maskValues[HETERO_NOCALL_VARIANT_CHAR_INDEX]); + String homoNoCallMaskStringRaw = new String(maskValues[HOMO_NOCALL_CHAR_INDEX]); + + heterozygousMask = variantMaskFromRawString(heteroMaskStringRaw); + homozygousMask = variantMaskFromRawString(homoMaskStringRaw); + heterozygousNoCallMask = variantMaskFromRawString(heteroNoCallMaskStringRaw); + homozygousNoCallMask = variantMaskFromRawString(homoNoCallMaskStringRaw); + } + + private VariantMask variantMaskFromRawString(String maskStringRaw) { + if (!maskStringRaw.contains("1")) { + return null; + } + + VariantMask variantMask; + BigInteger bitmask = new BigInteger(oneone + new StringBuilder(maskStringRaw).reverse() + oneone, 2); + if (bitmask.bitCount() - 4 > VariableVariantMasks.SPARSE_VARIANT_THRESHOLD) { + variantMask = new VariantMaskBitmaskImpl(bitmask); + } else { + Set patientIndexes = new HashSet<>(); + for (int i = 0; i < bitmask.bitLength() - 4; i++) { + // i + 2 because the mask is padded with 2 bits on each end + if (bitmask.testBit(i + 2)) { + patientIndexes.add(i); + } + } + variantMask = new VariantMaskSparseImpl(patientIndexes); + } + return variantMask; + } + + public VariableVariantMasks() {} + + @JsonProperty("ho") + @JsonInclude(JsonInclude.Include.NON_NULL) + public VariantMask homozygousMask; + + @JsonProperty("he") + @JsonInclude(JsonInclude.Include.NON_NULL) + public VariantMask heterozygousMask; + + @JsonProperty("hon") + @JsonInclude(JsonInclude.Include.NON_NULL) + public VariantMask homozygousNoCallMask; + + @JsonProperty("hen") + @JsonInclude(JsonInclude.Include.NON_NULL) + public VariantMask heterozygousNoCallMask; + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + VariableVariantMasks that = (VariableVariantMasks) o; + return Objects.equals(homozygousMask, that.homozygousMask) && Objects.equals(heterozygousMask, that.heterozygousMask) + && Objects.equals(homozygousNoCallMask, that.homozygousNoCallMask) + && Objects.equals(heterozygousNoCallMask, that.heterozygousNoCallMask); + } + + @Override + public int hashCode() { + return Objects.hash(homozygousMask, heterozygousMask, homozygousNoCallMask, heterozygousNoCallMask); + } + + public static BigInteger emptyBitmask(int length) { + BigInteger emptyBitmask = emptyBitmaskMap.get(length); + if (emptyBitmask == null) { + String emptyVariantMask = ""; + for (int i = 0; i < length; i++) { + emptyVariantMask = emptyVariantMask + "0"; + } + BigInteger newEmptyBitmask = new BigInteger("11" + emptyVariantMask + "11", 2); + emptyBitmaskMap.put(length, newEmptyBitmask); + return newEmptyBitmask; + } + return emptyBitmask; + } + + public static VariableVariantMasks append(VariableVariantMasks masks1, int length1, VariableVariantMasks masks2, int length2) { + VariableVariantMasks appendedMasks = new VariableVariantMasks(); + appendedMasks.homozygousMask = appendMask(masks1.homozygousMask, masks2.homozygousMask, length1, length2); + appendedMasks.heterozygousMask = appendMask(masks1.heterozygousMask, masks2.heterozygousMask, length1, length2); + appendedMasks.homozygousNoCallMask = appendMask(masks1.homozygousNoCallMask, masks2.homozygousNoCallMask, length1, length2); + appendedMasks.heterozygousNoCallMask = appendMask(masks1.heterozygousNoCallMask, masks2.heterozygousNoCallMask, length1, length2); + return appendedMasks; + } + + public static VariantMask appendMask(VariantMask variantMask1, VariantMask variantMask2, int length1, int length2) { + if (variantMask1 == null) { + variantMask1 = VariantMask.emptyInstance(); + } + if (variantMask2 == null) { + variantMask2 = VariantMask.emptyInstance(); + } + if (variantMask1.equals(VariantMask.emptyInstance()) && variantMask2.equals(VariantMask.emptyInstance())) { + return null; + } + + if (variantMask1 instanceof VariantMaskSparseImpl) { + if (variantMask2 instanceof VariantMaskSparseImpl) { + return append((VariantMaskSparseImpl) variantMask1, (VariantMaskSparseImpl) variantMask2, length1, length2); + } else if (variantMask2 instanceof VariantMaskBitmaskImpl) { + return append((VariantMaskSparseImpl) variantMask1, (VariantMaskBitmaskImpl) variantMask2, length1, length2); + } else { + throw new RuntimeException("Unknown VariantMask implementation"); + } + } else if (variantMask1 instanceof VariantMaskBitmaskImpl) { + if (variantMask2 instanceof VariantMaskSparseImpl) { + return append((VariantMaskBitmaskImpl) variantMask1, (VariantMaskSparseImpl) variantMask2, length1, length2); + } else if (variantMask2 instanceof VariantMaskBitmaskImpl) { + return append((VariantMaskBitmaskImpl) variantMask1, (VariantMaskBitmaskImpl) variantMask2, length1, length2); + } else { + throw new RuntimeException("Unknown VariantMask implementation"); + } + } else { + throw new RuntimeException("Unknown VariantMask implementation"); + } + } + + private static VariantMask append(VariantMaskSparseImpl variantMask1, VariantMaskBitmaskImpl variantMask2, int length1, int length2) { + BigInteger mask1 = emptyBitmask(length1); + for (Integer patientIndex : variantMask1.patientIndexes) { + mask1 = mask1.setBit(patientIndex + 2); + } + String binaryMask1 = mask1.toString(2); + + String binaryMask2 = variantMask2.bitmask.toString(2); + if (binaryMask2.length() - 4 != length2) { + throw new IllegalArgumentException("Bitmask does not match length (" + length2 + "): " + variantMask2.bitmask); + } + + String appendedString = binaryMask2.substring(0, binaryMask2.length() - 2) + binaryMask1.substring(2); + return new VariantMaskBitmaskImpl(new BigInteger(appendedString, 2)); + } + + private static VariantMask append(VariantMaskBitmaskImpl variantMask1, VariantMaskSparseImpl variantMask2, int length1, int length2) { + String binaryMask1 = variantMask1.bitmask.toString(2); + if (binaryMask1.length() - 4 != length1) { + throw new IllegalArgumentException("Bitmask does not match length (" + length1 + "): " + variantMask1.bitmask); + } + + BigInteger mask2 = emptyBitmask(length2); + for (Integer patientId : variantMask2.patientIndexes) { + mask2 = mask2.setBit(patientId + 2); + } + String binaryMask2 = mask2.toString(2); + + String appendedString = binaryMask2.substring(0, binaryMask2.length() - 2) + binaryMask1.substring(2); + return new VariantMaskBitmaskImpl(new BigInteger(appendedString, 2)); + } + + private static VariantMask append(VariantMaskBitmaskImpl variantMask1, VariantMaskBitmaskImpl variantMask2, int length1, int length2) { + String binaryMask1 = variantMask1.bitmask.toString(2); + String binaryMask2 = variantMask2.bitmask.toString(2); + + if (binaryMask1.length() - 4 != length1) { + throw new IllegalArgumentException("Bitmask does not match length (" + length1 + "): " + variantMask1.bitmask); + } + if (binaryMask2.length() - 4 != length2) { + throw new IllegalArgumentException("Bitmask does not match length (" + length2 + "): " + variantMask2.bitmask); + } + + String appendedString = binaryMask2.substring(0, binaryMask2.length() - 2) + binaryMask1.substring(2); + BigInteger bitmask = new BigInteger(appendedString, 2); + return new VariantMaskBitmaskImpl(bitmask); + } + + private static VariantMask append(VariantMaskSparseImpl variantMask1, VariantMaskSparseImpl variantMask2, int length1, int length2) { + if (variantMask1.patientIndexes.size() + variantMask2.patientIndexes.size() > SPARSE_VARIANT_THRESHOLD) { + BigInteger mask = emptyBitmask(length1 + length2); + for (Integer patientId : variantMask1.patientIndexes) { + mask = mask.setBit(patientId + 2); + } + // We start writing mask 2 where mask 1 ends. So the 0th index of mask 2 is now following the last bit of mask 1 + for (Integer patientId : variantMask2.patientIndexes) { + mask = mask.setBit(patientId + length1 + 2); + } + return new VariantMaskBitmaskImpl(mask); + } else { + Set patientIndexSet = new HashSet<>(); + patientIndexSet.addAll(variantMask1.patientIndexes); + // The indexes for mask 2 are shifted by the length of mask 1, corresponding to the corresponding patient id array + // for mask 2 being appended to those of mask 1 + patientIndexSet.addAll(variantMask2.patientIndexes.stream().map(i -> i + length1).collect(Collectors.toSet())); + return new VariantMaskSparseImpl(patientIndexSet); + } + } + +} diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMask.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMask.java new file mode 100644 index 000000000..376fcc432 --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMask.java @@ -0,0 +1,33 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; + +import com.fasterxml.jackson.annotation.JsonSubTypes; +import com.fasterxml.jackson.annotation.JsonTypeInfo; + +import java.math.BigInteger; +import java.util.List; +import java.util.Set; +import java.util.stream.Collectors; + +@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type", defaultImpl = VariantMaskBitmaskImpl.class) +@JsonSubTypes( + {@JsonSubTypes.Type(value = VariantMaskBitmaskImpl.class, name = "b"), + @JsonSubTypes.Type(value = VariantMaskSparseImpl.class, name = "s")} +) +public interface VariantMask { + + VariantMask intersection(VariantMask variantMask); + + VariantMask union(VariantMask variantMask); + + boolean testBit(int bit); + + int bitCount(); + + static VariantMask emptyInstance() { + return new VariantMaskSparseImpl(Set.of()); + } + + Set patientMaskToPatientIdSet(List patientIds); + + boolean isEmpty(); +} diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMaskBitmaskImpl.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMaskBitmaskImpl.java new file mode 100644 index 000000000..8fa2922ce --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMaskBitmaskImpl.java @@ -0,0 +1,113 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; + +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonIgnore; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.databind.annotation.JsonSerialize; +import com.fasterxml.jackson.databind.ser.std.ToStringSerializer; + +import java.math.BigInteger; +import java.util.HashSet; +import java.util.List; +import java.util.Objects; +import java.util.Set; + +public class VariantMaskBitmaskImpl implements VariantMask { + + + @JsonProperty("mask") + @JsonSerialize(using = ToStringSerializer.class) + protected final BigInteger bitmask; + + public BigInteger getBitmask() { + return bitmask; + } + + @JsonCreator + public VariantMaskBitmaskImpl(@JsonProperty("mask") String stringMask) { + this.bitmask = new BigInteger(stringMask); + } + + public VariantMaskBitmaskImpl(BigInteger bitmask) { + this.bitmask = bitmask; + } + + @Override + public VariantMask intersection(VariantMask variantMask) { + if (variantMask instanceof VariantMaskBitmaskImpl) { + return intersection((VariantMaskBitmaskImpl) variantMask); + } else if (variantMask instanceof VariantMaskSparseImpl) { + return variantMask.intersection(this); + } else { + throw new RuntimeException("Unknown VariantMask implementation"); + } + } + + @Override + public VariantMask union(VariantMask variantMask) { + if (variantMask instanceof VariantMaskBitmaskImpl) { + return union((VariantMaskBitmaskImpl) variantMask); + } else if (variantMask instanceof VariantMaskSparseImpl) { + return variantMask.union(this); + } else { + throw new RuntimeException("Unknown VariantMask implementation"); + } + } + + @Override + public boolean testBit(int bit) { + return bitmask.testBit(bit + 2); + } + + @Override + public int bitCount() { + return bitmask.bitCount(); + } + + @Override + public Set patientMaskToPatientIdSet(List patientIds) { + Set ids = new HashSet<>(); + for (int x = 0; x < bitmask.bitLength() - 4; x++) { + if (testBit(x)) { + String patientId = patientIds.get(x).trim(); + ids.add(Integer.parseInt(patientId)); + } + } + return ids; + } + + @Override + @JsonIgnore + public boolean isEmpty() { + // because the bitmasks are padded with 11 on each end + return bitmask.bitCount() <= 4; + } + + private VariantMask union(VariantMaskBitmaskImpl variantMaskBitmask) { + return new VariantMaskBitmaskImpl(variantMaskBitmask.bitmask.or(this.bitmask)); + } + + private VariantMask intersection(VariantMaskBitmaskImpl variantMaskBitmask) { + // we could consider using a sparse variant index here if we are ever going to be storing the + // result of this anywhere + return new VariantMaskBitmaskImpl(variantMaskBitmask.bitmask.and(this.bitmask)); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + VariantMaskBitmaskImpl that = (VariantMaskBitmaskImpl) o; + return Objects.equals(bitmask, that.bitmask); + } + + @Override + public int hashCode() { + return Objects.hash(bitmask); + } + + @Override + public String toString() { + return "VariantMaskBitmaskImpl{" + "bitmask=" + bitmask.toString() + '}'; + } +} diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMaskSparseImpl.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMaskSparseImpl.java new file mode 100644 index 000000000..9b78c51da --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMaskSparseImpl.java @@ -0,0 +1,89 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; + +import com.fasterxml.jackson.annotation.JsonIgnore; +import com.fasterxml.jackson.annotation.JsonProperty; + +import java.math.BigInteger; +import java.util.HashSet; +import java.util.List; +import java.util.Objects; +import java.util.Set; +import java.util.stream.Collectors; + +public class VariantMaskSparseImpl implements VariantMask { + + @JsonProperty("p") + protected Set patientIndexes; + + public VariantMaskSparseImpl(@JsonProperty("p") Set patientIndexes) { + this.patientIndexes = patientIndexes; + } + + public Set getPatientIndexes() { + return patientIndexes; + } + + @Override + public VariantMask intersection(VariantMask variantMask) { + return new VariantMaskSparseImpl(this.patientIndexes.stream().filter(variantMask::testBit).collect(Collectors.toSet())); + } + + @Override + public VariantMask union(VariantMask variantMask) { + if (variantMask instanceof VariantMaskBitmaskImpl) { + return union((VariantMaskBitmaskImpl) variantMask); + } else if (variantMask instanceof VariantMaskSparseImpl) { + return union((VariantMaskSparseImpl) variantMask); + } else { + throw new RuntimeException("Unknown VariantMask implementation"); + } + } + + @Override + public boolean testBit(int bit) { + return patientIndexes.contains(bit); + } + + @Override + public int bitCount() { + return patientIndexes.size(); + } + + @Override + public Set patientMaskToPatientIdSet(List patientIds) { + return patientIndexes.stream().map(patientIds::get).map(String::trim).map(Integer::parseInt).collect(Collectors.toSet()); + } + + @Override + @JsonIgnore + public boolean isEmpty() { + return this.patientIndexes.isEmpty(); + } + + private VariantMask union(VariantMaskSparseImpl variantMask) { + HashSet union = new HashSet<>(variantMask.patientIndexes); + union.addAll(this.patientIndexes); + return new VariantMaskSparseImpl(union); + } + + private VariantMask union(VariantMaskBitmaskImpl variantMaskBitmask) { + BigInteger union = variantMaskBitmask.bitmask; + for (Integer patientId : this.patientIndexes) { + union = union.setBit(patientId + 2); + } + return new VariantMaskBitmaskImpl(union); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + VariantMaskSparseImpl that = (VariantMaskSparseImpl) o; + return Objects.equals(patientIndexes, that.patientIndexes); + } + + @Override + public int hashCode() { + return Objects.hash(patientIndexes); + } +} diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMasks.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMasks.java new file mode 100644 index 000000000..a0d024984 --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMasks.java @@ -0,0 +1,250 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; + +import com.fasterxml.jackson.annotation.JsonInclude; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; +import com.fasterxml.jackson.databind.annotation.JsonSerialize; +import com.fasterxml.jackson.databind.ser.std.ToStringSerializer; + +import java.io.Serializable; +import java.math.BigInteger; +import java.util.Objects; + +public class VariantMasks implements Serializable { + private static final long serialVersionUID = 6225420483804601477L; + private static final String oneone = "11"; + private static final char one = '1'; + private static final char zero = '0'; + private static final String hetero = "0/1"; + private static final String heteroDel = "1/0"; + private static final String heteroPhased = "0|1"; + private static final String heteroPhased2 = "1|0"; + private static final String homo = "1/1"; + private static final String homoPhased = "1|1"; + private static final String homoNoCall = "./."; + private static final String heteroNoCall = "./1"; + + /* + * These indices result from the char values of the 3 characters in a VCF sample record summed as integers % 7 + * + * This allows us to not actually do string comparisons, instead we add 3 values, do one modulus operation, then use the result as the + * index into the result array. + */ + + // ./0 = (46 + 47 + 48) % 7 = 1 + // 0|. = (48 + 124 + 46) % 7 = 1 + // .|0 = (46 + 124 + 48) % 7 = 1 + public static final int HETERO_NOCALL_REF_CHAR_INDEX = 1; + + // ./1 = (46 + 47 + 49) % 7 = 2 + // 1|. = (49 + 124 + 46) % 7 = 2 + // .|1 = (46 + 124 + 49) % 7 = 2 + // ./1 = (46 + 47 + 49) % 7 = 2 + // 1|. = (49 + 124 + 46) % 7 = 2 + // .|1 = (46 + 124 + 49) % 7 = 2 + public static final int HETERO_NOCALL_VARIANT_CHAR_INDEX = 2; + + // 0/0 = (48 + 47 + 48) % 7 = 3 + // 0|0 = (48 + 124 + 48) % 7 = 3 + public static final int ZERO_ZERO_CHAR_INDEX = 3; + + // 0/1 = (48 + 47 + 49) % 7 = 4 + // 1|0 = (49 + 124 + 48) % 7 = 4 + // 0|1 = (48 + 124 + 49) % 7 = 4 + public static final int ZERO_ONE_CHAR_INDEX = 4; + + // 1/1 = (49 + 47 + 49) % 7 = 5 + // 1|1 = (49 + 124 + 49) % 7 = 5 + public static final int ONE_ONE_CHAR_INDEX = 5; + + // ./. = (46 + 47 + 46) % 7 = 6 + // .|. = (46 + 124 + 46) % 7 = 6 + public static final int HOMO_NOCALL_CHAR_INDEX = 6; + + public VariantMasks(String[] values) { + char[] homozygousBits = new char[values.length]; + char[] heterozygousBits = new char[values.length]; + char[] homozygousNoCallBits = new char[values.length]; + char[] heterozygousNoCallBits = new char[values.length]; + boolean hasHetero = false; + boolean hasHomo = false; + boolean hasHeteroNoCall = false; + boolean hasHomoNoCall = false; + + for (int x = 0; x < values.length; x++) { + homozygousBits[x] = zero; + heterozygousBits[x] = zero; + homozygousNoCallBits[x] = zero; + heterozygousNoCallBits[x] = zero; + if (values[x] != null) { + switch (values[x]) { + case hetero: { + heterozygousBits[x] = one; + hasHetero = true; + break; + } + case heteroPhased: { + heterozygousBits[x] = one; + hasHetero = true; + break; + } + case heteroPhased2: { + heterozygousBits[x] = one; + hasHetero = true; + break; + } + case heteroDel: { + heterozygousBits[x] = one; + hasHetero = true; + break; + } + case homo: { + homozygousBits[x] = one; + hasHomo = true; + break; + } + case homoPhased: { + homozygousBits[x] = one; + hasHomo = true; + break; + } + case heteroNoCall: { + heterozygousNoCallBits[x] = one; + hasHeteroNoCall = true; + break; + } + case homoNoCall: { + homozygousNoCallBits[x] = one; + hasHomoNoCall = true; + break; + } + } + } + + } + if (hasHetero) { + StringBuilder heteroString = new StringBuilder(values.length + 4); + heteroString.append(oneone); + heteroString.append(heterozygousBits); + heteroString.append(oneone); + heterozygousMask = new BigInteger(heteroString.toString(), 2); + } + if (hasHomo) { + StringBuilder homoString = new StringBuilder(values.length + 4); + homoString.append(oneone); + homoString.append(homozygousBits); + homoString.append(oneone); + homozygousMask = new BigInteger(homoString.toString(), 2); + } + if (hasHomoNoCall) { + StringBuilder homoNoCallString = new StringBuilder(values.length + 4); + homoNoCallString.append(oneone); + homoNoCallString.append(homozygousNoCallBits); + homoNoCallString.append(oneone); + homozygousNoCallMask = new BigInteger(homoNoCallString.toString(), 2); + } + if (hasHeteroNoCall) { + StringBuilder heteroNoCallString = new StringBuilder(values.length + 4); + heteroNoCallString.append(oneone); + heteroNoCallString.append(heterozygousNoCallBits); + heteroNoCallString.append(oneone); + heterozygousNoCallMask = new BigInteger(heteroNoCallString.toString(), 2); + } + } + + public VariantMasks(char[][] maskValues) { + String heteroMaskStringRaw = new String(maskValues[ZERO_ONE_CHAR_INDEX]); + String homoMaskStringRaw = new String(maskValues[ONE_ONE_CHAR_INDEX]); + String heteroNoCallMaskStringRaw = new String(maskValues[HETERO_NOCALL_VARIANT_CHAR_INDEX]); + String homoNoCallMaskStringRaw = new String(maskValues[HOMO_NOCALL_CHAR_INDEX]); + if (heteroMaskStringRaw.contains("1")) { + heterozygousMask = new BigInteger(oneone + heteroMaskStringRaw + oneone, 2); + } + if (homoMaskStringRaw.contains("1")) { + homozygousMask = new BigInteger(oneone + homoMaskStringRaw + oneone, 2); + } + if (heteroNoCallMaskStringRaw.contains("1")) { + heterozygousNoCallMask = new BigInteger(oneone + heteroNoCallMaskStringRaw + oneone, 2); + } + if (homoNoCallMaskStringRaw.contains("1")) { + homozygousNoCallMask = new BigInteger(oneone + homoNoCallMaskStringRaw + oneone, 2); + } + + } + + public VariantMasks() {} + + + public BigInteger homozygousMask; + + public BigInteger heterozygousMask; + + public BigInteger homozygousNoCallMask; + + public BigInteger heterozygousNoCallMask; + + + @JsonProperty("ho") + @JsonInclude(JsonInclude.Include.NON_NULL) + @JsonSerialize(using = ToStringSerializer.class) + public BigInteger getHomozygousMask() { + return homozygousMask; + } + + @JsonProperty("ho") + public void setHomozygousMask(String homozygousMask) { + this.homozygousMask = new BigInteger(homozygousMask); + } + + @JsonProperty("he") + @JsonSerialize(using = ToStringSerializer.class) + @JsonInclude(JsonInclude.Include.NON_NULL) + public BigInteger getHeterozygousMask() { + return heterozygousMask; + } + + @JsonProperty("he") + public void setHeterozygousMask(String heterozygousMask) { + this.heterozygousMask = new BigInteger(heterozygousMask); + } + + @JsonProperty("hon") + @JsonSerialize(using = ToStringSerializer.class) + @JsonInclude(JsonInclude.Include.NON_NULL) + public BigInteger getHomozygousNoCallMask() { + return homozygousNoCallMask; + } + + @JsonProperty("hon") + public void setHomozygousNoCallMask(String homozygousNoCallMask) { + this.homozygousNoCallMask = new BigInteger(homozygousNoCallMask); + } + + @JsonProperty("hen") + @JsonSerialize(using = ToStringSerializer.class) + @JsonInclude(JsonInclude.Include.NON_NULL) + public BigInteger getHeterozygousNoCallMask() { + return heterozygousNoCallMask; + } + + @JsonProperty("hen") + public void setHeterozygousNoCallMask(String heterozygousNoCallMask) { + this.heterozygousNoCallMask = new BigInteger(heterozygousNoCallMask); + } + + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + VariantMasks that = (VariantMasks) o; + return Objects.equals(homozygousMask, that.homozygousMask) && Objects.equals(heterozygousMask, that.heterozygousMask) + && Objects.equals(homozygousNoCallMask, that.homozygousNoCallMask) + && Objects.equals(heterozygousNoCallMask, that.heterozygousNoCallMask); + } + + @Override + public int hashCode() { + return Objects.hash(homozygousMask, heterozygousMask, homozygousNoCallMask, heterozygousNoCallMask); + } +} diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMetadataIndex.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMetadataIndex.java new file mode 100644 index 000000000..4207c6cbb --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMetadataIndex.java @@ -0,0 +1,267 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; + +import java.io.*; +import java.nio.file.Files; +import java.util.*; +import java.util.concurrent.ConcurrentHashMap; +import java.util.stream.Collectors; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; + +import com.google.common.base.Joiner; +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedJavaIndexedStorage; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedByteIndexedStorage; + +/** + * This class will create a set of FBBIS objects that allow lookups of variant-spec -> metadata, instead of the metadata -> variant-spec map + * that is used for searching and identifying patients. + * + * The loading and reading of this class must take place separately; the flush() function will write out the in-memory contents to a fast, + * disk-based backing store. + */ +public class VariantMetadataIndex implements Serializable { + public static final String VARIANT_METADATA_FILENAME = "VariantMetadata.javabin"; + public static String VARIANT_METADATA_BIN_FILE = "/opt/local/hpds/all/" + VARIANT_METADATA_FILENAME; + + private static final long serialVersionUID = 5917054606643971537L; + private static Logger log = LoggerFactory.getLogger(VariantMetadataIndex.class); + + // (String) contig --> (Integer) Bucket --> (String) variant spec --> INFO column data[]. + private final Map>> indexMap = new HashMap<>(); + + public static final String VARIANT_METADATA_STORAGE_FILE_PREFIX = "VariantMetadataStorage"; + private String fileStoragePrefix = "/opt/local/hpds/all/" + VARIANT_METADATA_STORAGE_FILE_PREFIX; + + /** + * This map allows us to load millions of variants without re-writing the fbbis each time (which would blow up the disk space). We need + * to remember to flush() between each contig this gets saved to the fbbis array. + */ + private transient Map>> loadingMap = new HashMap<>(); + + /** + * This constructor should only be used for testing; we expect the files to be in the default locations in production + * @param storageFile + * @throws IOException + */ + public VariantMetadataIndex(String storageFile) throws IOException { + fileStoragePrefix = storageFile; + } + + /** + * creates a default metadata index that maps variant spec -> metadata using an array of one file per contig. + * @throws IOException + */ + public VariantMetadataIndex() throws IOException {} + + /** + * This will always return a value, including an empty array if there is no data or an error. + * @param variantSpec + * @return + */ + public Set findBySingleVariantSpec(String variantSpec, VariantBucketHolder bucketCache) { + try { + String[] segments = variantSpec.split(","); + if (segments.length < 2) { + log.error("Less than 2 segments found in this variant : " + variantSpec); + } + + int chrOffset = Integer.parseInt(segments[1]) / VariantStore.BUCKET_SIZE; + String contig = segments[0]; + + // see if we can reuse the cache + if ( + bucketCache.lastValue == null || !contig.contentEquals(bucketCache.lastContig) || chrOffset != bucketCache.lastChunkOffset + ) { + FileBackedByteIndexedStorage> ContigFbbis = indexMap.get(contig); + if (ContigFbbis == null) { + return Set.of(); + } + bucketCache.lastValue = ContigFbbis.get(chrOffset); + bucketCache.lastContig = contig; + bucketCache.lastChunkOffset = chrOffset; + } + + if (bucketCache.lastValue != null) { + if (bucketCache.lastValue.get(variantSpec) == null) { + log.warn("No variant data found for spec " + variantSpec); + return Set.of(); + } + return Set.of(bucketCache.lastValue.get(variantSpec)); + } + log.warn("No bucket found for spec " + variantSpec + " in bucket " + chrOffset); + return Set.of(); + + } catch (UncheckedIOException e) { + log.warn("IOException caught looking up variantSpec : " + variantSpec, e); + return Set.of(); + } + } + + public Map> findByMultipleVariantSpec(Collection varientSpecList) { + // log.debug("SPEC list " + varientSpecList.size() + " :: " + Arrays.deepToString(varientSpecList.toArray())); + + VariantBucketHolder bucketCache = new VariantBucketHolder(); + return varientSpecList.stream().collect(Collectors.toMap(variant -> { + return variant; + }, variant -> { + return findBySingleVariantSpec(variant, bucketCache); + })); + } + + /** + * Get/put symmetry is broken here, since we want the ETL process to build the fbbis objects, so we only have to write them to disk + * once. The data will be written to disk only when the flush() method is called. + * + * @param variantSpec + * @throws IOException + */ + public void put(String variantSpec, String metaData) throws IOException { + + String[] segments = variantSpec.split(","); + if (segments.length < 2) { + log.error("Less than 2 segments found in this variant : " + variantSpec); + } + + int chrOffset = Integer.parseInt(segments[1]) / VariantStore.BUCKET_SIZE; + String contig = segments[0]; + + ConcurrentHashMap> contigMap = loadingMap.get(contig); + if (contigMap == null) { + contigMap = new ConcurrentHashMap>(); + loadingMap.put(contig, contigMap); + } + + ConcurrentHashMap bucket = contigMap.get(chrOffset); + if (bucket == null) { + bucket = new ConcurrentHashMap(); + contigMap.put(chrOffset, bucket); + } + + List existingRecords = new ArrayList(); + if (bucket.get(variantSpec) != null) { + Collections.addAll(existingRecords, bucket.get(variantSpec)); + } + existingRecords.add(metaData); + bucket.put(variantSpec, existingRecords.toArray(new String[existingRecords.size()])); + } + + /** + * This will write out the current contents of the in-memory cache to file based storage. it should be called between processing each + * contig so that the memory usage doesn't overwhelm the system. + * + * This will overwrite any existing data, so it should only be called once per contig. + * @throws IOException + */ + public synchronized void flush() throws IOException { + + for (String contig : loadingMap.keySet()) { + log.debug("writing contig " + contig); + + FileBackedByteIndexedStorage> contigFbbis = indexMap.get(contig); + if (contigFbbis == null) { + log.info("creating new file for " + contig); + String filePath = fileStoragePrefix + "_" + contig + ".bin"; + contigFbbis = new FileBackedJavaIndexedStorage(Integer.class, ConcurrentHashMap.class, new File(filePath)); + indexMap.put(contig, contigFbbis); + } + + ConcurrentHashMap> contigMap = loadingMap.get(contig); + for (Integer bucketNumber : contigMap.keySet()) { + // make sure we don't lose any existing data + ConcurrentHashMap bucketStorage = contigFbbis.get(bucketNumber); + if (bucketStorage == null) { + bucketStorage = contigMap.get(bucketNumber); + } else { + bucketStorage.putAll(contigMap.get(bucketNumber)); + } + + contigFbbis.put(bucketNumber, bucketStorage); + } + + log.debug("Saved " + contig + " to FBBIS"); + } + // now reset the map + loadingMap = new HashMap>>(); + } + + public void complete() throws IOException { + flush(); + + for (String contig : indexMap.keySet()) { + FileBackedByteIndexedStorage> contigFbbis = indexMap.get(contig); + contigFbbis.complete(); + } + + } + + public static VariantMetadataIndex createInstance(String metadataIndexPath) { + try ( + ObjectInputStream in = + new ObjectInputStream(new GZIPInputStream(new FileInputStream(metadataIndexPath + VARIANT_METADATA_FILENAME))) + ) { + VariantMetadataIndex variantMetadataIndex = (VariantMetadataIndex) in.readObject(); + variantMetadataIndex.updateStorageDirectory(new File(metadataIndexPath)); + return variantMetadataIndex; + } catch (Exception e) { + // todo: handle exceptions better + log.info("No Metadata Index found at " + metadataIndexPath); + return null; + } + } + + public static void merge(VariantMetadataIndex variantMetadataIndex1, VariantMetadataIndex variantMetadataIndex2, String outputDirectory) + throws IOException { + VariantMetadataIndex merged = new VariantMetadataIndex(outputDirectory + VARIANT_METADATA_STORAGE_FILE_PREFIX); + if (!variantMetadataIndex1.indexMap.keySet().equals(variantMetadataIndex2.indexMap.keySet())) { + log.warn( + "Merging incompatible variant indexes. Index1 keys: " + Joiner.on(",").join(variantMetadataIndex1.indexMap.keySet()) + + ". Index 2 keys: " + Joiner.on(",").join(variantMetadataIndex2.indexMap.keySet()) + ); + throw new IllegalStateException("Cannot merge variant metadata index with different contig keys"); + } + for (String contig : variantMetadataIndex1.indexMap.keySet()) { + String filePath = outputDirectory + VARIANT_METADATA_STORAGE_FILE_PREFIX + "_" + contig + ".bin"; + FileBackedByteIndexedStorage> mergedFbbis = + new FileBackedJavaIndexedStorage(Integer.class, ConcurrentHashMap.class, new File(filePath)); + + // Store the merged result here because FileBackedByteIndexedStorage must be written all at once + Map> mergedStagedFbbis = new HashMap<>(); + + FileBackedByteIndexedStorage> fbbis1 = variantMetadataIndex1.indexMap.get(contig); + FileBackedByteIndexedStorage> fbbis2 = variantMetadataIndex2.indexMap.get(contig); + + fbbis1.keys().forEach(key -> { + mergedStagedFbbis.put(key, fbbis1.get(key)); + }); + fbbis2.keys().forEach(key -> { + ConcurrentHashMap metadataMap = mergedStagedFbbis.get(key); + if (metadataMap == null) { + mergedStagedFbbis.put(key, fbbis2.get(key)); + } else { + metadataMap.putAll(fbbis2.get(key)); + } + }); + + mergedStagedFbbis.forEach(mergedFbbis::put); + mergedFbbis.complete(); + merged.indexMap.put(contig, mergedFbbis); + } + + try ( + ObjectOutputStream out = new ObjectOutputStream( + new GZIPOutputStream(Files.newOutputStream(new File(outputDirectory + VARIANT_METADATA_FILENAME).toPath())) + ) + ) { + out.writeObject(merged); + out.flush(); + } + } + + public void updateStorageDirectory(File genomicDataDirectory) { + indexMap.values().forEach(value -> value.updateStorageDirectory(genomicDataDirectory)); + } +} diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantSpec.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantSpec.java new file mode 100644 index 000000000..dcaedce25 --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantSpec.java @@ -0,0 +1,122 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; + +import java.io.Serializable; +import java.util.Objects; + +import org.apache.commons.csv.CSVRecord; + +public class VariantSpec implements Serializable, Comparable { + + public class VariantCoords implements Serializable { + public String chromosome; + public Integer offset; + public String name; + public String ref; + public String alt; + public int qual; + public String format; + public String gene; + public String consequence; + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + VariantCoords that = (VariantCoords) o; + return qual == that.qual && Objects.equals(chromosome, that.chromosome) && Objects.equals(offset, that.offset) + && Objects.equals(name, that.name) && Objects.equals(ref, that.ref) && Objects.equals(alt, that.alt) + && Objects.equals(format, that.format) && Objects.equals(gene, that.gene) && Objects.equals(consequence, that.consequence); + } + + @Override + public int hashCode() { + return Objects.hash(chromosome, offset, name, ref, alt, qual, format, gene, consequence); + } + } + + public static int CHR = 0, OFF = 1, NAME = 2, REF = 3, ALT = 4, QUAL = 5, FILTER = 6, INFO = 7, FORMAT = 8, DATA = 9; + public long heteroOffset; + public long homoOffset; + public VariantCoords metadata; + + public VariantSpec(CSVRecord r) { + this.metadata = new VariantCoords(); + this.metadata.chromosome = r.get(CHR); + this.metadata.offset = Integer.parseInt(r.get(OFF)); + this.metadata.name = r.get(NAME); + this.metadata.ref = r.get(REF); + this.metadata.alt = r.get(ALT); + try { + this.metadata.qual = Integer.parseInt(r.get(QUAL)); + } catch (NumberFormatException e) { + this.metadata.qual = -1; + } + + String[] variantInfo = r.get(INFO).split("[=;]"); + String gene = "NULL"; + String consequence = "NULL"; + for (int i = 0; i < variantInfo.length; i = i + 2) { + if ("Gene_with_variant".equals(variantInfo[i])) { + gene = variantInfo[i + 1]; + } + if ("Variant_consequence_calculated".equals(variantInfo[i])) { + consequence = variantInfo[i + 1]; + } + } + this.metadata.gene = gene; + this.metadata.consequence = consequence; + } + + public VariantSpec(String variant) { + this.metadata = new VariantCoords(); + String[] segments = variant.split(","); + this.metadata.chromosome = segments[0]; + this.metadata.offset = Integer.parseInt(segments[1]); + this.metadata.name = null; + this.metadata.ref = segments[2]; + this.metadata.alt = segments[3]; + this.metadata.qual = -1; + this.metadata.gene = segments[4]; + this.metadata.consequence = segments[5]; + } + + public String specNotation() { + return this.metadata.chromosome + "," + this.metadata.offset + "," + this.metadata.ref + "," + this.metadata.alt + "," + + this.metadata.gene + "," + this.metadata.consequence; + } + + public int compareTo(VariantSpec o) { + int ret = 0; + ret = this.metadata.chromosome.compareTo(o.metadata.chromosome); + if (ret == 0) { + ret = this.metadata.offset.compareTo(o.metadata.offset); + } + if (ret == 0) { + ret = this.metadata.ref.compareTo(o.metadata.ref); + } + if (ret == 0) { + ret = this.metadata.alt.compareTo(o.metadata.alt); + } + if (ret == 0) { + ret = this.metadata.gene.compareTo(o.metadata.gene); + } + if (ret == 0) { + ret = this.metadata.consequence.compareTo(o.metadata.consequence); + } + + return ret; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + VariantSpec that = (VariantSpec) o; + return heteroOffset == that.heteroOffset && homoOffset == that.homoOffset && Objects.equals(metadata, that.metadata); + } + + @Override + public int hashCode() { + return Objects.hash(heteroOffset, homoOffset, metadata); + } +} diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantStore.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantStore.java new file mode 100644 index 000000000..32e24c5a9 --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantStore.java @@ -0,0 +1,181 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; + +import com.google.common.collect.RangeSet; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedJsonIndexStorage; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.*; +import java.math.BigInteger; +import java.util.*; +import java.util.concurrent.ConcurrentHashMap; +import java.util.stream.Collectors; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; + +public class VariantStore implements Serializable { + private static final long serialVersionUID = -6970128712587609414L; + public static final String VARIANT_STORE_JAVABIN_FILENAME = "variantStore.javabin"; + public static final String VARIANT_SPEC_INDEX_JAVABIN_FILENAME = "variantSpecIndex.javabin"; + private static Logger log = LoggerFactory.getLogger(VariantStore.class); + public static final int BUCKET_SIZE = 1000; + + private BigInteger emptyBitmask; + private String[] patientIds; + + private transient String[] variantSpecIndex; + + private Map>> variantMaskStorage = + new TreeMap<>(); + + public Map>> getVariantMaskStorage() { + return variantMaskStorage; + } + + public void setVariantMaskStorage( + Map>> variantMaskStorage + ) { + this.variantMaskStorage = variantMaskStorage; + } + + public String[] getVariantSpecIndex() { + return variantSpecIndex; + } + + public void setVariantSpecIndex(String[] variantSpecIndex) { + this.variantSpecIndex = variantSpecIndex; + } + + public static VariantStore readInstance(String genomicDataDirectory) throws IOException, ClassNotFoundException { + try ( + GZIPInputStream gzipInputStream = + new GZIPInputStream(new FileInputStream(genomicDataDirectory + VARIANT_STORE_JAVABIN_FILENAME)); ObjectInputStream ois = + new ObjectInputStream(gzipInputStream) + ) { + VariantStore variantStore = (VariantStore) ois.readObject(); + ois.close(); + variantStore.getVariantMaskStorage().values().forEach(store -> { + store.updateStorageDirectory(new File(genomicDataDirectory)); + }); + variantStore.open(); + variantStore.setVariantSpecIndex(loadVariantIndexFromFile(genomicDataDirectory)); + return variantStore; + } + } + + public void writeInstance(String genomicDirectory) { + try ( + FileOutputStream fos = new FileOutputStream(new File(genomicDirectory, VARIANT_STORE_JAVABIN_FILENAME)); GZIPOutputStream gzos = + new GZIPOutputStream(fos); ObjectOutputStream oos = new ObjectOutputStream(gzos); + ) { + oos.writeObject(this); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + try ( + FileOutputStream fos = + new FileOutputStream(new File(genomicDirectory, VARIANT_SPEC_INDEX_JAVABIN_FILENAME)); GZIPOutputStream gzos = + new GZIPOutputStream(fos); ObjectOutputStream oos = new ObjectOutputStream(gzos); + ) { + oos.writeObject(Arrays.asList(variantSpecIndex)); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + } + + public String[] getPatientIds() { + return patientIds; + } + + public Optional getMasks(String variant, VariantBucketHolder bucketCache) + throws IOException { + String[] segments = variant.split(","); + if (segments.length < 2) { + log.error("Less than 2 segments found in this variant : " + variant); + } + + int chrOffset = Integer.parseInt(segments[1]) / BUCKET_SIZE; + String contig = segments[0]; + + if (bucketCache.lastValue != null && contig.contentEquals(bucketCache.lastContig) && chrOffset == bucketCache.lastChunkOffset) { + // TODO : This is a temporary efficiency hack, NOT THREADSAFE!!! + } else { + // todo: don't bother doing a lookup if this node does not have the chromosome specified + FileBackedJsonIndexStorage> indexedStorage = + variantMaskStorage.get(contig); + if (indexedStorage == null) { + return Optional.empty(); + } + bucketCache.lastValue = indexedStorage.get(chrOffset); + bucketCache.lastContig = contig; + bucketCache.lastChunkOffset = chrOffset; + } + return bucketCache.lastValue == null ? Optional.empty() : Optional.ofNullable(bucketCache.lastValue.get(variant)); + } + + public List getMasksForDbSnpSpec(String variant) { + String[] segments = variant.split(","); + if (segments.length < 2) { + log.error("Less than 2 segments found in this variant : " + variant); + } + + int chrOffset = Integer.parseInt(segments[1]) / BUCKET_SIZE; + String contig = segments[0]; + + // todo: don't bother doing a lookup if this node does not have the chromosome specified + FileBackedJsonIndexStorage> indexedStorage = + variantMaskStorage.get(contig); + if (indexedStorage == null) { + return List.of(); + } else { + ConcurrentHashMap specToMaskMap = indexedStorage.getOrELse(chrOffset, new ConcurrentHashMap<>()); + return specToMaskMap.entrySet().stream().filter(entry -> entry.getKey().startsWith(variant)).map(Map.Entry::getValue) + .collect(Collectors.toList()); + } + } + + public void open() { + variantMaskStorage.values().stream().forEach((fbbis -> { + if (fbbis != null) { + fbbis.open(); + } + })); + } + + public VariantStore() { + + } + + public void setPatientIds(String[] patientIds) { + this.patientIds = patientIds; + } + + public BigInteger emptyBitmask() { + if (emptyBitmask == null || emptyBitmask.testBit(emptyBitmask.bitLength() / 2)) { + String emptyVariantMask = ""; + for (String patientId : patientIds) { + emptyVariantMask = emptyVariantMask + "0"; + } + emptyBitmask = new BigInteger("11" + emptyVariantMask + "11", 2); + } + return emptyBitmask; + } + + @SuppressWarnings("unchecked") + public static String[] loadVariantIndexFromFile(String genomicDataDirectory) { + try ( + ObjectInputStream objectInputStream = new ObjectInputStream( + new GZIPInputStream(new FileInputStream(genomicDataDirectory + "/" + VARIANT_SPEC_INDEX_JAVABIN_FILENAME)) + ); + ) { + + List variants = (List) objectInputStream.readObject(); + return variants.toArray(new String[0]); + + } catch (IOException | ClassNotFoundException e) { + throw new RuntimeException(e); + } + } + +} diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/caching/VariantBucketHolder.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/caching/VariantBucketHolder.java new file mode 100644 index 000000000..c23cd4331 --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/caching/VariantBucketHolder.java @@ -0,0 +1,9 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching; + +import java.util.concurrent.ConcurrentHashMap; + +public class VariantBucketHolder { + public ConcurrentHashMap lastValue; + public String lastContig; + public int lastChunkOffset; +} diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMeta.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMeta.java new file mode 100644 index 000000000..94b6fd514 --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMeta.java @@ -0,0 +1,157 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.phenotype; + +import com.fasterxml.jackson.annotation.JsonIgnore; +import com.fasterxml.jackson.annotation.JsonInclude; + +import java.io.Serializable; +import java.util.List; + + +@JsonInclude(JsonInclude.Include.NON_NULL) +public class ColumnMeta implements Serializable { + + private static final long serialVersionUID = -124111104912063811L; + private String name; + private int widthInBytes; + private int columnOffset; + private boolean categorical; + private List categoryValues; + private Double min, max; + private long allObservationsOffset; + private long allObservationsLength; + private int observationCount; + private int patientCount; + private boolean hasTimestamp; + private Long timestampMin; + private Long timestampMax; + + public String getName() { + return name; + } + + public ColumnMeta setName(String header) { + this.name = header; + return this; + } + + @JsonIgnore + public int getWidthInBytes() { + return widthInBytes; + } + + public ColumnMeta setWidthInBytes(int widthInBytes) { + this.widthInBytes = widthInBytes; + return this; + } + + @JsonIgnore + public int getColumnOffset() { + return columnOffset; + } + + public ColumnMeta setColumnOffset(int columnOffset) { + this.columnOffset = columnOffset; + return this; + } + + public boolean isCategorical() { + return categorical; + } + + public ColumnMeta setCategorical(boolean isCategorical) { + this.categorical = isCategorical; + return this; + } + + @JsonIgnore + public long getAllObservationsOffset() { + return allObservationsOffset; + } + + public ColumnMeta setAllObservationsOffset(long allObservationsOffset) { + this.allObservationsOffset = allObservationsOffset; + return this; + } + + @JsonIgnore + public long getAllObservationsLength() { + return allObservationsLength; + } + + public ColumnMeta setAllObservationsLength(long allObservationsLength) { + this.allObservationsLength = allObservationsLength; + return this; + } + + public long getObservationCount() { + return observationCount; + } + + public ColumnMeta setObservationCount(int length) { + this.observationCount = length; + return this; + } + + public long getPatientCount() { + return patientCount; + } + + public ColumnMeta setPatientCount(int length) { + this.patientCount = length; + return this; + } + + public List getCategoryValues() { + return categoryValues; + } + + public void setCategoryValues(List categoryValues) { + this.categoryValues = categoryValues; + } + + public Double getMin() { + return min; + } + + public ColumnMeta setMin(double min) { + this.min = min; + return this; + } + + public Double getMax() { + return max; + } + + public ColumnMeta setMax(double max) { + this.max = max; + return this; + } + + public boolean hasTimestamp() { + return hasTimestamp; + } + + public ColumnMeta setHasTimestamp(boolean hasTimestamp) { + this.hasTimestamp = hasTimestamp; + return this; + } + + public Long getTimestampMin() { + return timestampMin; + } + + public ColumnMeta setTimestampMin(Long timestampMin) { + this.timestampMin = timestampMin; + return this; + } + + public Long getTimestampMax() { + return timestampMax; + } + + public ColumnMeta setTimestampMax(Long timestampMax) { + this.timestampMax = timestampMax; + return this; + } + +} diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/KeyAndValue.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/KeyAndValue.java new file mode 100644 index 000000000..2a11a0655 --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/KeyAndValue.java @@ -0,0 +1,62 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.phenotype; + +import java.io.Serializable; + +public class KeyAndValue> implements Serializable, Comparable> { + + private static final long serialVersionUID = -3714097509955396941L; + + int key; + + V value; + + Long timestamp; + + public KeyAndValue() { + + } + + public KeyAndValue(int key, V value) { + this.key = key; + this.value = value; + this.setTimestamp(Long.MIN_VALUE); + } + + + public KeyAndValue(int key, V value, Long timestamp) { + this.key = key; + this.value = value; + this.setTimestamp(timestamp); + } + + public V getValue() { + return value; + } + + public KeyAndValue setValue(V value) { + this.value = value; + return this; + } + + public Integer getKey() { + return key; + } + + public KeyAndValue setKey(Integer key) { + this.key = key; + return this; + } + + @Override + public int compareTo(KeyAndValue o) { + return this.key - o.key; + } + + public Long getTimestamp() { + return timestamp; + } + + public void setTimestamp(Long timestamp) { + this.timestamp = timestamp; + } +} diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/PhenoCube.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/PhenoCube.java new file mode 100644 index 000000000..810cf194a --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/PhenoCube.java @@ -0,0 +1,235 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.phenotype; + +import java.io.Serializable; +import java.lang.reflect.Array; +import java.util.*; +import java.util.stream.Collectors; + +public class PhenoCube> implements Serializable { + + private static final long serialVersionUID = -2584728054717230390L; + public final String name; + public final Class vType; + + int columnWidth; + + V[] lowDimValues; + boolean isLowDim = false; + + private KeyAndValue[] sortedByKey; + + private TreeMap> categoryMap; + + private transient List> loadingMap = Collections.synchronizedList(new ArrayList<>()); + + public PhenoCube(String name, Class vType) { + this.vType = vType; + this.name = name; + } + + public void add(Integer key, V value, Date date) { + loadingMap.add(new KeyAndValue(key, value, date != null ? date.getTime() : null)); + } + + public V getValueForKey(Integer key) { + int idx = Arrays.binarySearch(sortedByKey(), new KeyAndValue(key, null)); + if (idx < 0) return null; + return sortedByKey()[idx].value; + } + + public Set getKeysForValue(V value) { + + if (isStringType()) { + Set keys = categoryMap.get(value); + return keys == null ? new TreeSet() : keys; + } else { + int minIndex; + KeyAndValue keyAndValue = new KeyAndValue(1, value); + + if (value == null) { + return new TreeSet(); + } else { + KeyAndValue[] sortedByValue = sortedByValue(); + + int minSearchIndex = Arrays.binarySearch(sortedByValue, keyAndValue, (a, b) -> { + return a.value.compareTo(b.value); + }); + minIndex = seekForMinIndex(Math.abs(minSearchIndex), keyAndValue, sortedByValue); + + List keys = new ArrayList(); + for (int x = minIndex; x < sortedByValue.length && value.equals(sortedByValue[x].value); x++) { + keys.add(sortedByValue[x].key); + } + + return new TreeSet(keys); + } + } + + } + + public Set getKeysForRange(V min, V max) { + KeyAndValue[] entries = getEntriesForValueRange(min, max); + Set keys = new HashSet<>(); + for (KeyAndValue entry : entries) { + keys.add(entry.key); + } + return keys; + } + + public V[] getValuesForRange(V min, V max) { + KeyAndValue[] entries = getEntriesForValueRange(min, max); + @SuppressWarnings("unchecked") + V[] values = (V[]) Array.newInstance(vType, entries.length); + for (int x = 0; x < entries.length; x++) { + values[x] = entries[x].value; + } + return values; + } + + public KeyAndValue[] getEntriesForValueRange(V min, V max) { + KeyAndValue minKeyAndValue = new KeyAndValue(1, min); + KeyAndValue maxKeyAndValue = new KeyAndValue(2, max); + + int minIndex; + int maxIndex; + + KeyAndValue[] sortedByValue = sortedByValue(); + if (min == null) { + minIndex = 0; + } else { + int minSearchIndex = Arrays.binarySearch(sortedByValue, minKeyAndValue, (a, b) -> { + return a.value.compareTo(b.value); + }); + minIndex = seekForMinIndex(Math.abs(minSearchIndex), minKeyAndValue, sortedByValue); + } + + if (max == null) { + maxIndex = sortedByValue.length; + } else { + int maxSearchIndex = Arrays.binarySearch(sortedByValue, maxKeyAndValue, (a, b) -> { + return a.value.compareTo(b.value); + }); + /* + * Arrays.binarySearch returns the insertion index of the new value if there is no exact match for the value. + * + * Sometimes this is an index that already has a value higher than our max, which would be shifted to the right on insertion. To + * still make use of the advantage of the binary search we invert this insertion index AND decrement it once. + * + * This prevents us from including one extra value in these cases. + */ + if (maxSearchIndex < 0) { + maxSearchIndex = (maxSearchIndex * -1) - 1; + } + maxIndex = seekForMaxIndex(maxSearchIndex, maxKeyAndValue, sortedByValue); + } + + return Arrays.copyOfRange(sortedByValue, minIndex, maxIndex); + } + + private int seekForMinIndex(int minSearchIndex, KeyAndValue minEntry, KeyAndValue[] sortedByValue) { + + minSearchIndex--; + + Comparator> comparator = (a, b) -> { + return a.value.compareTo(b.value); + }; + while (minSearchIndex > -1 && comparator.compare(sortedByValue[minSearchIndex], minEntry) >= 0) { + minSearchIndex--; + } + return Math.max(0, minSearchIndex + 1); + } + + private int seekForMaxIndex(int maxSearchIndex, KeyAndValue maxEntry, KeyAndValue[] sortedByValue) { + Comparator> comparator = (a, b) -> { + return a.value.compareTo(b.value); + }; + while (maxSearchIndex < sortedByValue.length && comparator.compare(maxEntry, sortedByValue[maxSearchIndex]) >= 0) { + maxSearchIndex++; + } + return maxSearchIndex; + } + + public boolean isStringType() { + return vType.equals(String.class); + } + + public KeyAndValue[] sortedByValue() { + KeyAndValue[] sortedByValue = Arrays.copyOf(sortedByKey(), sortedByKey().length); + Arrays.sort(sortedByValue, (KeyAndValue o1, KeyAndValue o2) -> { + return o1.value.compareTo(o2.value); + }); + return sortedByValue; + } + + public KeyAndValue[] sortedByTimestamp() { + KeyAndValue[] sortedByTimestamp = Arrays.copyOf(sortedByKey(), sortedByKey().length); + Arrays.sort(sortedByTimestamp, (KeyAndValue o1, KeyAndValue o2) -> { + return o1.getTimestamp() == null ? -1 : o1.getTimestamp().compareTo(o2.getTimestamp()); + }); + return sortedByTimestamp; + } + + public List keyBasedIndex() { + return Arrays.asList(sortedByKey()).stream().map((KeyAndValue kv) -> { + return kv.key; + }).collect(Collectors.toList()); + } + + public List> keyBasedArray() { + return Arrays.asList(sortedByKey()).stream().map((KeyAndValue kv) -> { + return kv.value; + }).collect(Collectors.toList()); + } + + public KeyAndValue[] sortedByKey() { + return sortedByKey; + } + + public PhenoCube setSortedByKey(KeyAndValue[] sortedByKey) { + this.sortedByKey = sortedByKey; + return this; + } + + public int getColumnWidth() { + return columnWidth; + } + + public PhenoCube setColumnWidth(int columnWidth) { + this.columnWidth = columnWidth; + return this; + } + + public TreeMap> getCategoryMap() { + return categoryMap; + } + + public void setCategoryMap(TreeMap> categorySetMap) { + this.categoryMap = categorySetMap; + } + + public List> getLoadingMap() { + return loadingMap; + } + + public void setLoadingMap(List> newMap) { + this.loadingMap = newMap; + } + + public List> getValuesForKeys(Set patientIds) { + patientIds = new TreeSet<>(patientIds); + + List> values = new ArrayList<>(); + int x = 0; + for (Integer id : patientIds) { + while (x < sortedByKey.length && sortedByKey[x].key < id) { + x++; + } + while (x < sortedByKey.length && sortedByKey[x].key == id) { + values.add(sortedByKey[x]); + x++; + } + } + return values; + } + +} diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/TimelineEvent.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/TimelineEvent.java new file mode 100644 index 000000000..a348cf11c --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/TimelineEvent.java @@ -0,0 +1,42 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.phenotype; + +import java.util.Comparator; + +public class TimelineEvent { + + public TimelineEvent(KeyAndValue value2, long startTime) { + this.timestamp = value2.timestamp - startTime; + this.patient_num = value2.key; + this.value = value2.value.toString(); + } + + long timestamp; + int patient_num; + String value; + + public long getTimestamp() { + return timestamp; + } + + public void setTimestamp(long timestamp) { + this.timestamp = timestamp; + } + + public int getPatient_num() { + return patient_num; + } + + public void setPatient_num(int patient_num) { + this.patient_num = patient_num; + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } + + public static Comparator timestampComparator = Comparator.comparing(TimelineEvent::getTimestamp); +} diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/storage/FileBackedStorageVariantIndexImpl.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/storage/FileBackedStorageVariantIndexImpl.java new file mode 100644 index 000000000..d4b00542b --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/storage/FileBackedStorageVariantIndexImpl.java @@ -0,0 +1,23 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.storage; + +import com.fasterxml.jackson.core.type.TypeReference; +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedJsonIndexStorage; + +import java.io.File; +import java.io.FileNotFoundException; +import java.io.Serializable; + +public class FileBackedStorageVariantIndexImpl extends FileBackedJsonIndexStorage implements Serializable { + private static final long serialVersionUID = -893724459359928779L; + + public FileBackedStorageVariantIndexImpl(File storageFile) throws FileNotFoundException { + super(storageFile); + } + + private static final TypeReference typeRef = new TypeReference() {}; + + @Override + public TypeReference getTypeReference() { + return typeRef; + } +} diff --git a/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/storage/FileBackedStorageVariantMasksImpl.java b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/storage/FileBackedStorageVariantMasksImpl.java new file mode 100644 index 000000000..d667be057 --- /dev/null +++ b/services/pic-sure-hpds/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/storage/FileBackedStorageVariantMasksImpl.java @@ -0,0 +1,28 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.storage; + +import com.fasterxml.jackson.core.type.TypeReference; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariableVariantMasks; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMasks; +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedJsonIndexStorage; + +import java.io.File; +import java.io.FileNotFoundException; +import java.io.Serializable; +import java.util.concurrent.ConcurrentHashMap; + +public class FileBackedStorageVariantMasksImpl extends FileBackedJsonIndexStorage> + implements Serializable { + private static final long serialVersionUID = -1086729119489479152L; + + public FileBackedStorageVariantMasksImpl(File storageFile) throws FileNotFoundException { + super(storageFile); + } + + private static final TypeReference> typeRef = + new TypeReference>() {}; + + @Override + public TypeReference> getTypeReference() { + return typeRef; + } +} diff --git a/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/InfoColumnMetaTest.java b/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/InfoColumnMetaTest.java new file mode 100644 index 000000000..75a676c65 --- /dev/null +++ b/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/InfoColumnMetaTest.java @@ -0,0 +1,22 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import org.junit.jupiter.api.Test; +import static org.junit.jupiter.api.Assertions.*; + +public class InfoColumnMetaTest { + + @Test + public void jacksonSerializesAndDeserializes() throws JsonProcessingException { + ObjectMapper objectMapper = new ObjectMapper(); + + InfoColumnMeta infoColumnMeta = new InfoColumnMeta("abc123", "the description", true, 1.0f, 20.0f); + + String serialized = objectMapper.writeValueAsString(infoColumnMeta); + + InfoColumnMeta deserialized = objectMapper.readValue(serialized, InfoColumnMeta.class); + + assertEquals(infoColumnMeta, deserialized); + } +} diff --git a/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariableVariantMasksTest.java b/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariableVariantMasksTest.java new file mode 100644 index 000000000..31a2d4cca --- /dev/null +++ b/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariableVariantMasksTest.java @@ -0,0 +1,103 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; + +import org.junit.jupiter.api.Test; + +import java.math.BigInteger; +import java.util.Set; + +import static org.junit.jupiter.api.Assertions.*; + +class VariableVariantMasksTest { + + @Test + void appendMask_bitmaskImpl() { + BigInteger bitmask1 = new BigInteger( + "141128266537977664750676276621047930360647583370951385898970922432171641921591683601425661017874251620531446414001258481539117879583763813143907296662202568713257464719895142475222938754588184582833582945368733841208297077207159012919514593576142503835920156756519924916168242089239884330492690734761017788145472426679068150988914755013607752960816306592042734726724967292489382922774340753414934719473579642086577795740766564256929075326123036793589965882761953873677505969126336030099232419417531157749845223962002657158936982730111297974575206081858525359109608528262092083167977823315667519770531233235502931655993522963196732342798609807510543882273123542784003837220002062547832711681922161218010724226003150184777238854967623299970205873235909960398972219305810619458430315886318451687126866584390511424196256376003247717440484524668930504599413091194844245946142655802347109092922312106655798606759916931458730259588797621736772069847398957694392864416289605234581063232645315000563794292589544477569850783743632035729362609737922579552116678396740867191143283379987783383546964540333832022555110531730782339840166704631278663393147496643156685747417468473443887224102514355150110201463928311558935840684668441340082266117306282514075566574248767903320202249460451453420775463375086967869642395460246215345716051454824012618762098616749770441010729935100690497726813080659572063353154599964806728241328892738034442472863741591198849392657539785115946383059858121434147389809099727185407701653069953116828987459279642700621389676861517273949473071786975738343769782464350475716221573322857987917669867491560145456280976454077958400126376423873081869441464609193216436634914151839730185428390533788824490041131307997850622739795832813220163889874229711053167483400593799762457890098932032534121358716659875839129363445294836150352418351095797845291006220927734160887236196809213101473795" + ); + VariantMask mask1 = new VariantMaskBitmaskImpl(bitmask1); + BigInteger bitmask2 = new BigInteger( + "30986998537042903080350519548408047200882037374471443267447678987916097706689940814664693588471382927433911322922595655683" + ); + VariantMask mask2 = new VariantMaskBitmaskImpl(bitmask2); + BigInteger expected = new BigInteger( + "364428449062309565827240887371711117987574656019257508470944944605332301145049360947562613021825062352285550919581217473685332023988542714833984833584283993391279871691386067405572061472644828810015780133411925154335939452908415258964249206427971383684062861395477403040282307619178797392994855011010859741065713642937722555386553472167057412349499978682577859360114784650082282703011601887907648540462571623667509259030122346885116531561265495702316349933315144109402391832141090339015610768872781857606433548246400953322494469603219947770538558126916689855755477351331412849701993441724311536424509298383050084506206211767917732037267909332303742403672014600658318302593423194411973298402659688783532220840192809967726287753517722498547930875524876017589557370530361981799944335286739781131150443454009586308444310074980028948209472950776329093810066130759876455221806685349198404676070598652587630369814761497643023695920944554335463560556407863991874650393356359742532476840044738380631950001000889884841365536456755318891308758448828432322546827241786950989285280451703830359048521243704376576346418597615317052525572950500220422542100551941365526524572447973251506942320379483402120949518538372004537133062107782710822000749441206410146350956094013529342546401955361956752745578930129151472060056501664176391306323733630924234020572479814310832686356211870629168524382442619274880885230138170761194502147197237097179031772802871639774718532255582374871483153552524216278948609829889298505566944209429410943844015411379772232511986448333683276938151761604643176820833900087800015896793760190738573447504231241253241247411492029282990960833205840126804844971397564707229362865231720213379844987578324282466174232636950775929742330163059024377711272017786328444659381735736216404131832568759328992585474109193095809959345744181054394252160618715444166335074662636279289524790651946664188322635565248044921668500523867959008028963420119948417112017996816651287475428019005246560397815063629879127215220996440067" + ); + // length should equal the length of the binary representation - 4. Bitmasks are padded with 11 on each end + VariantMask merged = VariableVariantMasks.appendMask(mask1, mask2, 6282, 400); + + assertEquals(expected, ((VariantMaskBitmaskImpl) merged).getBitmask()); + } + + @Test + void appendMask_bitmaskImpl_invalidLength() { + BigInteger bitmask1 = new BigInteger( + "141128266537977664750676276621047930360647583370951385898970922432171641921591683601425661017874251620531446414001258481539117879583763813143907296662202568713257464719895142475222938754588184582833582945368733841208297077207159012919514593576142503835920156756519924916168242089239884330492690734761017788145472426679068150988914755013607752960816306592042734726724967292489382922774340753414934719473579642086577795740766564256929075326123036793589965882761953873677505969126336030099232419417531157749845223962002657158936982730111297974575206081858525359109608528262092083167977823315667519770531233235502931655993522963196732342798609807510543882273123542784003837220002062547832711681922161218010724226003150184777238854967623299970205873235909960398972219305810619458430315886318451687126866584390511424196256376003247717440484524668930504599413091194844245946142655802347109092922312106655798606759916931458730259588797621736772069847398957694392864416289605234581063232645315000563794292589544477569850783743632035729362609737922579552116678396740867191143283379987783383546964540333832022555110531730782339840166704631278663393147496643156685747417468473443887224102514355150110201463928311558935840684668441340082266117306282514075566574248767903320202249460451453420775463375086967869642395460246215345716051454824012618762098616749770441010729935100690497726813080659572063353154599964806728241328892738034442472863741591198849392657539785115946383059858121434147389809099727185407701653069953116828987459279642700621389676861517273949473071786975738343769782464350475716221573322857987917669867491560145456280976454077958400126376423873081869441464609193216436634914151839730185428390533788824490041131307997850622739795832813220163889874229711053167483400593799762457890098932032534121358716659875839129363445294836150352418351095797845291006220927734160887236196809213101473795" + ); + VariantMask mask1 = new VariantMaskBitmaskImpl(bitmask1); + BigInteger bitmask2 = new BigInteger( + "30986998537042903080350519548408047200882037374471443267447678987916097706689940814664693588471382927433911322922595655683" + ); + VariantMask mask2 = new VariantMaskBitmaskImpl(bitmask2); + BigInteger expected = new BigInteger( + "364428449062309565827240887371711117987574656019257508470944944605332301145049360947562613021825062352285550919581217473685332023988542714833984833584283993391279871691386067405572061472644828810015780133411925154335939452908415258964249206427971383684062861395477403040282307619178797392994855011010859741065713642937722555386553472167057412349499978682577859360114784650082282703011601887907648540462571623667509259030122346885116531561265495702316349933315144109402391832141090339015610768872781857606433548246400953322494469603219947770538558126916689855755477351331412849701993441724311536424509298383050084506206211767917732037267909332303742403672014600658318302593423194411973298402659688783532220840192809967726287753517722498547930875524876017589557370530361981799944335286739781131150443454009586308444310074980028948209472950776329093810066130759876455221806685349198404676070598652587630369814761497643023695920944554335463560556407863991874650393356359742532476840044738380631950001000889884841365536456755318891308758448828432322546827241786950989285280451703830359048521243704376576346418597615317052525572950500220422542100551941365526524572447973251506942320379483402120949518538372004537133062107782710822000749441206410146350956094013529342546401955361956752745578930129151472060056501664176391306323733630924234020572479814310832686356211870629168524382442619274880885230138170761194502147197237097179031772802871639774718532255582374871483153552524216278948609829889298505566944209429410943844015411379772232511986448333683276938151761604643176820833900087800015896793760190738573447504231241253241247411492029282990960833205840126804844971397564707229362865231720213379844987578324282466174232636950775929742330163059024377711272017786328444659381735736216404131832568759328992585474109193095809959345744181054394252160618715444166335074662636279289524790651946664188322635565248044921668500523867959008028963420119948417112017996816651287475428019005246560397815063629879127215220996440067" + ); + // length should equal the length of the binary representation - 4. Bitmasks are padded with 11 on each end + VariantMask merged = VariableVariantMasks.appendMask(mask1, mask2, 6282, 400); + + assertThrows(IllegalArgumentException.class, () -> VariableVariantMasks.appendMask(mask1, mask2, 6283, 400)); + assertThrows(IllegalArgumentException.class, () -> VariableVariantMasks.appendMask(mask1, mask2, 6282, 399)); + } + + @Test + void appendMask_sparseImpl() { + VariantMask mask1 = new VariantMaskSparseImpl(Set.of(1, 10, 99)); + VariantMask mask2 = new VariantMaskSparseImpl(Set.of(1, 99)); + VariantMask merged = VariableVariantMasks.appendMask(mask1, mask2, 100, 100); + + VariantMask expected = new VariantMaskSparseImpl(Set.of(1, 10, 99, 101, 199)); + assertEquals(expected, merged); + } + + @Test + void appendMask_sparseImplOneEmpty() { + VariantMask mask1 = new VariantMaskSparseImpl(Set.of()); + VariantMask mask2 = new VariantMaskSparseImpl(Set.of(1, 99)); + VariantMask merged = VariableVariantMasks.appendMask(mask1, mask2, 100, 100); + + VariantMask expected = new VariantMaskSparseImpl(Set.of(101, 199)); + assertEquals(expected, merged); + + mask1 = new VariantMaskSparseImpl(Set.of(1, 10, 99)); + mask2 = new VariantMaskSparseImpl(Set.of()); + merged = VariableVariantMasks.appendMask(mask1, mask2, 100, 100); + + expected = new VariantMaskSparseImpl(Set.of(1, 10, 99)); + assertEquals(expected, merged); + } + + @Test + void appendMask_sparseBitmask() { + VariantMask mask1 = new VariantMaskSparseImpl(Set.of(1, 9)); + BigInteger bitmask1 = new BigInteger("11100000010011", 2); + VariantMask mask2 = new VariantMaskBitmaskImpl(bitmask1); + VariantMask merged = VariableVariantMasks.appendMask(mask1, mask2, 10, 10); + + BigInteger bitmask = new BigInteger("111000000100" + "100000001011", 2); + VariantMask expected = new VariantMaskBitmaskImpl(bitmask); + System.out.println(((VariantMaskBitmaskImpl) merged).getBitmask().toString(2)); + assertEquals(expected, merged); + } + + @Test + void appendMask_bitmaskSparse() { + BigInteger bitmask1 = new BigInteger("11100000010011", 2); + VariantMask mask1 = new VariantMaskBitmaskImpl(bitmask1); + VariantMask mask2 = new VariantMaskSparseImpl(Set.of(1, 9)); + VariantMask merged = VariableVariantMasks.appendMask(mask1, mask2, 10, 10); + + BigInteger bitmask = new BigInteger("111000000010" + "100000010011", 2); + VariantMask expected = new VariantMaskBitmaskImpl(bitmask); + System.out.println(((VariantMaskBitmaskImpl) merged).getBitmask().toString(2)); + assertEquals(expected, merged); + } +} diff --git a/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMaskPerformanceTest.java b/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMaskPerformanceTest.java new file mode 100644 index 000000000..ddb7894f4 --- /dev/null +++ b/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMaskPerformanceTest.java @@ -0,0 +1,80 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; + +import java.math.BigInteger; +import java.util.Random; +import java.util.Set; + +public class VariantMaskPerformanceTest { + + /** + * This test shows the ideal maximum size for a sparse variant is between 5-10 items. The slight decrease in performance is generally + * worth the drastic reduction in disks space + */ + // @Test + public void test() { + VariantMaskBitmaskImpl mask100k = new VariantMaskBitmaskImpl(generateRandomBitmask(100_000)); + VariantMaskBitmaskImpl mask100k2 = new VariantMaskBitmaskImpl(generateRandomBitmask(100_000)); + VariantMaskBitmaskImpl mask1m = new VariantMaskBitmaskImpl(generateRandomBitmask(1_000_000)); + VariantMaskBitmaskImpl mask1m2 = new VariantMaskBitmaskImpl(generateRandomBitmask(1_000_000)); + VariantMaskSparseImpl sparseMask100k = new VariantMaskSparseImpl(Set.of(100, 200, 400, 50_000, 90_000)); + VariantMaskSparseImpl sparseMask100k2 = + new VariantMaskSparseImpl(Set.of(100, 101, 200, 300, 400, 1000, 20_000, 30_000, 50_000, 90_000)); + VariantMaskSparseImpl sparseMask1m = + new VariantMaskSparseImpl(Set.of(100, 200, 400, 50_000, 90_000, 300_000, 420_000, 555_555, 867_530, 999_999)); + + long time = System.currentTimeMillis(); + for (int k = 0; k < 1000; k++) { + VariantMask and = mask100k.union(mask100k2); + } + System.out + .println(mask100k.getBitmask().bitLength() + " bitmask union completed in " + (System.currentTimeMillis() - time) + " ms"); + + time = System.currentTimeMillis(); + for (int k = 0; k < 1000; k++) { + VariantMask and = sparseMask100k.union(mask100k); + } + System.out.println( + mask100k.getBitmask().bitLength() + " bitmask and " + sparseMask100k.patientIndexes.size() + " sparse union completed in " + + (System.currentTimeMillis() - time) + " ms" + ); + + time = System.currentTimeMillis(); + for (int k = 0; k < 1000; k++) { + VariantMask and = sparseMask100k2.union(mask100k); + } + System.out.println( + mask100k.getBitmask().bitLength() + " bitmask and " + sparseMask100k2.patientIndexes.size() + " sparse union completed in " + + (System.currentTimeMillis() - time) + " ms" + ); + + time = System.currentTimeMillis(); + for (int k = 0; k < 1000; k++) { + VariantMask and = mask1m.union(mask1m2); + } + System.out.println(mask1m.getBitmask().bitLength() + " bitmask union completed in " + (System.currentTimeMillis() - time) + " ms"); + + time = System.currentTimeMillis(); + for (int k = 0; k < 1000; k++) { + VariantMask and = sparseMask100k.union(mask1m); + } + System.out.println( + mask1m.getBitmask().bitLength() + " bitmask and " + sparseMask100k.patientIndexes.size() + " sparse union completed in " + + (System.currentTimeMillis() - time) + " ms" + ); + + time = System.currentTimeMillis(); + for (int k = 0; k < 1000; k++) { + VariantMask and = sparseMask1m.union(mask1m); + } + System.out.println( + mask1m.getBitmask().bitLength() + " bitmask and " + sparseMask1m.patientIndexes.size() + " sparse union completed in " + + (System.currentTimeMillis() - time) + " ms" + ); + + } + + private BigInteger generateRandomBitmask(int patients) { + return new BigInteger(patients + 4, new Random()); + } + +} diff --git a/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMaskTest.java b/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMaskTest.java new file mode 100644 index 000000000..4a8896e0c --- /dev/null +++ b/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMaskTest.java @@ -0,0 +1,85 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; + +import org.junit.jupiter.api.Test; + +import java.math.BigInteger; +import java.util.Set; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +public class VariantMaskTest { + + @Test + public void intersection_bitmaskVsBitmask() { + VariantMask mask1 = new VariantMaskBitmaskImpl(new BigInteger("111001100011", 2)); + VariantMask mask2 = new VariantMaskBitmaskImpl(new BigInteger("111010010011", 2)); + VariantMask expected = new VariantMaskBitmaskImpl(new BigInteger("111000000011", 2)); + + assertEquals(expected, mask1.intersection(mask2)); + } + + @Test + public void intersection_bitmaskVsSparse() { + // this is essentially a mask for patients 0, 2, 3, 7 (there is 11 padding on both ends) + VariantMask mask1 = new VariantMaskBitmaskImpl(new BigInteger("111000110111", 2)); + VariantMask mask2 = new VariantMaskSparseImpl(Set.of(0, 3, 6)); + VariantMask expected = new VariantMaskSparseImpl(Set.of(0, 3)); + + assertEquals(expected, mask1.intersection(mask2)); + } + + @Test + public void intersection_sparseVsBitmask() { + VariantMask mask1 = new VariantMaskSparseImpl(Set.of(4, 7)); + VariantMask mask2 = new VariantMaskBitmaskImpl(new BigInteger("110111110111", 2)); + VariantMask expected = new VariantMaskSparseImpl(Set.of(4)); + + assertEquals(expected, mask1.intersection(mask2)); + } + + @Test + public void intersection_sparseVsSparse() { + VariantMask mask1 = new VariantMaskSparseImpl(Set.of(0, 2, 4, 6)); + VariantMask mask2 = new VariantMaskSparseImpl(Set.of(0, 1, 3, 5, 7)); + VariantMask expected = new VariantMaskSparseImpl(Set.of(0)); + + assertEquals(expected, mask1.intersection(mask2)); + } + + @Test + public void union_bitmaskVsBitmask() { + VariantMask mask1 = new VariantMaskBitmaskImpl(new BigInteger("111001100011", 2)); + VariantMask mask2 = new VariantMaskBitmaskImpl(new BigInteger("111010010011", 2)); + VariantMask expected = new VariantMaskBitmaskImpl(new BigInteger("111011110011", 2)); + + assertEquals(expected, mask1.union(mask2)); + } + + @Test + public void union_bitmaskVsSparse() { + // this is essentially a mask for patients 0, 2, 3, 7 (there is 11 padding on both ends) + VariantMask mask1 = new VariantMaskBitmaskImpl(new BigInteger("111000110111", 2)); + VariantMask mask2 = new VariantMaskSparseImpl(Set.of(0, 3, 6)); + VariantMask expected = new VariantMaskBitmaskImpl(new BigInteger("111100110111", 2)); + + assertEquals(expected, mask1.union(mask2)); + } + + @Test + public void union_sparseVsBitmask() { + VariantMask mask1 = new VariantMaskSparseImpl(Set.of(4, 7)); + VariantMask mask2 = new VariantMaskBitmaskImpl(new BigInteger("110111110111", 2)); + VariantMask expected = new VariantMaskBitmaskImpl(new BigInteger("111111110111", 2)); + + assertEquals(expected, mask1.union(mask2)); + } + + @Test + public void union_sparseVsSparse() { + VariantMask mask1 = new VariantMaskSparseImpl(Set.of(0, 2, 4, 6)); + VariantMask mask2 = new VariantMaskSparseImpl(Set.of(1, 5, 7)); + VariantMask expected = new VariantMaskSparseImpl(Set.of(0, 1, 2, 4, 5, 6, 7)); + + assertEquals(expected, mask1.union(mask2)); + } +} diff --git a/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMasksSerializationTest.java b/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMasksSerializationTest.java new file mode 100644 index 000000000..1f01d5bd3 --- /dev/null +++ b/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMasksSerializationTest.java @@ -0,0 +1,67 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import org.junit.jupiter.api.Test; + +import java.math.BigInteger; +import java.util.Set; +import java.util.concurrent.ThreadLocalRandom; + +import static org.junit.jupiter.api.Assertions.*; + +public class VariantMasksSerializationTest { + + @Test + public void testFieldMaxLength() throws JsonProcessingException { + VariantMasks variantMasks = new VariantMasks(); + + StringBuilder homozygousStr = new StringBuilder(); + for (int i = 0; i < 50000; i++) { + homozygousStr.append(ThreadLocalRandom.current().nextInt(0, 10)); + } + variantMasks.homozygousMask = new BigInteger(homozygousStr.toString()); + + StringBuilder heterozygousStr = new StringBuilder(); + for (int i = 0; i < 50000; i++) { + heterozygousStr.append(ThreadLocalRandom.current().nextInt(0, 10)); + } + variantMasks.heterozygousMask = new BigInteger(heterozygousStr.toString()); + + StringBuilder homozygousNoCallStr = new StringBuilder(); + for (int i = 0; i < 50000; i++) { + homozygousNoCallStr.append(ThreadLocalRandom.current().nextInt(0, 10)); + } + variantMasks.homozygousNoCallMask = new BigInteger(homozygousNoCallStr.toString()); + + StringBuilder heterozygousNoCallStr = new StringBuilder(); + for (int i = 0; i < 50000; i++) { + heterozygousNoCallStr.append(ThreadLocalRandom.current().nextInt(0, 10)); + } + variantMasks.heterozygousNoCallMask = new BigInteger(heterozygousNoCallStr.toString()); + + ObjectMapper objectMapper = new ObjectMapper(); + String serialized = objectMapper.writeValueAsString(variantMasks); + VariantMasks deserialized = objectMapper.readValue(serialized, VariantMasks.class); + + assertEquals(variantMasks, deserialized); + } + + + + @Test + public void testVariableVariantMasks() throws JsonProcessingException { + VariableVariantMasks variableVariantMasks = new VariableVariantMasks(); + variableVariantMasks.heterozygousMask = new VariantMaskSparseImpl(Set.of(1, 2, 3)); + variableVariantMasks.homozygousMask = new VariantMaskBitmaskImpl(new BigInteger("1101010101010101011")); + variableVariantMasks.heterozygousNoCallMask = new VariantMaskSparseImpl(Set.of()); + variableVariantMasks.homozygousNoCallMask = null; + + ObjectMapper objectMapper = new ObjectMapper(); + String serialized = objectMapper.writeValueAsString(variableVariantMasks); + System.out.println(serialized); + VariableVariantMasks deserialized = objectMapper.readValue(serialized, VariableVariantMasks.class); + + assertEquals(variableVariantMasks, deserialized); + } +} diff --git a/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMetaTest.java b/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMetaTest.java new file mode 100644 index 000000000..5e2cd30d2 --- /dev/null +++ b/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMetaTest.java @@ -0,0 +1,173 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.phenotype; + +import org.junit.jupiter.api.Test; + +import java.io.*; + +import static org.junit.jupiter.api.Assertions.*; + +/** + * Unit tests for ColumnMeta timestamp field functionality. + * + *

    These tests validate the addition of timestamp tracking fields to ColumnMeta:

    • hasTimestamp: boolean flag indicating if + * temporal data is present
    • timestampMin: earliest timestamp value (epoch milliseconds)
    • timestampMax: latest + * timestamp value (epoch milliseconds)
    + * + *

    The implementation maintains backward compatibility with existing serialized ColumnMeta objects that do not contain timestamp fields. + * New fields default to hasTimestamp=false and timestampMin/timestampMax=null when deserializing legacy data. + * + * @see ColumnMeta + */ +class ColumnMetaTest { + + /** + * Verifies that newly instantiated ColumnMeta objects have correct default values for timestamp fields. + * + *

    This ensures backward compatibility when working with datasets that do not contain temporal data. Default values should be:

      + *
    • hasTimestamp: false
    • timestampMin: null
    • timestampMax: null
    + */ + @Test + void shouldCreateColumnMetaWithDefaultTimestampValues() { + ColumnMeta columnMeta = new ColumnMeta(); + + assertFalse(columnMeta.hasTimestamp()); + assertNull(columnMeta.getTimestampMin()); + assertNull(columnMeta.getTimestampMax()); + } + + /** + * Validates that timestamp field setters and getters function correctly. + * + *

    Tests the basic contract of the timestamp accessor methods to ensure values can be set and retrieved as expected. + */ + @Test + void shouldSetAndGetTimestampFields() { + ColumnMeta columnMeta = new ColumnMeta().setHasTimestamp(true).setTimestampMin(1000000L).setTimestampMax(2000000L); + + assertTrue(columnMeta.hasTimestamp()); + assertEquals(1000000L, columnMeta.getTimestampMin()); + assertEquals(2000000L, columnMeta.getTimestampMax()); + } + + /** + * Confirms that timestamp setters follow the builder pattern and can be chained with other ColumnMeta setters. + * + *

    The builder pattern allows for fluent configuration of ColumnMeta objects, improving code readability when initializing metadata + * with multiple properties. + */ + @Test + void shouldSupportMethodChaining() { + ColumnMeta columnMeta = new ColumnMeta().setName("test_column").setHasTimestamp(true).setTimestampMin(1000000L) + .setTimestampMax(2000000L).setCategorical(false).setObservationCount(100).setPatientCount(50); + + assertEquals("test_column", columnMeta.getName()); + assertTrue(columnMeta.hasTimestamp()); + assertEquals(1000000L, columnMeta.getTimestampMin()); + assertEquals(2000000L, columnMeta.getTimestampMax()); + assertFalse(columnMeta.isCategorical()); + assertEquals(100, columnMeta.getObservationCount()); + assertEquals(50, columnMeta.getPatientCount()); + } + + /** + * Verifies that ColumnMeta objects with timestamp fields can be serialized and deserialized correctly. + * + *

    This test ensures that the timestamp fields are properly included in the Java serialization process. When a ColumnMeta object + * containing timestamp data is serialized to disk (e.g., columnMeta.javabin) and later deserialized, all timestamp field values should + * be preserved. + * + *

    Uses realistic epoch millisecond values:

    • 1609459200000L = 2021-01-01 00:00:00 UTC
    • 1640995200000L = 2022-01-01 + * 00:00:00 UTC
    + */ + @Test + void shouldSerializeWithTimestampFields() throws IOException, ClassNotFoundException { + ColumnMeta original = new ColumnMeta().setName("timestamped_column").setHasTimestamp(true).setTimestampMin(1609459200000L) // 2021-01-01 + .setTimestampMax(1640995200000L) // 2022-01-01 + .setObservationCount(500).setPatientCount(250); + + ByteArrayOutputStream baos = new ByteArrayOutputStream(); + try (ObjectOutputStream oos = new ObjectOutputStream(baos)) { + oos.writeObject(original); + } + + ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray()); + ColumnMeta deserialized; + try (ObjectInputStream ois = new ObjectInputStream(bais)) { + deserialized = (ColumnMeta) ois.readObject(); + } + + assertEquals(original.getName(), deserialized.getName()); + assertEquals(original.hasTimestamp(), deserialized.hasTimestamp()); + assertEquals(original.getTimestampMin(), deserialized.getTimestampMin()); + assertEquals(original.getTimestampMax(), deserialized.getTimestampMax()); + assertEquals(original.getObservationCount(), deserialized.getObservationCount()); + assertEquals(original.getPatientCount(), deserialized.getPatientCount()); + } + + /** + * Tests backward compatibility by deserializing ColumnMeta objects that were serialized before timestamp fields were added. + * + *

    This is a critical test for production deployment. When HPDS loads existing columnMeta.javabin files created by older versions of + * the software, it must handle the absence of timestamp fields gracefully. Java serialization supports this by initializing new fields + * with their default values:

    • hasTimestamp: false (primitive boolean default)
    • timestampMin: null (object reference + * default)
    • timestampMax: null (object reference default)
    + * + *

    This test simulates loading legacy data by creating a ColumnMeta object, serializing it, and verifying that timestamp fields + * receive proper defaults upon deserialization. + */ + @Test + void shouldDeserializeLegacyColumnMetaWithoutTimestampFields() throws IOException, ClassNotFoundException { + ColumnMeta legacy = new ColumnMeta().setName("legacy_column").setCategorical(true).setObservationCount(1000).setPatientCount(500); + + ByteArrayOutputStream baos = new ByteArrayOutputStream(); + try (ObjectOutputStream oos = new ObjectOutputStream(baos)) { + oos.writeObject(legacy); + } + + ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray()); + ColumnMeta deserialized; + try (ObjectInputStream ois = new ObjectInputStream(bais)) { + deserialized = (ColumnMeta) ois.readObject(); + } + + assertEquals("legacy_column", deserialized.getName()); + assertTrue(deserialized.isCategorical()); + assertEquals(1000, deserialized.getObservationCount()); + assertEquals(500, deserialized.getPatientCount()); + + // Verify timestamp fields receive correct defaults + assertFalse(deserialized.hasTimestamp()); + assertNull(deserialized.getTimestampMin()); + assertNull(deserialized.getTimestampMax()); + } + + /** + * Validates that timestamp min/max fields can be explicitly set to null. + * + *

    This may occur when a column has temporal observations but timestamp values are not yet calculated or are unavailable. The + * hasTimestamp flag can be true while min/max values remain null. + */ + @Test + void shouldHandleNullTimestampMinMax() { + ColumnMeta columnMeta = new ColumnMeta().setHasTimestamp(true).setTimestampMin(null).setTimestampMax(null); + + assertTrue(columnMeta.hasTimestamp()); + assertNull(columnMeta.getTimestampMin()); + assertNull(columnMeta.getTimestampMax()); + } + + /** + * Tests that timestamp min/max values can be set independently of the hasTimestamp flag. + * + *

    While this may represent an inconsistent state in production usage, the fields are designed to be independently settable for + * flexibility. This test ensures the setters do not have hidden dependencies on each other. + */ + @Test + void shouldAllowTimestampFieldsWithoutHasTimestampFlag() { + ColumnMeta columnMeta = new ColumnMeta().setTimestampMin(1000000L).setTimestampMax(2000000L); + + assertFalse(columnMeta.hasTimestamp()); + assertEquals(1000000L, columnMeta.getTimestampMin()); + assertEquals(2000000L, columnMeta.getTimestampMax()); + } +} diff --git a/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/PhenoCubeTest.java b/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/PhenoCubeTest.java new file mode 100644 index 000000000..efa4faf4f --- /dev/null +++ b/services/pic-sure-hpds/data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/PhenoCubeTest.java @@ -0,0 +1,25 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.phenotype; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +import java.util.LinkedHashSet; +import java.util.List; +import java.util.Set; + +class PhenoCubeTest { + + @Test + void shouldGetValuesForKeys() { + KeyAndValue[] sortedByKey = + {new KeyAndValue<>(1, "a"), new KeyAndValue<>(1, "b"), new KeyAndValue<>(2, "c"), new KeyAndValue<>(3, "d"),}; + PhenoCube subject = new PhenoCube<>("phill the phenocube", String.class); + subject.setSortedByKey(sortedByKey); + + Set patientIds = new LinkedHashSet<>(List.of(3, 2, 1)); + List> actual = subject.getValuesForKeys(patientIds); + List> expected = List.of(sortedByKey); + + Assertions.assertEquals(expected, actual); + } +} diff --git a/services/pic-sure-hpds/docker/build.Dockerfile b/services/pic-sure-hpds/docker/build.Dockerfile new file mode 100644 index 000000000..053ecab8d --- /dev/null +++ b/services/pic-sure-hpds/docker/build.Dockerfile @@ -0,0 +1,3 @@ +FROM maven:3.9-amazoncorretto-25 + +RUN yum update -y && yum install -y git && yum clean all \ No newline at end of file diff --git a/services/pic-sure-hpds/docker/pic-sure-hpds-etl/Dockerfile b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/Dockerfile new file mode 100644 index 000000000..5928c9ae3 --- /dev/null +++ b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/Dockerfile @@ -0,0 +1,25 @@ +FROM amazoncorretto:25-alpine + +RUN apk add --no-cache --purge -uU bash curl wget unzip gnupg openssl && \ + rm -rf /var/cache/apk/* /tmp/* + +WORKDIR /app +COPY /docker/pic-sure-hpds-etl/SQLLoader-jar-with-dependencies.jar . +COPY /docker/pic-sure-hpds-etl/CSVLoader-jar-with-dependencies.jar . +COPY /docker/pic-sure-hpds-etl/CSVLoaderNewSearch-jar-with-dependencies.jar . +COPY /docker/pic-sure-hpds-etl/CSVDumper-jar-with-dependencies.jar . +COPY /docker/pic-sure-hpds-etl/VCFLocalLoader-jar-with-dependencies.jar . +COPY /docker/pic-sure-hpds-etl/SplitChromosomeVcfLoader-jar-with-dependencies.jar . +COPY /docker/pic-sure-hpds-etl/VariantMetadataLoader-jar-with-dependencies.jar . +COPY /docker/pic-sure-hpds-etl/GenomicDatasetFinalizer-jar-with-dependencies.jar . +COPY /docker/pic-sure-hpds-etl/UnifiedVCFLocalLoader-jar-with-dependencies.jar . +COPY /docker/pic-sure-hpds-etl/MultialleleCounter-jar-with-dependencies.jar . +COPY /docker/pic-sure-hpds-etl/RekeyDataset-jar-with-dependencies.jar . +COPY /docker/pic-sure-hpds-etl/RemoveConceptFromMetadata-jar-with-dependencies.jar . +COPY /docker/pic-sure-hpds-etl/HideAnnotationCategoryValue-jar-with-dependencies.jar . +COPY /docker/pic-sure-hpds-etl/SequentialLoader-jar-with-dependencies.jar . +COPY /docker/pic-sure-hpds-etl/LowRAMMultiCSVLoader-jar-with-dependencies.jar . +COPY /docker/pic-sure-hpds-etl/CreateColumnmetaCSV-jar-with-dependencies.jar . +COPY /docker/pic-sure-hpds-etl/create_key.sh . + +ENTRYPOINT ["sh", "-c", "java $JAVA_OPTS -Xmx${HEAPSIZE:-2048}m -jar ${LOADER_NAME:-CSVLoader}-jar-with-dependencies.jar $LOADER_ARGS"] diff --git a/services/pic-sure-hpds/docker/pic-sure-hpds-etl/README.md b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/README.md new file mode 100644 index 000000000..5b2fe9959 --- /dev/null +++ b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/README.md @@ -0,0 +1,34 @@ +HPDS ETL Process +================ + +*I2B2 Oracle SQL + +To load your I2B2 registry data, fill out the hpds/sql.properties file with your connection details and create an encryption key in the hpds/encryption_key file. + +The specific requirements for the sql.properties file will depend on your environment. The encryption_key file must have only 32 hexadecimal characters and no other content. + +Once this is done, run the loader: +``` +docker-compose -f docker-compose-sql-loader.yml up +``` +The logs will show all concepts as they are loaded and some other information. Once this process exits, you should have two new files in the hpds folder: +``` +columnMeta.javabin +allObservationsStore.javabin +``` +The first holds all of the metadata for all concepts. The second holds the actual concept data. These files are not readable using anything except HPDS. + +To make these files available to your HPDS container, volume map them into the following container path: +``` +/opt/local/phenocube +``` +You will of course need to unlock the HPDS instance once you have done that, which is outside the scope of this `README.md` file. + +It is a good idea to validate the following once you have your data hosted in an HPDS instance: + +Number of concepts vs expected number of concepts. +Number of patients vs expected number of patients. +Total number of facts. + +These values are dumped into the log of the loading process at the end, immediately preceded with statistics for each concept. + diff --git a/services/pic-sure-hpds/docker/pic-sure-hpds-etl/create_key.sh b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/create_key.sh new file mode 100644 index 000000000..90c90287c --- /dev/null +++ b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/create_key.sh @@ -0,0 +1,7 @@ +openssl rand -hex 16 > /opt/local/hpds/encryption_key +gpg --import /opt/local/hpds/gpg_pub_key.asc +gpg --list-keys +gpg --always-trust --batch --yes --no-tty -e -r "$GPG_USER" /opt/local/hpds/encryption_key +base64 /opt/local/hpds/encryption_key.gpg > /opt/local/hpds/encryption_key.gpg_base64 +echo "-----BEGIN PGP MESSAGE-----" > /opt/local/hpds/encryption_key.asc && cat /opt/local/hpds/encryption_key.gpg_base64 >> /opt/local/hpds/encryption_key.asc && echo "-----END PGP MESSAGE-----" >> /opt/local/hpds/encryption_key.asc +rm /opt/local/hpds/encryption_key.gpg /opt/local/hpds/encryption_key.gpg_base64 diff --git a/services/pic-sure-hpds/docker/pic-sure-hpds-etl/docker-compose-csv-dumper.yml b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/docker-compose-csv-dumper.yml new file mode 100644 index 000000000..8eec24f59 --- /dev/null +++ b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/docker-compose-csv-dumper.yml @@ -0,0 +1,10 @@ +version: '3.3' +services: + csv-loader: + image: dbmi/pic-sure-hpds-etl:jason-refactoring-project-structure_62b8ef6 + environment: + - HEAPSIZE=4096 + - LOADER_NAME=CSVDumper + volumes: + - ./hpds:/opt/local/phenocube + - ./hpds:/opt/local/hpds diff --git a/services/pic-sure-hpds/docker/pic-sure-hpds-etl/docker-compose-csv-loader.yml b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/docker-compose-csv-loader.yml new file mode 100644 index 000000000..695113381 --- /dev/null +++ b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/docker-compose-csv-loader.yml @@ -0,0 +1,10 @@ +version: '3.3' +services: + csv-loader: + image: dbmi/pic-sure-hpds-etl:jason-refactoring-project-structure_62b8ef6 + environment: + - HEAPSIZE=4096 + - LOADER_NAME=CSVLoader + volumes: + - ./hpds:/opt/local/phenocube + - ./hpds:/opt/local/hpds diff --git a/services/pic-sure-hpds/docker/pic-sure-hpds-etl/docker-compose-sql-loader.yml b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/docker-compose-sql-loader.yml new file mode 100644 index 000000000..767e38624 --- /dev/null +++ b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/docker-compose-sql-loader.yml @@ -0,0 +1,9 @@ +version: '3.3' +services: + sql-loader: + image: dbmi/pic-sure-hpds-etl:jason-refactoring-project-structure_62b8ef6 + environment: + - HEAPSIZE=4096 + - LOADER_NAME=SQLLoader + volumes: + - ./hpds:/opt/local/hpds diff --git a/services/pic-sure-hpds/docker/pic-sure-hpds-etl/docker-compose-variant-loader.yml b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/docker-compose-variant-loader.yml new file mode 100644 index 000000000..08e551501 --- /dev/null +++ b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/docker-compose-variant-loader.yml @@ -0,0 +1,11 @@ +version: '3.3' +services: + variant-loader: + image: dbmi/pic-sure-hpds-etl:master_62b8ef6 + environment: + - HEAPSIZE=26000 + - LOADER_NAME=VCFLocalLoader + volumes: + - ./hpds:/opt/local/hpds + - ./vcfLoad:/opt/local/hpds/vcfInput + - ./hpds/all:/opt/local/hpds/vcfOutput diff --git a/services/pic-sure-hpds/docker/pic-sure-hpds-etl/docker-compose-variantmetadata-loader.yml b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/docker-compose-variantmetadata-loader.yml new file mode 100644 index 000000000..24fa3d097 --- /dev/null +++ b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/docker-compose-variantmetadata-loader.yml @@ -0,0 +1,10 @@ +version: '3.3' +services: + variantmetadata-loader: + image: dbmi/pic-sure-hpds-etl:als-sprint-2_2f519a3 + environment: + - HEAPSIZE=4096 + - LOADER_NAME=VariantMetadataLoader + volumes: + - ./hpds:/opt/local/phenocube + - ./hpds:/opt/local/hpds diff --git a/services/pic-sure-hpds/docker/pic-sure-hpds-etl/hpds/encryption_key b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/hpds/encryption_key new file mode 100644 index 000000000..3274bbe72 --- /dev/null +++ b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/hpds/encryption_key @@ -0,0 +1 @@ + diff --git a/services/pic-sure-hpds/docker/pic-sure-hpds-etl/hpds/sql.properties b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/hpds/sql.properties new file mode 100644 index 000000000..386c62c77 --- /dev/null +++ b/services/pic-sure-hpds/docker/pic-sure-hpds-etl/hpds/sql.properties @@ -0,0 +1,5 @@ +datasource.password=< your password > +datasource.user=< your user > +datasource.url=< your db connection string (currently only oracle) > + + diff --git a/services/pic-sure-hpds/docker/pic-sure-hpds/Dockerfile b/services/pic-sure-hpds/docker/pic-sure-hpds/Dockerfile new file mode 100644 index 000000000..556a564ea --- /dev/null +++ b/services/pic-sure-hpds/docker/pic-sure-hpds/Dockerfile @@ -0,0 +1,7 @@ +FROM amazoncorretto:25-alpine + +WORKDIR /app + +COPY /service/target/service-*.jar /service.jar + +ENTRYPOINT ["sh", "-c", "java ${JAVA_OPTS} -jar /service.jar"] \ No newline at end of file diff --git a/services/pic-sure-hpds/docker/pic-sure-hpds/server.xml b/services/pic-sure-hpds/docker/pic-sure-hpds/server.xml new file mode 100644 index 000000000..8b8353462 --- /dev/null +++ b/services/pic-sure-hpds/docker/pic-sure-hpds/server.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/services/pic-sure-hpds/docker/pom.xml b/services/pic-sure-hpds/docker/pom.xml new file mode 100644 index 000000000..036daa76c --- /dev/null +++ b/services/pic-sure-hpds/docker/pom.xml @@ -0,0 +1,66 @@ + + + 4.0.0 + + pic-sure-hpds + edu.harvard.hms.dbmi.avillach.hpds + ${revision} + + + docker + + docker + + + + + org.codehaus.mojo + exec-maven-plugin + 1.6.0 + + + get-last-git-commit + + exec + + package + + git + + log + -1 + --pretty=format:%h + + ${basedir}/src/main/resources/gitCommit.properties + + + + + + org.apache.maven.plugins + maven-resources-plugin + + + copy-docker-build-artifacts + copy-resources + + ${basedir}/target/docker-builds + + + pic-sure-hpds + true + ${basedir}/target/docker-builds + + + pic-sure-hpds-etl + true + + + + + + + + + diff --git a/services/pic-sure-hpds/etl/pom.xml b/services/pic-sure-hpds/etl/pom.xml new file mode 100644 index 000000000..0a80af06f --- /dev/null +++ b/services/pic-sure-hpds/etl/pom.xml @@ -0,0 +1,433 @@ + + + 4.0.0 + + pic-sure-hpds + edu.harvard.hms.dbmi.avillach.hpds + ${revision} + + + etl + + etl + + + org.apache.commons + commons-compress + 1.26.0 + + + org.apache.httpcomponents + httpclient + 4.5.13 + + + com.fasterxml.jackson.core + jackson-databind + + + edu.harvard.hms.dbmi.avillach.hpds + data + + + edu.harvard.hms.dbmi.avillach.hpds + common + + + com.google.guava + guava + + + com.oracle.database.jdbc + ojdbc10 + + + org.postgresql + postgresql + 42.4.4 + + + com.microsoft.sqlserver + mssql-jdbc + 8.2.2.jre11 + + + com.github.samtools + htsjdk + 3.0.1 + + + + + + maven-clean-plugin + + + default-clean + clean + + clean + + + + + ../docker/pic-sure-hpds-etl + + *.jar + + + + + + + + + maven-assembly-plugin + + + buildPerPatientVCFLocalLoader + + + + edu.harvard.hms.dbmi.avillach.hpds.etl.genotype.NewVCFLoader + + + ${project.basedir}/../docker/pic-sure-hpds-etl + + jar-with-dependencies + + VCFLocalLoader + VCFLocalLoader + + package + + single + + + + buildSplitChromosomeVcfLoader + + + + edu.harvard.hms.dbmi.avillach.hpds.etl.genotype.SplitChromosomeVcfLoader + + + ${project.basedir}/../docker/pic-sure-hpds-etl + + jar-with-dependencies + + SplitChromosomeVcfLoader + SplitChromosomeVcfLoader + + package + + single + + + + buildPerPatientUnifiedVCFLocalLoader + + + + edu.harvard.hms.dbmi.avillach.hpds.etl.genotype.NewVCFLoader + + + ${project.basedir}/../docker/pic-sure-hpds-etl + + jar-with-dependencies + + UnifiedVCFLocalLoader + UnifiedVCFLocalLoader + + package + + single + + + + buildCSVLoaderNewSearch + + + + edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.csv.CSVLoaderNewSearch + + + ${project.basedir}/../docker/pic-sure-hpds-etl + + jar-with-dependencies + + CSVLoaderNewSearch + CSVLoaderNewSearch + + package + + single + + + + buildCSVLoader + + + + edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.csv.CSVLoader + + + ${project.basedir}/../docker/pic-sure-hpds-etl + + jar-with-dependencies + + CSVLoader + CSVLoader + + package + + single + + + + buildSQLLoader + + + + edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.sql.SQLLoader + + + ${project.basedir}/../docker/pic-sure-hpds-etl + + jar-with-dependencies + + SQLLoader + SQLLoader + + package + + single + + + + buildSequentialLoader + + + + edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.sequential.SequentialLoader + + + ${project.basedir}/../docker/pic-sure-hpds-etl + + jar-with-dependencies + + SequentialLoader + SequentialLoader + + package + + single + + + + buildLiteCSVLoader + + + + edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.litecsv.LowRAMMultiCSVLoader + + + ${project.basedir}/../docker/pic-sure-hpds-etl + + jar-with-dependencies + + LowRAMMultiCSVLoader + LowRAMMultiCSVLoader + + package + + single + + + + buildMultialleleCounter + + + + edu.harvard.hms.dbmi.avillach.hpds.etl.genotype.MultialleleCounter + + + ${project.basedir}/../docker/pic-sure-hpds-etl + + jar-with-dependencies + + MultialleleCounter + MultialleleCounter + + package + + single + + + + buildDumpCSV + + + + edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.util.DumpSourceCSV + + + ${project.basedir}/../docker/pic-sure-hpds-etl + + jar-with-dependencies + + CSVDumper + CSVDumper + + package + + single + + + + buildVariantMetadataLoader + + + + edu.harvard.hms.dbmi.avillach.hpds.etl.genotype.SplitChromosomeVariantMetadataLoader + + + ${project.basedir}/../docker/pic-sure-hpds-etl + + jar-with-dependencies + + VariantMetadataLoader + VariantMetadataLoader + + package + + single + + + + buildRekeyDatasets + + + + edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.util.RekeyDataset + + + ${project.basedir}/../docker/pic-sure-hpds-etl + + jar-with-dependencies + + RekeyDataset + RekeyDataset + + package + + single + + + + RemoveConceptFromMetadata + + + + edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.util.RemoveConceptFromMetadata + + + ${project.basedir}/../docker/pic-sure-hpds-etl + + jar-with-dependencies + + RemoveConceptFromMetadata + RemoveConceptFromMetadata + + package + + single + + + + HideAnnotationCategoryValue + + + + edu.harvard.hms.dbmi.avillach.hpds.data.genotype.util.HideAnnotationCategoryValue + + + ${project.basedir}/../docker/pic-sure-hpds-etl + + jar-with-dependencies + + HideAnnotationCategoryValue + HideAnnotationCategoryValue + + package + + single + + + + GenomicDatasetMergerRunner + + + + edu.harvard.hms.dbmi.avillach.hpds.etl.genotype.GenomicDatasetMergerRunner + + + ${project.basedir}/../docker/pic-sure-hpds-etl + + jar-with-dependencies + + GenomicDatasetMergerRunner + GenomicDatasetMergerRunner + + package + + single + + + + GenomicDatasetFinalizer + + + + edu.harvard.hms.dbmi.avillach.hpds.etl.genotype.GenomicDatasetFinalizer + + + ${project.basedir}/../docker/pic-sure-hpds-etl + + jar-with-dependencies + + GenomicDatasetFinalizer + GenomicDatasetFinalizer + + package + + single + + + + CreateColumnmetaCSV + + + + edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.columnmeta.CreateColumnmetaCSV + + + ${project.basedir}/../docker/pic-sure-hpds-etl + + jar-with-dependencies + + CreateColumnmetaCSV + CreateColumnmetaCSV + + package + + single + + + + + + + diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/util/ConvertMergedInfoStoresToFBBIS.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/util/ConvertMergedInfoStoresToFBBIS.java new file mode 100644 index 000000000..a82b3176f --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/util/ConvertMergedInfoStoresToFBBIS.java @@ -0,0 +1,17 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype.util; + +import edu.harvard.hms.dbmi.avillach.hpds.etl.genotype.NewVCFLoader; + +import java.io.FileNotFoundException; +import java.io.IOException; + + +public class ConvertMergedInfoStoresToFBBIS { + + public static void main(String[] args) throws IOException { + + new NewVCFLoader().convertInfoStoresToByteIndexed(); + + } + +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/util/HideAnnotationCategoryValue.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/util/HideAnnotationCategoryValue.java new file mode 100644 index 000000000..cad9d2c1a --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/util/HideAnnotationCategoryValue.java @@ -0,0 +1,46 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype.util; + +import java.io.FileInputStream; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.ObjectInputStream; +import java.io.ObjectOutputStream; +import java.util.TreeMap; +import java.util.TreeSet; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; + +import com.google.common.cache.LoadingCache; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.FileBackedByteIndexedInfoStore; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; + +public class HideAnnotationCategoryValue { + protected static LoadingCache> store; + + protected static TreeSet allIds; + + public static void main(String[] args) throws ClassNotFoundException, IOException { + String infoStoreToModify = args[0]; + String valueToScrub = args[1]; + + String infoStoreFilename = "/opt/local/hpds/all/" + infoStoreToModify.trim(); + + FileInputStream fis = new FileInputStream(infoStoreFilename); + GZIPInputStream gis = new GZIPInputStream(fis); + ObjectInputStream ois = new ObjectInputStream(gis); + + FileBackedByteIndexedInfoStore infoStore = (FileBackedByteIndexedInfoStore) ois.readObject(); + infoStore.getAllValues().keys().remove(valueToScrub); + + FileOutputStream fos = new FileOutputStream(infoStoreFilename); + GZIPOutputStream gos = new GZIPOutputStream(fos); + ObjectOutputStream oos = new ObjectOutputStream(gos); + + oos.writeObject(infoStore); + oos.flush(); + oos.close(); + } + +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/util/ReSplitMergeInfoStores.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/util/ReSplitMergeInfoStores.java new file mode 100644 index 000000000..b773baffd --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/util/ReSplitMergeInfoStores.java @@ -0,0 +1,20 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype.util; + +import edu.harvard.hms.dbmi.avillach.hpds.etl.genotype.NewVCFLoader; + +import java.io.IOException; + + +public class ReSplitMergeInfoStores { + + public static void main(String[] args) throws IOException { + + NewVCFLoader newVCFLoader = new NewVCFLoader(); + + newVCFLoader.splitInfoStoresByColumn(); + + newVCFLoader.convertInfoStoresToByteIndexed(); + + } + +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/util/RemapPatientIds.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/util/RemapPatientIds.java new file mode 100644 index 000000000..926e75de9 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/util/RemapPatientIds.java @@ -0,0 +1,63 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.genotype.util; + +import java.io.FileNotFoundException; +import java.io.FileOutputStream; +import java.io.FileReader; +import java.io.IOException; +import java.io.ObjectOutputStream; +import java.util.TreeMap; +import java.util.TreeSet; +import java.util.zip.GZIPOutputStream; + +import com.google.common.cache.LoadingCache; + +import de.siegmar.fastcsv.reader.CsvContainer; +import de.siegmar.fastcsv.reader.CsvReader; +import de.siegmar.fastcsv.reader.CsvRow; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantStore; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; + +public class RemapPatientIds { + protected static LoadingCache> store; + + protected static TreeMap metaStoreSource; + + protected static TreeSet allIds; + + private static final int PATIENT_NUM = 0; + + private static final int CONCEPT_PATH = 1; + + private static final int NUMERIC_VALUE = 2; + + private static final int TEXT_VALUE = 3; + + public static void main(String[] args) throws ClassNotFoundException, FileNotFoundException, IOException { + VariantStore variantStore = VariantStore.readInstance("/opt/local/hpds/all/"); + + String[] oldPatientIds = variantStore.getPatientIds(); + String[] newPatientIds = new String[oldPatientIds.length]; + + CsvReader reader = new CsvReader(); + CsvContainer csv = reader.read(new FileReader("/opt/local/hpds/mappings.csv")); + for (CsvRow row : csv.getRows()) { + String oldId = row.getField(0); + String newId = row.getField(1); + for (int x = 0; x < oldPatientIds.length; x++) { + if (oldPatientIds[x].contentEquals(oldId.trim())) { + newPatientIds[x] = newId; + System.out.println(oldId + ", " + newId); + } + } + } + variantStore.setPatientIds(newPatientIds); + + ObjectOutputStream out = + new ObjectOutputStream(new GZIPOutputStream(new FileOutputStream("/opt/local/hpds/all/variantStoreRemapped.javabin"))); + out.writeObject(variantStore); + out.flush(); + out.close(); + } + +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/DumpSourceCSV.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/DumpSourceCSV.java new file mode 100644 index 000000000..e2dd7df9d --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/DumpSourceCSV.java @@ -0,0 +1,118 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.util; + +import java.io.*; +import java.util.ArrayList; +import java.util.Set; +import java.util.TreeMap; +import java.util.TreeSet; +import java.util.Map.Entry; +import java.util.concurrent.ExecutionException; +import java.util.zip.GZIPInputStream; + +import org.apache.commons.csv.CSVFormat; +import org.apache.commons.csv.CSVPrinter; + +import com.google.common.cache.CacheBuilder; +import com.google.common.cache.CacheLoader; +import com.google.common.cache.LoadingCache; +import com.google.common.collect.ImmutableList; + +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.KeyAndValue; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.etl.LoadingStore; + +public class DumpSourceCSV { + protected static LoadingCache> store; + + protected static TreeMap metaStoreSource; + + protected static TreeSet allIds; + + private static final int PATIENT_NUM = 0; + + private static final int CONCEPT_PATH = 1; + + private static final int NUMERIC_VALUE = 2; + + private static final int TEXT_VALUE = 3; + + private static final int TIMESTAMP = 4; + + public static void main(String[] args) throws ClassNotFoundException, FileNotFoundException, IOException { + Object[] metadata = loadMetadata(); + metaStoreSource = (TreeMap) metadata[0]; + allIds = (TreeSet) metadata[1]; + store = initializeCache(); + FileWriter fWriter = new FileWriter("/opt/local/hpds/allConcepts.csv"); + CSVPrinter writer = CSVFormat.DEFAULT.print(fWriter); + writer.printRecord(ImmutableList.of(new String[] {"PATIENT_NUM", "CONCEPT_PATH", "NUMERIC_VALUE", "TEXT_VALUE", "TIMESTAMP"})); + metaStoreSource.keySet().forEach((String key) -> { + try { + PhenoCube cube = store.get(key); + ArrayList cubeLines = new ArrayList<>(); + for (KeyAndValue kv : cube.sortedByKey()) { + String[] line = new String[5]; + line[PATIENT_NUM] = kv.getKey().toString(); + line[CONCEPT_PATH] = key; + line[NUMERIC_VALUE] = cube.isStringType() ? "" : kv.getValue().toString(); + line[TEXT_VALUE] = cube.isStringType() ? kv.getValue().toString() : ""; + line[TIMESTAMP] = kv.getTimestamp() == null ? null : kv.getTimestamp().toString(); + cubeLines.add(line); + } + writer.printRecords(cubeLines); + } catch (ExecutionException e) { + throw new RuntimeException(e); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + }); + writer.flush(); + writer.close(); + } + + static LoadingStore loadingStoreSource = new LoadingStore(); + + protected static Object[] loadMetadata() { + try ( + ObjectInputStream objectInputStream = + new ObjectInputStream(new GZIPInputStream(new FileInputStream("/opt/local/hpds/columnMeta.javabin"))); + ) { + TreeMap metastore = (TreeMap) objectInputStream.readObject(); + TreeMap metastoreScrubbed = new TreeMap(); + for (Entry entry : metastore.entrySet()) { + metastoreScrubbed.put(entry.getKey().replaceAll("\\ufffd", ""), entry.getValue()); + } + Set allIds = (TreeSet) objectInputStream.readObject(); + return new Object[] {metastoreScrubbed, allIds}; + } catch (IOException | ClassNotFoundException e) { + throw new RuntimeException("Could not load metastore"); + } + } + + protected static LoadingCache> initializeCache() + throws ClassNotFoundException, FileNotFoundException, IOException { + return CacheBuilder.newBuilder().maximumSize(100).build(new CacheLoader>() { + public PhenoCube load(String key) throws Exception { + try (RandomAccessFile allObservationsStore = new RandomAccessFile("/opt/local/hpds/allObservationsStore.javabin", "r");) { + ColumnMeta columnMeta = metaStoreSource.get(key); + if (columnMeta != null) { + allObservationsStore.seek(columnMeta.getAllObservationsOffset()); + int length = (int) (columnMeta.getAllObservationsLength() - columnMeta.getAllObservationsOffset()); + byte[] buffer = new byte[length]; + allObservationsStore.read(buffer); + allObservationsStore.close(); + ObjectInputStream inStream = new ObjectInputStream(new ByteArrayInputStream(Crypto.decryptData(buffer))); + PhenoCube ret = (PhenoCube) inStream.readObject(); + inStream.close(); + return ret; + } else { + System.out.println("ColumnMeta not found for : [" + key + "]"); + return null; + } + } + } + }); + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/FixCategoricalConcepts.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/FixCategoricalConcepts.java new file mode 100644 index 000000000..c6e51ad95 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/FixCategoricalConcepts.java @@ -0,0 +1,200 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.util; + +import java.io.*; +import java.util.*; +import java.util.Map.Entry; +import java.util.concurrent.ExecutionException; +import java.util.zip.GZIPInputStream; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.common.cache.CacheBuilder; +import com.google.common.cache.CacheLoader; +import com.google.common.cache.CacheLoader.InvalidCacheLoadException; +import com.google.common.cache.LoadingCache; + +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.KeyAndValue; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.etl.LoadingStore; + +@SuppressWarnings({"unchecked", "rawtypes"}) +public class FixCategoricalConcepts { + + private static LoadingStore store = new LoadingStore(); + + private static Logger log = LoggerFactory.getLogger(FixCategoricalConcepts.class); + + protected static LoadingCache> sourceStore; + + protected static TreeMap sourceMetaStore; + + private static final int PATIENT_NUM = 0; + + private static final int CONCEPT_PATH = 1; + + private static final int NUMERIC_VALUE = 2; + + private static final int TEXT_VALUE = 3; + + private static final int TIMESTAMP = 4; + + private static String HPDS_DIRECTORY = "/opt/local/hpds/"; + + public static void main(String[] args) throws IOException, ClassNotFoundException, ExecutionException { + sourceStore = initializeCache(); + Object[] metadata = loadMetadata(); + sourceMetaStore = (TreeMap) metadata[0]; + store.allObservationsStore = new RandomAccessFile(HPDS_DIRECTORY + "allObservationsStore.javabin", "rw"); + initialLoad(); + store.saveStore(HPDS_DIRECTORY); + } + + private static void initialLoad() throws IOException, ExecutionException { + final PhenoCube[] currentConcept = new PhenoCube[1]; + Map> conceptsToMerge = new TreeMap>(); + for (String conceptPath : sourceMetaStore.keySet()) { + if (conceptPath.endsWith("/")) { + // this is a potentially bugged categorical concept + String correctConcept = conceptPath.substring(0, conceptPath.lastIndexOf("\\")); + List sisterConcepts = conceptsToMerge.get(correctConcept); + if (sisterConcepts == null) { + sisterConcepts = new ArrayList(); + conceptsToMerge.put(correctConcept, sisterConcepts); + } + sisterConcepts.add(conceptPath); + } else { + conceptsToMerge.put(conceptPath, List.of(conceptPath)); + } + } + for (String conceptPath : conceptsToMerge.keySet()) { + for (String concept : conceptsToMerge.get(conceptPath)) { + PhenoCube cubeForPath = sourceStore.get(concept); + for (KeyAndValue entry : cubeForPath.sortedByKey()) { + processRecord( + currentConcept, + List.of( + entry.getKey().toString(), conceptPath, cubeForPath.isStringType() ? "" : entry.getValue().toString(), + cubeForPath.isStringType() ? entry.getValue().toString() : "" + ) + ); + } + } + } + } + + private static void processRecord(final PhenoCube[] currentConcept, List record) { + try { + String conceptPathFromRow = record.get(CONCEPT_PATH); + String[] segments = conceptPathFromRow.split("\\\\"); + for (int x = 0; x < segments.length; x++) { + segments[x] = segments[x].trim(); + } + conceptPathFromRow = String.join("\\", segments) + "\\"; + conceptPathFromRow = conceptPathFromRow.replaceAll("\\ufffd", ""); + String textValueFromRow = record.get(TEXT_VALUE) == null ? null : record.get(TEXT_VALUE).trim(); + if (textValueFromRow != null) { + textValueFromRow = textValueFromRow.replaceAll("\\ufffd", ""); + } + String conceptPath = + conceptPathFromRow.endsWith("\\" + textValueFromRow + "\\") ? conceptPathFromRow.replaceAll("\\\\[^\\\\]*\\\\$", "\\\\") + : conceptPathFromRow; + // This is not getDouble because we need to handle null values, not coerce them into 0s + String numericValue = record.get(NUMERIC_VALUE); + if ((numericValue == null || numericValue.isEmpty()) && textValueFromRow != null) { + try { + numericValue = Double.parseDouble(textValueFromRow) + ""; + } catch (NumberFormatException e) { + + } + } + boolean isAlpha = (numericValue == null || numericValue.isEmpty()); + if (currentConcept[0] == null || !currentConcept[0].name.equals(conceptPath)) { + System.out.println(conceptPath); + try { + currentConcept[0] = store.store.get(conceptPath); + } catch (InvalidCacheLoadException e) { + currentConcept[0] = new PhenoCube(conceptPath, isAlpha ? String.class : Double.class); + store.store.put(conceptPath, currentConcept[0]); + } + } + String value = isAlpha ? record.get(TEXT_VALUE) : numericValue; + + if ( + value != null && !value.trim().isEmpty() + && ((isAlpha && currentConcept[0].vType == String.class) || (!isAlpha && currentConcept[0].vType == Double.class)) + ) { + value = value.trim(); + currentConcept[0] + .setColumnWidth(isAlpha ? Math.max(currentConcept[0].getColumnWidth(), value.getBytes().length) : Double.BYTES); + currentConcept[0].add( + Integer.parseInt(record.get(PATIENT_NUM)), isAlpha ? value : Double.parseDouble(value), new Date(record.get(TIMESTAMP)) + ); + store.allIds.add(Integer.parseInt(record.get(PATIENT_NUM))); + } + } catch (ExecutionException e) { + log.error("Error processing record", e); + } + } + + /** + * Load the variantStore object from disk and build the PhenoCube cache. + * + * @return + * @throws ClassNotFoundException + * @throws FileNotFoundException + * @throws IOException + */ + protected static LoadingCache> initializeCache() + throws ClassNotFoundException, FileNotFoundException, IOException { + return CacheBuilder.newBuilder().maximumSize(10).build(new CacheLoader>() { + public PhenoCube load(String key) throws Exception { + try (RandomAccessFile allObservationsStore = new RandomAccessFile("/opt/local/source/allObservationsStore.javabin", "r");) { + ColumnMeta columnMeta = sourceMetaStore.get(key); + if (columnMeta != null) { + allObservationsStore.seek(columnMeta.getAllObservationsOffset()); + int length = (int) (columnMeta.getAllObservationsLength() - columnMeta.getAllObservationsOffset()); + byte[] buffer = new byte[length]; + allObservationsStore.read(buffer); + allObservationsStore.close(); + ObjectInputStream inStream = new ObjectInputStream(new ByteArrayInputStream(Crypto.decryptData(buffer))); + PhenoCube ret = (PhenoCube) inStream.readObject(); + inStream.close(); + return ret; + } else { + System.out.println("ColumnMeta not found for : [" + key + "]"); + return null; + } + } + } + }); + } + + protected static Object[] loadMetadata() { + try ( + ObjectInputStream objectInputStream = + new ObjectInputStream(new GZIPInputStream(new FileInputStream("/opt/local/source/columnMeta.javabin"))); + ) { + TreeMap metastore = (TreeMap) objectInputStream.readObject(); + TreeMap metastoreScrubbed = new TreeMap(); + for (Entry entry : metastore.entrySet()) { + metastoreScrubbed.put(entry.getKey().replaceAll("\\ufffd", ""), entry.getValue()); + } + Set allIds = (TreeSet) objectInputStream.readObject(); + return new Object[] {metastoreScrubbed, allIds}; + } catch (IOException | ClassNotFoundException e) { + log.warn("************************************************"); + log.warn("************************************************"); + log.warn("Could not load metastore", e); + log.warn( + "If you meant to include phenotype data of any kind, please check that the file /opt/local/source/columnMeta.javabin exists and is readable by the service." + ); + log.warn("************************************************"); + log.warn("************************************************"); + return new Object[] {new TreeMap(), new TreeSet()}; + } + } + +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RekeyDataset.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RekeyDataset.java new file mode 100644 index 000000000..de230b1dc --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RekeyDataset.java @@ -0,0 +1,116 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.util; + +import java.io.*; +import java.util.Map.Entry; +import java.util.Set; +import java.util.TreeMap; +import java.util.TreeSet; +import java.util.concurrent.ExecutionException; +import java.util.zip.GZIPInputStream; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.common.cache.CacheBuilder; +import com.google.common.cache.CacheLoader; +import com.google.common.cache.LoadingCache; + +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.etl.LoadingStore; + +@SuppressWarnings({"unchecked"}) +public class RekeyDataset { + + private static final String SOURCE = "SOURCE"; + + private static LoadingStore store = new LoadingStore(); + + private static Logger log = LoggerFactory.getLogger(RekeyDataset.class); + + protected static LoadingCache> sourceStore; + + protected static TreeMap sourceMetaStore; + + private static String HPDS_DIRECTORY = "/opt/local/hpds/"; + + public static void main(String[] args) throws IOException, ClassNotFoundException, ExecutionException { + Crypto.loadDefaultKey(); + Crypto.loadKey(SOURCE, "/opt/local/source/encryption_key"); + sourceStore = initializeCache(); + Object[] metadata = loadMetadata(); + sourceMetaStore = (TreeMap) metadata[0]; + store.allObservationsStore = new RandomAccessFile(HPDS_DIRECTORY + "allObservationsStore.javabin", "rw"); + store.allIds = (TreeSet) metadata[1]; + initialLoad(); + + store.saveStore(HPDS_DIRECTORY); + } + + private static void initialLoad() throws IOException, ExecutionException { + for (String conceptPath : sourceMetaStore.keySet()) { + PhenoCube cube = sourceStore.get(conceptPath); + store.store.put(conceptPath, cube); + } + } + + /** + * Build the PhenoCube cache. + * + * @return + * @throws ClassNotFoundException + * @throws FileNotFoundException + * @throws IOException + */ + protected static LoadingCache> initializeCache() + throws ClassNotFoundException, FileNotFoundException, IOException { + return CacheBuilder.newBuilder().maximumSize(10).build(new CacheLoader>() { + public PhenoCube load(String key) throws Exception { + try (RandomAccessFile allObservationsStore = new RandomAccessFile("/opt/local/source/allObservationsStore.javabin", "r");) { + ColumnMeta columnMeta = sourceMetaStore.get(key); + if (columnMeta != null) { + allObservationsStore.seek(columnMeta.getAllObservationsOffset()); + int length = (int) (columnMeta.getAllObservationsLength() - columnMeta.getAllObservationsOffset()); + byte[] buffer = new byte[length]; + allObservationsStore.read(buffer); + allObservationsStore.close(); + ObjectInputStream inStream = new ObjectInputStream(new ByteArrayInputStream(Crypto.decryptData(SOURCE, buffer))); + PhenoCube ret = (PhenoCube) inStream.readObject(); + inStream.close(); + return ret; + } else { + System.out.println("ColumnMeta not found for : [" + key + "]"); + return null; + } + } + } + }); + } + + protected static Object[] loadMetadata() { + try ( + ObjectInputStream objectInputStream = + new ObjectInputStream(new GZIPInputStream(new FileInputStream("/opt/local/source/columnMeta.javabin"))); + ) { + TreeMap metastore = (TreeMap) objectInputStream.readObject(); + TreeMap metastoreScrubbed = new TreeMap(); + for (Entry entry : metastore.entrySet()) { + metastoreScrubbed.put(entry.getKey().replaceAll("\\ufffd", ""), entry.getValue()); + } + Set allIds = (TreeSet) objectInputStream.readObject(); + return new Object[] {metastoreScrubbed, allIds}; + } catch (IOException | ClassNotFoundException e) { + log.warn("************************************************"); + log.warn("************************************************"); + log.warn("Could not load metastore", e); + log.warn( + "If you meant to include phenotype data of any kind, please check that the file /opt/local/source/columnMeta.javabin exists and is readable by the service." + ); + log.warn("************************************************"); + log.warn("************************************************"); + return new Object[] {new TreeMap(), new TreeSet()}; + } + } + +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RemapIds.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RemapIds.java new file mode 100644 index 000000000..3d18719d1 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RemapIds.java @@ -0,0 +1,205 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.util; + +import java.io.*; +import java.util.*; +import java.util.Map.Entry; +import java.util.concurrent.ExecutionException; +import java.util.zip.GZIPInputStream; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.common.cache.CacheBuilder; +import com.google.common.cache.CacheLoader; +import com.google.common.cache.CacheLoader.InvalidCacheLoadException; +import com.google.common.cache.LoadingCache; + +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.KeyAndValue; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.etl.LoadingStore; + +@SuppressWarnings({"unchecked", "rawtypes"}) +public class RemapIds { + + private static LoadingStore store = new LoadingStore(); + + private static Logger log = LoggerFactory.getLogger(RemapIds.class); + + protected static LoadingCache> sourceStore; + + protected static TreeMap sourceMetaStore; + + private static HashMap patientIdMap; + + private static final int PATIENT_NUM = 0; + + private static final int CONCEPT_PATH = 1; + + private static final int NUMERIC_VALUE = 2; + + private static final int TEXT_VALUE = 3; + + private static final int TIMESTAMP = 4; + + private static String HPDS_DIRECTORY = "/opt/local/hpds/"; + + public static void main(String[] args) throws IOException, ClassNotFoundException, ExecutionException { + loadPatientIdMap(); + sourceStore = initializeCache(); + Object[] metadata = loadMetadata(); + sourceMetaStore = (TreeMap) metadata[0]; + store.allObservationsStore = new RandomAccessFile("/opt/local/hpds/allObservationsStore.javabin", "rw"); + initialLoad(); + store.saveStore(HPDS_DIRECTORY); + } + + private static void loadPatientIdMap() throws IOException { + patientIdMap = new HashMap(); + BufferedReader reader = new BufferedReader(new FileReader("/opt/local/source/idMapping.csv")); + String line = reader.readLine(); + while (line != null) { + String[] mapping = line.split(","); + patientIdMap.put(mapping[0].replaceAll("\"", ""), mapping[1].replaceAll("\"", "")); + line = reader.readLine(); + } + reader.close(); + } + + private static void initialLoad() throws IOException, ExecutionException { + final PhenoCube[] currentConcept = new PhenoCube[1]; + for (String conceptPath : sourceMetaStore.keySet()) { + PhenoCube cubeForPath = sourceStore.get(conceptPath); + for (KeyAndValue entry : cubeForPath.sortedByKey()) { + processRecord( + currentConcept, + List.of( + entry.getKey().toString(), conceptPath, cubeForPath.isStringType() ? "" : entry.getValue().toString(), + cubeForPath.isStringType() ? entry.getValue().toString() : "", + entry.getTimestamp() == null ? null : entry.getTimestamp().toString() + ) + ); + } + } + } + + private static void processRecord(final PhenoCube[] currentConcept, List record) { + try { + String conceptPathFromRow = record.get(CONCEPT_PATH); + String[] segments = conceptPathFromRow.split("\\\\"); + for (int x = 0; x < segments.length; x++) { + segments[x] = segments[x].trim(); + } + conceptPathFromRow = String.join("\\", segments) + "\\"; + conceptPathFromRow = conceptPathFromRow.replaceAll("\\ufffd", ""); + String textValueFromRow = record.get(TEXT_VALUE) == null ? null : record.get(TEXT_VALUE).trim(); + if (textValueFromRow != null) { + textValueFromRow = textValueFromRow.replaceAll("\\ufffd", ""); + } + String conceptPath = + conceptPathFromRow.endsWith("\\" + textValueFromRow + "\\") ? conceptPathFromRow.replaceAll("\\\\[^\\\\]*\\\\$", "\\\\") + : conceptPathFromRow; + // This is not getDouble because we need to handle null values, not coerce them into 0s + String numericValue = record.get(NUMERIC_VALUE); + if ((numericValue == null || numericValue.isEmpty()) && textValueFromRow != null) { + try { + numericValue = Double.parseDouble(textValueFromRow) + ""; + } catch (NumberFormatException e) { + + } + } + boolean isAlpha = (numericValue == null || numericValue.isEmpty()); + if (currentConcept[0] == null || !currentConcept[0].name.equals(conceptPath)) { + System.out.println(conceptPath); + try { + currentConcept[0] = store.store.get(conceptPath); + } catch (InvalidCacheLoadException e) { + currentConcept[0] = new PhenoCube(conceptPath, isAlpha ? String.class : Double.class); + store.store.put(conceptPath, currentConcept[0]); + } + } + String value = isAlpha ? record.get(TEXT_VALUE) : numericValue; + + if ( + value != null && !value.trim().isEmpty() + && ((isAlpha && currentConcept[0].vType == String.class) || (!isAlpha && currentConcept[0].vType == Double.class)) + ) { + value = value.trim(); + currentConcept[0] + .setColumnWidth(isAlpha ? Math.max(currentConcept[0].getColumnWidth(), value.getBytes().length) : Double.BYTES); + int patientId = Integer.parseInt(mapId(record.get(PATIENT_NUM))); + currentConcept[0].add( + patientId, isAlpha ? value : Double.parseDouble(value), + record.get(TIMESTAMP) == null ? null : new Date(Long.parseLong(record.get(TIMESTAMP))) + ); + store.allIds.add(patientId); + } + } catch (ExecutionException e) { + log.error("Error processing record", e); + } + } + + private static String mapId(String string) { + return patientIdMap.containsKey(string) ? patientIdMap.get(string) : string; + } + + /** + * Load the variantStore object from disk and build the PhenoCube cache. + * + * @return + * @throws ClassNotFoundException + * @throws FileNotFoundException + * @throws IOException + */ + protected static LoadingCache> initializeCache() + throws ClassNotFoundException, FileNotFoundException, IOException { + return CacheBuilder.newBuilder().maximumSize(10).build(new CacheLoader>() { + public PhenoCube load(String key) throws Exception { + try (RandomAccessFile allObservationsStore = new RandomAccessFile("/opt/local/source/allObservationsStore.javabin", "r");) { + ColumnMeta columnMeta = sourceMetaStore.get(key); + if (columnMeta != null) { + allObservationsStore.seek(columnMeta.getAllObservationsOffset()); + int length = (int) (columnMeta.getAllObservationsLength() - columnMeta.getAllObservationsOffset()); + byte[] buffer = new byte[length]; + allObservationsStore.read(buffer); + allObservationsStore.close(); + ObjectInputStream inStream = new ObjectInputStream(new ByteArrayInputStream(Crypto.decryptData(buffer))); + PhenoCube ret = (PhenoCube) inStream.readObject(); + inStream.close(); + return ret; + } else { + System.out.println("ColumnMeta not found for : [" + key + "]"); + return null; + } + } + } + }); + } + + protected static Object[] loadMetadata() { + try ( + ObjectInputStream objectInputStream = + new ObjectInputStream(new GZIPInputStream(new FileInputStream("/opt/local/source/columnMeta.javabin"))); + ) { + TreeMap metastore = (TreeMap) objectInputStream.readObject(); + TreeMap metastoreScrubbed = new TreeMap(); + for (Entry entry : metastore.entrySet()) { + metastoreScrubbed.put(entry.getKey().replaceAll("\\ufffd", ""), entry.getValue()); + } + Set allIds = (TreeSet) objectInputStream.readObject(); + return new Object[] {metastoreScrubbed, allIds}; + } catch (IOException | ClassNotFoundException e) { + log.warn("************************************************"); + log.warn("************************************************"); + log.warn("Could not load metastore", e); + log.warn( + "If you meant to include phenotype data of any kind, please check that the file /opt/local/source/columnMeta.javabin exists and is readable by the service." + ); + log.warn("************************************************"); + log.warn("************************************************"); + return new Object[] {new TreeMap(), new TreeSet()}; + } + } + +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RemoveConceptFromMetadata.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RemoveConceptFromMetadata.java new file mode 100644 index 000000000..208525b69 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RemoveConceptFromMetadata.java @@ -0,0 +1,85 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.util; + +import java.io.BufferedReader; +import java.io.File; +import java.io.FileInputStream; +import java.io.FileNotFoundException; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.ObjectInputStream; +import java.io.ObjectOutputStream; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.Set; +import java.util.TreeMap; +import java.util.TreeSet; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; + +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; + +/** + * + * This util will remove a concept path from the columnMetadata.java + * + * + * @author Thomas DeSain + * + */ +public class RemoveConceptFromMetadata { + + protected static final String COLUMN_META_FILE = "/opt/local/hpds/columnMeta.javabin"; + + protected static final String CONCEPTS_TO_REMOVE = "/opt/local/hpds/conceptsToRemove.txt"; + protected static Set allIds; + + public static void main(String[] args) throws ClassNotFoundException, FileNotFoundException, IOException { + + if (!Files.exists(Paths.get(CONCEPTS_TO_REMOVE))) { + throw new RuntimeException("Columns to remove file - " + CONCEPTS_TO_REMOVE + " - does not exist!"); + + } + if (!Files.exists(Paths.get(COLUMN_META_FILE))) { + throw new RuntimeException("Column Metadata file - " + COLUMN_META_FILE + " - does not exist!"); + } + + TreeMap metadata = removeMetadata(Paths.get(CONCEPTS_TO_REMOVE)); + + ObjectOutputStream metaOut = new ObjectOutputStream(new GZIPOutputStream(new FileOutputStream(new File(COLUMN_META_FILE)))); + + metaOut.writeObject(metadata); + + metaOut.writeObject(allIds); + metaOut.flush(); + metaOut.close(); + } + + protected static TreeMap removeMetadata(Path filePath) { + + try (ObjectInputStream objectInputStream = new ObjectInputStream(new GZIPInputStream(new FileInputStream(COLUMN_META_FILE)))) { + + TreeMap metastore = (TreeMap) objectInputStream.readObject(); + + allIds = (TreeSet) objectInputStream.readObject(); + + System.out.println("allIds size = " + allIds.size()); + + try (BufferedReader reader = Files.newBufferedReader(filePath)) { + + String conceptPathToRemove; + + while ((conceptPathToRemove = reader.readLine()) != null) { + + metastore.remove(conceptPathToRemove); + + } + + } + + return metastore; + } catch (IOException | ClassNotFoundException e) { + throw new RuntimeException("Could not load metastore"); + } + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RenameCategories.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RenameCategories.java new file mode 100644 index 000000000..414c1437c --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RenameCategories.java @@ -0,0 +1,102 @@ +package edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.util; + +import java.io.ByteArrayInputStream; +import java.io.FileInputStream; +import java.io.FileNotFoundException; +import java.io.IOException; +import java.io.ObjectInputStream; +import java.io.RandomAccessFile; +import java.util.Collections; +import java.util.Set; +import java.util.TreeMap; +import java.util.TreeSet; +import java.util.concurrent.ExecutionException; +import java.util.Map.Entry; + +import com.google.common.cache.CacheBuilder; +import com.google.common.cache.CacheLoader; +import com.google.common.cache.LoadingCache; + +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.etl.LoadingStore; + +public class RenameCategories { + + protected static LoadingCache> store; + + protected static TreeMap metaStoreSource; + + protected static TreeMap metaStoreTarget; + + protected static TreeSet allIds; + + public static void main(String[] args) throws ClassNotFoundException, FileNotFoundException, IOException { + String conceptPath = args[0]; + String oldCategoryName = args[1]; + String newCategoryName = args[2]; + Object[] metadata = loadMetadata(); + metaStoreSource = (TreeMap) metadata[0]; + allIds = (TreeSet) metadata[1]; + ColumnMeta meta = metaStoreSource.remove(conceptPath); + meta.getCategoryValues().remove(oldCategoryName); + meta.getCategoryValues().add(newCategoryName); + Collections.sort(meta.getCategoryValues()); + store = initializeCache(); + LoadingStore loadingStoreTarget = new LoadingStore(); + metaStoreSource.keySet().forEach((String key) -> { + try { + loadingStoreTarget.store.put(key, store.get(key)); + } catch (ExecutionException e) { + throw new RuntimeException(e); + } + }); + } + + static LoadingStore loadingStoreSource = new LoadingStore(); + + protected static Object[] loadMetadata() { + try ( + ObjectInputStream objectInputStream = new ObjectInputStream(new FileInputStream("/opt/local/hpds/source/columnMeta.javabin")); + ) { + TreeMap metastore = (TreeMap) objectInputStream.readObject(); + TreeMap metastoreScrubbed = new TreeMap(); + for (Entry entry : metastore.entrySet()) { + metastoreScrubbed.put(entry.getKey().replaceAll("\\ufffd", ""), entry.getValue()); + } + Set allIds = (TreeSet) objectInputStream.readObject(); + return new Object[] {metastoreScrubbed, allIds}; + } catch (IOException | ClassNotFoundException e) { + throw new RuntimeException("Could not load metastore"); + } + } + + protected static LoadingCache> initializeCache() + throws ClassNotFoundException, FileNotFoundException, IOException { + return CacheBuilder.newBuilder().maximumSize(100).build(new CacheLoader>() { + public PhenoCube load(String key) throws Exception { + try ( + RandomAccessFile allObservationsStore = + new RandomAccessFile("/opt/local/hpds/source/allObservationsStore.javabin", "r"); + ) { + ColumnMeta columnMeta = metaStoreSource.get(key); + if (columnMeta != null) { + allObservationsStore.seek(columnMeta.getAllObservationsOffset()); + int length = (int) (columnMeta.getAllObservationsLength() - columnMeta.getAllObservationsOffset()); + byte[] buffer = new byte[length]; + allObservationsStore.read(buffer); + allObservationsStore.close(); + ObjectInputStream inStream = new ObjectInputStream(new ByteArrayInputStream(Crypto.decryptData(buffer))); + PhenoCube ret = (PhenoCube) inStream.readObject(); + inStream.close(); + return ret; + } else { + System.out.println("ColumnMeta not found for : [" + key + "]"); + return null; + } + } + } + }); + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/LoadingStore.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/LoadingStore.java new file mode 100644 index 000000000..e2dca71ec --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/LoadingStore.java @@ -0,0 +1,225 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl; + +import java.io.*; +import java.nio.file.Files; +import java.nio.file.Paths; +import java.nio.file.StandardOpenOption; +import java.util.*; +import java.util.concurrent.atomic.AtomicInteger; +import java.util.stream.Collectors; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; + +import org.apache.commons.csv.CSVFormat; +import org.apache.commons.csv.CSVPrinter; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.common.cache.*; + +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.KeyAndValue; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; + +public class LoadingStore { + + public RandomAccessFile allObservationsStore; + + TreeMap metadataMap = new TreeMap<>(); + + private static Logger log = LoggerFactory.getLogger(LoadingStore.class); + + public LoadingCache store = + CacheBuilder.newBuilder().maximumSize(16).removalListener(new RemovalListener() { + + @Override + public void onRemoval(RemovalNotification arg0) { + log.debug("removing " + arg0.getKey()); + if (arg0.getValue().getLoadingMap() != null) { + complete(arg0.getValue()); + } + try { + ColumnMeta columnMeta = new ColumnMeta().setName(arg0.getKey()).setWidthInBytes(arg0.getValue().getColumnWidth()) + .setCategorical(arg0.getValue().isStringType()); + + columnMeta.setAllObservationsOffset(allObservationsStore.getFilePointer()); + columnMeta.setObservationCount(arg0.getValue().sortedByKey().length); + columnMeta.setPatientCount(Arrays.stream(arg0.getValue().sortedByKey()).map((kv) -> { + return kv.getKey(); + }).collect(Collectors.toSet()).size()); + if (columnMeta.isCategorical()) { + columnMeta.setCategoryValues(new ArrayList(new TreeSet(arg0.getValue().keyBasedArray()))); + } else { + List map = (List) arg0.getValue().keyBasedArray().stream().map((value) -> { + return (Double) value; + }).collect(Collectors.toList()); + double min = Double.MAX_VALUE; + double max = Double.MIN_VALUE; + for (double f : map) { + min = Double.min(min, f); + max = Double.max(max, f); + } + columnMeta.setMin(min); + columnMeta.setMax(max); + } + ByteArrayOutputStream byteStream = new ByteArrayOutputStream(); + + ObjectOutputStream out = new ObjectOutputStream(byteStream); + out.writeObject(arg0.getValue()); + out.flush(); + out.close(); + + allObservationsStore.write(Crypto.encryptData(byteStream.toByteArray())); + columnMeta.setAllObservationsLength(allObservationsStore.getFilePointer()); + metadataMap.put(columnMeta.getName(), columnMeta); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + } + + private > void complete(PhenoCube cube) { + ArrayList> entryList = new ArrayList>(cube.getLoadingMap().stream().map((entry) -> { + return new KeyAndValue(entry.getKey(), entry.getValue(), entry.getTimestamp()); + }).collect(Collectors.toList())); + + List> sortedByKey = + entryList.stream().sorted(Comparator.comparing(KeyAndValue::getKey)).collect(Collectors.toList()); + cube.setSortedByKey(sortedByKey.toArray(new KeyAndValue[0])); + + if (cube.isStringType()) { + TreeMap> categoryMap = new TreeMap<>(); + for (KeyAndValue entry : cube.sortedByValue()) { + if (!categoryMap.containsKey(entry.getValue())) { + categoryMap.put(entry.getValue(), new LinkedList()); + } + categoryMap.get(entry.getValue()).add(entry.getKey()); + } + TreeMap> categorySetMap = new TreeMap<>(); + categoryMap.entrySet().stream().forEach((entry) -> { + categorySetMap.put(entry.getKey(), new TreeSet(entry.getValue())); + }); + cube.setCategoryMap(categorySetMap); + } + + } + }).build(new CacheLoader() { + public PhenoCube load(String key) throws Exception { + log.debug("Loading cube: " + key); + return null; + } + }); + + public TreeSet allIds = new TreeSet(); + + public void saveStore(String hpdsDirectory) throws IOException { + System.out.println("Invalidating store"); + store.invalidateAll(); + store.cleanUp(); + System.out.println("Writing metadata"); + ObjectOutputStream metaOut = + new ObjectOutputStream(new GZIPOutputStream(new FileOutputStream(hpdsDirectory + "columnMeta.javabin"))); + metaOut.writeObject(metadataMap); + metaOut.writeObject(allIds); + metaOut.flush(); + metaOut.close(); + System.out.println("Closing Store"); + allObservationsStore.close(); + dumpStatsAndColumnMeta(hpdsDirectory); + } + + public void dumpStats() { + System.out.println("Dumping Stats"); + try ( + ObjectInputStream objectInputStream = + new ObjectInputStream(new GZIPInputStream(new FileInputStream("/opt/local/hpds/columnMeta.javabin"))); + ) { + TreeMap metastore = (TreeMap) objectInputStream.readObject(); + Set allIds = (TreeSet) objectInputStream.readObject(); + + long totalNumberOfObservations = 0; + + System.out.println("\n\nConceptPath\tObservationCount\tMinNumValue\tMaxNumValue\tCategoryValues"); + for (String key : metastore.keySet()) { + ColumnMeta columnMeta = metastore.get(key); + System.out.println( + String.join( + "\t", key.toString(), columnMeta.getObservationCount() + "", + columnMeta.getMin() == null ? "NaN" : columnMeta.getMin().toString(), + columnMeta.getMax() == null ? "NaN" : columnMeta.getMax().toString(), + columnMeta.getCategoryValues() == null ? "NUMERIC CONCEPT" + : String.join(",", columnMeta.getCategoryValues().stream().map((value) -> { + return value == null ? "NULL_VALUE" : "\"" + value + "\""; + }).collect(Collectors.toList())) + ) + ); + totalNumberOfObservations += columnMeta.getObservationCount(); + } + + System.out.println("Total Number of Concepts : " + metastore.size()); + System.out.println("Total Number of Patients : " + allIds.size()); + System.out.println("Total Number of Observations : " + totalNumberOfObservations); + + } catch (IOException | ClassNotFoundException e) { + throw new RuntimeException("Could not load metastore"); + } + } + + /** + * This method will display counts for the objects stored in the metadata. This will also write out a csv file used by the data + * dictionary importer. + */ + public void dumpStatsAndColumnMeta(String hpdsDirectory) { + try ( + ObjectInputStream objectInputStream = + new ObjectInputStream(new GZIPInputStream(new FileInputStream(hpdsDirectory + "columnMeta.javabin"))) + ) { + TreeMap metastore = (TreeMap) objectInputStream.readObject(); + try ( + BufferedWriter writer = Files.newBufferedWriter( + Paths.get(hpdsDirectory + "columnMeta.csv"), StandardOpenOption.CREATE, StandardOpenOption.TRUNCATE_EXISTING + ) + ) { + CSVPrinter printer = new CSVPrinter(writer, CSVFormat.DEFAULT); + for (String key : metastore.keySet()) { + ColumnMeta columnMeta = metastore.get(key); + Object[] columnMetaOut = new Object[11]; + + StringBuilder listQuoted = new StringBuilder(); + AtomicInteger x = new AtomicInteger(1); + + if (columnMeta.getCategoryValues() != null) { + if (!columnMeta.getCategoryValues().isEmpty()) { + columnMeta.getCategoryValues().forEach(string -> { + listQuoted.append(string); + if (x.get() != columnMeta.getCategoryValues().size()) listQuoted.append("µ"); + x.incrementAndGet(); + }); + } + } + + columnMetaOut[0] = columnMeta.getName(); + columnMetaOut[1] = String.valueOf(columnMeta.getWidthInBytes()); + columnMetaOut[2] = String.valueOf(columnMeta.getColumnOffset()); + columnMetaOut[3] = String.valueOf(columnMeta.isCategorical()); + // this should nest the list of values in a list inside the String array. + columnMetaOut[4] = listQuoted; + columnMetaOut[5] = String.valueOf(columnMeta.getMin()); + columnMetaOut[6] = String.valueOf(columnMeta.getMax()); + columnMetaOut[7] = String.valueOf(columnMeta.getAllObservationsOffset()); + columnMetaOut[8] = String.valueOf(columnMeta.getAllObservationsLength()); + columnMetaOut[9] = String.valueOf(columnMeta.getObservationCount()); + columnMetaOut[10] = String.valueOf(columnMeta.getPatientCount()); + + printer.printRecord(columnMetaOut); + } + + writer.flush(); + } + + } catch (IOException | ClassNotFoundException e) { + throw new RuntimeException("Could not load metastore", e); + } + } + +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetFinalizer.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetFinalizer.java new file mode 100644 index 000000000..95a93c05c --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetFinalizer.java @@ -0,0 +1,76 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.BucketIndexBySample; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantStore; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.File; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.ObjectOutputStream; +import java.util.concurrent.Executors; +import java.util.concurrent.Semaphore; +import java.util.concurrent.TimeUnit; +import java.util.zip.GZIPOutputStream; + +public class GenomicDatasetFinalizer { + + private static final Logger log = LoggerFactory.getLogger(GenomicDatasetFinalizer.class); + private static final String genomicDirectory = "/opt/local/hpds/all/"; + private final File[] chromosomeDirectories; + private final Semaphore sem; + + + public static void main(String[] args) throws IOException, ClassNotFoundException, InterruptedException { + new GenomicDatasetFinalizer(genomicDirectory, 10).processDirectory(); + } + + public GenomicDatasetFinalizer(String genomicDirectory, int maxThreads) { + chromosomeDirectories = new File(genomicDirectory).listFiles(File::isDirectory); + if (chromosomeDirectories == null) { + throw new IllegalArgumentException("Path " + genomicDirectory + " does not contain any directories"); + } + if (chromosomeDirectories.length > 50) { + throw new IllegalArgumentException( + "Number of chromosome partitions exceeds maximum of 50 (" + chromosomeDirectories.length + ")" + ); + } + sem = new Semaphore(maxThreads); + } + + + public void processDirectory() { + try (var executor = Executors.newVirtualThreadPerTaskExecutor()) { + for (File chromosomeDirectory : chromosomeDirectories) { + sem.acquire(); + executor.submit(() -> { + try { + String bucketIndexDirectory = chromosomeDirectory.getPath() + "/"; + VariantStore variantStore = VariantStore.readInstance(bucketIndexDirectory); + BucketIndexBySample bucketIndexBySample = new BucketIndexBySample(variantStore, bucketIndexDirectory); + String bucketIndexFilename = bucketIndexDirectory + "BucketIndexBySample.javabin"; + log.info("creating new " + bucketIndexFilename); + try ( + FileOutputStream fos = new FileOutputStream(bucketIndexFilename); GZIPOutputStream gzos = + new GZIPOutputStream(fos); ObjectOutputStream oos = new ObjectOutputStream(gzos); + ) { + oos.writeObject(bucketIndexBySample); + oos.flush(); + } + } catch (IOException | ClassNotFoundException e) { + executor.shutdown(); + throw new RuntimeException(e); + } + sem.release(); + }); + } + executor.shutdown(); + while (!executor.awaitTermination(1, TimeUnit.MINUTES)) { + log.info("Awaiting threadpool termination"); + } + } catch (InterruptedException e) { + throw new RuntimeException(e); + } + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMerger.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMerger.java new file mode 100644 index 000000000..4df7cd0f7 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMerger.java @@ -0,0 +1,281 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype; + +import com.google.common.base.Joiner; +import com.google.common.collect.Sets; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.*; +import edu.harvard.hms.dbmi.avillach.hpds.data.storage.FileBackedStorageVariantMasksImpl; +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedByteIndexedStorage; +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedJsonIndexStorage; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.*; +import java.util.*; +import java.util.concurrent.ConcurrentHashMap; +import java.util.concurrent.ConcurrentSkipListSet; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +public class GenomicDatasetMerger { + + private static Logger log = LoggerFactory.getLogger(GenomicDatasetMerger.class); + + private final VariantStore variantStore1; + private final VariantStore variantStore2; + + private final int variantStore1PatientCount; + private final int variantStore2PatientCount; + + private final Map infoStores1; + private final Map infoStores2; + + private final String outputDirectory; + + private final VariantStore mergedVariantStore; + + public GenomicDatasetMerger( + VariantStore variantStore1, VariantStore variantStore2, Map infoStores1, + Map infoStores2, String outputDirectory + ) { + this.variantStore1 = variantStore1; + this.variantStore1PatientCount = variantStore1.getPatientIds().length; + this.variantStore2 = variantStore2; + this.variantStore2PatientCount = variantStore2.getPatientIds().length; + this.mergedVariantStore = new VariantStore(); + this.infoStores1 = infoStores1; + this.infoStores2 = infoStores2; + this.outputDirectory = outputDirectory; + validate(); + } + + private void validate() { + if (!variantStore1.getVariantMaskStorage().keySet().equals(variantStore2.getVariantMaskStorage().keySet())) { + log.error("Variant store chromosomes do not match:"); + log.error(String.join(", ", variantStore1.getVariantMaskStorage().keySet())); + log.error(String.join(", ", variantStore2.getVariantMaskStorage().keySet())); + throw new IllegalStateException("Unable to merge variant stores with different numbers of chromosomes"); + } + Sets.SetView patientIntersection = + Sets.intersection(Sets.newHashSet(variantStore1.getPatientIds()), Sets.newHashSet(variantStore2.getPatientIds())); + if (!patientIntersection.isEmpty()) { + throw new IllegalStateException("Cannot merge genomic datasets containing the same patient id"); + } + } + + public VariantStore mergeVariantStore( + Map>> mergedChromosomeMasks + ) { + mergedVariantStore.setVariantMaskStorage(mergedChromosomeMasks); + return mergedVariantStore; + } + + public void mergePatients() { + mergedVariantStore.setPatientIds(mergePatientIds()); + } + + /** + * Since both sets of variant indexes reference a different variant spec list, we need to re-index the values in the second set of + * variant indexes. + * + * For each variant in the second list of variants: If it exists in list one, update any references to it by index to it's index in list + * 1 Otherwise, append it to list one, and update any references to it by index to it's new position in list 1 + * + * Ex: + * + * variantIndex1 = ["chr1,1000,A,G", "chr1,1002,A,G", "chr1,2000,A,G"] variantIndex2 = ["chr1,1000,A,G", "chr1,1004,A,G", + * "chr1,3000,A,G"] + * + * GeneWithVariant_store1 = [0, 1] GeneWithVariant_store2 = [0, 1, 2] + * + * mergedVariantIndex = ["chr1,1000,A,G", "chr1,1002,A,G", "chr1,2000,A,G", "chr1,1004,A,G", "chr1,3000,A,G"] GeneWithVariant_merged = + * [0, 1, 3, 4] + * + * @return + * @throws IOException + */ + public Map mergeVariantIndexes() throws IOException { + String[] variantIndex1 = variantStore1.getVariantSpecIndex(); + String[] variantIndex2 = variantStore2.getVariantSpecIndex(); + + Map variantSpecToIndexMap = new HashMap<>(); + LinkedList variantSpecList = new LinkedList<>(List.of(variantIndex1)); + for (int i = 0; i < variantIndex1.length; i++) { + variantSpecToIndexMap.put(variantIndex1[i], i); + } + + // Will contain any re-mapped indexes in the second variant index. For example, if a variant is contained in both + // data sets, the merged data set will use the index from dataset 1 to reference it, and any references in data + // set 2 for this variant needs to be re-mapped. Likewise, if a variant in set 2 is new, it will be appended to + // the list and also need to be re-mapped + Integer[] remappedIndexes = new Integer[variantIndex2.length]; + + for (int i = 0; i < variantIndex2.length; i++) { + String variantSpec = variantIndex2[i]; + Integer variantIndex = variantSpecToIndexMap.get(variantSpec); + if (variantIndex != null) { + remappedIndexes[i] = variantIndex; + } else { + variantSpecList.add(variantSpec); + // the new index is the now last item in the list + int newVariantSpecIndex = variantSpecList.size() - 1; + remappedIndexes[i] = newVariantSpecIndex; + variantSpecToIndexMap.put(variantSpec, newVariantSpecIndex); + } + } + + Map mergedInfoStores = new HashMap<>(); + + if (!infoStores1.keySet().equals(infoStores2.keySet())) { + throw new IllegalStateException("Info stores do not match"); + } + // for (Map.Entry infoStores1Entry : infoStores1.entrySet()) { + infoStores1.entrySet().stream().forEach(infoStores1Entry -> { + FileBackedByteIndexedInfoStore infoStore2 = infoStores2.get(infoStores1Entry.getKey()); + + FileBackedByteIndexedStorage allValuesStore1 = infoStores1Entry.getValue().getAllValues(); + FileBackedByteIndexedStorage allValuesStore2 = infoStore2.getAllValues(); + ConcurrentHashMap> mergedInfoStoreValues = new ConcurrentHashMap<>(); + + Sets.SetView allKeys = Sets.union(allValuesStore1.keys(), allValuesStore2.keys()); + for (String key : allKeys) { + Set store1Values = Set.of(allValuesStore1.getOrELse(key, new Integer[] {})); + Set store2Values = Set.of(allValuesStore2.getOrELse(key, new Integer[] {})); + Set remappedValuesStore2 = store2Values.stream().map(value -> remappedIndexes[value]).collect(Collectors.toSet()); + + Set mergedValues = Sets.union(store1Values, remappedValuesStore2); + mergedInfoStoreValues.put(key, new ConcurrentSkipListSet<>(mergedValues)); + } + + InfoStore infoStore = new InfoStore(infoStore2.description, null, infoStores1Entry.getKey()); + infoStore.allValues = mergedInfoStoreValues; + FileBackedByteIndexedInfoStore mergedStore = null; + try { + mergedStore = new FileBackedByteIndexedInfoStore(new File(outputDirectory), infoStore); + } catch (IOException e) { + throw new RuntimeException(e); + } + mergedInfoStores.put(infoStores1Entry.getKey(), mergedStore); + }); + + mergedVariantStore.setVariantSpecIndex(variantSpecList.toArray(new String[0])); + return mergedInfoStores; + } + + /** + * Merge patient ids from both variant stores. We are simply appending patients from store 2 to patients from store 1 + * + * @return the merged patient ids + */ + private String[] mergePatientIds() { + return Stream.concat(Arrays.stream(variantStore1.getPatientIds()), Arrays.stream(variantStore2.getPatientIds())) + .toArray(String[]::new); + } + + /** + * For each chromosome, call mergeChromosomeMask to merge the masks + * @return + */ + public Map>> mergeChromosomeMasks() { + Map>> mergedMaskStorage = + new ConcurrentHashMap<>(); + variantStore1.getVariantMaskStorage().keySet().forEach(chromosome -> { + try { + mergedMaskStorage.put(chromosome, mergeChromosomeMask(chromosome)); + } catch (FileNotFoundException e) { + throw new RuntimeException(e); + } + }); + return mergedMaskStorage; + } + + /** + * Merge the masks for a chormosome. The logic here is somewhat complex but straightforward, dealing with no values at various places in + * the maps. If a variant mask contains no matches (ie, is 000000...), it is not stored in the data. + * + * Examples: variantMaskStorage1: { 10001 -> { "chr22,10001031,A,G" -> "10101010", "chr22,10001143,G,A" -> "10101010" }, 10002 -> { + * "chr22,10002031,A,G" -> "10101010", "chr22,10002143,G,A" -> "10101010" } } variantMaskStorage2: { 10001 -> { "chr22,10001031,A,G" -> + * "00001111", "chr22,10001213,A,G" -> "00001111" }, 10003 -> { "chr22,10003031,A,G" -> "00001111", "chr22,10003213,A,G" -> "00001111" } + * } + * + * mergedVariantMaskStorage: { 10001 -> { "chr22,10001031,A,G" -> "1010101000001111", "chr22,10001213,A,G" -> "0000000000001111", + * "chr22,10001143,G,A" -> "1010101000000000" }, 10002 -> { "chr22,10002031,A,G" -> "1010101000000000", "chr22,10002143,G,A" -> + * "1010101000000000" } 10003 -> { "chr22,10003031,A,G" -> "0000000000001111", "chr22,10003213,A,G" -> "0000000000001111" } } + */ + public FileBackedJsonIndexStorage> mergeChromosomeMask(String chromosome) + throws FileNotFoundException { + FileBackedJsonIndexStorage> variantMaskStorage1 = + variantStore1.getVariantMaskStorage().get(chromosome); + FileBackedJsonIndexStorage> variantMaskStorage2 = + variantStore2.getVariantMaskStorage().get(chromosome); + + FileBackedJsonIndexStorage> merged = + new FileBackedStorageVariantMasksImpl(new File(outputDirectory + chromosome + "masks.bin")); + variantMaskStorage1.keys().stream().forEach(key -> { + Map masks1 = variantMaskStorage1.get(key); + Map masks2 = variantMaskStorage2.get(key); + if (masks2 == null) { + masks2 = Map.of(); + } + + ConcurrentHashMap mergedMasks = new ConcurrentHashMap<>(); + for (Map.Entry entry : masks1.entrySet()) { + VariableVariantMasks variantMasks2 = masks2.get(entry.getKey()); + if (variantMasks2 == null) { + // this will have all null masks, which will result in null when + // appended to a null, or be replaced with an empty bitmask otherwise + variantMasks2 = new VariableVariantMasks(); + } + + VariableVariantMasks mergeResult = + VariableVariantMasks.append(entry.getValue(), variantStore1PatientCount, variantMasks2, variantStore2PatientCount); + mergedMasks.put(entry.getKey(), mergeResult); + } + // Any entry in the second set that is not in the merged set can be merged with an empty variant mask, + // if there were a corresponding entry in set 1, it would have been merged in the previous loop + for (Map.Entry entry : masks2.entrySet()) { + if (!mergedMasks.containsKey(entry.getKey())) { + VariableVariantMasks appendedMasks = VariableVariantMasks + .append(new VariableVariantMasks(), variantStore1PatientCount, entry.getValue(), variantStore2PatientCount); + mergedMasks.put(entry.getKey(), appendedMasks); + } + } + if (merged.keys().contains(key)) { + log.warn("Merged already contains key: " + key); + } else { + merged.put(key, mergedMasks); + } + }); + + variantMaskStorage2.keys().forEach(key -> { + if (variantMaskStorage1.get(key) == null) { + ConcurrentHashMap mergedMasks = new ConcurrentHashMap<>(); + Map masks2 = variantMaskStorage2.get(key); + for (Map.Entry entry : masks2.entrySet()) { + if (!mergedMasks.containsKey(entry.getKey())) { + VariableVariantMasks appendedMasks = VariableVariantMasks + .append(new VariableVariantMasks(), variantStore1PatientCount, entry.getValue(), variantStore2PatientCount); + mergedMasks.put(entry.getKey(), appendedMasks); + } + } + if (merged.keys().contains(key)) { + log.warn("Second loop: merged already contains key: " + key); + } else { + merged.put(key, mergedMasks); + } + } + }); + + if (log.isTraceEnabled()) { + merged.keys().stream().sorted().limit(3).forEach(key -> { + ConcurrentHashMap maskMap = merged.get(key); + maskMap.keySet().stream().sorted().limit(5).forEach(variantSpec -> { + VariableVariantMasks variableVariantMasks = maskMap.get(variantSpec); + VariantMask heteroMask = Optional.ofNullable(variableVariantMasks.heterozygousMask).orElse(VariantMask.emptyInstance()); + Set patientsWithVariant = heteroMask.patientMaskToPatientIdSet(List.of(mergedVariantStore.getPatientIds())); + log.trace("Patients with variant [" + variantSpec + "]: " + Joiner.on(",").join(patientsWithVariant)); + }); + }); + } + return merged; + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMergerRunner.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMergerRunner.java new file mode 100644 index 000000000..7e2db7262 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMergerRunner.java @@ -0,0 +1,89 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype; + +import com.google.common.base.Preconditions; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.*; +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedByteIndexedStorage; +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedJsonIndexStorage; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; +import java.io.ObjectInputStream; +import java.util.Arrays; +import java.util.HashMap; +import java.util.Map; +import java.util.concurrent.ConcurrentHashMap; +import java.util.zip.GZIPInputStream; + +public class GenomicDatasetMergerRunner { + + private static Logger log = LoggerFactory.getLogger(GenomicDatasetMerger.class); + + public static final String INFO_STORE_JAVABIN_SUFFIX = "infoStore.javabin"; + + private static String genomicDirectory1; + private static String genomicDirectory2; + + /** + * args[0]: directory containing genomic dataset 1 args[1]: directory containing genomic dataset 2 args[2]: output directory + */ + public static void main(String[] args) throws IOException, ClassNotFoundException, InterruptedException { + if (args.length != 3) { + throw new IllegalArgumentException( + "Three arguments must be provided: source directory 1, source directory 2, output directory" + ); + } + genomicDirectory1 = args[0]; + genomicDirectory2 = args[1]; + String outputDirectory = args[2]; + + Map infoStores1 = loadInfoStores(genomicDirectory1); + Map infoStores2 = loadInfoStores(genomicDirectory2); + + GenomicDatasetMerger genomicDatasetMerger = new GenomicDatasetMerger( + VariantStore.readInstance(genomicDirectory1), VariantStore.readInstance(genomicDirectory2), infoStores1, infoStores2, + outputDirectory + ); + genomicDatasetMerger.mergePatients(); + + Map>> mergedChromosomeMasks = + genomicDatasetMerger.mergeChromosomeMasks(); + VariantStore mergedVariantStore = genomicDatasetMerger.mergeVariantStore(mergedChromosomeMasks); + Map variantIndexes = genomicDatasetMerger.mergeVariantIndexes(); + + mergedVariantStore.writeInstance(outputDirectory); + variantIndexes.values().forEach(variantIndex -> { + variantIndex.write(new File(outputDirectory + variantIndex.column_key + "_" + INFO_STORE_JAVABIN_SUFFIX)); + }); + + VariantMetadataIndex variantMetadataIndex1 = VariantMetadataIndex.createInstance(genomicDirectory1); + VariantMetadataIndex variantMetadataIndex2 = VariantMetadataIndex.createInstance(genomicDirectory2); + + VariantMetadataIndex.merge(variantMetadataIndex1, variantMetadataIndex2, outputDirectory); + } + + private static Map loadInfoStores(String directory) { + Map infoStores = new HashMap<>(); + File genomicDataDirectory = new File(directory); + if (genomicDataDirectory.exists() && genomicDataDirectory.isDirectory()) { + Arrays.stream(genomicDataDirectory.list((file, filename) -> { + return filename.endsWith(INFO_STORE_JAVABIN_SUFFIX); + })).forEach((String filename) -> { + try ( + FileInputStream fis = new FileInputStream(directory + filename); GZIPInputStream gis = + new GZIPInputStream(fis); ObjectInputStream ois = new ObjectInputStream(gis) + ) { + log.info("loading " + filename); + FileBackedByteIndexedInfoStore infoStore = (FileBackedByteIndexedInfoStore) ois.readObject(); + infoStore.updateStorageDirectory(genomicDataDirectory); + infoStores.put(filename.replace("_" + INFO_STORE_JAVABIN_SUFFIX, ""), infoStore); + } catch (IOException | ClassNotFoundException e) { + throw new RuntimeException(e); + } + }); + } + return infoStores; + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/NewVCFLoader.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/NewVCFLoader.java new file mode 100644 index 000000000..294574108 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/NewVCFLoader.java @@ -0,0 +1,636 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype; + +import java.io.*; +import java.math.BigInteger; +import java.util.*; +import java.util.concurrent.*; +import java.util.stream.Collectors; +import java.util.zip.GZIPOutputStream; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.*; +import edu.harvard.hms.dbmi.avillach.hpds.data.storage.FileBackedStorageVariantMasksImpl; +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedJsonIndexStorage; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedByteIndexedStorage; +import htsjdk.samtools.util.BlockCompressedInputStream; + +public class NewVCFLoader { + + public static final String DEFAULT_VCF_INDEX_FILE = "/opt/local/hpds/vcfIndex.tsv"; + public static final String DEFAULT_STORAGE_DIR = "/opt/local/hpds/all"; + public static final String DEFAULT_MERGED_DIR = "/opt/local/hpds/merged"; + private static Logger logger = LoggerFactory.getLogger(NewVCFLoader.class); + + protected File indexFile; + protected File storageDir; + protected String storageDirStr; + protected String mergedDirStr; + + protected VariantIndexBuilder variantIndexBuilder; + + // DO NOT CHANGE THIS unless you want to reload all the data everywhere. + protected static int CHUNK_SIZE = 1000; + + /** + * @param args - if testing, this should be an array ['vcfIndexFile path', 'output storage dir', 'merged dir']. by default this will be + * [/opt/local/hpds/vcfIndex.tsv, "/opt/local/hpds/all", "/opt/local/hpds/merged" ]. + */ + public static void main(String[] args) throws IOException { + + NewVCFLoader vcfLoader; + if (args != null && args.length >= 3) { + logger.info("Reading parameters from input"); + vcfLoader = new NewVCFLoader(new File(args[0]), args[1], args[2]); + } else { + logger.info(args.length + " arguments provided"); + logger.info("Using default values"); + vcfLoader = new NewVCFLoader(); + } + vcfLoader.loadAndMerge(); + } + + protected void loadAndMerge() throws IOException { + createWalkers(); + loadVCFs(); + } + + public NewVCFLoader() { + this.indexFile = new File(DEFAULT_VCF_INDEX_FILE); + this.storageDirStr = DEFAULT_STORAGE_DIR; + this.storageDir = new File(DEFAULT_STORAGE_DIR); + this.mergedDirStr = DEFAULT_MERGED_DIR; + this.variantIndexBuilder = new VariantIndexBuilder(); + } + + public NewVCFLoader(File indexFile, String storageDir, String mergedDirStr) { + this.indexFile = indexFile; + this.storageDirStr = storageDir; + this.storageDir = new File(storageDir); + this.mergedDirStr = mergedDirStr; + this.variantIndexBuilder = new VariantIndexBuilder(); + } + + protected ExecutorService chunkWriteEx = Executors.newFixedThreadPool(1); + + protected ConcurrentHashMap infoStoreMap = new ConcurrentHashMap(); + + protected HashMap zygosityMaskStrings; + + protected TreeMap>> variantMaskStorage = + new TreeMap<>(); + + protected long startTime; + + protected List walkers = new ArrayList<>(); + + private boolean contigIsHemizygous; + + protected void loadVCFs() throws IOException { + startTime = System.currentTimeMillis(); + TreeSet allPatientIds = new TreeSet<>(); + + // Pull the INFO columns out of the headers for each walker and add all patient ids + walkers.stream().forEach(walker -> { + try { + logger.info("Reading headers of VCF [" + walker.vcfIndexLine.getVcfPath() + "]"); + walker.readHeaders(infoStoreMap); + allPatientIds.addAll(Arrays.asList(walker.vcfIndexLine.getPatientIds())); + } catch (IOException e) { + logger.error("Error while reading headers of VCF [" + walker.vcfIndexLine.getVcfPath() + "]", e); + System.exit(-1); + } + }); + + Integer[] patientIds = allPatientIds.toArray(new Integer[0]); + String[] allSampleIds = new String[allPatientIds.size()]; + + walkers.parallelStream().forEach(walker -> { + logger.info("Setting bitmask offsets for VCF [" + walker.vcfIndexLine.getVcfPath() + "]"); + walker.setBitmaskOffsets(patientIds); + for (int x = 0; x < walker.vcfIndexLine.getSampleIds().length; x++) { + allSampleIds[Arrays.binarySearch(patientIds, walker.vcfIndexLine.getPatientIds()[x])] = + walker.vcfIndexLine.getSampleIds()[x]; + } + }); + + VariantStore store = new VariantStore(); + store.setPatientIds(allPatientIds.stream().map((id) -> { + return id.toString(); + }).collect(Collectors.toList()).toArray(new String[0])); + + String lastContigProcessed = null; + int lastChunkProcessed = 0; + int currentChunk = 0; + String[] currentContig = new String[1]; + int[] currentPosition = {-1}; + String[] currentRef = new String[1]; + String[] currentAlt = new String[1]; + + zygosityMaskStrings = new HashMap(); + + List positionsProcessedInChunk = new ArrayList<>(); + while (walkers.parallelStream().anyMatch(walker -> { + return walker.hasNext; + })) { + Collections.sort(walkers); + VCFWalker lowestWalker = walkers.get(0); + String currentSpecNotation = lowestWalker.currentSpecNotation(); + currentContig[0] = lowestWalker.currentContig; + currentPosition[0] = lowestWalker.currentPosition; + currentRef[0] = lowestWalker.currentRef; + currentAlt[0] = lowestWalker.currentAlt; + currentChunk = lowestWalker.currentPosition / CHUNK_SIZE; + positionsProcessedInChunk.add(currentPosition[0]); + + if (lastContigProcessed == null) { + lastContigProcessed = lowestWalker.currentContig; + } + + flipChunk(lastContigProcessed, lastChunkProcessed, currentChunk, currentContig[0], false, lowestWalker.currentLine); + lastContigProcessed = lowestWalker.currentContig; + lastChunkProcessed = currentChunk; + + char[][][] maskStringsForVariantSpec = {zygosityMaskStrings.get(currentSpecNotation)}; + if (maskStringsForVariantSpec[0] == null) { + maskStringsForVariantSpec[0] = new char[7][allPatientIds.size()]; + for (int x = 0; x < maskStringsForVariantSpec[0].length; x++) { + maskStringsForVariantSpec[0][x] = new char[allPatientIds.size()]; + for (int y = 0; y < allPatientIds.size(); y++) { + maskStringsForVariantSpec[0][x][y] = '0'; + } + } + } + walkers.stream().filter((walker) -> { + return walker.currentPosition == currentPosition[0] && walker.currentAlt == currentAlt[0] + && walker.currentRef == currentRef[0] && walker.currentContig.contentEquals(currentContig[0]); + }).forEach((walker) -> { + walker.updateRecords(maskStringsForVariantSpec[0], infoStoreMap); + try { + walker.nextLine(); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + }); + zygosityMaskStrings.put(currentSpecNotation, maskStringsForVariantSpec[0]); + walkers = walkers.parallelStream().filter((walker) -> { + return walker.hasNext; + }).collect(Collectors.toList()); + } + + flipChunk(lastContigProcessed, lastChunkProcessed, currentChunk, currentContig[0], true, null); + + shutdownChunkWriteExecutor(); + + saveInfoStores(); + + splitInfoStoresByColumn(); + + convertInfoStoresToByteIndexed(); + + if (logger.isDebugEnabled()) { + // Log out the first and last 50 variants + int[] count = {0}; + for (String contig : store.getVariantMaskStorage().keySet()) { + ArrayList chunkIds = new ArrayList<>(); + FileBackedByteIndexedStorage> chromosomeStorage = + store.getVariantMaskStorage().get(contig); + if (chromosomeStorage != null) { + // print out the top and bottom 50 variants in the store (that have masks) + chunkIds.addAll(chromosomeStorage.keys()); + for (Integer chunkId : chunkIds) { + for (String variantSpec : chromosomeStorage.get(chunkId).keySet()) { + count[0]++; + VariableVariantMasks variantMasks = chromosomeStorage.get(chunkId).get(variantSpec); + if (variantMasks != null) { + VariantMask heterozygousMask = variantMasks.heterozygousMask; + String heteroIdList = sampleIdsForMask(allSampleIds, heterozygousMask); + VariantMask homozygousMask = variantMasks.homozygousMask; + String homoIdList = sampleIdsForMask(allSampleIds, homozygousMask); + + if (!heteroIdList.isEmpty() && heteroIdList.length() < 1000) + logger.debug(variantSpec + " : heterozygous : " + heteroIdList); + if (!homoIdList.isEmpty() && homoIdList.length() < 1000) + logger.debug(variantSpec + " : homozygous : " + homoIdList); + } + } + if (count[0] > 50) break; + } + + count[0] = 0; + for (int x = chunkIds.size() - 1; x > 0; x--) { + int chunkId = chunkIds.get(x); + chromosomeStorage.get(chunkId).keySet().forEach((variantSpec) -> { + count[0]++; + VariableVariantMasks variantMasks = chromosomeStorage.get(chunkId).get(variantSpec); + if (variantMasks != null) { + VariantMask heterozygousMask = variantMasks.heterozygousMask; + String heteroIdList = sampleIdsForMask(allSampleIds, heterozygousMask); + VariantMask homozygousMask = variantMasks.homozygousMask; + String homoIdList = sampleIdsForMask(allSampleIds, homozygousMask); + + if (!heteroIdList.isEmpty() && heteroIdList.length() < 1000) + logger.debug(variantSpec + " : heterozygous : " + heteroIdList); + if (!homoIdList.isEmpty() && homoIdList.length() < 1000) + logger.debug(variantSpec + " : homozygous : " + homoIdList); + } + }); + if (count[0] > 50) break; + } + } + } + } + + store.setVariantSpecIndex(variantIndexBuilder.getVariantSpecIndex().toArray(new String[0])); + saveVariantStore(store, variantMaskStorage); + } + + private void createWalkers() { + List vcfIndexLines = new VcfIndexFileParser().parse(indexFile); + for (VCFIndexLine line : vcfIndexLines) { + walkers.add(new VCFWalker(line)); + } + } + + protected String sampleIdsForMask(String[] sampleIds, VariantMask variantMask) { + StringBuilder idList = new StringBuilder(); + if (variantMask != null) { + if (variantMask instanceof VariantMaskBitmaskImpl) { + BigInteger mask = ((VariantMaskBitmaskImpl) variantMask).getBitmask(); + for (int x = 0; x < mask.bitLength() - 4; x++) { + if (variantMask.testBit(x)) { + idList.append(sampleIds[x]).append(","); + } + } + } else if (variantMask instanceof VariantMaskSparseImpl) { + for (Integer patientIndex : ((VariantMaskSparseImpl) variantMask).getPatientIndexes()) { + idList.append(sampleIds[patientIndex]).append(","); + } + } + } + return idList.toString(); + } + + protected void flipChunk( + String lastContigProcessed, int lastChunkProcessed, int currentChunk, String currentContig, boolean isLastChunk, String currentLine + ) throws IOException, FileNotFoundException { + if (!currentContig.contentEquals(lastContigProcessed) || isLastChunk) { + if (infoStoreFlipped.get(lastContigProcessed) == null || !infoStoreFlipped.get(lastContigProcessed)) { + infoStoreFlipped.put(lastContigProcessed, true); + File infoFile = new File(storageDir, lastContigProcessed + "_infoStores.javabin"); + logger.debug( + Thread.currentThread().getName() + " : " + "Flipping info : " + infoFile.getAbsolutePath() + " " + lastContigProcessed + + " " + ); + try ( + FileOutputStream fos = new FileOutputStream(infoFile); GZIPOutputStream gzos = + new GZIPOutputStream(fos); ObjectOutputStream oos = new ObjectOutputStream(gzos); + ) { + oos.writeObject(infoStoreMap); + } + ConcurrentHashMap newInfoStores = new ConcurrentHashMap(); + for (String key : infoStoreMap.keySet()) { + newInfoStores.put(key, new InfoStore(infoStoreMap.get(key).description, ";", key)); + } + infoStoreMap = newInfoStores; + } + if (currentLine != null) { + String[] split = currentLine.split("\t"); + if (split[8].length() > 2) { + contigIsHemizygous = false; + } else { + contigIsHemizygous = true; + } + } + } + if (!currentContig.contentEquals(lastContigProcessed) || currentChunk > lastChunkProcessed || isLastChunk) { + // flip chunk + TreeMap>> variantMaskStorage_f = + variantMaskStorage; + HashMap zygosityMaskStrings_f = zygosityMaskStrings; + String lastContigProcessed_f = lastContigProcessed; + int lastChunkProcessed_f = lastChunkProcessed; + chunkWriteEx.execute(() -> { + try { + if (variantMaskStorage_f.get(lastContigProcessed_f) == null) { + String fileName = lastContigProcessed_f + "masks.bin"; + if (!fileName.startsWith("chr")) { + fileName = "chr" + fileName; + } + + variantMaskStorage_f + .put(lastContigProcessed_f, new FileBackedStorageVariantMasksImpl(new File(storageDir, fileName))); + } + variantMaskStorage_f.get(lastContigProcessed_f) + .put(lastChunkProcessed_f, convertLoadingMapToMaskMap(zygosityMaskStrings_f)); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + }); + if (lastChunkProcessed % 100 == 0) { + logger.info( + System.currentTimeMillis() + " Done loading chunk : " + lastChunkProcessed + " for chromosome " + lastContigProcessed + ); + } + zygosityMaskStrings = new HashMap(); + } + } + + protected void saveVariantStore( + VariantStore store, + TreeMap>> variantMaskStorage + ) throws IOException, FileNotFoundException { + store.setVariantMaskStorage(variantMaskStorage); + for (FileBackedByteIndexedStorage> storage : variantMaskStorage.values()) { + if (storage != null) storage.complete(); + } + store.writeInstance(storageDirStr); + logger.debug("Done saving variant masks."); + } + + protected void saveInfoStores() throws IOException, FileNotFoundException { + logger.debug("Saving info" + (System.currentTimeMillis() - startTime) + " seconds"); + try ( + FileOutputStream fos = new FileOutputStream(new File(storageDir, "infoStores.javabin")); GZIPOutputStream gzos = + new GZIPOutputStream(fos); ObjectOutputStream oos = new ObjectOutputStream(gzos); + ) { + oos.writeObject(infoStoreMap); + } + logger.debug("Done saving info."); + logger.info("completed load in " + (System.currentTimeMillis() - startTime) + " seconds"); + } + + public void splitInfoStoresByColumn() throws FileNotFoundException, IOException { + logger.debug("Splitting" + (System.currentTimeMillis() - startTime) + " seconds"); + try { + VCFPerPatientInfoStoreSplitter.splitAll(storageDir, new File(mergedDirStr)); + } catch (ClassNotFoundException | ExecutionException | InterruptedException e) { + throw new RuntimeException(e); + } + logger.debug("Split" + (System.currentTimeMillis() - startTime) + " seconds"); + } + + public void convertInfoStoresToByteIndexed() throws FileNotFoundException, IOException { + logger.debug("Converting" + (System.currentTimeMillis() - startTime) + " seconds"); + try { + VCFPerPatientInfoStoreToFBBIISConverter.convertAll(mergedDirStr, storageDirStr); + } catch (ClassNotFoundException | ExecutionException | InterruptedException e) { + throw new RuntimeException(e); + } + logger.debug("Converted " + ((System.currentTimeMillis() - startTime) / 1000) + " seconds"); + } + + protected void shutdownChunkWriteExecutor() { + chunkWriteEx.shutdown(); + while (!chunkWriteEx.isTerminated()) { + try { + logger.debug(((ThreadPoolExecutor) chunkWriteEx).getQueue().size() + " writes left to be written."); + chunkWriteEx.awaitTermination(20, TimeUnit.SECONDS); + } catch (InterruptedException e) { + logger.error("Error shutting down chunk write executor", e); + } + } + } + + private static ConcurrentHashMap convertLoadingMapToMaskMap( + HashMap zygosityMaskStrings_f + ) { + ConcurrentHashMap maskMap = new ConcurrentHashMap<>(zygosityMaskStrings_f.size()); + zygosityMaskStrings_f.entrySet().parallelStream().forEach((entry) -> { + maskMap.put(entry.getKey(), new VariableVariantMasks(entry.getValue())); + }); + return maskMap; + } + + static TreeMap infoStoreFlipped = new TreeMap(); + + protected class VCFWalker implements Comparable { + + protected List indices; + protected Integer[] vcfOffsets; + protected Integer[] bitmaskOffsets; + protected HashMap vcfIndexLookup; + protected String currentLine; + protected String[] currentLineSplit; + protected BufferedReader vcfReader; + protected VCFIndexLine vcfIndexLine; + boolean hasNext = true; + String currentContig; + Integer currentPosition; + String currentRef, currentAlt; + + public VCFWalker(VCFIndexLine vcfIndexLine) { + this.vcfIndexLine = vcfIndexLine; + this.vcfOffsets = new Integer[vcfIndexLine.getPatientIds().length]; + this.bitmaskOffsets = new Integer[vcfIndexLine.getPatientIds().length]; + vcfIndexLookup = new HashMap(vcfOffsets.length); + indices = new ArrayList<>(); + for (int x = 0; x < vcfOffsets.length; x++) { + indices.add(x); + } + try { + InputStream in = + this.vcfIndexLine.isGzipped() ? new BlockCompressedInputStream(new FileInputStream(this.vcfIndexLine.getVcfPath())) + : new FileInputStream(this.vcfIndexLine.getVcfPath()); + InputStreamReader reader = new InputStreamReader(in); + vcfReader = new BufferedReader(reader, 1024 * 1024 * 32); + } catch (IOException e) { + throw new RuntimeException("File not found, please fix the VCF index file : " + vcfIndexLine, e); + } + } + + public void updateRecords(char[][] zygosityMaskStrings, ConcurrentHashMap infoStores) { + int[] startOffsetForLine = {0}; + int columnNumber = 0; + int formatStartIndex = 0; + for (startOffsetForLine[0] = 0; columnNumber <= 8; startOffsetForLine[0]++) { + if (currentLine.charAt(startOffsetForLine[0]) == '\t') { + columnNumber++; + if (columnNumber == 8) { + formatStartIndex = startOffsetForLine[0]; + } + } + } + + // Because formatStartIndex is the index of the preceding \t and startOffsetForLine is + // after the next \t, this has to be 4 even though "\tGT" is only 3 characters. + boolean formatIsGTOnly = (startOffsetForLine[0] - formatStartIndex) == 4; + + if (!formatIsGTOnly) { + // index is sample index in vcf + int index = 0; + try { + + int currentLineOffset = startOffsetForLine[0]; + // added index boundary condition from master + for (; index < indices.size() && currentLineOffset < currentLine.length(); currentLineOffset++) { + if (currentLine.charAt(currentLineOffset - 1) == '\t') { + // and index lookup from variant explorer branch + if (vcfIndexLookup.containsKey(index)) { + setMasksForSample(zygosityMaskStrings, vcfIndexLookup.get(index), currentLineOffset); + } + index++; + } + } + + } catch (IndexOutOfBoundsException e) { + throw new RuntimeException("INDEX out of bounds " + currentLine.substring(0, Math.min(50, currentLine.length())), e); + } + } else { + indices.parallelStream().forEach((index) -> { + setMasksForSample(zygosityMaskStrings, index, startOffsetForLine[0] + vcfOffsets[index]); + }); + } + String[] infoColumns = currentLineSplit[7].split("[;&]"); + String currentSpecNotation = currentSpecNotation(); + int variantIndex = variantIndexBuilder.getIndex(currentSpecNotation); + infoStores.values().parallelStream().forEach(infoStore -> { + infoStore.processRecord(variantIndex, infoColumns); + }); + } + + private void setMasksForSample(char[][] zygosityMaskStrings, int index, int startOffsetForSample) { + int patientZygosityIndex = (currentLine.charAt(startOffsetForSample + 0) + currentLine.charAt(startOffsetForSample + 1) + + currentLine.charAt(startOffsetForSample + 2)) % 7; + zygosityMaskStrings[patientZygosityIndex][bitmaskOffsets[index]] = '1'; + } + + protected String currentSpecNotation() { + String[] variantInfo = currentLineSplit[7].split("[=;]"); + String gene = "NULL"; + String consequence = "NULL"; + for (int i = 0; i < variantInfo.length; i = i + 2) { + if ("Gene_with_variant".equals(variantInfo[i])) { + gene = variantInfo[i + 1]; + } + if ("Variant_consequence_calculated".equals(variantInfo[i])) { + consequence = variantInfo[i + 1]; + } + } + return currentLineSplit[0] + "," + currentLineSplit[1] + "," + currentLineSplit[3] + "," + currentLineSplit[4] + "," + gene + + "," + consequence; + } + + public void readHeaders(ConcurrentHashMap infoStores) throws IOException { + nextLine(); + // Parse VCF header extracting only INFO columns until we hit the header row for the TSV portion + while (currentLine != null && currentLine.startsWith("##")) { + if (currentLine.startsWith("##INFO") && vcfIndexLine.isAnnotated()) { + String[] info = currentLine.replaceAll("##INFO=<", "").replaceAll(">", "").split(","); + info[3] = String.join(",", Arrays.copyOfRange(info, 3, info.length)); + String columnKey = info[0].split("=")[1]; + if (!infoStores.containsKey(columnKey)) { + logger.info("Creating info store " + currentLine); + InfoStore infoStore = new InfoStore(info[3], ";", columnKey); + infoStores.put(columnKey, infoStore); + } + } + nextLine(); + } + + // Make sure all expected columns are included and in the right order, stop the presses otherwise + if (!currentLine.startsWith("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t")) { + logger.error( + "Invalid VCF format [" + this.vcfIndexLine.getVcfPath() + + "], please ensure all expected columns are included per VCF 4.1 specification : #CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t" + ); + System.exit(-1); + } + + String[] vcfHeaderSamples = Arrays.copyOfRange(currentLineSplit, 9, currentLineSplit.length - 1); + + // Set vcf offsets by sampleIds + for (int x = 0; x < vcfIndexLine.getSampleIds().length; x++) { + // y is index into vcf samples + // x is index into patient IDs + int y; + for (y = 0; y < vcfHeaderSamples.length && !vcfHeaderSamples[y].contentEquals(vcfIndexLine.getSampleIds()[x]); y++); + vcfOffsets[x] = y * 4; + vcfIndexLookup.put(y, x); + } + + // add not GT only logic + + nextLine(); + } + + public void setBitmaskOffsets(Integer[] allPatientIdsSorted) { + for (int x = 0; x < vcfIndexLine.getPatientIds().length; x++) { + bitmaskOffsets[x] = Arrays.binarySearch(allPatientIdsSorted, vcfIndexLine.getPatientIds()[x]); + } + + } + + public void nextLine() throws IOException { + currentLine = vcfReader.readLine(); + if (currentLine == null) { + hasNext = false; + } else if (currentLine.startsWith("#CHROM")) { + currentLineSplit = currentLine.split("\t"); + } else if (!currentLine.startsWith("#")) { + currentLineSplit = new String[8]; + int start = 0; + int end = 0; + for (int x = 0; x < currentLineSplit.length; x++) { + while (currentLine.charAt(end) != '\t') { + end++; + } + currentLineSplit[x] = currentLine.substring(start, end); + end++; + start = end; + } + currentContig = currentLineSplit[0]; + currentPosition = Integer.parseInt(currentLineSplit[1]); + currentRef = currentLineSplit[3]; + currentAlt = currentLineSplit[4]; + } + } + + private static LinkedList contigOrder = new LinkedList(); + + @Override + public int compareTo(VCFWalker o) { + int chromosomeCompared; + if (currentContig.contentEquals(o.currentContig)) { + chromosomeCompared = 0; + if (!contigOrder.contains(currentContig)) { + contigOrder.add(currentContig); + } + } else { + Integer currentContigIndex = -1; + Integer oCurrentContigIndex = -1; + for (int x = 0; x < contigOrder.size(); x++) { + if (currentContig.contentEquals(contigOrder.get(x))) { + currentContigIndex = x; + } + if (o.currentContig.contentEquals(contigOrder.get(x))) { + oCurrentContigIndex = x; + } + } + if (currentContigIndex == -1) { + contigOrder.add(currentContig); + currentContigIndex = contigOrder.size() - 1; + } + if (oCurrentContigIndex == -1) { + contigOrder.add(o.currentContig); + oCurrentContigIndex = contigOrder.size() - 1; + } + chromosomeCompared = currentContigIndex.compareTo(oCurrentContigIndex); + } + if (chromosomeCompared == 0) { + int positionCompared = currentPosition.compareTo(o.currentPosition); + if (positionCompared == 0) { + int refCompared = currentRef.compareTo(o.currentRef); + if (refCompared == 0) { + return currentAlt.compareTo(o.currentAlt); + } + return refCompared; + } + return positionCompared; + } + return chromosomeCompared; + } + } + +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/SplitChromosomeVariantMetadataLoader.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/SplitChromosomeVariantMetadataLoader.java new file mode 100644 index 000000000..f69162d2e --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/SplitChromosomeVariantMetadataLoader.java @@ -0,0 +1,107 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype; + + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMetadataIndex; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantSpec; +import org.apache.commons.csv.CSVFormat; +import org.apache.commons.csv.CSVParser; +import org.apache.commons.csv.CSVRecord; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.*; +import java.nio.charset.Charset; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; +import java.util.TreeSet; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; + +import static edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMetadataIndex.VARIANT_METADATA_FILENAME; +import static edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMetadataIndex.VARIANT_METADATA_STORAGE_FILE_PREFIX; + +/** + * + * This loader will read in the metadata associated with each variant and build a VariantMetadataIndex that can be used to populate data in + * the PIC-SURE Varaint Explorer. + */ +public class SplitChromosomeVariantMetadataLoader { + + public static final String DEFAULT_TSV_FILENAME = "vcfIndex.tsv"; + public static final String DEFAULT_HPDS_DIRECTORY = "/opt/local/hpds/"; + + public static final String DEFAULT_HPDS_DATA_DIRECTORY = DEFAULT_HPDS_DIRECTORY + "all/"; + private static Logger log = LoggerFactory.getLogger(SplitChromosomeVariantMetadataLoader.class); + + // fields to allow tests to override default file location + private static String hpdsDataPath = null; + + private static final int ANNOTATED_FLAG_COLUMN = 2, GZIP_FLAG_COLUMN = 3, FILE_COLUMN = 0; + + public static void main(String[] args) throws IOException { + File vcfIndexFile; + + log.info(new File(".").getAbsolutePath()); + if (args.length > 0 && new File(args[0]).exists()) { + log.info("using path from command line"); + vcfIndexFile = new File(args[0]); + hpdsDataPath = args[1]; + } else { + hpdsDataPath = DEFAULT_HPDS_DATA_DIRECTORY; + vcfIndexFile = new File(DEFAULT_HPDS_DIRECTORY + DEFAULT_TSV_FILENAME); + } + + List vcfIndexFiles = new ArrayList<>(); + + try ( + CSVParser parser = + CSVParser.parse(vcfIndexFile, Charset.forName("UTF-8"), CSVFormat.DEFAULT.withDelimiter('\t').withSkipHeaderRecord(true)) + ) { + final boolean[] horribleHeaderSkipFlag = {false}; + parser.forEach((CSVRecord r) -> { + if (horribleHeaderSkipFlag[0]) { + File vcfFileLocal = new File(r.get(FILE_COLUMN)); + if (Integer.parseInt(r.get(ANNOTATED_FLAG_COLUMN).trim()) == 1) { + VcfInputFile vcfInput = new VcfInputFile(vcfFileLocal, (Integer.parseInt(r.get(GZIP_FLAG_COLUMN).trim()) == 1)); + vcfIndexFiles.add(vcfInput); + } + } else { + horribleHeaderSkipFlag[0] = true; + } + }); + } + + vcfIndexFiles.stream().forEach(SplitChromosomeVariantMetadataLoader::createVariantMetadataIndexForContig); + + + } + + private static void createVariantMetadataIndexForContig(VcfInputFile vcfInput) { + try { + String contig = vcfInput.currentContig; + VariantMetadataIndex metadataIndex = + new VariantMetadataIndex(hpdsDataPath + contig + "/" + VARIANT_METADATA_STORAGE_FILE_PREFIX); + + while (vcfInput.hasNextVariant()) { + metadataIndex.put(vcfInput.currentVariantSpec, vcfInput.currentMetaData); + vcfInput.nextVariant(); + } + metadataIndex.put(vcfInput.currentVariantSpec, vcfInput.currentMetaData); + + metadataIndex.complete(); + + // store this in a path per contig (or a preset path + String binfilePath = hpdsDataPath + contig + "/" + VARIANT_METADATA_FILENAME; + + try (ObjectOutputStream out = new ObjectOutputStream(new GZIPOutputStream(new FileOutputStream(new File(binfilePath))))) { + out.writeObject(metadataIndex); + out.flush(); + } + + log.info("Finished processing: " + vcfInput.fileName); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/SplitChromosomeVcfLoader.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/SplitChromosomeVcfLoader.java new file mode 100644 index 000000000..5a8b690e4 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/SplitChromosomeVcfLoader.java @@ -0,0 +1,225 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariableVariantMasks; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMask; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantStore; +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedByteIndexedStorage; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.File; +import java.io.IOException; +import java.io.UncheckedIOException; +import java.util.*; +import java.util.concurrent.ConcurrentHashMap; +import java.util.concurrent.Executors; +import java.util.stream.Collectors; + +public class SplitChromosomeVcfLoader extends NewVCFLoader { + + private static Logger logger = LoggerFactory.getLogger(SplitChromosomeVcfLoader.class); + private String[] allSampleIds; + private Integer[] patientIds; + private TreeSet allPatientIds; + + private final String baseStorageDir; + private final String baseMergeDir; + + public SplitChromosomeVcfLoader(File file, String baseStorageDir, String baseMergeDir) { + super(file, baseStorageDir, baseMergeDir); + this.baseStorageDir = baseStorageDir; + this.baseMergeDir = baseMergeDir; + } + + public SplitChromosomeVcfLoader() { + super(); + this.baseStorageDir = DEFAULT_STORAGE_DIR; + this.baseMergeDir = DEFAULT_MERGED_DIR; + } + + + + public static void main(String[] args) throws IOException { + NewVCFLoader vcfLoader; + if (args != null && args.length >= 3) { + logger.info("Reading parameters from input"); + vcfLoader = new SplitChromosomeVcfLoader(new File(args[0]), args[1], args[2]); + } else { + logger.info(args.length + " arguments provided"); + logger.info("Using default values"); + vcfLoader = new SplitChromosomeVcfLoader(); + } + vcfLoader.loadAndMerge(); + + vcfLoader.shutdownChunkWriteExecutor(); + } + + + protected void loadVCFs() throws IOException { + startTime = System.currentTimeMillis(); + allPatientIds = new TreeSet<>(); + + // Pull the INFO columns out of the headers for each walker and add all patient ids + walkers.stream().forEach(walker -> { + try { + logger.info("Reading headers of VCF [" + walker.vcfIndexLine.getVcfPath() + "]"); + walker.readHeaders(infoStoreMap); + allPatientIds.addAll(Arrays.asList(walker.vcfIndexLine.getPatientIds())); + } catch (IOException e) { + logger.error("Error while reading headers of VCF [" + walker.vcfIndexLine.getVcfPath() + "]", e); + System.exit(-1); + } + }); + + patientIds = allPatientIds.toArray(new Integer[0]); + allSampleIds = new String[allPatientIds.size()]; + + walkers.parallelStream().forEach(walker -> { + logger.info("Setting bitmask offsets for VCF [" + walker.vcfIndexLine.getVcfPath() + "]"); + walker.setBitmaskOffsets(patientIds); + for (int x = 0; x < walker.vcfIndexLine.getSampleIds().length; x++) { + allSampleIds[Arrays.binarySearch(patientIds, walker.vcfIndexLine.getPatientIds()[x])] = + walker.vcfIndexLine.getSampleIds()[x]; + } + }); + + for (VCFWalker walker : walkers) { + chunkWriteEx = Executors.newFixedThreadPool(1); + storageDirStr = baseStorageDir + "/" + walker.currentContig; + storageDir = new File(storageDirStr); + storageDir.mkdirs(); + mergedDirStr = baseMergeDir + "/" + walker.currentContig; + new File(mergedDirStr).mkdirs(); + variantIndexBuilder = new VariantIndexBuilder(); + variantMaskStorage = new TreeMap<>(); + loadSingleContig(walker); + } + } + + private void loadSingleContig(VCFWalker walker) throws IOException { + VariantStore store = new VariantStore(); + store.setPatientIds(allPatientIds.stream().map((id) -> { + return id.toString(); + }).collect(Collectors.toList()).toArray(new String[0])); + + String lastContigProcessed = null; + int lastChunkProcessed = 0; + int currentChunk = 0; + String[] currentContig = new String[1]; + int[] currentPosition = {-1}; + String[] currentRef = new String[1]; + String[] currentAlt = new String[1]; + String[] currentVariantSpec = new String[1]; + + zygosityMaskStrings = new HashMap(); + + List positionsProcessedInChunk = new ArrayList<>(); + + while (walker.hasNext) { + String currentSpecNotation = walker.currentSpecNotation(); + currentContig[0] = walker.currentContig; + currentPosition[0] = walker.currentPosition; + currentRef[0] = walker.currentRef; + currentAlt[0] = walker.currentAlt; + currentVariantSpec[0] = walker.currentSpecNotation(); + currentChunk = walker.currentPosition / CHUNK_SIZE; + positionsProcessedInChunk.add(currentPosition[0]); + + if (lastContigProcessed == null) { + lastContigProcessed = walker.currentContig; + } + + flipChunk(lastContigProcessed, lastChunkProcessed, currentChunk, currentContig[0], false, walker.currentLine); + lastContigProcessed = walker.currentContig; + lastChunkProcessed = currentChunk; + + char[][][] maskStringsForVariantSpec = {zygosityMaskStrings.get(currentSpecNotation)}; + if (maskStringsForVariantSpec[0] == null) { + maskStringsForVariantSpec[0] = new char[7][allPatientIds.size()]; + for (int x = 0; x < maskStringsForVariantSpec[0].length; x++) { + maskStringsForVariantSpec[0][x] = new char[allPatientIds.size()]; + for (int y = 0; y < allPatientIds.size(); y++) { + maskStringsForVariantSpec[0][x][y] = '0'; + } + } + } + + while (Objects.equals(walker.currentSpecNotation(), currentVariantSpec[0]) && walker.hasNext) { + walker.updateRecords(maskStringsForVariantSpec[0], infoStoreMap); + try { + walker.nextLine(); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + } + + zygosityMaskStrings.put(currentSpecNotation, maskStringsForVariantSpec[0]); + } + + flipChunk(lastContigProcessed, lastChunkProcessed, currentChunk, currentContig[0], true, null); + + shutdownChunkWriteExecutor(); + + saveInfoStores(); + + splitInfoStoresByColumn(); + + convertInfoStoresToByteIndexed(); + + if (logger.isDebugEnabled()) { + // Log out the first and last 50 variants + int[] count = {0}; + for (String contig : store.getVariantMaskStorage().keySet()) { + ArrayList chunkIds = new ArrayList<>(); + FileBackedByteIndexedStorage> chromosomeStorage = + store.getVariantMaskStorage().get(contig); + if (chromosomeStorage != null) { + // print out the top and bottom 50 variants in the store (that have masks) + chunkIds.addAll(chromosomeStorage.keys()); + for (Integer chunkId : chunkIds) { + for (String variantSpec : chromosomeStorage.get(chunkId).keySet()) { + count[0]++; + VariableVariantMasks variantMasks = chromosomeStorage.get(chunkId).get(variantSpec); + if (variantMasks != null) { + VariantMask heterozygousMask = variantMasks.heterozygousMask; + String heteroIdList = sampleIdsForMask(allSampleIds, heterozygousMask); + VariantMask homozygousMask = variantMasks.homozygousMask; + String homoIdList = sampleIdsForMask(allSampleIds, homozygousMask); + + if (!heteroIdList.isEmpty() && heteroIdList.length() < 1000) + logger.debug(variantSpec + " : heterozygous : " + heteroIdList); + if (!homoIdList.isEmpty() && homoIdList.length() < 1000) + logger.debug(variantSpec + " : homozygous : " + homoIdList); + } + } + if (count[0] > 50) break; + } + + count[0] = 0; + for (int x = chunkIds.size() - 1; x > 0; x--) { + int chunkId = chunkIds.get(x); + chromosomeStorage.get(chunkId).keySet().forEach((variantSpec) -> { + count[0]++; + VariableVariantMasks variantMasks = chromosomeStorage.get(chunkId).get(variantSpec); + if (variantMasks != null) { + VariantMask heterozygousMask = variantMasks.heterozygousMask; + String heteroIdList = sampleIdsForMask(allSampleIds, heterozygousMask); + VariantMask homozygousMask = variantMasks.homozygousMask; + String homoIdList = sampleIdsForMask(allSampleIds, homozygousMask); + + if (!heteroIdList.isEmpty() && heteroIdList.length() < 1000) + logger.debug(variantSpec + " : heterozygous : " + heteroIdList); + if (!homoIdList.isEmpty() && homoIdList.length() < 1000) + logger.debug(variantSpec + " : homozygous : " + homoIdList); + } + }); + if (count[0] > 50) break; + } + } + } + } + + store.setVariantSpecIndex(variantIndexBuilder.getVariantSpecIndex().toArray(new String[0])); + saveVariantStore(store, variantMaskStorage); + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VCFIndexBuilder.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VCFIndexBuilder.java new file mode 100644 index 000000000..7be3220af --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VCFIndexBuilder.java @@ -0,0 +1,117 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype; + +import com.google.common.base.Joiner; + +import java.io.File; +import java.io.FileWriter; +import java.io.IOException; +import java.io.UncheckedIOException; +import java.nio.file.Files; +import java.util.*; +import java.util.stream.Collectors; + +public class VCFIndexBuilder { + + private final Set validPatientTypes; + + + private final File vcfPatientMappingFile; + private final File patientUUIDToIdMappingFile; + private final File vcfIndexOutputDirectory; + private Map> fileToPatientListMap; + private Map patientUUIDToPatientIdMapping; + + private static final String VCF_INDEX_DIRECTORY = "/opt/local/hpds"; + + private static final Joiner COMMA_JOINER = Joiner.on(","); + + public VCFIndexBuilder( + File vcfPatientMappingFile, File patientUUIDToIdMappingFile, File vcfIndexOutputDirectory, Set validPatientType + ) { + this.vcfPatientMappingFile = vcfPatientMappingFile; + this.patientUUIDToIdMappingFile = patientUUIDToIdMappingFile; + this.vcfIndexOutputDirectory = vcfIndexOutputDirectory; + this.validPatientTypes = validPatientType; + } + + public static void main(String[] args) { + if (args.length != 4) { + throw new IllegalArgumentException("There must be 4 parameters to VCFIndexBuilder"); + } + File vcfIndexOutputDirectoryFile = new File(args[2]); + if (!vcfIndexOutputDirectoryFile.isDirectory()) { + throw new IllegalArgumentException("Argument 3 must be a valid directory"); + } + new VCFIndexBuilder(new File(args[0]), new File(args[1]), vcfIndexOutputDirectoryFile, Set.of(args[3].split(","))).run(); + } + + private void run() { + + patientUUIDToPatientIdMapping = new HashMap<>(); + fileToPatientListMap = new HashMap<>(); + try { + Files.lines(patientUUIDToIdMappingFile.toPath()).skip(1).map(l -> l.split(",")).filter(columns -> columns.length == 2) + .forEach(columns -> { + patientUUIDToPatientIdMapping.put(columns[0], columns[1]); + }); + + Files.lines(vcfPatientMappingFile.toPath()).skip(1).map(l -> l.split(",")) + .filter(columns -> validPatientTypes.contains(columns[4])).forEach(columns -> { + String patientUuid = columns[0]; + String vcfFile = columns[1].substring(columns[1].lastIndexOf("/") + 1); + List patientList = Optional.ofNullable(fileToPatientListMap.get(vcfFile)).orElseGet(ArrayList::new); + patientList.add(patientUuid); + + if (patientUUIDToPatientIdMapping.get(patientUuid) != null) { + fileToPatientListMap.put(vcfFile, patientList); + } + }); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + + writeVcfIndexes(); + } + + private void writeVcfIndexes() { + Map> groupToVcfMapping = new HashMap<>(); + + for (String fileName : fileToPatientListMap.keySet()) { + String baseFile = fileName.substring(0, fileName.indexOf(".chr")); + List vcfFiles = groupToVcfMapping.getOrDefault(baseFile, new ArrayList<>()); + vcfFiles.add(fileName); + groupToVcfMapping.put(baseFile, vcfFiles); + } + + groupToVcfMapping.keySet().stream().forEach(vcfGroup -> { + writeVcfIndex(vcfGroup, groupToVcfMapping.get(vcfGroup)); + }); + } + + private void writeVcfIndex(String vcfGroup, List vcfFiles) { + try { + FileWriter fileWriter = new FileWriter(vcfIndexOutputDirectory.getAbsolutePath() + "/" + vcfGroup + "-vcfIndex.tsv"); + fileWriter.write( + "\"vcf_path\"\t\"chromosome\"\t\"isAnnotated\"\t\"isGzipped\"\t\"sample_ids\"\t\"patient_ids\"\t\"sample_relationship\"\t\"related_sample_ids\"\n" + ); + + for (String vcfFile : vcfFiles) { + Set validPatientUUIDs = fileToPatientListMap.get(vcfFile).stream() + .filter(patientUUIDToPatientIdMapping::containsKey).collect(Collectors.toSet()); + List patentIds = + validPatientUUIDs.stream().map(patientUUIDToPatientIdMapping::get).filter(Objects::nonNull).toList(); + fileWriter.write("\"" + VCF_INDEX_DIRECTORY + "/" + vcfFile + "\"\t\"" + extractChromosome(vcfFile) + "\"\t\"1\"\t\"1\"\t"); + fileWriter.write("\"" + COMMA_JOINER.join(validPatientUUIDs) + "\"\t\"" + COMMA_JOINER.join(patentIds) + "\"\n"); + } + + fileWriter.flush(); + fileWriter.close(); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + } + + private static String extractChromosome(String fileName) { + return fileName.substring(fileName.indexOf(".chr") + 4, fileName.lastIndexOf(".vcf.gz")); + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VCFIndexLine.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VCFIndexLine.java new file mode 100644 index 000000000..f30df63d7 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VCFIndexLine.java @@ -0,0 +1,88 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype; + +import java.util.Objects; + +public class VCFIndexLine implements Comparable { + private String vcfPath; + private String contig; + private boolean isAnnotated; + private boolean isGzipped; + private String[] sampleIds; + private Integer[] patientIds; + + public String getVcfPath() { + return vcfPath; + } + + public String getContig() { + return contig; + } + + public boolean isAnnotated() { + return isAnnotated; + } + + public boolean isGzipped() { + return isGzipped; + } + + public String[] getSampleIds() { + return sampleIds; + } + + public Integer[] getPatientIds() { + return patientIds; + } + + public VCFIndexLine setVcfPath(String vcfPath) { + this.vcfPath = vcfPath; + return this; + } + + public VCFIndexLine setContig(String contig) { + this.contig = contig; + return this; + } + + public VCFIndexLine setAnnotated(boolean annotated) { + isAnnotated = annotated; + return this; + } + + public VCFIndexLine setGzipped(boolean gzipped) { + isGzipped = gzipped; + return this; + } + + public VCFIndexLine setSampleIds(String[] sampleIds) { + this.sampleIds = sampleIds; + return this; + } + + public VCFIndexLine setPatientIds(Integer[] patientIds) { + this.patientIds = patientIds; + return this; + } + + @Override + public int compareTo(VCFIndexLine o) { + int chomosomeComparison = o.contig == null ? 1 : contig == null ? 0 : contig.compareTo(o.contig); + if (chomosomeComparison == 0) { + return vcfPath.compareTo(o.vcfPath); + } + return chomosomeComparison; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + VCFIndexLine that = (VCFIndexLine) o; + return Objects.equals(vcfPath, that.vcfPath) && Objects.equals(contig, that.contig); + } + + @Override + public int hashCode() { + return Objects.hash(vcfPath, contig); + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VCFPerPatientInfoStoreSplitter.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VCFPerPatientInfoStoreSplitter.java new file mode 100644 index 000000000..9cdae6c8f --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VCFPerPatientInfoStoreSplitter.java @@ -0,0 +1,105 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype; + +import java.io.*; +import java.util.concurrent.ConcurrentHashMap; +import java.util.concurrent.ExecutionException; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.InfoStore; + +public class VCFPerPatientInfoStoreSplitter { + private static Logger logger = LoggerFactory.getLogger(NewVCFLoader.class); + // private static File mergedFolder = new File("/opt/local/hpds/merged"); + + public static void splitAll(File javabinDir, File mergedFolder) + throws ClassNotFoundException, FileNotFoundException, IOException, InterruptedException, ExecutionException { + ConcurrentHashMap mergedFiles = new ConcurrentHashMap(); + + File[] inputFiles = javabinDir.listFiles((file) -> { + return file.getName().endsWith("_infoStores.javabin"); + }); + + mergedFolder.mkdir(); + + for (File file : inputFiles) { + try ( + FileInputStream fisi = new FileInputStream(file); GZIPInputStream gzisi = + new GZIPInputStream(fisi); ObjectInputStream objectInputStream = new ObjectInputStream(gzisi); + ) { + ConcurrentHashMap store = (ConcurrentHashMap) objectInputStream.readObject(); + logger.info("Loaded " + file.getName()); + store.keySet().parallelStream().forEach((key) -> { + if (key.contentEquals("PU") || key.contentEquals("IPU")) { + + } else { + try { + InfoStore partitionInfoStore = store.get(key); + File mergedStoreFile; + if (mergedFiles.containsKey(key)) { + mergedStoreFile = mergedFiles.get(key); + InfoStore mergedInfoStore = loadMergedStore(mergedFiles, key); + for (String value : partitionInfoStore.allValues.keySet()) { + if (mergedInfoStore.allValues.containsKey(value)) { + mergedInfoStore.allValues.get(value).addAll(partitionInfoStore.allValues.get(value)); + } else { + mergedInfoStore.allValues.put(value, partitionInfoStore.allValues.get(value)); + } + } + writeStore(mergedFiles, key, mergedInfoStore); + logger.info("Merged " + key + " for partition " + file.getName()); + } else { + mergedStoreFile = new File(mergedFolder, key + "_infoStore.javabin"); + mergedFiles.put(key, mergedStoreFile); + writeStore(mergedFiles, key, partitionInfoStore); + logger.info("Adding new store to merged set : " + key); + } + } catch (IOException e) { + logger.error("Error processing file [" + file.getName() + "], key [" + key + "]", e); + } catch (ClassNotFoundException e) { + logger.error("Error processing file [" + file.getName() + "], key [" + key + "]", e); + } + } + + }); + } catch (FileNotFoundException e) { + logger.error("Error processing file [" + file.getName() + "] : infoStores.javabin file not found", e); + } catch (IOException e) { + logger.error("Error processing file [" + file.getName() + "]", e); + } catch (ClassNotFoundException e) { + logger.error("Error processing file [" + file.getName() + "]", e); + } + } + + } + + private static InfoStore loadMergedStore(ConcurrentHashMap mergedFiles, String key) + throws FileNotFoundException, IOException, ClassNotFoundException { + FileInputStream fis = new FileInputStream(mergedFiles.get(key)); + GZIPInputStream gzis = new GZIPInputStream(fis); + ObjectInputStream ois = new ObjectInputStream(gzis); + InfoStore mergedInfoStore = (InfoStore) ois.readObject(); + ois.close(); + gzis.close(); + fis.close(); + return mergedInfoStore; + } + + private static synchronized void writeStore(ConcurrentHashMap mergedFiles, String key, InfoStore mergedInfoStore) + throws FileNotFoundException, IOException { + FileOutputStream fos = new FileOutputStream(mergedFiles.get(key)); + GZIPOutputStream gzos = new GZIPOutputStream(fos); + ObjectOutputStream oos = new ObjectOutputStream(gzos); + oos.writeObject(mergedInfoStore); + oos.flush(); + oos.close(); + gzos.flush(); + gzos.close(); + fos.flush(); + fos.close(); + } + +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VCFPerPatientInfoStoreToFBBIISConverter.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VCFPerPatientInfoStoreToFBBIISConverter.java new file mode 100644 index 000000000..6837e738e --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VCFPerPatientInfoStoreToFBBIISConverter.java @@ -0,0 +1,58 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype; + +import java.io.*; +import java.util.Arrays; +import java.util.List; +import java.util.concurrent.ExecutionException; +import java.util.zip.GZIPInputStream; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.FileBackedByteIndexedInfoStore; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.InfoStore; + +public class VCFPerPatientInfoStoreToFBBIISConverter { + private static Logger logger = LoggerFactory.getLogger(NewVCFLoader.class); + + public static void convertAll(String inputPath, String outputPath) + throws ClassNotFoundException, FileNotFoundException, IOException, InterruptedException, ExecutionException { + File[] inputFiles = new File(inputPath).listFiles((path) -> { + return path.getName().endsWith("infoStore.javabin"); + }); + Arrays.sort(inputFiles); + + File outputFolder = new File(outputPath); + + List inputFileList = Arrays.asList(inputFiles); + inputFileList.stream().forEach((file) -> { + convert(outputFolder, file); + }); + } + + public static void convert(File outputFolder, File file) { + logger.info("Converting InfoStore file: " + file.getAbsolutePath()); + try ( + FileInputStream fisi = new FileInputStream(file); GZIPInputStream gzisi = + new GZIPInputStream(fisi); ObjectInputStream objectInputStream = new ObjectInputStream(gzisi); + ) { + InfoStore store = (InfoStore) objectInputStream.readObject(); + + if (store.allValues.size() > 0) { + FileBackedByteIndexedInfoStore fbbiis = new FileBackedByteIndexedInfoStore(outputFolder, store); + + fbbiis.write(new File(outputFolder, file.getName())); + logger.info("Completed converting InfoStore file: " + file.getAbsolutePath()); + } else { + logger.info("Skipping empty InfoStore file: " + file.getAbsolutePath() + ""); + } + } catch (FileNotFoundException e) { + logger.error("InfoStore file not found: " + file.getAbsolutePath()); + } catch (IOException e) { + logger.error("Error converting InfoStore file: " + file.getAbsolutePath()); + } catch (ClassNotFoundException e) { + logger.error("Error converting InfoStore file: " + file.getAbsolutePath()); + } + } + +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VariantIndexBuilder.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VariantIndexBuilder.java new file mode 100644 index 000000000..71fec9596 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VariantIndexBuilder.java @@ -0,0 +1,30 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.LinkedList; +import java.util.Map; +import java.util.concurrent.ConcurrentHashMap; + +public class VariantIndexBuilder { + + private static Logger logger = LoggerFactory.getLogger(VariantIndexBuilder.class); + + private final LinkedList variantSpecIndex = new LinkedList<>(); + private final Map variantSpecToIndexMap = new ConcurrentHashMap<>(); + + public synchronized Integer getIndex(String variantSpec) { + Integer variantIndex = variantSpecToIndexMap.get(variantSpec); + if (variantIndex == null) { + variantIndex = variantSpecIndex.size(); + variantSpecIndex.add(variantSpec); + variantSpecToIndexMap.put(variantSpec, variantIndex); + } + return variantIndex; + } + + public LinkedList getVariantSpecIndex() { + return variantSpecIndex; + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VariantMetadataLoader.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VariantMetadataLoader.java new file mode 100644 index 000000000..e38799c3f --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VariantMetadataLoader.java @@ -0,0 +1,104 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype; + + +import java.io.*; +import java.nio.charset.Charset; +import java.util.Iterator; +import java.util.TreeSet; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; + +import org.apache.commons.csv.CSVFormat; +import org.apache.commons.csv.CSVParser; +import org.apache.commons.csv.CSVRecord; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMetadataIndex; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantSpec; + +/** + * + * This loader will read in the metadata associated with each variant and build a VariantMetadataIndex that can be used to populate data in + * the PIC-SURE Varaint Explorer. + */ +public class VariantMetadataLoader { + + private static Logger log = LoggerFactory.getLogger(VariantMetadataLoader.class); + + private static VariantMetadataIndex metadataIndex; + + // fields to allow tests to override default file location + private static String storagePathForTests = null; + private static String variantIndexPathForTests = null; + + private static final int ANNOTATED_FLAG_COLUMN = 2, GZIP_FLAG_COLUMN = 3, FILE_COLUMN = 0; + + public static void main(String[] args) throws IOException { + File vcfIndexFile; + + log.info(new File(".").getAbsolutePath()); + if (args.length > 0 && new File(args[0]).exists()) { + log.info("using path from command line"); + vcfIndexFile = new File(args[0]); + variantIndexPathForTests = args[1]; + storagePathForTests = args[2]; + metadataIndex = new VariantMetadataIndex(storagePathForTests); + } else { + metadataIndex = new VariantMetadataIndex(); + vcfIndexFile = new File("/opt/local/hpds/vcfIndex.tsv"); + } + + TreeSet vcfFileTree = new TreeSet<>(); + + try ( + CSVParser parser = + CSVParser.parse(vcfIndexFile, Charset.forName("UTF-8"), CSVFormat.DEFAULT.withDelimiter('\t').withSkipHeaderRecord(true)) + ) { + final boolean[] horribleHeaderSkipFlag = {false}; + parser.forEach((CSVRecord r) -> { + if (horribleHeaderSkipFlag[0]) { + File vcfFileLocal = new File(r.get(FILE_COLUMN)); + if (Integer.parseInt(r.get(ANNOTATED_FLAG_COLUMN).trim()) == 1) { + VcfInputFile vcfInput = new VcfInputFile(vcfFileLocal, (Integer.parseInt(r.get(GZIP_FLAG_COLUMN).trim()) == 1)); + vcfFileTree.add(vcfInput); + } + } else { + horribleHeaderSkipFlag[0] = true; + } + }); + } + + String currentContig = ""; + while (vcfFileTree.size() > 0) { + + // find and remove the lowest element + VcfInputFile vcfInput = vcfFileTree.pollFirst(); + + // write to disk each time the contig changes + if (!currentContig.equals(vcfInput.currentContig)) { + metadataIndex.flush(); + } + + currentContig = vcfInput.currentContig; + metadataIndex.put(vcfInput.currentVariantSpec, vcfInput.currentMetaData); + + if (vcfInput.hasNextVariant()) { + vcfInput.nextVariant(); + vcfFileTree.add(vcfInput); + } else { + log.info("Finished processing: " + vcfInput.fileName); + } + } + + metadataIndex.complete(); + + // store this in a path per contig (or a preset path + String binfilePath = variantIndexPathForTests == null ? VariantMetadataIndex.VARIANT_METADATA_BIN_FILE : variantIndexPathForTests; + + try (ObjectOutputStream out = new ObjectOutputStream(new GZIPOutputStream(new FileOutputStream(new File(binfilePath))))) { + out.writeObject(metadataIndex); + out.flush(); + } + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VcfIndexFileParser.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VcfIndexFileParser.java new file mode 100644 index 000000000..48f1b7f9e --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VcfIndexFileParser.java @@ -0,0 +1,92 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype; + +import org.apache.commons.csv.CSVFormat; +import org.apache.commons.csv.CSVParser; +import org.apache.commons.csv.CSVRecord; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.File; +import java.io.IOException; +import java.io.UncheckedIOException; +import java.nio.charset.Charset; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.TreeSet; +import java.util.function.Supplier; + +public class VcfIndexFileParser { + + + private static final Logger log = LoggerFactory.getLogger(VcfIndexFileParser.class); + + private static final int FILE_COLUMN = 0; + private static final int CHROMOSOME_COLUMN = 1; + private static final int ANNOTATED_FLAG_COLUMN = 2; + private static final int GZIP_FLAG_COLUMN = 3; + private static final int SAMPLE_IDS_COLUMN = 4; + private static final int PATIENT_IDS_COLUMN = 5; + + + + public List parse(File vcfIndexFile) { + TreeSet vcfSet = new TreeSet<>(); + CSVParser parser; + + int lineNumber = 0; + try { + parser = + CSVParser.parse(vcfIndexFile, Charset.forName("UTF-8"), CSVFormat.DEFAULT.withDelimiter('\t').withSkipHeaderRecord(true)); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + for (CSVRecord r : parser) { + // Because the CSV parser does not correctly skip the header + if (lineNumber == 0) { + lineNumber++; + continue; + } + VCFIndexLine line = new VCFIndexLine(); + + line.setVcfPath(runWithLogging(() -> r.get(FILE_COLUMN).trim(), r, FILE_COLUMN)); + line.setContig( + runWithLogging( + () -> r.get(CHROMOSOME_COLUMN).trim().contentEquals("ALL") ? null : r.get(CHROMOSOME_COLUMN).trim(), r, + CHROMOSOME_COLUMN + ) + ); + + line.setAnnotated(runWithLogging(() -> Integer.parseInt(r.get(ANNOTATED_FLAG_COLUMN).trim()) == 1, r, ANNOTATED_FLAG_COLUMN)); + line.setGzipped(runWithLogging(() -> Integer.parseInt(r.get(GZIP_FLAG_COLUMN).trim()) == 1, r, GZIP_FLAG_COLUMN)); + line.setSampleIds( + runWithLogging( + () -> Arrays.stream(r.get(SAMPLE_IDS_COLUMN).split(",")).map(String::trim).toList().toArray(new String[0]), r, + SAMPLE_IDS_COLUMN + ) + ); + line.setPatientIds( + runWithLogging( + () -> Arrays.stream(r.get(PATIENT_IDS_COLUMN).split(",")).map(String::trim).map(Integer::parseInt).toList() + .toArray(new Integer[0]), + r, PATIENT_IDS_COLUMN + ) + ); + vcfSet.add(line); + lineNumber++; + } + return new ArrayList<>(vcfSet); + } + + private T runWithLogging(Supplier supplier, CSVRecord r, int columnNumber) { + try { + return supplier.get(); + } catch (RuntimeException e) { + throw new IllegalArgumentException( + "Exception parsing vcfIndexFile on line " + r.getRecordNumber() + ", column " + (columnNumber + 1) + ". Value = \"" + + r.get(columnNumber) + "\"", + e + ); + } + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VcfInputFile.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VcfInputFile.java new file mode 100644 index 000000000..b29fe1d2d --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VcfInputFile.java @@ -0,0 +1,89 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantSpec; +import org.apache.commons.csv.CSVFormat; +import org.apache.commons.csv.CSVParser; +import org.apache.commons.csv.CSVRecord; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.*; +import java.util.Iterator; +import java.util.zip.GZIPInputStream; + +public class VcfInputFile implements Comparable { + + private static final int INFO_COLUMN = 7; + + private static Logger log = LoggerFactory.getLogger(VcfInputFile.class); + + Iterator iterator; + CSVParser parser; + + String fileName; + String currentContig; + String currentVariantSpec; + String currentMetaData; + + /** + * read in an vcfFile, skip the header rows, and queue up the first variant (with metadata) + * @param vcfFile + * @param gzipped + */ + public VcfInputFile(File vcfFile, boolean gzipped) { + fileName = vcfFile.getName(); + log.info("Processing VCF file: " + fileName); + try { + Reader reader = + new InputStreamReader(gzipped ? new GZIPInputStream(new FileInputStream(vcfFile)) : new FileInputStream(vcfFile)); + parser = new CSVParser(reader, CSVFormat.DEFAULT.withDelimiter('\t').withSkipHeaderRecord(false)); + + iterator = parser.iterator(); + while (iterator.hasNext()) { + CSVRecord csvRecord = iterator.next(); + // skip all header rows + if (csvRecord.get(0).startsWith("#")) { + continue; + } + + VariantSpec variantSpec = new VariantSpec(csvRecord); + currentContig = variantSpec.metadata.chromosome; + currentVariantSpec = variantSpec.specNotation(); + currentMetaData = csvRecord.get(INFO_COLUMN).trim(); + break; + } + + } catch (IOException e) { + log.error("Error processing VCF file: " + vcfFile.getName(), e); + } + + } + + boolean hasNextVariant() { + return iterator.hasNext(); + } + + void nextVariant() { + CSVRecord csvRecord = iterator.next(); + // skip all header rows + if (csvRecord.get(0).startsWith("#")) { + return; + } + + VariantSpec variantSpec = new VariantSpec(csvRecord); + currentContig = variantSpec.metadata.chromosome; + currentVariantSpec = variantSpec.specNotation(); + currentMetaData = csvRecord.get(INFO_COLUMN).trim(); + } + + /** + * These files will be sorted by the current variant spec. We need to make sure they are never actually equal values (since the TreeSet + * used to keep them sorted enforces uniqueness) + */ + @Override + public int compareTo(VcfInputFile arg0) { + return (currentVariantSpec + iterator.toString()).compareTo(arg0.currentVariantSpec + arg0.iterator.toString()); + } + + +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/columnmeta/CreateColumnmetaCSV.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/columnmeta/CreateColumnmetaCSV.java new file mode 100644 index 000000000..2911afda2 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/columnmeta/CreateColumnmetaCSV.java @@ -0,0 +1,26 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.columnmeta; + +import edu.harvard.hms.dbmi.avillach.hpds.etl.LoadingStore; +import edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.csv.CSVLoader; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.io.RandomAccessFile; + +public class CreateColumnmetaCSV { + private static LoadingStore store = new LoadingStore(); + + private static Logger log = LoggerFactory.getLogger(CSVLoader.class); + + private static String HPDS_DIRECTORY = "/opt/local/hpds/"; + + public static void main(String[] args) throws IOException { + if (args.length > 0) { + HPDS_DIRECTORY = args[0] + "/"; + } + store.allObservationsStore = new RandomAccessFile(HPDS_DIRECTORY + "allObservationsStore.javabin", "rw"); + store.dumpStatsAndColumnMeta(HPDS_DIRECTORY); + } + +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/config/CSVConfig.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/config/CSVConfig.java new file mode 100644 index 000000000..e79927873 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/config/CSVConfig.java @@ -0,0 +1,27 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.config; + +/** + * Configuration class for CSV processing. The names are using snake_case to match the JSON keys in the config file. This is used to map the + * JSON keys to the Java fields. + */ +public class CSVConfig { + + private String dataset_name; + private boolean dataset_name_as_root_node; + + public String getDataset_name() { + return dataset_name; + } + + public void setDataset_name(String dataset_name) { + this.dataset_name = dataset_name; + } + + public boolean getDataset_name_as_root_node() { + return dataset_name_as_root_node; + } + + public void setDataset_name_as_root_node(boolean dataset_name_as_root_node) { + this.dataset_name_as_root_node = dataset_name_as_root_node; + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/config/ConfigLoader.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/config/ConfigLoader.java new file mode 100644 index 000000000..7f46fbfac --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/config/ConfigLoader.java @@ -0,0 +1,82 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.config; + +import com.fasterxml.jackson.core.type.TypeReference; +import com.fasterxml.jackson.databind.ObjectMapper; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import software.amazon.awssdk.annotations.NotNull; + +import java.io.File; +import java.util.HashMap; +import java.util.Map; + +public class ConfigLoader { + + private static final Logger log = LoggerFactory.getLogger(ConfigLoader.class); + private static final String INPUT_DIR = "/opt/local/hpds_input"; + private Map csvConfigMap = new HashMap<>(); + + /** + * Constructor for ConfigLoader. It loads the configuration from a JSON file located in the INPUT_DIR. The JSON file should contain a + * mapping of CSV file names to their respective configurations. + */ + public ConfigLoader() { + File file = new File(INPUT_DIR); + if (file.exists()) { + ObjectMapper objectMapper = new ObjectMapper(); + try { + this.csvConfigMap = objectMapper.readValue(new File(INPUT_DIR + "/config.json"), new TypeReference<>() {}); + + // Remove the ".csv" extension from the keys in the map if they exist + for (String key : csvConfigMap.keySet()) { + if (key.endsWith(".csv")) { + String newKey = key.substring(0, key.length() - 4); + csvConfigMap.put(newKey, csvConfigMap.get(key)); + csvConfigMap.remove(key); + } + } + + log.info("Loaded config from {}", file.getAbsolutePath()); + log.info("CSV Config Map: {}", csvConfigMap); + } catch (Exception e) { + log.error(e.getMessage()); + } + } else { + log.error("ConfigLoader: Input directory does not exist: {}", INPUT_DIR); + } + } + + /** + * Returns the CSVConfig for the given csvName. If the config does not exist, it returns an empty Optional. + * + * @param fileName The name of the CSV file (without .csv extension) + * @return An Optional containing the CSVConfig if it exists, or an empty Optional if it does not + */ + public CSVConfig getConfigFor(@NotNull String fileName) { + if (fileName.endsWith(".csv") || fileName.endsWith(".sql")) { + fileName = fileName.substring(0, fileName.length() - 4); + } + + CSVConfig csvConfig = this.csvConfigMap.get(fileName); + if (csvConfig != null) { + log.info("Found config for file {}, using dataset_name {}", fileName, csvConfig.getDataset_name()); + } else { + log.warn("No config found for file {}, using default settings", fileName); + } + + return csvConfig; + } + + /** + * Returns all the CSV configurations loaded from the config.json file. + * @return A map of CSV file names to their respective configurations + */ + public Map getAllConfigs() { + return csvConfigMap; + } + + public void add(String fileName, CSVConfig csvConfig) { + this.csvConfigMap.put(fileName, csvConfig); + } + +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/csv/CSVLoader.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/csv/CSVLoader.java new file mode 100644 index 000000000..d63658699 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/csv/CSVLoader.java @@ -0,0 +1,119 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.csv; + +import java.io.*; +import java.util.Date; +import java.util.concurrent.ExecutionException; + +import edu.harvard.hms.dbmi.avillach.hpds.etl.LoadingStore; +import org.apache.commons.csv.CSVFormat; +import org.apache.commons.csv.CSVRecord; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.common.cache.CacheLoader.InvalidCacheLoadException; + +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; + +@SuppressWarnings({"unchecked", "rawtypes"}) +public class CSVLoader { + + private static LoadingStore store = new LoadingStore(); + + private static Logger log = LoggerFactory.getLogger(CSVLoader.class); + + private static final int PATIENT_NUM = 0; + + private static final int CONCEPT_PATH = 1; + + private static final int NUMERIC_VALUE = 2; + + private static final int TEXT_VALUE = 3; + + private static final int DATETIME = 4; + + private static String HPDS_DIRECTORY = "/opt/local/hpds/"; + + public static void main(String[] args) throws IOException { + if (args.length > 0) { + HPDS_DIRECTORY = args[0] + "/"; + } + store.allObservationsStore = new RandomAccessFile(HPDS_DIRECTORY + "allObservationsStore.javabin", "rw"); + initialLoad(HPDS_DIRECTORY); + store.saveStore(HPDS_DIRECTORY); + } + + private static void initialLoad(String hpdsDirectory) throws IOException { + Crypto.loadKey(Crypto.DEFAULT_KEY_NAME, hpdsDirectory + "encryption_key"); + Reader in = new FileReader(HPDS_DIRECTORY + "allConcepts.csv"); + Iterable records = CSVFormat.DEFAULT.withAllowMissingColumnNames().parse(new BufferedReader(in, 1024 * 1024)); + + final PhenoCube[] currentConcept = new PhenoCube[1]; + for (CSVRecord record : records) { + processRecord(currentConcept, record); + } + } + + private static void processRecord(final PhenoCube[] currentConcept, CSVRecord record) { + if (record.size() < 4) { + log.info("Record number " + record.getRecordNumber() + " had less records than we expected so we are skipping it."); + return; + } + + try { + String conceptPathFromRow = record.get(CONCEPT_PATH); + String[] segments = conceptPathFromRow.split("\\\\"); + for (int x = 0; x < segments.length; x++) { + segments[x] = segments[x].trim(); + } + conceptPathFromRow = String.join("\\", segments) + "\\"; + conceptPathFromRow = conceptPathFromRow.replaceAll("\\ufffd", ""); + String textValueFromRow = record.get(TEXT_VALUE) == null ? null : record.get(TEXT_VALUE).trim(); + if (textValueFromRow != null) { + textValueFromRow = textValueFromRow.replaceAll("\\ufffd", ""); + } + String conceptPath = + conceptPathFromRow.endsWith("\\" + textValueFromRow + "\\") ? conceptPathFromRow.replaceAll("\\\\[^\\\\]*\\\\$", "\\\\") + : conceptPathFromRow; + // This is not getDouble because we need to handle null values, not coerce them into 0s + String numericValue = record.get(NUMERIC_VALUE); + if ((numericValue == null || numericValue.isEmpty()) && textValueFromRow != null) { + try { + numericValue = Double.parseDouble(textValueFromRow) + ""; + } catch (NumberFormatException e) { + + } + } + boolean isAlpha = (numericValue == null || numericValue.isEmpty()); + if (currentConcept[0] == null || !currentConcept[0].name.equals(conceptPath)) { + log.debug(conceptPath); + try { + currentConcept[0] = store.store.get(conceptPath); + } catch (InvalidCacheLoadException e) { + currentConcept[0] = new PhenoCube(conceptPath, isAlpha ? String.class : Double.class); + store.store.put(conceptPath, currentConcept[0]); + } + } + String value = isAlpha ? record.get(TEXT_VALUE) : numericValue; + + if ( + value != null && !value.trim().isEmpty() + && ((isAlpha && currentConcept[0].vType == String.class) || (!isAlpha && currentConcept[0].vType == Double.class)) + ) { + value = value.trim(); + currentConcept[0] + .setColumnWidth(isAlpha ? Math.max(currentConcept[0].getColumnWidth(), value.getBytes().length) : Double.BYTES); + int patientId = Integer.parseInt(record.get(PATIENT_NUM)); + Date date = null; + if (record.size() > 4 && record.get(DATETIME) != null && !record.get(DATETIME).isEmpty()) { + date = new Date(Long.parseLong(record.get(DATETIME))); + } + currentConcept[0].add(patientId, isAlpha ? value : Double.parseDouble(value), date); + store.allIds.add(patientId); + } + } catch (ExecutionException e) { + // todo: do we really want to ignore this? + log.error("Error processing record", e); + } + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/csv/CSVLoaderNewSearch.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/csv/CSVLoaderNewSearch.java new file mode 100644 index 000000000..ec4712fbf --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/csv/CSVLoaderNewSearch.java @@ -0,0 +1,99 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.csv; + +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.etl.LoadingStore; +import edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.config.CSVConfig; +import edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.config.ConfigLoader; +import org.apache.commons.csv.CSVFormat; +import org.apache.commons.csv.CSVRecord; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.*; +import java.util.Date; +import java.util.Optional; + +@SuppressWarnings({"unchecked", "rawtypes"}) +public class CSVLoaderNewSearch { + + private static final Logger log = LoggerFactory.getLogger(CSVLoaderNewSearch.class); + + private static final LoadingStore store = new LoadingStore(); + private static final ConfigLoader configLoader = new ConfigLoader(); + + private static boolean DO_VARNAME_ROLLUP = false; + private static final String HPDS_DIRECTORY = "/opt/local/hpds/"; + + public static void main(String[] args) throws IOException { + if (args.length > 1) { + if (args[0].equalsIgnoreCase("NO_ROLLUP")) { + log.info("NO_ROLLUP SET."); + DO_VARNAME_ROLLUP = false; + } + } + + store.allObservationsStore = new RandomAccessFile(HPDS_DIRECTORY + "allObservationsStore.javabin", "rw"); + initialLoad(); + store.saveStore(HPDS_DIRECTORY); + } + + private static void initialLoad() throws IOException { + Crypto.loadDefaultKey(); + Reader in = new FileReader(HPDS_DIRECTORY + "allConcepts.csv"); + Iterable records = + CSVFormat.DEFAULT.withSkipHeaderRecord().withFirstRecordAsHeader().parse(new BufferedReader(in, 1024 * 1024)); + + CSVConfig csvConfig = configLoader.getConfigFor("allConcepts"); + final PhenoCube[] currentConcept = new PhenoCube[1]; + for (CSVRecord record : records) { + processRecord(currentConcept, record, csvConfig); + } + } + + private static void processRecord(final PhenoCube[] currentConcept, CSVRecord record, CSVConfig csvConfig) { + if (record.size() < 4) { + log.info("Record number {} had less records than we exgpected so we are skipping it.", record.getRecordNumber()); + return; + } + + String conceptPath = CSVParserUtil.parseConceptPath(record, DO_VARNAME_ROLLUP, csvConfig); + if (conceptPath == null || conceptPath.isEmpty()) { + log.info("Record number {} had no concept path so we are skipping it.", record.getRecordNumber()); + return; + } + + String numericValue = record.get(CSVParserUtil.NUMERIC_VALUE); + boolean isAlpha = (numericValue == null || numericValue.isEmpty()); + String value = isAlpha ? record.get(CSVParserUtil.TEXT_VALUE) : numericValue; + currentConcept[0] = getPhenoCube(currentConcept[0], conceptPath, isAlpha); + + if ( + value != null && !value.trim().isEmpty() + && ((isAlpha && currentConcept[0].vType == String.class) || (!isAlpha && currentConcept[0].vType == Double.class)) + ) { + value = value.trim(); + currentConcept[0] + .setColumnWidth(isAlpha ? Math.max(currentConcept[0].getColumnWidth(), value.getBytes().length) : Double.BYTES); + int patientId = Integer.parseInt(record.get(CSVParserUtil.PATIENT_NUM)); + Date date = null; + if (record.size() > 4 && record.get(CSVParserUtil.DATETIME) != null && !record.get(CSVParserUtil.DATETIME).isEmpty()) { + date = new Date(Long.parseLong(record.get(CSVParserUtil.DATETIME))); + } + currentConcept[0].add(patientId, isAlpha ? value : Double.parseDouble(value), date); + store.allIds.add(patientId); + } + } + + private static PhenoCube getPhenoCube(PhenoCube currentConcept, String conceptPath, boolean isAlpha) { + if (currentConcept == null || !currentConcept.name.equals(conceptPath)) { + currentConcept = store.store.getIfPresent(conceptPath); + if (currentConcept == null) { + currentConcept = new PhenoCube(conceptPath, isAlpha ? String.class : Double.class); + store.store.put(conceptPath, currentConcept); + } + } + + return currentConcept; + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/csv/CSVParserUtil.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/csv/CSVParserUtil.java new file mode 100644 index 000000000..c083959be --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/csv/CSVParserUtil.java @@ -0,0 +1,68 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.csv; + +import edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.config.CSVConfig; +import org.apache.commons.csv.CSVRecord; +import org.springframework.lang.NonNull; +import org.springframework.lang.Nullable; + +import java.util.Arrays; +import java.util.Date; +import java.util.stream.Collectors; + +public class CSVParserUtil { + public static final int PATIENT_NUM = 0; + public static final int CONCEPT_PATH = 1; + public static final int NUMERIC_VALUE = 2; + public static final int TEXT_VALUE = 3; + public static final int DATETIME = 4; + + private static final String MU = "µ"; + + public static String parseConceptPath(CSVRecord record, boolean doVarNameRollup, CSVConfig config) { + String conceptPathFromRow = record.get(CONCEPT_PATH); + + // replace the mu character with a backslash, see 1000 genome dataset + conceptPathFromRow = conceptPathFromRow.replace(MU, "\\"); + conceptPathFromRow = Arrays.stream(conceptPathFromRow.split("\\\\")).map(String::trim).collect(Collectors.joining("\\")) + "\\"; + conceptPathFromRow = stripWeirdUnicodeChars(conceptPathFromRow); + + // \\ufffd = � + String textValueFromRow = stripWeirdUnicodeChars(trim(record.get(TEXT_VALUE))); + if (doVarNameRollup && conceptPathFromRow.endsWith("\\" + textValueFromRow + "\\")) { + // This regex deletes the last node from the concept path, i.e. "rolling it up" + conceptPathFromRow = conceptPathFromRow.replaceAll("\\\\[^\\\\]*\\\\$", "\\\\"); + } + + if (config != null && config.getDataset_name_as_root_node()) { + String datasetName = config.getDataset_name(); + if (!conceptPathFromRow.startsWith("\\")) { + conceptPathFromRow = "\\" + conceptPathFromRow; + } + + conceptPathFromRow = "\\" + datasetName + conceptPathFromRow; + } + + return conceptPathFromRow; + } + + private static String stripWeirdUnicodeChars(@NonNull String raw) { + return raw.replaceAll("\\ufffd", ""); + } + + public static String trim(@Nullable String maybeString) { + return maybeString == null ? "" : maybeString.trim(); + } + + public static @Nullable Date parseDate(CSVRecord record) { + Date date = null; + try { + if (record.size() > 4 && record.get(DATETIME) != null && !record.get(DATETIME).isEmpty()) { + date = new Date(Long.parseLong(record.get(DATETIME))); + } + } catch (NumberFormatException e) { + return null; + } + + return date; + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/litecsv/IngestStatus.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/litecsv/IngestStatus.java new file mode 100644 index 000000000..33748767f --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/litecsv/IngestStatus.java @@ -0,0 +1,6 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.litecsv; + +import java.nio.file.Path; + +public record IngestStatus(Path file, long lineCount, int conceptCount, long duration) { +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/litecsv/LowRAMCSVProcessor.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/litecsv/LowRAMCSVProcessor.java new file mode 100644 index 000000000..364973598 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/litecsv/LowRAMCSVProcessor.java @@ -0,0 +1,178 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.litecsv; + +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.config.CSVConfig; +import edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.config.ConfigLoader; +import edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.csv.CSVParserUtil; +import org.apache.commons.csv.CSVFormat; +import org.apache.commons.csv.CSVParser; +import org.apache.commons.csv.CSVRecord; +import org.apache.logging.log4j.util.Strings; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.lang.Nullable; + +import java.io.*; +import java.nio.file.Files; +import java.util.*; +import java.util.stream.Stream; + +public class LowRAMCSVProcessor { + + private static final Logger log = LoggerFactory.getLogger(LowRAMCSVProcessor.class); + private final LowRAMLoadingStore store; + private final boolean doVarNameRollup; + private final double maxChunkSizeGigs; + private final ConfigLoader configLoader; + + public LowRAMCSVProcessor(LowRAMLoadingStore store, boolean doVarNameRollup, double maxChunkSizeGigs) { + this.store = store; + this.doVarNameRollup = doVarNameRollup; + this.maxChunkSizeGigs = maxChunkSizeGigs; + this.configLoader = null; + } + + public LowRAMCSVProcessor(LowRAMLoadingStore store, boolean doVarNameRollup, double maxChunkSizeGigs, ConfigLoader configLoader) { + this.store = store; + this.doVarNameRollup = doVarNameRollup; + this.maxChunkSizeGigs = maxChunkSizeGigs; + this.configLoader = configLoader; + } + + public IngestStatus process(File csv) { + long startTime = System.nanoTime(); + log.info("Attempting to ingest file {}", csv.getAbsolutePath()); + try (Reader r = new FileReader(csv); Stream rawLines = Files.lines(csv.toPath())) { + CSVParser parser = CSVFormat.DEFAULT.withSkipHeaderRecord().withFirstRecordAsHeader().parse(new BufferedReader(r)); + + CSVConfig csvConfig = configLoader != null ? configLoader.getConfigFor(csv.getName()) : null; + // we want to read the file in reasonably sized chunks so that we can handle chunks naively + // in memory without going OOM + // to do this, we're going to assume that over the course of thousands of lines, each line + // is more or less the same length + // so we'll just provision n chunks, where n is max(1, file_size/max_chunk_size) + log.info("Gathering stats about file {}", csv.getName()); + int chunks = Math.max(1, (int) Math.ceil((double) csv.length() / (maxChunkSizeGigs * 1024 * 1024 * 1024))); + final long totalLineCount = rawLines.count(); + final long linesPerChunk = totalLineCount / chunks; + log.info( + "File {} is {} bytes and {} lines. Dividing into {} chunks of {} lines each", csv.getName(), csv.length(), totalLineCount, + chunks, linesPerChunk + ); + long chunkLineCount = 0; + long lineCount = 0; + int chunkCount = 0; + Set concepts = new HashSet<>(); + List lines = new ArrayList<>(); + + log.info("Creating chunks"); + for (CSVRecord record : parser) { + chunkLineCount++; + lineCount++; + lines.add(record); + if (chunkLineCount > linesPerChunk || lineCount + 1 == totalLineCount) { + log.info("Finished creating chunk {}", chunkCount); + // sort by concept to prevent cache thrashing when ingesting + // loading each concept in its entirety for a chunk will minimize disk IO and + // let us keep more valuable things in RAM + lines.sort(Comparator.comparing(a -> a.get(1))); + log.info("Finished sorting chunk {}", chunkCount); + Set chunkConcepts = ingest(lines, csvConfig); + concepts.addAll(chunkConcepts); + log.info("Finished ingesting chunk {} with {} unique concepts", chunkCount, chunkConcepts.size()); + lines = new ArrayList<>(); + chunkLineCount = 0; + chunkCount++; + } + } + + return new IngestStatus(csv.toPath(), totalLineCount, concepts.size(), System.nanoTime() - startTime); + + } catch (IOException e) { + throw new RuntimeException(e); + } + } + + + private Set ingest(List sortedRecords, CSVConfig csvConfig) { + Set concepts = new HashSet<>(); + for (CSVRecord record : sortedRecords) { + if (record.size() < 4) { + log.warn("Record #{} has too few columns, skipping.", record.getRecordNumber()); + continue; + } + + String conceptPath = CSVParserUtil.parseConceptPath(record, doVarNameRollup, csvConfig); + IngestFn ingestFn = Strings.isBlank(record.get(CSVParserUtil.NUMERIC_VALUE)) ? this::ingestNonNumeric : this::ingestNumeric; + Date date = CSVParserUtil.parseDate(record); + int patientId = Integer.parseInt(record.get(CSVParserUtil.PATIENT_NUM)); + if (ingestFn.attemptIngest(record, conceptPath, patientId, date)) { + concepts.add(conceptPath); + } else { + log.warn("Could not ingest record #{}", record.getRecordNumber()); + } + } + return concepts; + } + + @FunctionalInterface + private interface IngestFn { + boolean attemptIngest(CSVRecord record, String path, int patientId, @Nullable Date date); + } + + private boolean ingestNumeric(CSVRecord record, String conceptPath, int patientId, Date date) { + PhenoCube concept = store.loadingCache.getIfPresent(conceptPath); + if (concept == null) { + concept = new PhenoCube<>(conceptPath, Double.class); + concept.setColumnWidth(Double.BYTES); + store.loadingCache.put(conceptPath, concept); + } + if (!concept.vType.equals(Double.class)) { + log.error(""" + Concept bucket {} was configured for non-numeric types, but received numeric value {} + This happens when, for a single concept, there rows that have a tval_char, and other + rows with an nval_num but no tval_char. + Offending record #{} + """, conceptPath, record.get(CSVParserUtil.NUMERIC_VALUE), record.getRecordNumber()); + + return false; + } + try { + String rawNumericValue = CSVParserUtil.trim(record.get(CSVParserUtil.NUMERIC_VALUE)); + double parsedValue = Double.parseDouble(rawNumericValue); + concept.add(patientId, parsedValue, date); + store.allIds.add(patientId); + return true; + } catch (NumberFormatException e) { + log.warn("Could not parse numeric value in line {}", record); + } + return false; + } + + private boolean ingestNonNumeric(CSVRecord record, String conceptPath, int patientId, Date date) { + PhenoCube concept = store.loadingCache.getIfPresent(conceptPath); + if (concept == null) { + concept = new PhenoCube<>(conceptPath, String.class); + store.loadingCache.put(conceptPath, concept); + } + + if (!concept.vType.equals(String.class)) { + log.error(""" + Concept bucket {} was configured for numeric types, but received non-numeric value {} + This happens when, for a single concept, there rows that have a tval_char, and other + rows with an nval_num but no tval_char. + Offending record #{} + """, conceptPath, record.get(CSVParserUtil.TEXT_VALUE), record.getRecordNumber()); + log.error("Entire record: {}", record); + return false; + } + String rawTextValue = CSVParserUtil.trim(record.get(CSVParserUtil.TEXT_VALUE)); + if (rawTextValue.isEmpty()) { + return false; + } + concept.setColumnWidth(Math.max(rawTextValue.getBytes().length, concept.getColumnWidth())); + concept.add(patientId, rawTextValue, date); + store.allIds.add(patientId); + return true; + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/litecsv/LowRAMLoadingStore.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/litecsv/LowRAMLoadingStore.java new file mode 100644 index 000000000..80cd0f774 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/litecsv/LowRAMLoadingStore.java @@ -0,0 +1,267 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.litecsv; + +import com.google.common.cache.*; +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.KeyAndValue; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import org.apache.commons.csv.CSVFormat; +import org.apache.commons.csv.CSVPrinter; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.*; +import java.nio.file.Files; +import java.nio.file.Paths; +import java.util.*; +import java.util.concurrent.atomic.AtomicInteger; +import java.util.stream.Collectors; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; + +import static edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto.DEFAULT_KEY_NAME; +import static java.nio.file.StandardOpenOption.*; + +/** + * This class provides similar functioanlity to the LoadingStore class, but is designed with sequential loading in mind. + * + * This will write out partial cubes to individual files instead of assuming that they can immediately be sequenced into the + * allObservationStore; This will allow us to pick them back up and add more patients to existing stores so that we can better handle + * fragmented data. + * + * + * @author nchu + * + */ +public class LowRAMLoadingStore { + + private final String columnmetaFilename; + protected final String observationsFilename; + protected final String obsTempFilename; + private final String encryptionKeyName; + + private final RandomAccessFile allObservationsTemp; + + TreeMap metadataMap = new TreeMap<>(); + + private static Logger log = LoggerFactory.getLogger(LowRAMLoadingStore.class); + + public LowRAMLoadingStore() { + this( + "/opt/local/hpds/allObservationsTemp.javabin", "/opt/local/hpds/columnMeta.javabin", + "/opt/local/hpds/allObservationsStore.javabin", DEFAULT_KEY_NAME + ); + } + + public LowRAMLoadingStore( + String observationsTempFile, String columnMetaTempFile, String observationsPermFile, String encryptionKeyName + ) { + obsTempFilename = observationsTempFile; + columnmetaFilename = columnMetaTempFile; + observationsFilename = observationsPermFile; + this.encryptionKeyName = encryptionKeyName; + try { + allObservationsTemp = new RandomAccessFile(obsTempFilename, "rw"); + } catch (FileNotFoundException e) { + throw new UncheckedIOException(e); + } + } + + public LoadingCache loadingCache = + CacheBuilder.newBuilder().maximumSize(1).removalListener(new RemovalListener() { + + @Override + public void onRemoval(RemovalNotification cubeRemoval) { + if (cubeRemoval.getValue().getLoadingMap() != null) { + try ( + ByteArrayOutputStream byteStream = new ByteArrayOutputStream(); ObjectOutputStream out = + new ObjectOutputStream(byteStream) + ) { + ColumnMeta columnMeta = new ColumnMeta().setName(cubeRemoval.getKey()) + .setWidthInBytes(cubeRemoval.getValue().getColumnWidth()).setCategorical(cubeRemoval.getValue().isStringType()); + columnMeta.setAllObservationsOffset(allObservationsTemp.getFilePointer()); + // write out the basic key/value map for loading; this will be compacted and finalized after all concepts are read + // in. + out.writeObject(cubeRemoval.getValue().getLoadingMap()); + out.flush(); + + allObservationsTemp.write(byteStream.toByteArray()); + columnMeta.setAllObservationsLength(allObservationsTemp.getFilePointer()); + metadataMap.put(columnMeta.getName(), columnMeta); + } catch (IOException e1) { + throw new UncheckedIOException(e1); + } + } + } + }).build(new CacheLoader<>() { + public PhenoCube load(String key) throws Exception { + ColumnMeta columnMeta = metadataMap.get(key); + if (columnMeta != null) { + log.debug("Loading concept : [" + key + "]"); + return getCubeFromTemp(columnMeta); + } else { + return null; + } + } + }); + + public TreeSet allIds = new TreeSet(); + + public void saveStore() throws FileNotFoundException, IOException, ClassNotFoundException { + log.info("flushing temp storage"); + loadingCache.invalidateAll(); + loadingCache.cleanUp(); + + RandomAccessFile allObservationsStore = new RandomAccessFile(observationsFilename, "rw"); + // we dumped it all in a temp file; now sort all the data and compress it into the real Store + for (String concept : metadataMap.keySet()) { + ColumnMeta columnMeta = metadataMap.get(concept); + log.debug("Writing concept : [{}]", concept); + PhenoCube cube = getCubeFromTemp(columnMeta); + complete(columnMeta, cube); + write(allObservationsStore, columnMeta, cube); + } + allObservationsStore.close(); + + log.info("Writing metadata"); + ObjectOutputStream metaOut = new ObjectOutputStream(new GZIPOutputStream(new FileOutputStream(new File(columnmetaFilename)))); + metaOut.writeObject(metadataMap); + metaOut.writeObject(allIds); + metaOut.flush(); + metaOut.close(); + + log.info("Cleaning up temporary file"); + + allObservationsTemp.close(); + File tempFile = new File(obsTempFilename); + tempFile.delete(); + dumpStatsAndColumnMeta("/opt/local/hpds/"); + } + + private void write(RandomAccessFile allObservationsStore, ColumnMeta columnMeta, PhenoCube cube) throws IOException { + columnMeta.setAllObservationsOffset(allObservationsStore.getFilePointer()); + + try (ByteArrayOutputStream byteStream = new ByteArrayOutputStream(); ObjectOutputStream out = new ObjectOutputStream(byteStream);) { + + out.writeObject(cube); + out.flush(); + allObservationsStore.write(Crypto.encryptData(encryptionKeyName, byteStream.toByteArray())); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + columnMeta.setAllObservationsLength(allObservationsStore.getFilePointer()); + } + + private PhenoCube getCubeFromTemp(ColumnMeta columnMeta) throws IOException, ClassNotFoundException { + allObservationsTemp.seek(columnMeta.getAllObservationsOffset()); + int length = (int) (columnMeta.getAllObservationsLength() - columnMeta.getAllObservationsOffset()); + byte[] buffer = new byte[length]; + allObservationsTemp.read(buffer); + allObservationsTemp.seek(allObservationsTemp.length()); + ObjectInputStream inStream = new ObjectInputStream(new ByteArrayInputStream(buffer)); + + PhenoCube cube = new PhenoCube(columnMeta.getName(), columnMeta.isCategorical() ? String.class : Double.class); + cube.setLoadingMap((List) inStream.readObject()); + cube.setColumnWidth(columnMeta.getWidthInBytes()); + inStream.close(); + return cube; + } + + private > void complete(ColumnMeta columnMeta, PhenoCube cube) { + ArrayList> entryList = new ArrayList>(cube.getLoadingMap().stream().map((entry) -> { + return new KeyAndValue(entry.getKey(), entry.getValue(), entry.getTimestamp()); + }).collect(Collectors.toList())); + + List> sortedByKey = + entryList.stream().sorted(Comparator.comparing(KeyAndValue::getKey)).collect(Collectors.toList()); + cube.setSortedByKey(sortedByKey.toArray(new KeyAndValue[0])); + + if (cube.isStringType()) { + TreeMap> categoryMap = new TreeMap<>(); + for (KeyAndValue entry : cube.sortedByValue()) { + if (!categoryMap.containsKey(entry.getValue())) { + categoryMap.put(entry.getValue(), new LinkedList()); + } + categoryMap.get(entry.getValue()).add(entry.getKey()); + } + TreeMap> categorySetMap = new TreeMap<>(); + categoryMap.entrySet().stream().forEach((entry) -> { + categorySetMap.put(entry.getKey(), new TreeSet(entry.getValue())); + }); + cube.setCategoryMap(categorySetMap); + } + + columnMeta.setObservationCount(cube.sortedByKey().length); + columnMeta.setPatientCount(Arrays.stream(cube.sortedByKey()).map((kv) -> { + return kv.getKey(); + }).collect(Collectors.toSet()).size()); + if (columnMeta.isCategorical()) { + columnMeta.setCategoryValues(new ArrayList(new TreeSet((List) cube.keyBasedArray()))); + } else { + List map = cube.keyBasedArray().stream().map((value) -> { + return (Double) value; + }).collect(Collectors.toList()); + double min = Double.MAX_VALUE; + double max = Double.MIN_VALUE; + for (double f : map) { + min = Double.min(min, f); + max = Double.max(max, f); + } + columnMeta.setMin(min); + columnMeta.setMax(max); + } + + } + + public void dumpStatsAndColumnMeta(String hpdsDirectory) { + try ( + FileInputStream fIn = new FileInputStream(hpdsDirectory + "columnMeta.javabin"); GZIPInputStream gIn = + new GZIPInputStream(fIn); ObjectInputStream oIn = new ObjectInputStream(gIn); BufferedWriter csvWriter = + Files.newBufferedWriter(Paths.get(hpdsDirectory + "columnMeta.csv"), CREATE, TRUNCATE_EXISTING) + ) { + TreeMap metastore = (TreeMap) oIn.readObject(); + CSVPrinter printer = new CSVPrinter(csvWriter, CSVFormat.DEFAULT); + for (String key : metastore.keySet()) { + String[] columnMetaOut = createRow(key, metastore); + printer.printRecord(columnMetaOut); + } + csvWriter.flush(); + } catch (IOException | ClassNotFoundException e) { + log.error("Error loading store or dumping store meta to CSV: ", e); + } + } + + private static String[] createRow(String key, TreeMap metastore) { + ColumnMeta columnMeta = metastore.get(key); + String[] columnMetaOut = new String[11]; + + StringBuilder listQuoted = new StringBuilder(); + AtomicInteger x = new AtomicInteger(1); + + if (columnMeta.getCategoryValues() != null) { + if (!columnMeta.getCategoryValues().isEmpty()) { + columnMeta.getCategoryValues().forEach(string -> { + listQuoted.append(string); + if (x.get() != columnMeta.getCategoryValues().size()) listQuoted.append("µ"); + x.incrementAndGet(); + }); + } + } + + columnMetaOut[0] = columnMeta.getName(); + columnMetaOut[1] = String.valueOf(columnMeta.getWidthInBytes()); + columnMetaOut[2] = String.valueOf(columnMeta.getColumnOffset()); + columnMetaOut[3] = String.valueOf(columnMeta.isCategorical()); + // this should nest the list of values in a list inside the String array. + columnMetaOut[4] = listQuoted.toString(); + columnMetaOut[5] = String.valueOf(columnMeta.getMin()); + columnMetaOut[6] = String.valueOf(columnMeta.getMax()); + columnMetaOut[7] = String.valueOf(columnMeta.getAllObservationsOffset()); + columnMetaOut[8] = String.valueOf(columnMeta.getAllObservationsLength()); + columnMetaOut[9] = String.valueOf(columnMeta.getObservationCount()); + columnMetaOut[10] = String.valueOf(columnMeta.getPatientCount()); + return columnMetaOut; + } + + +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/litecsv/LowRAMMultiCSVLoader.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/litecsv/LowRAMMultiCSVLoader.java new file mode 100644 index 000000000..c1bd460bf --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/litecsv/LowRAMMultiCSVLoader.java @@ -0,0 +1,80 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.litecsv; + +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.config.ConfigLoader; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.*; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.stream.Stream; + +public class LowRAMMultiCSVLoader { + + private static final Logger log = LoggerFactory.getLogger(LowRAMMultiCSVLoader.class); + private final LowRAMCSVProcessor processor; + private final String inputDir; + + public LowRAMMultiCSVLoader(LowRAMLoadingStore store, LowRAMCSVProcessor processor, String inputDir) { + this.inputDir = inputDir == null ? "/opt/local/hpds_input" : inputDir; + store = store == null ? new LowRAMLoadingStore() : store; + this.processor = processor == null ? new LowRAMCSVProcessor(store, false, 5D) : processor; + Crypto.loadDefaultKey(); + } + + public static void main(String[] args) { + boolean rollUpVarNames = true; + double maxChunkSize = 5D; + for (String arg : args) { + if (arg.equalsIgnoreCase("NO_ROLLUP")) { + log.info("Configured to not roll up variable names"); + rollUpVarNames = false; + } + + if (arg.contains("MAX_CHUNK_SIZE")) { + String[] parts = arg.split("="); + if (parts.length == 2) { + try { + maxChunkSize = Double.parseDouble(parts[1]); + log.info("Configured to use a max chunk size of {} GB", maxChunkSize); + } catch (NumberFormatException e) { + throw new IllegalArgumentException("Invalid max chunk size " + maxChunkSize); + } + } + } + } + + String inputDir = "/opt/local/hpds_input"; + ConfigLoader configLoader = new ConfigLoader(); + LowRAMLoadingStore store = new LowRAMLoadingStore(); + LowRAMCSVProcessor lowRAMCSVProcessor = new LowRAMCSVProcessor(store, rollUpVarNames, maxChunkSize, configLoader); + int exitCode = new LowRAMMultiCSVLoader(store, lowRAMCSVProcessor, inputDir).processCSVsFromHPDSDir(maxChunkSize); + try { + store.saveStore(); + } catch (IOException | ClassNotFoundException e) { + log.error("Error saving store: ", e); + System.exit(1); + } + System.exit(exitCode); + } + + protected int processCSVsFromHPDSDir(double maxChunkSize) { + // find all files + log.info("Looking for files to process. All files must be smaller than {}G", maxChunkSize); + log.info("Files larger than {}G should be split into a series of CSVs", maxChunkSize); + try (Stream input_files = Files.list(Path.of(inputDir))) { + input_files.map(Path::toFile).filter(File::isFile).peek(f -> log.info("Found file {}", f.getAbsolutePath())) + + .filter(f -> f.getName().endsWith(".csv")).peek(f -> log.info("Confirmed file {} is a .csv", f.getAbsolutePath())) + + .map(processor::process).forEach(status -> log.info("Finished processing file {}", status)); + return 0; + } catch (IOException e) { + log.error("Exception processing files: ", e); + return 1; + } + } + + +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/sequential/PhenoRecord.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/sequential/PhenoRecord.java new file mode 100644 index 000000000..297796130 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/sequential/PhenoRecord.java @@ -0,0 +1,96 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.sequential; + +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.Date; + +import org.apache.commons.csv.CSVRecord; + +/** + * This provides a common interface for csv and sql load jobs, which use different indexes. + * @author nchu + * + */ +public class PhenoRecord { + + private int patientNum; + private String conceptPath; + private String numericValue; + private String textValue; + private Date dateTime; + + public int getPatientNum() { + return patientNum; + } + + public void setPatientNum(int patientNum) { + this.patientNum = patientNum; + } + + public String getConceptPath() { + return conceptPath; + } + + public void setConceptPath(String conceptPath) { + this.conceptPath = conceptPath; + } + + public String getNumericValue() { + return numericValue; + } + + public void setNumericValue(String numericValue) { + this.numericValue = numericValue; + } + + public String getTextValue() { + return textValue; + } + + public void setTextValue(String textValue) { + this.textValue = textValue; + } + + public Date getDateTime() { + return dateTime; + } + + public void setDateTime(Date dateTime) { + this.dateTime = dateTime; + } + + + // SQL uses 1-based arrays + private static final int PATIENT_NUM_COL_SQL = 1; + private static final int CONCEPT_PATH_COL_SQL = 2; + private static final int NUMERIC_VALUE_COL_SQL = 3; + private static final int TEXT_VALUE_COL_SQL = 4; + private static final int DATETIME_COL_SQL = 5; + + // SQL constructor + public PhenoRecord(ResultSet result) throws SQLException { + conceptPath = result.getString(CONCEPT_PATH_COL_SQL); + dateTime = result.getDate(DATETIME_COL_SQL); + numericValue = result.getString(NUMERIC_VALUE_COL_SQL); + patientNum = result.getInt(PATIENT_NUM_COL_SQL); + textValue = result.getString(TEXT_VALUE_COL_SQL) == null ? null : result.getString(TEXT_VALUE_COL_SQL).trim(); + } + + // CSV uses 0-based arrays + private static final int PATIENT_NUM_COL = 0; + private static final int CONCEPT_PATH_COL = 1; + private static final int NUMERIC_VALUE_COL = 2; + private static final int TEXT_VALUE_COL = 3; + private static final int DATETIME_COL = 4; + + // CSV constructor + public PhenoRecord(CSVRecord record) { + conceptPath = record.get(CONCEPT_PATH_COL); + if (record.size() > DATETIME_COL && record.get(DATETIME_COL) != null && !record.get(DATETIME_COL).isEmpty()) { + dateTime = new Date(Long.parseLong(record.get(DATETIME_COL))); + } + numericValue = record.get(NUMERIC_VALUE_COL); + patientNum = Integer.parseInt(record.get(PATIENT_NUM_COL)); + textValue = record.get(TEXT_VALUE_COL) == null ? null : record.get(TEXT_VALUE_COL).trim(); + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/sequential/SequentialLoader.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/sequential/SequentialLoader.java new file mode 100644 index 000000000..778bb481c --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/sequential/SequentialLoader.java @@ -0,0 +1,318 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.sequential; + +import java.io.*; +import java.nio.charset.StandardCharsets; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.*; +import java.util.concurrent.ExecutionException; + +import edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.config.CSVConfig; +import edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.config.ConfigLoader; +import edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.litecsv.LowRAMMultiCSVLoader; +import org.apache.commons.csv.CSVFormat; +import org.apache.commons.csv.CSVRecord; +import org.apache.commons.io.IOUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.jdbc.core.JdbcTemplate; +import org.springframework.jdbc.datasource.DriverManagerDataSource; + +import com.google.common.cache.CacheLoader.InvalidCacheLoadException; + +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; + +/** + * Generates an HPDS data store "/opt/local/hpds/allObservationsStore.javabin" with all phenotype concepts from the provided input files. + * + * If no arguments are provided it will read a list of files from /opt/local/hpds/phenotypeInputs.txt, expecting one file per line. + * + * @author nchu + * + */ +@SuppressWarnings({"unchecked", "rawtypes"}) +public class SequentialLoader { + + private static final String INPUT_DIR = "/opt/local/hpds_input/"; + + private static final long LOG_INTERVAL = 1000000; + + private static SequentialLoadingStore store = new SequentialLoadingStore(); + + private static Logger log = LoggerFactory.getLogger(SequentialLoader.class); + + private static JdbcTemplate template = null; + + private static long processedRecords = 0; + + private static final int PATIENT_NUM = 0; + + private static final int CONCEPT_PATH = 1; + + private static final int NUMERIC_VALUE = 2; + + private static final int TEXT_VALUE = 3; + + private static final int DATETIME = 4; + + private static String HPDS_DIRECTORY = "/opt/local/hpds/"; + + public static void main(String[] args) throws IOException, ClassNotFoundException { + + Crypto.loadDefaultKey(); + + List inputFiles = new ArrayList(); + // read in input files + if (args.length > 0) { + inputFiles.addAll(Arrays.stream(args).filter(arg -> !arg.equals("NO_ROLLUP") && !arg.contains("MAX_CHUNK_SIZE")).toList()); + } else { + inputFiles.addAll(readFileList()); + } + + if (inputFiles.isEmpty()) { + // check for prior default file locations + File file = new File("/opt/local/hpds/loadQuery.sql"); + if (file.isFile()) { + inputFiles.add("/opt/local/hpds/loadQuery.sql"); + } else { + file = new File("/opt/local/hpds/allConcepts.csv"); + if (file.isFile()) { + inputFiles.add("/opt/local/hpds/allConcepts.csv"); + } + } + } + + log.info("Input files: {}", Arrays.deepToString(inputFiles.toArray())); + + // Remove the config.json file from the inputFiles list if it exists. + // We are only expecting to load CSV and SQL files. + inputFiles.removeIf(file -> file.contains("config.json")); + + if (inputFiles.stream().allMatch(f -> f.endsWith(".csv"))) { + LowRAMMultiCSVLoader.main(args); + } else { + log.info("Non-CSV files detected. Using SequentialLoader."); + } + + ConfigLoader configLoader = new ConfigLoader(); + // load each into the observation store + for (String filename : inputFiles) { + log.info("Loading file {}", filename); + Path path = Paths.get(HPDS_DIRECTORY + filename); + String fileName = path.getFileName().toString(); + + CSVConfig csvConfig = configLoader.getConfigFor(fileName); + if (filename.toLowerCase(Locale.ENGLISH).endsWith("sql")) { + loadSqlFile(filename, csvConfig); + } else if (filename.toLowerCase(Locale.ENGLISH).endsWith("csv")) { + loadCsvFile(filename, csvConfig); + } + } + + // then complete, which will compact, sort, and write out the data in the final place + log.info("found a total of {} entries", processedRecords); + store.saveStore(); + store.dumpStats(); + } + + private static List readFileList() throws IOException { + List inputFiles = new ArrayList(); + Files.list(new File(INPUT_DIR).toPath()).forEach(path -> { + inputFiles.add(INPUT_DIR + path.getFileName().toString()); + }); + return inputFiles; + } + + private static void loadCsvFile(String filename, CSVConfig csvConfig) throws IOException { + Reader in = new FileReader(filename); + BufferedReader reader = new BufferedReader(in, 1024 * 1024); + Iterable records = CSVFormat.DEFAULT.withSkipHeaderRecord().withFirstRecordAsHeader().parse(reader); + + // currentConcept is used to persist data across function calls and identify when we hit a new concept + final PhenoCube[] currentConcept = new PhenoCube[1]; + int count = 0; + for (CSVRecord record : records) { + count++; + if (count % 5000 == 0) { + log.info("Processed {} records for file {}", count, filename); + } + if (record.size() < 4) { + log.warn("Record number {} had less records than we expected so we are skipping it.", record.getRecordNumber()); + continue; + } + processRecord(currentConcept, record, csvConfig); + } + reader.close(); + in.close(); + } + + private static void loadSqlFile(String filename, CSVConfig csvConfig) throws IOException { + loadTemplate(); + String loadQuery = IOUtils.toString(new FileInputStream(filename), StandardCharsets.UTF_8); + + final PhenoCube[] currentConcept = new PhenoCube[1]; // used to identify new concepts + template.query(loadQuery, result -> { + processRecord(currentConcept, new PhenoRecord(result), csvConfig); + }); + } + + + private static void loadTemplate() throws FileNotFoundException, IOException { + if (template == null) { + Properties props = new Properties(); + props.load(new FileInputStream(INPUT_DIR + "sql.properties")); + template = new JdbcTemplate( + new DriverManagerDataSource( + props.getProperty("datasource.url"), props.getProperty("datasource.user"), props.getProperty("datasource.password") + ) + ); + } + } + + private static void processRecord(final PhenoCube[] currentConcept, CSVRecord record, CSVConfig csvConfig) { + if (record.size() < 4) { + log.info("Record number " + record.getRecordNumber() + " had less records than we expected so we are skipping it."); + return; + } + + try { + String conceptPathFromRow = record.get(CONCEPT_PATH); + String[] segments = conceptPathFromRow.split("\\\\"); + for (int x = 0; x < segments.length; x++) { + segments[x] = segments[x].trim(); + } + conceptPathFromRow = String.join("\\", segments) + "\\"; + conceptPathFromRow = conceptPathFromRow.replaceAll("\\ufffd", ""); + String textValueFromRow = record.get(TEXT_VALUE) == null ? null : record.get(TEXT_VALUE).trim(); + if (textValueFromRow != null) { + textValueFromRow = textValueFromRow.replaceAll("\\ufffd", ""); + } + String conceptPath = + conceptPathFromRow.endsWith("\\" + textValueFromRow + "\\") ? conceptPathFromRow.replaceAll("\\\\[^\\\\]*\\\\$", "\\\\") + : conceptPathFromRow; + // Check if the conceptPath should be prepended with dataset name + if (csvConfig != null && csvConfig.getDataset_name_as_root_node()) { + String datasetName = csvConfig.getDataset_name(); + if (!conceptPath.startsWith("\\")) { + conceptPath = "\\" + conceptPath; + } + + conceptPath = "\\" + datasetName + conceptPath; + } + + // This is not getDouble because we need to handle null values, not coerce them into 0s + String numericValue = record.get(NUMERIC_VALUE); + if ((numericValue == null || numericValue.isEmpty()) && textValueFromRow != null) { + try { + numericValue = Double.parseDouble(textValueFromRow) + ""; + } catch (NumberFormatException e) { + + } + } + boolean isAlpha = (numericValue == null || numericValue.isEmpty()); + if (currentConcept[0] == null || !currentConcept[0].name.equals(conceptPath)) { + try { + currentConcept[0] = store.loadingCache.get(conceptPath); + } catch (InvalidCacheLoadException e) { + currentConcept[0] = new PhenoCube(conceptPath, isAlpha ? String.class : Double.class); + store.loadingCache.put(conceptPath, currentConcept[0]); + } + } + String value = isAlpha ? record.get(TEXT_VALUE) : numericValue; + + if ( + value != null && !value.trim().isEmpty() + && ((isAlpha && currentConcept[0].vType == String.class) || (!isAlpha && currentConcept[0].vType == Double.class)) + ) { + value = value.trim(); + currentConcept[0] + .setColumnWidth(isAlpha ? Math.max(currentConcept[0].getColumnWidth(), value.getBytes().length) : Double.BYTES); + int patientId = Integer.parseInt(record.get(PATIENT_NUM)); + Date date = null; + if (record.size() > 4 && record.get(DATETIME) != null && !record.get(DATETIME).isEmpty()) { + date = new Date(Long.parseLong(record.get(DATETIME))); + } + currentConcept[0].add(patientId, isAlpha ? value : Double.parseDouble(value), date); + store.allIds.add(patientId); + } + } catch (ExecutionException e) { + // todo: do we really want to ignore this? + log.error("Error processing record", e); + } + } + + private static void processRecord(final PhenoCube[] currentConcept, PhenoRecord record, CSVConfig csvConfig) { + if (record == null) { + return; + } + + try { + String conceptPathFromRow = record.getConceptPath(); + String[] segments = conceptPathFromRow.split("\\\\"); + for (int x = 0; x < segments.length; x++) { + segments[x] = segments[x].trim(); + } + conceptPathFromRow = String.join("\\", segments) + "\\"; + conceptPathFromRow = conceptPathFromRow.replaceAll("\\ufffd", ""); + String textValueFromRow = record.getTextValue(); + if (textValueFromRow != null) { + textValueFromRow = textValueFromRow.replaceAll("\\ufffd", ""); + } + + String conceptPath = + conceptPathFromRow.endsWith("\\" + textValueFromRow + "\\") ? conceptPathFromRow.replaceAll("\\\\[^\\\\]*\\\\$", "\\\\") + : conceptPathFromRow; + // Check if the conceptPath should be prepended with a dataset name + if (csvConfig != null && csvConfig.getDataset_name_as_root_node()) { + String datasetName = csvConfig.getDataset_name(); + if (!conceptPath.startsWith("\\")) { + conceptPath = "\\" + conceptPath; + } + + conceptPath = "\\" + datasetName + conceptPath; + } + + // This is not getDouble because we need to handle null values, not coerce them into 0s + String numericValue = record.getNumericValue(); + if ((numericValue == null || numericValue.isEmpty()) && textValueFromRow != null) { + try { + numericValue = Double.parseDouble(textValueFromRow) + ""; + } catch (NumberFormatException e) { + + } + } + boolean isAlpha = (numericValue == null || numericValue.isEmpty()); + if (currentConcept[0] == null || !currentConcept[0].name.equals(conceptPath)) { + try { + currentConcept[0] = store.loadingCache.get(conceptPath); + } catch (InvalidCacheLoadException e) { + log.debug("New concept " + record.getConceptPath()); + currentConcept[0] = new PhenoCube(conceptPath, isAlpha ? String.class : Double.class); + store.loadingCache.put(conceptPath, currentConcept[0]); + } + } + String value = isAlpha ? record.getTextValue() : numericValue; + + if ( + value != null && !value.trim().isEmpty() + && ((isAlpha && currentConcept[0].vType == String.class) || (!isAlpha && currentConcept[0].vType == Double.class)) + ) { + value = value.trim(); + currentConcept[0] + .setColumnWidth(isAlpha ? Math.max(currentConcept[0].getColumnWidth(), value.getBytes().length) : Double.BYTES); + int patientId = record.getPatientNum(); + + currentConcept[0].add(patientId, isAlpha ? value : Double.parseDouble(value), record.getDateTime()); + store.allIds.add(patientId); + } + if (++processedRecords % LOG_INTERVAL == 0) { + log.info("Loaded " + processedRecords + " records"); + } + } catch (ExecutionException e) { + // todo: do we really want to ignore this? + log.error("Error processing record", e); + } + } +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/sequential/SequentialLoadingStore.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/sequential/SequentialLoadingStore.java new file mode 100644 index 000000000..9ecb38ee1 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/sequential/SequentialLoadingStore.java @@ -0,0 +1,237 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.sequential; + +import java.io.*; +import java.util.*; +import java.util.stream.Collectors; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.common.cache.*; + +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.KeyAndValue; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; + +/** + * This class provides similar functioanlity to the LoadingStore class, but is designed with sequential loading in mind. + * + * This will write out partial cubes to individual files instead of assuming that they can immediately be sequenced into the + * allObservationStore; This will allow us to pick them back up and add more patients to existing stores so that we can better handle + * fragmented data. + * + * + * @author nchu + * + */ +public class SequentialLoadingStore { + + private static final String COLUMNMETA_FILENAME = "/opt/local/hpds/columnMeta.javabin"; + protected static final String OBSERVATIONS_FILENAME = "/opt/local/hpds/allObservationsStore.javabin"; + protected static final String OBS_TEMP_FILENAME = "/opt/local/hpds/allObservationsTemp.javabin"; + + public RandomAccessFile allObservationsStore; + public RandomAccessFile allObservationsTemp; + + TreeMap metadataMap = new TreeMap<>(); + + private static Logger log = LoggerFactory.getLogger(SequentialLoadingStore.class); + + public SequentialLoadingStore() { + try { + allObservationsTemp = new RandomAccessFile(OBS_TEMP_FILENAME, "rw"); + } catch (FileNotFoundException e) { + throw new UncheckedIOException(e); + } + } + + public LoadingCache loadingCache = + CacheBuilder.newBuilder().maximumSize(16).removalListener(new RemovalListener() { + + @Override + public void onRemoval(RemovalNotification cubeRemoval) { + if (cubeRemoval.getValue().getLoadingMap() != null) { + try ( + ByteArrayOutputStream byteStream = new ByteArrayOutputStream(); ObjectOutputStream out = + new ObjectOutputStream(byteStream); + ) { + ColumnMeta columnMeta = new ColumnMeta().setName(cubeRemoval.getKey()) + .setWidthInBytes(cubeRemoval.getValue().getColumnWidth()).setCategorical(cubeRemoval.getValue().isStringType()); + columnMeta.setAllObservationsOffset(allObservationsTemp.getFilePointer()); + // write out the basic key/value map for loading; this will be compacted and finalized after all concepts are read + // in. + out.writeObject(cubeRemoval.getValue().getLoadingMap()); + out.flush(); + + allObservationsTemp.write(byteStream.toByteArray()); + columnMeta.setAllObservationsLength(allObservationsTemp.getFilePointer()); + metadataMap.put(columnMeta.getName(), columnMeta); + } catch (IOException e1) { + throw new UncheckedIOException(e1); + } + } + } + }).build(new CacheLoader() { + public PhenoCube load(String key) throws Exception { + ColumnMeta columnMeta = metadataMap.get(key); + if (columnMeta != null) { + log.debug("Loading concept : [" + key + "]"); + return getCubeFromTemp(columnMeta); + } else { + return null; + } + } + }); + + public TreeSet allIds = new TreeSet(); + + public void saveStore() throws FileNotFoundException, IOException, ClassNotFoundException { + log.info("flushing temp storage"); + loadingCache.invalidateAll(); + loadingCache.cleanUp(); + + allObservationsStore = new RandomAccessFile(OBSERVATIONS_FILENAME, "rw"); + // we dumped it all in a temp file; now sort all the data and compress it into the real Store + for (String concept : metadataMap.keySet()) { + ColumnMeta columnMeta = metadataMap.get(concept); + log.debug("Writing concept : [" + concept + "]"); + PhenoCube cube = getCubeFromTemp(columnMeta); + complete(columnMeta, cube); + write(columnMeta, cube); + } + allObservationsStore.close(); + + log.info("Writing metadata"); + ObjectOutputStream metaOut = new ObjectOutputStream(new GZIPOutputStream(new FileOutputStream(new File(COLUMNMETA_FILENAME)))); + metaOut.writeObject(metadataMap); + metaOut.writeObject(allIds); + metaOut.flush(); + metaOut.close(); + + log.info("Cleaning up temporary file"); + + allObservationsTemp.close(); + File tempFile = new File(OBS_TEMP_FILENAME); + tempFile.delete(); + } + + /** + * calculate the min/max, categories, observation count, etc for this cube and write it to disk + * @param columnMeta + * @param cube + * @throws IOException + */ + private void write(ColumnMeta columnMeta, PhenoCube cube) throws IOException { + columnMeta.setAllObservationsOffset(allObservationsStore.getFilePointer()); + + try (ByteArrayOutputStream byteStream = new ByteArrayOutputStream(); ObjectOutputStream out = new ObjectOutputStream(byteStream);) { + + out.writeObject(cube); + out.flush(); + allObservationsStore.write(Crypto.encryptData(byteStream.toByteArray())); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + columnMeta.setAllObservationsLength(allObservationsStore.getFilePointer()); + } + + private PhenoCube getCubeFromTemp(ColumnMeta columnMeta) throws IOException, ClassNotFoundException { + allObservationsTemp.seek(columnMeta.getAllObservationsOffset()); + int length = (int) (columnMeta.getAllObservationsLength() - columnMeta.getAllObservationsOffset()); + byte[] buffer = new byte[length]; + allObservationsTemp.read(buffer); + allObservationsTemp.seek(allObservationsTemp.length()); + ObjectInputStream inStream = new ObjectInputStream(new ByteArrayInputStream(buffer)); + + PhenoCube cube = new PhenoCube(columnMeta.getName(), columnMeta.isCategorical() ? String.class : Double.class); + cube.setLoadingMap((List) inStream.readObject()); + cube.setColumnWidth(columnMeta.getWidthInBytes()); + inStream.close(); + return cube; + } + + private > void complete(ColumnMeta columnMeta, PhenoCube cube) { + ArrayList> entryList = new ArrayList>(cube.getLoadingMap().stream().map((entry) -> { + return new KeyAndValue(entry.getKey(), entry.getValue(), entry.getTimestamp()); + }).collect(Collectors.toList())); + + List> sortedByKey = + entryList.stream().sorted(Comparator.comparing(KeyAndValue::getKey)).collect(Collectors.toList()); + cube.setSortedByKey(sortedByKey.toArray(new KeyAndValue[0])); + + if (cube.isStringType()) { + TreeMap> categoryMap = new TreeMap<>(); + for (KeyAndValue entry : cube.sortedByValue()) { + if (!categoryMap.containsKey(entry.getValue())) { + categoryMap.put(entry.getValue(), new LinkedList()); + } + categoryMap.get(entry.getValue()).add(entry.getKey()); + } + TreeMap> categorySetMap = new TreeMap<>(); + categoryMap.entrySet().stream().forEach((entry) -> { + categorySetMap.put(entry.getKey(), new TreeSet(entry.getValue())); + }); + cube.setCategoryMap(categorySetMap); + } + + columnMeta.setObservationCount(cube.sortedByKey().length); + columnMeta.setPatientCount(Arrays.stream(cube.sortedByKey()).map((kv) -> { + return kv.getKey(); + }).collect(Collectors.toSet()).size()); + if (columnMeta.isCategorical()) { + columnMeta.setCategoryValues(new ArrayList(new TreeSet((List) cube.keyBasedArray()))); + } else { + List map = (List) cube.keyBasedArray().stream().map((value) -> { + return (Double) value; + }).collect(Collectors.toList()); + double min = Double.MAX_VALUE; + double max = Double.MIN_VALUE; + for (double f : map) { + min = Double.min(min, f); + max = Double.max(max, f); + } + columnMeta.setMin(min); + columnMeta.setMax(max); + } + + } + + public void dumpStats() { + log.info("Dumping Stats"); + try (ObjectInputStream objectInputStream = new ObjectInputStream(new GZIPInputStream(new FileInputStream(COLUMNMETA_FILENAME)));) { + TreeMap metastore = (TreeMap) objectInputStream.readObject(); + Set allIds = (TreeSet) objectInputStream.readObject(); + + long totalNumberOfObservations = 0; + + log.info("\n\nConceptPath\tObservationCount\tMinNumValue\tMaxNumValue\tCategoryValues"); + for (String key : metastore.keySet()) { + ColumnMeta columnMeta = metastore.get(key); + log.info( + String.join( + "\t", key.toString(), columnMeta.getObservationCount() + "", + columnMeta.getMin() == null ? "NaN" : columnMeta.getMin().toString(), + columnMeta.getMax() == null ? "NaN" : columnMeta.getMax().toString(), + columnMeta.getCategoryValues() == null ? "NUMERIC CONCEPT" + : String.join(",", columnMeta.getCategoryValues().stream().map((value) -> { + return value == null ? "NULL_VALUE" : "\"" + value + "\""; + }).collect(Collectors.toList())) + ) + ); + totalNumberOfObservations += columnMeta.getObservationCount(); + } + + log.info("Total Number of Concepts : " + metastore.size()); + log.info("Total Number of Patients : " + allIds.size()); + log.info("Total Number of Observations : " + totalNumberOfObservations); + + } catch (IOException | ClassNotFoundException e) { + throw new RuntimeException("Could not load metastore"); + } + } + + +} diff --git a/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/sql/SQLLoader.java b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/sql/SQLLoader.java new file mode 100644 index 000000000..6def83fa4 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/sql/SQLLoader.java @@ -0,0 +1,238 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.sql; + +import java.sql.ResultSet; +import java.sql.SQLException; +import java.text.SimpleDateFormat; +import java.io.*; +import java.nio.charset.Charset; +import java.util.Properties; +import java.util.concurrent.ExecutionException; + +import com.google.common.cache.CacheLoader.InvalidCacheLoadException; + +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; + +import edu.harvard.hms.dbmi.avillach.hpds.etl.LoadingStore; +import org.apache.commons.io.IOUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.jdbc.core.JdbcTemplate; +import org.springframework.jdbc.core.RowCallbackHandler; +import org.springframework.jdbc.datasource.DriverManagerDataSource; + +public class SQLLoader { + + private static final Logger log = LoggerFactory.getLogger(SQLLoader.class); + + private static final SimpleDateFormat ORACLE_DATE_FORMAT = new SimpleDateFormat("dd-MMM-yy"); + + static JdbcTemplate template; + + private static LoadingStore store = new LoadingStore(); + + private static final int PATIENT_NUM = 1; + + private static final int CONCEPT_PATH = 2; + + private static final int NUMERIC_VALUE = 3; + + private static final int TEXT_VALUE = 4; + + private static final int DATETIME = 5; + + private static final Properties props = new Properties(); + + private static String HPDS_DIRECTORY = "/opt/local/hpds/"; + + public static void main(String[] args) throws IOException { + props.load(new FileInputStream(HPDS_DIRECTORY + "sql.properties")); + template = + new JdbcTemplate(new DriverManagerDataSource(prop("datasource.url"), prop("datasource.user"), prop("datasource.password"))); + store.allObservationsStore = new RandomAccessFile(HPDS_DIRECTORY + "allObservationsStore.javabin", "rw"); + Crypto.loadDefaultKey(); + initialLoad(); + store.saveStore(HPDS_DIRECTORY); + store.dumpStats(); + } + + private static String prop(String key) { + return props.getProperty(key); + } + + private static void initialLoad() throws IOException { + final PhenoCube[] currentConcept = new PhenoCube[1]; + String loadQuery = IOUtils.toString(new FileInputStream("/opt/local/hpds/loadQuery.sql"), Charset.forName("UTF-8")); + // + // ArrayBlockingQueue abq = new ArrayBlockingQueue<>(1000); + // + // ExecutorService chunkWriteEx = Executors.newFixedThreadPool(32); + // + // boolean[] stillProcessingRecords = {true}; + // + // for(int x = 0;x<32;x++) { + // chunkWriteEx.submit(new Runnable() { + // PhenoCube currentConcept = null; + // String[] arg0; + // @Override + // public void run() { + // while(stillProcessingRecords[0]) { + // try { + // arg0 = abq.poll(1, TimeUnit.SECONDS); + // if(arg0 != null) { + // String conceptPathFromRow = arg0[CONCEPT_PATH]; + // String[] segments = conceptPathFromRow.split("\\\\"); + // for(int x = 0;x + + + + + %d{HH:mm:ss.SSS} [%t] %-5level %logger{36} - %msg%n + + + + + + + + + \ No newline at end of file diff --git a/services/pic-sure-hpds/etl/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VcfIndexFileParserTest.java b/services/pic-sure-hpds/etl/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VcfIndexFileParserTest.java new file mode 100644 index 000000000..b4ff3b9d0 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VcfIndexFileParserTest.java @@ -0,0 +1,62 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.springframework.core.io.ClassPathResource; +import org.springframework.core.io.Resource; + +import java.io.IOException; +import java.util.List; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + + +class VcfIndexFileParserTest { + + + private VcfIndexFileParser vcfIndexFileParser; + + @BeforeEach + public void setup() { + vcfIndexFileParser = new VcfIndexFileParser(); + } + + @Test + public void parse_validFile() throws IOException { + Resource file = new ClassPathResource("vcf-index/valid.tsv"); + List vcfIndexLines = vcfIndexFileParser.parse(file.getFile()); + assertEquals(23, vcfIndexLines.size()); + VCFIndexLine line1 = vcfIndexLines.get(0); + // verify we are trimming whitespace + for (String sampleId : line1.getSampleIds()) { + assertFalse(sampleId.contains(" ")); + } + } + + @Test + public void parse_validFileNoQuotes() throws IOException { + Resource file = new ClassPathResource("vcf-index/valid-no-quotes.tsv"); + List vcfIndexLines = vcfIndexFileParser.parse(file.getFile()); + assertEquals(23, vcfIndexLines.size()); + } + + @Test + public void parse_invalidFileRow2Col3() { + Resource file = new ClassPathResource("vcf-index/invalid-row2-col3.tsv"); + IllegalArgumentException exception = assertThrows(IllegalArgumentException.class, () -> vcfIndexFileParser.parse(file.getFile())); + assertTrue(exception.getMessage().contains("line 2")); + assertTrue(exception.getMessage().contains("column 3")); + assertTrue(exception.getMessage().contains("Value = \"x\"")); + } + + @Test + public void parse_invalidFileRow6Col4() { + Resource file = new ClassPathResource("vcf-index/invalid-row6-col4.tsv"); + IllegalArgumentException exception = assertThrows(IllegalArgumentException.class, () -> vcfIndexFileParser.parse(file.getFile())); + assertTrue(exception.getMessage().contains("line 6")); + assertTrue(exception.getMessage().contains("column 4")); + assertTrue(exception.getMessage().contains("Value = \"\"")); + } +} diff --git a/services/pic-sure-hpds/etl/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/litecsv/LowRAMCSVProcessorTest.java b/services/pic-sure-hpds/etl/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/litecsv/LowRAMCSVProcessorTest.java new file mode 100644 index 000000000..c8c9526b7 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/litecsv/LowRAMCSVProcessorTest.java @@ -0,0 +1,220 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.litecsv; + + +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.config.CSVConfig; +import edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.config.ConfigLoader; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.io.TempDir; + +import java.io.*; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; +import java.util.TreeMap; +import java.util.zip.GZIPInputStream; + +class LowRAMCSVProcessorTest { + + private static final String TEST_KEY_PATH = "src/test/resources/test_named_encryption_key"; + + + @Test + void shouldProcessSimpleCSV(@TempDir File testDir) throws IOException, ClassNotFoundException { + String content = """ + PATIENT_NUM,CONCEPT_PATH,NUMERIC_VALUE,TEXT_VALUE,DATETIME + 1,\\foo\\1\\,,val,1 + 1,\\foo\\2\\,0,,1 + 2,\\foo\\1\\,,lav,1 + 2,\\foo\\2\\,99,,1 + """; + Path csvPath = Path.of(testDir.getAbsolutePath(), "test.csv"); + Files.writeString(csvPath, content); + LowRAMLoadingStore store = new LowRAMLoadingStore( + testDir.getAbsolutePath() + "/allObservationsTemp.javabin", testDir.getAbsolutePath() + "/columnMeta.javabin", + testDir.getAbsolutePath() + "/allObservationsStore.javabin", "TEST_KEY" + ); + + IngestStatus status = new LowRAMCSVProcessor(store, false, 1D).process(csvPath.toFile()); + + Assertions.assertEquals(2, status.conceptCount()); + Assertions.assertEquals(5, status.lineCount()); + Assertions.assertEquals(csvPath, status.file()); + + Crypto.loadKey("TEST_KEY", TEST_KEY_PATH); + store.saveStore(); + List expectedMetas = + List.of(new CategoricalMeta("\\foo\\1\\", 2, 2, List.of("lav", "val")), new NumericMeta("\\foo\\2\\", 2, 2, 0.0, 99.0)); + verifyStoreMeta(expectedMetas, testDir.getAbsolutePath() + "/columnMeta.javabin"); + } + + @Test + void shouldNotProcessCharAndInt(@TempDir File testDir) throws IOException, ClassNotFoundException { + String content = """ + PATIENT_NUM,CONCEPT_PATH,NUMERIC_VALUE,TEXT_VALUE,DATETIME + 1,\\foo\\1\\,,val,1 + 1,\\foo\\1\\,0,,1 + """; + Path csvPath = Path.of(testDir.getAbsolutePath(), "test.csv"); + Files.writeString(csvPath, content); + LowRAMLoadingStore store = new LowRAMLoadingStore( + testDir.getAbsolutePath() + "/allObservationsTemp.javabin", testDir.getAbsolutePath() + "/columnMeta.javabin", + testDir.getAbsolutePath() + "/allObservationsStore.javabin", "TEST_KEY" + ); + + IngestStatus status = new LowRAMCSVProcessor(store, false, 1D).process(csvPath.toFile()); + + Assertions.assertEquals(1, status.conceptCount()); + Assertions.assertEquals(3, status.lineCount()); + Assertions.assertEquals(csvPath, status.file()); + + Crypto.loadKey("TEST_KEY", TEST_KEY_PATH); + store.saveStore(); + List expectedMetas = List.of( + new CategoricalMeta("\\foo\\1\\", 1, 1, List.of("val")) // make sure "1" doesn't show up + ); + verifyStoreMeta(expectedMetas, testDir.getAbsolutePath() + "/columnMeta.javabin"); + } + + @Test + void shouldNotProcessIntAndChar(@TempDir File testDir) throws IOException, ClassNotFoundException { + String content = """ + PATIENT_NUM,CONCEPT_PATH,NUMERIC_VALUE,TEXT_VALUE,DATETIME + 1,\\foo\\1\\,0,,1 + 2,\\foo\\1\\,1,,1 + 1,\\foo\\1\\,,val,1 + """; + Path csvPath = Path.of(testDir.getAbsolutePath(), "test.csv"); + Files.writeString(csvPath, content); + LowRAMLoadingStore store = new LowRAMLoadingStore( + testDir.getAbsolutePath() + "/allObservationsTemp.javabin", testDir.getAbsolutePath() + "/columnMeta.javabin", + testDir.getAbsolutePath() + "/allObservationsStore.javabin", "TEST_KEY" + ); + + IngestStatus status = new LowRAMCSVProcessor(store, false, 1D).process(csvPath.toFile()); + + Assertions.assertEquals(1, status.conceptCount()); + Assertions.assertEquals(4, status.lineCount()); + Assertions.assertEquals(csvPath, status.file()); + + Crypto.loadKey("TEST_KEY", TEST_KEY_PATH); + store.saveStore(); + List expectedMetas = List.of( + new NumericMeta("\\foo\\1\\", 2, 2, 0.0, 1.0) // make sure "1" doesn't show up + ); + verifyStoreMeta(expectedMetas, testDir.getAbsolutePath() + "/columnMeta.javabin"); + } + + @Test + void shouldProcessLargeFile(@TempDir File testDir) throws IOException, ClassNotFoundException { + Path csvPath = Path.of(testDir.getAbsolutePath(), "test.csv"); + + // Create a ~200M file sorted by patient + String header = "PATIENT_NUM,CONCEPT_PATH,NUMERIC_VALUE,TEXT_VALUE,DATETIME\n"; + Files.writeString(csvPath, header); + // 5 char patient col + 22 char concept col + 1 char numeric value + 10 char date + 4 commas + newline = + // 43 chars of ascii-utf8 = 43 bytes per line, except the debugger says 44 so uh 44 it is + // I want a file that splits into 2 chunks. The chunk size is set to 0.1 G, so 2 * (0.1 * 1024^3)/44 + // So we need 4880644 lines of this to make a 0.2G file that splits into 2 chunks + // ... give or take. I shot a little under + try (FileWriter fw = new FileWriter(csvPath.toString(), true); BufferedWriter writer = new BufferedWriter(fw)) { + for (int line = 0; line < 4880000; line++) { + int patient = line / 100; + int concept = line % 100; + int val = line % 9; + String date = "1739329199"; + String row = String.format("%05d", patient) + ",\\my\\concept\\path\\" + String.format("%05d", concept) + "\\," + val + ",," + + date + '\n'; + writer.write(row); + if (line % 1000000 == 0) { + System.out.println("Wrote line: " + line); + } + } + } + + LowRAMLoadingStore store = new LowRAMLoadingStore( + testDir.getAbsolutePath() + "/allObservationsTemp.javabin", testDir.getAbsolutePath() + "/columnMeta.javabin", + testDir.getAbsolutePath() + "/allObservationsStore.javabin", "TEST_KEY" + ); + + IngestStatus status = new LowRAMCSVProcessor(store, false, 0.1).process(csvPath.toFile()); + Assertions.assertEquals(4880001, status.lineCount()); + Assertions.assertEquals(100, status.conceptCount()); + Assertions.assertEquals(csvPath, status.file()); + + Crypto.loadKey("TEST_KEY", TEST_KEY_PATH); + store.saveStore(); + List expectedMetas = List.of( + new NumericMeta("\\my\\concept\\path\\00000\\", 24399, 24399, 0.0, 8.0), + new NumericMeta("\\my\\concept\\path\\00099\\", 24400, 24400, 0.0, 8.0) + ); + verifyStoreMeta(expectedMetas, testDir.getAbsolutePath() + "/columnMeta.javabin"); + } + + @Test + void shouldPrependDatasetNameWithConfigLoader(@TempDir File testDir) throws IOException, ClassNotFoundException { + String content = """ + PATIENT_NUM,CONCEPT_PATH,NUMERIC_VALUE,TEXT_VALUE,DATETIME + 1,\\foo\\1\\,,val,1 + 1,\\foo\\2\\,0,,1 + 2,\\foo\\1\\,,lav,1 + 2,\\foo\\2\\,99,,1 + """; + Path csvPath = Path.of(testDir.getAbsolutePath(), "test.csv"); + Files.writeString(csvPath, content); + LowRAMLoadingStore store = new LowRAMLoadingStore( + testDir.getAbsolutePath() + "/allObservationsTemp.javabin", testDir.getAbsolutePath() + "/columnMeta.javabin", + testDir.getAbsolutePath() + "/allObservationsStore.javabin", "TEST_KEY" + ); + + CSVConfig csvConfig = new CSVConfig(); + csvConfig.setDataset_name("TEST_DATASET_NAME"); + csvConfig.setDataset_name_as_root_node(true); + ConfigLoader configLoader = new ConfigLoader(); + configLoader.add("test", csvConfig); + IngestStatus status = new LowRAMCSVProcessor(store, false, 1D, configLoader).process(csvPath.toFile()); + + Assertions.assertEquals(2, status.conceptCount()); + Assertions.assertEquals(5, status.lineCount()); + Assertions.assertEquals(csvPath, status.file()); + + Crypto.loadKey("TEST_KEY", TEST_KEY_PATH); + store.saveStore(); + List expectedMetas = List.of( + new CategoricalMeta("\\TEST_DATASET_NAME\\foo\\1\\", 2, 2, List.of("lav", "val")), + new NumericMeta("\\TEST_DATASET_NAME\\foo\\2\\", 2, 2, 0.0, 99.0) + ); + verifyStoreMeta(expectedMetas, testDir.getAbsolutePath() + "/columnMeta.javabin"); + } + + private void verifyStoreMeta(List expectedMetas, String columnMetaPath) throws IOException, ClassNotFoundException { + ObjectInputStream objectInputStream = new ObjectInputStream(new GZIPInputStream(new FileInputStream(columnMetaPath))); + TreeMap metaStore = (TreeMap) objectInputStream.readObject(); + for (Meta expectedMeta : expectedMetas) { + ColumnMeta actualMeta = metaStore.get(expectedMeta.key()); + Assertions.assertNotNull(actualMeta); + Assertions.assertEquals(expectedMeta.patientCount(), actualMeta.getPatientCount()); + Assertions.assertEquals(expectedMeta.conceptCount(), actualMeta.getObservationCount()); + if (expectedMeta instanceof NumericMeta expectedNumeric) { + Assertions.assertEquals(expectedNumeric.min(), actualMeta.getMin()); + Assertions.assertEquals(expectedNumeric.max(), actualMeta.getMax()); + } else if (expectedMeta instanceof CategoricalMeta expectedCategorical) { + Assertions.assertEquals(expectedCategorical.values(), actualMeta.getCategoryValues()); + } + } + } + + private sealed interface Meta permits NumericMeta, CategoricalMeta { + String key(); + + int patientCount(); + + int conceptCount(); + } + private record NumericMeta(String key, int patientCount, int conceptCount, Double min, Double max) implements Meta { + } + private record CategoricalMeta(String key, int patientCount, int conceptCount, List values) implements Meta { + } +} diff --git a/services/pic-sure-hpds/etl/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/litecsv/LowRAMMultiCSVLoaderTest.java b/services/pic-sure-hpds/etl/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/litecsv/LowRAMMultiCSVLoaderTest.java new file mode 100644 index 000000000..d4a003ca8 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/litecsv/LowRAMMultiCSVLoaderTest.java @@ -0,0 +1,64 @@ +package edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.litecsv; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.io.TempDir; +import org.mockito.Mockito; + +import java.io.File; +import java.io.IOException; +import java.io.RandomAccessFile; +import java.nio.file.Path; + +class LowRAMMultiCSVLoaderTest { + + @Test + void shouldFilterOutNonCSVs(@TempDir File testDir) throws IOException { + Path csvPath = Path.of(testDir.getAbsolutePath(), "test.txt"); + RandomAccessFile largeFile = new RandomAccessFile(csvPath.toString(), "rw"); + largeFile.setLength(6L * 1024); + + LowRAMCSVProcessor processor = Mockito.mock(LowRAMCSVProcessor.class); + LowRAMLoadingStore store = Mockito.mock(LowRAMLoadingStore.class); + + LowRAMMultiCSVLoader subject = new LowRAMMultiCSVLoader(store, processor, testDir.getAbsolutePath()); + int actual = subject.processCSVsFromHPDSDir(5D); + + Assertions.assertEquals(0, actual); + Mockito.verify(processor, Mockito.times(0)).process(Mockito.any()); + } + + @Test + void shouldProcessSmallCSVs(@TempDir File testDir) throws IOException { + Path csvPath = Path.of(testDir.getAbsolutePath(), "test.csv"); + RandomAccessFile largeFile = new RandomAccessFile(csvPath.toString(), "rw"); + largeFile.setLength(6L * 1024); + + LowRAMCSVProcessor processor = Mockito.mock(LowRAMCSVProcessor.class); + Mockito.when(processor.process(Mockito.any())).thenReturn(new IngestStatus(csvPath, 10, 10, 10L)); + LowRAMLoadingStore store = Mockito.mock(LowRAMLoadingStore.class); + + LowRAMMultiCSVLoader subject = new LowRAMMultiCSVLoader(store, processor, testDir.getAbsolutePath()); + int actual = subject.processCSVsFromHPDSDir(5D); + + Assertions.assertEquals(0, actual); + Mockito.verify(processor, Mockito.times(1)).process(Mockito.any()); + } + + @Test + void shouldProcessSmallCSVs_withReducedChunkSize(@TempDir File testDir) throws IOException { + Path csvPath = Path.of(testDir.getAbsolutePath(), "test.csv"); + RandomAccessFile largeFile = new RandomAccessFile(csvPath.toString(), "rw"); + largeFile.setLength(6L * 1024); + + LowRAMCSVProcessor processor = Mockito.mock(LowRAMCSVProcessor.class); + Mockito.when(processor.process(Mockito.any())).thenReturn(new IngestStatus(csvPath, 10, 10, 10L)); + LowRAMLoadingStore store = Mockito.mock(LowRAMLoadingStore.class); + + LowRAMMultiCSVLoader subject = new LowRAMMultiCSVLoader(store, processor, testDir.getAbsolutePath()); + int actual = subject.processCSVsFromHPDSDir(1D); + + Assertions.assertEquals(0, actual); + Mockito.verify(processor, Mockito.times(1)).process(Mockito.any()); + } +} diff --git a/services/pic-sure-hpds/etl/src/test/resources/test_named_encryption_key b/services/pic-sure-hpds/etl/src/test/resources/test_named_encryption_key new file mode 100644 index 000000000..d3720b6d6 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/test/resources/test_named_encryption_key @@ -0,0 +1 @@ +1111111111111111 \ No newline at end of file diff --git a/services/pic-sure-hpds/etl/src/test/resources/vcf-index/invalid-row2-col3.tsv b/services/pic-sure-hpds/etl/src/test/resources/vcf-index/invalid-row2-col3.tsv new file mode 100644 index 000000000..420935c66 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/test/resources/vcf-index/invalid-row2-col3.tsv @@ -0,0 +1,24 @@ +"vcf_path" "chromosome" "isAnnotated" "isGzipped" "sample_ids" "patient_ids" "sample_relationship" "related_sample_ids" +"chr1.vcf.gz" "1" "x" "1" " sample1, sample2, sample3 " " 1 , 2,3 " +"chr2.vcf.gz" "2" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr3.vcf.gz" "3" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr4.vcf.gz" "4" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr5.vcf.gz" "5" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr6.vcf.gz" "6" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr7.vcf.gz" "7" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr8.vcf.gz" "8" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr9.vcf.gz" "9" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr10.vcf.gz" "10" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr11.vcf.gz" "11" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr12.vcf.gz" "12" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr13.vcf.gz" "13" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr14.vcf.gz" "14" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr15.vcf.gz" "15" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr16.vcf.gz" "16" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr17.vcf.gz" "17" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr18.vcf.gz" "18" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr19.vcf.gz" "19" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr20.vcf.gz" "20" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr21.vcf.gz" "21" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr22.vcf.gz" "22" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chrX.vcf.gz" "X" "1" "1" "sample1, sample2, sample3" "1 , 2,3" diff --git a/services/pic-sure-hpds/etl/src/test/resources/vcf-index/invalid-row6-col4.tsv b/services/pic-sure-hpds/etl/src/test/resources/vcf-index/invalid-row6-col4.tsv new file mode 100644 index 000000000..8a736726f --- /dev/null +++ b/services/pic-sure-hpds/etl/src/test/resources/vcf-index/invalid-row6-col4.tsv @@ -0,0 +1,24 @@ +"vcf_path" "chromosome" "isAnnotated" "isGzipped" "sample_ids" "patient_ids" "sample_relationship" "related_sample_ids" +"chr1.vcf.gz" "1" "1" "1" " sample1, sample2, sample3 " " 1 , 2,3 " +"chr2.vcf.gz" "2" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr3.vcf.gz" "3" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr4.vcf.gz" "4" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr5.vcf.gz" "5" "1" "" "sample1, sample2, sample3" "1 , 2,3" +"chr6.vcf.gz" "6" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr7.vcf.gz" "7" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr8.vcf.gz" "8" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr9.vcf.gz" "9" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr10.vcf.gz" "10" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr11.vcf.gz" "11" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr12.vcf.gz" "12" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr13.vcf.gz" "13" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr14.vcf.gz" "14" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr15.vcf.gz" "15" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr16.vcf.gz" "16" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr17.vcf.gz" "17" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr18.vcf.gz" "18" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr19.vcf.gz" "19" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr20.vcf.gz" "20" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr21.vcf.gz" "21" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr22.vcf.gz" "22" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chrX.vcf.gz" "X" "1" "1" "sample1, sample2, sample3" "1 , 2,3" diff --git a/services/pic-sure-hpds/etl/src/test/resources/vcf-index/valid-no-quotes.tsv b/services/pic-sure-hpds/etl/src/test/resources/vcf-index/valid-no-quotes.tsv new file mode 100644 index 000000000..bd7ed9392 --- /dev/null +++ b/services/pic-sure-hpds/etl/src/test/resources/vcf-index/valid-no-quotes.tsv @@ -0,0 +1,24 @@ +vcf_path chromosome isAnnotated isGzipped sample_ids patient_ids sample_relationship related_sample_ids +chr1.vcf.gz 1 1 1 sample1, sample2, sample3 1 , 2,3 +chr2.vcf.gz 2 1 1 sample1, sample2, sample3 1 , 2,3 +chr3.vcf.gz 3 1 1 sample1, sample2, sample3 1 , 2,3 +chr4.vcf.gz 4 1 1 sample1, sample2, sample3 1 , 2,3 +chr5.vcf.gz 5 1 1 sample1, sample2, sample3 1 , 2,3 +chr6.vcf.gz 6 1 1 sample1, sample2, sample3 1 , 2,3 +chr7.vcf.gz 7 1 1 sample1, sample2, sample3 1 , 2,3 +chr8.vcf.gz 8 1 1 sample1, sample2, sample3 1 , 2,3 +chr9.vcf.gz 9 1 1 sample1, sample2, sample3 1 , 2,3 +chr10.vcf.gz 10 1 1 sample1, sample2, sample3 1 , 2,3 +chr11.vcf.gz 11 1 1 sample1, sample2, sample3 1 , 2,3 +chr12.vcf.gz 12 1 1 sample1, sample2, sample3 1 , 2,3 +chr13.vcf.gz 13 1 1 sample1, sample2, sample3 1 , 2,3 +chr14.vcf.gz 14 1 1 sample1, sample2, sample3 1 , 2,3 +chr15.vcf.gz 15 1 1 sample1, sample2, sample3 1 , 2,3 +chr16.vcf.gz 16 1 1 sample1, sample2, sample3 1 , 2,3 +chr17.vcf.gz 17 1 1 sample1, sample2, sample3 1 , 2,3 +chr18.vcf.gz 18 1 1 sample1, sample2, sample3 1 , 2,3 +chr19.vcf.gz 19 1 1 sample1, sample2, sample3 1 , 2,3 +chr20.vcf.gz 20 1 1 sample1, sample2, sample3 1 , 2,3 +chr21.vcf.gz 21 1 1 sample1, sample2, sample3 1 , 2,3 +chr22.vcf.gz 22 1 1 sample1, sample2, sample3 1 , 2,3 +chrX.vcf.gz X 1 1 sample1, sample2, sample3 1 , 2,3 diff --git a/services/pic-sure-hpds/etl/src/test/resources/vcf-index/valid.tsv b/services/pic-sure-hpds/etl/src/test/resources/vcf-index/valid.tsv new file mode 100644 index 000000000..1011c673c --- /dev/null +++ b/services/pic-sure-hpds/etl/src/test/resources/vcf-index/valid.tsv @@ -0,0 +1,24 @@ +"vcf_path" "chromosome" "isAnnotated" "isGzipped" "sample_ids" "patient_ids" "sample_relationship" "related_sample_ids" +"chr1.vcf.gz" "1" "1" "1" " sample1, sample2, sample3 " " 1 , 2,3 " +"chr2.vcf.gz" "2" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr3.vcf.gz" "3" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr4.vcf.gz" "4" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr5.vcf.gz" "5" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr6.vcf.gz" "6" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr7.vcf.gz" "7" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr8.vcf.gz" "8" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr9.vcf.gz" "9" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr10.vcf.gz" "10" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr11.vcf.gz" "11" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr12.vcf.gz" "12" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr13.vcf.gz" "13" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr14.vcf.gz" "14" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr15.vcf.gz" "15" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr16.vcf.gz" "16" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr17.vcf.gz" "17" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr18.vcf.gz" "18" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr19.vcf.gz" "19" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr20.vcf.gz" "20" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr21.vcf.gz" "21" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chr22.vcf.gz" "22" "1" "1" "sample1, sample2, sample3" "1 , 2,3" +"chrX.vcf.gz" "X" "1" "1" "sample1, sample2, sample3" "1 , 2,3" diff --git a/services/pic-sure-hpds/genomic-processor/pom.xml b/services/pic-sure-hpds/genomic-processor/pom.xml new file mode 100644 index 000000000..1291045e5 --- /dev/null +++ b/services/pic-sure-hpds/genomic-processor/pom.xml @@ -0,0 +1,62 @@ + + + + pic-sure-hpds + edu.harvard.hms.dbmi.avillach.hpds + ${revision} + + 4.0.0 + + genomic-processor + + + UTF-8 + + + + + + org.springframework.boot + spring-boot-starter-web + + + org.springframework.boot + spring-boot-starter-test + test + + + org.springframework + spring-webflux + + + + edu.harvard.hms.dbmi.avillach.hpds + service + + + edu.harvard.dbmi.avillach + pic-sure-logging-client + + + edu.harvard.hms.dbmi.avillach.hpds + etl + + + edu.harvard.hms.dbmi.avillach.hpds + data + + + + + + + + org.springframework.boot + spring-boot-maven-plugin + + + + + \ No newline at end of file diff --git a/services/pic-sure-hpds/genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/GenomicProcessorController.java b/services/pic-sure-hpds/genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/GenomicProcessorController.java new file mode 100644 index 000000000..cce8793ba --- /dev/null +++ b/services/pic-sure-hpds/genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/GenomicProcessorController.java @@ -0,0 +1,63 @@ +package edu.harvard.hms.dbmi.avillach.hpds.genomic; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.InfoColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMask; +import edu.harvard.hms.dbmi.avillach.hpds.processing.DistributableQuery; +import edu.harvard.hms.dbmi.avillach.hpds.processing.GenomicProcessor; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.web.bind.annotation.*; +import reactor.core.publisher.Mono; + +import java.math.BigInteger; +import java.util.Collection; +import java.util.List; +import java.util.Set; + + +@RestController +public class GenomicProcessorController { + + private GenomicProcessor genomicProcessor; + + @Autowired + public GenomicProcessorController(GenomicProcessor genomicProcessor) { + this.genomicProcessor = genomicProcessor; + } + + @AuditEvent(type = "QUERY", action = "genomic.patient.mask") + @PostMapping("/patients") + public Mono queryForPatientMask(@RequestBody DistributableQuery distributableQuery) { + return genomicProcessor.getPatientMask(distributableQuery); + } + + @AuditEvent(type = "QUERY", action = "genomic.variant.list") + @PostMapping("/variants") + public Mono> queryForVariants(@RequestBody DistributableQuery distributableQuery) { + return genomicProcessor.getVariantList(distributableQuery); + } + + @AuditEvent(type = "DATA_ACCESS", action = "genomic.patient.ids") + @GetMapping("/patients/ids") + public List getPatientIds() { + return genomicProcessor.getPatientIds(); + } + + @AuditEvent(type = "OTHER", action = "genomic.info") + @GetMapping("/info/columns") + public Set getInfoStoreColumns() { + return genomicProcessor.getInfoStoreColumns(); + } + + @AuditEvent(type = "OTHER", action = "genomic.info") + @GetMapping("/info/values") + public Set getInfoStoreValues(@RequestParam("conceptPath") String conceptPath) { + return genomicProcessor.getInfoStoreValues(conceptPath); + } + + @AuditEvent(type = "OTHER", action = "genomic.info") + @GetMapping("/info/meta") + public List getInfoMetadata() { + return genomicProcessor.getInfoColumnMeta(); + } +} diff --git a/services/pic-sure-hpds/genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/HpdsGenomicProcessorApplication.java b/services/pic-sure-hpds/genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/HpdsGenomicProcessorApplication.java new file mode 100644 index 000000000..18c06cc20 --- /dev/null +++ b/services/pic-sure-hpds/genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/HpdsGenomicProcessorApplication.java @@ -0,0 +1,13 @@ +package edu.harvard.hms.dbmi.avillach.hpds.genomic; + +import org.springframework.boot.SpringApplication; +import org.springframework.boot.autoconfigure.SpringBootApplication; + +@SpringBootApplication +public class HpdsGenomicProcessorApplication { + + public static void main(String[] args) { + SpringApplication.run(HpdsGenomicProcessorApplication.class, args); + } + +} diff --git a/services/pic-sure-hpds/genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/ServletInitializer.java b/services/pic-sure-hpds/genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/ServletInitializer.java new file mode 100644 index 000000000..09c14b2c7 --- /dev/null +++ b/services/pic-sure-hpds/genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/ServletInitializer.java @@ -0,0 +1,13 @@ +package edu.harvard.hms.dbmi.avillach.hpds.genomic; + +import org.springframework.boot.builder.SpringApplicationBuilder; +import org.springframework.boot.web.servlet.support.SpringBootServletInitializer; + +public class ServletInitializer extends SpringBootServletInitializer { + + @Override + protected SpringApplicationBuilder configure(SpringApplicationBuilder application) { + return application.sources(HpdsGenomicProcessorApplication.class); + } + +} diff --git a/services/pic-sure-hpds/genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/config/ApplicationConfig.java b/services/pic-sure-hpds/genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/config/ApplicationConfig.java new file mode 100644 index 000000000..129f12117 --- /dev/null +++ b/services/pic-sure-hpds/genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/config/ApplicationConfig.java @@ -0,0 +1,21 @@ +package edu.harvard.hms.dbmi.avillach.hpds.genomic.config; + +import edu.harvard.hms.dbmi.avillach.hpds.processing.GenomicProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.GenomicProcessorNodeImpl; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.autoconfigure.SpringBootApplication; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.PropertySource; + +@SpringBootApplication +@PropertySource("classpath:application.properties") +public class ApplicationConfig { + + @Value("${hpds.genomicDataDirectory}") + private String genomicDataDirectory; + + @Bean + public GenomicProcessor genomicProcessor() { + return new GenomicProcessorNodeImpl(genomicDataDirectory); + } +} diff --git a/services/pic-sure-hpds/genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/config/LoggingConfig.java b/services/pic-sure-hpds/genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/config/LoggingConfig.java new file mode 100644 index 000000000..fde8af798 --- /dev/null +++ b/services/pic-sure-hpds/genomic-processor/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/config/LoggingConfig.java @@ -0,0 +1,49 @@ +package edu.harvard.hms.dbmi.avillach.hpds.genomic.config; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingClientFactory; +import edu.harvard.hms.dbmi.avillach.hpds.processing.audit.AuditInterceptor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.audit.AuditLoggingFilter; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.web.servlet.FilterRegistrationBean; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.web.servlet.config.annotation.InterceptorRegistry; +import org.springframework.web.servlet.config.annotation.WebMvcConfigurer; + +@Configuration +public class LoggingConfig implements WebMvcConfigurer { + + @Value("${DEST_IP:#{null}}") + private String destIp; + + @Value("${DEST_PORT:#{null}}") + private Integer destPort; + + @Bean + public LoggingClient loggingClient() { + return LoggingClientFactory.create("hpds-genomic"); + } + + @Bean + public AuditLoggingFilter auditLoggingFilter(LoggingClient loggingClient) { + return new AuditLoggingFilter(loggingClient, destIp, destPort); + } + + @Bean + public FilterRegistrationBean auditLoggingFilterRegistration(AuditLoggingFilter filter) { + FilterRegistrationBean registration = new FilterRegistrationBean<>(filter); + registration.addUrlPatterns("/*"); + return registration; + } + + @Bean + public AuditInterceptor auditInterceptor() { + return new AuditInterceptor(); + } + + @Override + public void addInterceptors(InterceptorRegistry registry) { + registry.addInterceptor(auditInterceptor()); + } +} diff --git a/services/pic-sure-hpds/genomic-processor/src/main/resources/application.properties b/services/pic-sure-hpds/genomic-processor/src/main/resources/application.properties new file mode 100644 index 000000000..f5c890b49 --- /dev/null +++ b/services/pic-sure-hpds/genomic-processor/src/main/resources/application.properties @@ -0,0 +1,2 @@ +hpds.genomicDataDirectory = /opt/local/hpds/phs0000946/17/ +server.port=8090 \ No newline at end of file diff --git a/services/pic-sure-hpds/genomic-processor/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/GenomicControllerAuditEventTest.java b/services/pic-sure-hpds/genomic-processor/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/GenomicControllerAuditEventTest.java new file mode 100644 index 000000000..dd538c721 --- /dev/null +++ b/services/pic-sure-hpds/genomic-processor/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/GenomicControllerAuditEventTest.java @@ -0,0 +1,72 @@ +package edu.harvard.hms.dbmi.avillach.hpds.genomic; + +import static org.junit.jupiter.api.Assertions.*; + +import java.lang.reflect.Method; + +import edu.harvard.hms.dbmi.avillach.hpds.processing.DistributableQuery; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import org.junit.jupiter.api.Test; + +class GenomicControllerAuditEventTest { + + @Test + void queryForPatientMaskHasCorrectAuditEvent() throws Exception { + Method method = GenomicProcessorController.class.getMethod("queryForPatientMask", DistributableQuery.class); + AuditEvent event = method.getAnnotation(AuditEvent.class); + + assertNotNull(event, "queryForPatientMask should have @AuditEvent"); + assertEquals("QUERY", event.type()); + assertEquals("genomic.patient.mask", event.action()); + } + + @Test + void queryForVariantsHasCorrectAuditEvent() throws Exception { + Method method = GenomicProcessorController.class.getMethod("queryForVariants", DistributableQuery.class); + AuditEvent event = method.getAnnotation(AuditEvent.class); + + assertNotNull(event, "queryForVariants should have @AuditEvent"); + assertEquals("QUERY", event.type()); + assertEquals("genomic.variant.list", event.action()); + } + + @Test + void getPatientIdsHasCorrectAuditEvent() throws Exception { + Method method = GenomicProcessorController.class.getMethod("getPatientIds"); + AuditEvent event = method.getAnnotation(AuditEvent.class); + + assertNotNull(event, "getPatientIds should have @AuditEvent"); + assertEquals("DATA_ACCESS", event.type()); + assertEquals("genomic.patient.ids", event.action()); + } + + @Test + void getInfoStoreColumnsHasCorrectAuditEvent() throws Exception { + Method method = GenomicProcessorController.class.getMethod("getInfoStoreColumns"); + AuditEvent event = method.getAnnotation(AuditEvent.class); + + assertNotNull(event, "getInfoStoreColumns should have @AuditEvent"); + assertEquals("OTHER", event.type()); + assertEquals("genomic.info", event.action()); + } + + @Test + void getInfoStoreValuesHasCorrectAuditEvent() throws Exception { + Method method = GenomicProcessorController.class.getMethod("getInfoStoreValues", String.class); + AuditEvent event = method.getAnnotation(AuditEvent.class); + + assertNotNull(event, "getInfoStoreValues should have @AuditEvent"); + assertEquals("OTHER", event.type()); + assertEquals("genomic.info", event.action()); + } + + @Test + void getInfoMetadataHasCorrectAuditEvent() throws Exception { + Method method = GenomicProcessorController.class.getMethod("getInfoMetadata"); + AuditEvent event = method.getAnnotation(AuditEvent.class); + + assertNotNull(event, "getInfoMetadata should have @AuditEvent"); + assertEquals("OTHER", event.type()); + assertEquals("genomic.info", event.action()); + } +} diff --git a/services/pic-sure-hpds/genomic-processor/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/HpdsGenomicProcessorApplicationTests.java b/services/pic-sure-hpds/genomic-processor/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/HpdsGenomicProcessorApplicationTests.java new file mode 100644 index 000000000..f4c1e2015 --- /dev/null +++ b/services/pic-sure-hpds/genomic-processor/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/genomic/HpdsGenomicProcessorApplicationTests.java @@ -0,0 +1,14 @@ +package edu.harvard.hms.dbmi.avillach.hpds.genomic; + +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; +import org.springframework.boot.test.context.SpringBootTest; + +@Disabled +@SpringBootTest +class HpdsGenomicProcessorApplicationTests { + + @Test + void contextLoads() {} + +} diff --git a/services/pic-sure-hpds/pom.xml b/services/pic-sure-hpds/pom.xml new file mode 100644 index 000000000..073fd3ce9 --- /dev/null +++ b/services/pic-sure-hpds/pom.xml @@ -0,0 +1,275 @@ + + + 4.0.0 + + edu.harvard.hms.dbmi.avillach + pic-sure-api + ${revision} + ../../pom.xml + + edu.harvard.hms.dbmi.avillach.hpds + pic-sure-hpds + pom + pic-sure-hpds + + common + service + etl + data + processing + genomic-processor + docker + war + + + 25 + 25 + UTF-8 + 1.4.10 + 2.20.153 + 2.46.1 + + + + github + GitHub HMS-DBMI Apache Maven Packages + https://maven.pkg.github.com/hms-dbmi/pic-sure-common + + true + + + + + + + + org.apache.maven.plugins + maven-dependency-plugin + 3.8.1 + + + copy-installed + install + + copy + + + + + ${project.groupId} + ${project.artifactId} + ${project.version} + ${project.packaging} + + + pic-sure-hpds + + + + + + com.diffplug.spotless + spotless-maven-plugin + ${spotless.version} + + + + 4.26 + code-formatting/eclipse-formatter.xml + + + + + + + + + maven-clean-plugin + 3.5.0 + + + + maven-resources-plugin + 3.3.1 + + + maven-compiler-plugin + 3.15.0 + + + 25 + + + + org.apache.maven.plugins + maven-surefire-plugin + 3.5.3 + + + maven-jar-plugin + 3.4.2 + + + maven-install-plugin + 3.1.4 + + + maven-deploy-plugin + 3.1.4 + + + + maven-site-plugin + 3.21.0 + + + maven-project-info-reports-plugin + 3.9.0 + + + + + + + org.springframework.boot + spring-boot-starter-test + test + + + org.springframework.boot + spring-boot-starter-web + + + + + + + commons-logging + commons-logging + 1.2 + + + org.apache.commons + commons-compress + 1.26.0 + + + org.springframework.boot + spring-boot-starter-tomcat + provided + + + edu.harvard.hms.dbmi.avillach.hpds + common + ${project.version} + + + edu.harvard.hms.dbmi.avillach.hpds + service + ${project.version} + + + edu.harvard.hms.dbmi.avillach.hpds + processing + ${project.version} + + + edu.harvard.hms.dbmi.avillach.hpds + etl + ${project.version} + + + edu.harvard.hms.dbmi.avillach.hpds + data + ${project.version} + + + com.google.guava + guava + 33.4.8-jre + + + org.apache.commons + commons-math3 + 3.6.1 + + + de.siegmar + fastcsv + 1.0.2 + + + org.apache.commons + commons-csv + 1.5 + + + commons-io + commons-io + 2.20.0 + + + javax.xml.bind + jaxb-api + 2.3.0 + + + com.sun.xml.bind + jaxb-core + 2.3.0 + + + com.sun.xml.bind + jaxb-impl + 2.3.0 + + + javax.activation + activation + 1.1.1 + + + com.oracle.database.jdbc + ojdbc10 + 19.17.0.0 + + + org.apache.avro + avro + 1.12.1 + + + org.xerial.snappy + snappy-java + 1.1.10.5 + + + software.amazon.awssdk + s3 + ${aws.version} + + + + commons-logging + commons-logging + + + + + io.swagger.core.v3 + swagger-annotations + 2.2.40 + + + + + + github + GitHub HMS-DBMI Apache Maven Packages + https://maven.pkg.github.com/hms-dbmi/pic-sure-hpds + + + \ No newline at end of file diff --git a/services/pic-sure-hpds/processing/pom.xml b/services/pic-sure-hpds/processing/pom.xml new file mode 100644 index 000000000..6d5fc1344 --- /dev/null +++ b/services/pic-sure-hpds/processing/pom.xml @@ -0,0 +1,60 @@ + + + 4.0.0 + + pic-sure-hpds + edu.harvard.hms.dbmi.avillach.hpds + ${revision} + + + processing + + processing + + + edu.harvard.hms.dbmi.avillach.hpds + data + + + edu.harvard.hms.dbmi.avillach.hpds + pic-sure-hpds-model + + + edu.harvard.hms.dbmi.avillach + pic-sure-api-model + + + org.mockito + mockito-core + test + + + org.springframework + spring-webflux + + + io.projectreactor.netty + reactor-netty + + + edu.harvard.dbmi.avillach + pic-sure-logging-client + + + jakarta.servlet + jakarta.servlet-api + provided + + + org.apache.avro + avro + + + + org.xerial.snappy + snappy-java + + + + diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessor.java new file mode 100644 index 000000000..a4f363560 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessor.java @@ -0,0 +1,377 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import java.io.*; +import java.util.*; +import java.util.concurrent.*; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +import com.google.common.util.concurrent.UncheckedExecutionException; +import edu.harvard.hms.dbmi.avillach.hpds.data.genomic.VariantUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.common.cache.*; +import com.google.common.cache.CacheLoader.InvalidCacheLoadException; +import com.google.common.collect.Sets; + +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.*; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Component; +import reactor.core.publisher.Mono; + + +@Component +public class AbstractProcessor { + + private static Logger log = LoggerFactory.getLogger(AbstractProcessor.class); + + private final int cacheSize; + + private final String hpdsDataDirectory; + + + @Value("${HPDS_GENOMIC_DATA_DIRECTORY:/opt/local/hpds/all/}") + private String hpdsGenomicDataDirectory; + + private LoadingCache> store; + + private final PhenotypeMetaStore phenotypeMetaStore; + + private final GenomicProcessor genomicProcessor; + + + @Autowired + public AbstractProcessor( + PhenotypeMetaStore phenotypeMetaStore, GenomicProcessor genomicProcessor, + @Value("${HPDS_DATA_DIRECTORY:/opt/local/hpds/}") String hpdsDataDirectory, @Value("${CACHE_SIZE:100}") int cacheSize + ) throws ClassNotFoundException, IOException, InterruptedException { + + this.hpdsDataDirectory = hpdsDataDirectory; + this.phenotypeMetaStore = phenotypeMetaStore; + this.genomicProcessor = genomicProcessor; + + this.cacheSize = cacheSize; + + store = initializeCache(); + + if (Crypto.hasKey(Crypto.DEFAULT_KEY_NAME)) { + List cubes = new ArrayList(phenotypeMetaStore.getColumnNames()); + int conceptsToCache = Math.min(cubes.size(), this.cacheSize); + for (int x = 0; x < conceptsToCache; x++) { + try { + if (phenotypeMetaStore.getColumnMeta(cubes.get(x)).getObservationCount() == 0) { + log.info("Rejecting : " + cubes.get(x) + " because it has no entries."); + } else { + store.get(cubes.get(x)); + log.debug("loaded: " + cubes.get(x)); + // +1 offset when logging to print _after_ each 10% + if ((x + 1) % (conceptsToCache * .1) == 0) { + log.info("cached: " + (x + 1) + " out of " + conceptsToCache); + } + } + } catch (ExecutionException e) { + log.error("an error occurred", e); + } + + } + + } + } + + public AbstractProcessor( + PhenotypeMetaStore phenotypeMetaStore, LoadingCache> store, + Map infoStores, List infoStoreColumns, GenomicProcessor genomicProcessor, + String hpdsDataDirectory, @Value("${CACHE_SIZE:100}") int cacheSize + ) { + this.phenotypeMetaStore = phenotypeMetaStore; + this.store = store; + this.genomicProcessor = genomicProcessor; + + this.cacheSize = cacheSize; + + this.hpdsDataDirectory = hpdsDataDirectory; + } + + public Set getInfoStoreColumns() { + return genomicProcessor.getInfoStoreColumns(); + } + + + /** + * Merges a list of sets of patient ids by intersection. If we implemented OR semantics this would be where the change happens. + * + * @param filteredIdSets + * @return + */ + protected Set applyBooleanLogic(List> filteredIdSets) { + Set[] ids = new Set[] {filteredIdSets.get(0)}; + filteredIdSets.forEach((keySet) -> { + // I believe this is not ideal for large numbers of sets. Sets.intersection creates a view of the 2 sets, so + // doing this repeatedly would create views on views on views of the backing sets. retainAll() returns a new + // set with only the common elements, and if we sort by set size and start with the smallest I believe that + // will be more efficient + ids[0] = Sets.intersection(ids[0], keySet); + }); + return ids[0]; + } + + /** + * + * @param query + * @return + */ + protected Set idSetsForEachFilter(Query query) { + DistributableQuery distributableQuery = getDistributableQuery(query); + + // NULL (representing no phenotypic filters, i.e. all patients) or not empty patient ID sets require a genomic query. + // Otherwise, short circuit and return no patients + if ( + (distributableQuery.getPatientIds() == null || !distributableQuery.getPatientIds().isEmpty()) && distributableQuery.hasFilters() + ) { + Mono patientMaskForVariantInfoFilters = genomicProcessor.getPatientMask(distributableQuery); + return patientMaskForVariantInfoFilters.map(genomicProcessor::patientMaskToPatientIdSet).block(); + } + return distributableQuery.getPatientIds(); + } + + private DistributableQuery getDistributableQuery(Query query) { + DistributableQuery distributableQuery = new DistributableQuery(); + List> patientIdSets = new ArrayList<>(); + + try { + query.getAllAnyRecordOf().forEach(anyRecordOfFilterList -> { + getPatientIdsForAnyRecordOf(anyRecordOfFilterList, distributableQuery).map(patientIdSets::add); + }); + patientIdSets.addAll(getIdSetsForNumericFilters(query)); + patientIdSets.addAll(getIdSetsForRequiredFields(query, distributableQuery)); + patientIdSets.addAll(getIdSetsForCategoryFilters(query, distributableQuery)); + } catch (InvalidCacheLoadException e) { + log.warn("Invalid query supplied: " + e.getLocalizedMessage()); + patientIdSets.add(new HashSet<>()); // if an invalid path is supplied, no patients should match. + } + + Set phenotypicPatientSet = null; + // AND logic to make sure all patients match each filter + if (!patientIdSets.isEmpty()) { + phenotypicPatientSet = applyBooleanLogic(patientIdSets); + } else { + // if there are no patient filters, represent with null. 0 patients means no patients matched the filter + } + distributableQuery.setVariantInfoFilters(query.getVariantInfoFilters()); + distributableQuery.setPatientIds(phenotypicPatientSet); + return distributableQuery; + } + + /** + * Process each filter in the query and return a list of patient ids that should be included in the result. + * + * @param query + * @return + */ + public Set getPatientSubsetForQuery(Query query) { + Set patientIdSet = idSetsForEachFilter(query); + + // todo: make sure this can safely be ignored + /* + * TreeSet idList; if(patientIdSet.isEmpty()) { if(variantService.getPatientIds().length > 0 ) { idList = new TreeSet( + * Sets.union(phenotypeMetaStore.getPatientIds(), new TreeSet(Arrays.asList( variantService.getPatientIds()).stream() + * .collect(Collectors.mapping( (String id)->{return Integer.parseInt(id.trim());}, Collectors.toList()))) )); }else { idList = + * phenotypeMetaStore.getPatientIds(); } }else { idList = new TreeSet<>(applyBooleanLogic(patientIdSet)); } + */ + if (patientIdSet == null) { + return phenotypeMetaStore.getPatientIds(); + } + return patientIdSet; + } + + private List> getIdSetsForRequiredFields(Query query, DistributableQuery distributableQuery) { + if (!query.getRequiredFields().isEmpty()) { + return query.getRequiredFields().stream().map(path -> { + if (VariantUtils.pathIsVariantSpec(path)) { + distributableQuery.addRequiredVariantField(path); + return null; + } else { + return new HashSet(getCube(path).keyBasedIndex()); + } + }).filter(Objects::nonNull).collect(Collectors.toList()); + } + return List.of(); + } + + private Optional> getPatientIdsForAnyRecordOf(List anyRecordOfFilters, DistributableQuery distributableQuery) { + if (!anyRecordOfFilters.isEmpty()) { + // This is an OR aggregation of anyRecordOf filters + Set anyRecordOfPatientSet = anyRecordOfFilters.parallelStream().flatMap(path -> { + if (VariantUtils.pathIsVariantSpec(path)) { + throw new IllegalArgumentException("Variant paths not allowed for anyRecordOf queries"); + } + try { + return (Stream) getCube(path).keyBasedIndex().stream(); + } catch (Exception e) { + return Stream.empty(); + } + }).collect(Collectors.toSet()); + return Optional.of(anyRecordOfPatientSet); + } + return Optional.empty(); + } + + private List> getIdSetsForNumericFilters(Query query) { + if (!query.getNumericFilters().isEmpty()) { + return query.getNumericFilters().entrySet().stream().map(entry -> { + Set keysForRange = getCube(entry.getKey()).getKeysForRange(entry.getValue().getMin(), entry.getValue().getMax()); + return keysForRange; + }).collect(Collectors.toList()); + } + return List.of(); + } + + private List> getIdSetsForCategoryFilters(Query query, DistributableQuery distributableQuery) { + if (!query.getCategoryFilters().isEmpty()) { + return query.getCategoryFilters().entrySet().stream().map((entry) -> { + Set ids = new TreeSet<>(); + if (VariantUtils.pathIsVariantSpec(entry.getKey())) { + distributableQuery.addVariantSpecCategoryFilter(entry.getKey(), entry.getValue()); + return null; + } else { + for (String category : entry.getValue()) { + ids.addAll(getCube(entry.getKey()).getKeysForValue(category)); + } + } + return ids; + }).filter(Objects::nonNull).collect(Collectors.toList()); + } + return List.of(); + } + + public Collection getVariantList(Query query) { + DistributableQuery distributableQuery = getDistributableQuery(query); + return genomicProcessor.getVariantList(distributableQuery).block(); + } + + public List getInfoStoreMeta() { + return genomicProcessor.getInfoColumnMeta(); + } + + public List searchInfoConceptValues(String conceptPath, String query) { + try { + return genomicProcessor.getInfoStoreValues(conceptPath).stream() + .filter(variableValue -> variableValue.toUpperCase(Locale.ENGLISH).contains(query.toUpperCase(Locale.ENGLISH))) + .collect(Collectors.toList()); + } catch (UncheckedExecutionException e) { + if (e.getCause() instanceof RuntimeException) { + throw (RuntimeException) e.getCause(); + } + throw e; + } + } + + // + // private boolean pathIsGeneName(String key) { + // return new GeneLibrary().geneNameSearch(key).size()==1; + // } + + /** + * If there are concepts in the list of paths which are already in the cache, push those to the front of the list so that we don't evict + * and then reload them for concepts which are not yet in the cache. + * + * @param paths + * @param columnCount + * @return + */ + protected ArrayList useResidentCubesFirst(List paths, int columnCount) { + int x; + TreeSet pathSet = new TreeSet(paths); + Set residentKeys = Sets.intersection(pathSet, store.asMap().keySet()); + + ArrayList columnIndex = new ArrayList(); + + residentKeys.forEach(key -> { + columnIndex.add(paths.indexOf(key) + 1); + }); + + Sets.difference(pathSet, residentKeys).forEach(key -> { + columnIndex.add(paths.indexOf(key) + 1); + }); + + for (x = 1; x < columnCount; x++) { + columnIndex.add(x); + } + return columnIndex; + } + + /** + * Load the variantStore object from disk and build the PhenoCube cache. + * + * @return + */ + protected LoadingCache> initializeCache() { + return CacheBuilder.newBuilder().maximumSize(cacheSize).build(new CacheLoader>() { + public PhenoCube load(String key) throws Exception { + try ( + RandomAccessFile allObservationsStore = new RandomAccessFile(hpdsDataDirectory + "allObservationsStore.javabin", "r"); + ) { + ColumnMeta columnMeta = phenotypeMetaStore.getColumnMeta(key); + if (columnMeta != null) { + allObservationsStore.seek(columnMeta.getAllObservationsOffset()); + int length = (int) (columnMeta.getAllObservationsLength() - columnMeta.getAllObservationsOffset()); + byte[] buffer = new byte[length]; + allObservationsStore.read(buffer); + allObservationsStore.close(); + try (ObjectInputStream inStream = new ObjectInputStream(new ByteArrayInputStream(Crypto.decryptData(buffer)))) { + return (PhenoCube) inStream.readObject(); + } + } else { + log.warn("ColumnMeta not found for : [{}]", key); + return null; + } + } + } + }); + } + + + protected PhenoCube getCube(String path) { + try { + return store.get(path); + } catch (ExecutionException e) { + throw new RuntimeException(e); + } + } + + /** + * Get a cube without throwing an error if not found. Useful for federated pic-sure's where there are fewer guarantees about concept + * paths. + */ + public Optional> nullableGetCube(String path) { + try { + return Optional.ofNullable(store.get(path)); + } catch (InvalidCacheLoadException | ExecutionException e) { + return Optional.empty(); + } + } + + public TreeMap getDictionary() { + return phenotypeMetaStore.getMetaStore(); + } + + public List getPatientIds() { + return genomicProcessor.getPatientIds(); + } + + public Optional getMasks(String path, VariantBucketHolder variantMasksVariantBucketHolder) { + return genomicProcessor.getMasks(path, variantMasksVariantBucketHolder); + } + + // todo: handle this locally, we do not want this in the genomic processor + protected VariantMask createMaskForPatientSet(Set patientSubset) { + return genomicProcessor.createMaskForPatientSet(patientSubset); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AsyncResult.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AsyncResult.java new file mode 100644 index 000000000..a3334d550 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AsyncResult.java @@ -0,0 +1,295 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import java.io.File; +import java.io.IOException; +import java.nio.file.Path; +import java.io.UncheckedIOException; +import java.util.List; +import java.util.Map; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.RejectedExecutionException; + +import edu.harvard.dbmi.avillach.domain.PicSureStatus; +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.hms.dbmi.avillach.hpds.processing.io.ResultWriter; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.annotation.JsonIgnore; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import org.springframework.http.MediaType; + +public class AsyncResult implements Runnable, Comparable { + + private static Logger log = LoggerFactory.getLogger(AsyncResult.class); + + public byte[] readAllBytes() { + try { + return stream.readAllBytes(); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + } + + public void closeWriter() { + stream.closeWriter(); + } + + private MediaType responseType; + + public MediaType getResponseType() { + return responseType; + } + + public File getFile() { + return stream.getFile(); + } + + public static enum Status { + SUCCESS { + @Override + public PicSureStatus toPicSureStatus() { + return PicSureStatus.AVAILABLE; + } + }, + ERROR { + @Override + public PicSureStatus toPicSureStatus() { + return PicSureStatus.ERROR; + } + }, + PENDING { + @Override + public PicSureStatus toPicSureStatus() { + return PicSureStatus.QUEUED; + } + }, + RUNNING { + @Override + public PicSureStatus toPicSureStatus() { + return PicSureStatus.PENDING; + } + }, + RETRY { + @Override + public PicSureStatus toPicSureStatus() { + return PicSureStatus.QUEUED; + } + }; + + public abstract PicSureStatus toPicSureStatus(); + } + + private Query query; + + public Query getQuery() { + return query; + } + + private Status status; + + public Status getStatus() { + return status; + } + + public AsyncResult setStatus(Status status) { + this.status = status; + return this; + } + + private long queuedTime; + + public long getQueuedTime() { + return queuedTime; + } + + public AsyncResult setQueuedTime(long queuedTime) { + this.queuedTime = queuedTime; + return this; + } + + private long completedTime; + + public long getCompletedTime() { + return completedTime; + } + + private int retryCount; + + private int queueDepth; + + public int getQueueDepth() { + return queueDepth; + } + + public AsyncResult setQueueDepth(int queueDepth) { + this.queueDepth = queueDepth; + return this; + } + + private int positionInQueue; + + public AsyncResult setPositionInQueue(int positionInQueue) { + this.positionInQueue = positionInQueue; + return this; + } + + private int numRows; + + private int numColumns; + + private String id; + + public String getId() { + return id; + } + + public AsyncResult setId(String id) { + this.id = id; + return this; + } + + @JsonIgnore + private ResultStoreStream stream; + + public ResultStoreStream getStream() { + return stream; + } + + @JsonIgnore + private String[] headerRow; + + /* + * The result needs access to the jobQueue so it can requeue itself if it fails due to insufficient available heap to build its result + * array. + * + * The actual exception is thrown in @see ResultStore#constructor + */ + @JsonIgnore + private ExecutorService jobQueue; + + public ExecutorService getJobQueue() { + return jobQueue; + } + + public AsyncResult setJobQueue(ExecutorService jobQueue) { + this.jobQueue = jobQueue; + return this; + } + + @JsonIgnore + private LoggingClient loggingClient; + + public AsyncResult setLoggingClient(LoggingClient loggingClient) { + this.loggingClient = loggingClient; + return this; + } + + @JsonIgnore + private HpdsProcessor processor; + + public HpdsProcessor getProcessor() { + return processor; + } + + public AsyncResult(Query query, HpdsProcessor processor, ResultWriter writer) { + this.query = query; + this.processor = processor; + this.headerRow = processor.getHeaderRow(query); + this.responseType = writer.getResponseType(); + try { + stream = new ResultStoreStream(headerRow, writer); + } catch (IOException e) { + log.error("Exception creating result stream", e); + } + } + + public void appendResults(List dataEntries) { + stream.appendResults(dataEntries); + } + + public void appendMultiValueResults(List>> dataEntries) { + stream.appendMultiValueResults(dataEntries); + } + + public void appendResultStore(ResultStore resultStore) { + stream.appendResultStore(resultStore); + } + + + private void sendEvent(String eventType, String action, Map metadata) { + if (loggingClient != null && loggingClient.isEnabled()) { + try { + loggingClient.send(LoggingEvent.builder(eventType).action(action).metadata(Map.copyOf(metadata)).build()); + } catch (Exception e) { + log.warn("Failed to send audit log event", e); + } + } + } + + @Override + public void run() { + status = AsyncResult.Status.RUNNING; + long startTime = System.currentTimeMillis(); + + sendEvent( + "QUERY", "query.execution.started", + Map.of("query_id", id != null ? id : "unknown", "result_type", String.valueOf(query.getExpectedResultType())) + ); + + try { + processor.runQuery(query, this); + this.numColumns = this.headerRow.length; + this.numRows = stream.getNumRows(); + long durationMs = System.currentTimeMillis() - startTime; + log.info("Ran Query in " + durationMs + "ms for " + numRows + " rows and " + numColumns + " columns"); + this.status = AsyncResult.Status.SUCCESS; + + sendEvent( + "QUERY", "query.completed", + Map.of( + "query_id", id != null ? id : "unknown", "result_type", String.valueOf(query.getExpectedResultType()), "status", + "success", "duration_ms", String.valueOf(durationMs), "row_count", String.valueOf(numRows) + ) + ); + } catch (Exception e) { + long durationMs = System.currentTimeMillis() - startTime; + log.error("Query failed in " + durationMs + "ms", e); + this.status = AsyncResult.Status.ERROR; + + sendEvent( + "QUERY", "query.completed", + Map.of( + "query_id", id != null ? id : "unknown", "result_type", String.valueOf(query.getExpectedResultType()), "status", + "error", "duration_ms", String.valueOf(durationMs) + ) + ); + } finally { + this.completedTime = System.currentTimeMillis(); + } + } + + public void enqueue() { + try { + this.jobQueue.execute(this); + } catch (RejectedExecutionException e) { + this.status = AsyncResult.Status.ERROR; + } + } + + public void open() { + stream.open(); + } + + @Override + public int compareTo(AsyncResult o) { + return this.query.getId().compareTo(o.query.getId()); + } + + public Path getTempFilePath() { + return stream.getTempFilePath(); + } + +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/ColumnSorter.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/ColumnSorter.java new file mode 100644 index 000000000..17cba67ff --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/ColumnSorter.java @@ -0,0 +1,39 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Component; + +import java.util.*; +import java.util.stream.Collectors; + +@Component +public class ColumnSorter { + private final Map infoColumnsOrder; + + @Autowired + public ColumnSorter(@Value("#{'${variant.info_column_order:}'}") String infoColumnOrderString) { + if (infoColumnOrderString == null || infoColumnOrderString.isEmpty()) { + infoColumnsOrder = Map.of(); + } else { + String[] infoColumnOrder = infoColumnOrderString.split(","); + HashMap order = new HashMap<>(); + for (int i = 0; i < infoColumnOrder.length; i++) { + order.put(infoColumnOrder[i], i); + } + this.infoColumnsOrder = order; + } + } + + public List sortInfoColumns(Set columns) { + // backwards compatibility check. + if (infoColumnsOrder.isEmpty()) { + return new ArrayList<>(columns); + } + return columns.stream().filter(infoColumnsOrder::containsKey) + .sorted( + (a, b) -> Integer + .compare(infoColumnsOrder.getOrDefault(a, Integer.MAX_VALUE), infoColumnsOrder.getOrDefault(b, Integer.MAX_VALUE)) + ).collect(Collectors.toList()); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/CountProcessor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/CountProcessor.java new file mode 100644 index 000000000..5b4a05021 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/CountProcessor.java @@ -0,0 +1,207 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import com.google.common.collect.Sets; +import edu.harvard.hms.dbmi.avillach.hpds.data.genomic.VariantUtils; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.KeyAndValue; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Filter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Component; + +import java.util.*; +import java.util.concurrent.ConcurrentHashMap; + +@Component +public class CountProcessor implements HpdsProcessor { + + Logger log = LoggerFactory.getLogger(CountProcessor.class); + + private final AbstractProcessor abstractProcessor; + + @Autowired + public CountProcessor(AbstractProcessor abstractProcessor) { + this.abstractProcessor = abstractProcessor; + } + + /** + * Count processor always returns same headers + */ + @Override + public String[] getHeaderRow(Query query) { + return new String[] {"Patient ID", "Count"}; + } + + /** + * Retrieves a list of patient ids that are valid for the query result and returns the size of that list. + * + * @param query + * @return + */ + public int runCounts(Query query) { + return abstractProcessor.getPatientSubsetForQuery(query).size(); + } + + /** + * Returns a separate observation count for each field in query.crossCountFields when that field is added as a requiredFields entry for + * the base query. + * + * @param query + * @return + */ + public Map runObservationCrossCounts(Query query) { + TreeMap counts = new TreeMap<>(); + Set baseQueryPatientSet = abstractProcessor.getPatientSubsetForQuery(query); + query.getCrossCountFields().parallelStream().forEach((String concept) -> { + try { + // breaking these statements to allow += operator to cast long to int. + int observationCount = 0; + observationCount += (Long) Arrays.stream(abstractProcessor.getCube(concept).sortedByKey()).filter(keyAndValue -> { + return baseQueryPatientSet.contains(keyAndValue.getKey()); + }).count(); + counts.put(concept, observationCount); + } catch (Exception e) { + counts.put(concept, -1); + } + }); + return counts; + } + + /** + * Returns a separate count for each field in query.crossCountFields when that field is added as a requiredFields entry for the base + * query. + * + * @param query + * @return + */ + public Map runCrossCounts(Query query) { + ConcurrentHashMap counts = new ConcurrentHashMap<>(); + Set baseQueryPatientSet = abstractProcessor.getPatientSubsetForQuery(query); + query.getCrossCountFields().parallelStream().forEach((String concept) -> { + try { + Query safeCopy = new Query(); + safeCopy.setRequiredFields(List.of(concept)); + counts.put(concept, Sets.intersection(abstractProcessor.getPatientSubsetForQuery(safeCopy), baseQueryPatientSet).size()); + } catch (Exception e) { + counts.put(concept, -1); + } + }); + return counts; + } + + /** + * Returns a separate count for each field in the requiredFields and categoryFilters query. + * + * @param query + * @return a map of categorical data and their counts + */ + public Map> runCategoryCrossCounts(Query query) { + Map> categoryCounts = new TreeMap<>(); + Set baseQueryPatientSet = abstractProcessor.getPatientSubsetForQuery(query); + query.getRequiredFields().parallelStream().forEach(concept -> { + Map varCount = new TreeMap<>();; + TreeMap> categoryMap = abstractProcessor.getCube(concept).getCategoryMap(); + // We do not have all the categories (aka variables) for required fields, so we need to get them and + // then ensure that our base patient set, which is filtered down by our filters. Which may include + // not only other required filters, but categorical filters, numerical filters, or genomic filters. + // We then need to get the amount a patients for each category and map that to the concept path. + categoryMap.forEach((String category, TreeSet patientSet) -> { + // If all the patients are in the base then no need to loop, this would always be true for single + // filter queries. + if (baseQueryPatientSet.containsAll(patientSet)) { + varCount.put(category, patientSet.size()); + } else { + for (Integer patient : patientSet) { + if (baseQueryPatientSet.contains(patient)) { + // If we have a patient in the base set, we add 1 to the count. + // We are only worried about patients in the base set + varCount.put(category, varCount.getOrDefault(category, 1) + 1); + } else { + // If we don't have a patient in the base set, we add 0 to the count. + // This is necessary because we need to ensure that all categories are included in the + // map, even if they have a count of 0. This is because we are displaying the counts + // in a table (or other form). + varCount.put(category, varCount.getOrDefault(category, 0)); + } + } + } + }); + categoryCounts.put(concept, varCount); + }); + // For categoryFilters we need to ensure the variables included in the filter are the ones included in our count + // map. Then we make sure that the patients who have that variable are also in our base set. + query.getCategoryFilters().entrySet().parallelStream().forEach(categoryFilterEntry -> { + // Variant spec filter should not be included in cross count map + if (VariantUtils.pathIsVariantSpec(categoryFilterEntry.getKey())) { + return; + } + Map varCount; + TreeMap> categoryMap = abstractProcessor.getCube(categoryFilterEntry.getKey()).getCategoryMap(); + varCount = new TreeMap<>(); + categoryMap.forEach((String category, TreeSet patientSet) -> { + if (Arrays.asList(categoryFilterEntry.getValue()).contains(category)) { + varCount.put(category, Sets.intersection(patientSet, baseQueryPatientSet).size()); + } + }); + categoryCounts.put(categoryFilterEntry.getKey(), varCount); + }); + return categoryCounts; + } + + /** + * Returns a separate count for each range in numericFilters in query. + * + * @param query + * @return a map of numerical data and their counts + */ + public Map> runContinuousCrossCounts(Query query) { + TreeMap> conceptMap = new TreeMap<>(); + Set baseQueryPatientSet = abstractProcessor.getPatientSubsetForQuery(query); + query.getNumericFilters().forEach((String concept, Filter.DoubleFilter range) -> { + KeyAndValue[] pairs = abstractProcessor.getCube(concept).getEntriesForValueRange(range.getMin(), range.getMax()); + Map countMap = new TreeMap<>(); + Arrays.stream(pairs).forEach(patientConceptPair -> { + // The key of the patientConceptPair is the patient id. We need to make sure the patient matches our query. + if (baseQueryPatientSet.contains(patientConceptPair.getKey())) { + if (countMap.containsKey(patientConceptPair.getValue())) { + countMap.put((double) patientConceptPair.getValue(), countMap.get(patientConceptPair.getValue()) + 1); + } else { + countMap.put((double) patientConceptPair.getValue(), 1); + } + } + }); + conceptMap.put(concept, countMap); + }); + return conceptMap; + } + + /** + * Until we have a count based query that takes longer than 30 seconds to run, we should discourage running them asynchronously in the + * backend as this results in unnecessary request-response cycles. + */ + @Override + public void runQuery(Query query, AsyncResult asyncResult) { + throw new UnsupportedOperationException("Counts do not run asynchronously."); + } + + /** + * Process only variantInfoFilters to count the number of variants that would be included in evaluating the query. + * + * This does not actually evaluate a patient set for the query. + * + * @param query + * @return the number of variants that would be used to filter patients if the incomingQuery was run as a COUNT query. + */ + public Map runVariantCount(Query query) { + TreeMap response = new TreeMap(); + if (!query.getVariantInfoFilters().isEmpty()) { + response.put("count", abstractProcessor.getVariantList(query).size()); + response.put("message", "Query ran successfully"); + } else { + response.put("count", "0"); + response.put("message", "No variant filters were supplied, so no query was run."); + } + return response; + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/DenseVariantIndex.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/DenseVariantIndex.java new file mode 100644 index 000000000..8ec68832d --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/DenseVariantIndex.java @@ -0,0 +1,74 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import com.google.common.collect.Sets; + +import java.util.Set; +import java.util.concurrent.ConcurrentHashMap; + +public class DenseVariantIndex extends VariantIndex { + + /** + * Todo: this could more efficiently be represented as an array of bit-encoded bytes, although it would not be as simple to use. + */ + private final boolean[] variantIndexMask; + + public DenseVariantIndex(boolean[] variantIndexMask) { + this.variantIndexMask = variantIndexMask; + } + + public boolean[] getVariantIndexMask() { + return variantIndexMask; + } + + @Override + public VariantIndex union(VariantIndex variantIndex) { + if (variantIndex instanceof SparseVariantIndex) { + return union((SparseVariantIndex) variantIndex, this); + } else if (variantIndex instanceof DenseVariantIndex) { + // todo: implement with arrays of different lengths + boolean[] copy = new boolean[variantIndexMask.length]; + for (int i = 0; i < copy.length; i++) { + copy[i] = variantIndexMask[i] || ((DenseVariantIndex) variantIndex).variantIndexMask[i]; + } + return new DenseVariantIndex(copy); + } else { + throw new IllegalArgumentException("Union not implemented between DenseVariantIndex and " + variantIndex.getClass()); + } + } + + @Override + public VariantIndex intersection(VariantIndex variantIndex) { + if (variantIndex instanceof SparseVariantIndex) { + return intersection((SparseVariantIndex) variantIndex, this); + } else if (variantIndex instanceof DenseVariantIndex) { + // todo: implement with arrays of different lengths + boolean[] copy = new boolean[variantIndexMask.length]; + for (int i = 0; i < copy.length; i++) { + copy[i] = variantIndexMask[i] && ((DenseVariantIndex) variantIndex).variantIndexMask[i]; + } + // todo: return sparse index if small + return new DenseVariantIndex(copy); + } else { + throw new IllegalArgumentException("Intersection not implemented between SparseVariantIndex and " + variantIndex.getClass()); + } + } + + @Override + public Set mapToVariantSpec(String[] variantIndex) { + ConcurrentHashMap setMap = new ConcurrentHashMap<>(variantIndexMask.length / 10); + for (int i = 0; i < variantIndexMask.length; i++) { + if (variantIndexMask[i]) setMap.put(variantIndex[i], ""); + } + return setMap.keySet(); + } + + @Override + public boolean isEmpty() { + for (boolean b : variantIndexMask) { + if (b) { + return false; + } + } + return true; + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/DistributableQuery.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/DistributableQuery.java new file mode 100644 index 000000000..9dba0adcf --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/DistributableQuery.java @@ -0,0 +1,61 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; + +import java.util.*; +import java.util.stream.Collectors; + +public class DistributableQuery { + + private List variantInfoFilters = new ArrayList<>(); + + private final Map categoryFilters = new HashMap<>(); + + private final Set requiredFields = new HashSet<>(); + + private Set patientIds; + + + public void addRequiredVariantField(String path) { + requiredFields.add(path); + } + + public Set getRequiredFields() { + return requiredFields; + } + + public void addVariantSpecCategoryFilter(String key, String[] values) { + categoryFilters.put(key, values); + } + + public Map getCategoryFilters() { + return categoryFilters; + } + + public DistributableQuery setVariantInfoFilters(Collection variantInfoFilters) { + this.variantInfoFilters = variantInfoFilters.stream() + .filter( + variantInfoFilter -> !variantInfoFilter.categoryVariantInfoFilters.isEmpty() + || !variantInfoFilter.numericVariantInfoFilters.isEmpty() + ).collect(Collectors.toList()); + return this; + } + + public List getVariantInfoFilters() { + return new ArrayList<>(variantInfoFilters); + } + + + public DistributableQuery setPatientIds(Set patientIds) { + this.patientIds = patientIds; + return this; + } + + public Set getPatientIds() { + return patientIds; + } + + public boolean hasFilters() { + return !variantInfoFilters.isEmpty() || !categoryFilters.isEmpty() || !requiredFields.isEmpty(); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessor.java new file mode 100644 index 000000000..855acea4b --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessor.java @@ -0,0 +1,33 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.InfoColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariableVariantMasks; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMask; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMasks; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; +import reactor.core.publisher.Mono; + +import java.math.BigInteger; +import java.util.*; + +public interface GenomicProcessor { + Mono getPatientMask(DistributableQuery distributableQuery); + + Set patientMaskToPatientIdSet(VariantMask patientMask); + + VariantMask createMaskForPatientSet(Set patientSubset); + + Mono> getVariantList(DistributableQuery distributableQuery); + + List getPatientIds(); + + Optional getMasks(String path, VariantBucketHolder variantMasksVariantBucketHolder); + + Set getInfoStoreColumns(); + + Set getInfoStoreValues(String conceptPath); + + List getInfoColumnMeta(); + + Map> getVariantMetadata(Collection variantList); +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorConfig.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorConfig.java new file mode 100644 index 000000000..1d6d422c1 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorConfig.java @@ -0,0 +1,113 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import edu.harvard.hms.dbmi.avillach.hpds.processing.genomic.GenomicProcessorRestClient; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean; +import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import reactor.core.publisher.Flux; +import reactor.core.publisher.Mono; +import reactor.core.scheduler.Schedulers; + +import java.io.File; +import java.util.ArrayList; +import java.util.List; + +@Configuration +public class GenomicProcessorConfig { + + @Value("${HPDS_GENOMIC_DATA_DIRECTORY:/opt/local/hpds/all/}") + private String hpdsGenomicDataDirectory; + + private static Logger log = LoggerFactory.getLogger(GenomicProcessorConfig.class); + + + @Bean(name = "localGenomicProcessor") + @ConditionalOnProperty(prefix = "hpds.genomicProcessor", name = "impl", havingValue = "local") + public GenomicProcessor localGenomicProcessor() { + return new GenomicProcessorNodeImpl(hpdsGenomicDataDirectory); + } + + @Bean(name = "localDistributedGenomicProcessor") + @ConditionalOnProperty(prefix = "hpds.genomicProcessor", name = "impl", havingValue = "localDistributed") + public GenomicProcessor localDistributedGenomicProcessor() { + List genomicProcessors = getGenomicProcessors(new File(hpdsGenomicDataDirectory)); + return new GenomicProcessorParentImpl(genomicProcessors); + } + + @Bean(name = "localPatientDistributedGenomicProcessor") + @ConditionalOnProperty(prefix = "hpds.genomicProcessor", name = "impl", havingValue = "localPatientDistributed") + public GenomicProcessor localPatientDistributedGenomicProcessor() { + // assumed for now that all first level directories contain a genomic dataset for a group of studies + File[] directories = new File(hpdsGenomicDataDirectory).listFiles(File::isDirectory); + if (directories.length > 10) { + throw new IllegalArgumentException( + "Number of genomic partitions by studies exceeds maximum of 10 (" + directories.length + ")" + ); + } + + List studyGroupedGenomicProcessors = new ArrayList<>(); + + for (File directory : directories) { + List genomicProcessors = getGenomicProcessors(directory); + studyGroupedGenomicProcessors.add(new GenomicProcessorParentImpl(genomicProcessors)); + } + + return new GenomicProcessorPatientMergingParentImpl(studyGroupedGenomicProcessors); + } + + private static List getGenomicProcessors(File directory) { + File[] secondLevelDirectories = directory.listFiles(File::isDirectory); + if (secondLevelDirectories.length > 50) { + throw new IllegalArgumentException( + "Number of chromosome partitions exceeds maximum of 50 (" + secondLevelDirectories.length + ")" + ); + } + + return Flux.fromArray(secondLevelDirectories).flatMap(i -> Mono.fromCallable(() -> { + return (GenomicProcessor) new GenomicProcessorNodeImpl(i.getAbsolutePath() + "/"); + }).subscribeOn(Schedulers.boundedElastic())).collectList().block(); + } + + @Bean(name = "localPatientOnlyDistributedGenomicProcessor") + @ConditionalOnProperty(prefix = "hpds.genomicProcessor", name = "impl", havingValue = "localPatientOnlyDistributed") + public GenomicProcessor localPatientOnlyDistributedGenomicProcessor() { + // assumed for now that all first level directories contain a genomic dataset for a group of studies + File[] directories = new File(hpdsGenomicDataDirectory).listFiles(File::isDirectory); + if (directories.length > 10) { + throw new IllegalArgumentException( + "Number of genomic partitions by studies exceeds maximum of 10 (" + directories.length + ")" + ); + } + + List studyGroupedGenomicProcessors = new ArrayList<>(); + + for (File directory : directories) { + log.info("Loading partition: " + directory.getName()); + studyGroupedGenomicProcessors.add(new GenomicProcessorNodeImpl(directory.getAbsolutePath() + "/")); + } + + return new GenomicProcessorPatientMergingParentImpl(studyGroupedGenomicProcessors); + } + + @Bean(name = "remoteGenomicProcessor") + @ConditionalOnProperty(prefix = "hpds.genomicProcessor", name = "impl", havingValue = "remote") + public GenomicProcessor remoteGenomicProcessor(@Value("${hpds.genomicProcessor.remoteHosts}") List remoteHosts) { + List genomicProcessors = Flux.fromIterable(remoteHosts) + .flatMap( + remoteHost -> Mono.fromCallable(() -> (GenomicProcessor) new GenomicProcessorRestClient(remoteHost)) + .subscribeOn(Schedulers.boundedElastic()) + ).collectList().block(); + // todo: validate remote processors are valid + return new GenomicProcessorParentImpl(genomicProcessors); + } + + @Bean + @ConditionalOnMissingBean + public GenomicProcessor noOpGenomicProcessor() { + return new GenomicProcessorNoOp(); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorNoOp.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorNoOp.java new file mode 100644 index 000000000..1db3dfcad --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorNoOp.java @@ -0,0 +1,63 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.InfoColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariableVariantMasks; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMask; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMasks; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; +import reactor.core.publisher.Mono; + +import java.math.BigInteger; +import java.util.*; + +public class GenomicProcessorNoOp implements GenomicProcessor { + @Override + public Mono getPatientMask(DistributableQuery distributableQuery) { + return null; + } + + @Override + public Set patientMaskToPatientIdSet(VariantMask patientMask) { + return null; + } + + @Override + public VariantMask createMaskForPatientSet(Set patientSubset) { + return null; + } + + @Override + public Mono> getVariantList(DistributableQuery distributableQuery) { + return null; + } + + @Override + public List getPatientIds() { + return null; + } + + @Override + public Optional getMasks(String path, VariantBucketHolder variantMasksVariantBucketHolder) { + return Optional.empty(); + } + + @Override + public Set getInfoStoreColumns() { + return Set.of(); + } + + @Override + public Set getInfoStoreValues(String conceptPath) { + return Set.of(); + } + + @Override + public List getInfoColumnMeta() { + return List.of(); + } + + @Override + public Map> getVariantMetadata(Collection variantList) { + return null; + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorNodeImpl.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorNodeImpl.java new file mode 100644 index 000000000..57742021c --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorNodeImpl.java @@ -0,0 +1,417 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import com.google.common.base.Joiner; +import com.google.common.collect.Range; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.*; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Filter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import reactor.core.publisher.Mono; +import reactor.core.scheduler.Schedulers; + +import java.io.*; +import java.util.*; +import java.util.concurrent.ConcurrentSkipListSet; +import java.util.stream.Collectors; +import java.util.zip.GZIPInputStream; + +import static edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMetadataIndex.VARIANT_METADATA_FILENAME; + +public class GenomicProcessorNodeImpl implements GenomicProcessor { + + private static Logger log = LoggerFactory.getLogger(GenomicProcessorNodeImpl.class); + + private final PatientVariantJoinHandler patientVariantJoinHandler; + + private final VariantIndexCache variantIndexCache; + + private final Map infoStores; + + private final Set infoStoreColumns; + + private final String genomicDataDirectory; + + private final VariantService variantService; + + + private final String HOMOZYGOUS_VARIANT = "1/1"; + private final String HETEROZYGOUS_VARIANT = "0/1"; + private final String HOMOZYGOUS_REFERENCE = "0/0"; + + public GenomicProcessorNodeImpl(String genomicDataDirectory) { + this.genomicDataDirectory = genomicDataDirectory; + this.variantService = new VariantService(genomicDataDirectory); + this.patientVariantJoinHandler = new PatientVariantJoinHandler(variantService); + + infoStores = new HashMap<>(); + File genomicDataDirectoryFile = new File(this.genomicDataDirectory); + if (genomicDataDirectoryFile.exists() && genomicDataDirectoryFile.isDirectory()) { + Arrays.stream(genomicDataDirectoryFile.list((file, filename) -> { + return filename.endsWith("infoStore.javabin"); + })).forEach((String filename) -> { + try ( + FileInputStream fis = new FileInputStream(this.genomicDataDirectory + filename); GZIPInputStream gis = + new GZIPInputStream(fis); ObjectInputStream ois = new ObjectInputStream(gis) + ) { + log.info("loading " + filename); + FileBackedByteIndexedInfoStore infoStore = (FileBackedByteIndexedInfoStore) ois.readObject(); + infoStore.updateStorageDirectory(genomicDataDirectoryFile); + infoStores.put(filename.replace("_infoStore.javabin", ""), infoStore); + ois.close(); + } catch (IOException e) { + throw new UncheckedIOException(e); + } catch (ClassNotFoundException e) { + throw new RuntimeException(e); + } + }); + } else { + throw new IllegalArgumentException("Not a valid genomicDataDirectory: " + this.genomicDataDirectory); + } + infoStoreColumns = new HashSet<>(infoStores.keySet()); + + variantIndexCache = new VariantIndexCache(variantService.getVariantIndex(), infoStores); + } + + @Override + public Mono getPatientMask(DistributableQuery distributableQuery) { + return Mono.fromCallable(() -> runGetPatientMask(distributableQuery)).subscribeOn(Schedulers.boundedElastic()); + } + + public VariantMask runGetPatientMask(DistributableQuery distributableQuery) { + /* VARIANT INFO FILTER HANDLING IS MESSY */ + if (distributableQuery.hasFilters()) { + VariantIndex intersectionOfInfoFilters = null; + for (Query.VariantInfoFilter filter : distributableQuery.getVariantInfoFilters()) { + List variantSets = getVariantsMatchingFilters(filter); + log.debug("Found " + variantSets.size() + " groups of sets for patient identification"); + if (!variantSets.isEmpty()) { + // INTERSECT all the variant sets. + if (intersectionOfInfoFilters == null) { + intersectionOfInfoFilters = variantSets.get(0); + } + for (VariantIndex variantSet : variantSets) { + intersectionOfInfoFilters = intersectionOfInfoFilters.intersection(variantSet); + } + } else { + intersectionOfInfoFilters = VariantIndex.empty(); + } + } + + // todo: handle empty getVariantInfoFilters() + + // add filteredIdSet for patients who have matching variants, heterozygous or homozygous for now. + VariantMask patientMask = null; + if (intersectionOfInfoFilters != null) { + patientMask = patientVariantJoinHandler + .getPatientIdsForIntersectionOfVariantSets(distributableQuery.getPatientIds(), intersectionOfInfoFilters); + } else { + patientMask = createMaskForPatientSet(distributableQuery.getPatientIds()); + } + + for (String snp : distributableQuery.getCategoryFilters().keySet()) { + VariantMask patientsForVariantSpec = getVariantIndexesForSpec(distributableQuery.getCategoryFilters().get(snp), snp); + if (patientMask == null) { + patientMask = patientsForVariantSpec; + } else { + patientMask = patientMask.intersection(patientsForVariantSpec); + } + } + + VariantBucketHolder variantMasksVariantBucketHolder = new VariantBucketHolder<>(); + if (!distributableQuery.getRequiredFields().isEmpty()) { + for (String variantSpec : distributableQuery.getRequiredFields()) { + VariantMask patientsForVariantSpec = getVariantIndexesForSpec(new String[] {"0/1", "1/1"}, variantSpec); + if (patientMask == null) { + patientMask = patientsForVariantSpec; + } else { + patientMask = patientMask.intersection(patientsForVariantSpec); + } + } + } + + return patientMask; + } + return createMaskForPatientSet(distributableQuery.getPatientIds()); + /* END OF VARIANT INFO FILTER HANDLING */ + } + + private VariantMask getVariantIndexesForSpec(String[] zygosities, String variantSpec) { + List masksForDbSnpSpec = variantService.getMasksForDbSnpSpec(variantSpec); + VariantMask variantMask = VariantMask.emptyInstance(); + + for (VariableVariantMasks masks : masksForDbSnpSpec) { + for (String zygosity : zygosities) { + if (zygosity.equals(HOMOZYGOUS_REFERENCE)) { + /* + * // todo: implement this -- difficult with sparse variants of unknown length VariantMask homozygousReferenceBitmask = + * calculateIndiscriminateBitmask(masks); for(int x = 2;x patientMaskToPatientIdSet(VariantMask patientMask) { + return patientMask.patientMaskToPatientIdSet(getPatientIds()); + } + + private List getVariantsMatchingFilters(Query.VariantInfoFilter filter) { + List variantIndices = new ArrayList<>(); + // Add variant sets for each filter + if (filter.categoryVariantInfoFilters != null && !filter.categoryVariantInfoFilters.isEmpty()) { + filter.categoryVariantInfoFilters.entrySet().stream().forEach((Map.Entry entry) -> { + variantIndices.add(getComputedVariantIndexForCategoryFilter(entry)); + }); + } + if (filter.numericVariantInfoFilters != null && !filter.numericVariantInfoFilters.isEmpty()) { + filter.numericVariantInfoFilters.forEach((String column, Filter.FloatFilter doubleFilter) -> { + Optional infoStoreOptional = getInfoStore(column); + + doubleFilter.getMax(); + Range filterRange = Range.closed(doubleFilter.getMin(), doubleFilter.getMax()); + infoStoreOptional.ifPresentOrElse(infoStore -> { + List valuesInRange = infoStore.continuousValueIndex.getValuesInRange(filterRange); + for (String value : valuesInRange) { + variantIndices.add(variantIndexCache.get(column, value)); + } + }, () -> { + variantIndices.add(VariantIndex.empty()); + }); + + }); + } + return variantIndices; + } + + private VariantIndex getComputedVariantIndexForCategoryFilter(Map.Entry entry) { + String column = entry.getKey(); + String[] values = Arrays.copyOf(entry.getValue(), entry.getValue().length); + Arrays.sort(values); + Optional infoStoreOptional = getInfoStore(column); + + List infoKeys = infoStoreOptional.map(infoStore -> filterInfoCategoryKeys(values, infoStore)).orElseGet(ArrayList::new); + + if (infoKeys.size() > 1) { + // These should be ANDed + return infoKeys.stream().map(key -> variantIndexCache.get(column, key)).reduce(VariantIndex::union).orElseGet(() -> { + log.warn("No variant index computed for category filter. This should never happen"); + return VariantIndex.empty(); + }); + } else if (infoKeys.size() == 1) { + return variantIndexCache.get(column, infoKeys.get(0)); + } else { // infoKeys.size() == 0 + log.debug("No indexes found for column [" + column + "] for values [" + Joiner.on(",").join(values) + "]"); + return VariantIndex.empty(); + } + } + + private List filterInfoCategoryKeys(String[] values, FileBackedByteIndexedInfoStore infoStore) { + List infoKeys = infoStore.getAllValues().keys().stream().filter((String key) -> { + // iterate over the values for the specific category and find which ones match the search + int insertionIndex = Arrays.binarySearch(values, key); + return insertionIndex > -1 && insertionIndex < values.length; + }).collect(Collectors.toList()); + log.debug("found " + infoKeys.size() + " keys for info category filters"); + return infoKeys; + } + + @Override + public VariantMask createMaskForPatientSet(Set patientSubset) { + return new VariantMaskBitmaskImpl(patientVariantJoinHandler.createMaskForPatientSet(patientSubset)); + } + + private Optional getInfoStore(String column) { + return Optional.ofNullable(infoStores.get(column)); + } + + private VariantIndex addVariantsForInfoFilter(VariantIndex unionOfInfoFilters, Query.VariantInfoFilter filter) { + List variantSets = getVariantsMatchingFilters(filter); + + if (!variantSets.isEmpty()) { + VariantIndex intersectionOfInfoFilters = variantSets.get(0); + for (VariantIndex variantSet : variantSets) { + intersectionOfInfoFilters = intersectionOfInfoFilters.intersection(variantSet); + } + unionOfInfoFilters = unionOfInfoFilters.union(intersectionOfInfoFilters); + } else { + log.warn("No info filters included in query."); + } + return unionOfInfoFilters; + } + + @Override + public Mono> getVariantList(DistributableQuery query) { + return Mono.fromCallable(() -> runGetVariantList(query)).subscribeOn(Schedulers.boundedElastic()); + } + + public Set runGetVariantList(DistributableQuery query) { + boolean queryContainsVariantInfoFilters = query.getVariantInfoFilters().stream().anyMatch( + variantInfoFilter -> !variantInfoFilter.categoryVariantInfoFilters.isEmpty() + || !variantInfoFilter.numericVariantInfoFilters.isEmpty() + ); + if (queryContainsVariantInfoFilters) { + VariantIndex unionOfInfoFilters = VariantIndex.empty(); + + for (Query.VariantInfoFilter filter : query.getVariantInfoFilters()) { + unionOfInfoFilters = addVariantsForInfoFilter(unionOfInfoFilters, filter); + } + + VariantMask patientMask = runGetPatientMask(query); + + // If we have all patients then no variants would be filtered, so no need to do further processing + /* + * if(patientSubset.size()==variantService.getPatientIds().length) { log.info("query selects all patient IDs, returning...."); + * return unionOfInfoFilters.mapToVariantSpec(variantService.getVariantIndex()); } + */ + + Set unionOfInfoFiltersVariantSpecs = unionOfInfoFilters.mapToVariantSpec(variantService.getVariantIndex()); + Collection variantsInScope = + variantService.filterVariantSetForPatientSet(unionOfInfoFiltersVariantSpecs, patientMaskToPatientIdSet(patientMask)); + + // NC - this is the original variant filtering, which checks the patient mask from each variant against the patient mask from + // the query + if (variantsInScope.size() < 100000) { + ConcurrentSkipListSet variantsWithPatients = new ConcurrentSkipListSet<>(); + variantsInScope.parallelStream().forEach(variantKey -> { + variantService.getMasks(variantKey, new VariantBucketHolder<>()).ifPresent(masks -> { + if (masks.heterozygousMask != null && !masks.heterozygousMask.intersection(patientMask).isEmpty()) { + variantsWithPatients.add(variantKey); + } else if (masks.homozygousMask != null && !masks.homozygousMask.intersection(patientMask).isEmpty()) { + variantsWithPatients.add(variantKey); + } else if ( + masks.heterozygousNoCallMask != null && !masks.heterozygousNoCallMask.intersection(patientMask).isEmpty() + ) { + // so heterozygous no calls we want, homozygous no calls we don't + variantsWithPatients.add(variantKey); + } + }); + }); + return variantsWithPatients; + } else { + return unionOfInfoFiltersVariantSpecs; + } + } + return new HashSet<>(); + } + + private VariantMask getIdSetForVariantSpecCategoryFilter( + String[] zygosities, String key, VariantBucketHolder bucketCache + ) { + List variantBitmasks = getBitmasksForVariantSpecCategoryFilter(zygosities, key, bucketCache); + Set patientIds = new HashSet<>(); + if (!variantBitmasks.isEmpty()) { + VariantMask variantMask = variantBitmasks.get(0); + if (variantBitmasks.size() > 1) { + for (int x = 1; x < variantBitmasks.size(); x++) { + variantMask = variantMask.union(variantBitmasks.get(x)); + } + } + return variantMask; + } + return VariantMask.emptyInstance(); + } + + private ArrayList getBitmasksForVariantSpecCategoryFilter( + String[] zygosities, String variantName, VariantBucketHolder bucketCache + ) { + ArrayList variantBitmasks = new ArrayList<>(); + variantName = variantName.replaceAll(",\\d/\\d$", ""); + log.debug("looking up mask for : " + variantName); + Optional optionalMasks = variantService.getMasks(variantName, bucketCache); + Arrays.stream(zygosities).forEach((zygosity) -> { + optionalMasks.ifPresent(masks -> { + if (zygosity.equals(HOMOZYGOUS_REFERENCE)) { + // todo: implement for VariantMask. I don't think this logic was sound previously + /* + * VariantMask homozygousReferenceBitmask = calculateIndiscriminateBitmask(masks); for(int x = + * 2;x getPatientIds() { + return List.of(variantService.getPatientIds()); + } + + @Override + public Optional getMasks(String path, VariantBucketHolder variantMasksVariantBucketHolder) { + return variantService.getMasks(path, variantMasksVariantBucketHolder); + } + + @Override + public Set getInfoStoreColumns() { + return infoStoreColumns; + } + + @Override + public Set getInfoStoreValues(String conceptPath) { + return infoStores.get(conceptPath).getAllValues().keys().stream().sorted(String::compareToIgnoreCase).collect(Collectors.toSet()); + } + + @Override + public List getInfoColumnMeta() { + return getInfoStoreColumns().stream().map(infoStores::get) + .map( + fileBackedByteIndexedInfoStore -> new InfoColumnMeta( + fileBackedByteIndexedInfoStore.column_key, fileBackedByteIndexedInfoStore.description, + fileBackedByteIndexedInfoStore.isContinuous, fileBackedByteIndexedInfoStore.min, fileBackedByteIndexedInfoStore.max + ) + ).collect(Collectors.toList()); + } + + @Override + public Map> getVariantMetadata(Collection variantList) { + return variantService.findByMultipleVariantSpec(variantList); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorParentImpl.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorParentImpl.java new file mode 100644 index 000000000..df1002795 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorParentImpl.java @@ -0,0 +1,155 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import com.google.common.cache.CacheBuilder; +import com.google.common.cache.CacheLoader; +import com.google.common.cache.LoadingCache; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.*; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import reactor.core.publisher.Flux; +import reactor.core.publisher.Mono; +import reactor.core.scheduler.Schedulers; + +import java.math.BigInteger; +import java.util.*; +import java.util.concurrent.ConcurrentHashMap; +import java.util.stream.Collectors; + +/** + * This genomic processor assumes child nodes all have the same patient set + */ +public class GenomicProcessorParentImpl implements GenomicProcessor { + + private static Logger log = LoggerFactory.getLogger(GenomicProcessorParentImpl.class); + + private final List nodes; + + private final LoadingCache> infoStoreValuesCache = CacheBuilder.newBuilder().build(new CacheLoader<>() { + @Override + public Set load(String conceptPath) { + return nodes.parallelStream().map(node -> node.getInfoStoreValues(conceptPath)).flatMap(Set::stream) + .collect(Collectors.toSet()); + } + }); + + private final List infoColumnsMeta; + private final List patientIds; + private final Set infoStoreColumns; + + public GenomicProcessorParentImpl(List nodes) { + this.nodes = nodes; + + patientIds = initializePatientIds(); + infoStoreColumns = initializeInfoStoreColumns(); + infoColumnsMeta = initInfoColumnsMeta(); + } + + @Override + public Mono getPatientMask(DistributableQuery distributableQuery) { + Mono result = Flux.just(nodes.toArray(GenomicProcessor[]::new)) + .flatMap(node -> node.getPatientMask(distributableQuery)).reduce(VariantMask::union); + return result; + } + + @Override + public Set patientMaskToPatientIdSet(VariantMask patientMask) { + return patientMask.patientMaskToPatientIdSet(getPatientIds()); + } + + @Override + public VariantMask createMaskForPatientSet(Set patientSubset) { + // all nodes have the same patient set -- + VariantMask result = + nodes.stream().findFirst().map(node -> node.createMaskForPatientSet(patientSubset)).orElseGet(VariantMask::emptyInstance); + return result; + } + + @Override + public Mono> getVariantList(DistributableQuery distributableQuery) { + Mono> result = Flux.just(nodes.toArray(GenomicProcessor[]::new)) + .flatMap(node -> node.getVariantList(distributableQuery)).reduce((variantList1, variantList2) -> { + Set mergedResult = new HashSet<>(variantList1.size() + variantList2.size()); + mergedResult.addAll(variantList1); + mergedResult.addAll(variantList2); + return mergedResult; + }); + return result; + } + + @Override + public List getPatientIds() { + return patientIds; + } + + private List initializePatientIds() { + List patientIds = Flux.just(nodes.toArray(GenomicProcessor[]::new)) + .flatMap(node -> Mono.fromCallable(node::getPatientIds).subscribeOn(Schedulers.boundedElastic())) + .reduce((patientIds1, patientIds2) -> { + if (patientIds1.size() != patientIds2.size()) { + throw new IllegalStateException("Patient lists from partitions do not match"); + } else { + for (int i = 0; i < patientIds1.size(); i++) { + if (!patientIds1.get(i).equals(patientIds2.get(i))) { + throw new IllegalStateException("Patient lists from partitions do not match"); + } + } + } + return patientIds1; + }).block(); + + return patientIds; + } + + @Override + public Optional getMasks(String path, VariantBucketHolder variantMasksVariantBucketHolder) { + // TODO: test. only used in variant explorer + for (GenomicProcessor node : nodes) { + Optional masks = node.getMasks(path, variantMasksVariantBucketHolder); + if (masks.isPresent()) { + return masks; + } + } + return Optional.empty(); + } + + @Override + public Set getInfoStoreColumns() { + return infoStoreColumns; + } + + private Set initializeInfoStoreColumns() { + return nodes.parallelStream().map(GenomicProcessor::getInfoStoreColumns).flatMap(Set::stream).collect(Collectors.toSet()); + } + + @Override + public Set getInfoStoreValues(String conceptPath) { + return infoStoreValuesCache.getUnchecked(conceptPath); + } + + @Override + public List getInfoColumnMeta() { + return infoColumnsMeta; + } + + @Override + public Map> getVariantMetadata(Collection variantList) { + ConcurrentHashMap> result = new ConcurrentHashMap<>(); + nodes.stream().map(node -> node.getVariantMetadata(variantList)).forEach(variantMap -> { + variantMap.entrySet().forEach(entry -> { + Set metadata = result.get(entry.getKey()); + if (metadata != null) { + metadata.addAll(entry.getValue()); + } else { + result.put(entry.getKey(), new HashSet<>(entry.getValue())); + } + }); + }); + return result; + } + + private List initInfoColumnsMeta() { + return nodes.parallelStream().map(GenomicProcessor::getInfoColumnMeta).map(HashSet::new).flatMap(Set::stream) + .collect(Collectors.toList()); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorPatientMergingParentImpl.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorPatientMergingParentImpl.java new file mode 100644 index 000000000..15693bf1b --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorPatientMergingParentImpl.java @@ -0,0 +1,174 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import com.google.common.cache.CacheBuilder; +import com.google.common.cache.CacheLoader; +import com.google.common.cache.LoadingCache; +import com.google.common.collect.ImmutableList; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.*; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import reactor.core.publisher.Flux; +import reactor.core.publisher.Mono; +import reactor.core.scheduler.Schedulers; + +import java.util.*; +import java.util.stream.Collectors; + +public class GenomicProcessorPatientMergingParentImpl implements GenomicProcessor { + + private static Logger log = LoggerFactory.getLogger(GenomicProcessorPatientMergingParentImpl.class); + + private final List nodes; + + private final LoadingCache> infoStoreValuesCache = CacheBuilder.newBuilder().build(new CacheLoader<>() { + @Override + public Set load(String conceptPath) { + return nodes.parallelStream().map(node -> node.getInfoStoreValues(conceptPath)).flatMap(Set::stream) + .collect(Collectors.toSet()); + } + }); + + private final List infoColumnsMeta; + + private final List patientIds; + private final Set infoStoreColumns; + + public GenomicProcessorPatientMergingParentImpl(List nodes) { + this.nodes = nodes; + + patientIds = initializePatientIds(); + infoStoreColumns = initializeInfoStoreColumns(); + infoColumnsMeta = initInfoColumnsMeta(); + } + + private class SizedResult { + private final T result; + private final int size; + + public T getResult() { + return result; + } + + public int getSize() { + return size; + } + + public SizedResult(T result, int size) { + this.result = result; + this.size = size; + } + } + + @Override + public Mono getPatientMask(DistributableQuery distributableQuery) { + Mono result = Flux.just(nodes.toArray(GenomicProcessor[]::new)).flatMapSequential(node -> { + return node.getPatientMask(distributableQuery).map(mask -> { + return new SizedResult<>(mask, node.getPatientIds().size()); + }); + }).reduce(this::appendMask).map(SizedResult::getResult); + return result; + } + + /** + * A little bit of a hack for now since the masks don't have sizes at this point and they are needed to merge + */ + private SizedResult appendMask(SizedResult mask1, SizedResult mask2) { + VariantMask variantMask = VariableVariantMasks.appendMask(mask1.result, mask2.result, mask1.size, mask2.size); + return new SizedResult<>(variantMask != null ? variantMask : VariantMask.emptyInstance(), mask1.size + mask2.size); + } + + @Override + public Set patientMaskToPatientIdSet(VariantMask patientMask) { + return patientMask.patientMaskToPatientIdSet(getPatientIds()); + } + + @Override + public VariantMask createMaskForPatientSet(Set patientSubset) { + return nodes.stream().map(node -> new SizedResult<>(node.createMaskForPatientSet(patientSubset), node.getPatientIds().size())) + .reduce(this::appendMask).map(SizedResult::getResult).orElseGet(VariantMask::emptyInstance); + } + + @Override + public Mono> getVariantList(DistributableQuery distributableQuery) { + Mono> result = Flux.just(nodes.toArray(GenomicProcessor[]::new)) + .flatMap(node -> node.getVariantList(distributableQuery)).reduce((variantList1, variantList2) -> { + Set mergedResult = new HashSet<>(variantList1.size() + variantList2.size()); + mergedResult.addAll(variantList1); + mergedResult.addAll(variantList2); + return mergedResult; + }); + return result; + } + + @Override + public List getPatientIds() { + return patientIds; + } + + private List initializePatientIds() { + List result = Flux.just(nodes.toArray(GenomicProcessor[]::new)) + .flatMapSequential(node -> Mono.fromCallable(node::getPatientIds).subscribeOn(Schedulers.boundedElastic())) + .reduce((list1, list2) -> { + List concatenatedList = new ArrayList<>(list1); + concatenatedList.addAll(list2); + return concatenatedList; + }).block(); + Set distinctPatientIds = new HashSet<>(result); + if (distinctPatientIds.size() != result.size()) { + log.warn((result.size() - distinctPatientIds.size()) + " duplicate patients found in patient partitions"); + } + log.info(distinctPatientIds.size() + " patient ids loaded from patient partitions"); + return ImmutableList.copyOf(result); + } + + @Override + public Optional getMasks(String path, VariantBucketHolder variantMasksVariantBucketHolder) { + return Optional.ofNullable(Flux.just(nodes.toArray(GenomicProcessor[]::new)).flatMapSequential(node -> { + VariableVariantMasks masks = node.getMasks(path, new VariantBucketHolder<>()).orElseGet(VariableVariantMasks::new); + return Mono.fromCallable(() -> new SizedResult<>(masks, node.getPatientIds().size())).subscribeOn(Schedulers.boundedElastic()); + }).reduce((masks1, masks2) -> { + int combinedSize = masks1.size + masks2.size; + VariableVariantMasks appendedMasks = VariableVariantMasks.append(masks1.result, masks1.size, masks2.result, masks2.size); + return new SizedResult<>(appendedMasks, combinedSize); + }).map(SizedResult::getResult).block()); + } + + @Override + public Set getInfoStoreColumns() { + return infoStoreColumns; + } + + private Set initializeInfoStoreColumns() { + return nodes.parallelStream().map(GenomicProcessor::getInfoStoreColumns).flatMap(Set::stream).collect(Collectors.toSet()); + } + + @Override + public Set getInfoStoreValues(String conceptPath) { + return infoStoreValuesCache.getUnchecked(conceptPath); + } + + @Override + public List getInfoColumnMeta() { + return infoColumnsMeta; + } + + @Override + public Map> getVariantMetadata(Collection variantList) { + return nodes.parallelStream().map(node -> node.getVariantMetadata(variantList)).reduce((p1, p2) -> { + Map> mapCopy = new HashMap<>(p1); + + for (Map.Entry> map2Entry : p2.entrySet()) { + Set metadataValues = new HashSet<>(mapCopy.getOrDefault(map2Entry.getKey(), new HashSet<>())); + metadataValues.addAll(map2Entry.getValue()); + mapCopy.put(map2Entry.getKey(), metadataValues); + } + return mapCopy; + }).orElseGet(Map::of); + } + + private List initInfoColumnsMeta() { + return nodes.parallelStream().map(GenomicProcessor::getInfoColumnMeta).map(HashSet::new).flatMap(Set::stream) + .collect(Collectors.toList()); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/HpdsProcessor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/HpdsProcessor.java new file mode 100644 index 000000000..bbd48684b --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/HpdsProcessor.java @@ -0,0 +1,14 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; + +public interface HpdsProcessor { + /** + * This should return a String array of the columns that will be exported in a DATAFRAME or COUNT type query. default is NULL. + * @param query + * @return + */ + String[] getHeaderRow(Query query); + + void runQuery(Query query, AsyncResult asyncResult); +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/MultiValueQueryProcessor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/MultiValueQueryProcessor.java new file mode 100644 index 000000000..ae43b067f --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/MultiValueQueryProcessor.java @@ -0,0 +1,111 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import com.google.common.collect.Lists; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.KeyAndValue; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Component; + +import java.util.*; +import java.util.concurrent.ConcurrentHashMap; +import java.util.stream.Collectors; + +@Component +public class MultiValueQueryProcessor implements HpdsProcessor { + + public static final String PATIENT_ID_FIELD_NAME = "patient_id"; + private final int idBatchSize; + private final AbstractProcessor abstractProcessor; + + private Logger log = LoggerFactory.getLogger(MultiValueQueryProcessor.class); + + + @Autowired + public MultiValueQueryProcessor(AbstractProcessor abstractProcessor, @Value("${ID_BATCH_SIZE:0}") int idBatchSize) { + this.abstractProcessor = abstractProcessor; + this.idBatchSize = idBatchSize; + } + + @Override + public String[] getHeaderRow(Query query) { + String[] header = new String[query.getFields().size() + 1]; + header[0] = PATIENT_ID_FIELD_NAME; + System.arraycopy(query.getFields().toArray(), 0, header, 1, query.getFields().size()); + return header; + } + + @Override + public void runQuery(Query query, AsyncResult result) { + Set idList = abstractProcessor.getPatientSubsetForQuery(query); + log.info("Processing " + idList.size() + " rows for result " + result.getId()); + Lists.partition(new ArrayList<>(idList), idBatchSize).stream().forEach(patientIds -> { + Map>> pathToPatientToValueMap = buildResult(result, query, new TreeSet<>(patientIds)); + List>> fieldValuesPerPatient = patientIds.stream().map(patientId -> { + List> objectStream = Arrays.stream(getHeaderRow(query)).map(field -> { + if (PATIENT_ID_FIELD_NAME.equals(field)) { + return List.of(patientId.toString()); + } else { + return pathToPatientToValueMap.get(field).get(patientId); + } + }).collect(Collectors.toList()); + return objectStream; + }).collect(Collectors.toList()); + result.appendMultiValueResults(fieldValuesPerPatient); + }); + result.closeWriter(); + } + + private Map>> buildResult(AsyncResult result, Query query, TreeSet ids) { + ConcurrentHashMap>> pathToPatientToValueMap = new ConcurrentHashMap<>(); + List columns = + query.getFields().stream().map(abstractProcessor.getDictionary()::get).filter(Objects::nonNull).collect(Collectors.toList()); + List paths = columns.stream().map(ColumnMeta::getName).collect(Collectors.toList()); + int columnCount = paths.size() + 1; + + ArrayList columnIndex = abstractProcessor.useResidentCubesFirst(paths, columnCount); + + // todo: investigate if the parallel stream will thrash the cache if the number of executors is > number of resident cubes + columnIndex.parallelStream().forEach((columnId) -> { + String columnPath = paths.get(columnId - 1); + Map> patientIdToValueMap = processColumn(ids, columnPath); + pathToPatientToValueMap.put(columnPath, patientIdToValueMap); + }); + + return pathToPatientToValueMap; + } + + private Map> processColumn(TreeSet patientIds, String path) { + + Map> patientIdToValueMap = new HashMap<>(); + PhenoCube cube = abstractProcessor.getCube(path); + + KeyAndValue[] cubeValues = cube.sortedByKey(); + + int idPointer = 0; + for (int patientId : patientIds) { + while (idPointer < cubeValues.length) { + int key = cubeValues[idPointer].getKey(); + if (key < patientId) { + idPointer++; + } else if (key == patientId) { + String value = getResultField(cube, cubeValues, idPointer); + patientIdToValueMap.computeIfAbsent(patientId, k -> new ArrayList<>()).add(value); + idPointer++; + } else { + break; + } + } + } + return patientIdToValueMap; + } + + private String getResultField(PhenoCube cube, KeyAndValue[] cubeValues, int idPointer) { + Comparable value = cubeValues[idPointer].getValue(); + return value.toString(); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PatientAndConceptCount.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PatientAndConceptCount.java new file mode 100644 index 000000000..bcbb37c0a --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PatientAndConceptCount.java @@ -0,0 +1,21 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +public class PatientAndConceptCount { + private long patientCount, conceptCount; + + public long getPatientCount() { + return patientCount; + } + + public void setPatientCount(long patientCount) { + this.patientCount = patientCount; + } + + public long getConceptCount() { + return conceptCount; + } + + public void setConceptCount(long conceptCount) { + this.conceptCount = conceptCount; + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PatientVariantJoinHandler.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PatientVariantJoinHandler.java new file mode 100644 index 000000000..0b5db1abb --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PatientVariantJoinHandler.java @@ -0,0 +1,136 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import com.google.common.base.Joiner; +import com.google.common.collect.Lists; +import com.google.common.collect.Sets; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.*; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Component; + +import java.math.BigInteger; +import java.util.*; +import java.util.stream.Collectors; + +public class PatientVariantJoinHandler { + + private static Logger log = LoggerFactory.getLogger(PatientVariantJoinHandler.class); + + private final VariantService variantService; + + public PatientVariantJoinHandler(VariantService variantService) { + this.variantService = variantService; + } + + public VariantMask getPatientIdsForIntersectionOfVariantSets(Set patientSubset, VariantIndex intersectionOfInfoFilters) { + + if (!intersectionOfInfoFilters.isEmpty()) { + Set patientsInScope; + // todo: don't do this every time + Set patientIds = Arrays.asList(variantService.getPatientIds()).stream().map((String id) -> { + return Integer.parseInt(id); + }).collect(Collectors.toSet()); + if (patientSubset != null) { + patientsInScope = Sets.intersection(patientIds, patientSubset); + } else { + // for now, null means there were no phenotypic filters and all patients are eligible + // this should be heavily tested/reconsidered for sharding genomic data by study + patientsInScope = patientIds; + } + + // If genomic data is sharded by studies, it may be possible that the node this is running in does not have genomic + // data for any of the patients in the phenotypic query. In which case, we don't have to look for matching patients + if (patientsInScope.isEmpty()) { + return new VariantMaskSparseImpl(Set.of()); + } + + VariantMask[] matchingPatients = new VariantMask[] {new VariantMaskSparseImpl(Set.of())}; + + Set variantsInScope = intersectionOfInfoFilters.mapToVariantSpec(variantService.getVariantIndex()); + + /* + * // todo: determine ideal ratio to bother with this if (patientsInScope.size() < variantService.getPatientIds().length) { + * variantsInScope = variantService.filterVariantSetForPatientSet(variantsInScope, patientsInScope); } + */ + Collection> values = variantsInScope.stream().collect(Collectors.groupingByConcurrent((variantSpec) -> { + return new VariantSpec(variantSpec).metadata.offset / 1000; + })).values(); + ArrayList> variantBucketsInScope = new ArrayList>(values); + + + // don't error on small result sets (make sure we have at least one element in each partition) + int partitionSize = variantBucketsInScope.size() / Runtime.getRuntime().availableProcessors(); + List>> variantBucketPartitions = + Lists.partition(variantBucketsInScope, partitionSize > 0 ? partitionSize : 1); + + log.debug( + "found " + variantBucketsInScope.size() + " buckets and partitioned those into " + variantBucketPartitions.size() + + " groups" + ); + + VariantMask patientsInScopeMask = new VariantMaskBitmaskImpl(createMaskForPatientSet(patientsInScope)); + for (int x = 0; x < variantBucketPartitions.size() /* && matchingPatients[0].bitCount() < patientsInScopeSize + 4 */; x++) { + List> variantBuckets = variantBucketPartitions.get(x); + variantBuckets.parallelStream().forEach(variantBucket -> { + VariantBucketHolder bucketCache = new VariantBucketHolder<>(); + List missingVariants = new ArrayList<>(); + variantBucket.forEach(variantSpec -> { + Optional variantMask = variantService.getMasks(variantSpec, bucketCache); + variantMask.ifPresentOrElse(masks -> { + VariantMask heterozygousMask = masks.heterozygousMask; + VariantMask homozygousMask = masks.homozygousMask; + if (heterozygousMask != null) { + synchronized (matchingPatients) { + matchingPatients[0] = matchingPatients[0].union(heterozygousMask); + } + } + if (homozygousMask != null) { + synchronized (matchingPatients) { + matchingPatients[0] = matchingPatients[0].union(homozygousMask); + } + } + }, () -> missingVariants.add(variantSpec)); + }); + if (!missingVariants.isEmpty()) { + log.debug(missingVariants.size() + " variant masks not found"); + log.debug( + "Variants missing masks: " + + Joiner.on(",").join(missingVariants.subList(0, Math.min(100, missingVariants.size()))) + ); + } + }); + } + return matchingPatients[0].intersection(patientsInScopeMask); + } else { + // This will happen regularly, for example if someone is searching for a gene that is not on this partition + log.debug("No matches found for info filters."); + return new VariantMaskSparseImpl(Set.of()); + } + } + + // todo: return VariantMask + public BigInteger createMaskForPatientSet(Set patientSet) { + Set patientSubset = patientSet; + if (patientSet == null) { + patientSubset = Arrays.asList(variantService.getPatientIds()).stream().map((String id) -> { + return Integer.parseInt(id); + }).collect(Collectors.toSet()); + } + StringBuilder builder = new StringBuilder("11"); // variant bitmasks are bookended with '11' + + for (int i = variantService.getPatientIds().length - 1; i >= 0; i--) { + Integer idInt = Integer.parseInt(variantService.getPatientIds()[i]); + if (patientSubset.contains(idInt)) { + builder.append("1"); + } else { + builder.append("0"); + } + } + builder.append("11"); // masks are bookended with '11' set this so we don't count those + + BigInteger patientMasks = new BigInteger(builder.toString(), 2); + return patientMasks; + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PhenotypeMetaStore.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PhenotypeMetaStore.java new file mode 100644 index 000000000..2ede405d1 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PhenotypeMetaStore.java @@ -0,0 +1,110 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import com.google.common.cache.CacheBuilder; +import com.google.common.cache.CacheLoader; +import com.google.common.cache.LoadingCache; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Component; + +import java.io.FileInputStream; +import java.io.IOException; +import java.io.ObjectInputStream; +import java.util.*; +import java.util.concurrent.ExecutionException; +import java.util.stream.Collectors; +import java.util.zip.GZIPInputStream; + +@Component +public class PhenotypeMetaStore { + + private static final Logger log = LoggerFactory.getLogger(PhenotypeMetaStore.class); + + + // Todo: Test using hash map/sets here + private TreeMap metaStore; + + private TreeSet patientIds; + + private final LoadingCache> childConceptCache; + + public TreeMap getMetaStore() { + return metaStore; + } + + public TreeSet getPatientIds() { + return patientIds; + } + + public Set getColumnNames() { + return metaStore.keySet(); + } + + public ColumnMeta getColumnMeta(String columnName) { + return metaStore.get(columnName); + } + + public Set loadChildConceptPaths(String conceptPath) { + return metaStore.keySet().stream().filter(column -> column.startsWith(conceptPath)).collect(Collectors.toSet()); + } + + public Set getChildConceptPaths(String conceptPath) { + try { + return childConceptCache.get(conceptPath); + } catch (ExecutionException e) { + throw new RuntimeException(e); + } + } + + @Autowired + @SuppressWarnings("unchecked") + public PhenotypeMetaStore( + @Value("${HPDS_DATA_DIRECTORY:/opt/local/hpds/}") String hpdsDataDirectory, + @Value("${CHILD_CONCEPT_CACHE_SIZE:500}") int childConceptCacheSize + ) { + String columnMetaFile = hpdsDataDirectory + "columnMeta.javabin"; + try (ObjectInputStream objectInputStream = new ObjectInputStream(new GZIPInputStream(new FileInputStream(columnMetaFile)))) { + TreeMap _metastore = (TreeMap) objectInputStream.readObject(); + TreeMap metastoreScrubbed = new TreeMap<>(); + for (Map.Entry entry : _metastore.entrySet()) { + metastoreScrubbed.put(entry.getKey().replaceAll("\\ufffd", ""), entry.getValue()); + } + metaStore = metastoreScrubbed; + patientIds = (TreeSet) objectInputStream.readObject(); + } catch (IOException | ClassNotFoundException e) { + log.warn("************************************************"); + log.warn("Could not load metastore", e); + log.warn( + "If you meant to include phenotype data of any kind, please check that the file " + columnMetaFile + + " exists and is readable by the service." + ); + log.warn("************************************************"); + metaStore = new TreeMap<>(); + patientIds = new TreeSet<>(); + } + childConceptCache = CacheBuilder.newBuilder().maximumSize(childConceptCacheSize).build(new CacheLoader<>() { + @Override + public Set load(String key) { + return loadChildConceptPaths(key); + } + }); + } + + public PhenotypeMetaStore( + TreeMap metaStore, TreeSet patientIds, + @Value("${CHILD_CONCEPT_CACHE_SIZE:500}") int childConceptCacheSize + ) { + this.metaStore = metaStore; + this.patientIds = patientIds; + + this.childConceptCache = CacheBuilder.newBuilder().maximumSize(childConceptCacheSize).build(new CacheLoader<>() { + @Override + public Set load(String key) { + return loadChildConceptPaths(key); + } + }); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/Processor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/Processor.java new file mode 100644 index 000000000..45af248d3 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/Processor.java @@ -0,0 +1,10 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import edu.harvard.hms.dbmi.avillach.hpds.exception.NotEnoughMemoryException; + +public interface Processor { + + public void runQuery(Query query, AsyncResult asyncResult) throws NotEnoughMemoryException; + +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/QueryProcessor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/QueryProcessor.java new file mode 100644 index 000000000..a21978afe --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/QueryProcessor.java @@ -0,0 +1,208 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import java.nio.ByteBuffer; +import java.util.*; +import java.util.stream.Collectors; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genomic.VariantUtils; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariableVariantMasks; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.common.collect.Lists; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.KeyAndValue; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Component; + +/** + * This class handles DATAFRAME export queries for HPDS. + * @author nchu + * + */ +@Component +public class QueryProcessor implements HpdsProcessor { + + private static final byte[] EMPTY_STRING_BYTES = "".getBytes(); + private Logger log = LoggerFactory.getLogger(QueryProcessor.class); + + private final int idBatchSize; + + private final AbstractProcessor abstractProcessor; + + @Autowired + public QueryProcessor(AbstractProcessor abstractProcessor, @Value("${ID_BATCH_SIZE:0}") int idBatchSize) { + this.abstractProcessor = abstractProcessor; + this.idBatchSize = idBatchSize; + } + + @Override + public String[] getHeaderRow(Query query) { + String[] header = new String[query.getFields().size() + 1]; + header[0] = "Patient ID"; + System.arraycopy(query.getFields().toArray(), 0, header, 1, query.getFields().size()); + return header; + } + + public void runQuery(Query query, AsyncResult result) { + Set idList = abstractProcessor.getPatientSubsetForQuery(query); + log.info("Processing " + idList.size() + " rows for result " + result.getId()); + Lists.partition(new ArrayList<>(idList), idBatchSize).parallelStream().map(list -> buildResult(result, query, new TreeSet<>(list))) + .sequential().forEach(result::appendResultStore); + } + + + private ResultStore buildResult(AsyncResult result, Query query, TreeSet ids) { + List columns = + query.getFields().stream().map(abstractProcessor.getDictionary()::get).filter(Objects::nonNull).collect(Collectors.toList()); + List paths = columns.stream().map(ColumnMeta::getName).collect(Collectors.toList()); + int columnCount = paths.size() + 1; + + ArrayList columnIndex = abstractProcessor.useResidentCubesFirst(paths, columnCount); + ResultStore results = new ResultStore(result.getId(), columns, ids); + + columnIndex.parallelStream().forEach((column) -> { + clearColumn(paths, ids, results, column); + processColumn(paths, ids, results, column); + }); + + return results; + } + + private void clearColumn(List paths, TreeSet ids, ResultStore results, Integer x) { + String path = paths.get(x - 1); + if (VariantUtils.pathIsVariantSpec(path)) { + ByteBuffer doubleBuffer = ByteBuffer.allocate(Double.BYTES); + int idInSubsetPointer = 0; + for (int id : ids) { + writeVariantNullResultField(results, x, doubleBuffer, idInSubsetPointer); + idInSubsetPointer++; + } + } else { + PhenoCube cube = abstractProcessor.getCube(path); + ByteBuffer doubleBuffer = ByteBuffer.allocate(Double.BYTES); + int idInSubsetPointer = 0; + for (int id : ids) { + writeNullResultField(results, x, cube, doubleBuffer, idInSubsetPointer); + idInSubsetPointer++; + } + } + } + + private void processColumn(List paths, TreeSet ids, ResultStore results, Integer x) { + String path = paths.get(x - 1); + if (VariantUtils.pathIsVariantSpec(path)) { + // todo: confirm this entire if block is even used. I don't think it is + Optional masks = abstractProcessor.getMasks(path, new VariantBucketHolder<>()); + List patientIds = abstractProcessor.getPatientIds(); + int idPointer = 0; + + ByteBuffer doubleBuffer = ByteBuffer.allocate(Double.BYTES); + int idInSubsetPointer = 0; + for (int id : ids) { + while (idPointer < patientIds.size()) { + int key = Integer.parseInt(patientIds.get(idPointer)); + if (key < id) { + idPointer++; + } else if (key == id) { + idPointer = writeVariantResultField(results, x, masks, idPointer, idInSubsetPointer); + break; + } else { + writeVariantNullResultField(results, x, doubleBuffer, idInSubsetPointer); + break; + } + } + idInSubsetPointer++; + } + } else { + PhenoCube cube = abstractProcessor.getCube(path); + + KeyAndValue[] cubeValues = cube.sortedByKey(); + + int idPointer = 0; + + ByteBuffer doubleBuffer = ByteBuffer.allocate(Double.BYTES); + int idInSubsetPointer = 0; + for (int id : ids) { + while (idPointer < cubeValues.length) { + int key = cubeValues[idPointer].getKey(); + if (key < id) { + idPointer++; + } else if (key == id) { + idPointer = writeResultField(results, x, cube, cubeValues, idPointer, doubleBuffer, idInSubsetPointer); + break; + } else { + writeNullResultField(results, x, cube, doubleBuffer, idInSubsetPointer); + break; + } + } + idInSubsetPointer++; + } + } + } + + private void writeVariantNullResultField(ResultStore results, Integer x, ByteBuffer doubleBuffer, int idInSubsetPointer) { + byte[] valueBuffer = null; + valueBuffer = EMPTY_STRING_BYTES; + results.writeField(x, idInSubsetPointer, valueBuffer); + } + + private int writeVariantResultField( + ResultStore results, Integer x, Optional variantMasks, int idPointer, int idInSubsetPointer + ) { + byte[] valueBuffer = variantMasks.map(masks -> { + if (masks.heterozygousMask != null && masks.heterozygousMask.testBit(idPointer)) { + return "0/1".getBytes(); + } else if (masks.homozygousMask != null && masks.homozygousMask.testBit(idPointer)) { + return "1/1".getBytes(); + } else { + return "0/0".getBytes(); + } + }).orElse("".getBytes()); + results.writeField(x, idInSubsetPointer, valueBuffer); + return idPointer; + } + + private int writeResultField( + ResultStore results, Integer x, PhenoCube cube, KeyAndValue[] cubeValues, int idPointer, ByteBuffer doubleBuffer, + int idInSubsetPointer + ) { + byte[] valueBuffer; + Comparable value = cubeValues[idPointer++].getValue(); + if (cube.isStringType()) { + valueBuffer = value.toString().getBytes(); + } else { + valueBuffer = doubleBuffer.putDouble((Double) value).array(); + doubleBuffer.clear(); + } + results.writeField(x, idInSubsetPointer, valueBuffer); + return idPointer; + } + + /** + * Correctly handle null records. A numerical value should be a NaN if it is missing to distinguish from a zero. A String based + * value(categorical) should be empty instead of null because the word null might be a valid value. + * + * @param results + * @param x + * @param cube + * @param doubleBuffer + * @param idInSubsetPointer + */ + private void writeNullResultField(ResultStore results, Integer x, PhenoCube cube, ByteBuffer doubleBuffer, int idInSubsetPointer) { + byte[] valueBuffer = null; + if (cube.isStringType()) { + valueBuffer = EMPTY_STRING_BYTES; + } else { + Double nullDouble = Double.NaN; + valueBuffer = doubleBuffer.putDouble(nullDouble).array(); + doubleBuffer.clear(); + } + results.writeField(x, idInSubsetPointer, valueBuffer); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/ResultStore.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/ResultStore.java new file mode 100644 index 000000000..2c5c52d52 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/ResultStore.java @@ -0,0 +1,173 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import java.io.IOException; +import java.nio.ByteBuffer; +import java.text.DecimalFormat; +import java.util.*; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.exception.NotEnoughMemoryException; +import edu.harvard.hms.dbmi.avillach.hpds.exception.ResultSetTooLargeException; + +/** + * This class handles composing a segment of a data export file in memory. The goal here is to prevent memory errors during data export and + * maximize concurrency for processing concepts. + * + * Each ResultStore instance allocates a byte[] called resultArray. The size of this array is: + * + * (maximum width of a row in the results) * (number of patients in the result segment) + * + * The maximum width of a row in the result is the sum of the maximum widths in bytes of all columns. This width is stored when the data is + * loaded initially in the column meta for the concept. + * + * If the size of the array exceeds the maximum size for an array(Integer.MAX_VALUE) then a {@link ResultSetTooLargeException} is thrown + * with a message that suggests the user select fewer fields. + * + * If the size of the resultArray exceeds the available heap in the JVM a NotEnoughMemoryException is thrown. The only recourse here is to + * increase the amount of available heap or make the BATCH_SIZE system property smaller. One way to increase the amount of available heap is + * to reduce the CACHE_SIZE system property, but that has to be balanced against the performance of non-export queries. Finding the ideal + * settings for these properties is a trial and error process for each dataset and user-base. + * + * The resultArray approach allows us to build the entire CSV segment concurrently for multiple concepts without any synchronization + * overhead. Each concept is written into a dedicated fixed-width region of the resultArray. These regions do not overlap and a single + * thread is used for each concept, so there are never two threads writing to the same location at the same time. + * + * The data is then read out of this fixed width structure into a String[] at the time it is written to a temp file for the result by the + * {@link ResultStoreStream} class. + * + */ +public class ResultStore { + + private static Logger log = LoggerFactory.getLogger(ResultStore.class); + + private List columns; + int rowWidth; + private int numRows; + + private static final ColumnMeta PATIENT_ID_COLUMN_META = + new ColumnMeta().setColumnOffset(0).setName("PatientId").setWidthInBytes(Integer.BYTES); + byte[] resultArray; + + /** + * + * @param resultId The result id here is only used for logging + * @param columns The ColumnMeta entries involed in the result, these are used to calculate rowWidth + * @param ids The subject ids for in the current batch of the result + * @throws NotEnoughMemoryException If the size of available heap cannot support a byte array of size (rowWidth x numRows) + */ + public ResultStore(String resultId, List columns, TreeSet ids) throws NotEnoughMemoryException { + this.columns = new ArrayList(); + this.numRows = ids.size(); + this.getColumns().add(PATIENT_ID_COLUMN_META); + int rowWidth = Integer.BYTES; + for (ColumnMeta column : columns) { + column.setColumnOffset(rowWidth); + rowWidth += column.getWidthInBytes(); + this.getColumns().add(column); + } + this.rowWidth = rowWidth; + if (1L * this.rowWidth * this.getNumRows() > Integer.MAX_VALUE) { + throw new ResultSetTooLargeException((1L * this.rowWidth * this.getNumRows()) / (Integer.MAX_VALUE / 2)); + } + try { + log.info("Allocating result array : " + resultId); + resultArray = new byte[this.rowWidth * this.getNumRows()]; + } catch (Error e) { + throw new NotEnoughMemoryException(); + } + log.info("Store created for " + this.getNumRows() + " rows and " + columns.size() + " columns "); + int x = 0; + for (Integer id : ids) { + writeField(0, x++, ByteBuffer.allocate(Integer.BYTES).putInt(id).array()); + } + } + + /** + * Copies fieldValue into the resultArray of this instance using System.arraycopy + * @param column + * @param row + * @param fieldValue + */ + public void writeField(int column, int row, byte[] fieldValue) { + int offset = getFieldOffset(row, column); + try { + System.arraycopy(fieldValue, 0, resultArray, offset, fieldValue.length); + } catch (Exception e) { + log.info( + "Exception caught writing field : " + column + ", " + row + " : " + fieldValue.length + " bytes into result at offset " + + offset + " of " + resultArray.length + ); + throw e; + } + } + + /** + * Finds the resultArray offset of the passed in row and column + * @param row + * @param column + * @return + */ + private int getFieldOffset(int row, int column) { + int rowOffset = row * rowWidth; + int columnOffset = getColumns().get(column).getColumnOffset(); + return rowOffset + columnOffset; + } + + ByteBuffer wrappedResultArray; + + /** + * Populate + * + * @param rowNumber + * @param row + * @throws IOException + */ + public void readRowIntoStringArray(int rowNumber, int[] columnWidths, String[] row) { + if (wrappedResultArray == null) { + wrappedResultArray = ByteBuffer.wrap(resultArray); + } + row[0] = wrappedResultArray.getInt(getFieldOffset(rowNumber, 0)) + ""; + + stringifyRow(rowNumber, columnWidths, row); + } + + /** + * Copy each field of a single row from the resultArray into a String[] to be written out to the CSV + * + * @param rowNumber row number to copy + * @param row String[] to populate with field values + * @param columnBuffers a set of buffers corresponding to each column where each buffer is {@link ColumnMeta.widthInBytes} bytes + */ + private void stringifyRow(int rowNumber, int[] columnWidths, String[] row) { + for (int x = 1; x < row.length; x++) { + ColumnMeta columnMeta = getColumns().get(x); + int fieldOffset = getFieldOffset(rowNumber, x); + if (columnMeta.isCategorical()) { + stringifyString(row, columnWidths, x, fieldOffset); + } else { + stringifyDouble(row, x, fieldOffset); + } + } + } + + DecimalFormat decimalFormat = new DecimalFormat("########.####"); + + private void stringifyDouble(String[] row, int x, int fieldOffset) { + row[x] = Double.valueOf(wrappedResultArray.getDouble(fieldOffset)).toString(); + } + + private void stringifyString(String[] row, int[] columnWidths, int x, int fieldOffset) { + row[x] = new String(Arrays.copyOfRange(resultArray, fieldOffset, fieldOffset + columnWidths[x])).trim(); + } + + public int getNumRows() { + return numRows; + } + + public List getColumns() { + return columns; + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/ResultStoreStream.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/ResultStoreStream.java new file mode 100644 index 000000000..e0558190a --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/ResultStoreStream.java @@ -0,0 +1,130 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import java.io.*; +import java.nio.file.Path; +import java.util.ArrayList; +import java.util.List; +import edu.harvard.hms.dbmi.avillach.hpds.processing.io.CsvWriter; +import edu.harvard.hms.dbmi.avillach.hpds.processing.io.ResultWriter; + +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; + +public class ResultStoreStream extends InputStream { + + private ResultWriter writer; + private InputStream in; + private int value; + private boolean streamIsClosed = false; + private int numRows; + private String[] originalHeader; + + public ResultStoreStream(String[] header, ResultWriter writer) throws IOException { + this.writer = writer; + this.originalHeader = header; + writeHeader(this.originalHeader); + numRows = 0; + } + + private void writeHeader(String[] header) { + writer.writeHeader(header); + } + + public void appendResultStore(ResultStore results) { + int batchSize = 100; + List entries = new ArrayList<>(batchSize); + for (int x = 0; x < batchSize; x++) { + entries.add(new String[results.getColumns().size()]); + } + writeResultsToTempFile(results, batchSize, entries); + } + + /** + * A more compact method to append data to the temp file without making assumptions about the composition. + * @param entries + */ + public void appendResults(List entries) { + writer.writeEntity(entries); + } + + /** + * Appending data to the writer that supports multiple values per patient/variable combination + */ + public void appendMultiValueResults(List>> entries) { + writer.writeMultiValueEntity(entries); + } + + private List writeResultsToTempFile(ResultStore results, int batchSize, List entries) { + + List columns = results.getColumns(); + int[] columnWidths = new int[columns.size()]; + for (int x = 0; x < columns.size(); x++) { + columnWidths[x] = columns.get(x).getWidthInBytes(); + } + + for (int x = 0; x < (results.getNumRows()); x += batchSize) { + int rowsInBatch = Math.min(batchSize, results.getNumRows() - x); + for (int y = 0; y < rowsInBatch; y++) { + results.readRowIntoStringArray(y + x, columnWidths, entries.get(y)); + } + if (rowsInBatch < batchSize) { + entries = entries.subList(0, rowsInBatch); + } + writer.writeEntity(entries); + numRows += rowsInBatch; + } + return entries; + } + + public void close() { + try { + in.close(); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + } + + public void open() { + try { + in = new BufferedInputStream(new FileInputStream(writer.getFile().getAbsolutePath()), 1024 * 1024 * 8); + streamIsClosed = false; + } catch (FileNotFoundException e) { + throw new RuntimeException("temp file for result not found : " + writer.getFile().getAbsolutePath()); + } + } + + + + @Override + public int read() throws IOException { + if (streamIsClosed) { + return -1; + } + value = in.read(); + if (value == -1) { + in.close(); + streamIsClosed = true; + } + return value; + } + + public int getNumRows() { + return numRows; + } + + public long estimatedSize() { + return writer.getFile().length(); + } + + public void closeWriter() { + writer.close(); + } + + public File getFile() { + return writer.getFile(); + } + + public Path getTempFilePath() { + return Path.of(getFile().getAbsolutePath()); + } + +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/SparseVariantIndex.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/SparseVariantIndex.java new file mode 100644 index 000000000..0f78d915a --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/SparseVariantIndex.java @@ -0,0 +1,71 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import com.google.common.collect.Sets; + +import java.util.Objects; +import java.util.Set; +import java.util.concurrent.ConcurrentHashMap; + +public class SparseVariantIndex extends VariantIndex { + + private final Set variantIds; + + public SparseVariantIndex(Set variantIds) { + this.variantIds = variantIds; + } + + public Set getVariantIds() { + return variantIds; + } + + @Override + public VariantIndex union(VariantIndex variantIndex) { + if (variantIndex instanceof SparseVariantIndex) { + return new SparseVariantIndex(Sets.union(((SparseVariantIndex) variantIndex).variantIds, variantIds)); + } else if (variantIndex instanceof DenseVariantIndex) { + return union(this, (DenseVariantIndex) variantIndex); + } else { + throw new IllegalArgumentException("Union not implemented between SparseVariantIndex and " + variantIndex.getClass()); + } + } + + @Override + public VariantIndex intersection(VariantIndex variantIndex) { + if (variantIndex instanceof SparseVariantIndex) { + return new SparseVariantIndex(Sets.intersection(((SparseVariantIndex) variantIndex).variantIds, variantIds)); + } else if (variantIndex instanceof DenseVariantIndex) { + return intersection(this, (DenseVariantIndex) variantIndex); + } else { + throw new IllegalArgumentException("Intersection not implemented between SparseVariantIndex and " + variantIndex.getClass()); + } + } + + /** + * Converts a set of variant IDs to a set of String representations of variant spec. This implementation looks wonky, but performs much + * better than other more obvious approaches (ex: Collectors.toSet()) on large sets. + */ + @Override + public Set mapToVariantSpec(String[] variantIndex) { + ConcurrentHashMap setMap = new ConcurrentHashMap<>(variantIds.size()); + variantIds.stream().parallel().forEach(index -> setMap.put(variantIndex[index], "")); + return setMap.keySet(); + } + + @Override + public boolean isEmpty() { + return variantIds.isEmpty(); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + SparseVariantIndex that = (SparseVariantIndex) o; + return Objects.equals(variantIds, that.variantIds); + } + + @Override + public int hashCode() { + return Objects.hash(variantIds); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantIndex.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantIndex.java new file mode 100644 index 000000000..4e772678e --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantIndex.java @@ -0,0 +1,35 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import com.google.common.collect.Sets; +import com.google.errorprone.annotations.Var; + +import java.util.Set; +import java.util.stream.Collectors; + +public abstract class VariantIndex { + public abstract VariantIndex union(VariantIndex variantIndex); + + public abstract VariantIndex intersection(VariantIndex variantIndex); + + public abstract Set mapToVariantSpec(String[] variantIndex); + + public abstract boolean isEmpty(); + + protected VariantIndex union(SparseVariantIndex sparseVariantIndex, DenseVariantIndex denseVariantIndex) { + boolean[] copy = new boolean[denseVariantIndex.getVariantIndexMask().length]; + System.arraycopy(denseVariantIndex.getVariantIndexMask(), 0, copy, 0, copy.length); + sparseVariantIndex.getVariantIds().forEach(id -> copy[id] = true); + return new DenseVariantIndex(copy); + } + + + protected VariantIndex intersection(SparseVariantIndex sparseVariantIndex, DenseVariantIndex denseVariantIndex) { + Set intersection = sparseVariantIndex.getVariantIds().stream().filter(id -> denseVariantIndex.getVariantIndexMask()[id]) + .collect(Collectors.toSet()); + return new SparseVariantIndex(intersection); + } + + public static VariantIndex empty() { + return new SparseVariantIndex(Set.of()); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantIndexCache.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantIndexCache.java new file mode 100644 index 000000000..01be22ede --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantIndexCache.java @@ -0,0 +1,93 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import com.google.common.cache.CacheBuilder; +import com.google.common.cache.CacheLoader; +import com.google.common.cache.LoadingCache; +import com.google.common.cache.Weigher; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.FileBackedByteIndexedInfoStore; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Component; + +import java.io.IOException; +import java.util.Arrays; +import java.util.HashSet; +import java.util.Map; +import java.util.Set; + +public class VariantIndexCache { + + private static Logger log = LoggerFactory.getLogger(VariantIndexCache.class); + + private final LoadingCache infoCache; + + private final String[] variantIndex; + + private final Map infoStores; + + private static final String COLUMN_AND_KEY_DELIMITER = "_____"; + /** + * The maximum percentage of variants to use a sparse index vs a dense index. See {@link VariantIndex} + */ + private static final double MAX_SPARSE_INDEX_RATIO = 0.1; + + public VariantIndexCache(String[] variantIndex, Map infoStores) { + this.variantIndex = variantIndex; + this.infoStores = infoStores; + this.infoCache = CacheBuilder.newBuilder().weigher(weigher).maximumWeight(10000000000000L).build(cacheLoader); + } + + public VariantIndex get(String key) { + return infoCache.getUnchecked(key); + } + + public VariantIndex get(String column, String key) { + return infoCache.getUnchecked(columnAndKey(column, key)); + } + + private String columnAndKey(String column, String key) { + return column + COLUMN_AND_KEY_DELIMITER + key; + } + + private final Weigher weigher = new Weigher() { + @Override + public int weigh(String key, VariantIndex value) { + if (value instanceof DenseVariantIndex) { + return ((DenseVariantIndex) value).getVariantIndexMask().length; + } else if (value instanceof SparseVariantIndex) { + return ((SparseVariantIndex) value).getVariantIds().size(); + } else { + throw new IllegalArgumentException("Unknown VariantIndex implementation: " + value.getClass()); + } + } + }; + private final CacheLoader cacheLoader = new CacheLoader<>() { + @Override + public VariantIndex load(String infoColumn_valueKey) throws IOException { + log.debug("Calculating value for cache for key " + infoColumn_valueKey); + long time = System.currentTimeMillis(); + String[] column_and_value = infoColumn_valueKey.split(COLUMN_AND_KEY_DELIMITER); + Integer[] variantIndexIntArray = infoStores.get(column_and_value[0]).getAllValues().get(column_and_value[1]); + + if ((double) variantIndexIntArray.length / (double) variantIndex.length < MAX_SPARSE_INDEX_RATIO) { + Set variantIds = new HashSet<>(); + for (Integer variantIndex : variantIndexIntArray) { + variantIds.add(variantIndex); + } + return new SparseVariantIndex(variantIds); + } else { + boolean[] variantIndexArray = new boolean[variantIndex.length]; + int x = 0; + for (Integer variantIndex : variantIndexIntArray) { + if (variantIndex >= 0) { + variantIndexArray[variantIndex] = true; + } + } + log.debug("Cache value for key " + infoColumn_valueKey + " calculated in " + (System.currentTimeMillis() - time) + " ms"); + return new DenseVariantIndex(variantIndexArray); + } + } + }; + +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantListProcessor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantListProcessor.java new file mode 100644 index 000000000..a9ec81eea --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantListProcessor.java @@ -0,0 +1,293 @@ + +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import java.io.*; +import java.util.*; +import java.util.stream.Collectors; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.*; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import edu.harvard.hms.dbmi.avillach.hpds.exception.NotEnoughMemoryException; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Component; + +@Component +public class VariantListProcessor implements HpdsProcessor { + + private final GenomicProcessor genomicProcessor; + + private static Logger log = LoggerFactory.getLogger(VariantListProcessor.class); + + private final boolean vcfExcerptEnabled; + private final boolean aggregateVcfExcerptEnabled; + private final boolean variantListEnabled; + private final String idCubeName; + + private final AbstractProcessor abstractProcessor; + private final ColumnSorter columnSorter; + + + @Autowired + public VariantListProcessor( + AbstractProcessor abstractProcessor, GenomicProcessor genomicProcessor, ColumnSorter columnSorter, + @Value("${VCF_EXCERPT_ENABLED:false}") boolean vcfExcerptEnabled, + @Value("${AGGREGATE_VCF_EXCERPT_ENABLED:false}") boolean aggregateVcfExcerptEnabled, + @Value("${ID_CUBE_NAME:NONE}") String idCubeName + ) { + this.abstractProcessor = abstractProcessor; + this.genomicProcessor = genomicProcessor; + this.columnSorter = columnSorter; + + this.vcfExcerptEnabled = vcfExcerptEnabled; + // always enable aggregate queries if full queries are permitted. + this.aggregateVcfExcerptEnabled = this.vcfExcerptEnabled || aggregateVcfExcerptEnabled; + variantListEnabled = this.vcfExcerptEnabled || this.aggregateVcfExcerptEnabled; + this.idCubeName = idCubeName; + + } + + @Override + public void runQuery(Query query, AsyncResult asyncResult) throws NotEnoughMemoryException { + throw new RuntimeException("Not implemented"); + } + + /** + * The incomingQuery is a normal query, the same as COUNT result type. + * + * This should not actually do any filtering based on bitmasks, just INFO columns. + * + * @param query + * @return a List of VariantSpec strings that would be eligible to filter patients if the incomingQuery was run as a COUNT query. + */ + public String runVariantListQuery(Query query) { + + if (!variantListEnabled) { + log.warn("VARIANT_LIST query attempted, but not enabled."); + return "VARIANT_LIST query type not allowed"; + } + + return Arrays.toString(abstractProcessor.getVariantList(query).toArray()); + } + + /** + * This method takes a Query input (expected but not validated to be expected result type = VCF_EXCERPT) and returns a tab separated + * string representing a table describing the variants described by the query and the associated zygosities of subjects identified by + * the query. it includes a header row describing each column. + * + * The output columns start with the variant description (chromosome, position reference allele, and subsitution), continuing with a + * series of columns describing the Info columns associated with the variant data. A count of how many subjects in the result set + * have/do not have comes next, followed by one column per patient. + * + * The default patientId header value can be overridden by passing the ID_CUBE_NAME environment variable to the java VM. + * + * @param query A VCF_EXCERPT type query + * @param includePatientData whether to include patient specific data + * @return A Tab-separated string with one line per variant and one column per patient (plus variant data columns) + * @throws IOException + */ + public String runVcfExcerptQuery(Query query, boolean includePatientData) throws IOException { + + if (includePatientData && !vcfExcerptEnabled) { + log.warn("VCF_EXCERPT query attempted, but not enabled."); + return "VCF_EXCERPT query type not allowed"; + } else if (!includePatientData && !aggregateVcfExcerptEnabled) { + log.warn("AGGREGATE_VCF_EXCERPT query attempted, but not enabled."); + return "AGGREGATE_VCF_EXCERPT query type not allowed"; + } + + + log.info("Running VCF Extract query"); + + Collection variantList = abstractProcessor.getVariantList(query); + + log.debug("variantList Size " + variantList.size()); + + Map> metadata = genomicProcessor.getVariantMetadata(variantList); + + log.debug("metadata size " + metadata.size()); + + // Sort the variantSpecs so that the user doesn't lose their mind + TreeMap> metadataSorted = new TreeMap<>((o1, o2) -> { + return new VariantSpec(o1).compareTo(new VariantSpec(o2)); + }); + metadataSorted.putAll(metadata); + metadata = metadataSorted; + + if (metadata == null || metadata.isEmpty()) { + return "No Variants Found\n"; // UI uses newlines to show result count + } else { + log.debug("Found " + metadata.size() + " varaints"); + } + + PhenoCube idCube = null; + if (!idCubeName.contentEquals("NONE")) { + idCube = (PhenoCube) abstractProcessor.getCube(idCubeName); + } + + // + // Build the header row + // + StringBuilder builder = new StringBuilder(); + + // 5 columns for gene info + builder.append("CHROM\tPOSITION\tREF\tALT"); + + List infoStoreColumns = columnSorter.sortInfoColumns(abstractProcessor.getInfoStoreColumns()); + // now add the variant metadata column headers + for (String key : infoStoreColumns) { + builder.append("\t" + key); + } + + // patient count columns + builder.append("\tPatients with this variant in subset\tPatients with this variant NOT in subset"); + + // then one column per patient. We also need to identify the patient ID and + // map it to the right index in the bit mask fields. + Set patientSubset = abstractProcessor.getPatientSubsetForQuery(query); + log.debug("identified " + patientSubset.size() + " patients from query"); + Map patientIndexMap = new LinkedHashMap(); // keep a map for quick index lookups + VariantMask patientMasks = abstractProcessor.createMaskForPatientSet(patientSubset); + int index = 0; + + + for (String patientId : abstractProcessor.getPatientIds()) { + Integer idInt = Integer.parseInt(patientId); + if (patientSubset.contains(idInt)) { + patientIndexMap.put(patientId, index); + if (includePatientData) { + if (idCube == null) { + builder.append("\t" + patientId); + } else { + String value = idCube.getValueForKey(idInt); + if (value == null) { + builder.append("\t" + patientId); + } else { + builder.append("\t" + idCube.getValueForKey(idInt)); + } + } + } + } + index++; + + if (patientIndexMap.size() >= patientSubset.size()) { + log.debug("Found all " + patientIndexMap.size() + " patient Indices at index " + index); + break; + } + } + // End of headers + builder.append("\n"); + VariantBucketHolder variantMaskBucketHolder = new VariantBucketHolder(); + + // loop over the variants identified, and build an output row + metadata.forEach((String variantSpec, Set variantMetadata) -> { + + String[] variantDataColumns = variantSpec.split(","); + // 4 fixed columns in variant ID (CHROM POSITION REF ALT) + for (int i = 0; i < 4; i++) { + if (i > 0) { + builder.append("\t"); + } + if (i < variantDataColumns.length) { + builder.append(variantDataColumns[i]); + } + } + Map> variantColumnMap = new HashMap>(); + for (String infoColumns : variantMetadata) { + // data is in a single semi-colon delimited string. + // e.g., key1=value1;key2=value2;.... + + String[] metaDataColumns = infoColumns.split(";"); + + for (String key : metaDataColumns) { + String[] keyValue = key.split("="); + if (keyValue.length == 2 && keyValue[1] != null) { + Set existingValues = variantColumnMap.get(keyValue[0]); + if (existingValues == null) { + existingValues = new HashSet(); + variantColumnMap.put(keyValue[0], existingValues); + } + existingValues.add(keyValue[1]); + } + } + } + + // need to make sure columns are pushed out in the right order; use same iterator as headers + for (String key : infoStoreColumns) { + Set columnMeta = variantColumnMap.get(key); + if (columnMeta != null) { + // collect our sets to a single entry + builder.append("\t" + columnMeta.stream().map(String::toString).collect(Collectors.joining(","))); + } else { + builder.append("\tnull"); + } + } + + VariableVariantMasks masks = abstractProcessor.getMasks(variantSpec, variantMaskBucketHolder).get(); + + // make strings of 000100 so we can just check 'char at' + // so heterozygous no calls we want, homozygous no calls we don't + VariantMask heteroMask = masks.heterozygousMask != null ? masks.heterozygousMask + : masks.heterozygousNoCallMask != null ? masks.heterozygousNoCallMask : null; + VariantMask homoMask = masks.homozygousMask != null ? masks.homozygousMask : null; + + // Patient count = (hetero mask | homo mask) & patient mask + VariantMask heteroOrHomoMask = orNullableMasks(heteroMask, homoMask); + int patientCount = heteroOrHomoMask == null ? 0 : (heteroOrHomoMask.intersection(patientMasks).bitCount()); + + int bitCount = masks.heterozygousMask == null ? 0 : (masks.heterozygousMask.bitCount()); + bitCount += masks.homozygousMask == null ? 0 : (masks.homozygousMask.bitCount()); + + // count how many patients have genomic data available + Integer patientsWithVariantsCount = patientMasks.bitCount(); + + + // (patients with/total) in subset \t (patients with/total) out of subset. + builder.append( + "\t" + patientCount + "/" + patientIndexMap.size() + "\t" + (bitCount - patientCount) + "/" + + (patientsWithVariantsCount - patientIndexMap.size()) + ); + + if (includePatientData) { + // track the number of subjects without the variant; use a second builder to keep the column order + StringBuilder patientListBuilder = new StringBuilder(); + + for (Integer patientIndex : patientIndexMap.values()) { + if (heteroMask != null && heteroMask.testBit(patientIndex)) { + patientListBuilder.append("\t0/1"); + } else if (homoMask != null && homoMask.testBit(patientIndex)) { + patientListBuilder.append("\t1/1"); + } else { + patientListBuilder.append("\t0/0"); + } + } + builder.append(patientListBuilder); + } + + builder.append("\n"); + }); + + + return builder.toString(); + } + + private VariantMask orNullableMasks(VariantMask heteroMask, VariantMask homoMask) { + if (heteroMask != null) { + if (homoMask != null) { + return heteroMask.union(homoMask); + } + return heteroMask; + } else { + return homoMask; + } + } + + public String[] getHeaderRow(Query query) { + return null; + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantService.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantService.java new file mode 100644 index 000000000..cdbd0d3b9 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantService.java @@ -0,0 +1,231 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.*; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedByteIndexedStorage; +import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedJavaIndexedStorage; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.*; +import java.math.BigInteger; +import java.util.*; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.Executors; +import java.util.concurrent.TimeUnit; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; + +public class VariantService { + + private static Logger log = LoggerFactory.getLogger(VariantService.class); + + private static final Integer VARIANT_INDEX_BLOCK_SIZE = 1000000; + + private final String genomicDataDirectory; + + private final String VARIANT_INDEX_FBBIS_STORAGE_FILE; + private final String VARIANT_INDEX_FBBIS_FILE; + private final String BUCKET_INDEX_BY_SAMPLE_FILE; + + + private final VariantStore variantStore; + + // why is this not VariantSpec[]? + private String[] variantIndex = null; + private BucketIndexBySample bucketIndex; + + private final VariantMetadataIndex variantMetadataIndex; + + public String[] getVariantIndex() { + return variantIndex; + } + + public BucketIndexBySample getBucketIndex() { + return bucketIndex; + } + + public Set filterVariantSetForPatientSet(Set variantSet, Collection patientSet) { + try { + return bucketIndex.filterVariantSetForPatientSet(variantSet, patientSet); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + } + + public VariantService(String genomicDataDirectory) { + this.genomicDataDirectory = genomicDataDirectory; + VARIANT_INDEX_FBBIS_STORAGE_FILE = genomicDataDirectory + "variantIndex_fbbis_storage.javabin"; + VARIANT_INDEX_FBBIS_FILE = genomicDataDirectory + "variantIndex_fbbis.javabin"; + BUCKET_INDEX_BY_SAMPLE_FILE = genomicDataDirectory + "BucketIndexBySample.javabin"; + + variantStore = loadVariantStore(); + + this.variantMetadataIndex = VariantMetadataIndex.createInstance(genomicDataDirectory); + try { + loadGenomicCacheFiles(); + } catch (Exception e) { + log.error("Failed to load genomic data: " + e.getLocalizedMessage(), e); + } + } + + private VariantStore loadVariantStore() { + VariantStore variantStore; + try { + variantStore = VariantStore.readInstance(genomicDataDirectory); + } catch (Exception e) { + variantStore = new VariantStore(); + variantStore.setPatientIds(new String[0]); + log.warn("Unable to load variant store"); + } + return variantStore; + } + + public String[] loadVariantIndex() { + // skip if we have no variants + if (variantStore.getPatientIds().length == 0) { + log.warn("No Genomic Data found. Skipping variant Indexing"); + return new String[0]; + } + + String[] variantIndex = VariantStore.loadVariantIndexFromFile(genomicDataDirectory); + + log.info("Index created with " + variantIndex.length + " total variants."); + return variantIndex; + } + + /** + * This process takes a while (even after the cache is built), so let's spin it out into it's own thread. (not done yet) + * @throws FileNotFoundException + * @throws IOException + * @throws InterruptedException + */ + private void loadGenomicCacheFiles() throws FileNotFoundException, IOException, InterruptedException { + if (bucketIndex == null) { + if (variantIndex == null) { + if (!new File(VARIANT_INDEX_FBBIS_FILE).exists()) { + log.info("Creating new " + VARIANT_INDEX_FBBIS_FILE); + this.variantIndex = loadVariantIndex(); + FileBackedByteIndexedStorage fbbis = + new FileBackedJavaIndexedStorage<>(Integer.class, String[].class, new File(VARIANT_INDEX_FBBIS_STORAGE_FILE)); + try ( + ObjectOutputStream oos = + new ObjectOutputStream(new GZIPOutputStream(new FileOutputStream(VARIANT_INDEX_FBBIS_FILE))); + ) { + + log.debug("Writing Cache Object in blocks of " + VARIANT_INDEX_BLOCK_SIZE); + + int bucketCount = (variantIndex.length / VARIANT_INDEX_BLOCK_SIZE) + 1; // need to handle overflow + int index = 0; + for (int i = 0; i < bucketCount; i++) { + int blockSize = + i == (bucketCount - 1) ? (variantIndex.length % VARIANT_INDEX_BLOCK_SIZE) : VARIANT_INDEX_BLOCK_SIZE; + + String[] variantArrayBlock = new String[blockSize]; + System.arraycopy(variantIndex, index, variantArrayBlock, 0, blockSize); + fbbis.put(i, variantArrayBlock); + + index += blockSize; + log.debug("saved " + index + " variants"); + } + fbbis.complete(); + oos.writeObject("" + variantIndex.length); + oos.writeObject(fbbis); + oos.flush(); + oos.close(); + } + } else { + ExecutorService ex = Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors()); + try ( + ObjectInputStream objectInputStream = + new ObjectInputStream(new GZIPInputStream(new FileInputStream(VARIANT_INDEX_FBBIS_FILE))); + ) { + Integer variantCount = Integer.parseInt((String) objectInputStream.readObject()); + FileBackedByteIndexedStorage indexStore = + (FileBackedByteIndexedStorage) objectInputStream.readObject(); + log.info("loading " + VARIANT_INDEX_FBBIS_FILE); + + variantIndex = new String[variantCount]; + String[] _varaiantIndex2 = variantIndex; + + // variant index has to be a single array (we use a binary search for lookups) + // but reading/writing to disk should be batched for performance + int bucketCount = (variantCount / VARIANT_INDEX_BLOCK_SIZE) + 1; // need to handle overflow + + for (int i = 0; i < bucketCount; i++) { + final int _i = i; + ex.submit(() -> { + String[] variantIndexBucket = indexStore.get(_i); + System.arraycopy( + variantIndexBucket, 0, _varaiantIndex2, (_i * VARIANT_INDEX_BLOCK_SIZE), variantIndexBucket.length + ); + log.debug("loaded " + (_i * VARIANT_INDEX_BLOCK_SIZE) + " block"); + }); + } + objectInputStream.close(); + ex.shutdown(); + while (!ex.awaitTermination(60, TimeUnit.SECONDS)) { + log.info("Waiting for tasks to complete"); + Thread.sleep(10000); + } + } catch (IOException | ClassNotFoundException | NumberFormatException e) { + log.error("an error occurred", e); + } + log.info("Found " + variantIndex.length + " total variants."); + } + } + // todo: not loading bucket index when there is no variant metadata index is a temporary fix for non-variant explorer + // environments + // once we start building the bucket index as part of the ETL, we can remove this check and leverage the bucket index + // for all genomic queries + if ( + variantStore.getPatientIds().length > 0 && variantMetadataIndex != null && !new File(BUCKET_INDEX_BY_SAMPLE_FILE).exists() + ) { + log.info("creating new " + BUCKET_INDEX_BY_SAMPLE_FILE); + bucketIndex = new BucketIndexBySample(variantStore, genomicDataDirectory); + try ( + FileOutputStream fos = new FileOutputStream(BUCKET_INDEX_BY_SAMPLE_FILE); GZIPOutputStream gzos = + new GZIPOutputStream(fos); ObjectOutputStream oos = new ObjectOutputStream(gzos); + ) { + oos.writeObject(bucketIndex); + oos.flush(); + } + } else if (new File(BUCKET_INDEX_BY_SAMPLE_FILE).exists()) { + try ( + ObjectInputStream objectInputStream = + new ObjectInputStream(new GZIPInputStream(new FileInputStream(BUCKET_INDEX_BY_SAMPLE_FILE))); + ) { + log.info("loading " + BUCKET_INDEX_BY_SAMPLE_FILE); + bucketIndex = (BucketIndexBySample) objectInputStream.readObject(); + bucketIndex.updateStorageDirectory(new File(genomicDataDirectory)); + } catch (IOException | ClassNotFoundException e) { + log.error("an error occurred", e); + } + } + } + } + + public String[] getPatientIds() { + return variantStore.getPatientIds(); + } + + public Optional getMasks(String variantName, VariantBucketHolder bucketCache) { + try { + return variantStore.getMasks(variantName, bucketCache); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + } + + public List getMasksForDbSnpSpec(String variantName) { + return variantStore.getMasksForDbSnpSpec(variantName); + } + + public BigInteger emptyBitmask() { + return variantStore.emptyBitmask(); + } + + public Map> findByMultipleVariantSpec(Collection variantList) { + return variantMetadataIndex.findByMultipleVariantSpec(variantList); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/audit/AuditAttributes.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/audit/AuditAttributes.java new file mode 100644 index 000000000..9bcdf3357 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/audit/AuditAttributes.java @@ -0,0 +1,35 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.audit; + +import java.util.HashMap; +import java.util.Map; + +import jakarta.servlet.http.HttpServletRequest; + +/** + * Utility for setting audit metadata on the current request. Controllers call {@link #putMetadata} to attach domain-specific context + * (query_id, result_type, etc.) that the {@link AuditLoggingFilter} merges into the logging event. + */ +public final class AuditAttributes { + + public static final String EVENT_TYPE = "audit.event_type"; + public static final String ACTION = "audit.action"; + private static final String METADATA = "audit.metadata"; + + private AuditAttributes() {} + + public static void putMetadata(HttpServletRequest request, String key, Object value) { + if (request != null && key != null && value != null) { + getMetadata(request).put(key, value); + } + } + + @SuppressWarnings("unchecked") + public static Map getMetadata(HttpServletRequest request) { + Map metadata = (Map) request.getAttribute(METADATA); + if (metadata == null) { + metadata = new HashMap<>(); + request.setAttribute(METADATA, metadata); + } + return metadata; + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/audit/AuditInterceptor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/audit/AuditInterceptor.java new file mode 100644 index 000000000..96b40e73d --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/audit/AuditInterceptor.java @@ -0,0 +1,27 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.audit; + +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import org.springframework.web.method.HandlerMethod; +import org.springframework.web.servlet.HandlerInterceptor; + +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +/** + * Reads {@link AuditEvent} annotations from controller methods and sets the event type and action as request attributes for the + * {@link AuditLoggingFilter}. + */ +public class AuditInterceptor implements HandlerInterceptor { + + @Override + public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) { + if (handler instanceof HandlerMethod handlerMethod) { + AuditEvent auditEvent = handlerMethod.getMethodAnnotation(AuditEvent.class); + if (auditEvent != null) { + request.setAttribute(AuditAttributes.EVENT_TYPE, auditEvent.type()); + request.setAttribute(AuditAttributes.ACTION, auditEvent.action()); + } + } + return true; + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/audit/AuditLoggingFilter.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/audit/AuditLoggingFilter.java new file mode 100644 index 000000000..9f748491a --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/audit/AuditLoggingFilter.java @@ -0,0 +1,152 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.audit; + +import java.io.IOException; +import java.util.HashMap; +import java.util.Map; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.web.filter.OncePerRequestFilter; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.dbmi.avillach.logging.RequestInfo; +import edu.harvard.dbmi.avillach.logging.SessionIdResolver; +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +/** + * Generic audit logging filter shared by both the HPDS service and the genomic processor.

    Event categorization is NOT done here — it is + * set by {@link AuditInterceptor} (reading {@link AuditEvent} annotations) as request attributes. This filter reads those attributes and + * falls back to OTHER / HTTP method if none are set.

    Domain-specific metadata (query_id, result_type, etc.) is set by controllers via + * {@link AuditAttributes#putMetadata}.

    Not annotated {@code @Component} — each application registers it via its own + * {@code LoggingConfig} to allow sharing across separately-scanned Spring Boot apps. + */ +public class AuditLoggingFilter extends OncePerRequestFilter { + + private static final Logger log = LoggerFactory.getLogger(AuditLoggingFilter.class); + + private final String destIpConfig; + private final Integer destPortConfig; + private final LoggingClient loggingClient; + + public AuditLoggingFilter(LoggingClient loggingClient, String destIp, Integer destPort) { + this.loggingClient = loggingClient; + this.destIpConfig = destIp; + this.destPortConfig = destPort; + } + + @Override + protected boolean shouldNotFilter(HttpServletRequest request) { + return request.getRequestURI().startsWith("/actuator"); + } + + @Override + protected void doFilterInternal(HttpServletRequest request, HttpServletResponse response, FilterChain filterChain) + throws ServletException, IOException { + + long startTime = System.currentTimeMillis(); + + try { + filterChain.doFilter(request, response); + } finally { + try { + if (loggingClient == null || !loggingClient.isEnabled()) { + return; + } + + String fullPath = request.getRequestURI(); + String method = request.getMethod(); + long duration = System.currentTimeMillis() - startTime; + + // Read event categorization set by AuditInterceptor (from @AuditEvent annotations) + String eventType = (String) request.getAttribute(AuditAttributes.EVENT_TYPE); + String action = (String) request.getAttribute(AuditAttributes.ACTION); + if (eventType == null) { + eventType = "OTHER"; + } + if (action == null) { + action = method; + } + + // Source IP + String srcIp = extractSourceIp(request); + + // Destination IP and port + String destIp = destIpConfig != null ? destIpConfig : request.getLocalAddr(); + int destPort = destPortConfig != null ? destPortConfig : request.getLocalPort(); + + // Response info + int responseStatus = response.getStatus(); + String contentType = response.getContentType(); + Long bytes = parseContentLength(response.getHeader("Content-Length")); + + String queryString = request.getQueryString(); + RequestInfo requestInfo = RequestInfo.builder().method(method).url(fullPath).queryString(queryString).srcIp(srcIp) + .destIp(destIp).destPort(destPort).httpUserAgent(request.getHeader("User-Agent")).status(responseStatus) + .duration(duration).httpContentType(contentType).bytes(bytes).build(); + + // Build metadata: api version + domain metadata from controllers + String sessionId = SessionIdResolver.resolve(request.getHeader("X-Session-Id"), srcIp, request.getHeader("User-Agent")); + Map metadata = new HashMap<>(); + if (fullPath.contains("/v3/")) { + metadata.put("api_version", "v3"); + } + + // Merge domain-specific metadata set by controllers via AuditAttributes.putMetadata() + AuditAttributes.getMetadata(request).forEach(metadata::putIfAbsent); + + // Error map for 4xx/5xx + Map errorMap = null; + if (responseStatus >= 400) { + errorMap = new HashMap<>(); + errorMap.put("status", responseStatus); + errorMap.put("error_type", responseStatus >= 500 ? "server_error" : "client_error"); + } + + LoggingEvent.Builder eventBuilder = + LoggingEvent.builder(eventType).action(action).sessionId(sessionId).request(requestInfo).metadata(metadata); + + if (errorMap != null) { + eventBuilder.error(errorMap); + } + + LoggingEvent event = eventBuilder.build(); + + // Send with bearer token passthrough + String authHeader = request.getHeader("Authorization"); + String requestId = request.getHeader("X-Request-Id"); + + if (authHeader != null || requestId != null) { + loggingClient.send(event, authHeader, requestId); + } else { + loggingClient.send(event); + } + + } catch (Exception e) { + log.warn("AuditLoggingFilter failed to log request", e); + } + } + } + + static String extractSourceIp(HttpServletRequest request) { + String xForwardedFor = request.getHeader("X-Forwarded-For"); + if (xForwardedFor != null && !xForwardedFor.isEmpty()) { + return xForwardedFor.split(",")[0].trim(); + } + return request.getRemoteAddr(); + } + + static Long parseContentLength(String header) { + if (header == null) { + return null; + } + try { + return Long.parseLong(header); + } catch (NumberFormatException e) { + return null; + } + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/dictionary/Concept.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/dictionary/Concept.java new file mode 100644 index 000000000..0e9da98cc --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/dictionary/Concept.java @@ -0,0 +1,9 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.dictionary; + +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; + +import java.util.Map; + +@JsonIgnoreProperties(ignoreUnknown = true) +public record Concept(String conceptPath, String name, String display, String dataset, String description, Map meta) { +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/dictionary/DictionaryService.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/dictionary/DictionaryService.java new file mode 100644 index 000000000..8ae536dc6 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/dictionary/DictionaryService.java @@ -0,0 +1,39 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.dictionary; + +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty; +import org.springframework.core.ParameterizedTypeReference; +import org.springframework.http.HttpEntity; +import org.springframework.http.HttpMethod; +import org.springframework.stereotype.Component; +import org.springframework.stereotype.Service; +import org.springframework.web.client.RestTemplate; + +import java.util.List; + +@Service +@ConditionalOnProperty("dictionary.host") +public class DictionaryService { + + public static final ParameterizedTypeReference> CONCEPT_LIST_TYPE_REFERENCE = new ParameterizedTypeReference<>() {}; + private final String dictionaryHost; + private final RestTemplate restTemplate; + + @Autowired + public DictionaryService(@Value("${dictionary.host}") String dictionaryHostTemplate, @Value("${TARGET_STACK:}") String targetStack) { + if (targetStack != null && !targetStack.isEmpty()) { + this.dictionaryHost = dictionaryHostTemplate.replace("___TARGET_STACK___", targetStack); + } else { + this.dictionaryHost = dictionaryHostTemplate; + } + this.restTemplate = new RestTemplate(); + } + + public List getConcepts(List conceptPaths) { + return restTemplate.exchange( + dictionaryHost + "/pic-sure-api-2/PICSURE/proxy/dictionary-api/concepts/detail", HttpMethod.POST, + new HttpEntity<>(conceptPaths), CONCEPT_LIST_TYPE_REFERENCE + ).getBody(); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/genomic/GenomicProcessorRestClient.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/genomic/GenomicProcessorRestClient.java new file mode 100644 index 000000000..bc0ac81bf --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/genomic/GenomicProcessorRestClient.java @@ -0,0 +1,93 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.genomic; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.InfoColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariableVariantMasks; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMask; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; +import edu.harvard.hms.dbmi.avillach.hpds.processing.DistributableQuery; +import edu.harvard.hms.dbmi.avillach.hpds.processing.GenomicProcessor; +import org.springframework.core.ParameterizedTypeReference; +import org.springframework.http.HttpHeaders; +import org.springframework.http.MediaType; +import org.springframework.web.reactive.function.client.WebClient; +import reactor.core.publisher.Mono; + +import java.util.*; + +public class GenomicProcessorRestClient implements GenomicProcessor { + + private final WebClient webClient; + + private static final ParameterizedTypeReference> VARIANT_SET_TYPE_REFERENCE = new ParameterizedTypeReference<>() {}; + private static final ParameterizedTypeReference> INFO_COLUMNS_META_TYPE_REFERENCE = + new ParameterizedTypeReference<>() {}; + private static final ParameterizedTypeReference> LIST_OF_STRING_TYPE_REFERENCE = new ParameterizedTypeReference<>() {}; + private static final ParameterizedTypeReference> SET_OF_STRING_TYPE_REFERENCE = new ParameterizedTypeReference<>() {}; + + public GenomicProcessorRestClient(String serviceUrl) { + this.webClient = + WebClient.builder().baseUrl(serviceUrl).defaultHeader(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE).build(); + } + + @Override + public Mono getPatientMask(DistributableQuery distributableQuery) { + Mono result = webClient.post().uri("/patients").contentType(MediaType.APPLICATION_JSON) + .body(Mono.just(distributableQuery), DistributableQuery.class).retrieve().bodyToMono(VariantMask.class); + return result; + } + + @Override + public Set patientMaskToPatientIdSet(VariantMask patientMask) { + throw new RuntimeException("Not Implemented"); + } + + @Override + public VariantMask createMaskForPatientSet(Set patientSubset) { + throw new RuntimeException("Not Implemented"); + } + + @SuppressWarnings("unchecked") + @Override + public Mono> getVariantList(DistributableQuery distributableQuery) { + Mono> result = webClient.post().uri("/variants").contentType(MediaType.APPLICATION_JSON) + .body(Mono.just(distributableQuery), DistributableQuery.class).retrieve().bodyToMono(VARIANT_SET_TYPE_REFERENCE); + return result; + } + + @Override + public List getPatientIds() { + List result = webClient.get().uri("/patients/ids").retrieve().bodyToMono(LIST_OF_STRING_TYPE_REFERENCE).block(); + return result; + } + + @Override + public Optional getMasks(String path, VariantBucketHolder variantMasksVariantBucketHolder) { + throw new RuntimeException("Not Implemented"); + } + + @Override + public Set getInfoStoreColumns() { + Set result = webClient.get().uri(uriBuilder -> uriBuilder.path("/info/columns").build()).retrieve() + .bodyToMono(SET_OF_STRING_TYPE_REFERENCE).block(); + return result; + } + + @Override + public Set getInfoStoreValues(String conceptPath) { + Set result = + webClient.get().uri(uriBuilder -> uriBuilder.path("/info/values").queryParam("conceptPath", conceptPath).build(conceptPath)) + .retrieve().bodyToMono(SET_OF_STRING_TYPE_REFERENCE).block(); + return result; + } + + @Override + public List getInfoColumnMeta() { + List result = webClient.get().uri("/info/meta").retrieve().bodyToMono(INFO_COLUMNS_META_TYPE_REFERENCE).block(); + return result; + } + + @Override + public Map> getVariantMetadata(Collection variantList) { + throw new RuntimeException("Not implemented yet"); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/CsvWriter.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/CsvWriter.java new file mode 100644 index 000000000..a9123d91a --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/CsvWriter.java @@ -0,0 +1,88 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.io; + +import com.google.common.base.Joiner; +import org.springframework.http.MediaType; + +import java.io.File; +import java.io.FileWriter; +import java.io.IOException; +import java.io.UncheckedIOException; +import java.util.ArrayList; +import java.util.Collection; +import java.util.List; +import java.util.stream.Collectors; + +public class CsvWriter implements ResultWriter { + + private final de.siegmar.fastcsv.writer.CsvWriter csvWriter; + + private final FileWriter fileWriter; + + private final File file; + + public CsvWriter(File file) { + this.file = file; + csvWriter = new de.siegmar.fastcsv.writer.CsvWriter(); + try { + this.fileWriter = new FileWriter(file); + } catch (IOException e) { + throw new RuntimeException("IOException while appending temp file : " + file.getAbsolutePath(), e); + } + } + + @Override + public void writeHeader(String[] data) { + try { + List dataList = new ArrayList<>(); + dataList.add(data); + csvWriter.write(fileWriter, dataList); + } catch (IOException e) { + throw new RuntimeException("IOException while appending to CSV file", e); + } + } + + @Override + public void writeEntity(Collection data) { + try { + csvWriter.write(fileWriter, data); + } catch (IOException e) { + throw new UncheckedIOException("IOException while appending to CSV file", e); + } + } + + @Override + public void writeMultiValueEntity(Collection>> data) { + List collect = data.stream().map(line -> { + return line.stream().map(cell -> { + if (cell == null) { + return ""; + } + return Joiner.on('\t').join(cell); + }).toArray(String[]::new); + }).toList(); + try { + csvWriter.write(fileWriter, collect); + } catch (IOException e) { + throw new UncheckedIOException("IOException while appending to CSV file", e); + } + } + + @Override + public File getFile() { + return file; + } + + @Override + public MediaType getResponseType() { + return MediaType.TEXT_PLAIN; + } + + @Override + public void close() { + try { + fileWriter.close(); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/PfbWriter.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/PfbWriter.java new file mode 100644 index 000000000..6c044dee5 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/PfbWriter.java @@ -0,0 +1,344 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.io; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.hms.dbmi.avillach.hpds.processing.dictionary.Concept; +import edu.harvard.hms.dbmi.avillach.hpds.processing.dictionary.DictionaryService; +import org.apache.avro.Schema; +import org.apache.avro.SchemaBuilder; +import org.apache.avro.file.CodecFactory; +import org.apache.avro.file.DataFileWriter; +import org.apache.avro.generic.GenericData; +import org.apache.avro.generic.GenericDatumWriter; +import org.apache.avro.generic.GenericRecord; +import org.apache.avro.io.DatumWriter; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.http.MediaType; + +import java.io.File; +import java.io.IOException; +import java.io.UncheckedIOException; +import java.util.*; +import java.util.function.Function; +import java.util.stream.Collectors; + +/** + * Writes HPDS data in PFB format. PFB is an Avro schema specifically created for biomedical data. See https://uc-cdis.github.io/pypfb/ for more details. + * + * Our PFB format has 4 entities currently:

    • pic-sure-patients: Contains patient data, with one row per patient
      • + *
    • pic-sure-data-dictionary: Contains variable metadata with one row per variable exported
    • metadata: Contains ontological + * metadata about variables. Currently empty
    • relations: Contains relational data about entities. Currently empty
    + */ +public class PfbWriter implements ResultWriter { + + public static final String PATIENT_TABLE_PREFIX = "pic-sure-patients-"; + public static final String DATA_DICTIONARY_TABLE_PREFIX = "pic-sure-data-dictionary-"; + public static final List DATA_DICTIONARY_FIELDS = List.of("concept_path", "display", "dataset", "description", "drs_uri"); + private static final Logger log = LoggerFactory.getLogger(PfbWriter.class); + + private final DictionaryService dictionaryService; + + private final Schema metadataSchema; + private final Schema nodeSchema; + + private final Schema propertiesSchema; + + private final String patientTableName; + private final String dataDictionaryTableName; + private SchemaBuilder.FieldAssembler entityFieldAssembler; + + /** + * The original (before formatting for avro) concept path values + */ + private List originalFields; + /** + * The avro formatted concept path values. Avro only allows alphanumeric values and underscores as field names + */ + private List formattedFields; + private DataFileWriter dataFileWriter; + /** + * Location of the file being written to + */ + private File file; + /** + * The entity schema is a union of our custom entities, plus the PFB defined relation and metadata entities + */ + private Schema entitySchema; + /** + * Schema containing one row per patient and one column per concept path exported + */ + private Schema patientDataSchema; + /** + * Data dictionary schema containing one row per concept path exported and various metadata columns + */ + private Schema dataDictionarySchema; + /** + * Relational data about entities. Currently empty + */ + private Schema relationSchema; + + /** + * A hardcoded set of fields that should be a single value instead of an array. + * + * todo: introduce an attribute on concept paths specifying if they can contain multiple values + */ + private static final Set SINGULAR_FIELDS = Set.of("patient_id"); + + public PfbWriter(File tempFile, String queryId, DictionaryService dictionaryService) { + this.file = tempFile; + this.dictionaryService = dictionaryService; + this.patientTableName = formatFieldName(PATIENT_TABLE_PREFIX + queryId); + this.dataDictionaryTableName = formatFieldName(DATA_DICTIONARY_TABLE_PREFIX + queryId); + entityFieldAssembler = SchemaBuilder.record("entity").namespace("edu.harvard.dbmi").fields(); + + + Schema linksSchema = SchemaBuilder.record("Link").fields().requiredString("dst").name("multiplicity") + .type(SchemaBuilder.enumeration("Multiplicity").symbols("ONE_TO_ONE", "ONE_TO_MANY", "MANY_TO_ONE", "MANY_TO_MANY")).noDefault() + .endRecord(); + + propertiesSchema = SchemaBuilder.record("Property").fields().requiredString("name").requiredString("ontology_reference") + .name("values").type(SchemaBuilder.map().values(SchemaBuilder.nullable().stringType())).noDefault().endRecord(); + + SchemaBuilder.FieldAssembler nodeRecord = SchemaBuilder.record("nodes").fields().requiredString("name") + .nullableString("ontology_reference", "null").name("links").type(SchemaBuilder.array().items(linksSchema)).noDefault() + .name("properties").type(SchemaBuilder.array().items(propertiesSchema)).noDefault().name("values") + .type(SchemaBuilder.map().values(SchemaBuilder.nullable().stringType())).noDefault(); + nodeSchema = nodeRecord.endRecord(); + + SchemaBuilder.FieldAssembler metadataRecord = SchemaBuilder.record("metadata").fields(); + metadataRecord.requiredString("misc"); + metadataRecord = metadataRecord.name("nodes").type(SchemaBuilder.array().items(nodeSchema)).noDefault(); + metadataSchema = metadataRecord.endRecord(); + + + SchemaBuilder.FieldAssembler relationRecord = + SchemaBuilder.record("Relation").fields().requiredString("dst_name").requiredString("dst_id"); + relationSchema = relationRecord.endRecord(); + } + + @Override + public void writeHeader(String[] data) { + originalFields = List.of(data); + formattedFields = originalFields.stream().map(this::formatFieldName).collect(Collectors.toList()); + + dataDictionarySchema = SchemaBuilder.record(dataDictionaryTableName).fields().requiredString("concept_path").name("drs_uri") + .type(SchemaBuilder.array().items(SchemaBuilder.nullable().stringType())).noDefault().nullableString("display", "null") + .nullableString("dataset", "null").nullableString("description", "null").endRecord(); + + SchemaBuilder.FieldAssembler patientRecords = SchemaBuilder.record(patientTableName).fields(); + formattedFields.forEach(field -> { + if (isSingularField(field)) { + patientRecords.nullableString(field, "null"); + } else { + patientRecords.name(field).type(SchemaBuilder.array().items(SchemaBuilder.nullable().stringType())).noDefault(); + } + + }); + patientDataSchema = patientRecords.endRecord(); + + Schema objectSchema = Schema.createUnion(metadataSchema, patientDataSchema, dataDictionarySchema); + + entityFieldAssembler = entityFieldAssembler.name("object").type(objectSchema).noDefault(); + entityFieldAssembler.nullableString("id", "null"); + entityFieldAssembler.requiredString("name"); + entityFieldAssembler = entityFieldAssembler.name("relations").type(SchemaBuilder.array().items(relationSchema)).noDefault(); + entitySchema = entityFieldAssembler.endRecord(); + + DatumWriter datumWriter = new GenericDatumWriter(entitySchema); + dataFileWriter = new DataFileWriter(datumWriter); + try { + log.info("Creating temp avro file at " + file.getAbsoluteFile()); + dataFileWriter.setCodec(CodecFactory.deflateCodec(CodecFactory.DEFAULT_DEFLATE_LEVEL)); + dataFileWriter.create(entitySchema, file); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + + writeMetadata(); + writeDataDictionary(); + } + + private void writeDataDictionary() { + GenericRecord entityRecord = new GenericData.Record(entitySchema);; + Map conceptMap = Map.of(); + try { + conceptMap = + dictionaryService.getConcepts(originalFields).stream().collect(Collectors.toMap(Concept::conceptPath, Function.identity())); + } catch (RuntimeException e) { + log.error("Error fetching concepts from dictionary service", e); + } + + for (int i = 0; i < formattedFields.size(); i++) { + String formattedField = formattedFields.get(i); + if ("patient_id".equals(formattedField)) { + continue; + } + GenericRecord dataDictionaryData = new GenericData.Record(dataDictionarySchema); + dataDictionaryData.put("concept_path", formattedField); + + Concept concept = conceptMap.get(originalFields.get(i)); + List drsUris = List.of(); + if (concept != null) { + Map meta = concept.meta(); + if (meta != null) { + String drsUriJson = meta.get("drs_uri"); + if (drsUriJson != null) { + try { + String[] drsUriArray = new ObjectMapper().readValue(drsUriJson, String[].class); + drsUris = List.of(drsUriArray); + } catch (JsonProcessingException e) { + log.error("Error parsing drs_uri as json: " + drsUriJson); + } + } + } + dataDictionaryData.put("display", concept.display()); + dataDictionaryData.put("dataset", concept.dataset()); + dataDictionaryData.put("description", concept.description()); + } + dataDictionaryData.put("drs_uri", drsUris); + + log.info("Writing " + formattedField + " to data dictonary table with drs_uris: " + drsUris); + entityRecord.put("object", dataDictionaryData); + entityRecord.put("name", dataDictionaryTableName); + entityRecord.put("id", formattedField); + entityRecord.put("relations", List.of()); + + try { + dataFileWriter.append(entityRecord); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + } + } + + private boolean isSingularField(String field) { + return SINGULAR_FIELDS.contains(field); + } + + /** + * Transforms our variable names to once that are valid avro fields. We replace invalid characters with underscores and add a leading + * underscore if the variable starts with a number + */ + protected String formatFieldName(String s) { + String formattedFieldName = s.replaceAll("\\W", "_"); + if (Character.isDigit(formattedFieldName.charAt(0))) { + return "_" + formattedFieldName; + } + return formattedFieldName; + } + + private void writeMetadata() { + GenericRecord entityRecord = new GenericData.Record(entitySchema); + + List nodeList = new ArrayList<>(); + List propertiesList = new ArrayList<>(); + GenericRecord nodeData = new GenericData.Record(nodeSchema); + nodeData.put("name", this.patientTableName); + nodeData.put("ontology_reference", ""); + nodeData.put("values", Map.of()); + nodeData.put("links", List.of()); + for (String field : formattedFields) { + GenericRecord properties = new GenericData.Record(propertiesSchema); + properties.put("name", field); + properties.put("ontology_reference", ""); + properties.put("values", Map.of()); + propertiesList.add(properties); + } + nodeData.put("properties", propertiesList); + nodeList.add(nodeData); + + + propertiesList = new ArrayList<>(); + nodeData = new GenericData.Record(nodeSchema); + nodeData.put("name", this.dataDictionaryTableName); + nodeData.put("ontology_reference", ""); + nodeData.put("values", Map.of()); + nodeData.put("links", List.of()); + for (String field : DATA_DICTIONARY_FIELDS) { + GenericRecord properties = new GenericData.Record(propertiesSchema); + properties.put("name", field); + properties.put("ontology_reference", ""); + properties.put("values", Map.of()); + propertiesList.add(properties); + } + nodeData.put("properties", propertiesList); + nodeList.add(nodeData); + + GenericRecord metadata = new GenericData.Record(metadataSchema); + metadata.put("misc", ""); + metadata.put("nodes", nodeList); + + entityRecord.put("object", metadata); + entityRecord.put("name", "metadata"); + entityRecord.put("id", "null"); + entityRecord.put("relations", List.of()); + + try { + dataFileWriter.append(entityRecord); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + } + + @Override + public void writeEntity(Collection entities) { + throw new RuntimeException("Method not supported, use writeMultiValueEntity instead"); + } + + @Override + public void writeMultiValueEntity(Collection>> entities) { + entities.forEach(entity -> { + if (entity.size() != formattedFields.size()) { + throw new IllegalArgumentException("Entity length much match the number of fields in this document"); + } + GenericRecord patientData = new GenericData.Record(patientDataSchema); + String patientId = ""; + for (int i = 0; i < formattedFields.size(); i++) { + if ("patient_id".equals(formattedFields.get(i))) { + patientId = (entity.get(i) != null && !entity.get(i).isEmpty()) ? entity.get(i).get(0) : ""; + } + if (isSingularField(formattedFields.get(i))) { + String entityValue = (entity.get(i) != null && !entity.get(i).isEmpty()) ? entity.get(i).get(0) : ""; + patientData.put(formattedFields.get(i), entityValue); + } else { + List fieldValue = entity.get(i) != null ? entity.get(i) : List.of(); + patientData.put(formattedFields.get(i), fieldValue); + } + } + + + GenericRecord entityRecord = new GenericData.Record(entitySchema); + entityRecord.put("object", patientData); + entityRecord.put("name", patientTableName); + entityRecord.put("id", patientId); + entityRecord.put("relations", List.of()); + + try { + dataFileWriter.append(entityRecord); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + }); + } + + @Override + public void close() { + try { + dataFileWriter.close(); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + } + + @Override + public File getFile() { + return file; + } + + @Override + public MediaType getResponseType() { + return MediaType.APPLICATION_OCTET_STREAM; + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/ResultWriter.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/ResultWriter.java new file mode 100644 index 000000000..617c4afa6 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/ResultWriter.java @@ -0,0 +1,22 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.io; + +import org.springframework.http.MediaType; + +import java.io.File; +import java.io.IOException; +import java.util.Collection; +import java.util.List; + +public interface ResultWriter { + void writeHeader(String[] data); + + void writeEntity(Collection data); + + void writeMultiValueEntity(Collection>> data); + + File getFile(); + + MediaType getResponseType(); + + void close(); +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/patient/PatientProcessor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/patient/PatientProcessor.java new file mode 100644 index 000000000..92b9e4ba1 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/patient/PatientProcessor.java @@ -0,0 +1,41 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.patient; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import edu.harvard.hms.dbmi.avillach.hpds.processing.AbstractProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.AsyncResult; +import edu.harvard.hms.dbmi.avillach.hpds.processing.HpdsProcessor; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Component; + +import java.util.List; + +@Component +public class PatientProcessor implements HpdsProcessor { + + private static final Logger LOG = LoggerFactory.getLogger(PatientProcessor.class); + private final AbstractProcessor abstractProcessor; + + @Autowired + public PatientProcessor(AbstractProcessor abstractProcessor) { + this.abstractProcessor = abstractProcessor; + } + + @Override + public String[] getHeaderRow(Query query) { + return new String[] {"PATIENT_NUM"}; + } + + @Override + public void runQuery(Query query, AsyncResult asyncResult) { + LOG.info("Pulling results for query {}", query.getId()); + // floating all this in memory is a bit gross, but the whole list of + // patient IDs was already there, so I don't feel too bad + List allPatients = + abstractProcessor.getPatientSubsetForQuery(query).stream().map(patient -> new String[] {patient.toString()}).toList(); + LOG.info("Writing results for query {}", query.getId()); + asyncResult.appendResults(allPatients); + LOG.info("Completed query {}", query.getId()); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/timeseries/TimeSeriesConversionService.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/timeseries/TimeSeriesConversionService.java new file mode 100644 index 000000000..816a66fab --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/timeseries/TimeSeriesConversionService.java @@ -0,0 +1,18 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.timeseries; + +import org.springframework.stereotype.Service; + +import java.time.Instant; +import java.time.format.DateTimeFormatter; + +@Service +public class TimeSeriesConversionService { + + public String toISOString(Long unixTimeStamp) { + if (unixTimeStamp == null) { + return ""; + } + Instant instant = Instant.ofEpochMilli(unixTimeStamp); + return DateTimeFormatter.ISO_INSTANT.format(instant); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/timeseries/TimeseriesProcessor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/timeseries/TimeseriesProcessor.java new file mode 100644 index 000000000..74bd743a3 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/timeseries/TimeseriesProcessor.java @@ -0,0 +1,140 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.timeseries; + +import java.io.IOException; +import java.util.*; +import java.util.stream.Collectors; + +import edu.harvard.hms.dbmi.avillach.hpds.processing.AbstractProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.AsyncResult; +import edu.harvard.hms.dbmi.avillach.hpds.processing.HpdsProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.QueryProcessor; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.KeyAndValue; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Component; + +/** + * A class for exporting datapoints from HPDS; this will export each individual input data as a unique row, allowing multiple data points + * (with time data) to be exported for a single patient/concept combination. + * + * This returns data in no meaningful order; it is exported by field parameters. Concepts which are present multiple times in a query will + * only be exported once. + * + * + * + * @author nchu + * + */ +@Component +public class TimeseriesProcessor implements HpdsProcessor { + + private static final Logger log = LoggerFactory.getLogger(QueryProcessor.class); + + private AbstractProcessor abstractProcessor; + private final TimeSeriesConversionService conversionService; + + + private final int idBatchSize; + + @Autowired + public TimeseriesProcessor( + AbstractProcessor abstractProcessor, TimeSeriesConversionService conversionService, @Value("${ID_BATCH_SIZE:0}") int idBatchSize + ) { + this.abstractProcessor = abstractProcessor; + this.conversionService = conversionService; + this.idBatchSize = idBatchSize; + } + + /** + * FOr this type of export, the header is always the same + */ + @Override + public String[] getHeaderRow(Query query) { + return new String[] {"PATIENT_NUM", "CONCEPT_PATH", "NVAL_NUM", "TVAL_CHAR", "TIMESTAMP"}; + } + + @Override + public void runQuery(Query query, AsyncResult result) { + Set idList = abstractProcessor.getPatientSubsetForQuery(query); + + if (idBatchSize > 0) { + try { + exportTimeData(query, result, idList); + } catch (IOException e) { + log.error("Exception exporting time data", e); + } + } else { + throw new RuntimeException("Data Export is not authorized for this system"); + } + return; + } + + /** + * //no variant data exported in this processor + * + * @param query + * @param result + * @param idList + * @throws IOException + */ + private void exportTimeData(Query query, AsyncResult result, Set idList) throws IOException { + log.info("Starting export for time series data of query {} (HPDS ID {})", query.getPicSureId(), query.getId()); + Set exportedConceptPaths = new HashSet(); + // get a list of all fields mentioned in the query; export all data associated with any included field + List pathList = new LinkedList(); + pathList.addAll(query.getAnyRecordOf()); + pathList.addAll(query.getAnyRecordOfMulti().stream().flatMap(Collection::stream).collect(Collectors.toList())); + pathList.addAll(query.getFields()); + pathList.addAll(query.getRequiredFields()); + pathList.addAll(query.getCategoryFilters().keySet()); + pathList.addAll(query.getNumericFilters().keySet()); + + addDataForConcepts(pathList, exportedConceptPaths, idList, result); + } + + private void addDataForConcepts(Collection pathList, Set exportedConceptPaths, Set idList, AsyncResult result) + throws IOException { + for (String conceptPath : pathList) { + // skip concepts we may already have encountered + if (exportedConceptPaths.contains(conceptPath)) { + continue; + } + ArrayList dataEntries = new ArrayList(); + Optional> maybeCube = abstractProcessor.nullableGetCube(conceptPath); + if (maybeCube.isEmpty()) { + log.warn("Attempting export of non-existant concept: {}", conceptPath); + continue; + } + PhenoCube cube = maybeCube.get(); + log.debug("Exporting " + conceptPath); + List valuesForKeys = cube.getValuesForKeys(idList); + for (Object kvObj : valuesForKeys) { + if (cube.isStringType()) { + KeyAndValue keyAndValue = (KeyAndValue) kvObj; + // "PATIENT_NUM","CONCEPT_PATH","NVAL_NUM","TVAL_CHAR","TIMESTAMP" + String[] entryData = {keyAndValue.getKey().toString(), conceptPath, "", keyAndValue.getValue(), + conversionService.toISOString(keyAndValue.getTimestamp())}; + dataEntries.add(entryData); + } else { // numeric + KeyAndValue keyAndValue = (KeyAndValue) kvObj; + // "PATIENT_NUM","CONCEPT_PATH","NVAL_NUM","TVAL_CHAR","TIMESTAMP" + String[] entryData = {keyAndValue.getKey().toString(), conceptPath, keyAndValue.getValue().toString(), "", + conversionService.toISOString(keyAndValue.getTimestamp())}; + dataEntries.add(entryData); + } + // batch exports so we don't take double memory (valuesForKeys + dataEntries could be a lot of data points) + if (dataEntries.size() >= (idBatchSize > 0 ? 10 : idBatchSize)) { + result.appendResults(dataEntries); + dataEntries = new ArrayList(); + } + } + result.appendResults(dataEntries); + exportedConceptPaths.add(conceptPath); + } + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/upload/SignUrlService.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/upload/SignUrlService.java new file mode 100644 index 000000000..88325af88 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/upload/SignUrlService.java @@ -0,0 +1,87 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.upload; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Component; +import software.amazon.awssdk.core.sync.RequestBody; +import software.amazon.awssdk.regions.Region; +import software.amazon.awssdk.services.s3.S3Client; +import software.amazon.awssdk.services.s3.model.GetObjectRequest; +import software.amazon.awssdk.services.s3.model.PutObjectRequest; +import software.amazon.awssdk.services.s3.presigner.S3Presigner; +import software.amazon.awssdk.services.s3.presigner.model.GetObjectPresignRequest; +import software.amazon.awssdk.services.s3.presigner.model.PresignedGetObjectRequest; + +import java.io.File; +import java.time.Duration; +import java.util.HashMap; +import java.util.Map; + +@Component +public class SignUrlService { + + private final String bucketName; + private final int signedUrlExpiryMinutes; + private final Region region; + private final LoggingClient loggingClient; + + private static Logger log = LoggerFactory.getLogger(SignUrlService.class); + + @Autowired + public SignUrlService( + @Value("${data-export.s3.bucket-name:}") String bucketName, @Value("${data-export.s3.region:us-east-1}") String region, + @Value("${data-export.s3.signedUrl-expiry-minutes:60}") int signedUrlExpiryMinutes, LoggingClient loggingClient + ) { + this.bucketName = bucketName; + this.signedUrlExpiryMinutes = signedUrlExpiryMinutes; + this.region = Region.of(region); + this.loggingClient = loggingClient; + } + + public void uploadFile(File file, String objectKey) { + S3Client s3 = S3Client.builder().region(this.region).build(); + putS3Object(s3, bucketName, objectKey, file); + if (loggingClient != null && loggingClient.isEnabled()) { + try { + loggingClient.send( + LoggingEvent.builder("DATA_ACCESS").action("data.s3.uploaded") + .metadata(Map.of("bucket", bucketName, "object_key", objectKey)).build() + ); + } catch (Exception e) { + log.warn("Failed to send audit log event", e); + } + } + s3.close(); + } + + // This example uses RequestBody.fromFile to avoid loading the whole file into + // memory. + public void putS3Object(S3Client s3, String bucketName, String objectKey, File file) { + Map metadata = new HashMap<>(); + PutObjectRequest putOb = PutObjectRequest.builder().bucket(bucketName).key(objectKey).metadata(metadata).build(); + + s3.putObject(putOb, RequestBody.fromFile(file)); + log.info("Successfully placed " + objectKey + " into bucket " + bucketName); + } + + public String createPresignedGetUrl(String keyName) { + PresignedGetObjectRequest presignedRequest; + try (S3Presigner presigner = S3Presigner.builder().region(region).build()) { + GetObjectRequest objectRequest = GetObjectRequest.builder().bucket(bucketName).key(keyName).build(); + + GetObjectPresignRequest presignRequest = + GetObjectPresignRequest.builder().signatureDuration(Duration.ofMinutes(signedUrlExpiryMinutes)) // The URL will expire in 10 + // minutes. + .getObjectRequest(objectRequest).build(); + + presignedRequest = presigner.presignGetObject(presignRequest); + } + log.info("Presigned URL: [{}]", presignedRequest.url().toString()); + + return presignedRequest.url().toExternalForm(); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/util/SetUtils.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/util/SetUtils.java new file mode 100644 index 000000000..cac95569f --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/util/SetUtils.java @@ -0,0 +1,21 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.util; + +import java.util.HashSet; +import java.util.Set; +import java.util.stream.Collectors; + +public class SetUtils { + + public static Set union(final Set set1, final Set set2) { + Set union = new HashSet<>(set1); + union.addAll(set2); + return union; + } + + public static Set intersection(final Set set1, final Set set2) { + if (set1.isEmpty() || set2.isEmpty()) { + return new HashSet<>(); + } + return set1.parallelStream().filter(set2::contains).collect(Collectors.toSet()); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/AsyncResult.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/AsyncResult.java new file mode 100644 index 000000000..7870e77cf --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/AsyncResult.java @@ -0,0 +1,294 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.v3; + +import com.fasterxml.jackson.annotation.JsonIgnore; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import edu.harvard.hms.dbmi.avillach.hpds.processing.ResultStore; +import edu.harvard.hms.dbmi.avillach.hpds.processing.ResultStoreStream; +import edu.harvard.hms.dbmi.avillach.hpds.processing.io.ResultWriter; +import edu.harvard.dbmi.avillach.domain.PicSureStatus; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.http.MediaType; + +import java.io.File; +import java.io.IOException; +import java.io.UncheckedIOException; +import java.nio.file.Path; +import java.util.List; +import java.util.Map; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.RejectedExecutionException; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; + +/** + * Note: This class was copied from {@link edu.harvard.hms.dbmi.avillach.hpds.processing.AsyncResult} and updated to use new Query entity + */ +public class AsyncResult implements Runnable, Comparable { + + private static final Logger log = LoggerFactory.getLogger(AsyncResult.class); + + public byte[] readAllBytes() { + try { + return stream.readAllBytes(); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + } + + public void closeWriter() { + stream.closeWriter(); + } + + private final MediaType responseType; + + public MediaType getResponseType() { + return responseType; + } + + public File getFile() { + return stream.getFile(); + } + + public enum Status { + SUCCESS { + @Override + public PicSureStatus toPicSureStatus() { + return PicSureStatus.AVAILABLE; + } + }, + ERROR { + @Override + public PicSureStatus toPicSureStatus() { + return PicSureStatus.ERROR; + } + }, + PENDING { + @Override + public PicSureStatus toPicSureStatus() { + return PicSureStatus.QUEUED; + } + }, + RUNNING { + @Override + public PicSureStatus toPicSureStatus() { + return PicSureStatus.PENDING; + } + }, + RETRY { + @Override + public PicSureStatus toPicSureStatus() { + return PicSureStatus.QUEUED; + } + }; + + public abstract PicSureStatus toPicSureStatus(); + } + + private final Query query; + + public Query getQuery() { + return query; + } + + private Status status; + + public Status getStatus() { + return status; + } + + public AsyncResult setStatus(Status status) { + this.status = status; + return this; + } + + private long queuedTime; + + public long getQueuedTime() { + return queuedTime; + } + + public AsyncResult setQueuedTime(long queuedTime) { + this.queuedTime = queuedTime; + return this; + } + + private long completedTime; + + public long getCompletedTime() { + return completedTime; + } + + private int queueDepth; + + public int getQueueDepth() { + return queueDepth; + } + + public AsyncResult setQueueDepth(int queueDepth) { + this.queueDepth = queueDepth; + return this; + } + + private int positionInQueue; + + public AsyncResult setPositionInQueue(int positionInQueue) { + this.positionInQueue = positionInQueue; + return this; + } + + private int numRows; + + private int numColumns; + + private String id; + + public String getId() { + return id; + } + + public AsyncResult setId(String id) { + this.id = id; + return this; + } + + @JsonIgnore + private ResultStoreStream stream; + + public ResultStoreStream getStream() { + return stream; + } + + @JsonIgnore + private final String[] headerRow; + + /* + * The result needs access to the jobQueue so it can requeue itself if it fails due to insufficient available heap to build its result + * array. + * + * The actual exception is thrown in @see ResultStore#constructor + */ + @JsonIgnore + private ExecutorService jobQueue; + + public ExecutorService getJobQueue() { + return jobQueue; + } + + public AsyncResult setJobQueue(ExecutorService jobQueue) { + this.jobQueue = jobQueue; + return this; + } + + @JsonIgnore + private LoggingClient loggingClient; + + public AsyncResult setLoggingClient(LoggingClient loggingClient) { + this.loggingClient = loggingClient; + return this; + } + + @JsonIgnore + private final HpdsV3Processor processor; + + public HpdsV3Processor getProcessor() { + return processor; + } + + public AsyncResult(Query query, HpdsV3Processor processor, ResultWriter writer) { + this.query = query; + this.processor = processor; + this.headerRow = processor.getHeaderRow(query); + this.responseType = writer.getResponseType(); + try { + stream = new ResultStoreStream(headerRow, writer); + } catch (IOException e) { + log.error("Exception creating result stream", e); + } + } + + public void appendResults(List dataEntries) { + stream.appendResults(dataEntries); + } + + public void appendMultiValueResults(List>> dataEntries) { + stream.appendMultiValueResults(dataEntries); + } + + public void appendResultStore(ResultStore resultStore) { + stream.appendResultStore(resultStore); + } + + + private void sendEvent(String eventType, String action, Map metadata) { + if (loggingClient != null && loggingClient.isEnabled()) { + try { + loggingClient.send(LoggingEvent.builder(eventType).action(action).metadata(Map.copyOf(metadata)).build()); + } catch (Exception e) { + log.warn("Failed to send audit log event", e); + } + } + } + + @Override + public void run() { + status = Status.RUNNING; + long startTime = System.currentTimeMillis(); + + sendEvent("QUERY", "query.execution.started", Map.of("query_id", id, "result_type", String.valueOf(query.expectedResultType()))); + + try { + processor.runQuery(query, this); + this.numColumns = this.headerRow.length; + this.numRows = stream.getNumRows(); + long durationMs = System.currentTimeMillis() - startTime; + log.info("Ran Query in " + durationMs + "ms for " + numRows + " rows and " + numColumns + " columns"); + this.status = Status.SUCCESS; + + sendEvent( + "QUERY", "query.completed", + Map.of( + "query_id", id, "result_type", String.valueOf(query.expectedResultType()), "status", "success", "duration_ms", + String.valueOf(durationMs), "row_count", String.valueOf(numRows) + ) + ); + } catch (Exception e) { + long durationMs = System.currentTimeMillis() - startTime; + log.error("Query failed in " + durationMs + "ms", e); + this.status = Status.ERROR; + + sendEvent( + "QUERY", "query.completed", + Map.of( + "query_id", id, "result_type", String.valueOf(query.expectedResultType()), "status", "error", "duration_ms", + String.valueOf(durationMs) + ) + ); + } finally { + this.completedTime = System.currentTimeMillis(); + } + } + + public void enqueue() { + try { + this.jobQueue.execute(this); + } catch (RejectedExecutionException e) { + this.status = Status.ERROR; + } + } + + public void open() { + stream.open(); + } + + @Override + public int compareTo(AsyncResult o) { + return this.query.id().compareTo(o.query.id()); + } + + public Path getTempFilePath() { + return stream.getTempFilePath(); + } + +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/CountV3Processor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/CountV3Processor.java new file mode 100644 index 000000000..e5d6b2264 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/CountV3Processor.java @@ -0,0 +1,242 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.v3; + +import com.google.common.collect.Sets; +import edu.harvard.hms.dbmi.avillach.hpds.data.genomic.VariantUtils; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.KeyAndValue; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicFilterType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import edu.harvard.hms.dbmi.avillach.hpds.processing.PatientAndConceptCount; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Component; + +import java.util.*; +import java.util.concurrent.ConcurrentHashMap; +import java.util.stream.Collectors; + +/** + * Note: This class was copied from {@link edu.harvard.hms.dbmi.avillach.hpds.processing.CountProcessor} and updated to use new Query entity + */ +@Component +public class CountV3Processor implements HpdsV3Processor { + + private final static Logger log = LoggerFactory.getLogger(CountV3Processor.class); + + private final QueryExecutor queryExecutor; + + private final PhenotypicObservationStore phenotypicObservationStore; + + @Autowired + public CountV3Processor(QueryExecutor queryExecutor, PhenotypicObservationStore phenotypicObservationStore) { + this.queryExecutor = queryExecutor; + this.phenotypicObservationStore = phenotypicObservationStore; + } + + /** + * Count processor always returns same headers + */ + @Override + public String[] getHeaderRow(Query query) { + return new String[] {"Patient ID", "Count"}; + } + + /** + * Retrieves a list of patient ids that are valid for the query result and returns the size of that list. + * + * @param query + * @return + */ + public int runCounts(Query query) { + return queryExecutor.getPatientSubsetForQuery(query).size(); + } + + + /** + * Returns a separate observation count for each field in query.crossCountFields when that field is added as a requiredFields entry for + * the base query. + * + * @param query + * @return + */ + public Map runObservationCrossCounts(Query query) { + TreeMap counts = new TreeMap<>(); + Set baseQueryPatientSet = queryExecutor.getPatientSubsetForQuery(query); + query.select().parallelStream().forEach((String concept) -> { + try { + phenotypicObservationStore.getCube(concept).ifPresent(cube -> { + int observationCount = (int) Arrays.stream(cube.sortedByKey()).filter(keyAndValue -> { + return baseQueryPatientSet.contains(keyAndValue.getKey()); + }).count(); + counts.put(concept, observationCount); + }); + } catch (Exception e) { + counts.put(concept, -1); + } + }); + return counts; + } + + /** + * Returns a separate count for each field in query.crossCountFields when that field is added as a requiredFields entry for the base + * query. + * + * @param query + * @return + */ + public Map runCrossCounts(Query query) { + ConcurrentHashMap counts = new ConcurrentHashMap<>(); + Set baseQueryPatientSet = queryExecutor.getPatientSubsetForQuery(query); + query.select().parallelStream().forEach((String concept) -> { + try { + Query safeCopy = new Query( + List.of(), List.of(), new PhenotypicFilter(PhenotypicFilterType.REQUIRED, concept, null, null, null, null), List.of(), + null, null, null + ); + int matchingPatients = Sets.intersection(queryExecutor.getPatientSubsetForQuery(safeCopy), baseQueryPatientSet).size(); + counts.put(concept, matchingPatients); + } catch (Exception e) { + counts.put(concept, -1); + } + }); + return counts; + } + + /** + * Returns a separate count for each field in the requiredFields and categoryFilters query.

    The v3 query lets a user add multiple + * filters on the same variable (e.g. sex=male OR sex=female). Filters are grouped by concept path so each variable produces exactly one + * entry rather than later filters overwriting earlier ones.

    A cross count reports each concept's distribution across the cohort. A + * category is included when it has members in the cohort, OR when it was explicitly named ("called out") by a value filter. This means + * a value filter never hides cohort members that arrived via an OR branch on another concept (sex=male OR age-required still shows + * females that have an age), while a value the user specifically asked for is always shown even when its cohort count is zero. + * Categories that are neither called out nor present in the cohort are omitted, so AND-narrowed concepts do not sprout empty bars. + * + * @param query + * @return a map of categorical data and their counts + */ + public Map> runCategoryCrossCounts(Query query) { + Set baseQueryPatientSet = queryExecutor.getPatientSubsetForQuery(query); + + Map> filtersByConcept = query.allFilters().stream().filter(this::isCategoryCrossCountFilter) + .collect(Collectors.groupingBy(PhenotypicFilter::conceptPath)); + + Map> categoryCounts = new TreeMap<>(); + for (Map.Entry> entry : filtersByConcept.entrySet()) { + String conceptPath = entry.getKey(); + + TreeMap> categoryMap = (TreeMap>) phenotypicObservationStore + .getCube(conceptPath).map(PhenoCube::getCategoryMap).orElseGet(TreeMap::new); + + Set calledOutValues = entry.getValue().stream().filter(PhenotypicFilter::isCategoricalFilter) + .flatMap(filter -> filter.values().stream()).collect(Collectors.toSet()); + + Map varCount = new TreeMap<>(); + categoryMap.forEach((String category, TreeSet patientSet) -> { + int count = Sets.intersection(patientSet, baseQueryPatientSet).size(); + if (count > 0 || calledOutValues.contains(category)) { + varCount.put(category, count); + } + }); + categoryCounts.put(conceptPath, varCount); + } + return categoryCounts; + } + + /** + * A categorical cross count is produced for value filters and for REQUIRED filters on categorical concepts, excluding variant-spec + * paths. A REQUIRED filter on a continuous concept is gated out here (it is handled by {@link #runContinuousCrossCounts}); otherwise it + * would be admitted and rely on the cube having no category map to avoid emitting a meaningless empty entry. + */ + private boolean isCategoryCrossCountFilter(PhenotypicFilter filter) { + if (VariantUtils.pathIsVariantSpec(filter.conceptPath())) { + return false; + } + if (filter.isCategoricalFilter()) { + return true; + } + return PhenotypicFilterType.REQUIRED.equals(filter.phenotypicFilterType()) + && Optional.ofNullable(queryExecutor.getDictionary().get(filter.conceptPath())).map(meta -> meta.isCategorical()).orElse(false); + } + + /** + * Returns the distribution of observed values for each continuous concept in the query.

    A continuous concept reports the + * distribution of every observed value across the cohort. Each filter's min/max only constrains the cohort (handled by the query + * executor); it does not limit which values are shown. So a range filter never hides cohort members that arrived via an OR branch on + * another concept (age>50 OR sex=male still shows the younger ages of the OR'd males), and multiple range filters on the same + * concept collapse to one entry since every patient is counted once from the cube. + * + * @param query + * @return a map of numerical data and their counts + */ + public Map> runContinuousCrossCounts(Query query) { + Set baseQueryPatientSet = queryExecutor.getPatientSubsetForQuery(query); + + Set conceptPaths = query.allFilters().stream().filter(this::isContinuousCrossCountFilter).map(PhenotypicFilter::conceptPath) + .collect(Collectors.toCollection(LinkedHashSet::new)); + + Map> conceptMap = new TreeMap<>(); + for (String conceptPath : conceptPaths) { + KeyAndValue[] pairs = phenotypicObservationStore.getCube(conceptPath) + .map(phenoCube -> ((PhenoCube) phenoCube).getEntriesForValueRange(null, null)) + .orElseGet(() -> new KeyAndValue[] {}); + Map countMap = new TreeMap<>(); + for (KeyAndValue patientConceptPair : pairs) { + if (baseQueryPatientSet.contains(patientConceptPair.getKey())) { + countMap.merge((double) patientConceptPair.getValue(), 1, Integer::sum); + } + } + conceptMap.put(conceptPath, countMap); + } + return conceptMap; + } + + private boolean isContinuousCrossCountFilter(PhenotypicFilter phenotypicFilter) { + return Optional.ofNullable(queryExecutor.getDictionary().get(phenotypicFilter.conceptPath())).map(meta -> !meta.isCategorical()) + .orElse(false); + } + + /** + * Until we have a count based query that takes longer than 30 seconds to run, we should discourage running them asynchronously in the + * backend as this results in unnecessary request-response cycles. + */ + @Override + public void runQuery(Query query, AsyncResult asyncResult) { + throw new UnsupportedOperationException("Counts do not run asynchronously."); + } + + /** + * Process only variantInfoFilters to count the number of variants that would be included in evaluating the query. + * + * This does not actually evaluate a patient set for the query. + * + * @param query + * @return the number of variants that would be used to filter patients if the incomingQuery was run as a COUNT query. + */ + public Map runVariantCount(Query query) { + TreeMap response = new TreeMap(); + // if(!query.getVariantInfoFilters().isEmpty()) { + if (!query.genomicFilters().isEmpty()) { + response.put("count", queryExecutor.getVariantList(query).size()); + response.put("message", "Query ran successfully"); + } else { + response.put("count", "0"); + response.put("message", "No variant filters were supplied, so no query was run."); + } + return response; + } + + public PatientAndConceptCount runPatientAndConceptCount(Query incomingQuery) { + log.info("Starting Patient and Concept Count query {}", incomingQuery.picsureId()); + log.info("Calculating available concepts"); + long concepts = incomingQuery.select().stream().map(phenotypicObservationStore::getCube).filter(Optional::isPresent).count(); + log.info("Calculating patient counts"); + int patients = runCounts(incomingQuery); + PatientAndConceptCount patientAndConceptCount = new PatientAndConceptCount(); + patientAndConceptCount.setConceptCount(concepts); + patientAndConceptCount.setPatientCount(patients); + log.info("Completed Patient and Concept Count query {}", incomingQuery.picsureId()); + return patientAndConceptCount; + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/HpdsV3Processor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/HpdsV3Processor.java new file mode 100644 index 000000000..69baf28ce --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/HpdsV3Processor.java @@ -0,0 +1,10 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.v3; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; + +public interface HpdsV3Processor { + + String[] getHeaderRow(Query query); + + void runQuery(Query query, AsyncResult asyncResult); +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/MultiValueQueryV3Processor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/MultiValueQueryV3Processor.java new file mode 100644 index 000000000..5d7b82fac --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/MultiValueQueryV3Processor.java @@ -0,0 +1,124 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.v3; + +import com.google.common.collect.Lists; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.KeyAndValue; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Component; + +import java.util.*; +import java.util.concurrent.ConcurrentHashMap; +import java.util.stream.Collectors; + +/** + * Note: This class was copied from {@link edu.harvard.hms.dbmi.avillach.hpds.processing.MultiValueQueryProcessor} and updated to use new + * Query entity + */ +@Component +public class MultiValueQueryV3Processor implements HpdsV3Processor { + + public static final String PATIENT_ID_FIELD_NAME = "patient_id"; + private final int idBatchSize; + private final QueryExecutor queryExecutor; + + private final PhenotypicObservationStore phenotypicObservationStore; + + private static final Logger log = LoggerFactory.getLogger(MultiValueQueryV3Processor.class); + + + @Autowired + public MultiValueQueryV3Processor( + QueryExecutor queryExecutor, PhenotypicObservationStore phenotypicObservationStore, @Value("${ID_BATCH_SIZE:0}") int idBatchSize + ) { + this.queryExecutor = queryExecutor; + this.idBatchSize = idBatchSize; + this.phenotypicObservationStore = phenotypicObservationStore; + } + + @Override + public String[] getHeaderRow(Query query) { + String[] header = new String[query.select().size() + 1]; + header[0] = PATIENT_ID_FIELD_NAME; + System.arraycopy(query.select().toArray(new String[0]), 0, header, 1, query.select().size()); + return header; + } + + @Override + public void runQuery(Query query, AsyncResult result) { + Set idList = queryExecutor.getPatientSubsetForQuery(query); + log.info("Processing " + idList.size() + " rows for result " + result.getId()); + Lists.partition(new ArrayList<>(idList), idBatchSize).forEach(patientIds -> { + Map>> pathToPatientToValueMap = buildResult(query, new TreeSet<>(patientIds)); + // A list of values per concept path, per patient + List>> fieldValuesPerPatient = + patientIds.stream().map(patientId -> Arrays.stream(getHeaderRow(query)).map(field -> { + if (PATIENT_ID_FIELD_NAME.equals(field)) { + return List.of(patientId.toString()); + } else { + Map> integerListMap = pathToPatientToValueMap.get(field); + if (integerListMap != null) { + return integerListMap.get(patientId); + } + return new ArrayList(); + } + }).collect(Collectors.toList())).collect(Collectors.toList()); + result.appendMultiValueResults(fieldValuesPerPatient); + }); + result.closeWriter(); + } + + private Map>> buildResult(Query query, TreeSet ids) { + ConcurrentHashMap>> pathToPatientToValueMap = new ConcurrentHashMap<>(); + List columns = query.select().stream().map(queryExecutor.getDictionary()::get).filter(Objects::nonNull).toList(); + List paths = columns.stream().map(ColumnMeta::getName).collect(Collectors.toList()); + int columnCount = paths.size() + 1; + + ArrayList columnIndex = queryExecutor.useResidentCubesFirst(paths, columnCount); + + // todo: investigate if the parallel stream will thrash the cache if the number of executors is > number of resident cubes + columnIndex.parallelStream().forEach((columnId) -> { + String columnPath = paths.get(columnId - 1); + Map> patientIdToValueMap = processColumn(ids, columnPath); + pathToPatientToValueMap.put(columnPath, patientIdToValueMap); + }); + + return pathToPatientToValueMap; + } + + private Map> processColumn(TreeSet patientIds, String path) { + + Map> patientIdToValueMap = new HashMap<>(); + Optional> cubeOptional = phenotypicObservationStore.getCube(path); + + return cubeOptional.map(cube -> { + KeyAndValue[] cubeValues = cube.sortedByKey(); + + int idPointer = 0; + for (int patientId : patientIds) { + while (idPointer < cubeValues.length) { + int key = cubeValues[idPointer].getKey(); + if (key < patientId) { + idPointer++; + } else if (key == patientId) { + String value = getResultField(cubeValues, idPointer); + patientIdToValueMap.computeIfAbsent(patientId, k -> new ArrayList<>()).add(value); + idPointer++; + } else { + break; + } + } + } + return patientIdToValueMap; + }).orElseGet(Map::of); + } + + private String getResultField(KeyAndValue[] cubeValues, int idPointer) { + Comparable value = cubeValues[idPointer].getValue(); + return value.toString(); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/PatientV3Processor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/PatientV3Processor.java new file mode 100644 index 000000000..072446a08 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/PatientV3Processor.java @@ -0,0 +1,42 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.v3; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Component; + +import java.util.List; + +/** + * Note: This class was copied from {@link edu.harvard.hms.dbmi.avillach.hpds.processing.patient.PatientProcessor} and updated to use new + * Query entity + */ +@Component +public class PatientV3Processor implements HpdsV3Processor { + + private static final Logger LOG = LoggerFactory.getLogger(PatientV3Processor.class); + private final QueryExecutor queryExecutor; + + @Autowired + public PatientV3Processor(QueryExecutor queryExecutor) { + this.queryExecutor = queryExecutor; + } + + @Override + public String[] getHeaderRow(Query query) { + return new String[] {"PATIENT_NUM"}; + } + + @Override + public void runQuery(Query query, AsyncResult asyncResult) { + LOG.info("Pulling results for query {}", query.id()); + // floating all this in memory is a bit gross, but the whole list of + // patient IDs was already there, so I don't feel too bad + List allPatients = + queryExecutor.getPatientSubsetForQuery(query).stream().map(patient -> new String[] {patient.toString()}).toList(); + LOG.info("Writing results for query {}", query.id()); + asyncResult.appendResults(allPatients); + LOG.info("Completed query {}", query.id()); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/PhenotypicFilterValidator.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/PhenotypicFilterValidator.java new file mode 100644 index 000000000..20a111b1b --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/PhenotypicFilterValidator.java @@ -0,0 +1,73 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.v3; + +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.AuthorizationFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicFilter; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.stereotype.Component; + +import java.util.Map; + +@Component +public class PhenotypicFilterValidator { + + private static final Logger log = LoggerFactory.getLogger(PhenotypicFilterValidator.class); + + public void validate(PhenotypicFilter phenotypicFilter, Map metaStore) { + switch (phenotypicFilter.phenotypicFilterType()) { + case FILTER -> validateFilterFilter(phenotypicFilter, metaStore); + case REQUIRED -> validateRequiredFilter(phenotypicFilter, metaStore); + case ANY_RECORD_OF -> validateAnyRecordOfFilter(phenotypicFilter); + } + } + + public void validate(AuthorizationFilter authorizationFilter, Map metaStore) { + if (authorizationFilter.values() == null || authorizationFilter.values().isEmpty()) { + throw new IllegalArgumentException("AuthorizationFilter values cannot be null or empty"); + } + if (!metaStore.containsKey(authorizationFilter.conceptPath())) { + throw new IllegalArgumentException(authorizationFilter.conceptPath() + " is not a valid concept path"); + } + if (!metaStore.get(authorizationFilter.conceptPath()).isCategorical()) { + throw new IllegalArgumentException( + authorizationFilter.conceptPath() + " is not a categorical variable. Authorization filters must be categorical" + ); + } + } + + private void validateFilterFilter(PhenotypicFilter phenotypicFilter, Map metaStore) { + if ( + (phenotypicFilter.min() != null || phenotypicFilter.max() != null) && phenotypicFilter.values() != null + && !phenotypicFilter.values().isEmpty() + ) { + throw new IllegalArgumentException( + "Filter with concept path " + phenotypicFilter.conceptPath() + " cannot have both categorical values and min/max set" + ); + } else if (!metaStore.containsKey(phenotypicFilter.conceptPath())) { + log.debug(phenotypicFilter.conceptPath() + " is not a valid concept path"); + } else if (phenotypicFilter.isCategoricalFilter() && !metaStore.get(phenotypicFilter.conceptPath()).isCategorical()) { + throw new IllegalArgumentException(phenotypicFilter.conceptPath() + " is not a categorical variable"); + } else if (phenotypicFilter.isNumericFilter() && metaStore.get(phenotypicFilter.conceptPath()).isCategorical()) { + throw new IllegalArgumentException(phenotypicFilter.conceptPath() + " is not a numeric variable"); + } + } + + private void validateRequiredFilter(PhenotypicFilter phenotypicFilter, Map metaStore) { + if (phenotypicFilter.min() != null || phenotypicFilter.max() != null || phenotypicFilter.values() != null) { + throw new IllegalArgumentException( + "Required filter with concept path " + phenotypicFilter.conceptPath() + " cannot have categorical values or min/max set" + ); + } else if (!metaStore.containsKey(phenotypicFilter.conceptPath())) { + log.debug(phenotypicFilter.conceptPath() + " is not a valid concept path"); + } + } + + private void validateAnyRecordOfFilter(PhenotypicFilter phenotypicFilter) { + if (phenotypicFilter.min() != null || phenotypicFilter.max() != null || phenotypicFilter.values() != null) { + throw new IllegalArgumentException( + "Required filter with concept path " + phenotypicFilter.conceptPath() + " cannot have categorical values or min/max set" + ); + } + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/PhenotypicObservationStore.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/PhenotypicObservationStore.java new file mode 100644 index 000000000..ffd9f37dd --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/PhenotypicObservationStore.java @@ -0,0 +1,131 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.v3; + +import com.google.common.cache.CacheBuilder; +import com.google.common.cache.CacheLoader; +import com.google.common.cache.LoadingCache; +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.processing.PhenotypeMetaStore; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Component; + +import java.io.*; +import java.util.*; +import java.util.concurrent.ExecutionException; + +/** + * Class representing a store for phenotypic observations. The store manages caching of PhenoCube objects. + */ +@Component +public class PhenotypicObservationStore { + + private static final Logger log = LoggerFactory.getLogger(PhenotypicObservationStore.class); + + + private final LoadingCache> phenoCubeCache; + + private final String hpdsDataDirectory; + + private final PhenotypeMetaStore phenotypeMetaStore; + + @Autowired + public PhenotypicObservationStore( + PhenotypeMetaStore phenotypeMetaStore, @Value("${HPDS_DATA_DIRECTORY:/opt/local/hpds/}") String hpdsDataDirectory, + @Value("${CACHE_SIZE:100}") int cacheSize + ) { + this.phenotypeMetaStore = phenotypeMetaStore; + this.hpdsDataDirectory = hpdsDataDirectory; + phenoCubeCache = CacheBuilder.newBuilder().maximumSize(cacheSize).build(new CacheLoader<>() { + public PhenoCube load(String key) { + return loadPhenoCube(key); + } + }); + } + + // Constructor for testing only + public PhenotypicObservationStore( + PhenotypeMetaStore phenotypeMetaStore, LoadingCache> phenoCubeCache, int cacheSize + ) { + this.phenotypeMetaStore = phenotypeMetaStore; + this.phenoCubeCache = phenoCubeCache; + this.hpdsDataDirectory = ""; + } + + /** + * For a given key (concept path), loads a PhenoCube from allObservationsStore.javabin in the configured hpdsDataDirectory. Throws an + * exception if not found + * @param key concept path to load a PhenoCube for + * @return the PhenoCube for this key + */ + public PhenoCube loadPhenoCube(String key) { + try (RandomAccessFile allObservationsStore = new RandomAccessFile(hpdsDataDirectory + "allObservationsStore.javabin", "r");) { + ColumnMeta columnMeta = phenotypeMetaStore.getColumnMeta(key); + if (columnMeta != null) { + allObservationsStore.seek(columnMeta.getAllObservationsOffset()); + int length = (int) (columnMeta.getAllObservationsLength() - columnMeta.getAllObservationsOffset()); + byte[] buffer = new byte[length]; + allObservationsStore.read(buffer); + allObservationsStore.close(); + try (ObjectInputStream inStream = new ObjectInputStream(new ByteArrayInputStream(Crypto.decryptData(buffer)))) { + return (PhenoCube) inStream.readObject(); + } + } else { + log.warn("ColumnMeta not found for : [{}]", key); + return null; + } + } catch (IOException | ClassNotFoundException e) { + throw new RuntimeException(e); + } + } + + /** + * Gets all keys (patient ids) with at least one value inside the specified range for a given concept path. + */ + public Set getKeysForRange(String conceptPath, Double min, Double max) { + return getCube(conceptPath).map(cube -> ((PhenoCube) cube).getKeysForRange(min, max)).orElseGet(Set::of); + } + + /** + * Gets all keys (patient ids) with at least one matching value for a given concept path. + */ + public Set getKeysForValues(String conceptPath, Collection values) { + return getCube(conceptPath).map(cube -> { + return values.stream().map(value -> ((PhenoCube) cube).getKeysForValue(value)).reduce((set1, set2) -> { + Set union = new HashSet<>(set1); + union.addAll(set2); + return union; + }).orElseGet(Set::of); + }).orElseGet(Set::of); + } + + + /** + * Gets all keys (patient ids) for a given concept path. This returns any patient with at least one value for this concept path + */ + public List getAllKeys(String conceptPath) { + return getCube(conceptPath).map(PhenoCube::keyBasedIndex).orElseGet(List::of); + } + + /** + * Get a cube without throwing an error if not found. Useful for federated pic-sure's where there are fewer guarantees about concept + * paths. + */ + public Optional> getCube(String path) { + try { + return Optional.of(phenoCubeCache.get(path)); + } catch (CacheLoader.InvalidCacheLoadException | ExecutionException e) { + return Optional.empty(); + } + } + + /** + * Gets currently cached keys. This can be useful for ordering a large number of lookups and avoiding cache churn + */ + public Set getCachedKeys() { + return phenoCubeCache.asMap().keySet(); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/PhenotypicQueryExecutor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/PhenotypicQueryExecutor.java new file mode 100644 index 000000000..50df9bd3f --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/PhenotypicQueryExecutor.java @@ -0,0 +1,149 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.v3; + +import com.google.common.collect.Sets; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.*; +import edu.harvard.hms.dbmi.avillach.hpds.processing.PhenotypeMetaStore; +import edu.harvard.hms.dbmi.avillach.hpds.processing.util.SetUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Component; + +import java.util.*; +import java.util.function.BinaryOperator; +import java.util.stream.Collectors; + +@Component +public class PhenotypicQueryExecutor { + + private static Logger log = LoggerFactory.getLogger(PhenotypicQueryExecutor.class); + + private final PhenotypeMetaStore phenotypeMetaStore; + + private final PhenotypicObservationStore phenotypicObservationStore; + + @Autowired + public PhenotypicQueryExecutor(PhenotypeMetaStore phenotypeMetaStore, PhenotypicObservationStore phenotypicObservationStore) { + this.phenotypeMetaStore = phenotypeMetaStore; + this.phenotypicObservationStore = phenotypicObservationStore; + } + + public Set getPatientSet(Query query) { + List mergedClauses = new ArrayList<>(); + + List authorizationClauses = authorizationFiltersToPhenotypicClause(query.authorizationFilters()); + mergedClauses.addAll(authorizationClauses); + + if (query.phenotypicClause() != null) { + mergedClauses.add(query.phenotypicClause()); + } + + if (!mergedClauses.isEmpty()) { + PhenotypicSubquery authorizedSubquery = new PhenotypicSubquery(null, mergedClauses, Operator.AND); + return evaluatePhenotypicClause(authorizedSubquery); + } else { + // if there are no phenotypic queries, return all patients + return phenotypeMetaStore.getPatientIds(); + } + } + + private List authorizationFiltersToPhenotypicClause(List authorizationFilters) { + return authorizationFilters.parallelStream().map(authorizationFilter -> { + return new PhenotypicFilter( + PhenotypicFilterType.FILTER, authorizationFilter.conceptPath(), authorizationFilter.values(), null, null, null + ); + }).collect(Collectors.toList()); + } + + private Set evaluatePhenotypicClause(PhenotypicClause phenotypicClause) { + return switch (phenotypicClause) { + case PhenotypicSubquery phenotypicSubquery -> evaluatePhenotypicSubquery(phenotypicSubquery); + case PhenotypicFilter phenotypicFilter -> evaluatePhenotypicFilter(phenotypicFilter); + }; + } + + private Set evaluatePhenotypicFilter(PhenotypicFilter phenotypicFilter) { + return switch (phenotypicFilter.phenotypicFilterType()) { + case FILTER -> evaluateFilterFilter(phenotypicFilter); + case REQUIRED -> evaluateRequiredFilter(phenotypicFilter); + case ANY_RECORD_OF -> evaluateAnyRecordOfFilter(phenotypicFilter); + }; + } + + private Set evaluateAnyRecordOfFilter(PhenotypicFilter phenotypicFilter) { + Set matchingConcepts = phenotypeMetaStore.getChildConceptPaths(phenotypicFilter.conceptPath()); + Set ids = new TreeSet<>(); + for (String concept : matchingConcepts) { + ids.addAll(phenotypicObservationStore.getAllKeys(concept)); + } + return ids; + } + + private Set evaluateFilterFilter(PhenotypicFilter phenotypicFilter) { + if (phenotypicFilter.values() != null) { + return phenotypicObservationStore.getKeysForValues(phenotypicFilter.conceptPath(), phenotypicFilter.values()); + } else if (phenotypicFilter.max() != null || phenotypicFilter.min() != null) { + return phenotypicObservationStore + .getKeysForRange(phenotypicFilter.conceptPath(), phenotypicFilter.min(), phenotypicFilter.max()); + } else { + throw new IllegalArgumentException("Either values or one of min/max must be set for a filter"); + } + } + + private Set evaluateRequiredFilter(PhenotypicFilter phenotypicFilter) { + return new HashSet<>(phenotypicObservationStore.getAllKeys(phenotypicFilter.conceptPath())); + } + + private Set evaluatePhenotypicSubquery(PhenotypicSubquery phenotypicSubquery) { + return phenotypicSubquery.phenotypicClauses().parallelStream().map(this::evaluatePhenotypicClause) + .reduce(getReducer(phenotypicSubquery.operator())) + // todo: deal with empty lists + .get(); + } + + private BinaryOperator> getReducer(Operator operator) { + return switch (operator) { + case OR -> SetUtils::union; + case AND -> SetUtils::intersection; + }; + } + + /** + * If there are concepts in the list of paths which are already in the cache, push those to the front of the list so that we don't evict + * and then reload them for concepts which are not yet in the cache. + * + * @param paths + * @param columnCount + * @return + */ + public ArrayList useResidentCubesFirst(List paths, int columnCount) { + int x; + TreeSet pathSet = new TreeSet<>(paths); + Set residentKeys = Sets.intersection(pathSet, phenotypicObservationStore.getCachedKeys()); + + ArrayList columnIndex = new ArrayList(); + + residentKeys.forEach(key -> { + columnIndex.add(paths.indexOf(key) + 1); + }); + + Sets.difference(pathSet, residentKeys).forEach(key -> { + columnIndex.add(paths.indexOf(key) + 1); + }); + + for (x = 1; x < columnCount; x++) { + columnIndex.add(x); + } + return columnIndex; + } + + + public Map getMetaStore() { + return phenotypeMetaStore.getMetaStore(); + } + + public Set getPatientIds() { + return phenotypeMetaStore.getPatientIds(); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/QueryExecutor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/QueryExecutor.java new file mode 100644 index 000000000..9e55f16b8 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/QueryExecutor.java @@ -0,0 +1,167 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.v3; + +import com.google.common.util.concurrent.UncheckedExecutionException; +import edu.harvard.hms.dbmi.avillach.hpds.data.genomic.VariantUtils; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.InfoColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariableVariantMasks; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMask; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Filter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import edu.harvard.hms.dbmi.avillach.hpds.processing.DistributableQuery; +import edu.harvard.hms.dbmi.avillach.hpds.processing.GenomicProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.PhenotypeMetaStore; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Component; +import reactor.core.publisher.Mono; + +import java.util.*; +import java.util.stream.Collectors; + + +@Component +public class QueryExecutor { + + private static Logger log = LoggerFactory.getLogger(QueryExecutor.class); + + + private final GenomicProcessor genomicProcessor; + + private final PhenotypicQueryExecutor phenotypicQueryExecutor; + + private final PhenotypeMetaStore phenotypeMetaStore; + + + @Autowired + public QueryExecutor( + GenomicProcessor genomicProcessor, PhenotypicQueryExecutor phenotypicQueryExecutor, PhenotypeMetaStore phenotypeMetaStore + ) { + this.genomicProcessor = genomicProcessor; + this.phenotypicQueryExecutor = phenotypicQueryExecutor; + this.phenotypeMetaStore = phenotypeMetaStore; + } + + public Set getInfoStoreColumns() { + return genomicProcessor.getInfoStoreColumns(); + } + + + + /** + * Executes a query and returns the ids of all matching patients + * + * @param query + * @return + */ + public Set getPatientSubsetForQuery(Query query) { + Set patientIdSet = phenotypicQueryExecutor.getPatientSet(query); + DistributableQuery distributableQuery = queryToDistributableQuery(query, patientIdSet); + // NULL (representing no phenotypic filters, i.e. all patients) or not empty patient ID sets require a genomic query. + // Otherwise, short circuit and return no patients + if ( + (distributableQuery.getPatientIds() == null || !distributableQuery.getPatientIds().isEmpty()) && distributableQuery.hasFilters() + ) { + Mono patientMaskForVariantInfoFilters = genomicProcessor.getPatientMask(distributableQuery); + return patientMaskForVariantInfoFilters.map(genomicProcessor::patientMaskToPatientIdSet).block(); + } + + if (distributableQuery.getPatientIds() == null) { + return phenotypicQueryExecutor.getPatientIds(); + } + return distributableQuery.getPatientIds(); + } + + private DistributableQuery queryToDistributableQuery(Query query, Set patientIds) { + DistributableQuery distributableQuery = new DistributableQuery().setPatientIds(patientIds); + + if (query.genomicFilters().isEmpty()) { + return distributableQuery; + } + + edu.harvard.hms.dbmi.avillach.hpds.data.query.Query.VariantInfoFilter variantInfoFilters = + new edu.harvard.hms.dbmi.avillach.hpds.data.query.Query.VariantInfoFilter(); + variantInfoFilters.numericVariantInfoFilters = new HashMap<>(); + variantInfoFilters.categoryVariantInfoFilters = new HashMap<>(); + + query.genomicFilters().forEach(genomicFilter -> { + if (VariantUtils.pathIsVariantSpec(genomicFilter.key())) { + if (genomicFilter.values() == null || genomicFilter.values().isEmpty()) { + distributableQuery.addVariantSpecCategoryFilter(genomicFilter.key(), new String[] {"0/1", "1/1"}); + } else { + distributableQuery.addVariantSpecCategoryFilter(genomicFilter.key(), genomicFilter.values().toArray(new String[0])); + } + + } else { + if (genomicFilter.values() != null) { + variantInfoFilters.categoryVariantInfoFilters.put(genomicFilter.key(), genomicFilter.values().toArray(new String[0])); + } else if (genomicFilter.max() != null || genomicFilter.min() != null) { + variantInfoFilters.numericVariantInfoFilters + .put(genomicFilter.key(), new Filter.FloatFilter(genomicFilter.min(), genomicFilter.max())); + } + } + }); + + distributableQuery.setVariantInfoFilters(List.of(variantInfoFilters)); + return distributableQuery; + } + + public Collection getVariantList(Query query) { + Set patientIdSet = phenotypicQueryExecutor.getPatientSet(query); + DistributableQuery distributableQuery = queryToDistributableQuery(query, patientIdSet); + return genomicProcessor.getVariantList(distributableQuery).block(); + } + + public List getInfoStoreMeta() { + return genomicProcessor.getInfoColumnMeta(); + } + + public List searchInfoConceptValues(String conceptPath, String query) { + try { + return genomicProcessor.getInfoStoreValues(conceptPath).stream() + .filter(variableValue -> variableValue.toUpperCase(Locale.ENGLISH).contains(query.toUpperCase(Locale.ENGLISH))) + .collect(Collectors.toList()); + } catch (UncheckedExecutionException e) { + if (e.getCause() instanceof RuntimeException) { + throw (RuntimeException) e.getCause(); + } + throw e; + } + } + + + public ArrayList useResidentCubesFirst(List paths, int columnCount) { + return phenotypicQueryExecutor.useResidentCubesFirst(paths, columnCount); + } + + public Map getDictionary() { + return phenotypicQueryExecutor.getMetaStore(); + } + + public List getPatientIds() { + return genomicProcessor.getPatientIds(); + } + + public Optional getMasks(String path, VariantBucketHolder variantMasksVariantBucketHolder) { + return genomicProcessor.getMasks(path, variantMasksVariantBucketHolder); + } + + // todo: handle this locally, we do not want this in the genomic processor + protected VariantMask createMaskForPatientSet(Set patientSubset) { + return genomicProcessor.createMaskForPatientSet(patientSubset); + } + + public SequencedSet getAllConceptPaths(Query query) { + SequencedSet allConceptPaths = new LinkedHashSet<>(query.select()); + List allFilterPaths = + query.allFilters().stream().flatMap(phenotypicFilter -> (switch (phenotypicFilter.phenotypicFilterType()) { + case FILTER, REQUIRED -> List.of(phenotypicFilter.conceptPath()); + case ANY_RECORD_OF -> phenotypeMetaStore.getChildConceptPaths(phenotypicFilter.conceptPath()); + }).stream()).toList(); + allConceptPaths.addAll(allFilterPaths); + return allConceptPaths; + } + +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/QueryV3Processor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/QueryV3Processor.java new file mode 100644 index 000000000..ddb671f89 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/QueryV3Processor.java @@ -0,0 +1,215 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.v3; + +import com.google.common.collect.Lists; +import edu.harvard.hms.dbmi.avillach.hpds.data.genomic.VariantUtils; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariableVariantMasks; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.KeyAndValue; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import edu.harvard.hms.dbmi.avillach.hpds.processing.ResultStore; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Component; + +import java.nio.ByteBuffer; +import java.util.*; +import java.util.stream.Collectors; + +/** + * This class handles DATAFRAME export queries for HPDS. + * @author nchu + * + * Note: This class was copied from {@link edu.harvard.hms.dbmi.avillach.hpds.processing.QueryProcessor} and updated to use new + * Query entity + */ +@Component +public class QueryV3Processor implements HpdsV3Processor { + + private static final byte[] EMPTY_STRING_BYTES = "".getBytes(); + private static final Logger log = LoggerFactory.getLogger(QueryV3Processor.class); + + private final int idBatchSize; + + private final QueryExecutor queryExecutor; + + private final PhenotypicObservationStore phenotypicObservationStore; + + @Autowired + public QueryV3Processor( + QueryExecutor queryExecutor, PhenotypicObservationStore phenotypicObservationStore, @Value("${ID_BATCH_SIZE:0}") int idBatchSize + ) { + this.queryExecutor = queryExecutor; + this.phenotypicObservationStore = phenotypicObservationStore; + this.idBatchSize = idBatchSize; + } + + @Override + public String[] getHeaderRow(Query query) { + String[] header = new String[query.select().size() + 1]; + header[0] = "Patient ID"; + System.arraycopy(query.select().toArray(new String[0]), 0, header, 1, query.select().size()); + return header; + } + + public void runQuery(Query query, AsyncResult result) { + Set idList = queryExecutor.getPatientSubsetForQuery(query); + log.info("Processing " + idList.size() + " rows for result " + result.getId()); + Lists.partition(new ArrayList<>(idList), idBatchSize).parallelStream().map(list -> buildResult(result, query, new TreeSet<>(list))) + .sequential().forEach(result::appendResultStore); + } + + + private ResultStore buildResult(AsyncResult result, Query query, TreeSet ids) { + List columns = + query.select().stream().map(queryExecutor.getDictionary()::get).filter(Objects::nonNull).collect(Collectors.toList()); + List paths = columns.stream().map(ColumnMeta::getName).collect(Collectors.toList()); + int columnCount = paths.size() + 1; + + ArrayList columnIndex = queryExecutor.useResidentCubesFirst(paths, columnCount); + ResultStore results = new ResultStore(result.getId(), columns, ids); + + columnIndex.parallelStream().forEach((column) -> { + clearColumn(paths, ids, results, column); + processColumn(paths, ids, results, column); + }); + + return results; + } + + private void clearColumn(List paths, TreeSet ids, ResultStore results, Integer x) { + String path = paths.get(x - 1); + if (VariantUtils.pathIsVariantSpec(path)) { + ByteBuffer doubleBuffer = ByteBuffer.allocate(Double.BYTES); + int idInSubsetPointer = 0; + for (int id : ids) { + writeVariantNullResultField(results, x, doubleBuffer, idInSubsetPointer); + idInSubsetPointer++; + } + } else { + phenotypicObservationStore.getCube(path).ifPresent(cube -> { + ByteBuffer doubleBuffer = ByteBuffer.allocate(Double.BYTES); + int idInSubsetPointer = 0; + for (int id : ids) { + writeNullResultField(results, x, cube, doubleBuffer, idInSubsetPointer); + idInSubsetPointer++; + } + }); + } + } + + private void processColumn(List paths, TreeSet ids, ResultStore results, Integer x) { + String path = paths.get(x - 1); + if (VariantUtils.pathIsVariantSpec(path)) { + // todo: confirm this entire if block is even used. I don't think it is + Optional masks = queryExecutor.getMasks(path, new VariantBucketHolder<>()); + List patientIds = queryExecutor.getPatientIds(); + int idPointer = 0; + + ByteBuffer doubleBuffer = ByteBuffer.allocate(Double.BYTES); + int idInSubsetPointer = 0; + for (int id : ids) { + while (idPointer < patientIds.size()) { + int key = Integer.parseInt(patientIds.get(idPointer)); + if (key < id) { + idPointer++; + } else if (key == id) { + idPointer = writeVariantResultField(results, x, masks, idPointer, idInSubsetPointer); + break; + } else { + writeVariantNullResultField(results, x, doubleBuffer, idInSubsetPointer); + break; + } + } + idInSubsetPointer++; + } + } else { + phenotypicObservationStore.getCube(path).ifPresent(cube -> { + KeyAndValue[] cubeValues = cube.sortedByKey(); + + int idPointer = 0; + + ByteBuffer doubleBuffer = ByteBuffer.allocate(Double.BYTES); + int idInSubsetPointer = 0; + for (int id : ids) { + while (idPointer < cubeValues.length) { + int key = cubeValues[idPointer].getKey(); + if (key < id) { + idPointer++; + } else if (key == id) { + idPointer = writeResultField(results, x, cube, cubeValues, idPointer, doubleBuffer, idInSubsetPointer); + break; + } else { + writeNullResultField(results, x, cube, doubleBuffer, idInSubsetPointer); + break; + } + } + idInSubsetPointer++; + } + }); + } + } + + private void writeVariantNullResultField(ResultStore results, Integer x, ByteBuffer doubleBuffer, int idInSubsetPointer) { + byte[] valueBuffer = null; + valueBuffer = EMPTY_STRING_BYTES; + results.writeField(x, idInSubsetPointer, valueBuffer); + } + + private int writeVariantResultField( + ResultStore results, Integer x, Optional variantMasks, int idPointer, int idInSubsetPointer + ) { + byte[] valueBuffer = variantMasks.map(masks -> { + if (masks.heterozygousMask != null && masks.heterozygousMask.testBit(idPointer)) { + return "0/1".getBytes(); + } else if (masks.homozygousMask != null && masks.homozygousMask.testBit(idPointer)) { + return "1/1".getBytes(); + } else { + return "0/0".getBytes(); + } + }).orElse("".getBytes()); + results.writeField(x, idInSubsetPointer, valueBuffer); + return idPointer; + } + + private int writeResultField( + ResultStore results, Integer x, PhenoCube cube, KeyAndValue[] cubeValues, int idPointer, ByteBuffer doubleBuffer, + int idInSubsetPointer + ) { + byte[] valueBuffer; + Comparable value = cubeValues[idPointer++].getValue(); + if (cube.isStringType()) { + valueBuffer = value.toString().getBytes(); + } else { + valueBuffer = doubleBuffer.putDouble((Double) value).array(); + doubleBuffer.clear(); + } + results.writeField(x, idInSubsetPointer, valueBuffer); + return idPointer; + } + + /** + * Correctly handle null records. A numerical value should be a NaN if it is missing to distinguish from a zero. A String based + * value(categorical) should be empty instead of null because the word null might be a valid value. + * + * @param results + * @param x + * @param cube + * @param doubleBuffer + * @param idInSubsetPointer + */ + private void writeNullResultField(ResultStore results, Integer x, PhenoCube cube, ByteBuffer doubleBuffer, int idInSubsetPointer) { + byte[] valueBuffer = null; + if (cube.isStringType()) { + valueBuffer = EMPTY_STRING_BYTES; + } else { + Double nullDouble = Double.NaN; + valueBuffer = doubleBuffer.putDouble(nullDouble).array(); + doubleBuffer.clear(); + } + results.writeField(x, idInSubsetPointer, valueBuffer); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/QueryValidator.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/QueryValidator.java new file mode 100644 index 000000000..eb436490f --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/QueryValidator.java @@ -0,0 +1,58 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.v3; + +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Component; + +import java.util.*; + +@Component +public class QueryValidator { + + private static final Logger log = LoggerFactory.getLogger(QueryValidator.class); + + private final PhenotypicQueryExecutor phenotypicQueryExecutor; + + private final PhenotypicFilterValidator phenotypicFilterValidator; + + private final boolean requireAuthorizationFilter; + + @Autowired + public QueryValidator( + PhenotypicQueryExecutor phenotypicQueryExecutor, PhenotypicFilterValidator phenotypicFilterValidator, + @Value("${hpds.requireAuthorizationFilter:true}") boolean requireAuthorizationFilter + ) { + this.phenotypicQueryExecutor = phenotypicQueryExecutor; + this.phenotypicFilterValidator = phenotypicFilterValidator; + this.requireAuthorizationFilter = requireAuthorizationFilter; + } + + public void validate(Query query) { + Map metaStore = phenotypicQueryExecutor.getMetaStore(); + + if (requireAuthorizationFilter) { + if (query.authorizationFilters().isEmpty()) { + log.warn( + "Authorization filter is required for this query. To disable this requirement, set hpds.requireAuthorizationFilter=false" + ); + throw new IllegalArgumentException("Authorization filter is required for this query"); + } + } + + query.allFilters().forEach(phenotypicFilter -> phenotypicFilterValidator.validate(phenotypicFilter, metaStore)); + + query.authorizationFilters().forEach(authorizationFilter -> { + phenotypicFilterValidator.validate(authorizationFilter, metaStore); + }); + + query.select().forEach(select -> { + if (!metaStore.containsKey(select)) { + log.debug(select + " is not a valid concept path"); + } + }); + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/TimeseriesV3Processor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/TimeseriesV3Processor.java new file mode 100644 index 000000000..da1745149 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/TimeseriesV3Processor.java @@ -0,0 +1,124 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.v3; + +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.KeyAndValue; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import edu.harvard.hms.dbmi.avillach.hpds.processing.timeseries.TimeSeriesConversionService; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Component; + +import java.io.IOException; +import java.util.*; + +/** + * A class for exporting datapoints from HPDS; this will export each individual input data as a unique row, allowing multiple data points + * (with time data) to be exported for a single patient/concept combination. + * + * This returns data in no meaningful order; it is exported by field parameters. Concepts which are present multiple times in a query will + * only be exported once. + * + * @author nchu + * + * Note: This class was copied from {@link edu.harvard.hms.dbmi.avillach.hpds.processing.timeseries.TimeseriesProcessor} and updated + * to use new Query entity + * + */ +@Component +public class TimeseriesV3Processor implements HpdsV3Processor { + + private static final Logger log = LoggerFactory.getLogger(TimeseriesV3Processor.class); + + private final QueryExecutor queryExecutor; + private final TimeSeriesConversionService conversionService; + + private final PhenotypicObservationStore phenotypicObservationStore; + + private final int idBatchSize; + + @Autowired + public TimeseriesV3Processor( + QueryExecutor queryExecutor, TimeSeriesConversionService conversionService, PhenotypicObservationStore phenotypicObservationStore, + @Value("${ID_BATCH_SIZE:0}") int idBatchSize + ) { + this.queryExecutor = queryExecutor; + this.conversionService = conversionService; + this.phenotypicObservationStore = phenotypicObservationStore; + this.idBatchSize = idBatchSize; + } + + /** + * FOr this type of export, the header is always the same + */ + @Override + public String[] getHeaderRow(Query query) { + return new String[] {"PATIENT_NUM", "CONCEPT_PATH", "NVAL_NUM", "TVAL_CHAR", "TIMESTAMP"}; + } + + @Override + public void runQuery(Query query, AsyncResult result) { + Set idList = queryExecutor.getPatientSubsetForQuery(query); + + if (idBatchSize > 0) { + try { + exportTimeData(query, result, idList); + } catch (IOException e) { + log.error("Exception exporting time data", e); + } + } else { + throw new RuntimeException("Data Export is not authorized for this system"); + } + } + + private void exportTimeData(Query query, AsyncResult result, Set idList) throws IOException { + log.info("Starting export for time series data of query {} (HPDS ID {})", query.picsureId(), query.id()); + Set exportedConceptPaths = new HashSet<>(); + Collection pathList = queryExecutor.getAllConceptPaths(query); + + addDataForConcepts(pathList, exportedConceptPaths, idList, result); + } + + private void addDataForConcepts( + Collection pathList, Set exportedConceptPaths, Set idList, AsyncResult result + ) { + for (String conceptPath : pathList) { + // skip concepts we may already have encountered + if (exportedConceptPaths.contains(conceptPath)) { + continue; + } + ArrayList dataEntries = new ArrayList<>(); + Optional> maybeCube = phenotypicObservationStore.getCube(conceptPath); + if (maybeCube.isEmpty()) { + log.warn("Attempting export of non-existant concept: {}", conceptPath); + continue; + } + PhenoCube cube = maybeCube.get(); + log.debug("Exporting " + conceptPath); + List valuesForKeys = cube.getValuesForKeys(idList); + for (Object kvObj : valuesForKeys) { + if (cube.isStringType()) { + KeyAndValue keyAndValue = (KeyAndValue) kvObj; + // "PATIENT_NUM","CONCEPT_PATH","NVAL_NUM","TVAL_CHAR","TIMESTAMP" + String[] entryData = {keyAndValue.getKey().toString(), conceptPath, "", keyAndValue.getValue(), + conversionService.toISOString(keyAndValue.getTimestamp())}; + dataEntries.add(entryData); + } else { // numeric + KeyAndValue keyAndValue = (KeyAndValue) kvObj; + // "PATIENT_NUM","CONCEPT_PATH","NVAL_NUM","TVAL_CHAR","TIMESTAMP" + String[] entryData = {keyAndValue.getKey().toString(), conceptPath, keyAndValue.getValue().toString(), "", + conversionService.toISOString(keyAndValue.getTimestamp())}; + dataEntries.add(entryData); + } + // batch exports so we don't take double memory (valuesForKeys + dataEntries could be a lot of data points) + if (dataEntries.size() >= (idBatchSize > 0 ? 10 : idBatchSize)) { + result.appendResults(dataEntries); + dataEntries = new ArrayList<>(); + } + } + result.appendResults(dataEntries); + exportedConceptPaths.add(conceptPath); + } + } +} diff --git a/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/VariantListV3Processor.java b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/VariantListV3Processor.java new file mode 100644 index 000000000..580fcdc55 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/VariantListV3Processor.java @@ -0,0 +1,288 @@ + +package edu.harvard.hms.dbmi.avillach.hpds.processing.v3; + +import com.google.common.base.Joiner; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariableVariantMasks; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMask; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantSpec; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import edu.harvard.hms.dbmi.avillach.hpds.exception.NotEnoughMemoryException; +import edu.harvard.hms.dbmi.avillach.hpds.processing.ColumnSorter; +import edu.harvard.hms.dbmi.avillach.hpds.processing.GenomicProcessor; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Component; + +import java.util.*; +import java.util.stream.Collectors; + +/** + * Note: This class was copied from {@link edu.harvard.hms.dbmi.avillach.hpds.processing.VariantListProcessor} and updated to use new Query + * entity + */ +@Component +public class VariantListV3Processor implements HpdsV3Processor { + + private final GenomicProcessor genomicProcessor; + + private static final Logger log = LoggerFactory.getLogger(VariantListV3Processor.class); + + private static final Joiner VARIANT_LIST_JOINER = Joiner.on(", "); + + private final boolean vcfExcerptEnabled; + private final boolean aggregateVcfExcerptEnabled; + private final boolean variantListEnabled; + private final String idCubeName; + + private final QueryExecutor queryExecutor; + private final ColumnSorter columnSorter; + + private final PhenotypicObservationStore phenotypicObservationStore; + + + @Autowired + public VariantListV3Processor( + QueryExecutor queryExecutor, GenomicProcessor genomicProcessor, ColumnSorter columnSorter, + PhenotypicObservationStore phenotypicObservationStore, @Value("${VCF_EXCERPT_ENABLED:false}") boolean vcfExcerptEnabled, + @Value("${AGGREGATE_VCF_EXCERPT_ENABLED:false}") boolean aggregateVcfExcerptEnabled, + @Value("${ID_CUBE_NAME:NONE}") String idCubeName + ) { + this.queryExecutor = queryExecutor; + this.genomicProcessor = genomicProcessor; + this.columnSorter = columnSorter; + this.phenotypicObservationStore = phenotypicObservationStore; + + this.vcfExcerptEnabled = vcfExcerptEnabled; + // always enable aggregate queries if full queries are permitted. + this.aggregateVcfExcerptEnabled = this.vcfExcerptEnabled || aggregateVcfExcerptEnabled; + this.variantListEnabled = this.vcfExcerptEnabled || this.aggregateVcfExcerptEnabled; + this.idCubeName = idCubeName; + + } + + @Override + public void runQuery(Query query, AsyncResult asyncResult) throws NotEnoughMemoryException { + throw new RuntimeException("Not implemented"); + } + + /** + * Gets a list of variants for a given query. + * + * @return a List of VariantSpec strings that would be eligible to filter patients if the incomingQuery was run as a COUNT query. + */ + public String runVariantListQuery(Query query) { + + if (!variantListEnabled) { + log.warn("VARIANT_LIST query attempted, but not enabled."); + return "VARIANT_LIST query type not allowed"; + } + + return "[" + VARIANT_LIST_JOINER.join(queryExecutor.getVariantList(query)) + "]"; + } + + /** + * This method takes a Query input (expected but not validated to be expected result type = VCF_EXCERPT) and returns a tab separated + * string representing a table describing the variants described by the query and the associated zygosities of subjects identified by + * the query. it includes a header row describing each column.

    The output columns start with the variant description (chromosome, + * position reference allele, and subsitution), continuing with a series of columns describing the Info columns associated with the + * variant data. A count of how many subjects in the result set have/do not have comes next, followed by one column per patient.

    The + * default patientId header value can be overridden by passing the ID_CUBE_NAME environment variable to the java VM. + * + * @param query A VCF_EXCERPT type query + * @param includePatientData whether to include patient specific data + * @return A Tab-separated string with one line per variant and one column per patient (plus variant data columns) + */ + public String runVcfExcerptQuery(Query query, boolean includePatientData) { + + if (includePatientData && !vcfExcerptEnabled) { + log.warn("VCF_EXCERPT query attempted, but not enabled."); + return "VCF_EXCERPT query type not allowed"; + } else if (!includePatientData && !aggregateVcfExcerptEnabled) { + log.warn("AGGREGATE_VCF_EXCERPT query attempted, but not enabled."); + return "AGGREGATE_VCF_EXCERPT query type not allowed"; + } + + + log.info("Running VCF Extract query"); + + Collection variantList = queryExecutor.getVariantList(query); + + log.debug("variantList Size " + variantList.size()); + + Map> metadata = genomicProcessor.getVariantMetadata(variantList); + + log.debug("metadata size " + metadata.size()); + + // Sort the variantSpecs so that the user doesn't lose their mind + TreeMap> metadataSorted = new TreeMap<>(Comparator.comparing(VariantSpec::new)); + metadataSorted.putAll(metadata); + metadata = metadataSorted; + + if (metadata.isEmpty()) { + return "No Variants Found\n"; // UI uses newlines to show result count + } else { + log.debug("Found " + metadata.size() + " varaints"); + } + + Optional> idCube = Optional.empty(); + if (!idCubeName.contentEquals("NONE")) { + idCube = phenotypicObservationStore.getCube(idCubeName); + } + + // + // Build the header row + // + StringBuilder builder = new StringBuilder(); + + // 5 columns for gene info + builder.append("CHROM\tPOSITION\tREF\tALT"); + + List infoStoreColumns = columnSorter.sortInfoColumns(queryExecutor.getInfoStoreColumns()); + // now add the variant metadata column headers + for (String key : infoStoreColumns) { + builder.append("\t").append(key); + } + + // patient count columns + builder.append("\tPatients with this variant in subset\tPatients with this variant NOT in subset"); + + // then one column per patient. We also need to identify the patient ID and + // map it to the right index in the bit mask fields. + Set patientSubset = queryExecutor.getPatientSubsetForQuery(query); + log.debug("identified " + patientSubset.size() + " patients from query"); + Map patientIndexMap = new LinkedHashMap<>(); // keep a map for quick index lookups + VariantMask patientMasks = queryExecutor.createMaskForPatientSet(patientSubset); + int index = 0; + + + for (String patientId : queryExecutor.getPatientIds()) { + Integer idInt = Integer.parseInt(patientId); + if (patientSubset.contains(idInt)) { + patientIndexMap.put(patientId, index); + if (includePatientData) { + idCube.ifPresentOrElse(phenoCube -> { + String value = (String) phenoCube.getValueForKey(idInt); + if (value == null) { + builder.append("\t").append(patientId); + } else { + builder.append("\t").append(phenoCube.getValueForKey(idInt)); + } + }, () -> builder.append("\t").append(patientId)); + } + } + index++; + + if (patientIndexMap.size() >= patientSubset.size()) { + log.debug("Found all " + patientIndexMap.size() + " patient Indices at index " + index); + break; + } + } + // End of headers + builder.append("\n"); + VariantBucketHolder variantMaskBucketHolder = new VariantBucketHolder(); + + // loop over the variants identified, and build an output row + metadata.forEach((String variantSpec, Set variantMetadata) -> { + + String[] variantDataColumns = variantSpec.split(","); + // 4 fixed columns in variant ID (CHROM POSITION REF ALT) + for (int i = 0; i < 4; i++) { + if (i > 0) { + builder.append("\t"); + } + if (i < variantDataColumns.length) { + builder.append(variantDataColumns[i]); + } + } + Map> variantColumnMap = new HashMap>(); + for (String infoColumns : variantMetadata) { + // data is in a single semi-colon delimited string. + // e.g., key1=value1;key2=value2;.... + + String[] metaDataColumns = infoColumns.split(";"); + + for (String key : metaDataColumns) { + String[] keyValue = key.split("="); + if (keyValue.length == 2 && keyValue[1] != null) { + Set existingValues = variantColumnMap.computeIfAbsent(keyValue[0], k -> new HashSet<>()); + existingValues.add(keyValue[1]); + } + } + } + + // need to make sure columns are pushed out in the right order; use same iterator as headers + for (String key : infoStoreColumns) { + Set columnMeta = variantColumnMap.get(key); + if (columnMeta != null) { + // collect our sets to a single entry + builder.append("\t").append(columnMeta.stream().map(String::toString).collect(Collectors.joining(","))); + } else { + builder.append("\tnull"); + } + } + + VariableVariantMasks masks = queryExecutor.getMasks(variantSpec, variantMaskBucketHolder).get(); + + // make strings of 000100 so we can just check 'char at' + // so heterozygous no calls we want, homozygous no calls we don't + VariantMask heteroMask = masks.heterozygousMask != null ? masks.heterozygousMask + : masks.heterozygousNoCallMask != null ? masks.heterozygousNoCallMask : null; + VariantMask homoMask = masks.homozygousMask != null ? masks.homozygousMask : null; + + // Patient count = (hetero mask | homo mask) & patient mask + VariantMask heteroOrHomoMask = orNullableMasks(heteroMask, homoMask); + int patientCount = heteroOrHomoMask == null ? 0 : (heteroOrHomoMask.intersection(patientMasks).bitCount()); + + int bitCount = masks.heterozygousMask == null ? 0 : (masks.heterozygousMask.bitCount()); + bitCount += masks.homozygousMask == null ? 0 : (masks.homozygousMask.bitCount()); + + // count how many patients have genomic data available + int patientsWithVariantsCount = patientMasks.bitCount(); + + + // (patients with/total) in subset \t (patients with/total) out of subset. + builder.append("\t").append(patientCount).append("/").append(patientIndexMap.size()).append("\t") + .append(bitCount - patientCount).append("/").append(patientsWithVariantsCount - patientIndexMap.size()); + + if (includePatientData) { + // track the number of subjects without the variant; use a second builder to keep the column order + StringBuilder patientListBuilder = new StringBuilder(); + + for (Integer patientIndex : patientIndexMap.values()) { + if (heteroMask != null && heteroMask.testBit(patientIndex)) { + patientListBuilder.append("\t0/1"); + } else if (homoMask != null && homoMask.testBit(patientIndex)) { + patientListBuilder.append("\t1/1"); + } else { + patientListBuilder.append("\t0/0"); + } + } + builder.append(patientListBuilder); + } + + builder.append("\n"); + }); + + + return builder.toString(); + } + + private VariantMask orNullableMasks(VariantMask heteroMask, VariantMask homoMask) { + if (heteroMask != null) { + if (homoMask != null) { + return heteroMask.union(homoMask); + } + return heteroMask; + } else { + return homoMask; + } + } + + public String[] getHeaderRow(Query query) { + return null; + } +} diff --git a/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/Testing504MVariants.java b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/Testing504MVariants.java new file mode 100644 index 000000000..876797b8f --- /dev/null +++ b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/Testing504MVariants.java @@ -0,0 +1,49 @@ +package edu.harvard.hms.dbmi.avillach.hpds; + +import java.io.IOException; +import java.io.UncheckedIOException; +import java.math.BigInteger; +import java.nio.ByteBuffer; +import java.util.Random; + +import org.apache.commons.io.output.ByteArrayOutputStream; +import org.junit.jupiter.api.Test; + +public class Testing504MVariants { + + @Test + public void test() { + BigInteger mask = generateRandomBitmask(); + BigInteger mask2 = generateRandomBitmask(); + BigInteger mask3 = generateRandomBitmask(); + System.out.println(mask.bitCount()); + System.out.println(mask2.bitCount()); + System.out.println(mask2.and(mask).bitCount()); + System.out.println(mask3.bitCount()); + System.out.println(mask2.and(mask3).bitCount()); + } + + private BigInteger generateRandomBitmask() { + int[] ints = new int[504000000 / 32]; + Random r = new Random(); + for (int x = 0; x < ints.length; x++) { + ints[x] = r.nextInt(); + } + BigInteger mask = null;; + try (ByteArrayOutputStream out = new ByteArrayOutputStream();) { + ByteBuffer buf = ByteBuffer.allocate(4); + for (int x : ints) { + buf.clear(); + buf.putInt(x); + out.write(buf.array()); + } + mask = new BigInteger(out.toByteArray()); + System.out.println(out.size()); + + } catch (IOException e1) { + e1.printStackTrace(); + } + return mask; + } + +} diff --git a/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessorTest.java b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessorTest.java new file mode 100644 index 000000000..c6b71a851 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessorTest.java @@ -0,0 +1,94 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + + +import com.google.common.cache.CacheLoader; +import com.google.common.cache.LoadingCache; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.FileBackedByteIndexedInfoStore; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMaskBitmaskImpl; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; +import reactor.core.publisher.Mono; + +import java.math.BigInteger; +import java.util.*; +import java.util.concurrent.ExecutionException; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + +@ExtendWith(MockitoExtension.class) +public class AbstractProcessorTest { + + private AbstractProcessor abstractProcessor; + + @Mock + private Map infoStores; + + @Mock + private GenomicProcessor genomicProcessor; + + @Mock + private LoadingCache> mockLoadingCache; + + public static final String GENE_WITH_VARIANT_KEY = "Gene_with_variant"; + public static final List EXAMPLE_GENES_WITH_VARIANT = List.of("CDH8", "CDH9", "CDH10"); + + @BeforeEach + public void setup() { + abstractProcessor = new AbstractProcessor( + new PhenotypeMetaStore(new TreeMap<>(), new TreeSet<>(), 500), mockLoadingCache, infoStores, null, genomicProcessor, "", 100 + ); + } + + @Test + public void getPatientSubsetForQuery_oneVariantCategoryFilter_indexFound() { + Map categoryVariantInfoFilters = Map.of(GENE_WITH_VARIANT_KEY, new String[] {EXAMPLE_GENES_WITH_VARIANT.get(0)}); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = categoryVariantInfoFilters; + + when(genomicProcessor.getPatientMask(isA(DistributableQuery.class))) + .thenReturn(Mono.just(new VariantMaskBitmaskImpl(new BigInteger("1100110011")))); + when(genomicProcessor.patientMaskToPatientIdSet(eq(new VariantMaskBitmaskImpl(new BigInteger("1100110011"))))) + .thenReturn(Set.of(42, 99)); + + List variantInfoFilters = List.of(variantInfoFilter); + + Query query = new Query(); + query.setVariantInfoFilters(variantInfoFilters); + + Set patientSubsetForQuery = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(Set.of(42, 99), patientSubsetForQuery); + } + + @Test + public void getPatientSubsetForQuery_anyRecordOf_applyOrLogic() throws ExecutionException { + PhenoCube mockPhenoCube = mock(PhenoCube.class); + when(mockPhenoCube.keyBasedIndex()).thenReturn(List.of(42, 101)); + when(mockLoadingCache.get("good concept")).thenReturn(mockPhenoCube); + when(mockLoadingCache.get("bad concept")).thenThrow(CacheLoader.InvalidCacheLoadException.class); + + Query query = new Query(); + query.setAnyRecordOf(List.of("good concept", "bad concept")); + + Set patientSubsetForQuery = abstractProcessor.getPatientSubsetForQuery(query); + assertFalse(patientSubsetForQuery.isEmpty()); + } + + + + @Test + public void getPatientSubsetForQuery_anyRecordOfInvalidKey_returnEmpty() throws ExecutionException { + when(mockLoadingCache.get("bad concept")).thenThrow(CacheLoader.InvalidCacheLoadException.class); + + Query query = new Query(); + query.setAnyRecordOf(List.of("bad concept")); + + Set patientSubsetForQuery = abstractProcessor.getPatientSubsetForQuery(query); + assertTrue(patientSubsetForQuery.isEmpty()); + } +} diff --git a/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/ColumnSorterTest.java b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/ColumnSorterTest.java new file mode 100644 index 000000000..50ed964b5 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/ColumnSorterTest.java @@ -0,0 +1,53 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + + +import org.junit.jupiter.api.Test; + +import java.util.HashSet; +import java.util.List; +import java.util.Set; + +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.equalTo; +import static org.junit.jupiter.api.Assertions.assertEquals; + +import static org.hamcrest.CoreMatchers.*; + +public class ColumnSorterTest { + + @Test + public void shouldSortColumns() { + ColumnSorter subject = new ColumnSorter("a,b,c"); + List actual = subject.sortInfoColumns(Set.of("b", "c", "a")); + List expected = List.of("a", "b", "c"); + + assertEquals(expected, actual); + } + + @Test + public void shouldExcludeMissingColumns() { + ColumnSorter subject = new ColumnSorter("a,b,c"); + List actual = subject.sortInfoColumns(Set.of("d", "b", "c", "a")); + List expected = List.of("a", "b", "c"); + + assertEquals(expected, actual); + } + + @Test + public void shouldNotBreakForMissingColumns() { + ColumnSorter subject = new ColumnSorter("a,b,c,d"); + List actual = subject.sortInfoColumns(Set.of("d", "a")); + List expected = List.of("a", "d"); + + assertEquals(expected, actual); + } + + @Test + public void shouldNoOpWithoutConfig() { + ColumnSorter subject = new ColumnSorter(""); + List actual = subject.sortInfoColumns(Set.of("b", "c", "a")); + List expected = List.of("b", "c", "a"); + + assertThat(new HashSet<>(expected), is(equalTo(new HashSet<>(actual)))); + } +} diff --git a/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/CountProcessorTest.java b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/CountProcessorTest.java new file mode 100644 index 000000000..59ce7f82e --- /dev/null +++ b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/CountProcessorTest.java @@ -0,0 +1,106 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; + +import java.io.IOException; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.mockito.Mockito.when; + +@ExtendWith(MockitoExtension.class) +public class CountProcessorTest { + + private final CountProcessor countProcessor; + + private final AbstractProcessor mockAbstractProcessor; + + public CountProcessorTest(@Mock AbstractProcessor mockAbstractProcessor) { + this.mockAbstractProcessor = mockAbstractProcessor; + this.countProcessor = new CountProcessor(mockAbstractProcessor); + } + + @Test + public void testVariantCountWithEmptyQuery() { + Map countResponse = countProcessor.runVariantCount(new Query()); + assertEquals("0", countResponse.get("count")); + } + + @Test + public void testVariantCountWithEmptyVariantInfoFiltersInQuery() { + Query query = new Query(); + query.setVariantInfoFilters(new ArrayList<>()); + Map countResponse = countProcessor.runVariantCount(query); + assertEquals("0", countResponse.get("count")); + } + + @Test + public void testVariantCountReturningVariants() throws IOException { + Query query = new Query(); + query.setVariantInfoFilters(List.of(new Query.VariantInfoFilter())); + + when(mockAbstractProcessor.getVariantList(query)).thenReturn(List.of("variant1", "variant2")); + Map countResponse = countProcessor.runVariantCount(query); + assertEquals(2, countResponse.get("count")); + } + + // todo: test these directly in AbstractProcessor + /* + * @Test public void testVariantCountWithVariantInfoFiltersWithMultipleVariantsWithIntersectingKeys() throws Exception { + * ArrayList> data = new ArrayList<>(List.of( Set.of(1), Set.of(1, 2))); TestableCountProcessor t = new + * TestableCountProcessor(true, data); + * + * Map categoryVariantInfoFilters = Map.of("FILTERKEY", new String[] { "test1" }); VariantInfoFilter variantInfoFilter + * = new VariantInfoFilter(); variantInfoFilter.categoryVariantInfoFilters = categoryVariantInfoFilters; + * + * List variantInfoFilters = new ArrayList<>(); variantInfoFilters.add(variantInfoFilter); Query q = new Query(); + * q.variantInfoFilters = variantInfoFilters; + * + * Map countResponse = t.runVariantCount(q); assertEquals(1,countResponse.get("count") ); } + * + * @Test public void testVariantCountWithTwoVariantInfoFiltersWithMultipleVariantsWithIntersectingKeys() throws Exception { + * List>> data1 = new ArrayList>>(new ArrayList(List.of( new ArrayList(List.of(Set.of(1, + * 2))),new ArrayList(List.of(Set.of(1, 3)))))); TestableCountProcessor t = new TestableCountProcessor(true, data1); + * + * Map categoryVariantInfoFilters = Map.of("FILTERKEY", new String[] { "test1" }); VariantInfoFilter variantInfoFilter + * = new VariantInfoFilter(); variantInfoFilter.categoryVariantInfoFilters = categoryVariantInfoFilters; + * + * VariantInfoFilter variantInfoFilter2 = new VariantInfoFilter(); variantInfoFilter2.categoryVariantInfoFilters = + * categoryVariantInfoFilters; + * + * List variantInfoFilters = new ArrayList<>( List.of(variantInfoFilter, variantInfoFilter2)); Query q = new Query(); + * q.variantInfoFilters = variantInfoFilters; + * + * + * Map countResponse = t.runVariantCount(q); assertEquals(3,countResponse.get("count") ); } + * + * @Test public void testVariantCountWithVariantInfoFiltersWithOnlyOneFilterCriteria() throws Exception { ArrayList> data = + * new ArrayList(List.of( Set.of("2,1234,G,T"))); TestableCountProcessor t = new TestableCountProcessor(true, data); + * + * Map categoryVariantInfoFilters = Map.of("FILTERKEY", new String[] { "test1" }); VariantInfoFilter variantInfoFilter + * = new VariantInfoFilter(); variantInfoFilter.categoryVariantInfoFilters = categoryVariantInfoFilters; + * + * List variantInfoFilters = new ArrayList<>(); variantInfoFilters.add(variantInfoFilter); Query q = new Query(); + * q.variantInfoFilters = variantInfoFilters; + * + * Map countResponse = t.runVariantCount(q); assertEquals(1,countResponse.get("count") ); } + * + * @Test public void testVariantCountWithVariantInfoFiltersWhenFiltersDoNotMatchAnyVariants() throws Exception { TestableCountProcessor + * t = new TestableCountProcessor(true, new ArrayList>()); + * + * Map categoryVariantInfoFilters = Map.of("FILTERKEY", new String[] { "test1" }); VariantInfoFilter variantInfoFilter + * = new VariantInfoFilter(); variantInfoFilter.categoryVariantInfoFilters = categoryVariantInfoFilters; + * + * List variantInfoFilters = new ArrayList<>(); variantInfoFilters.add(variantInfoFilter); Query q = new Query(); + * + * Map countResponse = t.runVariantCount(q); assertEquals("0",countResponse.get("count") ); } + */ + +} diff --git a/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorParentImplTest.java b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorParentImplTest.java new file mode 100644 index 000000000..85e5fe5f6 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorParentImplTest.java @@ -0,0 +1,160 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMask; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMaskBitmaskImpl; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMaskSparseImpl; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; +import reactor.core.publisher.Mono; + +import java.math.BigInteger; +import java.util.Collection; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + +@ExtendWith(MockitoExtension.class) +class GenomicProcessorParentImplTest { + @Mock + private GenomicProcessor mockProcessor1; + @Mock + private GenomicProcessor mockProcessor2; + @Mock + private GenomicProcessor mockProcessor3; + + private GenomicProcessorParentImpl parentProcessor; + + @BeforeEach + public void setup() { + parentProcessor = new GenomicProcessorParentImpl(List.of(mockProcessor1, mockProcessor2, mockProcessor3)); + } + + @Test + public void patientIdInit_patientsMatch_noException() { + when(mockProcessor1.getPatientIds()).thenReturn(List.of("1", "42", "99")); + when(mockProcessor2.getPatientIds()).thenReturn(List.of("1", "42", "99")); + when(mockProcessor3.getPatientIds()).thenReturn(List.of("1", "42", "99")); + parentProcessor = new GenomicProcessorParentImpl(List.of( + mockProcessor1, mockProcessor2, mockProcessor3 + )); + } + + @Test + public void patientIdInit_patientsDiffer_exception() { + when(mockProcessor1.getPatientIds()).thenReturn(List.of("1", "42", "99")); + when(mockProcessor2.getPatientIds()).thenReturn(List.of("1", "43", "99")); + + assertThrows(IllegalStateException.class, () -> { + parentProcessor = new GenomicProcessorParentImpl(List.of( + mockProcessor1, mockProcessor2, mockProcessor3 + )); + }); + } + + + @Test + public void getPatientMask_validResponses_returnMerged() { + DistributableQuery distributableQuery = new DistributableQuery(); + when(mockProcessor1.getPatientMask(distributableQuery)) + .thenReturn(Mono.just(new VariantMaskBitmaskImpl(new BigInteger("110110000011", 2)))); + when(mockProcessor2.getPatientMask(distributableQuery)) + .thenReturn(Mono.just(new VariantMaskBitmaskImpl(new BigInteger("110001100011", 2)))); + when(mockProcessor3.getPatientMask(distributableQuery)) + .thenReturn(Mono.just(new VariantMaskBitmaskImpl(new BigInteger("110000000111", 2)))); + + VariantMask patientMask = parentProcessor.getPatientMask(distributableQuery).block(); + VariantMask expectedPatientMask = new VariantMaskBitmaskImpl(new BigInteger("110111100111", 2)); + assertEquals(expectedPatientMask, patientMask); + } + + @Test + public void getPatientMask_oneNode_returnPatients() { + DistributableQuery distributableQuery = new DistributableQuery(); + when(mockProcessor1.getPatientMask(distributableQuery)) + .thenReturn(Mono.just(new VariantMaskBitmaskImpl(new BigInteger("110110000011", 2)))); + parentProcessor = new GenomicProcessorParentImpl(List.of(mockProcessor1)); + + VariantMask patientMask = parentProcessor.getPatientMask(distributableQuery).block(); + VariantMask expectedPatientMask = new VariantMaskBitmaskImpl(new BigInteger("110110000011", 2)); + assertEquals(expectedPatientMask, patientMask); + } + + @Test + public void createMaskForPatientSet_oneNode_returnFirst() { + Set patientSet = Set.of(7, 8, 9); + when(mockProcessor1.createMaskForPatientSet(patientSet)).thenReturn(new VariantMaskBitmaskImpl(new BigInteger("110100000011", 2))); + + parentProcessor = new GenomicProcessorParentImpl(List.of(mockProcessor1)); + + VariantMask patientMask = parentProcessor.createMaskForPatientSet(patientSet); + VariantMask expectedPatientMask = new VariantMaskBitmaskImpl(new BigInteger("110100000011", 2)); + assertEquals(expectedPatientMask, patientMask); + } + + @Test + public void createMaskForPatientSet_multipleNodes_returnFirst() { + Set patientSet = Set.of(7, 8, 9); + when(mockProcessor1.createMaskForPatientSet(patientSet)).thenReturn(new VariantMaskBitmaskImpl(new BigInteger("110100000011", 2))); + + VariantMask patientMask = parentProcessor.createMaskForPatientSet(patientSet); + VariantMask expectedPatientMask = new VariantMaskBitmaskImpl(new BigInteger("110100000011", 2)); + assertEquals(expectedPatientMask, patientMask); + // this should just call the first node, since all nodes have identical patient sets + verify(mockProcessor2, never()).createMaskForPatientSet(any()); + verify(mockProcessor3, never()).createMaskForPatientSet(any()); + } + + @Test + public void getVariantList_overlappingVariants_mergeCorrectly() { + DistributableQuery distributableQuery = new DistributableQuery(); + when(mockProcessor1.getVariantList(distributableQuery)).thenReturn(Mono.just(Set.of("variant1", "variant2"))); + when(mockProcessor2.getVariantList(distributableQuery)).thenReturn(Mono.just(Set.of("variant2", "variant3"))); + when(mockProcessor3.getVariantList(distributableQuery)).thenReturn(Mono.just(Set.of("variant3", "variant4"))); + + Set variantList = parentProcessor.getVariantList(distributableQuery).block(); + assertEquals(Set.of("variant1", "variant2", "variant3", "variant4"), variantList); + } + + @Test + public void getVariantList_oneNode_returnVariants() { + DistributableQuery distributableQuery = new DistributableQuery(); + when(mockProcessor1.getVariantList(distributableQuery)).thenReturn(Mono.just(Set.of("variant1", "variant2"))); + + parentProcessor = new GenomicProcessorParentImpl(List.of(mockProcessor1)); + + Set variantList = parentProcessor.getVariantList(distributableQuery).block(); + assertEquals(Set.of("variant1", "variant2"), variantList); + } + + @Test + public void getVariantMetadata_mixedEmptyVariants_mergedCorrectly() { + List variantList = List.of("variant1", "variant2", "variant3"); + when(mockProcessor1.getVariantMetadata(variantList)).thenReturn(Map.of()); + when(mockProcessor2.getVariantMetadata(variantList)).thenReturn(Map.of("variant1", Set.of("metadata1", "metadata2"))); + when(mockProcessor3.getVariantMetadata(variantList)).thenReturn(Map.of("variant3", Set.of("metadata31", "metadata32"))); + + Map> variantMetadata = parentProcessor.getVariantMetadata(variantList); + assertEquals(Set.of("metadata1", "metadata2"), variantMetadata.get("variant1")); + assertEquals(Set.of("metadata31", "metadata32"), variantMetadata.get("variant3")); + assertEquals(2, variantMetadata.size()); + } + + @Test + public void getVariantMetadata_overlappingVariants_mergedCorrectly() { + List variantList = List.of("variant1", "variant2", "variant3"); + when(mockProcessor1.getVariantMetadata(variantList)).thenReturn(Map.of("variant1", Set.of("metadata1", "metadata2"))); + when(mockProcessor2.getVariantMetadata(variantList)).thenReturn(Map.of("variant1", Set.of("metadata1", "metadata3"))); + when(mockProcessor3.getVariantMetadata(variantList)).thenReturn(Map.of("variant3", Set.of("metadata31", "metadata32"))); + + Map> variantMetadata = parentProcessor.getVariantMetadata(variantList); + assertEquals(Set.of("metadata1", "metadata2", "metadata3"), variantMetadata.get("variant1")); + assertEquals(Set.of("metadata31", "metadata32"), variantMetadata.get("variant3")); + assertEquals(2, variantMetadata.size()); + } +} diff --git a/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorPatientMergingParentImplTest.java b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorPatientMergingParentImplTest.java new file mode 100644 index 000000000..aa1407cce --- /dev/null +++ b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorPatientMergingParentImplTest.java @@ -0,0 +1,330 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariableVariantMasks; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMask; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMaskBitmaskImpl; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMaskSparseImpl; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; +import org.springframework.boot.test.system.CapturedOutput; +import org.springframework.boot.test.system.OutputCaptureExtension; +import reactor.core.publisher.Mono; + +import java.math.BigInteger; +import java.util.List; +import java.util.Map; +import java.util.Optional; +import java.util.Set; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.ArgumentMatchers.eq; +import static org.mockito.Mockito.when; + +@ExtendWith({MockitoExtension.class, OutputCaptureExtension.class}) +public class GenomicProcessorPatientMergingParentImplTest { + + @Mock + private GenomicProcessor mockProcessor1; + @Mock + private GenomicProcessor mockProcessor2; + @Mock + private GenomicProcessor mockProcessor3; + + private GenomicProcessorPatientMergingParentImpl patientMergingParent; + + @BeforeEach + public void setup() { + patientMergingParent = new GenomicProcessorPatientMergingParentImpl(List.of(mockProcessor1, mockProcessor2, mockProcessor3)); + } + + @Test + public void getPatientMask_validResponses_returnMerged() { + DistributableQuery distributableQuery = new DistributableQuery(); + when(mockProcessor1.getPatientMask(distributableQuery)) + .thenReturn(Mono.just(new VariantMaskBitmaskImpl(new BigInteger("11011011", 2)))); + when(mockProcessor1.getPatientIds()).thenReturn(List.of("1", "2", "3", "4")); + when(mockProcessor2.getPatientMask(distributableQuery)) + .thenReturn(Mono.just(new VariantMaskBitmaskImpl(new BigInteger("110001100011", 2)))); + when(mockProcessor2.getPatientIds()).thenReturn(List.of("5", "6", "7", "8", "9", "10", "11", "12")); + when(mockProcessor3.getPatientMask(distributableQuery)) + .thenReturn(Mono.just(new VariantMaskBitmaskImpl(new BigInteger("11000111", 2)))); + when(mockProcessor3.getPatientIds()).thenReturn(List.of("15", "16", "17", "18")); + VariantMask patientMask = patientMergingParent.getPatientMask(distributableQuery).block(); + VariantMask expectedPatientMask = new VariantMaskBitmaskImpl(new BigInteger("11000100011000011011", 2)); + assertEquals(expectedPatientMask, patientMask); + } + + @Test + public void getPatientMask_noPatientResponses_returnMerged() { + DistributableQuery distributableQuery = new DistributableQuery(); + when(mockProcessor1.getPatientMask(distributableQuery)) + .thenReturn(Mono.just(new VariantMaskBitmaskImpl(new BigInteger("11011011", 2)))); + when(mockProcessor1.getPatientIds()).thenReturn(List.of("1", "2", "3", "4")); + when(mockProcessor2.getPatientMask(distributableQuery)) + .thenReturn(Mono.just(new VariantMaskBitmaskImpl(new BigInteger("110000000011", 2)))); + when(mockProcessor2.getPatientIds()).thenReturn(List.of("5", "6", "7", "8", "9", "10", "11", "12")); + when(mockProcessor3.getPatientMask(distributableQuery)) + .thenReturn(Mono.just(new VariantMaskBitmaskImpl(new BigInteger("11000011", 2)))); + when(mockProcessor3.getPatientIds()).thenReturn(List.of("15", "16", "17", "18")); + VariantMask patientMask = patientMergingParent.getPatientMask(distributableQuery).block(); + VariantMask expectedPatientMask = new VariantMaskBitmaskImpl(new BigInteger("11000000000000011011", 2)); + assertEquals(expectedPatientMask, patientMask); + } + + @Test + public void getPatientMask_emptyResponses_returnMerged() { + DistributableQuery distributableQuery = new DistributableQuery(); + when(mockProcessor1.getPatientMask(distributableQuery)) + .thenReturn(Mono.just(new VariantMaskBitmaskImpl(new BigInteger("11011011", 2)))); + when(mockProcessor1.getPatientIds()).thenReturn(List.of("1", "2", "3", "4")); + when(mockProcessor2.getPatientMask(distributableQuery)) + .thenReturn(Mono.just(new VariantMaskBitmaskImpl(new BigInteger("1111", 2)))); + when(mockProcessor2.getPatientIds()).thenReturn(List.of()); + when(mockProcessor3.getPatientMask(distributableQuery)) + .thenReturn(Mono.just(new VariantMaskBitmaskImpl(new BigInteger("11000111", 2)))); + when(mockProcessor3.getPatientIds()).thenReturn(List.of("5", "6", "7", "8")); + VariantMask patientMask = patientMergingParent.getPatientMask(distributableQuery).block(); + VariantMask expectedPatientMask = new VariantMaskBitmaskImpl(new BigInteger("110001011011", 2)); + assertEquals(expectedPatientMask, patientMask); + } + + @Test + public void patientIdInit_validPatients_noException(CapturedOutput output) { + when(mockProcessor1.getPatientIds()).thenReturn(List.of("1", "42", "99")); + when(mockProcessor2.getPatientIds()).thenReturn(List.of("2", "50", "100")); + when(mockProcessor3.getPatientIds()).thenReturn(List.of("1000", "10001", "1002", "1003")); + + patientMergingParent = new GenomicProcessorPatientMergingParentImpl(List.of( + mockProcessor1, mockProcessor2, mockProcessor3 + )); + + assertFalse(output.getOut().contains("duplicate patients found in patient partitions")); + } + + @Test + public void patientIdInit_invalidPatients_warnMessage(CapturedOutput output) { + when(mockProcessor1.getPatientIds()).thenReturn(List.of("1", "42", "99")); + when(mockProcessor2.getPatientIds()).thenReturn(List.of("2", "42", "100")); + when(mockProcessor3.getPatientIds()).thenReturn(List.of("1000", "10001", "1002", "1003")); + + patientMergingParent = new GenomicProcessorPatientMergingParentImpl(List.of( + mockProcessor1, mockProcessor2, mockProcessor3 + )); + + assertTrue(output.getOut().contains("1 duplicate patients found in patient partitions")); + } + + @Test + public void patientIdInit_multipleInvalidPatients_warnMessage(CapturedOutput output) { + when(mockProcessor1.getPatientIds()).thenReturn(List.of("1", "42", "99")); + when(mockProcessor2.getPatientIds()).thenReturn(List.of("2", "50", "100")); + when(mockProcessor3.getPatientIds()).thenReturn(List.of("1", "42", "99", "1003")); + + patientMergingParent = new GenomicProcessorPatientMergingParentImpl(List.of( + mockProcessor1, mockProcessor2, mockProcessor3 + )); + + assertTrue(output.getOut().contains("3 duplicate patients found in patient partitions")); + } + + + @Test + public void createMaskForPatientSet_validResponses_returnMerged() { + Set patientSubset = Set.of(2, 3, 8, 9, 15); + when(mockProcessor1.createMaskForPatientSet(patientSubset)).thenReturn(new VariantMaskBitmaskImpl(new BigInteger("11011011", 2))); + when(mockProcessor1.getPatientIds()).thenReturn(List.of("1", "2", "3", "4")); + when(mockProcessor2.createMaskForPatientSet(patientSubset)).thenReturn(new VariantMaskSparseImpl(Set.of(3, 4))); + when(mockProcessor2.getPatientIds()).thenReturn(List.of("5", "6", "7", "8", "9", "10", "11", "12")); + when(mockProcessor3.createMaskForPatientSet(patientSubset)).thenReturn(new VariantMaskBitmaskImpl(new BigInteger("11000111", 2))); + when(mockProcessor3.getPatientIds()).thenReturn(List.of("15", "16", "17", "18")); + VariantMask patientMask = patientMergingParent.createMaskForPatientSet(patientSubset); + VariantMask expectedPatientMask = new VariantMaskBitmaskImpl(new BigInteger("11000100011000011011", 2)); + assertEquals(expectedPatientMask, patientMask); + } + + @Test + public void createMaskForPatientSet_validResponsesOneEmpty_returnMerged() { + Set patientSubset = Set.of(2, 3, 15); + when(mockProcessor1.createMaskForPatientSet(patientSubset)).thenReturn(new VariantMaskBitmaskImpl(new BigInteger("11011011", 2))); + when(mockProcessor1.getPatientIds()).thenReturn(List.of("1", "2", "3", "4")); + when(mockProcessor2.createMaskForPatientSet(patientSubset)).thenReturn(VariantMask.emptyInstance()); + when(mockProcessor2.getPatientIds()).thenReturn(List.of("5", "6", "7", "8", "9", "10", "11", "12")); + when(mockProcessor3.createMaskForPatientSet(patientSubset)).thenReturn(new VariantMaskBitmaskImpl(new BigInteger("11000111", 2))); + when(mockProcessor3.getPatientIds()).thenReturn(List.of("15", "16", "17", "18")); + VariantMask patientMask = patientMergingParent.createMaskForPatientSet(patientSubset); + VariantMask expectedPatientMask = new VariantMaskBitmaskImpl(new BigInteger("11000100000000011011", 2)); + assertEquals(expectedPatientMask, patientMask); + } + + + @Test + public void getMasks_validEmptyResponses_returnEmpty() { + String path = "chr21,5032061,A,Z,LOC102723996,missense_variant"; + when(mockProcessor1.getMasks(eq(path), any(VariantBucketHolder.class))).thenReturn(Optional.empty()); + when(mockProcessor2.getMasks(eq(path), any(VariantBucketHolder.class))).thenReturn(Optional.empty()); + when(mockProcessor3.getMasks(eq(path), any(VariantBucketHolder.class))).thenReturn(Optional.empty()); + + Optional masks = patientMergingParent.getMasks(path, new VariantBucketHolder<>()); + assertEquals(Optional.of(new VariableVariantMasks()), masks); + } + + @Test + public void getMasks_validEmptyAndNullResponses_returnEmpty() { + String path = "chr21,5032061,A,Z,LOC102723996,missense_variant"; + when(mockProcessor1.getMasks(eq(path), any(VariantBucketHolder.class))).thenReturn(Optional.empty()); + when(mockProcessor2.getMasks(eq(path), any(VariantBucketHolder.class))).thenReturn(Optional.of(new VariableVariantMasks())); + when(mockProcessor3.getMasks(eq(path), any(VariantBucketHolder.class))).thenReturn(Optional.empty()); + + Optional masks = patientMergingParent.getMasks(path, new VariantBucketHolder<>()); + assertEquals(Optional.of(new VariableVariantMasks()), masks); + } + + + @Test + public void getMasks_validResponses_returnMerged() { + String path = "chr21,5032061,A,Z,LOC102723996,missense_variant"; + VariableVariantMasks variableVariantMasks1 = new VariableVariantMasks(); + variableVariantMasks1.heterozygousMask = new VariantMaskBitmaskImpl(new BigInteger("11011011", 2)); + VariableVariantMasks variableVariantMasks2 = new VariableVariantMasks(); + variableVariantMasks2.heterozygousMask = new VariantMaskSparseImpl(Set.of(3, 4)); + VariableVariantMasks variableVariantMasks3 = new VariableVariantMasks(); + variableVariantMasks3.heterozygousMask = new VariantMaskBitmaskImpl(new BigInteger("11000111", 2)); + + when(mockProcessor1.getPatientIds()).thenReturn(List.of("1", "2", "3", "4")); + when(mockProcessor2.getPatientIds()).thenReturn(List.of("5", "6", "7", "8", "9", "10", "11", "12")); + when(mockProcessor3.getPatientIds()).thenReturn(List.of("15", "16", "17", "18")); + + + when(mockProcessor1.getMasks(eq(path), any(VariantBucketHolder.class))).thenReturn(Optional.of(variableVariantMasks1)); + when(mockProcessor2.getMasks(eq(path), any(VariantBucketHolder.class))).thenReturn(Optional.of(variableVariantMasks2)); + when(mockProcessor3.getMasks(eq(path), any(VariantBucketHolder.class))).thenReturn(Optional.of(variableVariantMasks3)); + + Optional masks = patientMergingParent.getMasks(path, new VariantBucketHolder<>()); + + VariantMask expectedPatientMask = new VariantMaskBitmaskImpl(new BigInteger("11000100011000011011", 2)); + assertEquals(expectedPatientMask, masks.get().heterozygousMask); + } + + @Test + public void getMasks_validResponsesSinglePartition_returnResult() { + String path = "chr21,5032061,A,Z,LOC102723996,missense_variant"; + VariableVariantMasks variableVariantMasks1 = new VariableVariantMasks(); + variableVariantMasks1.heterozygousMask = new VariantMaskBitmaskImpl(new BigInteger("11011011", 2)); + + when(mockProcessor1.getPatientIds()).thenReturn(List.of("1", "2", "3", "4")); + + + when(mockProcessor1.getMasks(eq(path), any(VariantBucketHolder.class))).thenReturn(Optional.of(variableVariantMasks1)); + + Optional masks = + new GenomicProcessorPatientMergingParentImpl(List.of(mockProcessor1)).getMasks(path, new VariantBucketHolder<>()); + + assertEquals(variableVariantMasks1.heterozygousMask, masks.get().heterozygousMask); + } + + @Test + public void getMasks_validResponsesSinglePartitionEmpty_returnEmpty() { + String path = "chr21,5032061,A,Z,LOC102723996,missense_variant"; + + when(mockProcessor1.getPatientIds()).thenReturn(List.of("1", "2", "3", "4")); + when(mockProcessor1.getMasks(eq(path), any(VariantBucketHolder.class))).thenReturn(Optional.empty()); + + Optional masks = + new GenomicProcessorPatientMergingParentImpl(List.of(mockProcessor1)).getMasks(path, new VariantBucketHolder<>()); + + assertNull(masks.get().heterozygousMask); + } + + @Test + public void getMasks_validAndEmptyResponses_returnMerged() { + String path = "chr21,5032061,A,Z,LOC102723996,missense_variant"; + VariableVariantMasks variableVariantMasks1 = new VariableVariantMasks(); + variableVariantMasks1.heterozygousMask = new VariantMaskBitmaskImpl(new BigInteger("11011011", 2)); + VariableVariantMasks variableVariantMasks3 = new VariableVariantMasks(); + variableVariantMasks3.heterozygousMask = new VariantMaskBitmaskImpl(new BigInteger("11000111", 2)); + + when(mockProcessor1.getPatientIds()).thenReturn(List.of("1", "2", "3", "4")); + when(mockProcessor2.getPatientIds()).thenReturn(List.of("5", "6", "7", "8", "9", "10", "11", "12")); + when(mockProcessor3.getPatientIds()).thenReturn(List.of("15", "16", "17", "18")); + + + when(mockProcessor1.getMasks(eq(path), any(VariantBucketHolder.class))).thenReturn(Optional.of(variableVariantMasks1)); + when(mockProcessor2.getMasks(eq(path), any(VariantBucketHolder.class))).thenReturn(Optional.empty()); + when(mockProcessor3.getMasks(eq(path), any(VariantBucketHolder.class))).thenReturn(Optional.of(variableVariantMasks3)); + + Optional masks = patientMergingParent.getMasks(path, new VariantBucketHolder<>()); + + VariantMask expectedPatientMask = new VariantMaskBitmaskImpl(new BigInteger("11000100000000011011", 2)); + assertEquals(expectedPatientMask, masks.get().heterozygousMask); + } + + @Test + public void getMasks_validResponsesHomozygous_returnMerged() { + String path = "chr21,5032061,A,Z,LOC102723996,missense_variant"; + VariableVariantMasks variableVariantMasks1 = new VariableVariantMasks(); + variableVariantMasks1.homozygousMask = new VariantMaskBitmaskImpl(new BigInteger("11011011", 2)); + VariableVariantMasks variableVariantMasks2 = new VariableVariantMasks(); + variableVariantMasks2.homozygousMask = new VariantMaskSparseImpl(Set.of(3, 4)); + VariableVariantMasks variableVariantMasks3 = new VariableVariantMasks(); + variableVariantMasks3.homozygousMask = new VariantMaskBitmaskImpl(new BigInteger("11000111", 2)); + + when(mockProcessor1.getPatientIds()).thenReturn(List.of("1", "2", "3", "4")); + when(mockProcessor2.getPatientIds()).thenReturn(List.of("5", "6", "7", "8", "9", "10", "11", "12")); + when(mockProcessor3.getPatientIds()).thenReturn(List.of("15", "16", "17", "18")); + + + when(mockProcessor1.getMasks(eq(path), any(VariantBucketHolder.class))).thenReturn(Optional.of(variableVariantMasks1)); + when(mockProcessor2.getMasks(eq(path), any(VariantBucketHolder.class))).thenReturn(Optional.of(variableVariantMasks2)); + when(mockProcessor3.getMasks(eq(path), any(VariantBucketHolder.class))).thenReturn(Optional.of(variableVariantMasks3)); + + Optional masks = patientMergingParent.getMasks(path, new VariantBucketHolder<>()); + + VariantMask expectedPatientMask = new VariantMaskBitmaskImpl(new BigInteger("11000100011000011011", 2)); + assertEquals(expectedPatientMask, masks.get().homozygousMask); + assertNull(masks.get().heterozygousMask); + assertNull(masks.get().heterozygousNoCallMask); + assertNull(masks.get().homozygousNoCallMask); + } + + @Test + public void getVariantList_oneNode_returnVariants() { + DistributableQuery distributableQuery = new DistributableQuery(); + when(mockProcessor1.getVariantList(distributableQuery)).thenReturn(Mono.just(Set.of("variant1", "variant2"))); + + patientMergingParent = new GenomicProcessorPatientMergingParentImpl(List.of(mockProcessor1)); + + Set variantList = patientMergingParent.getVariantList(distributableQuery).block(); + assertEquals(Set.of("variant1", "variant2"), variantList); + } + + @Test + public void getVariantMetadata_mixedEmptyVariants_mergedCorrectly() { + List variantList = List.of("variant1", "variant2", "variant3"); + when(mockProcessor1.getVariantMetadata(variantList)).thenReturn(Map.of()); + when(mockProcessor2.getVariantMetadata(variantList)).thenReturn(Map.of("variant1", Set.of("metadata1", "metadata2"))); + when(mockProcessor3.getVariantMetadata(variantList)).thenReturn(Map.of("variant3", Set.of("metadata31", "metadata32"))); + + Map> variantMetadata = patientMergingParent.getVariantMetadata(variantList); + assertEquals(Set.of("metadata1", "metadata2"), variantMetadata.get("variant1")); + assertEquals(Set.of("metadata31", "metadata32"), variantMetadata.get("variant3")); + assertEquals(2, variantMetadata.size()); + } + + @Test + public void getVariantMetadata_overlappingVariants_mergedCorrectly() { + List variantList = List.of("variant1", "variant2", "variant3"); + when(mockProcessor1.getVariantMetadata(variantList)).thenReturn(Map.of("variant1", Set.of("metadata1", "metadata2"))); + when(mockProcessor2.getVariantMetadata(variantList)).thenReturn(Map.of("variant1", Set.of("metadata1", "metadata3"))); + when(mockProcessor3.getVariantMetadata(variantList)).thenReturn(Map.of("variant3", Set.of("metadata31", "metadata32"))); + + Map> variantMetadata = patientMergingParent.getVariantMetadata(variantList); + assertEquals(Set.of("metadata1", "metadata2", "metadata3"), variantMetadata.get("variant1")); + assertEquals(Set.of("metadata31", "metadata32"), variantMetadata.get("variant3")); + assertEquals(2, variantMetadata.size()); + } +} diff --git a/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PatientVariantJoinHandlerTest.java b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PatientVariantJoinHandlerTest.java new file mode 100644 index 000000000..ffc1adaca --- /dev/null +++ b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PatientVariantJoinHandlerTest.java @@ -0,0 +1,171 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariableVariantMasks; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMask; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMaskBitmaskImpl; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMasks; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; +import org.springframework.test.context.event.annotation.BeforeTestClass; + +import java.math.BigInteger; +import java.util.List; +import java.util.Optional; +import java.util.Set; +import java.util.TreeSet; +import java.util.stream.Collectors; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.mockito.Mockito.*; + +@ExtendWith(MockitoExtension.class) +public class PatientVariantJoinHandlerTest { + + private VariantService variantService; + + private PatientVariantJoinHandler patientVariantJoinHandler; + + public static final String[] PATIENT_IDS = {"101", "102", "103", "104", "105", "106", "107", "108"}; + public static final Set PATIENT_IDS_INTEGERS = Set.of(PATIENT_IDS).stream().map(Integer::parseInt).collect(Collectors.toSet()); + public static final String[] VARIANT_INDEX = {"16,61642243,A,T,ABC,consequence1", "16,61642252,A,G,ABC,consequence1", + "16,61642256,C,T,ABC,consequence2", "16,61642257,G,A,ABC,consequence3", "16,61642258,G,A,ABC,consequence3", + "16,61642259,G,A,ABC,consequence1", "16,61642260,G,A,ABC,consequence1", "16,61642261,G,A,ABC,consequence1"}; + + public PatientVariantJoinHandlerTest(@Mock VariantService variantService) { + this.variantService = variantService; + patientVariantJoinHandler = new PatientVariantJoinHandler(variantService); + when(variantService.getVariantIndex()).thenReturn(VARIANT_INDEX); + } + + @Test + public void getPatientIdsForIntersectionOfVariantSets_allPatientsMatchOneVariant() { + VariantIndex intersectionOfInfoFilters = new SparseVariantIndex(Set.of(0, 2, 4)); + when(variantService.getPatientIds()).thenReturn(PATIENT_IDS); + when(variantService.emptyBitmask()).thenReturn(emptyBitmask(PATIENT_IDS)); + + VariantMask maskForAllPatients = + new VariantMaskBitmaskImpl(patientVariantJoinHandler.createMaskForPatientSet(PATIENT_IDS_INTEGERS)); + VariantMask maskForNoPatients = VariantMask.emptyInstance(); + + VariableVariantMasks variantMasks = new VariableVariantMasks(); + variantMasks.heterozygousMask = maskForAllPatients; + VariableVariantMasks emptyVariantMasks = new VariableVariantMasks(); + emptyVariantMasks.heterozygousMask = maskForNoPatients; + when(variantService.getMasks(eq(VARIANT_INDEX[0]), any())).thenReturn(Optional.of(variantMasks)); + when(variantService.getMasks(eq(VARIANT_INDEX[2]), any())).thenReturn(Optional.of(emptyVariantMasks)); + when(variantService.getMasks(eq(VARIANT_INDEX[4]), any())).thenReturn(Optional.of(emptyVariantMasks)); + + Set patientIdsForIntersectionOfVariantSets = patientVariantJoinHandler + .getPatientIdsForIntersectionOfVariantSets(null, intersectionOfInfoFilters).patientMaskToPatientIdSet(List.of(PATIENT_IDS)); + // this should be all patients, as all patients match one of the variants + assertEquals(PATIENT_IDS_INTEGERS, patientIdsForIntersectionOfVariantSets); + } + + @Test + public void getPatientIdsForIntersectionOfVariantSets_allPatientsMatchOneVariantWithNoVariantFound() { + VariantIndex intersectionOfInfoFilters = new SparseVariantIndex(Set.of(0, 2, 4)); + when(variantService.getPatientIds()).thenReturn(PATIENT_IDS); + when(variantService.emptyBitmask()).thenReturn(emptyBitmask(PATIENT_IDS)); + + VariantMask maskForAllPatients = + new VariantMaskBitmaskImpl(patientVariantJoinHandler.createMaskForPatientSet(PATIENT_IDS_INTEGERS)); + VariantMask maskForNoPatients = VariantMask.emptyInstance(); + + VariableVariantMasks variantMasks = new VariableVariantMasks(); + variantMasks.heterozygousMask = maskForAllPatients; + VariableVariantMasks emptyVariantMasks = new VariableVariantMasks(); + emptyVariantMasks.heterozygousMask = maskForNoPatients; + when(variantService.getMasks(eq(VARIANT_INDEX[0]), any())).thenReturn(Optional.of(variantMasks)); + when(variantService.getMasks(eq(VARIANT_INDEX[2]), any())).thenReturn(Optional.empty()); + when(variantService.getMasks(eq(VARIANT_INDEX[4]), any())).thenReturn(Optional.empty()); + + Set patientIdsForIntersectionOfVariantSets = patientVariantJoinHandler + .getPatientIdsForIntersectionOfVariantSets(null, intersectionOfInfoFilters).patientMaskToPatientIdSet(List.of(PATIENT_IDS)); + // this should be all patients, as all patients match one of the variants + assertEquals(PATIENT_IDS_INTEGERS, patientIdsForIntersectionOfVariantSets); + } + + @Test + public void getPatientIdsForIntersectionOfVariantSets_noPatientsMatchVariants() { + VariantIndex intersectionOfInfoFilters = new SparseVariantIndex(Set.of(0, 2, 4)); + when(variantService.getPatientIds()).thenReturn(PATIENT_IDS); + when(variantService.emptyBitmask()).thenReturn(emptyBitmask(PATIENT_IDS)); + + VariantMask maskForNoPatients = VariantMask.emptyInstance(); + VariableVariantMasks emptyVariantMasks = new VariableVariantMasks(); + emptyVariantMasks.heterozygousMask = maskForNoPatients; + when(variantService.getMasks(eq(VARIANT_INDEX[0]), any())).thenReturn(Optional.of(emptyVariantMasks)); + when(variantService.getMasks(eq(VARIANT_INDEX[2]), any())).thenReturn(Optional.of(emptyVariantMasks)); + when(variantService.getMasks(eq(VARIANT_INDEX[4]), any())).thenReturn(Optional.of(emptyVariantMasks)); + + Set patientIdsForIntersectionOfVariantSets = patientVariantJoinHandler + .getPatientIdsForIntersectionOfVariantSets(Set.of(), intersectionOfInfoFilters).patientMaskToPatientIdSet(List.of(PATIENT_IDS)); + // this should be empty because all variants masks have no matching patients + assertEquals(Set.of(), patientIdsForIntersectionOfVariantSets); + } + + @Test + public void getPatientIdsForIntersectionOfVariantSets_somePatientsMatchVariants() { + VariantIndex intersectionOfInfoFilters = new SparseVariantIndex(Set.of(0, 2, 4)); + when(variantService.getPatientIds()).thenReturn(PATIENT_IDS); + when(variantService.emptyBitmask()).thenReturn(emptyBitmask(PATIENT_IDS)); + + VariantMask maskForPatients1 = new VariantMaskBitmaskImpl(patientVariantJoinHandler.createMaskForPatientSet(Set.of(101, 103))); + VariantMask maskForPatients2 = new VariantMaskBitmaskImpl(patientVariantJoinHandler.createMaskForPatientSet(Set.of(103, 105))); + VariableVariantMasks variantMasks = new VariableVariantMasks(); + variantMasks.heterozygousMask = maskForPatients1; + VariableVariantMasks variantMasks2 = new VariableVariantMasks(); + variantMasks2.heterozygousMask = maskForPatients2; + when(variantService.getMasks(eq(VARIANT_INDEX[0]), any())).thenReturn(Optional.of(variantMasks)); + when(variantService.getMasks(eq(VARIANT_INDEX[2]), any())).thenReturn(Optional.of(variantMasks2)); + + Set patientIdsForIntersectionOfVariantSets = patientVariantJoinHandler + .getPatientIdsForIntersectionOfVariantSets(null, intersectionOfInfoFilters).patientMaskToPatientIdSet(List.of(PATIENT_IDS)); + // this should be all patients who match at least one variant + assertEquals(Set.of(101, 103, 105), patientIdsForIntersectionOfVariantSets); + } + + @Test + public void getPatientIdsForIntersectionOfVariantSets_noVariants() { + VariantIndex intersectionOfInfoFilters = VariantIndex.empty(); + when(variantService.getPatientIds()).thenReturn(PATIENT_IDS); + + Set patientIdsForIntersectionOfVariantSets = patientVariantJoinHandler + .getPatientIdsForIntersectionOfVariantSets(null, intersectionOfInfoFilters).patientMaskToPatientIdSet(List.of(PATIENT_IDS)); + // this should be empty, as there are no variants + assertEquals(Set.of(), patientIdsForIntersectionOfVariantSets); + } + + @Test + public void getPatientIdsForIntersectionOfVariantSets_patientSubsetPassed() { + VariantIndex intersectionOfInfoFilters = new SparseVariantIndex(Set.of(0, 2, 4)); + when(variantService.getPatientIds()).thenReturn(PATIENT_IDS); + when(variantService.emptyBitmask()).thenReturn(emptyBitmask(PATIENT_IDS)); + + VariantMask maskForPatients1 = new VariantMaskBitmaskImpl(patientVariantJoinHandler.createMaskForPatientSet(Set.of(101, 103, 105))); + VariantMask maskForPatients2 = new VariantMaskBitmaskImpl(patientVariantJoinHandler.createMaskForPatientSet(Set.of(103, 105, 107))); + VariableVariantMasks variantMasks = new VariableVariantMasks(); + variantMasks.heterozygousMask = maskForPatients1; + VariableVariantMasks variantMasks2 = new VariableVariantMasks(); + variantMasks2.heterozygousMask = maskForPatients2; + when(variantService.getMasks(eq(VARIANT_INDEX[0]), any())).thenReturn(Optional.of(variantMasks)); + when(variantService.getMasks(eq(VARIANT_INDEX[2]), any())).thenReturn(Optional.of(variantMasks2)); + + Set patientIdsForIntersectionOfVariantSets = + patientVariantJoinHandler.getPatientIdsForIntersectionOfVariantSets(Set.of(102, 103, 104, 105, 106), intersectionOfInfoFilters) + .patientMaskToPatientIdSet(List.of(PATIENT_IDS)); + // this should be the union of patients matching variants (101, 103, 105, 107), intersected with the patient subset parameter (103, + // 104, 105) which is (103, 105) + assertEquals(Set.of(103, 105), patientIdsForIntersectionOfVariantSets); + } + + public BigInteger emptyBitmask(String[] patientIds) { + String emptyVariantMask = ""; + for (String patientId : patientIds) { + emptyVariantMask = emptyVariantMask + "0"; + } + return new BigInteger("11" + emptyVariantMask + "11", 2); + } +} diff --git a/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PhenotypeMetaStoreTest.java b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PhenotypeMetaStoreTest.java new file mode 100644 index 000000000..04b0f9f35 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PhenotypeMetaStoreTest.java @@ -0,0 +1,62 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import java.util.Set; +import java.util.TreeMap; +import java.util.TreeSet; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + +class PhenotypeMetaStoreTest { + + private TreeMap metaStore; + + private TreeSet patientIds; + + private PhenotypeMetaStore phenotypeMetaStore; + + @BeforeEach + public void setup() { + metaStore = new TreeMap<>(); + metaStore.put("\\study1\\demographics\\age\\", new ColumnMeta().setName("age")); + metaStore.put("\\study1\\demographics\\sex\\", new ColumnMeta().setName("sex")); + metaStore.put("\\study2\\demographics\\age\\", new ColumnMeta().setName("age")); + metaStore.put("\\study2\\demographics\\sex\\", new ColumnMeta().setName("sex")); + + patientIds = new TreeSet<>(); + phenotypeMetaStore = new PhenotypeMetaStore(metaStore, patientIds, 500); + } + + @Test + public void loadChildConceptPaths_matchingConcepts_shouldReturnConcepts() { + Set childConceptPaths = phenotypeMetaStore.loadChildConceptPaths("\\study1\\demographics\\"); + assertEquals(Set.of("\\study1\\demographics\\age\\", "\\study1\\demographics\\sex\\"), childConceptPaths); + } + + @Test + public void loadChildConceptPaths_noMatchingConcepts_shouldReturnNoConcepts() { + Set childConceptPaths = phenotypeMetaStore.loadChildConceptPaths("\\study3\\demographics\\"); + assertEquals(Set.of(), childConceptPaths); + } + + @Test + public void getChildConceptPaths_multipleCalls_shouldCacheResults() { + TreeMap metaStore = mock(TreeMap.class); + when(metaStore.keySet()).thenReturn( + Set.of( + "\\study1\\demographics\\age\\", "\\study1\\demographics\\sex\\", "\\study2\\demographics\\age\\", + "\\study2\\demographics\\sex\\" + ) + ); + phenotypeMetaStore = new PhenotypeMetaStore(metaStore, patientIds, 500); + + for (int k = 0; k < 5; k++) { + Set childConceptPaths = phenotypeMetaStore.getChildConceptPaths("\\study1\\demographics\\"); + assertEquals(Set.of("\\study1\\demographics\\age\\", "\\study1\\demographics\\sex\\"), childConceptPaths); + } + verify(metaStore, times(1)).keySet(); + } +} diff --git a/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantIndexTest.java b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantIndexTest.java new file mode 100644 index 000000000..61be5e369 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantIndexTest.java @@ -0,0 +1,66 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing; + +import org.junit.jupiter.api.Test; + +import java.util.Set; + +import static org.junit.jupiter.api.Assertions.assertArrayEquals; +import static org.junit.jupiter.api.Assertions.assertEquals; + +public class VariantIndexTest { + + + @Test + public void testSparseVariantUnion() { + SparseVariantIndex sparseVariantIndex1 = new SparseVariantIndex(Set.of(1, 3, 5)); + SparseVariantIndex sparseVariantIndex2 = new SparseVariantIndex(Set.of(2, 4, 8)); + VariantIndex union = sparseVariantIndex1.union(sparseVariantIndex2); + assertEquals(union.getClass(), SparseVariantIndex.class); + assertEquals(Set.of(1, 2, 3, 4, 5, 8), ((SparseVariantIndex) union).getVariantIds()); + } + + @Test + public void testSparseVariantIntersection() { + SparseVariantIndex sparseVariantIndex1 = new SparseVariantIndex(Set.of(1, 3, 5, 7)); + SparseVariantIndex sparseVariantIndex2 = new SparseVariantIndex(Set.of(2, 3, 4, 5, 6)); + VariantIndex intersection = sparseVariantIndex1.intersection(sparseVariantIndex2); + assertEquals(intersection.getClass(), SparseVariantIndex.class); + assertEquals(Set.of(3, 5), ((SparseVariantIndex) intersection).getVariantIds()); + } + + @Test + public void testDenseVariantUnion() { + DenseVariantIndex denseVariantIndex1 = new DenseVariantIndex(new boolean[] {true, false, true, false}); + DenseVariantIndex denseVariantIndex2 = new DenseVariantIndex(new boolean[] {true, false, false, true}); + VariantIndex union = denseVariantIndex1.union(denseVariantIndex2); + assertEquals(union.getClass(), DenseVariantIndex.class); + assertArrayEquals(new boolean[] {true, false, true, true}, ((DenseVariantIndex) union).getVariantIndexMask()); + } + + @Test + public void testDenseVariantIntersection() { + DenseVariantIndex denseVariantIndex1 = new DenseVariantIndex(new boolean[] {true, false, true, false}); + DenseVariantIndex denseVariantIndex2 = new DenseVariantIndex(new boolean[] {true, false, false, true}); + VariantIndex intersection = denseVariantIndex1.intersection(denseVariantIndex2); + assertEquals(intersection.getClass(), DenseVariantIndex.class); + assertArrayEquals(new boolean[] {true, false, false, false}, ((DenseVariantIndex) intersection).getVariantIndexMask()); + } + + @Test + public void testSparseAndDenseUnion() { + SparseVariantIndex sparseVariantIndex1 = new SparseVariantIndex(Set.of(0, 2)); + DenseVariantIndex denseVariantIndex = new DenseVariantIndex(new boolean[] {true, true, false, false}); + VariantIndex union = sparseVariantIndex1.union(denseVariantIndex); + assertEquals(union.getClass(), DenseVariantIndex.class); + assertArrayEquals(new boolean[] {true, true, true, false}, ((DenseVariantIndex) union).getVariantIndexMask()); + } + + @Test + public void testSparseAndDenseIntersection() { + SparseVariantIndex sparseVariantIndex1 = new SparseVariantIndex(Set.of(0, 2)); + DenseVariantIndex denseVariantIndex = new DenseVariantIndex(new boolean[] {false, true, true, false}); + VariantIndex intersection = sparseVariantIndex1.intersection(denseVariantIndex); + assertEquals(intersection.getClass(), SparseVariantIndex.class); + assertEquals(Set.of(2), ((SparseVariantIndex) intersection).getVariantIds()); + } +} diff --git a/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/dictionary/ConceptTest.java b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/dictionary/ConceptTest.java new file mode 100644 index 000000000..7ea336751 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/dictionary/ConceptTest.java @@ -0,0 +1,26 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.dictionary; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import org.junit.jupiter.api.Test; + +import java.util.List; +import java.util.Map; + +import static org.junit.jupiter.api.Assertions.*; + +public class ConceptTest { + + @Test + public void jsonSerialization() throws JsonProcessingException { + Concept[] concepts = new Concept[] {new Concept( + "\\demographics\\age\\", "age", "AGE", null, "patient age", Map.of("drs_uri", "[\"a-drs.uri\", \"another-drs.uri\"]") + )}; + ObjectMapper objectMapper = new ObjectMapper(); + + String serialized = objectMapper.writeValueAsString(concepts); + Concept[] deserialized = objectMapper.readValue(serialized, Concept[].class); + + assertEquals(List.of(concepts), List.of(deserialized)); + } +} diff --git a/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/genomic/GenomicProcessorRestClientTest.java b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/genomic/GenomicProcessorRestClientTest.java new file mode 100644 index 000000000..0957d0085 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/genomic/GenomicProcessorRestClientTest.java @@ -0,0 +1,64 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.genomic; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.InfoColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMask; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import edu.harvard.hms.dbmi.avillach.hpds.processing.DistributableQuery; +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; +import static org.junit.jupiter.api.Assertions.*; + +import java.math.BigInteger; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.stream.Collectors; +import java.util.stream.IntStream; + +@Disabled +public class GenomicProcessorRestClientTest { + + private GenomicProcessorRestClient genomicProcessorRestClient = new GenomicProcessorRestClient("http://localhost:8090/"); + + + @Test + public void simpleTest() { + DistributableQuery distributableQuery = new DistributableQuery(); + + List variantInfoFilters = new ArrayList<>(); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = + Map.of("Gene_with_variant", new String[] {"BRCA1"}, "Variant_consequence_calculated", new String[] {"splice_donor_variant"}); + variantInfoFilters.add(variantInfoFilter); + distributableQuery.setVariantInfoFilters(variantInfoFilters); + Set patientIds = IntStream.range(53000, 53635).boxed().collect(Collectors.toSet()); + distributableQuery.setPatientIds(patientIds); + + VariantMask patientMaskForVariantInfoFilters = genomicProcessorRestClient.getPatientMask(distributableQuery).block(); + System.out.println(patientMaskForVariantInfoFilters); + } + + @Test + public void getInfoStoreColumns() { + Set infoStoreColumns = genomicProcessorRestClient.getInfoStoreColumns(); + assertTrue(infoStoreColumns.contains("Variant_consequence_calculated")); + } + + @Test + public void getInfoStoreValues() { + Set infoStoreValues = genomicProcessorRestClient.getInfoStoreValues("Variant_consequence_calculated"); + assertTrue(infoStoreValues.contains("inframe_deletion")); + } + + @Test + public void getInfoColumnMeta() { + List infoColumnMeta = genomicProcessorRestClient.getInfoColumnMeta(); + for (InfoColumnMeta columnMeta : infoColumnMeta) { + if (columnMeta.key().equals("Variant_consequence_calculated")) { + return; + } + } + throw new RuntimeException("Variant_consequence_calculated not found in info column meta"); + } +} diff --git a/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/PfbWriterTest.java b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/PfbWriterTest.java new file mode 100644 index 000000000..93437aa0e --- /dev/null +++ b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/PfbWriterTest.java @@ -0,0 +1,75 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.io; + +import edu.harvard.hms.dbmi.avillach.hpds.processing.dictionary.Concept; +import edu.harvard.hms.dbmi.avillach.hpds.processing.dictionary.DictionaryService; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.Mockito; +import org.mockito.junit.jupiter.MockitoExtension; + +import java.io.File; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; +import java.util.UUID; + +import static org.junit.jupiter.api.Assertions.*; + + +@ExtendWith(MockitoExtension.class) +public class PfbWriterTest { + + @Mock + private DictionaryService dictionaryService; + + @Test + public void writeValidPFB() { + PfbWriter pfbWriter = new PfbWriter(new File("target/test-result.avro"), UUID.randomUUID().toString(), dictionaryService); + + Mockito.when(dictionaryService.getConcepts(List.of("patient_id", "\\demographics\\age\\", "\\phs123\\stroke\\"))).thenReturn( + List.of( + new Concept( + "\\demographics\\age\\", "age", "AGE", null, "patient age", Map.of("drs_uri", "[\"a-drs.uri\", \"another-drs.uri\"]") + ) + ) + ); + + pfbWriter.writeHeader(new String[] {"patient_id", "\\demographics\\age\\", "\\phs123\\stroke\\"}); + List> nullableList = new ArrayList<>(); + nullableList.add(List.of("123")); + nullableList.add(null); + nullableList.add(List.of("Y")); + pfbWriter.writeMultiValueEntity( + List.of(nullableList, List.of(List.of("456"), List.of("80"), List.of("N", "Y")), List.of(List.of(), List.of("75"), List.of())) + ); + pfbWriter.writeMultiValueEntity( + List.of( + List.of(List.of("123"), List.of("80"), List.of("Y")), List.of(List.of("456"), List.of("70"), List.of("N", "Y")), + List.of(List.of(), List.of("75"), List.of()) + ) + ); + pfbWriter.close(); + } + + @Test + public void formatFieldName_spacesAndBackslashes_replacedWithUnderscore() { + PfbWriter pfbWriter = new PfbWriter(new File("target/test-result.avro"), UUID.randomUUID().toString(), dictionaryService); + String formattedName = pfbWriter.formatFieldName("\\Topmed Study Accession with Subject ID\\\\"); + assertEquals("_Topmed_Study_Accession_with_Subject_ID__", formattedName); + } + + @Test + public void formatFieldName_startsWithDigit_prependUnderscore() { + PfbWriter pfbWriter = new PfbWriter(new File("target/test-result.avro"), UUID.randomUUID().toString(), dictionaryService); + String formattedName = pfbWriter.formatFieldName("123Topmed Study Accession with Subject ID\\\\"); + assertEquals("_123Topmed_Study_Accession_with_Subject_ID__", formattedName); + } + + @Test + public void formatFieldName_randomGarbage_replaceWithUnderscore() { + PfbWriter pfbWriter = new PfbWriter(new File("target/test-result.avro"), UUID.randomUUID().toString(), dictionaryService); + String formattedName = pfbWriter.formatFieldName("$$$my garbage @vro var!able nam#"); + assertEquals("___my_garbage__vro_var_able_nam_", formattedName); + } +} diff --git a/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/patient/PatientProcessorTest.java b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/patient/PatientProcessorTest.java new file mode 100644 index 000000000..2e620a33a --- /dev/null +++ b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/patient/PatientProcessorTest.java @@ -0,0 +1,45 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.patient; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.processing.AbstractProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.AsyncResult; +import org.junit.jupiter.api.Test; +import org.mockito.Mockito; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.autoconfigure.EnableAutoConfiguration; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; + +import java.util.List; +import java.util.TreeSet; + +@EnableAutoConfiguration +@SpringBootTest(classes = PatientProcessor.class) +class PatientProcessorTest { + + @MockBean + AbstractProcessor abstractProcessor; + + @Autowired + PatientProcessor subject; + + @Test + void shouldProcessPatientQuery() { + Query q = new Query(); + q.setId("frank"); + q.setPicSureId("frank"); + q.setExpectedResultType(ResultType.PATIENTS); + AsyncResult writeToThis = Mockito.mock(AsyncResult.class); + Mockito.when(abstractProcessor.getPatientSubsetForQuery(q)).thenReturn(new TreeSet<>(List.of(1, 2, 42))); + + subject.runQuery(q, writeToThis); + + Mockito.verify(writeToThis, Mockito.times(1)).appendResults( + Mockito.argThat( + strings -> strings.size() == 3 && strings.get(0)[0].equals("1") && strings.get(1)[0].equals("2") + && strings.get(2)[0].equals("42") + ) + ); + } +} diff --git a/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/timeseries/TimeSeriesConversionServiceTest.java b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/timeseries/TimeSeriesConversionServiceTest.java new file mode 100644 index 000000000..adadca3d0 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/timeseries/TimeSeriesConversionServiceTest.java @@ -0,0 +1,19 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.timeseries; + +import org.junit.jupiter.api.Test; + +import static org.junit.jupiter.api.Assertions.assertEquals; + + +public class TimeSeriesConversionServiceTest { + + TimeSeriesConversionService subject = new TimeSeriesConversionService(); + + @Test + public void shouldConvertToIsoString() { + String actual = subject.toISOString(0L); + String expected = "1970-01-01T00:00:00Z"; + + assertEquals(expected, actual); + } +} diff --git a/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/CountV3ProcessorTest.java b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/CountV3ProcessorTest.java new file mode 100644 index 000000000..d97125f31 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/CountV3ProcessorTest.java @@ -0,0 +1,237 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.v3; + +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.KeyAndValue; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Operator; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicFilterType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicSubquery; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; + +import java.util.Collection; +import java.util.List; +import java.util.Map; +import java.util.Optional; +import java.util.Set; +import java.util.TreeMap; +import java.util.TreeSet; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.when; + +@ExtendWith(MockitoExtension.class) +class CountV3ProcessorTest { + + private CountV3Processor countV3Processor; + + @Mock + private QueryExecutor queryExecutor; + + @Mock + private PhenotypicObservationStore phenotypicObservationStore; + + @BeforeEach + public void setup() { + countV3Processor = new CountV3Processor(queryExecutor, phenotypicObservationStore); + } + + + @Test + public void runCrossCounts_validPaths_returnPatientCounts() { + Set allPaientIds = Set.of(2, 3, 5, 8, 13, 21); + Set patientSubset1 = Set.of(1, 2, 3, 5, 8); + Set patientSubset2 = Set.of(8, 13, 21, 34); + String conceptPath1 = "\\_studies_consents\\phs001194\\HMB\\"; + String conceptPath2 = "\\_studies_consents\\phs000007\\HMB-IRB-MDS\\"; + + Query fullQuery = new Query(List.of(conceptPath1, conceptPath2), List.of(), null, List.of(), ResultType.CROSS_COUNT, null, null); + + Query queryConcept1 = new Query( + List.of(), List.of(), new PhenotypicFilter(PhenotypicFilterType.REQUIRED, conceptPath1, null, null, null, null), List.of(), + null, null, null + ); + Query queryConcept2 = new Query( + List.of(), List.of(), new PhenotypicFilter(PhenotypicFilterType.REQUIRED, conceptPath2, null, null, null, null), List.of(), + null, null, null + ); + + when(queryExecutor.getPatientSubsetForQuery(fullQuery)).thenReturn(allPaientIds); + when(queryExecutor.getPatientSubsetForQuery(queryConcept1)).thenReturn(patientSubset1); + when(queryExecutor.getPatientSubsetForQuery(queryConcept2)).thenReturn(patientSubset2); + + Map crossCountsMap = countV3Processor.runCrossCounts(fullQuery); + assertEquals(2, crossCountsMap.size()); + assertEquals(Set.of(conceptPath1, conceptPath2), crossCountsMap.keySet()); + // Should not include 1 as it is not in the base patient set + assertEquals(4, crossCountsMap.get(conceptPath1)); + // should not include 34 as it is not in the base patient set + assertEquals(3, crossCountsMap.get(conceptPath2)); + } + + @Test + public void runCrossCounts_validPathsNoMatchingPatients_returnZeros() { + Set allPaientIds = Set.of(1000, 1001, 1002, 1003); + Set patientSubset1 = Set.of(1, 2, 3, 5, 8); + Set patientSubset2 = Set.of(8, 13, 21, 34); + String conceptPath1 = "\\_studies_consents\\phs001194\\HMB\\"; + String conceptPath2 = "\\_studies_consents\\phs000007\\HMB-IRB-MDS\\"; + + Query fullQuery = new Query(List.of(conceptPath1, conceptPath2), List.of(), null, List.of(), ResultType.CROSS_COUNT, null, null); + + Query queryConcept1 = new Query( + List.of(), List.of(), new PhenotypicFilter(PhenotypicFilterType.REQUIRED, conceptPath1, null, null, null, null), List.of(), + null, null, null + ); + Query queryConcept2 = new Query( + List.of(), List.of(), new PhenotypicFilter(PhenotypicFilterType.REQUIRED, conceptPath2, null, null, null, null), List.of(), + null, null, null + ); + + when(queryExecutor.getPatientSubsetForQuery(fullQuery)).thenReturn(allPaientIds); + when(queryExecutor.getPatientSubsetForQuery(queryConcept1)).thenReturn(patientSubset1); + when(queryExecutor.getPatientSubsetForQuery(queryConcept2)).thenReturn(patientSubset2); + + Map crossCountsMap = countV3Processor.runCrossCounts(fullQuery); + assertEquals(2, crossCountsMap.size()); + assertEquals(Set.of(conceptPath1, conceptPath2), crossCountsMap.keySet()); + // Should not include 1 as it is not in the base patient set + assertEquals(0, crossCountsMap.get(conceptPath1)); + // should not include 34 as it is not in the base patient set + assertEquals(0, crossCountsMap.get(conceptPath2)); + } + + + @Test + public void runCrossCounts_invalidPath_returnNegativeOne() { + Set allPaientIds = Set.of(2, 3, 5, 8, 13, 21); + Set patientSubset1 = Set.of(1, 2, 3, 5, 8); + Set patientSubset2 = Set.of(8, 13, 21, 34); + String conceptPath1 = "\\_studies_consents\\phs001194\\HMB\\"; + String conceptPath2 = "\\_studies_consents\\phs000007\\HMB-IRB-MDS\\"; + + Query fullQuery = new Query(List.of(conceptPath1, conceptPath2), List.of(), null, List.of(), ResultType.CROSS_COUNT, null, null); + + Query queryConcept1 = new Query( + List.of(), List.of(), new PhenotypicFilter(PhenotypicFilterType.REQUIRED, conceptPath1, null, null, null, null), List.of(), + null, null, null + ); + Query queryConcept2 = new Query( + List.of(), List.of(), new PhenotypicFilter(PhenotypicFilterType.REQUIRED, conceptPath2, null, null, null, null), List.of(), + null, null, null + ); + + when(queryExecutor.getPatientSubsetForQuery(fullQuery)).thenReturn(allPaientIds); + when(queryExecutor.getPatientSubsetForQuery(queryConcept1)).thenReturn(patientSubset1); + when(queryExecutor.getPatientSubsetForQuery(queryConcept2)).thenThrow(RuntimeException.class); + + Map crossCountsMap = countV3Processor.runCrossCounts(fullQuery); + assertEquals(2, crossCountsMap.size()); + assertEquals(Set.of(conceptPath1, conceptPath2), crossCountsMap.keySet()); + // Should not include 1 as it is not in the base patient set + assertEquals(4, crossCountsMap.get(conceptPath1)); + // should not include 34 as it is not in the base patient set + assertEquals(-1, crossCountsMap.get(conceptPath2)); + } + + @Test + @SuppressWarnings("unchecked") + public void runContinuousCrossCounts_requiredNumericConcept_returnsObservedValues() { + String conceptPath = "\\demographics\\AGE\\"; + PhenotypicFilter required = new PhenotypicFilter(PhenotypicFilterType.REQUIRED, conceptPath, null, null, null, null); + Query query = new Query(List.of(), List.of(), required, List.of(), ResultType.CONTINUOUS_CROSS_COUNT, null, null); + + PhenoCube cube = new PhenoCube<>(conceptPath, Double.class); + cube.setSortedByKey(new KeyAndValue[] {new KeyAndValue<>(1, 18.0), new KeyAndValue<>(2, 19.0), new KeyAndValue<>(3, 19.0)}); + + when(queryExecutor.getPatientSubsetForQuery(query)).thenReturn(Set.of(1, 3)); + when(queryExecutor.getDictionary()).thenReturn(Map.of(conceptPath, new ColumnMeta().setName(conceptPath).setCategorical(false))); + when(phenotypicObservationStore.getCube(conceptPath)).thenReturn(java.util.Optional.of(cube)); + + Map> crossCounts = countV3Processor.runContinuousCrossCounts(query); + + assertEquals(1, crossCounts.get(conceptPath).get(18.0)); + assertEquals(1, crossCounts.get(conceptPath).get(19.0)); + } + + @Test + public void runCategoryCrossCounts_duplicateValueFiltersSamePath_mergesValues() { + String sexPath = "\\demographics\\SEX\\"; + PhenotypicFilter maleFilter = new PhenotypicFilter(PhenotypicFilterType.FILTER, sexPath, Set.of("male"), null, null, null); + PhenotypicFilter femaleFilter = new PhenotypicFilter(PhenotypicFilterType.FILTER, sexPath, Set.of("female"), null, null, null); + PhenotypicSubquery subquery = new PhenotypicSubquery(null, List.of(maleFilter, femaleFilter), Operator.OR); + Query query = new Query(List.of(), List.of(), subquery, List.of(), ResultType.CATEGORICAL_CROSS_COUNT, null, null); + + TreeMap> categoryMap = new TreeMap<>(); + categoryMap.put("male", new TreeSet<>(Set.of(1, 2, 3))); + categoryMap.put("female", new TreeSet<>(Set.of(4, 5))); + PhenoCube cube = new PhenoCube<>(sexPath, String.class); + cube.setCategoryMap(categoryMap); + + when(queryExecutor.getPatientSubsetForQuery(query)).thenReturn(Set.of(1, 2, 3, 4, 5)); + when(phenotypicObservationStore.getCube(sexPath)).thenReturn(Optional.of(cube)); + + Map> crossCounts = countV3Processor.runCategoryCrossCounts(query); + + // Both filter values land in a single SEX entry instead of one overwriting the other + assertEquals(1, crossCounts.size()); + assertEquals(Set.of("male", "female"), crossCounts.get(sexPath).keySet()); + assertEquals(3, crossCounts.get(sexPath).get("male")); + assertEquals(2, crossCounts.get(sexPath).get("female")); + } + + @Test + public void runCategoryCrossCounts_requiredFilterPartialBaseSet_countsEachPatientOnce() { + String sexPath = "\\demographics\\SEX\\"; + PhenotypicFilter requiredSex = new PhenotypicFilter(PhenotypicFilterType.REQUIRED, sexPath, null, null, null, null); + Query query = new Query(List.of(), List.of(), requiredSex, List.of(), ResultType.CATEGORICAL_CROSS_COUNT, null, null); + + TreeMap> categoryMap = new TreeMap<>(); + categoryMap.put("male", new TreeSet<>(Set.of(1, 2, 3))); + categoryMap.put("female", new TreeSet<>(Set.of(4, 5))); + PhenoCube cube = new PhenoCube<>(sexPath, String.class); + cube.setCategoryMap(categoryMap); + + // Base set is a partial subset of every category, forcing the per-patient counting path. + // Only patient 1 (male) and patient 4 (female) are in the cohort, so each category count must be exactly 1. + when(queryExecutor.getPatientSubsetForQuery(query)).thenReturn(Set.of(1, 4)); + when(queryExecutor.getDictionary()).thenReturn(Map.of(sexPath, new ColumnMeta().setName(sexPath).setCategorical(true))); + when(phenotypicObservationStore.getCube(sexPath)).thenReturn(Optional.of(cube)); + + Map> crossCounts = countV3Processor.runCategoryCrossCounts(query); + + assertEquals(1, crossCounts.get(sexPath).get("male")); + assertEquals(1, crossCounts.get(sexPath).get("female")); + } + + @Test + @SuppressWarnings("unchecked") + public void runContinuousCrossCounts_showsCohortValuesOutsideFilterRange() { + String agePath = "\\demographics\\AGE\\"; + // A range filter (age 10-20); the cohort, however, includes patient 2 (age 40) who is outside that range -- as happens when the + // range is OR'd with a filter on another concept. The age distribution must include 40 because patient 2 is in the cohort; the + // filter range only constrains the cohort, not which values are displayed. + PhenotypicFilter youngFilter = new PhenotypicFilter(PhenotypicFilterType.FILTER, agePath, null, 10.0, 20.0, null); + Query query = new Query(List.of(), List.of(), youngFilter, List.of(), ResultType.CONTINUOUS_CROSS_COUNT, null, null); + + PhenoCube cube = new PhenoCube<>(agePath, Double.class); + cube.setSortedByKey(new KeyAndValue[] {new KeyAndValue<>(1, 15.0), new KeyAndValue<>(2, 40.0), new KeyAndValue<>(3, 65.0)}); + + when(queryExecutor.getPatientSubsetForQuery(query)).thenReturn(Set.of(1, 2)); + when(queryExecutor.getDictionary()).thenReturn(Map.of(agePath, new ColumnMeta().setName(agePath).setCategorical(false))); + when(phenotypicObservationStore.getCube(agePath)).thenReturn(Optional.of(cube)); + + Map> crossCounts = countV3Processor.runContinuousCrossCounts(query); + + assertEquals(1, crossCounts.get(agePath).get(15.0)); + assertEquals(1, crossCounts.get(agePath).get(40.0)); + // patient 3 (65) is not in the cohort, so it is absent + assertNull(crossCounts.get(agePath).get(65.0)); + } +} diff --git a/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/PhenotypicFilterValidatorTest.java b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/PhenotypicFilterValidatorTest.java new file mode 100644 index 000000000..d395db84d --- /dev/null +++ b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/PhenotypicFilterValidatorTest.java @@ -0,0 +1,149 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.v3; + +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.*; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +import java.util.Map; +import java.util.Set; + +import static org.junit.jupiter.api.Assertions.*; + +class PhenotypicFilterValidatorTest { + + private PhenotypicFilterValidator phenotypicFilterValidator; + + private Map metaStore; + + @BeforeEach + public void setup() { + phenotypicFilterValidator = new PhenotypicFilterValidator(); + metaStore = Map.of( + "\\study123\\demographics\\sex\\", new ColumnMeta().setCategorical(true), "\\study123\\demographics\\age\\", + new ColumnMeta().setCategorical(false).setMin(0).setMax(130) + ); + } + + @Test + public void validate_validCategoricalFilter_isValid() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\study123\\demographics\\sex\\", Set.of("male"), null, null, null); + phenotypicFilterValidator.validate(phenotypicFilter, metaStore); + } + + @Test + public void validate_nonExistingCategoricalFilter_isValid() { + PhenotypicFilter phenotypicFilter = new PhenotypicFilter( + PhenotypicFilterType.FILTER, "\\study123\\demographics\\not_a_real_concept\\", Set.of("male"), null, null, null + ); + + phenotypicFilterValidator.validate(phenotypicFilter, metaStore); + } + + @Test + public void validate_invalidCategoricalFilter_throwsException() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\study123\\demographics\\age\\", Set.of("male"), null, null, null); + assertThrows(IllegalArgumentException.class, () -> phenotypicFilterValidator.validate(phenotypicFilter, metaStore)); + } + + @Test + public void validate_validNumericFilter_isValid() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\study123\\demographics\\age\\", null, 20.0, 25.0, null); + phenotypicFilterValidator.validate(phenotypicFilter, metaStore); + } + + @Test + public void validate_validNumericFilterMinOnly_isValid() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\study123\\demographics\\age\\", null, 20.0, null, null); + phenotypicFilterValidator.validate(phenotypicFilter, metaStore); + } + + @Test + public void validate_validNumericFilterMaxOnly_isValid() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\study123\\demographics\\age\\", null, null, 45.0, null); + phenotypicFilterValidator.validate(phenotypicFilter, metaStore); + } + + @Test + public void validate_nonExistingNumericFilter_isValid() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\study123\\demographics\\not_a_real_concept\\", null, 20.0, null, null); + + phenotypicFilterValidator.validate(phenotypicFilter, metaStore); + } + + @Test + public void validate_invalidNumericFilter_throwsException() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\study123\\demographics\\sex\\", null, null, 20.0, null); + assertThrows(IllegalArgumentException.class, () -> phenotypicFilterValidator.validate(phenotypicFilter, metaStore)); + } + + @Test + public void validate_invalidFilterValuesAndMinMax_throwsException() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\study123\\demographics\\sex\\", Set.of("male"), null, 20.0, null); + assertThrows(IllegalArgumentException.class, () -> phenotypicFilterValidator.validate(phenotypicFilter, metaStore)); + } + + @Test + public void validate_anyRecordOfFilter_isValid() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.ANY_RECORD_OF, "\\study123\\", null, null, null, null); + phenotypicFilterValidator.validate(phenotypicFilter, metaStore); + } + + @Test + public void validate_anyRecordOfFilterWithValues_throwsException() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.ANY_RECORD_OF, "\\study123\\", Set.of("purple"), null, null, null); + assertThrows(IllegalArgumentException.class, () -> phenotypicFilterValidator.validate(phenotypicFilter, metaStore)); + PhenotypicFilter phenotypicFilter2 = + new PhenotypicFilter(PhenotypicFilterType.ANY_RECORD_OF, "\\study123\\", null, 42.0, null, null); + assertThrows(IllegalArgumentException.class, () -> phenotypicFilterValidator.validate(phenotypicFilter2, metaStore)); + } + + + @Test + public void validate_requiredFilter_isValid() { + PhenotypicFilter phenotypicFilter = new PhenotypicFilter(PhenotypicFilterType.REQUIRED, "\\study123\\", null, null, null, null); + phenotypicFilterValidator.validate(phenotypicFilter, metaStore); + } + + @Test + public void validate_requiredFilterWithValues_throwsException() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.REQUIRED, "\\study123\\", Set.of("purple"), null, null, null); + assertThrows(IllegalArgumentException.class, () -> phenotypicFilterValidator.validate(phenotypicFilter, metaStore)); + PhenotypicFilter phenotypicFilter2 = new PhenotypicFilter(PhenotypicFilterType.REQUIRED, "\\study123\\", null, 42.0, null, null); + assertThrows(IllegalArgumentException.class, () -> phenotypicFilterValidator.validate(phenotypicFilter2, metaStore)); + } + + @Test + public void validate_validAuthorizationFilter_isValid() { + AuthorizationFilter authorizationFilter = new AuthorizationFilter("\\study123\\demographics\\sex\\", Set.of("male")); + phenotypicFilterValidator.validate(authorizationFilter, metaStore); + } + + @Test + public void validate_emptyValuesAuthorizationFilter_throwsException() { + // Authorization filters cannot be empty + AuthorizationFilter authorizationFilter = new AuthorizationFilter("\\study123\\demographics\\sex\\", Set.of()); + assertThrows(IllegalArgumentException.class, () -> phenotypicFilterValidator.validate(authorizationFilter, metaStore)); + AuthorizationFilter nullAuthorizationFilter = new AuthorizationFilter("\\study123\\demographics\\sex\\", null); + assertThrows(IllegalArgumentException.class, () -> phenotypicFilterValidator.validate(nullAuthorizationFilter, metaStore)); + } + + @Test + public void validate_continuousAuthorizationFilter_throwsException() { + AuthorizationFilter authorizationFilter = new AuthorizationFilter("\\study123\\demographics\\age\\", Set.of("male")); + assertThrows(IllegalArgumentException.class, () -> phenotypicFilterValidator.validate(authorizationFilter, metaStore)); + } + + +} diff --git a/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/PhenotypicQueryExecutorTest.java b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/PhenotypicQueryExecutorTest.java new file mode 100644 index 000000000..fef86eee3 --- /dev/null +++ b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/PhenotypicQueryExecutorTest.java @@ -0,0 +1,232 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.v3; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.*; +import edu.harvard.hms.dbmi.avillach.hpds.processing.PhenotypeMetaStore; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; + +import java.util.HashSet; +import java.util.List; +import java.util.Set; +import java.util.TreeSet; +import java.util.concurrent.ExecutionException; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + + +@ExtendWith(MockitoExtension.class) +class PhenotypicQueryExecutorTest { + + @Mock + private PhenotypeMetaStore phenotypeMetaStore; + + @Mock + private PhenotypicObservationStore phenotypicObservationStore; + + private PhenotypicQueryExecutor phenotypicQueryExecutor; + + @BeforeEach + public void setup() { + phenotypicQueryExecutor = new PhenotypicQueryExecutor(phenotypeMetaStore, phenotypicObservationStore); + } + + @Test + public void getPatientSet_noFilters_returnAllPatients() { + Query query = new Query(List.of(), List.of(), null, null, ResultType.COUNT, null, null); + + Set patientIds = Set.of(10, 100, 1000); + when(phenotypeMetaStore.getPatientIds()).thenReturn(new TreeSet<>(patientIds)); + + Set patientSet = phenotypicQueryExecutor.getPatientSet(query); + assertEquals(patientIds, patientSet); + } + + @Test + public void getPatientSet_validNumericFilter_returnPatients() throws ExecutionException { + String conceptPath = "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\"; + Query query = new Query( + List.of(), List.of(), new PhenotypicFilter(PhenotypicFilterType.FILTER, conceptPath, null, 35.0, 45.0, null), null, + ResultType.COUNT, null, null + ); + + Set patientIds = Set.of(2, 3, 5); + when(phenotypicObservationStore.getKeysForRange(conceptPath, 35.0, 45.0)).thenReturn(patientIds); + + Set patientSet = phenotypicQueryExecutor.getPatientSet(query); + assertEquals(patientIds, patientSet); + } + + @Test + public void getPatientSet_validCategoricalFilter_returnPatients() throws ExecutionException { + String conceptPath = "\\open_access-1000Genomes\\data\\POPULATION NAME\\"; + Query query = new Query( + List.of(), List.of(), new PhenotypicFilter(PhenotypicFilterType.FILTER, conceptPath, Set.of("Finnish"), null, null, null), null, + ResultType.COUNT, null, null + ); + + Set patientIds = Set.of(2, 3, 5, 8, 13); + when(phenotypicObservationStore.getKeysForValues(conceptPath, Set.of("Finnish"))).thenReturn(patientIds); + + Set patientSet = phenotypicQueryExecutor.getPatientSet(query); + assertEquals(patientIds, patientSet); + } + + @Test + public void getPatientSet_nonExistentCategoricalFilter_returnNoPatients() { + String conceptPath = "\\open_access-1000Genomes\\data\\NOT_A_CONCEPT_PATH\\"; + Query query = new Query( + List.of(), List.of(), new PhenotypicFilter(PhenotypicFilterType.FILTER, conceptPath, Set.of("Finnish"), null, null, null), null, + ResultType.COUNT, null, null + ); + + when(phenotypicObservationStore.getKeysForValues(conceptPath, Set.of("Finnish"))).thenReturn(Set.of()); + + Set patientSet = phenotypicQueryExecutor.getPatientSet(query); + assertEquals(Set.of(), patientSet); + } + + @Test + public void getPatientSet_nonExistentNumericFilter_returnNoPatients() { + String conceptPath = "\\open_access-1000Genomes\\data\\NOT_A_CONCEPT_PATH\\"; + Query query = new Query( + List.of(), List.of(), new PhenotypicFilter(PhenotypicFilterType.FILTER, conceptPath, null, 42.0, null, null), null, + ResultType.COUNT, null, null + ); + + when(phenotypicObservationStore.getKeysForRange(conceptPath, 42.0, null)).thenReturn(Set.of()); + + Set patientSet = phenotypicQueryExecutor.getPatientSet(query); + assertEquals(Set.of(), patientSet); + } + + + @Test + public void getPatientSet_complexNestedFilters_returnPatients() throws ExecutionException { + String categoricalConcept1 = "\\open_access-1000Genomes\\data\\POPULATION NAME\\"; + String categoricalConcept2 = "\\open_access-1000Genomes\\data\\SEX\\"; + String numericConcept1 = "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\"; + String numericConcept2 = "\\open_access-1000Genomes\\data\\SYNTHETIC_HEIGHT\\"; + + PhenotypicFilter categoricalFilter1 = + new PhenotypicFilter(PhenotypicFilterType.FILTER, categoricalConcept1, Set.of("Finnish"), null, null, null); + PhenotypicFilter numericFilter1 = new PhenotypicFilter(PhenotypicFilterType.FILTER, numericConcept1, null, 42.0, null, null); + PhenotypicFilter categoricalFilter2 = + new PhenotypicFilter(PhenotypicFilterType.FILTER, categoricalConcept2, Set.of("female"), null, null, null); + PhenotypicFilter numericFilter2 = new PhenotypicFilter(PhenotypicFilterType.FILTER, numericConcept2, null, null, 175.5, null); + PhenotypicClause phenotypicSubquery1 = new PhenotypicSubquery(null, List.of(categoricalFilter1, numericFilter1), Operator.AND); + PhenotypicClause phenotypicSubquery2 = new PhenotypicSubquery(null, List.of(categoricalFilter2, numericFilter2), Operator.AND); + PhenotypicClause topSubquery = new PhenotypicSubquery(null, List.of(phenotypicSubquery1, phenotypicSubquery2), Operator.OR); + + Query query = new Query(List.of(), List.of(), topSubquery, List.of(), ResultType.COUNT, null, null); + + Set catFilter1Ids = Set.of(3, 5, 8, 13, 21); + Set numFilter1Ids = Set.of(2, 3, 5, 8, 13); + Set catFilter2Ids = Set.of(10, 100, 1000); + Set numFilter2Ids = Set.of(999, 1000, 10001); + // (catFilter1Ids AND numFilter1Ids) OR (catFilter2Ids AND numFilter2Ids) + Set expectedPatients = Set.of(3, 5, 8, 13, 1000); + + when(phenotypicObservationStore.getKeysForValues(categoricalConcept1, Set.of("Finnish"))).thenReturn(catFilter1Ids); + when(phenotypicObservationStore.getKeysForValues(categoricalConcept2, Set.of("female"))).thenReturn(catFilter2Ids); + when(phenotypicObservationStore.getKeysForRange(numericConcept1, 42.0, null)).thenReturn(numFilter1Ids); + when(phenotypicObservationStore.getKeysForRange(numericConcept2, null, 175.5)).thenReturn(numFilter2Ids); + + Set patientSet = phenotypicQueryExecutor.getPatientSet(query); + assertEquals(expectedPatients, patientSet); + } + + @Test + public void getPatientSet_validCategoricalFilterMultipleValues_returnPatients() throws ExecutionException { + String conceptPath = "\\open_access-1000Genomes\\data\\POPULATION NAME\\"; + Query query = new Query( + List.of(), List.of(), + new PhenotypicFilter(PhenotypicFilterType.FILTER, conceptPath, Set.of("Finnish", "Zapotec"), null, null, null), null, + ResultType.COUNT, null, null + ); + + Set patientIds = Set.of(8, 13, 21); + when(phenotypicObservationStore.getKeysForValues(conceptPath, Set.of("Finnish", "Zapotec"))).thenReturn(patientIds); + + Set patientSet = phenotypicQueryExecutor.getPatientSet(query); + assertEquals(patientIds, patientSet); + } + + @Test + public void getPatientSet_validAnyRecordOfFilter_returnPatients() throws ExecutionException { + String categoricalConceptPath = "\\open_access-1000Genomes\\data\\POPULATION NAME\\"; + String numericConceptPath = "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\"; + String nonMatchingConceptPath = "\\synthea\\data\\SYNTHETIC_AGE\\"; + Query query = new Query( + List.of(), List.of(), + new PhenotypicFilter(PhenotypicFilterType.ANY_RECORD_OF, "\\open_access-1000Genomes\\", null, null, null, null), null, + ResultType.COUNT, null, null + ); + + when(phenotypeMetaStore.getChildConceptPaths("\\open_access-1000Genomes\\")) + .thenReturn(Set.of(categoricalConceptPath, numericConceptPath)); + List numericPatientIds = List.of(2, 3, 5); + List categoricalPatientIds = List.of(10, 100, 1000, 100000); + + when(phenotypicObservationStore.getAllKeys(categoricalConceptPath)).thenReturn(categoricalPatientIds); + when(phenotypicObservationStore.getAllKeys(numericConceptPath)).thenReturn(numericPatientIds); + + Set patientSet = phenotypicQueryExecutor.getPatientSet(query); + Set expectedPatients = new HashSet<>(); + expectedPatients.addAll(categoricalPatientIds); + expectedPatients.addAll(numericPatientIds); + assertEquals(expectedPatients, patientSet); + + verify(phenotypicObservationStore, times(0)).getAllKeys(nonMatchingConceptPath); + } + + @Test + public void getPatientSet_anyRecordOfFilterNoMatches_returnNoPatients() { + String nonMatchingConceptPath = "\\synthea\\data\\SYNTHETIC_AGE\\"; + Query query = new Query( + List.of(), List.of(), + new PhenotypicFilter(PhenotypicFilterType.ANY_RECORD_OF, "\\open_access-1000Genomes\\", null, null, null, null), null, + ResultType.COUNT, null, null + ); + + when(phenotypeMetaStore.getChildConceptPaths("\\open_access-1000Genomes\\")).thenReturn(Set.of()); + + Set patientSet = phenotypicQueryExecutor.getPatientSet(query); + assertEquals(Set.of(), patientSet); + } + + + @Test + public void getPatientSet_validRequiredFilter_returnPatients() throws ExecutionException { + String conceptPath = "\\open_access-1000Genomes\\data\\POPULATION NAME\\"; + Query query = new Query( + List.of(), List.of(), new PhenotypicFilter(PhenotypicFilterType.REQUIRED, conceptPath, null, null, null, null), null, + ResultType.COUNT, null, null + ); + + List keyList = List.of(2, 3, 5, 8, 13, 13, 8, 5); + when(phenotypicObservationStore.getAllKeys(conceptPath)).thenReturn(keyList); + + Set patientSet = phenotypicQueryExecutor.getPatientSet(query); + assertEquals(new HashSet<>(keyList), patientSet); + } + + @Test + public void getPatientSet_notFoundRequiredFilter_returnNoPatients() { + String conceptPath = "\\open_access-1000Genomes\\data\\POPULATION NAME\\"; + Query query = new Query( + List.of(), List.of(), new PhenotypicFilter(PhenotypicFilterType.REQUIRED, conceptPath, null, null, null, null), null, + ResultType.COUNT, null, null + ); + + when(phenotypicObservationStore.getAllKeys(conceptPath)).thenReturn(List.of()); + + Set patientSet = phenotypicQueryExecutor.getPatientSet(query); + assertEquals(Set.of(), patientSet); + } + +} diff --git a/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/QueryValidatorTest.java b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/QueryValidatorTest.java new file mode 100644 index 000000000..51c36ebcf --- /dev/null +++ b/services/pic-sure-hpds/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/v3/QueryValidatorTest.java @@ -0,0 +1,117 @@ +package edu.harvard.hms.dbmi.avillach.hpds.processing.v3; + +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.*; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; + +import java.util.List; +import java.util.Map; +import java.util.Set; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + +@ExtendWith(MockitoExtension.class) +class QueryValidatorTest { + + @Mock + private PhenotypicQueryExecutor phenotypicQueryExecutor; + + @Mock + private PhenotypicFilterValidator phenotypicFilterValidator; + + private QueryValidator queryValidator; + + private Map metaStore; + + + @BeforeEach + public void setup() { + metaStore = Map.of( + "\\study123\\demographics\\sex\\", new ColumnMeta().setCategorical(true), "\\study123\\demographics\\age\\", + new ColumnMeta().setCategorical(false).setMin(0).setMax(130) + ); + + queryValidator = new QueryValidator(phenotypicQueryExecutor, phenotypicFilterValidator, false); + when(phenotypicQueryExecutor.getMetaStore()).thenReturn(metaStore); + } + + @Test + public void validate_emptyQuery_isValid() { + Query query = new Query(List.of(), List.of(), null, List.of(), ResultType.COUNT, null, null); + queryValidator.validate(query); + } + + @Test + public void validate_validPhenotypicFilter_isValid() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\study123\\demographics\\sex\\", Set.of("male"), null, null, null); + Query query = new Query(List.of(), List.of(), phenotypicFilter, List.of(), ResultType.COUNT, null, null); + queryValidator.validate(query); + verify(phenotypicFilterValidator, times(1)).validate(phenotypicFilter, metaStore); + } + + @Test + public void validate_validNestedFilters_allValidated() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\study123\\demographics\\sex\\", Set.of("male"), null, null, null); + PhenotypicFilter phenotypicFilter2 = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\study123\\demographics\\age\\", null, 42.0, null, null); + PhenotypicClause phenotypicSubquery1 = new PhenotypicSubquery(null, List.of(phenotypicFilter, phenotypicFilter2), Operator.AND); + PhenotypicClause phenotypicSubquery2 = new PhenotypicSubquery(null, List.of(phenotypicSubquery1, phenotypicSubquery1), Operator.OR); + Query query = new Query(List.of(), List.of(), phenotypicSubquery2, List.of(), ResultType.COUNT, null, null); + queryValidator.validate(query); + verify(phenotypicFilterValidator, times(2)).validate(phenotypicFilter, metaStore); + verify(phenotypicFilterValidator, times(2)).validate(phenotypicFilter2, metaStore); + } + + @Test + public void validate_invalidFilter_throwsException() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\study123\\demographics\\age\\", Set.of("male"), null, null, null); + Query query = new Query(List.of(), List.of(), phenotypicFilter, List.of(), ResultType.COUNT, null, null); + doThrow(IllegalArgumentException.class).when(phenotypicFilterValidator).validate(phenotypicFilter, metaStore); + assertThrows(IllegalArgumentException.class, () -> queryValidator.validate(query)); + } + + @Test + public void validate_invalidNnestedCategoricalFilter_throwsException() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\study123\\demographics\\age\\", Set.of("male"), null, null, null); + PhenotypicFilter phenotypicFilter2 = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\study123\\demographics\\age\\", null, 42.0, null, null); + PhenotypicClause phenotypicSubquery1 = new PhenotypicSubquery(null, List.of(phenotypicFilter, phenotypicFilter2), Operator.AND); + PhenotypicClause phenotypicSubquery2 = new PhenotypicSubquery(null, List.of(phenotypicSubquery1, phenotypicSubquery1), Operator.OR); + Query query = new Query(List.of(), List.of(), phenotypicSubquery2, List.of(), ResultType.COUNT, null, null); + doThrow(IllegalArgumentException.class).when(phenotypicFilterValidator).validate(phenotypicFilter, metaStore); + assertThrows(IllegalArgumentException.class, () -> queryValidator.validate(query)); + } + + @Test + public void validate_requireAuthorizationFilter_isValid() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\study123\\demographics\\sex\\", Set.of("male"), null, null, null); + Query query = new Query( + List.of(), List.of(new AuthorizationFilter("\\_consent\\", Set.of("studyABC"))), phenotypicFilter, List.of(), ResultType.COUNT, + null, null + ); + + queryValidator = new QueryValidator(phenotypicQueryExecutor, phenotypicFilterValidator, true); + queryValidator.validate(query); + } + + @Test + public void validate_requireAuthorizationFilter_throwsException() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\study123\\demographics\\sex\\", Set.of("male"), null, null, null); + Query query = new Query(List.of(), List.of(), phenotypicFilter, List.of(), ResultType.COUNT, null, null); + + queryValidator = new QueryValidator(phenotypicQueryExecutor, phenotypicFilterValidator, true); + assertThrows(IllegalArgumentException.class, () -> queryValidator.validate(query)); + } +} diff --git a/services/pic-sure-hpds/service/pom.xml b/services/pic-sure-hpds/service/pom.xml new file mode 100644 index 000000000..5a87646c6 --- /dev/null +++ b/services/pic-sure-hpds/service/pom.xml @@ -0,0 +1,106 @@ + + + 4.0.0 + + pic-sure-hpds + edu.harvard.hms.dbmi.avillach.hpds + ${revision} + + + service + + service + + + edu.harvard.hms.dbmi.avillach.hpds + data + + + edu.harvard.hms.dbmi.avillach.hpds + etl + test + + + edu.harvard.hms.dbmi.avillach.hpds + pic-sure-hpds-model + + + edu.harvard.hms.dbmi.avillach.hpds + processing + + + edu.harvard.hms.dbmi.avillach.hpds + common + + + edu.harvard.hms.dbmi.avillach + pic-sure-api-model + + + org.apache.commons + commons-math3 + + + com.google.guava + guava + + + javax.xml.bind + jaxb-api + + + com.sun.xml.bind + jaxb-core + + + com.sun.xml.bind + jaxb-impl + + + javax.activation + activation + + + org.springframework + spring-web + + + org.springframework + spring-test + test + + + org.mockito + mockito-core + test + + + org.springframework.boot + spring-boot-starter-web + + + org.springframework.boot + spring-boot-starter-actuator + + + edu.harvard.dbmi.avillach + pic-sure-logging-client + + + + + + + + org.springframework.boot + spring-boot-maven-plugin + + edu.harvard.hms.dbmi.avillach.hpds.service.HpdsApplication + JAR + + + + + + diff --git a/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/HpdsApplication.java b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/HpdsApplication.java new file mode 100644 index 000000000..d2b343956 --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/HpdsApplication.java @@ -0,0 +1,22 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service; + +import org.springframework.boot.SpringApplication; +import org.springframework.boot.autoconfigure.SpringBootApplication; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.ComponentScan; +import org.springframework.context.support.PropertySourcesPlaceholderConfigurer; + +@SpringBootApplication +@ComponentScan("edu.harvard.hms.dbmi.avillach.hpds") +public class HpdsApplication { + + public static void main(String[] args) { + SpringApplication.run(HpdsApplication.class, args); + } + + @Bean + public static PropertySourcesPlaceholderConfigurer propertySourcesPlaceholderConfigurer() { + return new PropertySourcesPlaceholderConfigurer(); + } + +} diff --git a/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/LoggingConfig.java b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/LoggingConfig.java new file mode 100644 index 000000000..519dd1a7a --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/LoggingConfig.java @@ -0,0 +1,49 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.hms.dbmi.avillach.hpds.processing.audit.AuditInterceptor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.audit.AuditLoggingFilter; +import edu.harvard.dbmi.avillach.logging.LoggingClientFactory; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.web.servlet.FilterRegistrationBean; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.web.servlet.config.annotation.InterceptorRegistry; +import org.springframework.web.servlet.config.annotation.WebMvcConfigurer; + +@Configuration +public class LoggingConfig implements WebMvcConfigurer { + + @Value("${DEST_IP:#{null}}") + private String destIp; + + @Value("${DEST_PORT:#{null}}") + private Integer destPort; + + @Bean + public LoggingClient loggingClient() { + return LoggingClientFactory.create("hpds"); + } + + @Bean + public AuditLoggingFilter auditLoggingFilter(LoggingClient loggingClient) { + return new AuditLoggingFilter(loggingClient, destIp, destPort); + } + + @Bean + public FilterRegistrationBean auditLoggingFilterRegistration(AuditLoggingFilter filter) { + FilterRegistrationBean registration = new FilterRegistrationBean<>(filter); + registration.addUrlPatterns("/*"); + return registration; + } + + @Bean + public AuditInterceptor auditInterceptor() { + return new AuditInterceptor(); + } + + @Override + public void addInterceptors(InterceptorRegistry registry) { + registry.addInterceptor(auditInterceptor()); + } +} diff --git a/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureService.java b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureService.java new file mode 100644 index 000000000..f770ae542 --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureService.java @@ -0,0 +1,481 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service; + +import java.io.File; +import java.io.IOException; +import java.nio.charset.StandardCharsets; +import java.util.*; +import java.util.Map.Entry; +import java.util.stream.Collectors; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.InfoColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.QueryDecorator; +import edu.harvard.hms.dbmi.avillach.hpds.processing.audit.AuditAttributes; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.processing.upload.SignUrlService; +import edu.harvard.hms.dbmi.avillach.hpds.service.filesharing.FileSharingService; +import edu.harvard.hms.dbmi.avillach.hpds.service.filesharing.TestDataService; +import edu.harvard.hms.dbmi.avillach.hpds.service.util.Paginator; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.core.io.InputStreamResource; +import org.springframework.http.HttpHeaders; +import org.springframework.http.MediaType; + +import com.fasterxml.jackson.core.JsonParseException; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.JsonMappingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.ImmutableList; +import com.google.common.collect.ImmutableMap; + +import edu.harvard.dbmi.avillach.domain.*; +import edu.harvard.dbmi.avillach.util.UUIDv5; +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import edu.harvard.hms.dbmi.avillach.hpds.processing.*; +import jakarta.servlet.http.HttpServletRequest; +import org.springframework.http.ResponseEntity; +import org.springframework.web.bind.annotation.*; +import org.springframework.web.bind.annotation.RequestBody; + +@RequestMapping(value = "PIC-SURE", produces = "application/json") +@RestController +public class PicSureService { + + @Autowired + public PicSureService( + QueryService queryService, CountProcessor countProcessor, VariantListProcessor variantListProcessor, + AbstractProcessor abstractProcessor, Paginator paginator, SignUrlService signUrlService, FileSharingService fileSystemService, + TestDataService testDataService + ) { + this.queryService = queryService; + this.countProcessor = countProcessor; + this.variantListProcessor = variantListProcessor; + this.abstractProcessor = abstractProcessor; + this.paginator = paginator; + this.fileSystemService = fileSystemService; + this.queryDecorator = new QueryDecorator(); + this.signUrlService = signUrlService; + this.testDataService = testDataService; + Crypto.loadDefaultKey(); + } + + private final QueryService queryService; + + private final ObjectMapper mapper = new ObjectMapper(); + + private Logger log = LoggerFactory.getLogger(PicSureService.class); + + private final CountProcessor countProcessor; + + private final VariantListProcessor variantListProcessor; + + private final AbstractProcessor abstractProcessor; + + private final Paginator paginator; + + private final SignUrlService signUrlService; + + private final FileSharingService fileSystemService; + + private final QueryDecorator queryDecorator; + + private final TestDataService testDataService; + + @Autowired + private HttpServletRequest httpRequest; + + private static final String QUERY_METADATA_FIELD = "queryMetadata"; + private static final int RESPONSE_CACHE_SIZE = 50; + + @AuditEvent(type = "OTHER", action = "info") + @PostMapping("/info") + public ResourceInfo info(@RequestBody QueryRequest request) { + ResourceInfo info = new ResourceInfo(); + info.setName("PhenoCube v1.0-SNAPSHOT"); + info.setId(UUID.randomUUID()); + + try { + info.setQueryFormats( + ImmutableList.of( + new QueryFormat().setDescription("PhenoCube Query Format").setName("PhenoCube Query Format").setExamples( + ImmutableList.of( + ImmutableMap.of( + "Demographics and interesting variables for people with high blood pressure", + new ObjectMapper().readValue( + "{\"fields\":[\"\\\\demographics\\\\SEX\\\\\",\"\\\\demographics\\\\WTMEC2YR\\\\\",\"\\\\demographics\\\\WTMEC4YR\\\\\",\"\\\\demographics\\\\area\\\\\",\"\\\\demographics\\\\education\\\\\",\"\\\\examination\\\\blood pressure\\\\60 sec HR (30 sec HR * 2)\\\\\",\"\\\\examination\\\\blood pressure\\\\mean diastolic\\\\\",\"\\\\examination\\\\blood pressure\\\\mean systolic\\\\\",\"\\\\examination\\\\body measures\\\\Body Mass Index (kg per m**2)\\\\\",\"\\\\examination\\\\body measures\\\\Head BMD (g per cm^2)\\\\\",\"\\\\examination\\\\body measures\\\\Head Circumference (cm)\\\\\",\"\\\\examination\\\\body measures\\\\Lumber Pelvis BMD (g per cm^2)\\\\\",\"\\\\examination\\\\body measures\\\\Lumber Spine BMD (g per cm^2)\\\\\",\"\\\\examination\\\\body measures\\\\Maximal Calf Circumference (cm)\\\\\",\"\\\\examination\\\\body measures\\\\Recumbent Length (cm)\\\\\",\"\\\\examination\\\\body measures\\\\Standing Height (cm)\\\\\",\"\\\\examination\\\\body measures\\\\Subscapular Skinfold (mm)\\\\\"]," + + "\"numericFilters\":{\"\\\\examination\\\\blood pressure\\\\mean systolic\\\\\":{\"min\":120},\"\\\\examination\\\\blood pressure\\\\mean diastolic\\\\\":{\"min\":80}}}", + Map.class + ) + ), + ImmutableMap.of( + "Demographics and interesting variables for men with high blood pressure who live with a smoker and for whom we have BMI data", + ImmutableMap.of( + "fields", + ImmutableList.of( + "\\demographics\\SEX\\", "\\demographics\\WTMEC2YR\\", "\\demographics\\WTMEC4YR\\", + "\\demographics\\area\\", "\\demographics\\education\\", + "\\examination\\blood pressure\\60 sec HR (30 sec HR * 2)\\", + "\\examination\\blood pressure\\mean diastolic\\", "\\examination\\blood pressure\\mean systolic\\", + "\\examination\\body measures\\Body Mass Index (kg per m**2)\\", + "\\examination\\body measures\\Head BMD (g per cm^2)\\", + "\\examination\\body measures\\Head Circumference (cm)\\", + "\\examination\\body measures\\Lumber Pelvis BMD (g per cm^2)\\", + "\\examination\\body measures\\Lumber Spine BMD (g per cm^2)\\", + "\\examination\\body measures\\Maximal Calf Circumference (cm)\\", + "\\examination\\body measures\\Recumbent Length (cm)\\", + "\\examination\\body measures\\Standing Height (cm)\\", + "\\examination\\body measures\\Subscapular Skinfold (mm)\\" + ), "requiredFields", ImmutableList.of("\\examination\\body measures\\Body Mass Index (kg per m**2)\\"), + "numericFilters", + ImmutableMap.of( + "\\examination\\blood pressure\\mean systolic\\", ImmutableMap.of("min", 120), + "\\examination\\blood pressure\\mean diastolic\\", ImmutableMap.of("min", 80) + ), "categoryFilters", + ImmutableMap.of( + "\\demographics\\SEX\\", ImmutableList.of("male"), + "\\questionnaire\\smoking family\\Does anyone smoke in home?\\", ImmutableList.of("Yes") + ) + ) + ) + ) + ).setSpecification( + ImmutableMap.of( + "fields", + "A list of field names. Can be any key from the results map returned from the search endpoint of this resource. Unless filters are set, the included fields will be returned for all patients as a sparse matrix.", + "numericFilters", + "A map where each entry maps a field name to an object with min and/or max properties. Patients without a value between the min and max will not be included in the result set.", + "requiredFields", + "A list of field names for which a patient must have a value in order to be inclued in the result set.", + "categoryFilters", + "A map where each entry maps a field name to a list of values to be included in the result set." + ) + ) + ) + ); + } catch (JsonParseException e) { + log.error("JsonParseException caught: ", e); + } catch (JsonMappingException e) { + log.error("JsonMappingException caught: ", e); + } catch (IOException e) { + log.error("IOException caught: ", e); + } + // TODO examples, examples, examples, specification + return info; + } + + @AuditEvent(type = "SEARCH", action = "search") + @PostMapping("/search") + public SearchResults search(@RequestBody QueryRequest searchJson) { + if (searchJson.getQuery() != null) { + AuditAttributes.putMetadata(httpRequest, "search_term", searchJson.getQuery().toString()); + } + Set> allColumns = abstractProcessor.getDictionary().entrySet(); + + // Phenotype Values + Object phenotypeResults = searchJson.getQuery() != null ? allColumns.stream().filter((entry) -> { + String lowerCaseSearchTerm = searchJson.getQuery().toString().toLowerCase(Locale.ENGLISH); + return entry.getKey().toLowerCase(Locale.ENGLISH).contains(lowerCaseSearchTerm) + || (entry.getValue().isCategorical() && entry.getValue().getCategoryValues().stream().map(String::toLowerCase) + .collect(Collectors.toList()).contains(lowerCaseSearchTerm)); + }).collect(Collectors.toMap(Entry::getKey, Entry::getValue)) : allColumns; + + // Info Values + Map infoResults = new TreeMap(); + if (searchJson.getQuery() != null) { + abstractProcessor.getInfoStoreMeta().stream().forEach(infoColumnMeta -> { + String query = searchJson.getQuery().toString(); + String lowerCase = query.toLowerCase(Locale.ENGLISH); + boolean storeIsNumeric = infoColumnMeta.continuous(); + if ( + infoColumnMeta.description().toLowerCase(Locale.ENGLISH).contains(lowerCase) + || infoColumnMeta.key().toLowerCase(Locale.ENGLISH).contains(lowerCase) + ) { + infoResults + .put( + infoColumnMeta.key(), + ImmutableMap.of( + "description", infoColumnMeta.description(), "values", + storeIsNumeric ? new ArrayList() + : abstractProcessor.searchInfoConceptValues(infoColumnMeta.key(), ""), + "continuous", storeIsNumeric + ) + ); + } + }); + } + + return new SearchResults() + .setResults(ImmutableMap.of("phenotypes", phenotypeResults, /* "genes", resultMap, */ "info", infoResults)) + .setSearchQuery(searchJson.getQuery() != null ? searchJson.getQuery().toString() : ""); + } + + @AuditEvent(type = "QUERY", action = "query.submitted") + @PostMapping("/query") + public ResponseEntity query(@RequestBody QueryRequest queryJson) { + if (Crypto.hasKey(Crypto.DEFAULT_KEY_NAME)) { + try { + Query query = convertIncomingQuery(queryJson); + QueryStatus result = convertToQueryStatus(queryService.runQuery(query)); + AuditAttributes.putMetadata(httpRequest, "result_type", String.valueOf(query.getExpectedResultType())); + AuditAttributes.putMetadata(httpRequest, "query_id", result.getResourceResultId()); + return ResponseEntity.ok(result); + } catch (IOException e) { + log.error("IOException caught in query processing:", e); + return ResponseEntity.status(500).build(); + } + } else { + QueryStatus status = new QueryStatus(); + status.setResourceStatus("Resource is locked."); + return ResponseEntity.ok(status); + } + } + + private Query convertIncomingQuery(QueryRequest queryJson) + throws IOException, JsonParseException, JsonMappingException, JsonProcessingException { + return mapper.readValue(mapper.writeValueAsString(queryJson.getQuery()), Query.class); + } + + private QueryStatus convertToQueryStatus(AsyncResult entity) { + QueryStatus status = new QueryStatus(); + status.setDuration(entity.getCompletedTime() == 0 ? 0 : entity.getCompletedTime() - entity.getQueuedTime()); + status.setResourceResultId(entity.getId()); + status.setResourceStatus(entity.getStatus().name()); + if (entity.getStatus() == AsyncResult.Status.SUCCESS) { + status.setSizeInBytes(entity.getStream().estimatedSize()); + } + status.setStartTime(entity.getQueuedTime()); + status.setStatus(entity.getStatus().toPicSureStatus()); + + Map metadata = new HashMap(); + queryDecorator.setId(entity.getQuery()); + metadata.put("picsureQueryId", UUIDv5.UUIDFromString(entity.getQuery().getId())); + status.setResultMetadata(metadata); + return status; + } + + @AuditEvent(type = "DATA_ACCESS", action = "query.result") + @PostMapping(value = "/query/{resourceQueryId}/result") + public ResponseEntity queryResult(@PathVariable("resourceQueryId") UUID queryId, @RequestBody QueryRequest resultRequest) + throws IOException { + AuditAttributes.putMetadata(httpRequest, "query_id", queryId.toString()); + AsyncResult result = queryService.getResultFor(queryId.toString()); + if (result == null) { + return ResponseEntity.status(404).build(); + } + if (result.getStatus() == AsyncResult.Status.SUCCESS) { + result.open(); + return ResponseEntity.ok().contentType(result.getResponseType()).body(new InputStreamResource(result.getStream())); + } else { + return ResponseEntity.status(400).body("Status : " + result.getStatus().name()); + } + } + + private Optional roundTripUUID(String uuid) { + try { + return Optional.ofNullable(UUID.fromString(uuid).toString()); + } catch (IllegalArgumentException ignored) { + return Optional.empty(); + } + } + + @AuditEvent(type = "DATA_ACCESS", action = "data.write") + @PostMapping("/write/{dataType}") + public ResponseEntity writeQueryResult(@RequestBody() Query query, @PathVariable("dataType") String datatype) { + AuditAttributes.putMetadata(httpRequest, "data_type", datatype); + AuditAttributes.putMetadata(httpRequest, "result_type", String.valueOf(query.getExpectedResultType())); + if ("test_upload".equals(datatype)) { + return testDataService.uploadTestFile(query.getPicSureId()) ? ResponseEntity.ok().build() : ResponseEntity.status(500).build(); + } + if (roundTripUUID(query.getPicSureId()).map(id -> !id.equalsIgnoreCase(query.getPicSureId())).orElse(true)) { + return ResponseEntity.status(400).body("The query pic-sure ID is not a UUID"); + } + if (!List.of(ResultType.DATAFRAME_TIMESERIES, ResultType.PATIENTS).contains(query.getExpectedResultType())) { + return ResponseEntity.status(400).body("The write endpoint only writes time series dataframes. Fix result type."); + } + String hpdsQueryID; + try { + QueryStatus queryStatus = convertToQueryStatus(queryService.runQuery(query)); + String status = queryStatus.getResourceStatus(); + hpdsQueryID = queryStatus.getResourceResultId(); + while ("RUNNING".equalsIgnoreCase(status) || "PENDING".equalsIgnoreCase(status)) { + Thread.sleep(10000); // Yea, this is not restful. Sorry. + status = convertToQueryStatus(queryService.getStatusFor(hpdsQueryID)).getResourceStatus(); + } + } catch (IOException | InterruptedException e) { + log.warn("Error waiting for response", e); + return ResponseEntity.internalServerError().build(); + } + + AsyncResult result = queryService.getResultFor(hpdsQueryID); + // the queryResult has this DIY retry logic that blocks a system thread. + // I'm not going to do that here. If the service can't find it, you get a 404. + // Retry it client side. + if (result == null) { + return ResponseEntity.status(404).build(); + } + if (AsyncResult.Status.ERROR.equals(result.getStatus())) { + return ResponseEntity.status(500).build(); + } + if (!AsyncResult.Status.SUCCESS.equals(result.getStatus())) { + return ResponseEntity.status(503).build(); // 503 = unavailable + } + + // at least for now, this is going to block until we finish writing + // Not very restful, but it will make this API very easy to consume + boolean success = false; + query.setId(hpdsQueryID); + if ("phenotypic".equals(datatype)) { + success = fileSystemService.createPhenotypicData(query); + } else if ("genomic".equals(datatype)) { + success = fileSystemService.createGenomicData(query); + } else if ("patients".equals(datatype)) { + success = ResultType.PATIENTS.equals(query.getExpectedResultType()) && fileSystemService.createPatientList(query); + } + return success ? ResponseEntity.ok().build() : ResponseEntity.internalServerError().build(); + } + + @AuditEvent(type = "DATA_ACCESS", action = "query.signed.url") + @PostMapping(value = "/query/{resourceQueryId}/signed-url") + public ResponseEntity querySignedURL(@PathVariable("resourceQueryId") UUID queryId, @RequestBody QueryRequest resultRequest) + throws IOException { + AuditAttributes.putMetadata(httpRequest, "query_id", queryId.toString()); + AsyncResult result = queryService.getResultFor(queryId.toString()); + if (result == null) { + return ResponseEntity.status(404).build(); + } + if (result.getStatus() == AsyncResult.Status.SUCCESS) { + File file = result.getFile(); + signUrlService.uploadFile(file, file.getName()); + String presignedGetUrl = signUrlService.createPresignedGetUrl(file.getName()); + log.info("Presigned url: " + presignedGetUrl); + return ResponseEntity.ok().contentType(MediaType.APPLICATION_JSON).body(new SignedUrlResponse(presignedGetUrl)); + } else { + return ResponseEntity.status(400).body("Status : " + result.getStatus().name()); + } + } + + @AuditEvent(type = "QUERY", action = "query.status") + @PostMapping("/query/{resourceQueryId}/status") + public QueryStatus queryStatus(@PathVariable("resourceQueryId") UUID queryId, @RequestBody QueryRequest request) { + AuditAttributes.putMetadata(httpRequest, "query_id", queryId.toString()); + return convertToQueryStatus(queryService.getStatusFor(queryId.toString())); + } + + @AuditEvent(type = "OTHER", action = "query.format") + @PostMapping("/query/format") + public ResponseEntity queryFormat(@RequestBody QueryRequest resultRequest) { + try { + // The toString() method here has been overridden to produce a human readable + // value + return ResponseEntity.ok(convertIncomingQuery(resultRequest).toString()); + } catch (IOException e) { + return ResponseEntity.status(500).body("An error occurred formatting the query for display: " + e.getLocalizedMessage()); + } + } + + @AuditEvent(type = "QUERY", action = "query.sync") + @PostMapping(value = "/query/sync", produces = MediaType.TEXT_PLAIN_VALUE) + public ResponseEntity querySync(@RequestBody QueryRequest resultRequest) { + if (Crypto.hasKey(Crypto.DEFAULT_KEY_NAME)) { + try { + return _querySync(resultRequest); + } catch (IOException e) { + log.error("IOException caught: ", e); + return ResponseEntity.status(500).build(); + } + } else { + return ResponseEntity.status(403).body("Resource is locked"); + } + } + + @AuditEvent(type = "SEARCH", action = "search.values") + @GetMapping("/search/values/") + public PaginatedSearchResult searchGenomicConceptValues( + @RequestParam("genomicConceptPath") String genomicConceptPath, @RequestParam("query") String query, @RequestParam("page") int page, + @RequestParam("size") int size + ) { + AuditAttributes.putMetadata(httpRequest, "genomic_concept_path", genomicConceptPath); + if (page < 1) { + throw new IllegalArgumentException("Page must be greater than 0"); + } + if (size < 1) { + throw new IllegalArgumentException("Size must be greater than 0"); + } + final List matchingValues = abstractProcessor.searchInfoConceptValues(genomicConceptPath, query); + return paginator.paginate(matchingValues, page, size); + } + + private ResponseEntity _querySync(QueryRequest resultRequest) throws IOException { + Query incomingQuery; + incomingQuery = convertIncomingQuery(resultRequest); + AuditAttributes.putMetadata(httpRequest, "result_type", String.valueOf(incomingQuery.getExpectedResultType())); + log.info("Query Converted"); + switch (incomingQuery.getExpectedResultType()) { + + case INFO_COLUMN_LISTING: + List infoColumnMeta = abstractProcessor.getInfoStoreMeta(); + return ResponseEntity.ok().contentType(MediaType.APPLICATION_JSON).body(infoColumnMeta); + + case DATAFRAME: + case SECRET_ADMIN_DATAFRAME: + case DATAFRAME_TIMESERIES: + case PATIENTS: + QueryStatus status = query(resultRequest).getBody(); + while (status.getResourceStatus().equalsIgnoreCase("RUNNING") || status.getResourceStatus().equalsIgnoreCase("PENDING")) { + status = queryStatus(UUID.fromString(status.getResourceResultId()), null); + } + log.info(status.toString()); + + AsyncResult result = queryService.getResultFor(status.getResourceResultId()); + if (result.getStatus() == AsyncResult.Status.SUCCESS) { + result.getStream().open(); + return queryOkResponse( + new String(result.getStream().readAllBytes(), StandardCharsets.UTF_8), incomingQuery, MediaType.TEXT_PLAIN + ); + } + return ResponseEntity.status(400).contentType(MediaType.APPLICATION_JSON).body("Status : " + result.getStatus().name()); + + case CROSS_COUNT: + return queryOkResponse(countProcessor.runCrossCounts(incomingQuery), incomingQuery, MediaType.APPLICATION_JSON); + + case CATEGORICAL_CROSS_COUNT: + return queryOkResponse(countProcessor.runCategoryCrossCounts(incomingQuery), incomingQuery, MediaType.APPLICATION_JSON); + + case CONTINUOUS_CROSS_COUNT: + return queryOkResponse(countProcessor.runContinuousCrossCounts(incomingQuery), incomingQuery, MediaType.APPLICATION_JSON); + + case OBSERVATION_CROSS_COUNT: + return queryOkResponse(countProcessor.runObservationCrossCounts(incomingQuery), incomingQuery, MediaType.APPLICATION_JSON); + + case VARIANT_COUNT_FOR_QUERY: + return queryOkResponse(countProcessor.runVariantCount(incomingQuery), incomingQuery, MediaType.APPLICATION_JSON); + + case VARIANT_LIST_FOR_QUERY: + return queryOkResponse(variantListProcessor.runVariantListQuery(incomingQuery), incomingQuery, MediaType.TEXT_PLAIN); + + case VCF_EXCERPT: + return queryOkResponse(variantListProcessor.runVcfExcerptQuery(incomingQuery, true), incomingQuery, MediaType.TEXT_PLAIN); + + case AGGREGATE_VCF_EXCERPT: + return queryOkResponse(variantListProcessor.runVcfExcerptQuery(incomingQuery, false), incomingQuery, MediaType.TEXT_PLAIN); + + case COUNT: + return queryOkResponse(String.valueOf(countProcessor.runCounts(incomingQuery)), incomingQuery, MediaType.TEXT_PLAIN); + + default: + // no valid type + return ResponseEntity.status(500).build(); + } + } + + private ResponseEntity queryOkResponse(Object obj, Query incomingQuery, MediaType mediaType) { + queryDecorator.setId(incomingQuery); + HttpHeaders responseHeaders = new HttpHeaders(); + responseHeaders.set(QUERY_METADATA_FIELD, UUIDv5.UUIDFromString(incomingQuery.toString()).toString()); + return ResponseEntity.ok().contentType(mediaType).headers(responseHeaders).body(obj); + } +} diff --git a/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureV3Service.java b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureV3Service.java new file mode 100644 index 000000000..d354aa3b4 --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureV3Service.java @@ -0,0 +1,458 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service; + +import com.fasterxml.jackson.core.JsonParseException; +import com.fasterxml.jackson.databind.JsonMappingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.ImmutableList; +import com.google.common.collect.ImmutableMap; +import edu.harvard.dbmi.avillach.domain.*; +import edu.harvard.dbmi.avillach.util.UUIDv5; +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.processing.audit.AuditAttributes; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.InfoColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import edu.harvard.hms.dbmi.avillach.hpds.processing.upload.SignUrlService; +import edu.harvard.hms.dbmi.avillach.hpds.processing.v3.AsyncResult; +import edu.harvard.hms.dbmi.avillach.hpds.processing.v3.CountV3Processor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.v3.QueryExecutor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.v3.VariantListV3Processor; +import edu.harvard.hms.dbmi.avillach.hpds.service.filesharing.FileSharingV3Service; +import edu.harvard.hms.dbmi.avillach.hpds.service.filesharing.TestDataService; +import edu.harvard.hms.dbmi.avillach.hpds.service.util.Paginator; +import jakarta.servlet.http.HttpServletRequest; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.core.io.InputStreamResource; +import org.springframework.http.HttpHeaders; +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import org.springframework.web.bind.annotation.*; + +import java.io.File; +import java.io.IOException; +import java.nio.charset.StandardCharsets; +import java.util.*; +import java.util.Map.Entry; +import java.util.stream.Collectors; + +@RequestMapping(value = "PIC-SURE/v3", produces = "application/json") +@RestController +public class PicSureV3Service { + + @Autowired + public PicSureV3Service( + QueryV3Service queryService, CountV3Processor countProcessor, VariantListV3Processor variantListProcessor, + QueryExecutor queryExecutor, Paginator paginator, SignUrlService signUrlService, FileSharingV3Service fileSharingService, + TestDataService testDataService + ) { + this.queryService = queryService; + this.countProcessor = countProcessor; + this.variantListProcessor = variantListProcessor; + this.queryExecutor = queryExecutor; + this.paginator = paginator; + this.fileSharingService = fileSharingService; + this.signUrlService = signUrlService; + this.testDataService = testDataService; + Crypto.loadDefaultKey(); + } + + private final QueryV3Service queryService; + + private final ObjectMapper mapper = new ObjectMapper(); + + private static final Logger log = LoggerFactory.getLogger(PicSureV3Service.class); + + private final CountV3Processor countProcessor; + + private final VariantListV3Processor variantListProcessor; + + private final QueryExecutor queryExecutor; + + private final Paginator paginator; + + private final SignUrlService signUrlService; + + private final FileSharingV3Service fileSharingService; + + private final TestDataService testDataService; + + @Autowired + private HttpServletRequest httpRequest; + + private static final String QUERY_METADATA_FIELD = "queryMetadata"; + + @AuditEvent(type = "OTHER", action = "info") + @PostMapping("/info") + public ResourceInfo info(@RequestBody QueryRequest request) { + ResourceInfo info = new ResourceInfo(); + info.setName("PhenoCube v1.0-SNAPSHOT"); + info.setId(UUID.randomUUID()); + + try { + info.setQueryFormats( + ImmutableList.of( + new QueryFormat().setDescription("PhenoCube Query Format").setName("PhenoCube Query Format").setExamples( + ImmutableList.of( + ImmutableMap.of( + "Demographics and interesting variables for people with high blood pressure", + new ObjectMapper().readValue( + "{\"fields\":[\"\\\\demographics\\\\SEX\\\\\",\"\\\\demographics\\\\WTMEC2YR\\\\\",\"\\\\demographics\\\\WTMEC4YR\\\\\",\"\\\\demographics\\\\area\\\\\",\"\\\\demographics\\\\education\\\\\",\"\\\\examination\\\\blood pressure\\\\60 sec HR (30 sec HR * 2)\\\\\",\"\\\\examination\\\\blood pressure\\\\mean diastolic\\\\\",\"\\\\examination\\\\blood pressure\\\\mean systolic\\\\\",\"\\\\examination\\\\body measures\\\\Body Mass Index (kg per m**2)\\\\\",\"\\\\examination\\\\body measures\\\\Head BMD (g per cm^2)\\\\\",\"\\\\examination\\\\body measures\\\\Head Circumference (cm)\\\\\",\"\\\\examination\\\\body measures\\\\Lumber Pelvis BMD (g per cm^2)\\\\\",\"\\\\examination\\\\body measures\\\\Lumber Spine BMD (g per cm^2)\\\\\",\"\\\\examination\\\\body measures\\\\Maximal Calf Circumference (cm)\\\\\",\"\\\\examination\\\\body measures\\\\Recumbent Length (cm)\\\\\",\"\\\\examination\\\\body measures\\\\Standing Height (cm)\\\\\",\"\\\\examination\\\\body measures\\\\Subscapular Skinfold (mm)\\\\\"]," + + "\"numericFilters\":{\"\\\\examination\\\\blood pressure\\\\mean systolic\\\\\":{\"min\":120},\"\\\\examination\\\\blood pressure\\\\mean diastolic\\\\\":{\"min\":80}}}", + Map.class + ) + ), + ImmutableMap.of( + "Demographics and interesting variables for men with high blood pressure who live with a smoker and for whom we have BMI data", + ImmutableMap.of( + "fields", + ImmutableList.of( + "\\demographics\\SEX\\", "\\demographics\\WTMEC2YR\\", "\\demographics\\WTMEC4YR\\", + "\\demographics\\area\\", "\\demographics\\education\\", + "\\examination\\blood pressure\\60 sec HR (30 sec HR * 2)\\", + "\\examination\\blood pressure\\mean diastolic\\", "\\examination\\blood pressure\\mean systolic\\", + "\\examination\\body measures\\Body Mass Index (kg per m**2)\\", + "\\examination\\body measures\\Head BMD (g per cm^2)\\", + "\\examination\\body measures\\Head Circumference (cm)\\", + "\\examination\\body measures\\Lumber Pelvis BMD (g per cm^2)\\", + "\\examination\\body measures\\Lumber Spine BMD (g per cm^2)\\", + "\\examination\\body measures\\Maximal Calf Circumference (cm)\\", + "\\examination\\body measures\\Recumbent Length (cm)\\", + "\\examination\\body measures\\Standing Height (cm)\\", + "\\examination\\body measures\\Subscapular Skinfold (mm)\\" + ), "requiredFields", ImmutableList.of("\\examination\\body measures\\Body Mass Index (kg per m**2)\\"), + "numericFilters", + ImmutableMap.of( + "\\examination\\blood pressure\\mean systolic\\", ImmutableMap.of("min", 120), + "\\examination\\blood pressure\\mean diastolic\\", ImmutableMap.of("min", 80) + ), "categoryFilters", + ImmutableMap.of( + "\\demographics\\SEX\\", ImmutableList.of("male"), + "\\questionnaire\\smoking family\\Does anyone smoke in home?\\", ImmutableList.of("Yes") + ) + ) + ) + ) + ).setSpecification( + ImmutableMap.of( + "fields", + "A list of field names. Can be any key from the results map returned from the search endpoint of this resource. Unless filters are set, the included fields will be returned for all patients as a sparse matrix.", + "numericFilters", + "A map where each entry maps a field name to an object with min and/or max properties. Patients without a value between the min and max will not be included in the result set.", + "requiredFields", + "A list of field names for which a patient must have a value in order to be inclued in the result set.", + "categoryFilters", + "A map where each entry maps a field name to a list of values to be included in the result set." + ) + ) + ) + ); + } catch (JsonParseException e) { + log.error("JsonParseException caught: ", e); + } catch (JsonMappingException e) { + log.error("JsonMappingException caught: ", e); + } catch (IOException e) { + log.error("IOException caught: ", e); + } + // TODO examples, examples, examples, specification + return info; + } + + @AuditEvent(type = "SEARCH", action = "search") + @PostMapping("/search") + public SearchResults search(@RequestBody QueryRequest searchJson) { + if (searchJson.getQuery() != null) { + AuditAttributes.putMetadata(httpRequest, "search_term", searchJson.getQuery().toString()); + } + Set> allColumns = queryExecutor.getDictionary().entrySet(); + + // Phenotype Values + Object phenotypeResults = searchJson.getQuery() != null ? allColumns.stream().filter((entry) -> { + String lowerCaseSearchTerm = searchJson.getQuery().toString().toLowerCase(Locale.ENGLISH); + return entry.getKey().toLowerCase(Locale.ENGLISH).contains(lowerCaseSearchTerm) || (entry.getValue().isCategorical() + && entry.getValue().getCategoryValues().stream().map(String::toLowerCase).toList().contains(lowerCaseSearchTerm)); + }).collect(Collectors.toMap(Entry::getKey, Entry::getValue)) : allColumns; + + // Info Values + Map> infoResults = new TreeMap<>(); + if (searchJson.getQuery() != null) { + queryExecutor.getInfoStoreMeta().forEach(infoColumnMeta -> { + String query = searchJson.getQuery().toString(); + String lowerCase = query.toLowerCase(Locale.ENGLISH); + boolean storeIsNumeric = infoColumnMeta.continuous(); + if ( + infoColumnMeta.description().toLowerCase(Locale.ENGLISH).contains(lowerCase) + || infoColumnMeta.key().toLowerCase(Locale.ENGLISH).contains(lowerCase) + ) { + infoResults.put( + infoColumnMeta.key(), + ImmutableMap.of( + "description", infoColumnMeta.description(), "values", + storeIsNumeric ? new ArrayList() : queryExecutor.searchInfoConceptValues(infoColumnMeta.key(), ""), + "continuous", storeIsNumeric + ) + ); + } + }); + } + + return new SearchResults().setResults(ImmutableMap.of("phenotypes", phenotypeResults, "info", infoResults)) + .setSearchQuery(searchJson.getQuery() != null ? searchJson.getQuery().toString() : ""); + } + + @AuditEvent(type = "QUERY", action = "query.submitted") + @PostMapping("/query") + public ResponseEntity query(@RequestBody QueryRequest queryJson) { + if (Crypto.hasKey(Crypto.DEFAULT_KEY_NAME)) { + try { + Query query = convertIncomingQuery(queryJson); + QueryStatus result = convertToQueryStatus(queryService.runQuery(query)); + AuditAttributes.putMetadata(httpRequest, "result_type", String.valueOf(query.expectedResultType())); + AuditAttributes.putMetadata(httpRequest, "query_id", result.getResourceResultId()); + return ResponseEntity.ok(result); + } catch (IOException e) { + log.error("IOException caught in query processing:", e); + return ResponseEntity.status(500).build(); + } + } else { + QueryStatus status = new QueryStatus(); + status.setResourceStatus("Resource is locked."); + return ResponseEntity.ok(status); + } + } + + private Query convertIncomingQuery(QueryRequest queryJson) throws IOException { + Object query = queryJson.getQuery(); + if (query instanceof String) { + // The query is now being reset in wildfly and encoded as a string in JWTFilter + return mapper.readValue((String) query, Query.class); + } else { + String queryString = mapper.writeValueAsString(query); + return mapper.readValue(queryString, Query.class); + } + } + + private QueryStatus convertToQueryStatus(AsyncResult entity) { + QueryStatus status = new QueryStatus(); + status.setDuration(entity.getCompletedTime() == 0 ? 0 : entity.getCompletedTime() - entity.getQueuedTime()); + status.setResourceResultId(entity.getId()); + status.setResourceStatus(entity.getStatus().name()); + if (entity.getStatus() == AsyncResult.Status.SUCCESS) { + status.setSizeInBytes(entity.getStream().estimatedSize()); + } + status.setStartTime(entity.getQueuedTime()); + status.setStatus(entity.getStatus().toPicSureStatus()); + + Map metadata = new HashMap<>(); + metadata.put("picsureQueryId", entity.getQuery().id()); + status.setResultMetadata(metadata); + return status; + } + + @AuditEvent(type = "DATA_ACCESS", action = "query.result") + @PostMapping(value = "/query/{resourceQueryId}/result") + public ResponseEntity queryResult(@PathVariable("resourceQueryId") UUID queryId, @RequestBody QueryRequest resultRequest) { + AuditAttributes.putMetadata(httpRequest, "query_id", queryId.toString()); + AsyncResult result = queryService.getResultFor(queryId); + if (result == null) { + return ResponseEntity.status(404).build(); + } + if (result.getStatus() == AsyncResult.Status.SUCCESS) { + result.open(); + return ResponseEntity.ok().contentType(result.getResponseType()).body(new InputStreamResource(result.getStream())); + } else { + return ResponseEntity.status(400).body("Status : " + result.getStatus().name()); + } + } + + @AuditEvent(type = "DATA_ACCESS", action = "data.write") + @PostMapping("/write/{dataType}") + public ResponseEntity writeQueryResult(@RequestBody() Query query, @PathVariable("dataType") String datatype) { + AuditAttributes.putMetadata(httpRequest, "data_type", datatype); + AuditAttributes.putMetadata(httpRequest, "result_type", String.valueOf(query.expectedResultType())); + if ("test_upload".equals(datatype)) { + return testDataService.uploadTestFile(query.picsureId().toString()) ? ResponseEntity.ok().build() + : ResponseEntity.status(500).build(); + } + if (!List.of(ResultType.DATAFRAME_TIMESERIES, ResultType.PATIENTS).contains(query.expectedResultType())) { + return ResponseEntity.status(400).body("The write endpoint only writes time series dataframes. Fix result type."); + } + String hpdsQueryID; + try { + QueryStatus queryStatus = convertToQueryStatus(queryService.runQuery(query)); + String status = queryStatus.getResourceStatus(); + hpdsQueryID = queryStatus.getResourceResultId(); + while ("RUNNING".equalsIgnoreCase(status) || "PENDING".equalsIgnoreCase(status)) { + Thread.sleep(10000); // Yea, this is not restful. Sorry. + status = convertToQueryStatus(queryService.getStatusFor(hpdsQueryID)).getResourceStatus(); + } + } catch (IOException | InterruptedException e) { + log.warn("Error waiting for response", e); + return ResponseEntity.internalServerError().build(); + } + + AsyncResult result = queryService.getResultFor(UUID.fromString(hpdsQueryID)); + if (result == null) { + return ResponseEntity.status(404).build(); + } + if (AsyncResult.Status.ERROR.equals(result.getStatus())) { + return ResponseEntity.status(500).build(); + } + if (!AsyncResult.Status.SUCCESS.equals(result.getStatus())) { + return ResponseEntity.status(503).build(); // 503 = unavailable + } + + boolean success = false; + Query queryCopy = query.generateId(); + if ("phenotypic".equals(datatype)) { + success = fileSharingService.createPhenotypicData(queryCopy); + } else if ("genomic".equals(datatype)) { + success = fileSharingService.createGenomicData(queryCopy); + } else if ("patients".equals(datatype)) { + success = ResultType.PATIENTS.equals(queryCopy.expectedResultType()) && fileSharingService.createPatientList(queryCopy); + } + return success ? ResponseEntity.ok().build() : ResponseEntity.internalServerError().build(); + } + + @AuditEvent(type = "DATA_ACCESS", action = "query.signed.url") + @PostMapping(value = "/query/{resourceQueryId}/signed-url") + public ResponseEntity querySignedURL(@PathVariable("resourceQueryId") UUID queryId, @RequestBody QueryRequest resultRequest) + throws IOException { + AuditAttributes.putMetadata(httpRequest, "query_id", queryId.toString()); + AsyncResult result = queryService.getResultFor(queryId); + if (result == null) { + return ResponseEntity.status(404).build(); + } + if (result.getStatus() == AsyncResult.Status.SUCCESS) { + File file = result.getFile(); + signUrlService.uploadFile(file, file.getName()); + String presignedGetUrl = signUrlService.createPresignedGetUrl(file.getName()); + log.info("Presigned url: " + presignedGetUrl); + return ResponseEntity.ok().contentType(MediaType.APPLICATION_JSON).body(new SignedUrlResponse(presignedGetUrl)); + } else { + return ResponseEntity.status(400).body("Status : " + result.getStatus().name()); + } + } + + @AuditEvent(type = "QUERY", action = "query.status") + @PostMapping("/query/{resourceQueryId}/status") + public QueryStatus queryStatus(@PathVariable("resourceQueryId") UUID queryId, @RequestBody QueryRequest request) { + AuditAttributes.putMetadata(httpRequest, "query_id", queryId.toString()); + return convertToQueryStatus(queryService.getStatusFor(queryId.toString())); + } + + @AuditEvent(type = "OTHER", action = "query.format") + @PostMapping("/query/format") + public ResponseEntity queryFormat(@RequestBody QueryRequest resultRequest) { + try { + return ResponseEntity.ok(convertIncomingQuery(resultRequest).toString()); + } catch (IOException e) { + return ResponseEntity.status(500).body("An error occurred formatting the query for display: " + e.getLocalizedMessage()); + } + } + + @AuditEvent(type = "QUERY", action = "query.sync") + @PostMapping(value = "/query/sync", produces = {MediaType.APPLICATION_JSON_VALUE, MediaType.TEXT_PLAIN_VALUE}) + public ResponseEntity querySync(@RequestBody QueryRequest resultRequest) { + if (Crypto.hasKey(Crypto.DEFAULT_KEY_NAME)) { + try { + return _querySync(resultRequest); + } catch (IOException e) { + log.error("IOException caught: ", e); + return ResponseEntity.status(500).build(); + } + } else { + return ResponseEntity.status(403).body("Resource is locked"); + } + } + + @AuditEvent(type = "SEARCH", action = "search.values") + @GetMapping("/search/values/") + public PaginatedSearchResult searchGenomicConceptValues( + @RequestParam("genomicConceptPath") String genomicConceptPath, @RequestParam("query") String query, @RequestParam("page") int page, + @RequestParam("size") int size + ) { + AuditAttributes.putMetadata(httpRequest, "genomic_concept_path", genomicConceptPath); + if (page < 1) { + throw new IllegalArgumentException("Page must be greater than 0"); + } + if (size < 1) { + throw new IllegalArgumentException("Size must be greater than 0"); + } + final List matchingValues = queryExecutor.searchInfoConceptValues(genomicConceptPath, query); + return paginator.paginate(matchingValues, page, size); + } + + private ResponseEntity _querySync(QueryRequest resultRequest) throws IOException { + Query incomingQuery; + incomingQuery = convertIncomingQuery(resultRequest); + AuditAttributes.putMetadata(httpRequest, "result_type", String.valueOf(incomingQuery.expectedResultType())); + log.info("Query Converted"); + switch (incomingQuery.expectedResultType()) { + + case INFO_COLUMN_LISTING: + List infoColumnMeta = queryExecutor.getInfoStoreMeta(); + return ResponseEntity.ok().contentType(MediaType.APPLICATION_JSON).body(infoColumnMeta); + + case DATAFRAME: + case SECRET_ADMIN_DATAFRAME: + case DATAFRAME_TIMESERIES: + case PATIENTS: + QueryStatus status = query(resultRequest).getBody(); + while (status.getResourceStatus().equalsIgnoreCase("RUNNING") || status.getResourceStatus().equalsIgnoreCase("PENDING")) { + status = queryStatus(UUID.fromString(status.getResourceResultId()), null); + } + log.info(status.toString()); + + AsyncResult result = queryService.getResultFor(UUID.fromString(status.getResourceResultId())); + if (result.getStatus() == AsyncResult.Status.SUCCESS) { + result.getStream().open(); + return queryOkResponse( + new String(result.getStream().readAllBytes(), StandardCharsets.UTF_8), incomingQuery, MediaType.TEXT_PLAIN + ); + } + return ResponseEntity.status(400).contentType(MediaType.APPLICATION_JSON).body("Status : " + result.getStatus().name()); + + case CROSS_COUNT: + return queryOkResponse(countProcessor.runCrossCounts(incomingQuery), incomingQuery, MediaType.APPLICATION_JSON); + + case CATEGORICAL_CROSS_COUNT: + return queryOkResponse(countProcessor.runCategoryCrossCounts(incomingQuery), incomingQuery, MediaType.APPLICATION_JSON); + + case CONTINUOUS_CROSS_COUNT: + return queryOkResponse(countProcessor.runContinuousCrossCounts(incomingQuery), incomingQuery, MediaType.APPLICATION_JSON); + + case OBSERVATION_CROSS_COUNT: + return queryOkResponse(countProcessor.runObservationCrossCounts(incomingQuery), incomingQuery, MediaType.APPLICATION_JSON); + + case VARIANT_COUNT_FOR_QUERY: + return queryOkResponse(countProcessor.runVariantCount(incomingQuery), incomingQuery, MediaType.APPLICATION_JSON); + + case VARIANT_LIST_FOR_QUERY: + return queryOkResponse(variantListProcessor.runVariantListQuery(incomingQuery), incomingQuery, MediaType.TEXT_PLAIN); + + case VCF_EXCERPT: + return queryOkResponse(variantListProcessor.runVcfExcerptQuery(incomingQuery, true), incomingQuery, MediaType.TEXT_PLAIN); + + case AGGREGATE_VCF_EXCERPT: + return queryOkResponse(variantListProcessor.runVcfExcerptQuery(incomingQuery, false), incomingQuery, MediaType.TEXT_PLAIN); + + case COUNT: + return queryOkResponse(String.valueOf(countProcessor.runCounts(incomingQuery)), incomingQuery, MediaType.TEXT_PLAIN); + + default: + // no valid type + return ResponseEntity.status(500).build(); + } + } + + private ResponseEntity queryOkResponse(Object obj, Query incomingQuery, MediaType mediaType) { + Query query = incomingQuery.generateId(); + HttpHeaders responseHeaders = new HttpHeaders(); + responseHeaders.set(QUERY_METADATA_FIELD, UUIDv5.UUIDFromString(query.toString()).toString()); + return ResponseEntity.ok().contentType(mediaType).headers(responseHeaders).body(obj); + } +} diff --git a/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/QueryService.java b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/QueryService.java new file mode 100644 index 000000000..b2ea9fb63 --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/QueryService.java @@ -0,0 +1,253 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service; + +import java.io.File; +import java.io.FileNotFoundException; +import java.io.IOException; +import java.util.*; +import java.util.concurrent.*; +import java.util.function.Predicate; +import java.util.stream.Collectors; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.hms.dbmi.avillach.hpds.data.genomic.VariantUtils; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.QueryDecorator; +import edu.harvard.hms.dbmi.avillach.hpds.processing.patient.PatientProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.timeseries.TimeseriesProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.processing.dictionary.DictionaryService; +import edu.harvard.hms.dbmi.avillach.hpds.processing.io.CsvWriter; +import edu.harvard.hms.dbmi.avillach.hpds.processing.io.PfbWriter; +import edu.harvard.hms.dbmi.avillach.hpds.processing.io.ResultWriter; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import edu.harvard.dbmi.avillach.util.UUIDv5; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import edu.harvard.hms.dbmi.avillach.hpds.processing.*; +import edu.harvard.hms.dbmi.avillach.hpds.processing.AsyncResult.Status; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Service; + +@Service +public class QueryService { + + private final int SMALL_JOB_LIMIT; + private final int LARGE_TASK_THREADS; + private final int SMALL_TASK_THREADS; + + private final Logger log = LoggerFactory.getLogger(this.getClass()); + + private final BlockingQueue largeTaskExecutionQueue; + + private final ExecutorService largeTaskExecutor; + + private final BlockingQueue smallTaskExecutionQueue; + + private final ExecutorService smallTaskExecutor; + + private final AbstractProcessor abstractProcessor; + private final QueryProcessor queryProcessor; + private final TimeseriesProcessor timeseriesProcessor; + private final CountProcessor countProcessor; + private final MultiValueQueryProcessor multiValueQueryProcessor; + private final PatientProcessor patientProcessor; + + private final DictionaryService dictionaryService; + private final QueryDecorator queryDecorator; + private final LoggingClient loggingClient; + + HashMap results = new HashMap<>(); + + + @Autowired + public QueryService( + AbstractProcessor abstractProcessor, QueryProcessor queryProcessor, TimeseriesProcessor timeseriesProcessor, + CountProcessor countProcessor, MultiValueQueryProcessor multiValueQueryProcessor, + @Autowired(required = false) DictionaryService dictionaryService, @Value("${SMALL_JOB_LIMIT}") Integer smallJobLimit, + @Value("${SMALL_TASK_THREADS}") Integer smallTaskThreads, @Value("${LARGE_TASK_THREADS}") Integer largeTaskThreads, + PatientProcessor patientProcessor, @Autowired(required = false) LoggingClient loggingClient + ) { + this.abstractProcessor = abstractProcessor; + this.queryProcessor = queryProcessor; + this.timeseriesProcessor = timeseriesProcessor; + this.countProcessor = countProcessor; + this.multiValueQueryProcessor = multiValueQueryProcessor; + this.dictionaryService = dictionaryService; + this.queryDecorator = new QueryDecorator(); + + SMALL_JOB_LIMIT = smallJobLimit; + SMALL_TASK_THREADS = smallTaskThreads; + LARGE_TASK_THREADS = largeTaskThreads; + this.patientProcessor = patientProcessor; + this.loggingClient = loggingClient; + + + /* + * These have to be of type Runnable(nothing more specific) in order to be compatible with ThreadPoolExecutor constructor prototype + */ + largeTaskExecutionQueue = new PriorityBlockingQueue(1000); + smallTaskExecutionQueue = new PriorityBlockingQueue(1000); + + largeTaskExecutor = createExecutor(largeTaskExecutionQueue, LARGE_TASK_THREADS); + smallTaskExecutor = createExecutor(smallTaskExecutionQueue, SMALL_TASK_THREADS); + } + + public AsyncResult runQuery(Query query) throws IOException { + // Merging fields from filters into selected fields for user validation of results + List fields = query.getFields(); + Collections.sort(fields); + query.setFields(fields); + + AsyncResult result = initializeResult(query); + + // This is all the validation we do for now. + if (!ensureAllFieldsExist(query)) { + result.setStatus(Status.ERROR); + } else { + if (query.getFields().size() > SMALL_JOB_LIMIT) { + result.setJobQueue(largeTaskExecutor); + } else { + result.setJobQueue(smallTaskExecutor); + } + + result.enqueue(); + + if (loggingClient != null && loggingClient.isEnabled()) { + try { + loggingClient.send( + LoggingEvent.builder("QUERY").action("query.enqueued") + .metadata( + Map.of( + "query_id", result.getId(), "result_type", String.valueOf(query.getExpectedResultType()), "field_count", + String.valueOf(query.getFields().size()), "queue", + query.getFields().size() > SMALL_JOB_LIMIT ? "large" : "small" + ) + ).build() + ); + } catch (Exception e) { + log.warn("Failed to send audit log event", e); + } + } + } + return getStatusFor(result.getId()); + } + + private AsyncResult initializeResult(Query query) throws IOException { + + HpdsProcessor p; + switch (query.getExpectedResultType()) { + case PATIENTS: + p = patientProcessor; + break; + case SECRET_ADMIN_DATAFRAME: + p = queryProcessor; + break; + case DATAFRAME_TIMESERIES: + p = timeseriesProcessor; + break; + case COUNT: + case CATEGORICAL_CROSS_COUNT: + case CONTINUOUS_CROSS_COUNT: + p = countProcessor; + break; + case DATAFRAME_PFB: + case DATAFRAME: + p = multiValueQueryProcessor; + break; + default: + throw new RuntimeException("UNSUPPORTED RESULT TYPE"); + } + + String queryId = UUIDv5.UUIDFromString(query.toString()).toString(); + ResultWriter writer; + if (ResultType.DATAFRAME_PFB.equals(query.getExpectedResultType())) { + writer = new PfbWriter(File.createTempFile("result-" + System.nanoTime(), ".avro"), queryId, dictionaryService); + } else { + writer = new CsvWriter(File.createTempFile("result-" + System.nanoTime(), ".sstmp")); + } + + queryDecorator.setId(query); + AsyncResult result = new AsyncResult(query, p, writer).setStatus(AsyncResult.Status.PENDING) + .setQueuedTime(System.currentTimeMillis()).setId(queryId).setLoggingClient(loggingClient); + results.put(result.getId(), result); + return result; + } + + private boolean ensureAllFieldsExist(Query query) { + TreeSet allFields = new TreeSet<>(); + List badNumericFilters = new ArrayList(); + List badCategoryFilters = new ArrayList(); + Set dictionaryFields = abstractProcessor.getDictionary().keySet(); + + allFields.addAll(query.getFields()); + allFields.addAll(query.getRequiredFields()); + + allFields.addAll(query.getNumericFilters().keySet()); + for (String field : includingOnlyDictionaryFields(query.getNumericFilters().keySet(), dictionaryFields)) { + if (abstractProcessor.getDictionary().get(field).isCategorical()) { + badNumericFilters.add(field); + } + } + + Set catFieldNames = + query.getCategoryFilters().keySet().stream().filter(Predicate.not(VariantUtils::pathIsVariantSpec)).collect(Collectors.toSet()); + + allFields.addAll(catFieldNames); + for (String field : includingOnlyDictionaryFields(catFieldNames, dictionaryFields)) { + if (!abstractProcessor.getDictionary().get(field).isCategorical()) { + badCategoryFilters.add(field); + } + } + + List missingFields = allFields.stream().filter(Predicate.not(dictionaryFields::contains)).collect(Collectors.toList()); + + if (badNumericFilters.isEmpty() && badCategoryFilters.isEmpty()) { + log.info("All fields passed validation"); + return true; + } else { + log.info("Query failed due to field validation : " + query.getId()); + log.info("Non-existant fields : " + String.join(",", missingFields)); + log.info("Bad numeric fields : " + String.join(",", badNumericFilters)); + log.info("Bad category fields : " + String.join(",", badCategoryFilters)); + return false; + } + } + + private List includingOnlyDictionaryFields(Set fields, Set dictionaryFields) { + return fields.stream().filter((value) -> { + return dictionaryFields.contains(value); + }).collect(Collectors.toList()); + } + + public AsyncResult getStatusFor(String queryId) { + AsyncResult asyncResult = results.get(queryId); + AsyncResult[] queue = asyncResult.getQuery().getFields().size() > SMALL_JOB_LIMIT + ? largeTaskExecutionQueue.toArray(new AsyncResult[largeTaskExecutionQueue.size()]) + : smallTaskExecutionQueue.toArray(new AsyncResult[smallTaskExecutionQueue.size()]); + if (asyncResult.getStatus() == Status.PENDING) { + // this code obviously does not work + ArrayList queueSnapshot = new ArrayList(); + for (int x = 0; x < queueSnapshot.size(); x++) { + if (queueSnapshot.get(x).getId().equals(queryId)) { + asyncResult.setPositionInQueue(x); + break; + } + } + } else { + asyncResult.setPositionInQueue(-1); + } + asyncResult.setQueueDepth(queue.length); + return asyncResult; + } + + public AsyncResult getResultFor(String queryId) { + return results.get(queryId); + } + + private ExecutorService createExecutor(BlockingQueue taskQueue, int numThreads) { + return new ThreadPoolExecutor(1, Math.max(2, numThreads), 10, TimeUnit.MINUTES, taskQueue); + } + +} diff --git a/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/QueryV3Service.java b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/QueryV3Service.java new file mode 100644 index 000000000..a8ca2b8eb --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/QueryV3Service.java @@ -0,0 +1,160 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import edu.harvard.hms.dbmi.avillach.hpds.processing.dictionary.DictionaryService; +import edu.harvard.hms.dbmi.avillach.hpds.processing.io.CsvWriter; +import edu.harvard.hms.dbmi.avillach.hpds.processing.io.PfbWriter; +import edu.harvard.hms.dbmi.avillach.hpds.processing.io.ResultWriter; +import edu.harvard.hms.dbmi.avillach.hpds.processing.v3.*; +import edu.harvard.dbmi.avillach.util.UUIDv5; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Service; + +import java.io.File; +import java.io.IOException; +import java.util.*; +import java.util.concurrent.*; + +@Service +public class QueryV3Service { + + + private final int SMALL_JOB_LIMIT; + + private static final Logger log = LoggerFactory.getLogger(QueryV3Service.class); + + private final BlockingQueue largeTaskExecutionQueue; + + private final ExecutorService largeTaskExecutor; + + private final BlockingQueue smallTaskExecutionQueue; + + private final ExecutorService smallTaskExecutor; + + private final QueryV3Processor queryProcessor; + private final TimeseriesV3Processor timeseriesProcessor; + private final CountV3Processor countProcessor; + private final MultiValueQueryV3Processor multiValueQueryProcessor; + private final PatientV3Processor patientProcessor; + + private final DictionaryService dictionaryService; + + private final QueryValidator queryValidator; + private final LoggingClient loggingClient; + + HashMap results = new HashMap<>(); + + + @Autowired + public QueryV3Service( + QueryV3Processor queryProcessor, TimeseriesV3Processor timeseriesProcessor, CountV3Processor countProcessor, + MultiValueQueryV3Processor multiValueQueryProcessor, @Autowired(required = false) DictionaryService dictionaryService, + QueryValidator queryValidator, @Value("${SMALL_JOB_LIMIT}") Integer smallJobLimit, + @Value("${SMALL_TASK_THREADS}") Integer smallTaskThreads, @Value("${LARGE_TASK_THREADS}") Integer largeTaskThreads, + PatientV3Processor patientProcessor, @Autowired(required = false) LoggingClient loggingClient + ) { + this.queryProcessor = queryProcessor; + this.timeseriesProcessor = timeseriesProcessor; + this.countProcessor = countProcessor; + this.multiValueQueryProcessor = multiValueQueryProcessor; + this.dictionaryService = dictionaryService; + this.queryValidator = queryValidator; + + SMALL_JOB_LIMIT = smallJobLimit; + this.patientProcessor = patientProcessor; + this.loggingClient = loggingClient; + + + /* + * These have to be of type Runnable(nothing more specific) in order to be compatible with ThreadPoolExecutor constructor prototype + */ + largeTaskExecutionQueue = new PriorityBlockingQueue(1000); + smallTaskExecutionQueue = new PriorityBlockingQueue(1000); + + largeTaskExecutor = createExecutor(largeTaskExecutionQueue, largeTaskThreads); + smallTaskExecutor = createExecutor(smallTaskExecutionQueue, smallTaskThreads); + } + + public AsyncResult runQuery(Query query) throws IOException { + AsyncResult result = initializeResult(query); + + try { + queryValidator.validate(query); + if (query.select().size() > SMALL_JOB_LIMIT) { + result.setJobQueue(largeTaskExecutor); + } else { + result.setJobQueue(smallTaskExecutor); + } + + result.enqueue(); + + if (loggingClient != null && loggingClient.isEnabled()) { + try { + loggingClient.send( + LoggingEvent.builder("QUERY").action("query.enqueued").metadata( + Map.of( + "query_id", result.getId(), "result_type", String.valueOf(query.expectedResultType()), "field_count", + String.valueOf(query.select().size()), "queue", query.select().size() > SMALL_JOB_LIMIT ? "large" : "small" + ) + ).build() + ); + } catch (Exception e) { + log.warn("Failed to send audit log event", e); + } + } + } catch (IllegalArgumentException e) { + result.setStatus(AsyncResult.Status.ERROR); + return result; + } + return getStatusFor(result.getId()); + } + + private AsyncResult initializeResult(Query query) throws IOException { + + HpdsV3Processor p = switch (query.expectedResultType()) { + case PATIENTS -> patientProcessor; + case SECRET_ADMIN_DATAFRAME -> queryProcessor; + case DATAFRAME_TIMESERIES -> timeseriesProcessor; + case COUNT, CATEGORICAL_CROSS_COUNT, CONTINUOUS_CROSS_COUNT -> countProcessor; + case DATAFRAME_PFB, DATAFRAME -> multiValueQueryProcessor; + default -> throw new RuntimeException("UNSUPPORTED RESULT TYPE"); + }; + + String queryId = UUIDv5.UUIDFromString(query.toString()).toString(); + ResultWriter writer; + if (ResultType.DATAFRAME_PFB.equals(query.expectedResultType())) { + writer = new PfbWriter(File.createTempFile("result-" + System.nanoTime(), ".avro"), queryId, dictionaryService); + } else { + writer = new CsvWriter(File.createTempFile("result-" + System.nanoTime(), ".sstmp")); + } + + query = query.generateId(); + AsyncResult result = new AsyncResult(query, p, writer).setStatus(AsyncResult.Status.PENDING) + .setQueuedTime(System.currentTimeMillis()).setId(queryId).setLoggingClient(loggingClient); + results.put(result.getId(), result); + return result; + } + + public AsyncResult getStatusFor(String queryId) { + AsyncResult asyncResult = results.get(queryId); + int queueDepth = + asyncResult.getQuery().select().size() > SMALL_JOB_LIMIT ? largeTaskExecutionQueue.size() : smallTaskExecutionQueue.size(); + // note: code copied from this method in QueryService was removed, it was obviously not working + return asyncResult.setQueueDepth(queueDepth); + } + + public AsyncResult getResultFor(UUID queryId) { + return results.get(queryId.toString()); + } + + private ExecutorService createExecutor(BlockingQueue taskQueue, int numThreads) { + return new ThreadPoolExecutor(1, Math.max(2, numThreads), 10, TimeUnit.MINUTES, taskQueue); + } + +} diff --git a/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSharingService.java b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSharingService.java new file mode 100644 index 000000000..93a4abd1f --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSharingService.java @@ -0,0 +1,89 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service.filesharing; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import edu.harvard.hms.dbmi.avillach.hpds.processing.AsyncResult; +import edu.harvard.hms.dbmi.avillach.hpds.processing.VariantListProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.service.QueryService; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.stereotype.Service; + +import java.io.IOException; +import java.util.Map; +import java.util.Optional; + +/** + * Used for sharing data. Given a query, this service will write phenotypic and genomic data into a directory + */ +@Service +public class FileSharingService { + + private static final Logger LOG = LoggerFactory.getLogger(FileSharingService.class); + + private final QueryService queryService; + private final FileSystemService fileWriter; + private final VariantListProcessor variantListProcessor; + private final LoggingClient loggingClient; + + public FileSharingService( + QueryService queryService, FileSystemService fileWriter, VariantListProcessor variantListProcessor, LoggingClient loggingClient + ) { + this.queryService = queryService; + this.fileWriter = fileWriter; + this.variantListProcessor = variantListProcessor; + this.loggingClient = loggingClient; + } + + public boolean createPhenotypicData(Query query) { + boolean success = createAndWriteData(query, "phenotypic_data.csv"); + if (success) { + sendFileWrittenEvent(query.getId(), "phenotypic"); + } + return success; + } + + public boolean createPatientList(Query query) { + boolean success = createAndWriteData(query, "patients.txt"); + if (success) { + sendFileWrittenEvent(query.getId(), "patients"); + } + return success; + } + + public boolean createGenomicData(Query query) { + try { + String vcf = variantListProcessor.runVcfExcerptQuery(query, true); + boolean success = fileWriter.writeResultToFile("genomic_data.tsv", vcf, query.getPicSureId()); + if (success) { + sendFileWrittenEvent(query.getId(), "genomic"); + } + return success; + } catch (IOException e) { + LOG.error("Error running genomic query", e); + return false; + } + } + + private void sendFileWrittenEvent(String queryId, String dataType) { + if (loggingClient != null && loggingClient.isEnabled()) { + try { + loggingClient.send( + LoggingEvent.builder("DATA_ACCESS").action("data.file.written") + .metadata(Map.of("query_id", queryId, "data_type", dataType)).build() + ); + } catch (Exception e) { + LOG.warn("Failed to send audit log event", e); + } + } + } + + private boolean createAndWriteData(Query query, String fileName) { + AsyncResult result = queryService.getResultFor(query.getId()); + if (result == null || result.getStatus() != AsyncResult.Status.SUCCESS) { + return false; + } + return fileWriter.writeResultToFile(fileName, result, query.getPicSureId()); + } +} diff --git a/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSharingV3Service.java b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSharingV3Service.java new file mode 100644 index 000000000..f9e65535f --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSharingV3Service.java @@ -0,0 +1,86 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service.filesharing; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import edu.harvard.hms.dbmi.avillach.hpds.processing.v3.AsyncResult; +import edu.harvard.hms.dbmi.avillach.hpds.processing.v3.VariantListV3Processor; +import edu.harvard.hms.dbmi.avillach.hpds.service.QueryV3Service; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.stereotype.Service; + +import java.util.Map; + +/** + * Used for sharing data. Given a query, this service will write phenotypic and genomic data into a directory + * + * Note: This class was copied from {@link edu.harvard.hms.dbmi.avillach.hpds.service.filesharing.FileSharingService} and updated to use new + * Query entity + */ +@Service +public class FileSharingV3Service { + + private static final Logger LOG = LoggerFactory.getLogger(FileSharingV3Service.class); + + private final QueryV3Service queryService; + private final FileSystemV3Service fileWriter; + private final VariantListV3Processor variantListProcessor; + private final LoggingClient loggingClient; + + public FileSharingV3Service( + QueryV3Service queryService, FileSystemV3Service fileWriter, VariantListV3Processor variantListProcessor, + LoggingClient loggingClient + ) { + this.queryService = queryService; + this.fileWriter = fileWriter; + this.variantListProcessor = variantListProcessor; + this.loggingClient = loggingClient; + } + + public boolean createPhenotypicData(Query query) { + boolean success = createAndWriteData(query, "phenotypic_data.csv"); + if (success) { + sendFileWrittenEvent(query.id().toString(), "phenotypic"); + } + return success; + } + + public boolean createPatientList(Query query) { + boolean success = createAndWriteData(query, "patients.txt"); + if (success) { + sendFileWrittenEvent(query.id().toString(), "patients"); + } + return success; + } + + public boolean createGenomicData(Query query) { + String vcf = variantListProcessor.runVcfExcerptQuery(query, true); + boolean success = fileWriter.writeResultToFile("genomic_data.tsv", vcf, query.picsureId().toString()); + if (success) { + sendFileWrittenEvent(query.id().toString(), "genomic"); + } + return success; + } + + private void sendFileWrittenEvent(String queryId, String dataType) { + if (loggingClient != null && loggingClient.isEnabled()) { + try { + loggingClient.send( + LoggingEvent.builder("DATA_ACCESS").action("data.file.written") + .metadata(Map.of("query_id", queryId, "data_type", dataType)).build() + ); + } catch (Exception e) { + LOG.warn("Failed to send audit log event", e); + } + } + } + + private boolean createAndWriteData(Query query, String fileName) { + AsyncResult result = queryService.getResultFor(query.id()); + if (result == null || result.getStatus() != AsyncResult.Status.SUCCESS) { + return false; + } + return fileWriter.writeResultToFile(fileName, result, query.picsureId().toString()); + } +} diff --git a/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSystemConfig.java b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSystemConfig.java new file mode 100644 index 000000000..1448c8f2c --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSystemConfig.java @@ -0,0 +1,30 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service.filesharing; + +import org.springframework.beans.factory.annotation.Value; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; + +import java.nio.file.Path; + +@Configuration +public class FileSystemConfig { + @Value("${file_sharing_root:/gic_query_results/}") + private String fileSharingRootDir; + + @Value("${enable_file_sharing:false}") + private boolean enableFileSharing; + + @Bean() + Path sharingRoot() { + if (!enableFileSharing) { + return Path.of("/dev/null"); + } + + Path path = Path.of(fileSharingRootDir); + if (!path.toFile().exists()) { + throw new RuntimeException(fileSharingRootDir + " DNE."); + } + + return path; + } +} diff --git a/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSystemService.java b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSystemService.java new file mode 100644 index 000000000..b2f08f8d9 --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSystemService.java @@ -0,0 +1,93 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service.filesharing; + +import edu.harvard.hms.dbmi.avillach.hpds.processing.AsyncResult; +import org.apache.commons.io.IOUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Service; + +import java.io.ByteArrayInputStream; +import java.io.IOException; +import java.io.InputStream; +import java.nio.file.Files; +import java.nio.file.Path; + +import static java.nio.file.StandardCopyOption.REPLACE_EXISTING; + +@Service +public class FileSystemService { + + private static final Logger LOG = LoggerFactory.getLogger(FileSystemService.class); + + @Autowired + private Path sharingRoot; + + @Value("${enable_file_sharing:false}") + private boolean enableFileSharing; + + public boolean writeResultToFile(String fileName, AsyncResult result, String id) { + if (Files.exists(result.getTempFilePath())) { + LOG.info("A temp file already exists for query {}. Moving that rather than rewriting.", id); + return moveFile(fileName, result.getTempFilePath(), id); + } + result.getStream().open(); + return writeStreamToFile(fileName, result.getStream(), id); + } + + public boolean writeResultToFile(String fileName, String result, String id) { + return writeStreamToFile(fileName, new ByteArrayInputStream(result.getBytes()), id); + } + + + private boolean moveFile(String destinationName, Path sourceFile, String queryId) { + if (!enableFileSharing) { + LOG.warn("Attempted to write query result to file while file sharing is disabled. No-op."); + return false; + } + + Path dirPath = Path.of(sharingRoot.toString(), queryId); + Path filePath = Path.of(sharingRoot.toString(), queryId, destinationName); + + try { + LOG.info("Moving query {} to file: {}", queryId, filePath); + makeDirIfDNE(dirPath); + Path result = Files.copy(sourceFile, filePath, REPLACE_EXISTING); + // we have to copy and then delete because of how mv works with mounted drives + // (it doesn't work) + Files.delete(sourceFile); + return Files.exists(result); + } catch (IOException e) { + LOG.error("Error moving.", e); + return false; + } + } + + private boolean writeStreamToFile(String fileName, InputStream content, String queryId) { + if (!enableFileSharing) { + LOG.warn("Attempted to write query result to file while file sharing is disabled. No-op."); + return false; + } + + Path dirPath = Path.of(sharingRoot.toString(), queryId); + Path filePath = Path.of(sharingRoot.toString(), queryId, fileName); + + try { + LOG.info("Writing query {} to file: {}", queryId, filePath); + makeDirIfDNE(dirPath); + return Files.copy(content, filePath) > 0; + } catch (IOException e) { + LOG.error("Error writing result.", e); + return false; + } finally { + IOUtils.closeQuietly(content); + } + } + + private synchronized void makeDirIfDNE(Path dirPath) throws IOException { + if (!Files.exists(dirPath)) { + Files.createDirectory(dirPath); + } + } +} diff --git a/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSystemV3Service.java b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSystemV3Service.java new file mode 100644 index 000000000..f2517ec64 --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSystemV3Service.java @@ -0,0 +1,97 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service.filesharing; + +import edu.harvard.hms.dbmi.avillach.hpds.processing.v3.AsyncResult; +import org.apache.commons.io.IOUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Service; + +import java.io.ByteArrayInputStream; +import java.io.IOException; +import java.io.InputStream; +import java.nio.file.Files; +import java.nio.file.Path; + +import static java.nio.file.StandardCopyOption.REPLACE_EXISTING; + +/** + * Note: This class was copied from {@link edu.harvard.hms.dbmi.avillach.hpds.service.filesharing.FileSystemService} and updated to use new + * Query entity + */ +@Service +public class FileSystemV3Service { + + private static final Logger LOG = LoggerFactory.getLogger(FileSystemV3Service.class); + + @Autowired + private Path sharingRoot; + + @Value("${enable_file_sharing:false}") + private boolean enableFileSharing; + + public boolean writeResultToFile(String fileName, AsyncResult result, String id) { + if (Files.exists(result.getTempFilePath())) { + LOG.info("A temp file already exists for query {}. Moving that rather than rewriting.", id); + return moveFile(fileName, result.getTempFilePath(), id); + } + result.getStream().open(); + return writeStreamToFile(fileName, result.getStream(), id); + } + + public boolean writeResultToFile(String fileName, String result, String id) { + return writeStreamToFile(fileName, new ByteArrayInputStream(result.getBytes()), id); + } + + + private boolean moveFile(String destinationName, Path sourceFile, String queryId) { + if (!enableFileSharing) { + LOG.warn("Attempted to write query result to file while file sharing is disabled. No-op."); + return false; + } + + Path dirPath = Path.of(sharingRoot.toString(), queryId); + Path filePath = Path.of(sharingRoot.toString(), queryId, destinationName); + + try { + LOG.info("Moving query {} to file: {}", queryId, filePath); + makeDirIfDNE(dirPath); + Path result = Files.copy(sourceFile, filePath, REPLACE_EXISTING); + // we have to copy and then delete because of how mv works with mounted drives + // (it doesn't work) + Files.delete(sourceFile); + return Files.exists(result); + } catch (IOException e) { + LOG.error("Error moving.", e); + return false; + } + } + + private boolean writeStreamToFile(String fileName, InputStream content, String queryId) { + if (!enableFileSharing) { + LOG.warn("Attempted to write query result to file while file sharing is disabled. No-op."); + return false; + } + + Path dirPath = Path.of(sharingRoot.toString(), queryId); + Path filePath = Path.of(sharingRoot.toString(), queryId, fileName); + + try { + LOG.info("Writing query {} to file: {}", queryId, filePath); + makeDirIfDNE(dirPath); + return Files.copy(content, filePath) > 0; + } catch (IOException e) { + LOG.error("Error writing result.", e); + return false; + } finally { + IOUtils.closeQuietly(content); + } + } + + private synchronized void makeDirIfDNE(Path dirPath) throws IOException { + if (!Files.exists(dirPath)) { + Files.createDirectory(dirPath); + } + } +} diff --git a/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/TestDataService.java b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/TestDataService.java new file mode 100644 index 000000000..f9e5da60f --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/TestDataService.java @@ -0,0 +1,29 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service.filesharing; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Service; + +import java.util.UUID; + +/** + * Writes test data to the directory shared with the uploader to test uploading features + */ +@Service +public class TestDataService { + + private static final Logger LOG = LoggerFactory.getLogger(TestDataService.class); + + private final FileSystemService fileSystemService; + + @Autowired + public TestDataService(FileSystemService fileSystemService) { + this.fileSystemService = fileSystemService; + } + + public boolean uploadTestFile(String uuid) { + LOG.info("Writing test file for uuid {}", uuid); + return fileSystemService.writeResultToFile("test_data.txt", "This is a disposable test file", uuid); + } +} diff --git a/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/health/HpdsReadinessHealthIndicator.java b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/health/HpdsReadinessHealthIndicator.java new file mode 100644 index 000000000..0a250e494 --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/health/HpdsReadinessHealthIndicator.java @@ -0,0 +1,34 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service.health; + +import edu.harvard.hms.dbmi.avillach.hpds.processing.AbstractProcessor; +import org.springframework.boot.actuate.health.Health; +import org.springframework.boot.actuate.health.HealthIndicator; +import org.springframework.stereotype.Component; + +/** + * Deep readiness for HPDS (spec 3.8): UP only when phenotype OR genomic data is actually loaded — a real "data ready" signal, not just + * port-up. HPDS has no DataSource, so this replaces the built-in db indicator. + */ +@Component("hpdsReadiness") +public class HpdsReadinessHealthIndicator implements HealthIndicator { + + private final AbstractProcessor abstractProcessor; + + public HpdsReadinessHealthIndicator(AbstractProcessor abstractProcessor) { + this.abstractProcessor = abstractProcessor; + } + + @Override + public Health health() { + try { + int phenotypeColumns = abstractProcessor.getDictionary().size(); + int genomicColumns = abstractProcessor.getInfoStoreColumns().size(); + if (phenotypeColumns > 0 || genomicColumns > 0) { + return Health.up().withDetail("phenotypeColumns", phenotypeColumns).withDetail("genomicColumns", genomicColumns).build(); + } + return Health.down().withDetail("reason", "no phenotype or genomic data loaded").build(); + } catch (Exception ex) { + return Health.down(ex).build(); + } + } +} diff --git a/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/util/Paginator.java b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/util/Paginator.java new file mode 100644 index 000000000..f396ce070 --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/util/Paginator.java @@ -0,0 +1,31 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service.util; + +import edu.harvard.dbmi.avillach.domain.PaginatedSearchResult; +import org.springframework.stereotype.Component; + +import java.util.List; + +@Component +public class Paginator { + + /** + * Creates a paginated search result with the specified page from a list + * + * @param list the list from which to select a page + * @param page the page to select, the first page is 1 + * @param size the size of a page to select, minimum 1 + * @return A paginated search result containing the specified page + */ + public PaginatedSearchResult paginate(List list, int page, int size) { + if (page < 1) { + throw new IllegalArgumentException("Page must be greater than 0"); + } + if (size < 1) { + throw new IllegalArgumentException("Size must be greater than 0"); + } + int start = Math.min((page - 1) * size, list.size()); + int end = Math.min(page * size, list.size()); + List results = list.subList(start, end); + return new PaginatedSearchResult<>(results, page, list.size()); + } +} diff --git a/services/pic-sure-hpds/service/src/main/resources/META-INF/additional-spring-configuration-metadata.json b/services/pic-sure-hpds/service/src/main/resources/META-INF/additional-spring-configuration-metadata.json new file mode 100644 index 000000000..65869fafb --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/resources/META-INF/additional-spring-configuration-metadata.json @@ -0,0 +1,8 @@ +{ + "properties": [ + { + "name": "log.pattern", + "type": "java.lang.String", + "description": "Description for log.pattern." + } +] } \ No newline at end of file diff --git a/services/pic-sure-hpds/service/src/main/resources/application-bch-dev.properties b/services/pic-sure-hpds/service/src/main/resources/application-bch-dev.properties new file mode 100644 index 000000000..7a68ec357 --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/resources/application-bch-dev.properties @@ -0,0 +1,7 @@ +SMALL_JOB_LIMIT = 100 +SMALL_TASK_THREADS = 1 +LARGE_TASK_THREADS = 1 +VCF_EXCERPT_ENABLED=true + +hpds.genomicProcessor.impl=localPatientDistributed +HPDS_GENOMIC_DATA_DIRECTORY=/opt/local/hpds/all/ \ No newline at end of file diff --git a/services/pic-sure-hpds/service/src/main/resources/application-bdc-auth-dev.properties b/services/pic-sure-hpds/service/src/main/resources/application-bdc-auth-dev.properties new file mode 100644 index 000000000..6e884d694 --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/resources/application-bdc-auth-dev.properties @@ -0,0 +1,14 @@ +SMALL_JOB_LIMIT = 100 +SMALL_TASK_THREADS = 1 +LARGE_TASK_THREADS = 1 + +hpds.genomicProcessor.impl=localPatientDistributed +HPDS_GENOMIC_DATA_DIRECTORY=/opt/local/hpds/all/ + +data-export.s3.bucket-name=pic-sure-auth-dev-data-export +data-export.s3.region=us-east-1 +data-export.s3.signedUrl-expiry-minutes=60 + +dictionary.host = http://wildfly.___TARGET_STACK___:8080/ + +log.pattern=%d{yyyy-MM-dd'T'HH:mm:ss.SSS'Z', UTC} %-5level --- [auth-hpds] [%thread] %logger{36} : %msg%n \ No newline at end of file diff --git a/services/pic-sure-hpds/service/src/main/resources/application-bdc-auth-prod.properties b/services/pic-sure-hpds/service/src/main/resources/application-bdc-auth-prod.properties new file mode 100644 index 000000000..7fa735131 --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/resources/application-bdc-auth-prod.properties @@ -0,0 +1,14 @@ +SMALL_JOB_LIMIT = 100 +SMALL_TASK_THREADS = 1 +LARGE_TASK_THREADS = 1 + +hpds.genomicProcessor.impl=localPatientDistributed +HPDS_GENOMIC_DATA_DIRECTORY=/opt/local/hpds/all/ + +data-export.s3.bucket-name=pic-sure-auth-prod-data-export +data-export.s3.region=us-east-1 +data-export.s3.signedUrl-expiry-minutes=60 + +dictionary.host = http://wildfly.___TARGET_STACK___:8080/ + +log.pattern=%d{yyyy-MM-dd'T'HH:mm:ss.SSS'Z', UTC} %-5level --- [auth-hpds] [%thread] %logger{36} : %msg%n \ No newline at end of file diff --git a/services/pic-sure-hpds/service/src/main/resources/application-development.properties b/services/pic-sure-hpds/service/src/main/resources/application-development.properties new file mode 100644 index 000000000..5768ef1bd --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/resources/application-development.properties @@ -0,0 +1,5 @@ +SMALL_JOB_LIMIT = 100 +SMALL_TASK_THREADS = 1 +LARGE_TASK_THREADS = 1 + +dictionary.host = http://wildfly.___TARGET_STACK___:8080/ \ No newline at end of file diff --git a/services/pic-sure-hpds/service/src/main/resources/application-gic-site.properties b/services/pic-sure-hpds/service/src/main/resources/application-gic-site.properties new file mode 100644 index 000000000..c00b1a012 --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/resources/application-gic-site.properties @@ -0,0 +1,9 @@ +SMALL_JOB_LIMIT = 100 +SMALL_TASK_THREADS = 1 +LARGE_TASK_THREADS = 1 +VCF_EXCERPT_ENABLED=true + +hpds.genomicProcessor.impl=localPatientDistributed +HPDS_GENOMIC_DATA_DIRECTORY=/opt/local/hpds/all/ + +enable_file_sharing=true \ No newline at end of file diff --git a/services/pic-sure-hpds/service/src/main/resources/application-integration-test.properties b/services/pic-sure-hpds/service/src/main/resources/application-integration-test.properties new file mode 100644 index 000000000..912f01624 --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/resources/application-integration-test.properties @@ -0,0 +1,12 @@ +SMALL_JOB_LIMIT = 100 +SMALL_TASK_THREADS = 1 +LARGE_TASK_THREADS = 1 +ID_BATCH_SIZE=1000 +VCF_EXCERPT_ENABLED=true + +hpds.genomicProcessor.impl=localDistributed +HPDS_GENOMIC_DATA_DIRECTORY=target/all/ +HPDS_DATA_DIRECTORY=target/test-classes/phenotypic/ + +enable_file_sharing=false +hpds.requireAuthorizationFilter=false \ No newline at end of file diff --git a/services/pic-sure-hpds/service/src/main/resources/application-integrationB.properties b/services/pic-sure-hpds/service/src/main/resources/application-integrationB.properties new file mode 100644 index 000000000..16c335d22 --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/resources/application-integrationB.properties @@ -0,0 +1,6 @@ +SMALL_JOB_LIMIT = 100 +SMALL_TASK_THREADS = 1 +LARGE_TASK_THREADS = 1 + +hpds.genomicProcessor.impl=localDistributed +HPDS_GENOMIC_DATA_DIRECTORY=/opt/local/hpds/all/ \ No newline at end of file diff --git a/services/pic-sure-hpds/service/src/main/resources/application-open.properties b/services/pic-sure-hpds/service/src/main/resources/application-open.properties new file mode 100644 index 000000000..99a34b595 --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/resources/application-open.properties @@ -0,0 +1,5 @@ +SMALL_JOB_LIMIT = 100 +SMALL_TASK_THREADS = 1 +LARGE_TASK_THREADS = 1 + +log.pattern=%d{yyyy-MM-dd'T'HH:mm:ss.SSS'Z', UTC} %-5level --- [open-hpds] [%thread] %logger{36} : %msg%n \ No newline at end of file diff --git a/services/pic-sure-hpds/service/src/main/resources/application.properties b/services/pic-sure-hpds/service/src/main/resources/application.properties new file mode 100644 index 000000000..cedc66056 --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/resources/application.properties @@ -0,0 +1,22 @@ +SMALL_JOB_LIMIT = 100 +SMALL_TASK_THREADS = 1 +LARGE_TASK_THREADS = 1 + +# Logging File Output https://docs.spring.io/spring-boot/reference/features/logging.html#features.logging.file-output +# If you are adding additional log files please add them to /var/log/ directory. +logging.file.name=/var/log/hpds.log +logging.level.root=info +log.pattern=%d{yyyy-MM-dd'T'HH:mm:ss.SSS'Z', UTC} %-5level --- [hpds] [%thread] %logger{36} : %msg%n +enable_file_sharing=false + +# This should only be set to true if you wish to control patient data access granularly +# See edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query.authorizationFilters for more information +# hpds.requireAuthorizationFilter=false + +# Actuator: OFF BY DEFAULT. HPDS has no Spring Security in front of it, so nothing is exposed unless the +# deployment opts in. AIO's hpds.env sets PICSURE_ACTUATOR_EXPOSURE=health to enable a shallow readiness +# probe; details stay hidden (PICSURE_ACTUATOR_DETAILS defaults to never) so no datasource/disk/component +# internals leak even when health is reachable. +management.endpoints.web.exposure.include=${PICSURE_ACTUATOR_EXPOSURE:none} +management.endpoint.health.show-details=${PICSURE_ACTUATOR_DETAILS:never} +management.endpoint.health.probes.enabled=true \ No newline at end of file diff --git a/services/pic-sure-hpds/service/src/main/resources/logback-spring.xml b/services/pic-sure-hpds/service/src/main/resources/logback-spring.xml new file mode 100644 index 000000000..582c4ab27 --- /dev/null +++ b/services/pic-sure-hpds/service/src/main/resources/logback-spring.xml @@ -0,0 +1,32 @@ + + + + + + + ${LOG_PATTERN} + + + + + ${LOG_FILE:-var/log/hpds.log} + + ${LOG_PATTERN} + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/AuditAttributesTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/AuditAttributesTest.java new file mode 100644 index 000000000..426575b2e --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/AuditAttributesTest.java @@ -0,0 +1,81 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service; + +import static org.junit.jupiter.api.Assertions.*; + +import java.util.Map; + +import org.junit.jupiter.api.Test; +import org.springframework.mock.web.MockHttpServletRequest; + +import edu.harvard.hms.dbmi.avillach.hpds.processing.audit.AuditAttributes; + +class AuditAttributesTest { + + @Test + void testPutAndGetMetadata() { + MockHttpServletRequest request = new MockHttpServletRequest(); + + AuditAttributes.putMetadata(request, "query_id", "abc-123"); + AuditAttributes.putMetadata(request, "result_type", "COUNT"); + + Map metadata = AuditAttributes.getMetadata(request); + assertEquals("abc-123", metadata.get("query_id")); + assertEquals("COUNT", metadata.get("result_type")); + } + + @Test + void testNullKeyIsIgnored() { + MockHttpServletRequest request = new MockHttpServletRequest(); + + AuditAttributes.putMetadata(request, null, "value"); + + assertTrue(AuditAttributes.getMetadata(request).isEmpty()); + } + + @Test + void testNullValueIsIgnored() { + MockHttpServletRequest request = new MockHttpServletRequest(); + + AuditAttributes.putMetadata(request, "key", null); + + assertTrue(AuditAttributes.getMetadata(request).isEmpty()); + } + + @Test + void testNullRequestIsIgnored() { + // Should not throw + AuditAttributes.putMetadata(null, "key", "value"); + } + + @Test + void testGetMetadataCreatesMapOnFirstCall() { + MockHttpServletRequest request = new MockHttpServletRequest(); + + Map metadata = AuditAttributes.getMetadata(request); + + assertNotNull(metadata); + assertTrue(metadata.isEmpty()); + } + + @Test + void testGetMetadataReturnsSameMapOnSubsequentCalls() { + MockHttpServletRequest request = new MockHttpServletRequest(); + + Map first = AuditAttributes.getMetadata(request); + first.put("key", "value"); + Map second = AuditAttributes.getMetadata(request); + + assertSame(first, second); + assertEquals("value", second.get("key")); + } + + @Test + void testOverwritesExistingKey() { + MockHttpServletRequest request = new MockHttpServletRequest(); + + AuditAttributes.putMetadata(request, "result_type", "COUNT"); + AuditAttributes.putMetadata(request, "result_type", "DATAFRAME"); + + assertEquals("DATAFRAME", AuditAttributes.getMetadata(request).get("result_type")); + } +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/AuditIntegrationTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/AuditIntegrationTest.java new file mode 100644 index 000000000..7441b3672 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/AuditIntegrationTest.java @@ -0,0 +1,161 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + +import java.util.Map; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import jakarta.servlet.FilterChain; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.ArgumentCaptor; +import org.springframework.mock.web.MockHttpServletRequest; +import org.springframework.mock.web.MockHttpServletResponse; +import org.springframework.web.method.HandlerMethod; + +import edu.harvard.hms.dbmi.avillach.hpds.processing.audit.AuditAttributes; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import edu.harvard.hms.dbmi.avillach.hpds.processing.audit.AuditInterceptor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.audit.AuditLoggingFilter; + +class AuditIntegrationTest { + + private AuditInterceptor interceptor; + private LoggingClient loggingClient; + private AuditLoggingFilter filter; + + // Test controller with @AuditEvent annotation + static class TestController { + + @AuditEvent(type = "QUERY", action = "query.submitted") + public void queryEndpoint() {} + + @AuditEvent(type = "DATA_ACCESS", action = "query.result") + public void resultEndpoint() {} + } + + @BeforeEach + void setup() { + interceptor = new AuditInterceptor(); + loggingClient = mock(LoggingClient.class); + when(loggingClient.isEnabled()).thenReturn(true); + filter = new AuditLoggingFilter(loggingClient, null, null); + } + + @Test + void happyPathFullChain() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/PIC-SURE/v3/query"); + request.setRemoteAddr("10.0.0.1"); + request.addHeader("User-Agent", "test-agent"); + request.addHeader("Authorization", "Bearer abc123"); + request.addHeader("X-Request-Id", "req-42"); + request.addHeader("X-Session-Id", "session-99"); + + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + // Step 1: Interceptor reads @AuditEvent and sets request attributes + HandlerMethod handlerMethod = new HandlerMethod(new TestController(), "queryEndpoint"); + interceptor.preHandle(request, response, handlerMethod); + + // Step 2: Controller sets domain metadata + AuditAttributes.putMetadata(request, "query_id", "q-abc"); + AuditAttributes.putMetadata(request, "result_type", "COUNT"); + + // Step 3: Filter runs and sends LoggingEvent + FilterChain chain = mock(FilterChain.class); + filter.doFilter(request, response, chain); + + // Step 4: Capture and verify the LoggingEvent + ArgumentCaptor eventCaptor = ArgumentCaptor.forClass(LoggingEvent.class); + ArgumentCaptor bearerCaptor = ArgumentCaptor.forClass(String.class); + ArgumentCaptor requestIdCaptor = ArgumentCaptor.forClass(String.class); + verify(loggingClient).send(eventCaptor.capture(), bearerCaptor.capture(), requestIdCaptor.capture()); + + LoggingEvent event = eventCaptor.getValue(); + assertEquals("QUERY", event.getEventType()); + assertEquals("query.submitted", event.getAction()); + assertNull(event.getError()); + + // Verify request info + assertNotNull(event.getRequest()); + assertEquals("POST", event.getRequest().getMethod()); + assertEquals("/PIC-SURE/v3/query", event.getRequest().getUrl()); + assertEquals("10.0.0.1", event.getRequest().getSrcIp()); + assertEquals(200, event.getRequest().getStatus()); + + // Verify session ID (top-level on event, not in metadata) + assertEquals("session-99", event.getSessionId()); + + // Verify metadata + Map metadata = event.getMetadata(); + assertNotNull(metadata); + assertEquals("v3", metadata.get("api_version")); + assertEquals("q-abc", metadata.get("query_id")); + assertEquals("COUNT", metadata.get("result_type")); + + // Verify bearer token and request ID passthrough + assertEquals("Bearer abc123", bearerCaptor.getValue()); + assertEquals("req-42", requestIdCaptor.getValue()); + + // Verify the filter chain was invoked + verify(chain).doFilter(request, response); + } + + @Test + void v3PathDetection() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("GET", "/PIC-SURE/v3/search/values/"); + request.setRemoteAddr("192.168.1.1"); + + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + // Interceptor with DATA_ACCESS annotation + HandlerMethod handlerMethod = new HandlerMethod(new TestController(), "resultEndpoint"); + interceptor.preHandle(request, response, handlerMethod); + + FilterChain chain = mock(FilterChain.class); + filter.doFilter(request, response, chain); + + ArgumentCaptor eventCaptor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(eventCaptor.capture()); + + LoggingEvent event = eventCaptor.getValue(); + assertEquals("DATA_ACCESS", event.getEventType()); + assertEquals("query.result", event.getAction()); + assertEquals("v3", event.getMetadata().get("api_version")); + } + + @Test + void errorResponseIncludesErrorMap() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/PIC-SURE/query"); + request.setRemoteAddr("10.0.0.5"); + + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(500); + + // Interceptor sets annotation attributes + HandlerMethod handlerMethod = new HandlerMethod(new TestController(), "queryEndpoint"); + interceptor.preHandle(request, response, handlerMethod); + + FilterChain chain = mock(FilterChain.class); + filter.doFilter(request, response, chain); + + ArgumentCaptor eventCaptor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(eventCaptor.capture()); + + LoggingEvent event = eventCaptor.getValue(); + assertEquals("QUERY", event.getEventType()); + + // Verify error map is populated for 5xx + Map error = event.getError(); + assertNotNull(error, "Error map should be present for 500 status"); + assertEquals(500, error.get("status")); + assertEquals("server_error", error.get("error_type")); + + // Verify no v3 api_version for non-v3 path + assertNull(event.getMetadata().get("api_version")); + } +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/AuditInterceptorTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/AuditInterceptorTest.java new file mode 100644 index 000000000..931e4b80d --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/AuditInterceptorTest.java @@ -0,0 +1,97 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.mock.web.MockHttpServletRequest; +import org.springframework.mock.web.MockHttpServletResponse; +import org.springframework.web.method.HandlerMethod; + +import edu.harvard.hms.dbmi.avillach.hpds.processing.audit.AuditAttributes; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import edu.harvard.hms.dbmi.avillach.hpds.processing.audit.AuditInterceptor; + +class AuditInterceptorTest { + + private AuditInterceptor interceptor; + + @BeforeEach + void setup() { + interceptor = new AuditInterceptor(); + } + + // Test controller with annotated methods + static class TestController { + + @AuditEvent(type = "QUERY", action = "query.submitted") + public void queryEndpoint() {} + + @AuditEvent(type = "DATA_ACCESS", action = "query.result") + public void resultEndpoint() {} + + public void unannotatedEndpoint() {} + } + + private HandlerMethod handlerFor(String methodName) throws Exception { + return new HandlerMethod(new TestController(), methodName); + } + + @Test + void testSetsEventTypeAndActionFromAnnotation() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest(); + MockHttpServletResponse response = new MockHttpServletResponse(); + + boolean result = interceptor.preHandle(request, response, handlerFor("queryEndpoint")); + + assertTrue(result); + assertEquals("QUERY", request.getAttribute(AuditAttributes.EVENT_TYPE)); + assertEquals("query.submitted", request.getAttribute(AuditAttributes.ACTION)); + } + + @Test + void testDifferentAnnotationValues() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest(); + MockHttpServletResponse response = new MockHttpServletResponse(); + + interceptor.preHandle(request, response, handlerFor("resultEndpoint")); + + assertEquals("DATA_ACCESS", request.getAttribute(AuditAttributes.EVENT_TYPE)); + assertEquals("query.result", request.getAttribute(AuditAttributes.ACTION)); + } + + @Test + void testUnannotatedMethodSetsNoAttributes() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest(); + MockHttpServletResponse response = new MockHttpServletResponse(); + + boolean result = interceptor.preHandle(request, response, handlerFor("unannotatedEndpoint")); + + assertTrue(result); + assertNull(request.getAttribute(AuditAttributes.EVENT_TYPE)); + assertNull(request.getAttribute(AuditAttributes.ACTION)); + } + + @Test + void testNonHandlerMethodObjectIsIgnored() { + MockHttpServletRequest request = new MockHttpServletRequest(); + MockHttpServletResponse response = new MockHttpServletResponse(); + + // Pass a non-HandlerMethod object (e.g., a string) + boolean result = interceptor.preHandle(request, response, "not-a-handler"); + + assertTrue(result); + assertNull(request.getAttribute(AuditAttributes.EVENT_TYPE)); + } + + @Test + void testAlwaysReturnsTrue() throws Exception { + MockHttpServletRequest request = new MockHttpServletRequest(); + MockHttpServletResponse response = new MockHttpServletResponse(); + + assertTrue(interceptor.preHandle(request, response, handlerFor("queryEndpoint"))); + assertTrue(interceptor.preHandle(request, response, handlerFor("unannotatedEndpoint"))); + assertTrue(interceptor.preHandle(request, response, "not-a-handler")); + } +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/AuditLoggingFilterTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/AuditLoggingFilterTest.java new file mode 100644 index 000000000..bc81cd17d --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/AuditLoggingFilterTest.java @@ -0,0 +1,356 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + +import java.util.Map; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.ArgumentCaptor; +import org.springframework.mock.web.MockFilterChain; +import org.springframework.mock.web.MockHttpServletRequest; +import org.springframework.mock.web.MockHttpServletResponse; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.dbmi.avillach.logging.SessionIdResolver; +import edu.harvard.hms.dbmi.avillach.hpds.processing.audit.AuditAttributes; +import edu.harvard.hms.dbmi.avillach.hpds.processing.audit.AuditLoggingFilter; + +class AuditLoggingFilterTest { + + private AuditLoggingFilter filter; + private LoggingClient loggingClient; + + @BeforeEach + void setup() { + loggingClient = mock(LoggingClient.class); + when(loggingClient.isEnabled()).thenReturn(true); + filter = new AuditLoggingFilter(loggingClient, null, null); + } + + private MockHttpServletRequest mockRequest(String path, String method) { + MockHttpServletRequest request = new MockHttpServletRequest(method, path); + request.setRemoteAddr("192.168.1.1"); + request.setLocalAddr("10.0.0.1"); + request.setLocalPort(8080); + return request; + } + + // ---- Reads event type/action from request attributes (set by AuditInterceptor) ---- + + @Test + void testReadsEventTypeAndActionFromAttributes() throws Exception { + MockHttpServletRequest request = mockRequest("/PIC-SURE/query", "POST"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "QUERY"); + request.setAttribute(AuditAttributes.ACTION, "query.submitted"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + LoggingEvent event = captor.getValue(); + assertEquals("QUERY", event.getEventType()); + assertEquals("query.submitted", event.getAction()); + } + + @Test + void testFallsBackToOtherAndMethodWhenNoAttributes() throws Exception { + MockHttpServletRequest request = mockRequest("/unknown/path", "GET"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + LoggingEvent event = captor.getValue(); + assertEquals("OTHER", event.getEventType()); + assertEquals("GET", event.getAction()); + } + + @Test + void testDataAccessEventType() throws Exception { + MockHttpServletRequest request = mockRequest("/PIC-SURE/query/abc/result", "POST"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "DATA_ACCESS"); + request.setAttribute(AuditAttributes.ACTION, "query.result"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("DATA_ACCESS", captor.getValue().getEventType()); + assertEquals("query.result", captor.getValue().getAction()); + } + + // ---- API version detection ---- + + @Test + void testV3PathSetsApiVersion() throws Exception { + MockHttpServletRequest request = mockRequest("/PIC-SURE/v3/query", "POST"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "QUERY"); + request.setAttribute(AuditAttributes.ACTION, "query.submitted"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("v3", captor.getValue().getMetadata().get("api_version")); + } + + @Test + void testNonV3PathHasNoApiVersion() throws Exception { + MockHttpServletRequest request = mockRequest("/PIC-SURE/query", "POST"); + request.setAttribute(AuditAttributes.EVENT_TYPE, "QUERY"); + request.setAttribute(AuditAttributes.ACTION, "query.submitted"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertNull(captor.getValue().getMetadata().get("api_version")); + } + + // ---- IP extraction ---- + + @Test + void testXForwardedForSingleIpUsedAsSrcIp() throws Exception { + MockHttpServletRequest request = mockRequest("/PIC-SURE/query", "POST"); + request.addHeader("X-Forwarded-For", "203.0.113.50"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("203.0.113.50", captor.getValue().getRequest().getSrcIp()); + } + + @Test + void testXForwardedForMultipleIpsUsesFirst() throws Exception { + MockHttpServletRequest request = mockRequest("/PIC-SURE/query", "POST"); + request.addHeader("X-Forwarded-For", "203.0.113.50, 70.41.3.18, 150.172.238.178"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("203.0.113.50", captor.getValue().getRequest().getSrcIp()); + } + + @Test + void testNoXForwardedForFallsBackToRemoteAddr() throws Exception { + MockHttpServletRequest request = mockRequest("/PIC-SURE/query", "POST"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("192.168.1.1", captor.getValue().getRequest().getSrcIp()); + } + + // ---- Session ID ---- + + @Test + void testXSessionIdHeaderUsedWhenPresent() throws Exception { + MockHttpServletRequest request = mockRequest("/PIC-SURE/query", "POST"); + request.addHeader("X-Session-Id", "my-session-123"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("my-session-123", captor.getValue().getSessionId()); + } + + @Test + void testNoXSessionIdGeneratesHashFromIpAndUserAgent() throws Exception { + MockHttpServletRequest request = mockRequest("/PIC-SURE/query", "POST"); + request.addHeader("User-Agent", "TestBrowser/1.0"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + + String expectedHash = SessionIdResolver.resolve(null, "192.168.1.1", "TestBrowser/1.0"); + assertEquals(expectedHash, captor.getValue().getSessionId()); + } + + // ---- Error detection ---- + + @Test + void testStatus200HasNoErrorMap() throws Exception { + MockHttpServletRequest request = mockRequest("/PIC-SURE/query", "POST"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertNull(captor.getValue().getError()); + } + + @Test + void testStatus404HasClientErrorMap() throws Exception { + MockHttpServletRequest request = mockRequest("/PIC-SURE/query", "POST"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(404); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + Map error = captor.getValue().getError(); + assertNotNull(error); + assertEquals(404, error.get("status")); + assertEquals("client_error", error.get("error_type")); + } + + @Test + void testStatus500HasServerErrorMap() throws Exception { + MockHttpServletRequest request = mockRequest("/PIC-SURE/query", "POST"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(500); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + Map error = captor.getValue().getError(); + assertNotNull(error); + assertEquals(500, error.get("status")); + assertEquals("server_error", error.get("error_type")); + } + + // ---- Bearer token passthrough ---- + + @Test + void testAuthorizationHeaderPresentCallsSendWithAuthAndRequestId() throws Exception { + MockHttpServletRequest request = mockRequest("/PIC-SURE/query", "POST"); + request.addHeader("Authorization", "Bearer token123"); + request.addHeader("X-Request-Id", "req-456"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture(), eq("Bearer token123"), eq("req-456")); + verify(loggingClient, never()).send(any(LoggingEvent.class)); + } + + @Test + void testNoAuthHeaderAndNoRequestIdCallsSendWithoutExtra() throws Exception { + MockHttpServletRequest request = mockRequest("/PIC-SURE/query", "POST"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + verify(loggingClient, never()).send(any(LoggingEvent.class), anyString(), anyString()); + } + + // ---- Disabled logging client ---- + + @Test + void testDisabledLoggingClientDoesNotSend() throws Exception { + when(loggingClient.isEnabled()).thenReturn(false); + + MockHttpServletRequest request = mockRequest("/PIC-SURE/query", "POST"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + verify(loggingClient, never()).send(any(LoggingEvent.class)); + verify(loggingClient, never()).send(any(LoggingEvent.class), anyString(), anyString()); + } + + // ---- AuditAttributes metadata merge ---- + + @Test + void testMergesControllerMetadata() throws Exception { + MockHttpServletRequest request = mockRequest("/PIC-SURE/query", "POST"); + // Simulate what a controller would do + AuditAttributes.putMetadata(request, "query_id", "def-456"); + AuditAttributes.putMetadata(request, "result_type", "COUNT"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + LoggingEvent event = captor.getValue(); + assertEquals("def-456", event.getMetadata().get("query_id")); + assertEquals("COUNT", event.getMetadata().get("result_type")); + // Session ID is a top-level field + assertNotNull(event.getSessionId()); + } + + @Test + void testSessionIdFromHeaderTakesPrecedence() throws Exception { + MockHttpServletRequest request = mockRequest("/PIC-SURE/query", "POST"); + request.addHeader("X-Session-Id", "filter-session"); + // Controller tries to set session_id in metadata — filter's top-level field takes precedence + AuditAttributes.putMetadata(request, "session_id", "controller-session"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + assertEquals("filter-session", captor.getValue().getSessionId()); + } + + // ---- RequestInfo fields ---- + + @Test + void testRequestInfoPopulatedCorrectly() throws Exception { + MockHttpServletRequest request = mockRequest("/PIC-SURE/query", "POST"); + request.addHeader("User-Agent", "TestAgent/2.0"); + MockHttpServletResponse response = new MockHttpServletResponse(); + response.setStatus(200); + response.setContentType("application/json"); + + filter.doFilter(request, response, new MockFilterChain()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(captor.capture()); + LoggingEvent event = captor.getValue(); + + assertEquals("POST", event.getRequest().getMethod()); + assertEquals("/PIC-SURE/query", event.getRequest().getUrl()); + assertEquals("192.168.1.1", event.getRequest().getSrcIp()); + assertEquals("10.0.0.1", event.getRequest().getDestIp()); + assertEquals(Integer.valueOf(8080), event.getRequest().getDestPort()); + assertEquals("TestAgent/2.0", event.getRequest().getHttpUserAgent()); + assertEquals(Integer.valueOf(200), event.getRequest().getStatus()); + assertEquals("application/json", event.getRequest().getHttpContentType()); + assertNotNull(event.getRequest().getDuration()); + } + +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/AuditMockMvcTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/AuditMockMvcTest.java new file mode 100644 index 000000000..c1ccc6a51 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/AuditMockMvcTest.java @@ -0,0 +1,146 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.hms.dbmi.avillach.hpds.processing.AbstractProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.CountProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.VariantListProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.upload.SignUrlService; +import edu.harvard.hms.dbmi.avillach.hpds.service.filesharing.FileSharingService; +import edu.harvard.hms.dbmi.avillach.hpds.service.filesharing.TestDataService; +import edu.harvard.hms.dbmi.avillach.hpds.service.util.Paginator; +import org.junit.jupiter.api.Test; +import org.mockito.ArgumentCaptor; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.http.MediaType; +import org.springframework.test.web.servlet.MockMvc; + +/** + * Verifies that Spring actually registers the AuditLoggingFilter and AuditInterceptor, and that @AuditEvent annotations on real controller + * methods produce correct logging events through the full HTTP pipeline. + */ +@SpringBootTest +@AutoConfigureMockMvc +class AuditMockMvcTest { + + @Autowired + MockMvc mockMvc; + + @MockBean + LoggingClient loggingClient; + + // Mock all service dependencies so we don't need real data + @MockBean + QueryService queryService; + @MockBean + CountProcessor countProcessor; + @MockBean + VariantListProcessor variantListProcessor; + @MockBean + AbstractProcessor abstractProcessor; + @MockBean + Paginator paginator; + @MockBean + SignUrlService signUrlService; + @MockBean + FileSharingService fileSystemService; + @MockBean + TestDataService testDataService; + + @Test + void postInfoEndpointProducesAuditEvent() throws Exception { + when(loggingClient.isEnabled()).thenReturn(true); + + mockMvc.perform( + post("/PIC-SURE/info").contentType(MediaType.APPLICATION_JSON).content("{\"query\":\"test\"}") + ).andExpect(status().isOk()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient, atLeastOnce()).send(captor.capture()); + + LoggingEvent event = captor.getValue(); + assertEquals("OTHER", event.getEventType()); + assertEquals("info", event.getAction()); + assertEquals("POST", event.getRequest().getMethod()); + assertEquals(200, event.getRequest().getStatus()); + assertNotNull(event.getSessionId()); + } + + @Test + void searchEndpointIncludesSearchTermMetadata() throws Exception { + when(loggingClient.isEnabled()).thenReturn(true); + when(abstractProcessor.getDictionary()).thenReturn(new java.util.TreeMap<>()); + when(abstractProcessor.getInfoStoreMeta()).thenReturn(java.util.List.of()); + + mockMvc.perform( + post("/PIC-SURE/search").contentType(MediaType.APPLICATION_JSON).content("{\"query\":\"blood pressure\"}") + ).andExpect(status().isOk()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient, atLeastOnce()).send(captor.capture()); + + LoggingEvent event = captor.getValue(); + assertEquals("SEARCH", event.getEventType()); + assertEquals("search", event.getAction()); + assertEquals("blood pressure", event.getMetadata().get("search_term")); + } + + @Test + void v3EndpointIncludesApiVersion() throws Exception { + when(loggingClient.isEnabled()).thenReturn(true); + + mockMvc.perform( + post("/PIC-SURE/v3/info").contentType(MediaType.APPLICATION_JSON).content("{\"query\":\"test\"}") + ).andExpect(status().isOk()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient, atLeastOnce()).send(captor.capture()); + + LoggingEvent event = captor.getValue(); + assertEquals("v3", event.getMetadata().get("api_version")); + } + + @Test + void bearerTokenIsPassedThrough() throws Exception { + when(loggingClient.isEnabled()).thenReturn(true); + + mockMvc.perform( + post("/PIC-SURE/info").contentType(MediaType.APPLICATION_JSON).content("{\"query\":\"test\"}") + .header("Authorization", "Bearer mytoken") + .header("X-Request-Id", "req-99") + ).andExpect(status().isOk()); + + ArgumentCaptor eventCaptor = ArgumentCaptor.forClass(LoggingEvent.class); + ArgumentCaptor authCaptor = ArgumentCaptor.forClass(String.class); + ArgumentCaptor reqIdCaptor = ArgumentCaptor.forClass(String.class); + verify(loggingClient, atLeastOnce()).send(eventCaptor.capture(), authCaptor.capture(), reqIdCaptor.capture()); + + assertEquals("Bearer mytoken", authCaptor.getValue()); + assertEquals("req-99", reqIdCaptor.getValue()); + } + + @Test + void notFoundReturnsOtherEventTypeWithNoAnnotation() throws Exception { + when(loggingClient.isEnabled()).thenReturn(true); + + mockMvc.perform(get("/PIC-SURE/nonexistent")).andExpect(status().isNotFound()); + + ArgumentCaptor captor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient, atLeastOnce()).send(captor.capture()); + + LoggingEvent event = captor.getValue(); + // No @AuditEvent on a 404, so falls back to defaults + assertEquals("OTHER", event.getEventType()); + assertNotNull(event.getError()); + assertEquals(404, event.getError().get("status")); + } +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/AuditWiringTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/AuditWiringTest.java new file mode 100644 index 000000000..a738b3845 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/AuditWiringTest.java @@ -0,0 +1,123 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service; + +import static org.junit.jupiter.api.Assertions.*; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.hms.dbmi.avillach.hpds.processing.*; +import edu.harvard.hms.dbmi.avillach.hpds.processing.dictionary.DictionaryService; +import edu.harvard.hms.dbmi.avillach.hpds.processing.patient.PatientProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.timeseries.TimeseriesProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.upload.SignUrlService; +import edu.harvard.hms.dbmi.avillach.hpds.processing.v3.*; +import edu.harvard.hms.dbmi.avillach.hpds.service.filesharing.FileSharingService; +import edu.harvard.hms.dbmi.avillach.hpds.service.filesharing.FileSharingV3Service; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.test.context.TestPropertySource; +import org.springframework.test.util.ReflectionTestUtils; + +@SpringBootTest +@TestPropertySource(properties = {"SMALL_JOB_LIMIT=100", "SMALL_TASK_THREADS=2", "LARGE_TASK_THREADS=2",}) +class AuditWiringTest { + + // -- Bean under verification -------------------------------------------------- + @MockBean + LoggingClient loggingClient; + + // -- Services wired by Spring (these are the subjects of the test) ------------ + @Autowired + QueryService queryService; + + @Autowired + QueryV3Service queryV3Service; + + @Autowired + FileSharingService fileSharingService; + + @Autowired + FileSharingV3Service fileSharingV3Service; + + // -- Mock all processor-level dependencies so the context can load ------------- + @MockBean + GenomicProcessor genomicProcessor; + @MockBean + AbstractProcessor abstractProcessor; + @MockBean + QueryProcessor queryProcessor; + @MockBean + CountProcessor countProcessor; + @MockBean + TimeseriesProcessor timeseriesProcessor; + @MockBean + MultiValueQueryProcessor multiValueQueryProcessor; + @MockBean + PatientProcessor patientProcessor; + @MockBean + VariantListProcessor variantListProcessor; + @MockBean + QueryV3Processor queryV3Processor; + @MockBean + CountV3Processor countV3Processor; + @MockBean + TimeseriesV3Processor timeseriesV3Processor; + @MockBean + MultiValueQueryV3Processor multiValueQueryV3Processor; + @MockBean + PatientV3Processor patientV3Processor; + @MockBean + VariantListV3Processor variantListV3Processor; + @MockBean + QueryValidator queryValidator; + @MockBean + QueryExecutor queryExecutor; + @MockBean + PhenotypicQueryExecutor phenotypicQueryExecutor; + @MockBean + PhenotypicFilterValidator phenotypicFilterValidator; + @MockBean + PhenotypicObservationStore phenotypicObservationStore; + + // Shared processing dependencies + @MockBean + PhenotypeMetaStore phenotypeMetaStore; + @MockBean + ColumnSorter columnSorter; + @MockBean + DictionaryService dictionaryService; + @MockBean + SignUrlService signUrlService; + + @Test + void contextLoads_servicesAreWired() { + assertNotNull(queryService, "QueryService should be wired"); + assertNotNull(queryV3Service, "QueryV3Service should be wired"); + assertNotNull(fileSharingService, "FileSharingService should be wired"); + assertNotNull(fileSharingV3Service, "FileSharingV3Service should be wired"); + } + + @Test + void loggingClientIsInjectedIntoQueryService() { + Object client = ReflectionTestUtils.getField(queryService, "loggingClient"); + assertSame(loggingClient, client, "QueryService.loggingClient should be the mock"); + } + + @Test + void loggingClientIsInjectedIntoQueryV3Service() { + Object client = ReflectionTestUtils.getField(queryV3Service, "loggingClient"); + assertSame(loggingClient, client, "QueryV3Service.loggingClient should be the mock"); + } + + @Test + void loggingClientIsInjectedIntoFileSharingService() { + Object client = ReflectionTestUtils.getField(fileSharingService, "loggingClient"); + assertSame(loggingClient, client, "FileSharingService.loggingClient should be the mock"); + } + + @Test + void loggingClientIsInjectedIntoFileSharingV3Service() { + Object client = ReflectionTestUtils.getField(fileSharingV3Service, "loggingClient"); + assertSame(loggingClient, client, "FileSharingV3Service.loggingClient should be the mock"); + } +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureServiceAuditTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureServiceAuditTest.java new file mode 100644 index 000000000..f34f9aefc --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureServiceAuditTest.java @@ -0,0 +1,164 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + +import java.io.IOException; +import java.util.List; +import java.util.Map; +import java.util.TreeMap; +import java.util.UUID; + +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.processing.*; +import edu.harvard.hms.dbmi.avillach.hpds.processing.audit.AuditAttributes; +import edu.harvard.hms.dbmi.avillach.hpds.processing.upload.SignUrlService; +import edu.harvard.hms.dbmi.avillach.hpds.service.filesharing.FileSharingService; +import edu.harvard.hms.dbmi.avillach.hpds.service.filesharing.TestDataService; +import edu.harvard.hms.dbmi.avillach.hpds.service.util.Paginator; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockedStatic; +import org.springframework.mock.web.MockHttpServletRequest; +import org.springframework.test.util.ReflectionTestUtils; + +class PicSureServiceAuditTest { + + private PicSureService service; + private QueryService queryService; + private AbstractProcessor abstractProcessor; + private MockHttpServletRequest request; + + @BeforeEach + void setup() { + queryService = mock(QueryService.class); + abstractProcessor = mock(AbstractProcessor.class); + service = new PicSureService( + queryService, mock(CountProcessor.class), mock(VariantListProcessor.class), abstractProcessor, mock(Paginator.class), + mock(SignUrlService.class), mock(FileSharingService.class), mock(TestDataService.class) + ); + + request = new MockHttpServletRequest(); + ReflectionTestUtils.setField(service, "httpRequest", request); + } + + @Test + void queryPopulatesResultTypeAndQueryId() throws IOException { + AsyncResult asyncResult = mock(AsyncResult.class); + when(asyncResult.getId()).thenReturn("query-123"); + when(asyncResult.getStatus()).thenReturn(AsyncResult.Status.RUNNING); + when(asyncResult.getQueuedTime()).thenReturn(1000L); + when(asyncResult.getCompletedTime()).thenReturn(0L); + Query mockQuery = mock(Query.class); + when(asyncResult.getQuery()).thenReturn(mockQuery); + when(mockQuery.getId()).thenReturn("internal-id"); + when(queryService.runQuery(any())).thenReturn(asyncResult); + + QueryRequest queryRequest = mock(QueryRequest.class); + when(queryRequest.getQuery()).thenReturn(Map.of("expectedResultType", "COUNT")); + + try (MockedStatic crypto = mockStatic(Crypto.class)) { + crypto.when(() -> Crypto.hasKey(Crypto.DEFAULT_KEY_NAME)).thenReturn(true); + service.query(queryRequest); + } + + Map metadata = AuditAttributes.getMetadata(request); + assertEquals("query-123", metadata.get("query_id")); + assertEquals("COUNT", metadata.get("result_type")); + } + + @Test + void queryResultPopulatesQueryId() throws IOException { + UUID queryId = UUID.randomUUID(); + when(queryService.getResultFor(queryId.toString())).thenReturn(null); + + service.queryResult(queryId, mock(QueryRequest.class)); + + assertEquals(queryId.toString(), AuditAttributes.getMetadata(request).get("query_id")); + } + + @Test + void queryStatusPopulatesQueryId() { + UUID queryId = UUID.randomUUID(); + AsyncResult asyncResult = mock(AsyncResult.class); + when(asyncResult.getStatus()).thenReturn(AsyncResult.Status.RUNNING); + when(asyncResult.getQueuedTime()).thenReturn(1000L); + when(asyncResult.getCompletedTime()).thenReturn(0L); + Query mockQuery = mock(Query.class); + when(asyncResult.getQuery()).thenReturn(mockQuery); + when(mockQuery.getId()).thenReturn("internal-id"); + when(queryService.getStatusFor(queryId.toString())).thenReturn(asyncResult); + + service.queryStatus(queryId, mock(QueryRequest.class)); + + assertEquals(queryId.toString(), AuditAttributes.getMetadata(request).get("query_id")); + } + + @Test + void querySignedUrlPopulatesQueryId() throws IOException { + UUID queryId = UUID.randomUUID(); + when(queryService.getResultFor(queryId.toString())).thenReturn(null); + + service.querySignedURL(queryId, mock(QueryRequest.class)); + + assertEquals(queryId.toString(), AuditAttributes.getMetadata(request).get("query_id")); + } + + @Test + void writeQueryResultPopulatesDataTypeAndResultType() { + Query query = mock(Query.class); + when(query.getExpectedResultType()).thenReturn(ResultType.COUNT); + when(query.getPicSureId()).thenReturn(":)"); + + service.writeQueryResult(query, "phenotypic"); + + Map metadata = AuditAttributes.getMetadata(request); + assertEquals("phenotypic", metadata.get("data_type")); + assertEquals("COUNT", metadata.get("result_type")); + } + + @Test + void searchPopulatesSearchTerm() { + when(abstractProcessor.getDictionary()).thenReturn(new TreeMap<>()); + when(abstractProcessor.getInfoStoreMeta()).thenReturn(List.of()); + + QueryRequest searchRequest = mock(QueryRequest.class); + when(searchRequest.getQuery()).thenReturn("blood pressure"); + + service.search(searchRequest); + + assertEquals("blood pressure", AuditAttributes.getMetadata(request).get("search_term")); + } + + @Test + void searchWithNullQueryDoesNotSetSearchTermOrThrow() { + when(abstractProcessor.getDictionary()).thenReturn(new TreeMap<>()); + + QueryRequest searchRequest = mock(QueryRequest.class); + when(searchRequest.getQuery()).thenReturn(null); + + service.search(searchRequest); + + assertNull(AuditAttributes.getMetadata(request).get("search_term")); + } + + @Test + void searchGenomicConceptValuesPopulatesConceptPath() { + when(abstractProcessor.searchInfoConceptValues(anyString(), anyString())).thenReturn(List.of("val1")); + + Paginator paginator = new Paginator(); + PicSureService serviceWithRealPaginator = new PicSureService( + queryService, mock(CountProcessor.class), mock(VariantListProcessor.class), + abstractProcessor, paginator, mock(SignUrlService.class), mock(FileSharingService.class), + mock(TestDataService.class) + ); + + ReflectionTestUtils.setField(serviceWithRealPaginator, "httpRequest", request); + serviceWithRealPaginator.searchGenomicConceptValues("\\gene\\BRCA1\\", "val", 1, 10); + + assertEquals("\\gene\\BRCA1\\", AuditAttributes.getMetadata(request).get("genomic_concept_path")); + } +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureServiceTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureServiceTest.java new file mode 100644 index 000000000..05bfb1ba5 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureServiceTest.java @@ -0,0 +1,80 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.processing.AbstractProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.CountProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.VariantListProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.upload.SignUrlService; +import edu.harvard.hms.dbmi.avillach.hpds.service.filesharing.FileSharingService; +import edu.harvard.hms.dbmi.avillach.hpds.service.filesharing.TestDataService; +import edu.harvard.hms.dbmi.avillach.hpds.service.util.Paginator; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.mockito.Mockito; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; + + +import java.util.UUID; + +import static org.junit.jupiter.api.Assertions.*; + +@SpringBootTest +class PicSureServiceTest { + + @Autowired + PicSureService subject; + + @MockBean + QueryService queryService; + @MockBean + CountProcessor countProcessor; + @MockBean + VariantListProcessor variantListProcessor; + @MockBean + AbstractProcessor abstractProcessor; + @MockBean + Paginator paginator; + @MockBean + SignUrlService signUrlService; + @MockBean + FileSharingService fileSystemService; + @MockBean + TestDataService testDataService; + + @Test + void shouldUploadTestFile() { + Query query = Mockito.mock(Query.class); + query.setPicSureId(UUID.randomUUID().toString()); + Mockito.when(testDataService.uploadTestFile(query.getPicSureId())).thenReturn(true); + + ResponseEntity actual = subject.writeQueryResult(query, "test_upload"); + Assertions.assertEquals(HttpStatus.OK, actual.getStatusCode()); + } + + @Test + void shouldValidateUUID() { + Query query = Mockito.mock(Query.class); + Mockito.when(query.getExpectedResultType()).thenReturn(ResultType.COUNT); + Mockito.when(query.getPicSureId()).thenReturn(":)"); + ResponseEntity actual = subject.writeQueryResult(query, "patients"); + + Assertions.assertEquals(HttpStatus.BAD_REQUEST, actual.getStatusCode()); + Assertions.assertEquals("The query pic-sure ID is not a UUID", actual.getBody()); + } + + @Test + void should400ForBadResultType() { + Query query = Mockito.mock(Query.class); + Mockito.when(query.getExpectedResultType()).thenReturn(ResultType.COUNT); + Mockito.when(query.getPicSureId()).thenReturn(UUID.randomUUID().toString()); + ResponseEntity actual = subject.writeQueryResult(query, "patients"); + Assertions.assertEquals(HttpStatus.BAD_REQUEST, actual.getStatusCode()); + Assertions.assertEquals("The write endpoint only writes time series dataframes. Fix result type.", actual.getBody()); + + } +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureV3ServiceAuditTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureV3ServiceAuditTest.java new file mode 100644 index 000000000..5de32549b --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureV3ServiceAuditTest.java @@ -0,0 +1,155 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + +import java.io.IOException; +import java.util.List; +import java.util.Map; +import java.util.TreeMap; +import java.util.UUID; + +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import edu.harvard.hms.dbmi.avillach.hpds.processing.audit.AuditAttributes; +import edu.harvard.hms.dbmi.avillach.hpds.processing.upload.SignUrlService; +import edu.harvard.hms.dbmi.avillach.hpds.processing.v3.AsyncResult; +import edu.harvard.hms.dbmi.avillach.hpds.processing.v3.CountV3Processor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.v3.QueryExecutor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.v3.VariantListV3Processor; +import edu.harvard.hms.dbmi.avillach.hpds.service.filesharing.FileSharingV3Service; +import edu.harvard.hms.dbmi.avillach.hpds.service.filesharing.TestDataService; +import edu.harvard.hms.dbmi.avillach.hpds.service.util.Paginator; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockedStatic; +import org.springframework.mock.web.MockHttpServletRequest; +import org.springframework.test.util.ReflectionTestUtils; + +class PicSureV3ServiceAuditTest { + + private PicSureV3Service service; + private QueryV3Service queryService; + private QueryExecutor queryExecutor; + private MockHttpServletRequest request; + + @BeforeEach + void setup() { + queryService = mock(QueryV3Service.class); + queryExecutor = mock(QueryExecutor.class); + service = new PicSureV3Service( + queryService, mock(CountV3Processor.class), mock(VariantListV3Processor.class), queryExecutor, mock(Paginator.class), + mock(SignUrlService.class), mock(FileSharingV3Service.class), mock(TestDataService.class) + ); + + request = new MockHttpServletRequest(); + ReflectionTestUtils.setField(service, "httpRequest", request); + } + + @Test + void queryPopulatesResultTypeAndQueryId() throws IOException { + AsyncResult asyncResult = mock(AsyncResult.class); + when(asyncResult.getId()).thenReturn("query-123"); + when(asyncResult.getStatus()).thenReturn(AsyncResult.Status.RUNNING); + when(asyncResult.getQueuedTime()).thenReturn(1000L); + when(asyncResult.getCompletedTime()).thenReturn(0L); + Query mockQuery = mock(Query.class); + when(asyncResult.getQuery()).thenReturn(mockQuery); + when(mockQuery.id()).thenReturn(UUID.randomUUID()); + when(queryService.runQuery(any())).thenReturn(asyncResult); + + QueryRequest queryRequest = mock(QueryRequest.class); + when(queryRequest.getQuery()).thenReturn(Map.of("expectedResultType", "COUNT")); + + try (MockedStatic crypto = mockStatic(Crypto.class)) { + crypto.when(() -> Crypto.hasKey(Crypto.DEFAULT_KEY_NAME)).thenReturn(true); + service.query(queryRequest); + } + + Map metadata = AuditAttributes.getMetadata(request); + assertEquals("query-123", metadata.get("query_id")); + assertEquals("COUNT", metadata.get("result_type")); + } + + @Test + void queryResultPopulatesQueryId() { + UUID queryId = UUID.randomUUID(); + when(queryService.getResultFor(queryId)).thenReturn(null); + + service.queryResult(queryId, mock(QueryRequest.class)); + + assertEquals(queryId.toString(), AuditAttributes.getMetadata(request).get("query_id")); + } + + @Test + void queryStatusPopulatesQueryId() { + UUID queryId = UUID.randomUUID(); + AsyncResult asyncResult = mock(AsyncResult.class); + when(asyncResult.getStatus()).thenReturn(AsyncResult.Status.RUNNING); + when(asyncResult.getQueuedTime()).thenReturn(1000L); + when(asyncResult.getCompletedTime()).thenReturn(0L); + Query mockQuery = mock(Query.class); + when(asyncResult.getQuery()).thenReturn(mockQuery); + when(mockQuery.id()).thenReturn(UUID.randomUUID()); + when(queryService.getStatusFor(queryId.toString())).thenReturn(asyncResult); + + service.queryStatus(queryId, mock(QueryRequest.class)); + + assertEquals(queryId.toString(), AuditAttributes.getMetadata(request).get("query_id")); + } + + @Test + void querySignedUrlPopulatesQueryId() throws IOException { + UUID queryId = UUID.randomUUID(); + when(queryService.getResultFor(queryId)).thenReturn(null); + + service.querySignedURL(queryId, mock(QueryRequest.class)); + + assertEquals(queryId.toString(), AuditAttributes.getMetadata(request).get("query_id")); + } + + @Test + void writeQueryResultPopulatesDataTypeAndResultType() { + Query query = mock(Query.class); + when(query.expectedResultType()).thenReturn(ResultType.COUNT); + when(query.picsureId()).thenReturn(UUID.randomUUID()); + + service.writeQueryResult(query, "phenotypic"); + + Map metadata = AuditAttributes.getMetadata(request); + assertEquals("phenotypic", metadata.get("data_type")); + assertEquals("COUNT", metadata.get("result_type")); + } + + @Test + void searchPopulatesSearchTerm() { + when(queryExecutor.getDictionary()).thenReturn(new TreeMap<>()); + when(queryExecutor.getInfoStoreMeta()).thenReturn(List.of()); + + QueryRequest searchRequest = mock(QueryRequest.class); + when(searchRequest.getQuery()).thenReturn("blood pressure"); + + service.search(searchRequest); + + assertEquals("blood pressure", AuditAttributes.getMetadata(request).get("search_term")); + } + + @Test + void searchGenomicConceptValuesPopulatesConceptPath() { + when(queryExecutor.searchInfoConceptValues(anyString(), anyString())).thenReturn(List.of("val1")); + + Paginator paginator = new Paginator(); + PicSureV3Service serviceWithRealPaginator = new PicSureV3Service( + queryService, mock(CountV3Processor.class), mock(VariantListV3Processor.class), + queryExecutor, paginator, mock(SignUrlService.class), mock(FileSharingV3Service.class), + mock(TestDataService.class) + ); + + ReflectionTestUtils.setField(serviceWithRealPaginator, "httpRequest", request); + serviceWithRealPaginator.searchGenomicConceptValues("\\gene\\BRCA1\\", "val", 1, 10); + + assertEquals("\\gene\\BRCA1\\", AuditAttributes.getMetadata(request).get("genomic_concept_path")); + } +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/QueryServiceTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/QueryServiceTest.java new file mode 100644 index 000000000..0bf021a53 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/QueryServiceTest.java @@ -0,0 +1,71 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service; + +import de.siegmar.fastcsv.reader.CsvContainer; +import de.siegmar.fastcsv.reader.CsvReader; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.processing.AsyncResult; +import edu.harvard.hms.dbmi.avillach.hpds.test.util.BuildIntegrationTestEnvironment; +import org.apache.commons.io.IOUtils; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.autoconfigure.EnableAutoConfiguration; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.ActiveProfiles; +import org.springframework.test.context.junit.jupiter.SpringExtension; + +import java.io.FileInputStream; +import java.io.IOException; +import java.nio.charset.StandardCharsets; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; + +import static org.junit.jupiter.api.Assertions.*; + +@ExtendWith(SpringExtension.class) +@EnableAutoConfiguration +@SpringBootTest(classes = edu.harvard.hms.dbmi.avillach.hpds.service.HpdsApplication.class) +@ActiveProfiles("integration-test") +class QueryServiceTest { + + @Autowired + private QueryService queryService; + + @BeforeAll + public static void beforeAll() { + BuildIntegrationTestEnvironment instance = BuildIntegrationTestEnvironment.INSTANCE; + } + + @Test + public void dataframeMulti() throws IOException, InterruptedException { + Query query = new Query(); + List variantInfoFilters = new ArrayList<>(); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = Map.of("Gene_with_variant", new String[] {"LOC102723996", "LOC101928576"}); + variantInfoFilters.add(variantInfoFilter); + query.setVariantInfoFilters(variantInfoFilters); + query.setFields(List.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\")); + query.setExpectedResultType(ResultType.DATAFRAME); + + AsyncResult asyncResult = queryService.runQuery(query); + + int retries = 0; + while ( + (AsyncResult.Status.RUNNING.equals(asyncResult.getStatus()) || AsyncResult.Status.PENDING.equals(asyncResult.getStatus())) + && retries < 10 + ) { + retries++; + Thread.sleep(200); + } + + assertEquals(AsyncResult.Status.SUCCESS, asyncResult.getStatus()); + CsvReader csvReader = new CsvReader(); + CsvContainer csvContainer = csvReader.read(asyncResult.getFile(), StandardCharsets.UTF_8); + // 22 plus header + assertEquals(23, csvContainer.getRows().size()); + } + +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSharingServiceTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSharingServiceTest.java new file mode 100644 index 000000000..ff816beb5 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSharingServiceTest.java @@ -0,0 +1,123 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service.filesharing; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.processing.AsyncResult; +import edu.harvard.hms.dbmi.avillach.hpds.processing.VariantListProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.processing.io.ResultWriter; +import edu.harvard.hms.dbmi.avillach.hpds.processing.patient.PatientProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.service.QueryService; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.InjectMocks; +import org.mockito.Mock; +import org.mockito.Mockito; +import org.mockito.junit.jupiter.MockitoExtension; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.autoconfigure.EnableAutoConfiguration; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; + +import java.io.IOException; + +import static org.junit.jupiter.api.Assertions.assertFalse; +import static org.junit.jupiter.api.Assertions.assertTrue; + +@EnableAutoConfiguration +@SpringBootTest(classes = FileSharingService.class) +public class FileSharingServiceTest { + + @MockBean + QueryService queryService; + + @MockBean + FileSystemService fileWriter; + + @MockBean + VariantListProcessor variantListProcessor; + + @MockBean + PatientProcessor patientProcessor; + + @MockBean + ResultWriter resultWriter; + + @MockBean + LoggingClient loggingClient; + + @Autowired + FileSharingService subject; + + @Test + public void shouldCreatePhenotypicData() { + Query query = new Query(); + query.setId("my-id"); + query.setPicSureId("my-ps-id"); + AsyncResult result = new AsyncResult(query, variantListProcessor, resultWriter); + result.setStatus(AsyncResult.Status.SUCCESS); + + Mockito.when(queryService.getResultFor("my-id")).thenReturn(result); + Mockito.when(fileWriter.writeResultToFile("phenotypic_data.csv", result, "my-ps-id")).thenReturn(true); + + boolean actual = subject.createPhenotypicData(query); + + assertTrue(actual); + } + + @Test + public void shouldNotCreatePhenotypicData() { + Query query = new Query(); + query.setId("my-id"); + query.setPicSureId("my-ps-id"); + AsyncResult result = new AsyncResult(query, variantListProcessor, resultWriter); + result.setStatus(AsyncResult.Status.ERROR); + + Mockito.when(queryService.getResultFor("my-id")).thenReturn(result); + + boolean actual = subject.createPhenotypicData(query); + + assertFalse(actual); + } + + @Test + public void shouldCreateGenomicData() throws IOException { + Query query = new Query(); + query.setPicSureId("my-id"); + String vcf = "lol lets put the whole vcf in a string"; + Mockito.when(variantListProcessor.runVcfExcerptQuery(query, true)).thenReturn(vcf); + Mockito.when(fileWriter.writeResultToFile("genomic_data.tsv", vcf, "my-id")).thenReturn(true); + + boolean actual = subject.createGenomicData(query); + + assertTrue(actual); + } + + @Test + public void shouldNotCreateGenomicData() throws IOException { + Query query = new Query(); + query.setPicSureId("my-id"); + Mockito.when(variantListProcessor.runVcfExcerptQuery(query, true)).thenThrow(new IOException("oh no!")); + + boolean actual = subject.createGenomicData(query); + + assertFalse(actual); + } + + @Test + void shouldCreatePatientsList() { + Query query = new Query(); + query.setId("jasdijasd"); + query.setPicSureId("jasdijasd"); + query.setExpectedResultType(ResultType.PATIENTS); + AsyncResult result = new AsyncResult(query, patientProcessor, resultWriter); + result.setStatus(AsyncResult.Status.SUCCESS); + Mockito.when(queryService.getResultFor("jasdijasd")).thenReturn(result); + Mockito.when(fileWriter.writeResultToFile("patients.txt", result, "jasdijasd")).thenReturn(true); + + boolean actual = subject.createPatientList(query); + + Assertions.assertTrue(actual); + } +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSystemServiceTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSystemServiceTest.java new file mode 100644 index 000000000..5911bcbe3 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/FileSystemServiceTest.java @@ -0,0 +1,42 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service.filesharing; + +import org.junit.jupiter.api.Test; +import org.springframework.test.util.ReflectionTestUtils; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import static org.junit.jupiter.api.Assertions.*; + +public class FileSystemServiceTest { + + @Test + public void shouldWriteToFile() throws IOException { + Path dir = Files.createTempDirectory("my-upload-dir"); + FileSystemService subject = new FileSystemService(); + ReflectionTestUtils.setField(subject, "sharingRoot", dir); + ReflectionTestUtils.setField(subject, "enableFileSharing", true); + String fileContent = "I just got an ad that tried to sell a baguette with moz, dressing, " + + "and tomatoes as a healthy lunch, and that's just so far from the truth that it's bugging me. " + + "Like, come on. It's bread and cheese and oil. I don't care how fresh the tomatoes are."; + + boolean actual = subject.writeResultToFile("out.tsv", fileContent, "my-id"); + String actualContent = Files.readString(dir.resolve("my-id/out.tsv")); + + assertTrue(actual); + assertEquals(fileContent, actualContent); + } + + @Test + public void shouldNotWriteToFile() throws IOException { + Path dir = Files.createTempDirectory("my-upload-dir"); + FileSystemService subject = new FileSystemService(); + ReflectionTestUtils.setField(subject, "sharingRoot", dir); + ReflectionTestUtils.setField(subject, "enableFileSharing", false); + + boolean actual = subject.writeResultToFile("out.tsv", "", "my-id"); + + assertFalse(actual); + } +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/TestDataServiceTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/TestDataServiceTest.java new file mode 100644 index 000000000..2d70ff66b --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/filesharing/TestDataServiceTest.java @@ -0,0 +1,30 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service.filesharing; + +import org.junit.jupiter.api.Test; +import org.mockito.Mockito; + +import java.util.UUID; + +import static org.junit.jupiter.api.Assertions.assertTrue; + + +public class TestDataServiceTest { + FileSystemService fileSystemService; + + TestDataService subject; + + @Test + public void shouldCreateTestFileForUpload() { + fileSystemService = Mockito.mock(FileSystemService.class); + subject = new TestDataService(fileSystemService); + + String uuid = UUID.randomUUID().toString(); + Mockito.when(fileSystemService.writeResultToFile("test_data.txt", "This is a disposable test file", uuid.toString())) + .thenReturn(true); + + boolean success = subject.uploadTestFile(uuid); + assertTrue(success); + Mockito.verify(fileSystemService, Mockito.times(1)) + .writeResultToFile("test_data.txt", "This is a disposable test file", uuid.toString()); + } +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/health/HpdsReadinessHealthIndicatorTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/health/HpdsReadinessHealthIndicatorTest.java new file mode 100644 index 000000000..10e83679a --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/health/HpdsReadinessHealthIndicatorTest.java @@ -0,0 +1,45 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service.health; + +import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.ColumnMeta; +import edu.harvard.hms.dbmi.avillach.hpds.processing.AbstractProcessor; +import org.junit.jupiter.api.Test; +import org.springframework.boot.actuate.health.Status; + +import java.util.Set; +import java.util.TreeMap; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.when; + +class HpdsReadinessHealthIndicatorTest { + + @Test + void upWhenPhenotypeDataLoaded() { + AbstractProcessor proc = mock(AbstractProcessor.class); + TreeMap dict = new TreeMap<>(); + dict.put("\\demographics\\AGE\\", mock(ColumnMeta.class)); + when(proc.getDictionary()).thenReturn(dict); + when(proc.getInfoStoreColumns()).thenReturn(Set.of()); + + assertThat(new HpdsReadinessHealthIndicator(proc).health().getStatus()).isEqualTo(Status.UP); + } + + @Test + void upWhenGenomicDataLoaded() { + AbstractProcessor proc = mock(AbstractProcessor.class); + when(proc.getDictionary()).thenReturn(new TreeMap<>()); + when(proc.getInfoStoreColumns()).thenReturn(Set.of("Gene_with_variant")); + + assertThat(new HpdsReadinessHealthIndicator(proc).health().getStatus()).isEqualTo(Status.UP); + } + + @Test + void downWhenNoDataLoaded() { + AbstractProcessor proc = mock(AbstractProcessor.class); + when(proc.getDictionary()).thenReturn(new TreeMap<>()); + when(proc.getInfoStoreColumns()).thenReturn(Set.of()); + + assertThat(new HpdsReadinessHealthIndicator(proc).health().getStatus()).isEqualTo(Status.DOWN); + } +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/util/PaginatorTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/util/PaginatorTest.java new file mode 100644 index 000000000..4cf7614f8 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/util/PaginatorTest.java @@ -0,0 +1,95 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service.util; + +import edu.harvard.dbmi.avillach.domain.PaginatedSearchResult; +import org.junit.jupiter.api.Test; + +import java.util.List; +import java.util.stream.Collectors; +import java.util.stream.IntStream; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertThrows; + +public class PaginatorTest { + + private final Paginator paginator = new Paginator(); + + @Test + public void paginate_validParams() { + List values = IntStream.range(0, 50).boxed().map(String::valueOf).collect(Collectors.toList()); + PaginatedSearchResult paginatedSearchResult = paginator.paginate(values, 1, 20); + assertEquals(50, paginatedSearchResult.getTotal()); + assertEquals(1, paginatedSearchResult.getPage()); + assertEquals(IntStream.range(0, 20).boxed().map(String::valueOf).collect(Collectors.toList()), paginatedSearchResult.getResults()); + } + + @Test + public void paginate_lastPage() { + List values = IntStream.range(0, 50).boxed().map(String::valueOf).collect(Collectors.toList()); + PaginatedSearchResult paginatedSearchResult = paginator.paginate(values, 3, 20); + assertEquals(50, paginatedSearchResult.getTotal()); + assertEquals(3, paginatedSearchResult.getPage()); + assertEquals(IntStream.range(40, 50).boxed().map(String::valueOf).collect(Collectors.toList()), paginatedSearchResult.getResults()); + } + + + @Test + public void paginate_middlePage() { + List values = IntStream.range(0, 50).boxed().map(String::valueOf).collect(Collectors.toList()); + PaginatedSearchResult paginatedSearchResult = paginator.paginate(values, 2, 20); + assertEquals(50, paginatedSearchResult.getTotal()); + assertEquals(2, paginatedSearchResult.getPage()); + assertEquals(IntStream.range(20, 40).boxed().map(String::valueOf).collect(Collectors.toList()), paginatedSearchResult.getResults()); + } + + @Test + public void paginate_pageOutOfBounds() { + List values = IntStream.range(0, 50).boxed().map(String::valueOf).collect(Collectors.toList()); + PaginatedSearchResult paginatedSearchResult = paginator.paginate(values, 5, 20); + assertEquals(50, paginatedSearchResult.getTotal()); + assertEquals(5, paginatedSearchResult.getPage()); + assertEquals(List.of(), paginatedSearchResult.getResults()); + } + + @Test + public void paginate_noResults() { + List values = List.of(); + PaginatedSearchResult paginatedSearchResult = paginator.paginate(values, 1, 20); + assertEquals(0, paginatedSearchResult.getTotal()); + assertEquals(1, paginatedSearchResult.getPage()); + assertEquals(List.of(), paginatedSearchResult.getResults()); + } + + @Test + public void paginate_invalidPageZero() { + assertThrows(IllegalArgumentException.class, () -> { + List values = List.of(); + paginator.paginate(values, 0, 20); + }); + } + + @Test + public void paginate_invalidPageNegative() { + assertThrows(IllegalArgumentException.class, () -> { + List values = List.of(); + paginator.paginate(values, -2, 20); + }); + + } + + @Test + public void paginate_invalidSizeZero() { + assertThrows(IllegalArgumentException.class, () -> { + List values = List.of(); + paginator.paginate(values, 1, 0); + }); + } + + @Test + public void paginate_invalidSizeNegative() { + assertThrows(IllegalArgumentException.class, () -> { + List values = List.of(); + paginator.paginate(values, 1, -5); + }); + } +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/v3/QueryServiceTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/v3/QueryServiceTest.java new file mode 100644 index 000000000..7889ba227 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/service/v3/QueryServiceTest.java @@ -0,0 +1,99 @@ +package edu.harvard.hms.dbmi.avillach.hpds.service.v3; + +import de.siegmar.fastcsv.reader.CsvContainer; +import de.siegmar.fastcsv.reader.CsvReader; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.GenomicFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicFilterType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import edu.harvard.hms.dbmi.avillach.hpds.processing.v3.AsyncResult; +import edu.harvard.hms.dbmi.avillach.hpds.service.HpdsApplication; +import edu.harvard.hms.dbmi.avillach.hpds.service.QueryV3Service; +import edu.harvard.hms.dbmi.avillach.hpds.test.util.BuildIntegrationTestEnvironment; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.autoconfigure.EnableAutoConfiguration; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.ActiveProfiles; +import org.springframework.test.context.junit.jupiter.SpringExtension; + +import java.io.IOException; +import java.nio.charset.StandardCharsets; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +@ExtendWith(SpringExtension.class) +@EnableAutoConfiguration +@SpringBootTest(classes = HpdsApplication.class) +@ActiveProfiles("integration-test") +class QueryServiceTest { + + @Autowired + private QueryV3Service queryService; + + @BeforeAll + public static void beforeAll() { + BuildIntegrationTestEnvironment instance = BuildIntegrationTestEnvironment.INSTANCE; + } + + @Test + public void dataframeMulti() throws IOException, InterruptedException { + Query query = new Query( + List.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\"), List.of(), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", null, 35.0, 45.0, null), + List.of(new GenomicFilter("Gene_with_variant", List.of("LOC102723996", "LOC101928576"), null, null)), ResultType.DATAFRAME, + null, null + ); + + AsyncResult asyncResult = queryService.runQuery(query); + + int retries = 0; + while ( + (AsyncResult.Status.RUNNING.equals(asyncResult.getStatus()) || AsyncResult.Status.PENDING.equals(asyncResult.getStatus())) + && retries < 10 + ) { + retries++; + Thread.sleep(200); + } + + assertEquals(AsyncResult.Status.SUCCESS, asyncResult.getStatus()); + CsvReader csvReader = new CsvReader(); + CsvContainer csvContainer = csvReader.read(asyncResult.getFile(), StandardCharsets.UTF_8); + // 22 plus header + assertEquals(8, csvContainer.getRows().size()); + } + + @Test + public void runQuery_dataframeSelectInvalidConcept_doNotFail() throws IOException, InterruptedException { + Query query = new Query( + List.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", "\\open_access-1000Genomes\\data\\NOT_A_CONCEPT_PATH\\"), List.of(), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", null, 35.0, 45.0, null), + List.of(new GenomicFilter("Gene_with_variant", List.of("LOC102723996", "LOC101928576"), null, null)), ResultType.DATAFRAME, + null, null + ); + + AsyncResult asyncResult = queryService.runQuery(query); + + int retries = 0; + while ( + (AsyncResult.Status.RUNNING.equals(asyncResult.getStatus()) || AsyncResult.Status.PENDING.equals(asyncResult.getStatus())) + && retries < 10 + ) { + retries++; + Thread.sleep(200); + } + + assertEquals(AsyncResult.Status.SUCCESS, asyncResult.getStatus()); + CsvReader csvReader = new CsvReader(); + CsvContainer csvContainer = csvReader.read(asyncResult.getFile(), StandardCharsets.UTF_8); + // 22 plus header + assertEquals(8, csvContainer.getRows().size()); + } + +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/AbstractProcessorIntegrationTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/AbstractProcessorIntegrationTest.java new file mode 100644 index 000000000..f3eab7dd6 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/AbstractProcessorIntegrationTest.java @@ -0,0 +1,437 @@ +package edu.harvard.hms.dbmi.avillach.hpds.test; + +import com.google.common.collect.Sets; +import edu.harvard.hms.dbmi.avillach.hpds.processing.AbstractProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.test.util.BuildIntegrationTestEnvironment; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Filter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; + +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.autoconfigure.EnableAutoConfiguration; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.ActiveProfiles; +import org.springframework.test.context.junit.jupiter.SpringExtension; + +import java.util.*; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; + + +@ExtendWith(SpringExtension.class) +@EnableAutoConfiguration +@SpringBootTest(classes = edu.harvard.hms.dbmi.avillach.hpds.service.HpdsApplication.class) +@ActiveProfiles("integration-test") +public class AbstractProcessorIntegrationTest { + + @Autowired + private AbstractProcessor abstractProcessor; + + @BeforeAll + public static void beforeAll() { + BuildIntegrationTestEnvironment instance = BuildIntegrationTestEnvironment.INSTANCE; + } + + @Test + public void getPatientSubsetForQuery_validEmptyQuery() { + Query query = new Query(); + List variantInfoFilters = new ArrayList<>(); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = Map.of(); + variantInfoFilter.numericVariantInfoFilters = Map.of(); + variantInfoFilters.add(variantInfoFilter); + query.setVariantInfoFilters(variantInfoFilters); + + Set idList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(4978, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_validGeneWithVariantQuery() { + Query query = new Query(); + List variantInfoFilters = new ArrayList<>(); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = Map.of("Gene_with_variant", new String[] {"LOC102723996"}); + variantInfoFilters.add(variantInfoFilter); + query.setVariantInfoFilters(variantInfoFilters); + + Set idList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(16, idList.size()); + assertTrue(idList.contains(200972)); + assertTrue(idList.contains(200971)); + assertTrue(idList.contains(200975)); + } + + @Test + public void getPatientSubsetForQuery_validGeneWithMultipleVariantQuery() { + Query query = new Query(); + List variantInfoFilters = new ArrayList<>(); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = Map.of("Gene_with_variant", new String[] {"LOC102723996", "LOC101928576"}); + variantInfoFilters.add(variantInfoFilter); + query.setVariantInfoFilters(variantInfoFilters); + + Set idList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(22, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_validGeneWithVariantQueryAndNumericQuery() { + Query query = new Query(); + List variantInfoFilters = new ArrayList<>(); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = Map.of("Gene_with_variant", new String[] {"LOC102723996"}); + variantInfoFilters.add(variantInfoFilter); + query.setVariantInfoFilters(variantInfoFilters); + query.setNumericFilters(Map.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", new Filter.DoubleFilter(35.0, 45.0))); + + Set idList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(4, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_validNumericPhenotypicQuery() { + Query query = new Query(); + query.setNumericFilters(Map.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", new Filter.DoubleFilter(35.0, 45.0))); + + Set idList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(562, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_validCategoricalPhenotypicQuery() { + Query query = new Query(); + query.setCategoryFilters(Map.of("\\open_access-1000Genomes\\data\\POPULATION NAME\\", new String[] {"Finnish"})); + Set idList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(102, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_validMultipleValueCategoricalPhenotypicQuery() { + Query query = new Query(); + query.setCategoryFilters(Map.of("\\open_access-1000Genomes\\data\\POPULATION NAME\\", new String[] {"Finnish"})); + Set finnishIdList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(102, finnishIdList.size()); + + query = new Query(); + query.setCategoryFilters(Map.of("\\open_access-1000Genomes\\data\\POPULATION NAME\\", new String[] {"Colombian"})); + Set columbianIdList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(153, columbianIdList.size()); + + query = new Query(); + query.setCategoryFilters(Map.of("\\open_access-1000Genomes\\data\\POPULATION NAME\\", new String[] {"Finnish", "Colombian"})); + Set bothIdList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(255, bothIdList.size()); + assertEquals(Sets.union(finnishIdList, columbianIdList), bothIdList); + } + + @Test + public void getPatientSubsetForQuery_validMultipleCategoricalPhenotypicQuery() { + Query query = new Query(); + query.setCategoryFilters(Map.of("\\open_access-1000Genomes\\data\\POPULATION NAME\\", new String[] {"Finnish"})); + Set finnishIdList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(102, finnishIdList.size()); + + query = new Query(); + query.setCategoryFilters(Map.of("\\open_access-1000Genomes\\data\\SEX\\", new String[] {"female"})); + Set femaleIdList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(2330, femaleIdList.size()); + + query = new Query(); + query.setCategoryFilters( + Map.of( + "\\open_access-1000Genomes\\data\\POPULATION NAME\\", new String[] {"Finnish"}, "\\open_access-1000Genomes\\data\\SEX\\", + new String[] {"female"} + ) + ); + Set bothIdList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(64, bothIdList.size()); + assertEquals(Sets.intersection(finnishIdList, femaleIdList), bothIdList); + } + + @Test + public void getPatientSubsetForQuery_validMultiplePhenotypicQuery() { + Query query = new Query(); + query.setNumericFilters(Map.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", new Filter.DoubleFilter(35.0, 45.0))); + Set ageIdList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(562, ageIdList.size()); + + query = new Query(); + query.setCategoryFilters(Map.of("\\open_access-1000Genomes\\data\\SEX\\", new String[] {"male"})); + Set sexIdList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(2648, sexIdList.size()); + + query = new Query(); + query.setNumericFilters(Map.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", new Filter.DoubleFilter(35.0, 45.0))); + query.setCategoryFilters(Map.of("\\open_access-1000Genomes\\data\\SEX\\", new String[] {"male"})); + Set bothIdList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(269, bothIdList.size()); + assertEquals(Sets.intersection(ageIdList, sexIdList), bothIdList); + } + + @Test + public void getPatientSubsetForQuery_validMultipleNumericPhenotypicQuery() { + Query query = new Query(); + query.setNumericFilters(Map.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", new Filter.DoubleFilter(35.0, 45.0))); + Set ageIdList = abstractProcessor.getPatientSubsetForQuery(query); + + query = new Query(); + query.setNumericFilters(Map.of("\\open_access-1000Genomes\\data\\SYNTHETIC_HEIGHT\\", new Filter.DoubleFilter(180.0, null))); + Set heightIdList = abstractProcessor.getPatientSubsetForQuery(query); + + query = new Query(); + query.setNumericFilters( + Map.of( + "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", new Filter.DoubleFilter(35.0, 45.0), + "\\open_access-1000Genomes\\data\\SYNTHETIC_HEIGHT\\", new Filter.DoubleFilter(180.0, null) + ) + ); + Set bothIdList = abstractProcessor.getPatientSubsetForQuery(query); + + assertEquals(Sets.intersection(ageIdList, heightIdList), bothIdList); + } + + @Test + public void getPatientSubsetForQuery_validRequiredVariant() { + Query query = new Query(); + query.setRequiredFields(List.of("chr21,5032061,A,G,LOC102723996,missense_variant")); + + Set idList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(7, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_invalidRequiredVariant() { + Query query = new Query(); + query.setRequiredFields(List.of("chr21,5061,A,G")); + + Set idList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(0, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_validRequiredVariantOldFormat() { + Query query = new Query(); + query.setRequiredFields(List.of("chr21,5032061,A,G")); + + Set idList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(8, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_invalidVariantSpecQuery() { + Query query = new Query(); + query.setCategoryFilters(Map.of("chr21,5061,AAAA,GGGG", new String[] {"0/1", "1/1"})); + + Set idList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(0, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_validRequiredVariantOldFormatCategoryFilter() { + Query query = new Query(); + query.setCategoryFilters(Map.of("chr21,5032061,A,G", new String[] {"0/1", "1/1"})); + + Set idList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(8, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_validRequiredVariantOldFormatCategoryFilterHomozygous() { + Query query = new Query(); + query.setCategoryFilters(Map.of("chr21,5032061,A,G", new String[] {"1/1"})); + + Set idList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(3, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_validRequiredVariantOldFormatCategoryFilterHeterozygous() { + Query query = new Query(); + query.setCategoryFilters(Map.of("chr21,5032061,A,G", new String[] {"0/1"})); + + Set idList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(5, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_verifySeparateQueriesAreEquivalent() { + Query query = new Query(); + query.setNumericFilters(Map.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", new Filter.DoubleFilter(35.0, 45.0))); + + Set numericIdList = abstractProcessor.getPatientSubsetForQuery(query); + + query = new Query(); + query.setRequiredFields(List.of("chr21,5032061,A,G")); + + Set variantIdList = abstractProcessor.getPatientSubsetForQuery(query); + + + query = new Query(); + query.setNumericFilters(Map.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", new Filter.DoubleFilter(35.0, 45.0))); + query.setRequiredFields(List.of("chr21,5032061,A,G")); + + Set bothIdList = abstractProcessor.getPatientSubsetForQuery(query); + + assertEquals(Sets.intersection(numericIdList, variantIdList), bothIdList); + } + + + @Test + public void getPatientSubsetForQuery_validAnyRecordOfQuery() { + Query query = new Query(); + query.setAnyRecordOf(List.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\")); + + Set anyRecordOfList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(1126, anyRecordOfList.size()); + + query = new Query(); + query.setAnyRecordOf( + List.of( + "\\open_access-1000Genomes\\data\\THE HUMAN GENOME STRUCTURAL VARIATION CONSORTIUM\\", + "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\" + ) + ); + + anyRecordOfList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(4978, anyRecordOfList.size()); + } + + public void getPatientSubsetForQuery_validAnyRecordOfAndCategoryQuery() { + Query query = new Query(); + query.setCategoryFilters(Map.of("\\open_access-1000Genomes\\data\\POPULATION NAME\\", new String[] {"Yoruba"})); + + Set yorubaIdList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(208, yorubaIdList.size()); + + query = new Query(); + query.setAnyRecordOf(List.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\")); + + Set anyRecordOf = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(1126, anyRecordOf.size()); + + + query = new Query(); + query.setCategoryFilters(Map.of("\\open_access-1000Genomes\\data\\POPULATION NAME\\", new String[] {"Yoruba"})); + query.setAnyRecordOf(List.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\")); + + Set bothIdList = abstractProcessor.getPatientSubsetForQuery(query); + + assertEquals(Sets.intersection(yorubaIdList, anyRecordOf), bothIdList); + } + + @Test + public void getPatientSubsetForQuery_validAnyRecordOfMultiQuery() { + Query query = new Query(); + query.setAnyRecordOfMulti( + List.of( + List.of( + "\\open_access-1000Genomes\\data\\THE HUMAN GENOME STRUCTURAL VARIATION CONSORTIUM\\", + "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\" + ) + ) + ); + + Set anyRecordOfList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(4978, anyRecordOfList.size()); + + query = new Query(); + query.setAnyRecordOfMulti( + List.of( + List.of("\\open_access-1000Genomes\\data\\THE HUMAN GENOME STRUCTURAL VARIATION CONSORTIUM\\"), + List.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", "\\open_access-1000Genomes\\data\\SYNTHETIC_SEX\\") + ) + ); + + anyRecordOfList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(1126, anyRecordOfList.size()); + } + + + @Test + public void getVariantList_validGeneWithVariantQuery() { + Query query = new Query(); + List variantInfoFilters = new ArrayList<>(); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = Map.of("Gene_with_variant", new String[] {"LOC102723996"}); + variantInfoFilters.add(variantInfoFilter); + query.setVariantInfoFilters(variantInfoFilters); + + Collection variantList = abstractProcessor.getVariantList(query); + assertEquals(4, variantList.size()); + } + + + @Test + public void getVariantList_invalidGeneQuery() { + Query query = new Query(); + List variantInfoFilters = new ArrayList<>(); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = Map.of("Gene_with_variant", new String[] {"NOTAGENE"}); + variantInfoFilters.add(variantInfoFilter); + query.setVariantInfoFilters(variantInfoFilters); + + Collection variantList = abstractProcessor.getVariantList(query); + assertEquals(0, variantList.size()); + } + + @Test + public void getVariantList_validGeneWithMultipleVariantQuery() { + Query query = new Query(); + List variantInfoFilters = new ArrayList<>(); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = Map.of("Gene_with_variant", new String[] {"LOC102723996", "LOC101928576"}); + variantInfoFilters.add(variantInfoFilter); + query.setVariantInfoFilters(variantInfoFilters); + + Collection variantList = abstractProcessor.getVariantList(query); + assertEquals(5, variantList.size()); + } + + + @Test + public void getVariantList_validGeneWithVariantQueryAndNumericQuery() { + Query query = new Query(); + List variantInfoFilters = new ArrayList<>(); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = Map.of("Gene_with_variant", new String[] {"LOC102723996"}); + variantInfoFilters.add(variantInfoFilter); + query.setVariantInfoFilters(variantInfoFilters); + query.setNumericFilters(Map.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", new Filter.DoubleFilter(35.0, 45.0))); + + + Collection variantList = abstractProcessor.getVariantList(query); + assertEquals(2, variantList.size()); + } + + @Test + public void getVariantList_validContinuousGenomicFilter() { + Query query = new Query(); + List variantInfoFilters = new ArrayList<>(); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = Map.of(); + variantInfoFilter.numericVariantInfoFilters = Map.of("Variant_frequency_in_gnomAD", new Filter.FloatFilter(0.0001345F, 0.0001347f)); + variantInfoFilters.add(variantInfoFilter); + query.setVariantInfoFilters(variantInfoFilters); + + Collection variantList = abstractProcessor.getVariantList(query); + assertEquals(4, variantList.size()); + } + + @Test + public void getPatientSubsetForQuery_validContinuousGenomicFilter() { + Query query = new Query(); + List variantInfoFilters = new ArrayList<>(); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = Map.of(); + variantInfoFilter.numericVariantInfoFilters = Map.of("Variant_frequency_in_gnomAD", new Filter.FloatFilter(0.0001345F, 0.0001347f)); + variantInfoFilters.add(variantInfoFilter); + query.setVariantInfoFilters(variantInfoFilters); + + Set idList = abstractProcessor.getPatientSubsetForQuery(query); + assertEquals(8, idList.size()); + } +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/BucketIndexBySampleTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/BucketIndexBySampleTest.java new file mode 100644 index 000000000..c6ea4a8a2 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/BucketIndexBySampleTest.java @@ -0,0 +1,226 @@ +package edu.harvard.hms.dbmi.avillach.hpds.test; + +import java.io.IOException; +import java.util.ArrayList; +import java.util.Collection; +import java.util.HashSet; +import java.util.List; +import java.util.Set; + + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.BucketIndexBySample; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantStore; +import edu.harvard.hms.dbmi.avillach.hpds.test.util.BuildIntegrationTestEnvironment; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; + +import static org.springframework.test.util.AssertionErrors.*; + +/** + * These tests are in the ETL project so that we can read in data from disk each time instead of storing binfiles that may become outdated. + * + * the BucketIndexBySample.filterVariantSetForPatientSet method removes variants base on the patent BUCKET MASK; just because a patient does + * not have a particular variant doesn't mean it will be filtered out e.g., when a patient has a different variant in the same bucket. + * + * Filtering the specific variants is typically done by the calling function after filtering out the unneeded buckets. + * + * @author nchu + * + */ +public class BucketIndexBySampleTest { + + private static final String STORAGE_DIR = "./target/all/"; + + private static BucketIndexBySample bucketIndexBySampleChr4; + private static BucketIndexBySample bucketIndexBySampleChr20; + private static BucketIndexBySample bucketIndexBySampleChr21; + + // Some known variant specs from the input file. + // Some known variant specs from the input file. These have been designed for testing partially overlapping specs + private static final String spec1 = "chr4,9856624,CAAAAA,C,TVP23A,splice_acceptor_variant"; + private static final String spec2 = "chr4,9856624,CAAA,C,TVP23A,splice_acceptor_variant"; + private static final String spec3 = "chr4,9856624,CA,C,TVP23A,splice_acceptor_variant"; + private static final String spec4 = "chr4,9856624,C,CA,TVP23A,splice_acceptor_variant"; + private static final String spec5 = "chr4,9856624,CAAAAA,CA,TVP23A,splice_acceptor_variant"; + + private static final String spec6 = "chr21,5032061,A,G,LOC102723996,missense_variant"; + private static final String spec6b = "chr21,5032061,A,G,ABCDEF123456,synonymous_variant"; + private static final String spec7 = "chr21,5033914,A,G,LOC102723996,missense_variant"; + private static final String spec8 = "chr21,5033988,C,G,LOC102723996,synonymous_variant"; + private static final String spec9 = "chr21,5034028,C,T,LOC102723996,missense_variant"; + + + // these parameters to the BucketIndexBySample methods are configured by each test + Set variantSet; + List patientSet; + + @BeforeAll + public static void initializeBinfile() throws Exception { + BuildIntegrationTestEnvironment instance = BuildIntegrationTestEnvironment.INSTANCE; + VariantStore variantStoreChr4 = VariantStore.readInstance(STORAGE_DIR + "chr4/"); + bucketIndexBySampleChr4 = new BucketIndexBySample(variantStoreChr4, STORAGE_DIR + "chr4/"); + + VariantStore variantStoreChr20 = VariantStore.readInstance(STORAGE_DIR + "chr20/"); + bucketIndexBySampleChr20 = new BucketIndexBySample(variantStoreChr20, STORAGE_DIR + "chr20/"); + + VariantStore variantStoreChr21 = VariantStore.readInstance(STORAGE_DIR + "chr21/"); + bucketIndexBySampleChr21 = new BucketIndexBySample(variantStoreChr21, STORAGE_DIR + "chr21/"); + } + + @BeforeEach + public void setUpTest() { + // start with fresh, empty collections + variantSet = new HashSet<>(); + patientSet = new ArrayList<>(); + } + + @Test + public void test_filterVariantSetForPatientSet_noPatients() throws IOException { + variantSet.add(spec1); + variantSet.add(spec2); + variantSet.add(spec3); + + Collection filteredVariantSet = bucketIndexBySampleChr4.filterVariantSetForPatientSet(variantSet, patientSet); + + assertTrue("Empty Patient List should filter out all variants", filteredVariantSet.isEmpty()); + } + + @Test + public void test_filterVariantSetForPatientSet_noVariants() throws IOException { + patientSet.add(200392); + patientSet.add(200689); + patientSet.add(200972); + + Collection filteredVariantSet = bucketIndexBySampleChr4.filterVariantSetForPatientSet(variantSet, patientSet); + + assertTrue("Empty Variant Set should remain empty", filteredVariantSet.isEmpty()); + } + + @Test + public void test_filterVariantSetForPatientSet_VariantsWithoutPatientsLastBucket() throws IOException { + System.out.println("test_filterVariantSetForPatientSet_VariantsWithoutPatientsLastBucket"); + + variantSet.add(spec1); + variantSet.add(spec2); + variantSet.add(spec3); + variantSet.add(spec4); + variantSet.add(spec5); + + patientSet.add(200706); + patientSet.add(200709); + + Collection filteredVariantSet = bucketIndexBySampleChr4.filterVariantSetForPatientSet(variantSet, patientSet); + + assertTrue("Patients should not match any variants in the list", filteredVariantSet.isEmpty()); + } + + @Test + public void test_filterVariantSetForPatientSet_PatientsWithNoVariantsFirstBucket() throws IOException { + System.out.println("test_filterVariantSetForPatientSet_PatientsWithNoVariantsFirstBucket"); + + variantSet.add(spec6); + variantSet.add(spec6b); + + patientSet.add(197506); + patientSet.add(197508); + patientSet.add(197509); + + Collection filteredVariantSet = bucketIndexBySampleChr4.filterVariantSetForPatientSet(variantSet, patientSet); + + assertTrue("Patients should not match any variants in the list", filteredVariantSet.isEmpty()); + } + + @Test + public void filterVariantSetForPatientSet_variantsDoNotExist_returnNoVariants() throws IOException { + System.out.println("test_filterVariantSetForPatientSet_PatientsWithNoVariantsFirstBucket"); + + variantSet.add(spec6); + variantSet.add(spec6b); + + patientSet.add(197506); + patientSet.add(197508); + patientSet.add(197509); + + Collection filteredVariantSet = bucketIndexBySampleChr4.filterVariantSetForPatientSet(variantSet, patientSet); + + assertTrue("Patients should not match any variants in the list", filteredVariantSet.isEmpty()); + } + + @Test + public void test_filterVariantSetForPatientSet_allValidFirstBucket() throws IOException { + System.out.println("test_filterVariantSetForPatientSet_allValidFirstBucket"); + + variantSet.add(spec6); + variantSet.add(spec6b); + + patientSet.add(200392); + patientSet.add(200689); + patientSet.add(200972); + + Collection filteredVariantSet = bucketIndexBySampleChr21.filterVariantSetForPatientSet(variantSet, patientSet); + + assertEquals("No variants should be filtered out", 2, filteredVariantSet.size()); + } + + @Test + public void test_filterVariantSetForPatientSet_allValidFirstBucketWithNoCall() throws IOException { + System.out.println("test_filterVariantSetForPatientSet_allValidFirstBucket"); + + variantSet.add("chr20,5032061,A,G,ABC1,missense_variant"); + variantSet.add("chr20,5032061,A,G,DEF1,synonymous_variant"); + + patientSet.add(200392); + patientSet.add(200689); + patientSet.add(200972); + + Collection filteredVariantSet = bucketIndexBySampleChr20.filterVariantSetForPatientSet(variantSet, patientSet); + + assertEquals("No variants should be filtered out", 2, filteredVariantSet.size()); + } + + @Test + public void test_filterVariantSetForPatientSet_allValidDifferentPatients() throws IOException { + System.out.println("test_filterVariantSetForPatientSet_allValidDifferentPatients"); + + variantSet.add(spec1); + variantSet.add(spec4); + variantSet.add(spec5); + variantSet.add(spec7); + + patientSet.add(200194); + patientSet.add(200450); + patientSet.add(200710); + patientSet.add(198206); + + Collection filteredVariantSet = bucketIndexBySampleChr4.filterVariantSetForPatientSet(variantSet, patientSet); + filteredVariantSet.addAll(bucketIndexBySampleChr21.filterVariantSetForPatientSet(variantSet, patientSet)); + + assertEquals("No variants should be filtered out", (long) 4, (long) filteredVariantSet.size()); + } + + @Test + @Disabled + public void test_filterVariantSetForPatientSet_someValidDifferentPatients() throws IOException { + System.out.println("test_filterVariantSetForPatientSet_allValidDifferentPatients"); + + // specs 1-5 are in the last bucket + variantSet.add(spec1); + variantSet.add(spec4); + variantSet.add(spec5); + variantSet.add(spec8); + variantSet.add(spec9); // none + + patientSet.add(3); + patientSet.add(9); + patientSet.add(10); + + Collection filteredVariantSet = bucketIndexBySampleChr4.filterVariantSetForPatientSet(variantSet, patientSet); + filteredVariantSet.addAll(bucketIndexBySampleChr21.filterVariantSetForPatientSet(variantSet, patientSet)); + + assertEquals("One variant should be filtered out", (long) 4, (long) filteredVariantSet.size()); + assertFalse("Spec 9 should have been filtered out", filteredVariantSet.contains(spec9)); + } + +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/CountProcessorIntegrationTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/CountProcessorIntegrationTest.java new file mode 100644 index 000000000..2f26218a9 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/CountProcessorIntegrationTest.java @@ -0,0 +1,67 @@ +package edu.harvard.hms.dbmi.avillach.hpds.test; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.processing.CountProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.test.util.BuildIntegrationTestEnvironment; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.autoconfigure.EnableAutoConfiguration; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.ActiveProfiles; +import org.springframework.test.context.junit.jupiter.SpringExtension; + +import java.util.List; +import java.util.Map; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +@ExtendWith(SpringExtension.class) +@EnableAutoConfiguration +@SpringBootTest(classes = edu.harvard.hms.dbmi.avillach.hpds.service.HpdsApplication.class) +@ActiveProfiles("integration-test") +public class CountProcessorIntegrationTest { + + @Autowired + private CountProcessor countProcessor; + + @BeforeAll + public static void beforeAll() { + BuildIntegrationTestEnvironment instance = BuildIntegrationTestEnvironment.INSTANCE; + } + + @Test + public void runCategoryCrossCounts_twoFilters() { + Query query = new Query(); + query.setCrossCountFields(List.of()); + query.setCategoryFilters( + Map.of( + "\\open_access-1000Genomes\\data\\SEX\\", new String[] {"male", "female"}, + "\\open_access-1000Genomes\\data\\POPULATION NAME\\", new String[] {"Finnish"} + ) + ); + query.setExpectedResultType(ResultType.CROSS_COUNT); + + Map> crossCounts = countProcessor.runCategoryCrossCounts(query); + assertEquals(2, crossCounts.size()); + assertEquals(38, crossCounts.get("\\open_access-1000Genomes\\data\\SEX\\").get("male")); + assertEquals(64, crossCounts.get("\\open_access-1000Genomes\\data\\SEX\\").get("female")); + assertEquals(102, crossCounts.get("\\open_access-1000Genomes\\data\\POPULATION NAME\\").get("Finnish")); + } + + @Test + public void runCategoryCrossCounts_snpFilter() { + Query query = new Query(); + query.setCategoryFilters( + Map.of("chr21,5032061,A,G", new String[] {"0/1", "1/1"}, "\\open_access-1000Genomes\\data\\SEX\\", new String[] {"male"}) + ); + query.setExpectedResultType(ResultType.CROSS_COUNT); + + Map> crossCounts = countProcessor.runCategoryCrossCounts(query); + assertEquals(1, crossCounts.size()); + assertEquals(2, crossCounts.get("\\open_access-1000Genomes\\data\\SEX\\").get("male")); + } + +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/CountV3ProcessorIntegrationTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/CountV3ProcessorIntegrationTest.java new file mode 100644 index 000000000..ac2ba4df8 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/CountV3ProcessorIntegrationTest.java @@ -0,0 +1,311 @@ +package edu.harvard.hms.dbmi.avillach.hpds.test; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.*; +import edu.harvard.hms.dbmi.avillach.hpds.processing.v3.CountV3Processor; +import edu.harvard.hms.dbmi.avillach.hpds.test.util.BuildIntegrationTestEnvironment; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.autoconfigure.EnableAutoConfiguration; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.ActiveProfiles; +import org.springframework.test.context.junit.jupiter.SpringExtension; + +import java.util.List; +import java.util.Map; +import java.util.Set; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertFalse; +import static org.junit.jupiter.api.Assertions.assertTrue; + +@ExtendWith(SpringExtension.class) +@EnableAutoConfiguration +@SpringBootTest(classes = edu.harvard.hms.dbmi.avillach.hpds.service.HpdsApplication.class) +@ActiveProfiles("integration-test") +public class CountV3ProcessorIntegrationTest { + + @Autowired + private CountV3Processor countProcessor; + + @BeforeAll + public static void beforeAll() { + BuildIntegrationTestEnvironment instance = BuildIntegrationTestEnvironment.INSTANCE; + } + + @Test + public void runCategoryCrossCounts_multipleConceptsNoFilters() { + Query query = new Query( + List.of("\\open_access-1000Genomes\\data\\SEX\\", "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\"), List.of(), null, null, + ResultType.CROSS_COUNT, null, null + ); + + Map crossCountsMap = countProcessor.runCrossCounts(query); + assertEquals(2, crossCountsMap.size()); + assertEquals(4978, crossCountsMap.get("\\open_access-1000Genomes\\data\\SEX\\")); + assertEquals(1126, crossCountsMap.get("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\")); + } + + @Test + public void runCategoryCrossCounts_unknownConceptNoFilters() { + Query query = new Query( + List.of("\\open_access-1000Genomes\\data\\SEX\\", "\\open_access-1000Genomes\\data\\NOT_REAL_DOESNT_EXIST\\"), List.of(), null, + null, ResultType.CROSS_COUNT, null, null + ); + + Map crossCountsMap = countProcessor.runCrossCounts(query); + assertEquals(2, crossCountsMap.size()); + assertEquals(4978, crossCountsMap.get("\\open_access-1000Genomes\\data\\SEX\\")); + assertEquals(0, crossCountsMap.get("\\open_access-1000Genomes\\data\\NOT_REAL_DOESNT_EXIST\\")); + } + + @Test + public void runCategoryCrossCounts_multipleConceptsWithFilters() { + PhenotypicFilter sexFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SEX\\", Set.of("male"), null, null, null); + PhenotypicFilter populationFilter = + new PhenotypicFilter(PhenotypicFilterType.REQUIRED, "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", null, null, null, null); + + PhenotypicSubquery phenotypicSubquery = new PhenotypicSubquery(null, List.of(sexFilter, populationFilter), Operator.AND); + + Query query = new Query( + List.of("\\open_access-1000Genomes\\data\\SEX\\", "\\open_access-1000Genomes\\data\\SYNTHETIC_HEIGHT\\"), List.of(), + phenotypicSubquery, null, ResultType.CROSS_COUNT, null, null + ); + + Map crossCountsMap = countProcessor.runCrossCounts(query); + assertEquals(2, crossCountsMap.size()); + assertEquals(551, crossCountsMap.get("\\open_access-1000Genomes\\data\\SEX\\")); + assertEquals(551, crossCountsMap.get("\\open_access-1000Genomes\\data\\SYNTHETIC_HEIGHT\\")); + } + + @Test + public void runCategoryCrossCounts_conceptsNoResults() { + PhenotypicFilter sexFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SEX\\", Set.of("vulcan"), null, null, null); + PhenotypicFilter populationFilter = new PhenotypicFilter( + PhenotypicFilterType.REQUIRED, "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", null, null, 500.0, null + ); + + PhenotypicSubquery phenotypicSubquery = new PhenotypicSubquery(null, List.of(sexFilter, populationFilter), Operator.AND); + + Query query = new Query( + List.of("\\open_access-1000Genomes\\data\\SEX\\", "\\open_access-1000Genomes\\data\\SYNTHETIC_HEIGHT\\"), List.of(), + phenotypicSubquery, null, ResultType.CROSS_COUNT, null, null + ); + + Map crossCountsMap = countProcessor.runCrossCounts(query); + assertEquals(2, crossCountsMap.size()); + assertEquals(0, crossCountsMap.get("\\open_access-1000Genomes\\data\\SEX\\")); + assertEquals(0, crossCountsMap.get("\\open_access-1000Genomes\\data\\SYNTHETIC_HEIGHT\\")); + } + + @Test + public void runCategoryCrossCounts_twoFilters() { + PhenotypicFilter sexFilter = new PhenotypicFilter( + PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SEX\\", Set.of("male", "female"), null, null, null + ); + PhenotypicFilter populationFilter = new PhenotypicFilter( + PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\POPULATION NAME\\", Set.of("Finnish"), null, null, null + ); + + PhenotypicSubquery phenotypicSubquery = new PhenotypicSubquery(null, List.of(sexFilter, populationFilter), Operator.AND); + Query query = new Query(List.of(), List.of(), phenotypicSubquery, null, ResultType.COUNT, null, null); + + Map> crossCounts = countProcessor.runCategoryCrossCounts(query); + assertEquals(2, crossCounts.size()); + assertEquals(38, crossCounts.get("\\open_access-1000Genomes\\data\\SEX\\").get("male")); + assertEquals(64, crossCounts.get("\\open_access-1000Genomes\\data\\SEX\\").get("female")); + assertEquals(102, crossCounts.get("\\open_access-1000Genomes\\data\\POPULATION NAME\\").get("Finnish")); + } + + /** + * With an OR clause the cohort is broader than any single filter's values, so a cross count reports each concept's full distribution + * across that cohort: SEX shows female (present via the OR'd POPULATION branch) alongside the called-out male, and POPULATION shows the + * populations of the OR'd males alongside the called-out Finnish. + */ + @Test + public void runCategoryCrossCounts_twoFiltersOr_reportsFullCohortDistribution() { + String sexPath = "\\open_access-1000Genomes\\data\\SEX\\"; + String populationPath = "\\open_access-1000Genomes\\data\\POPULATION NAME\\"; + PhenotypicFilter sexFilter = new PhenotypicFilter(PhenotypicFilterType.FILTER, sexPath, Set.of("male"), null, null, null); + PhenotypicFilter populationFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, populationPath, Set.of("Finnish"), null, null, null); + + PhenotypicSubquery phenotypicSubquery = new PhenotypicSubquery(null, List.of(sexFilter, populationFilter), Operator.OR); + Query query = new Query(List.of(), List.of(), phenotypicSubquery, null, ResultType.COUNT, null, null); + + Map> crossCounts = countProcessor.runCategoryCrossCounts(query); + + assertEquals(2, crossCounts.size()); + Map sexCounts = crossCounts.get(sexPath); + // female is in the cohort via the OR'd POPULATION branch, so it appears even though only male was filtered + assertEquals(Set.of("male", "female"), sexCounts.keySet()); + assertEquals(2648, sexCounts.get("male")); + assertTrue(sexCounts.get("female") > 0, "females in the OR cohort should be reported"); + + Map populationCounts = crossCounts.get(populationPath); + // the OR'd males bring in their own populations alongside the called-out Finnish + assertEquals(102, populationCounts.get("Finnish")); + assertTrue(populationCounts.size() > 1, "populations of the OR'd males should be reported"); + } + + @Test + public void runCategoryCrossCounts_snpFilter() { + PhenotypicFilter sexFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SEX\\", Set.of("male"), null, null, null); + Query query = new Query( + List.of(), List.of(), sexFilter, List.of(new GenomicFilter("chr21,5032061,A,G", List.of("0/1", "1/1"), null, null)), + ResultType.COUNT, null, null + ); + + Map> crossCounts = countProcessor.runCategoryCrossCounts(query); + assertEquals(1, crossCounts.size()); + assertEquals(2, crossCounts.get("\\open_access-1000Genomes\\data\\SEX\\").get("male")); + } + + /** + * Two categorical filters on the SAME concept path, OR'd together. With the v3 query a user can add sex=male OR sex=female as two + * separate filters; the result must be a SINGLE chart entry for SEX that contains BOTH values, not just the last filter's value. + */ + @Test + public void runCategoryCrossCounts_duplicateCategoricalSamePathOr() { + String sexPath = "\\open_access-1000Genomes\\data\\SEX\\"; + PhenotypicFilter maleFilter = new PhenotypicFilter(PhenotypicFilterType.FILTER, sexPath, Set.of("male"), null, null, null); + PhenotypicFilter femaleFilter = new PhenotypicFilter(PhenotypicFilterType.FILTER, sexPath, Set.of("female"), null, null, null); + PhenotypicSubquery subquery = new PhenotypicSubquery(null, List.of(maleFilter, femaleFilter), Operator.OR); + Query query = new Query(List.of(), List.of(), subquery, null, ResultType.COUNT, null, null); + + Map> crossCounts = countProcessor.runCategoryCrossCounts(query); + + assertEquals(1, crossCounts.size()); + Map sexCounts = crossCounts.get(sexPath); + assertEquals(Set.of("male", "female"), sexCounts.keySet()); + assertEquals(2648, sexCounts.get("male")); + assertEquals(2330, sexCounts.get("female")); + } + + /** + * Two categorical filters on the same path, AND'd with disjoint values (sex=male AND sex=female) yields an empty cohort. The single SEX + * entry must still list both values, each at zero, rather than dropping one to a map-key collision. + */ + @Test + public void runCategoryCrossCounts_duplicateCategoricalSamePathAndDisjoint() { + String sexPath = "\\open_access-1000Genomes\\data\\SEX\\"; + PhenotypicFilter maleFilter = new PhenotypicFilter(PhenotypicFilterType.FILTER, sexPath, Set.of("male"), null, null, null); + PhenotypicFilter femaleFilter = new PhenotypicFilter(PhenotypicFilterType.FILTER, sexPath, Set.of("female"), null, null, null); + PhenotypicSubquery subquery = new PhenotypicSubquery(null, List.of(maleFilter, femaleFilter), Operator.AND); + Query query = new Query(List.of(), List.of(), subquery, null, ResultType.COUNT, null, null); + + Map> crossCounts = countProcessor.runCategoryCrossCounts(query); + + assertEquals(1, crossCounts.size()); + Map sexCounts = crossCounts.get(sexPath); + assertEquals(Set.of("male", "female"), sexCounts.keySet()); + assertEquals(0, sexCounts.get("male")); + assertEquals(0, sexCounts.get("female")); + } + + /** + * A REQUIRED filter and a value filter on the same path, AND'd, narrow the cohort to males. female has no members in that cohort and + * was not explicitly selected, so it is omitted (it is not "called out" by a value filter). + */ + @Test + public void runCategoryCrossCounts_requiredPlusFilterSamePath() { + String sexPath = "\\open_access-1000Genomes\\data\\SEX\\"; + PhenotypicFilter requiredSex = new PhenotypicFilter(PhenotypicFilterType.REQUIRED, sexPath, null, null, null, null); + PhenotypicFilter maleFilter = new PhenotypicFilter(PhenotypicFilterType.FILTER, sexPath, Set.of("male"), null, null, null); + PhenotypicSubquery subquery = new PhenotypicSubquery(null, List.of(requiredSex, maleFilter), Operator.AND); + Query query = new Query(List.of(), List.of(), subquery, null, ResultType.COUNT, null, null); + + Map> crossCounts = countProcessor.runCategoryCrossCounts(query); + + assertEquals(1, crossCounts.size()); + Map sexCounts = crossCounts.get(sexPath); + assertEquals(Set.of("male"), sexCounts.keySet()); + assertEquals(2648, sexCounts.get("male")); + } + + /** + * Mirrors the reported bug: a value filter (SEX=male) OR'd with a REQUIRED filter on a different concept. The REQUIRED branch pulls + * females into the cohort, so the SEX chart must show female alongside male rather than male alone. + */ + @Test + public void runCategoryCrossCounts_valueFilterOrRequiredOnOtherConcept_showsUnfilteredValues() { + String sexPath = "\\open_access-1000Genomes\\data\\SEX\\"; + String populationPath = "\\open_access-1000Genomes\\data\\POPULATION NAME\\"; + PhenotypicFilter maleFilter = new PhenotypicFilter(PhenotypicFilterType.FILTER, sexPath, Set.of("male"), null, null, null); + PhenotypicFilter requiredPopulation = new PhenotypicFilter(PhenotypicFilterType.REQUIRED, populationPath, null, null, null, null); + + PhenotypicSubquery subquery = new PhenotypicSubquery(null, List.of(maleFilter, requiredPopulation), Operator.OR); + Query query = new Query(List.of(), List.of(), subquery, null, ResultType.COUNT, null, null); + + Map> crossCounts = countProcessor.runCategoryCrossCounts(query); + + Map sexCounts = crossCounts.get(sexPath); + assertEquals(Set.of("male", "female"), sexCounts.keySet()); + assertEquals(2648, sexCounts.get("male")); + assertTrue(sexCounts.get("female") > 0, "females pulled into the cohort by the REQUIRED branch should be reported"); + } + + /** + * A REQUIRED filter on a continuous concept must not produce a categorical cross-count entry: continuous concepts have no categorical + * distribution and are handled by runContinuousCrossCounts instead. + */ + @Test + public void runCategoryCrossCounts_requiredContinuousConcept_isExcluded() { + String agePath = "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\"; + PhenotypicFilter requiredAge = new PhenotypicFilter(PhenotypicFilterType.REQUIRED, agePath, null, null, null, null); + Query query = new Query(List.of(), List.of(), requiredAge, null, ResultType.COUNT, null, null); + + Map> crossCounts = countProcessor.runCategoryCrossCounts(query); + + assertFalse(crossCounts.containsKey(agePath), "a continuous concept should not appear in categorical cross counts"); + } + + /** + * Two numeric range filters on the same path, OR'd, must produce a single entry whose keys are the UNION of the two ranges, not a + * widened [min,max] span: a value sitting in the gap between the ranges must NOT appear. + */ + @Test + public void runContinuousCrossCounts_duplicateRangesSamePathOr() { + String agePath = "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\"; + PhenotypicFilter youngFilter = new PhenotypicFilter(PhenotypicFilterType.FILTER, agePath, null, 31.0, 35.0, null); + PhenotypicFilter oldFilter = new PhenotypicFilter(PhenotypicFilterType.FILTER, agePath, null, 55.0, 62.0, null); + PhenotypicSubquery subquery = new PhenotypicSubquery(null, List.of(youngFilter, oldFilter), Operator.OR); + Query query = new Query(List.of(), List.of(), subquery, null, ResultType.COUNT, null, null); + + Map> crossCounts = countProcessor.runContinuousCrossCounts(query); + + assertEquals(1, crossCounts.size()); + Map ageCounts = crossCounts.get(agePath); + assertTrue(ageCounts.containsKey(31.0), "low range endpoint should be present"); + assertTrue(ageCounts.containsKey(62.0), "high range endpoint should be present"); + assertFalse(ageCounts.containsKey(44.0), "a value in the gap between the two ranges must not appear"); + } + + /** + * A continuous range filter OR'd with a filter on another concept: the age distribution must include ages outside the filtered [55,62] + * range, because the OR'd males (of all ages) are in the cohort. The range only constrains the cohort, not which values are displayed. + */ + @Test + public void runContinuousCrossCounts_rangeOrOtherConcept_showsValuesOutsideRange() { + String agePath = "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\"; + String sexPath = "\\open_access-1000Genomes\\data\\SEX\\"; + PhenotypicFilter oldFilter = new PhenotypicFilter(PhenotypicFilterType.FILTER, agePath, null, 55.0, 62.0, null); + PhenotypicFilter maleFilter = new PhenotypicFilter(PhenotypicFilterType.FILTER, sexPath, Set.of("male"), null, null, null); + PhenotypicSubquery subquery = new PhenotypicSubquery(null, List.of(oldFilter, maleFilter), Operator.OR); + Query query = new Query(List.of(), List.of(), subquery, null, ResultType.COUNT, null, null); + + Map> crossCounts = countProcessor.runContinuousCrossCounts(query); + + Map ageCounts = crossCounts.get(agePath); + assertTrue( + ageCounts.keySet().stream().anyMatch(age -> age < 55.0), + "ages below the filtered range should appear via the OR'd males in the cohort" + ); + } + +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/QueryExecutorIntegrationTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/QueryExecutorIntegrationTest.java new file mode 100644 index 000000000..306aa5e38 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/QueryExecutorIntegrationTest.java @@ -0,0 +1,544 @@ +package edu.harvard.hms.dbmi.avillach.hpds.test; + +import com.google.common.collect.Sets; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.*; +import edu.harvard.hms.dbmi.avillach.hpds.processing.v3.QueryExecutor; +import edu.harvard.hms.dbmi.avillach.hpds.test.util.BuildIntegrationTestEnvironment; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.autoconfigure.EnableAutoConfiguration; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.ActiveProfiles; +import org.springframework.test.context.junit.jupiter.SpringExtension; + +import java.util.*; + +import static org.junit.jupiter.api.Assertions.*; + +@ExtendWith(SpringExtension.class) +@EnableAutoConfiguration +@SpringBootTest(classes = edu.harvard.hms.dbmi.avillach.hpds.service.HpdsApplication.class) +@ActiveProfiles("integration-test") +public class QueryExecutorIntegrationTest { + + private static final Logger log = LoggerFactory.getLogger(QueryExecutorIntegrationTest.class); + + @Autowired + private QueryExecutor queryExecutor; + + @BeforeAll + public static void beforeAll() { + BuildIntegrationTestEnvironment instance = BuildIntegrationTestEnvironment.INSTANCE; + } + + // Existing tests from AbstractProcessor + + @Test + public void getPatientSubsetForQuery_validEmptyQuery() { + Query query = new Query( + List.of(), List.of(), null, List.of(new GenomicFilter("Gene_with_variant", List.of("LOC102723996"), null, null)), + ResultType.COUNT, null, null + ); + + Set idList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(16, idList.size()); + assertTrue(idList.contains(200972)); + assertTrue(idList.contains(200971)); + assertTrue(idList.contains(200975)); + } + + @Test + public void getPatientSubsetForQuery_validGeneWithMultipleVariantQuery() { + Query query = new Query( + List.of(), List.of(), null, + List.of(new GenomicFilter("Gene_with_variant", List.of("LOC102723996", "LOC101928576"), null, null)), ResultType.COUNT, null, + null + ); + + Set idList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(22, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_validGeneWithVariantQueryAndNumericQuery() { + Query query = new Query( + List.of(), List.of(), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", null, 35.0, 45.0, null), + List.of(new GenomicFilter("Gene_with_variant", List.of("LOC102723996"), null, null)), ResultType.COUNT, null, null + ); + + Set idList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(4, idList.size()); + } + + + + @Test + public void getPatientSubsetForQuery_validNumericPhenotypicQuery() { + Query query = new Query( + List.of(), List.of(), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", null, 35.0, 45.0, null), + null, ResultType.COUNT, null, null + ); + + Set idList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(562, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_validCategoricalPhenotypicQuery() { + Query query = new Query( + List.of(), List.of(), + new PhenotypicFilter( + PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\POPULATION NAME\\", Set.of("Finnish"), null, null, null + ), null, ResultType.COUNT, null, null + ); + Set idList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(102, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_nonExistentCategoricalPhenotypicQuery() { + Query query = new Query( + List.of(), List.of(), + new PhenotypicFilter( + PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\NOTAREAL_CONCEPT\\", Set.of("Finnish"), null, null, null + ), null, ResultType.COUNT, null, null + ); + Set idList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(0, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_validMultipleValueCategoricalPhenotypicQuery() { + Query query = new Query( + List.of(), List.of(), + new PhenotypicFilter( + PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\POPULATION NAME\\", Set.of("Finnish"), null, null, null + ), null, ResultType.COUNT, null, null + ); + Set finnishIdList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(102, finnishIdList.size()); + + query = new Query( + List.of(), List.of(), + new PhenotypicFilter( + PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\POPULATION NAME\\", Set.of("Colombian"), null, null, null + ), null, ResultType.COUNT, null, null + ); + Set columbianIdList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(153, columbianIdList.size()); + + query = new Query( + List.of(), List.of(), + new PhenotypicFilter( + PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\POPULATION NAME\\", Set.of("Finnish", "Colombian"), null, + null, null + ), null, ResultType.COUNT, null, null + ); + Set bothIdList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(255, bothIdList.size()); + assertEquals(Sets.union(finnishIdList, columbianIdList), bothIdList); + } + + @Test + public void getPatientSubsetForQuery_validMultipleCategoricalPhenotypicQuery() { + PhenotypicFilter finnishFilter = new PhenotypicFilter( + PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\POPULATION NAME\\", Set.of("Finnish"), null, null, null + ); + Query query = new Query(List.of(), List.of(), finnishFilter, null, ResultType.COUNT, null, null); + Set finnishIdList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(102, finnishIdList.size()); + + PhenotypicFilter femaleFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SEX\\", Set.of("female"), null, null, null); + query = new Query(List.of(), List.of(), femaleFilter, null, ResultType.COUNT, null, null); + Set femaleIdList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(2330, femaleIdList.size()); + + PhenotypicSubquery phenotypicSubquery = new PhenotypicSubquery(null, List.of(finnishFilter, femaleFilter), Operator.AND); + query = new Query(List.of(), List.of(), phenotypicSubquery, null, ResultType.COUNT, null, null); + Set bothIdList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(64, bothIdList.size()); + assertEquals(Sets.intersection(finnishIdList, femaleIdList), bothIdList); + } + + @Test + public void getPatientSubsetForQuery_validMultiplePhenotypicQuery() { + PhenotypicFilter ageFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", null, 35.0, 45.0, null); + Query query = new Query(List.of(), List.of(), ageFilter, null, ResultType.COUNT, null, null); + Set ageIdList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(562, ageIdList.size()); + + PhenotypicFilter maleFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SEX\\", Set.of("male"), null, null, null); + query = new Query(List.of(), List.of(), maleFilter, null, ResultType.COUNT, null, null); + Set sexIdList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(2648, sexIdList.size()); + + PhenotypicSubquery phenotypicSubquery = new PhenotypicSubquery(null, List.of(ageFilter, maleFilter), Operator.AND); + query = new Query(List.of(), List.of(), phenotypicSubquery, null, ResultType.COUNT, null, null); + Set bothIdList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(269, bothIdList.size()); + assertEquals(Sets.intersection(ageIdList, sexIdList), bothIdList); + } + + @Test + public void getPatientSubsetForQuery_validMultipleNumericPhenotypicQuery() { + PhenotypicFilter ageFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", null, 35.0, 45.0, null); + Query query = new Query(List.of(), List.of(), ageFilter, null, ResultType.COUNT, null, null); + Set ageIdList = queryExecutor.getPatientSubsetForQuery(query); + + PhenotypicFilter heightFilter = new PhenotypicFilter( + PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SYNTHETIC_HEIGHT\\", null, 180.0, null, null + ); + query = new Query(List.of(), List.of(), heightFilter, null, ResultType.COUNT, null, null); + Set heightIdList = queryExecutor.getPatientSubsetForQuery(query); + + PhenotypicSubquery phenotypicSubquery = new PhenotypicSubquery(null, List.of(ageFilter, heightFilter), Operator.AND); + query = new Query(List.of(), List.of(), phenotypicSubquery, null, ResultType.COUNT, null, null); + Set bothIdList = queryExecutor.getPatientSubsetForQuery(query); + + assertEquals(Sets.intersection(ageIdList, heightIdList), bothIdList); + } + + @Test + public void getPatientSubsetForQuery_validRequiredVariant() { + Query query = new Query( + List.of(), List.of(), null, List.of(new GenomicFilter("chr21,5032061,A,G,LOC102723996,missense_variant", null, null, null)), + ResultType.COUNT, null, null + ); + + Set idList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(7, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_invalidRequiredVariant() { + Query query = new Query( + List.of(), List.of(), null, List.of(new GenomicFilter("chr21,5061,A,G", null, null, null)), ResultType.COUNT, null, null + ); + + Set idList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(0, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_validRequiredVariantOldFormat() { + Query query = new Query( + List.of(), List.of(), null, List.of(new GenomicFilter("chr21,5032061,A,G", null, null, null)), ResultType.COUNT, null, null + ); + + Set idList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(8, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_invalidVariantSpecQuery() { + Query query = new Query( + List.of(), List.of(), null, List.of(new GenomicFilter("chr21,5061,AAAA,GGGG", List.of("0/1", "1/1"), null, null)), + ResultType.COUNT, null, null + ); + + Set idList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(0, idList.size()); + } + + + @Test + public void getPatientSubsetForQuery_validRequiredVariantOldFormatCategoryFilter() { + Query query = new Query( + List.of(), List.of(), null, List.of(new GenomicFilter("chr21,5032061,A,G", List.of("0/1", "1/1"), null, null)), + ResultType.COUNT, null, null + ); + + Set idList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(8, idList.size()); + } + + + @Test + public void getPatientSubsetForQuery_validRequiredVariantOldFormatCategoryFilterHomozygous() { + Query query = new Query( + List.of(), List.of(), null, List.of(new GenomicFilter("chr21,5032061,A,G", List.of("1/1"), null, null)), ResultType.COUNT, null, + null + ); + + Set idList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(3, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_validRequiredVariantOldFormatCategoryFilterHeterozygous() { + Query query = new Query( + List.of(), List.of(), null, List.of(new GenomicFilter("chr21,5032061,A,G", List.of("0/1"), null, null)), ResultType.COUNT, null, + null + ); + + Set idList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(5, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_verifySeparateQueriesAreEquivalent() { + Query query = new Query( + List.of(), List.of(), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", null, 35.0, 45.0, null), + List.of(), ResultType.COUNT, null, null + ); + + Set numericIdList = queryExecutor.getPatientSubsetForQuery(query); + + query = new Query( + List.of(), List.of(), null, List.of(new GenomicFilter("chr21,5032061,A,G", List.of("0/1"), null, null)), ResultType.COUNT, null, + null + ); + + Set variantIdList = queryExecutor.getPatientSubsetForQuery(query); + + + query = new Query( + List.of(), List.of(), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", null, 35.0, 45.0, null), + List.of(new GenomicFilter("chr21,5032061,A,G", List.of("0/1"), null, null)), ResultType.COUNT, null, null + ); + + Set bothIdList = queryExecutor.getPatientSubsetForQuery(query); + + assertEquals(Sets.intersection(numericIdList, variantIdList), bothIdList); + } + + + @Test + public void getVariantList_validGeneWithVariantQuery() { + Query query = new Query( + List.of(), List.of(), null, List.of(new GenomicFilter("Gene_with_variant", List.of("LOC102723996"), null, null)), + ResultType.COUNT, null, null + ); + + Collection variantList = queryExecutor.getVariantList(query); + assertEquals(4, variantList.size()); + } + + @Test + public void getVariantList_invalidGeneQuery() { + Query query = new Query( + List.of(), List.of(), null, List.of(new GenomicFilter("Gene_with_variant", List.of("NOTAGENE"), null, null)), ResultType.COUNT, + null, null + ); + + Collection variantList = queryExecutor.getVariantList(query); + assertEquals(0, variantList.size()); + } + + @Test + public void getVariantList_validGeneWithMultipleVariantQuery() { + Query query = new Query( + List.of(), List.of(), null, + List.of(new GenomicFilter("Gene_with_variant", List.of("LOC102723996", "LOC101928576"), null, null)), ResultType.COUNT, null, + null + ); + + Collection variantList = queryExecutor.getVariantList(query); + assertEquals(5, variantList.size()); + } + + @Test + public void getVariantList_validGeneWithVariantQueryAndNumericQuery() { + Query query = new Query( + List.of(), List.of(), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", null, 35.0, 45.0, null), + List.of(new GenomicFilter("Gene_with_variant", List.of("LOC102723996"), null, null)), ResultType.COUNT, null, null + ); + + + Collection variantList = queryExecutor.getVariantList(query); + assertEquals(2, variantList.size()); + } + + @Test + public void getVariantList_validContinuousGenomicFilter() { + Query query = new Query( + List.of(), List.of(), null, List.of(new GenomicFilter("Variant_frequency_in_gnomAD", null, 0.0001345F, 0.0001347f)), + ResultType.COUNT, null, null + ); + + Collection variantList = queryExecutor.getVariantList(query); + assertEquals(4, variantList.size()); + } + + @Test + public void getPatientSubsetForQuery_validContinuousGenomicFilter() { + Query query = new Query( + List.of(), List.of(), null, List.of(new GenomicFilter("Variant_frequency_in_gnomAD", null, 0.0001345F, 0.0001347f)), + ResultType.COUNT, null, null + ); + + Set idList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(8, idList.size()); + } + + // New tests, testing OR functionality + + + @Test + public void getPatientSubsetForQuery_validPhenotypicOrQuery() { + PhenotypicFilter finnishFilter = new PhenotypicFilter( + PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\POPULATION NAME\\", Set.of("Finnish"), null, null, null + ); + Query query = new Query(List.of(), List.of(), finnishFilter, null, ResultType.COUNT, null, null); + Set finnishIdList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(102, finnishIdList.size()); + + PhenotypicFilter ageFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", null, 35.0, 45.0, null); + query = new Query(List.of(), List.of(), ageFilter, null, ResultType.COUNT, null, null); + Set femaleIdList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(562, femaleIdList.size()); + + PhenotypicSubquery phenotypicSubquery = new PhenotypicSubquery(null, List.of(finnishFilter, ageFilter), Operator.OR); + query = new Query(List.of(), List.of(), phenotypicSubquery, null, ResultType.COUNT, null, null); + Set bothIdList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(Sets.union(finnishIdList, femaleIdList), bothIdList); + } + + @Test + public void getPatientSubsetForQuery_validPhenotypicRequiredQuery() { + PhenotypicFilter yorubaFilter = new PhenotypicFilter( + PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\POPULATION NAME\\", Set.of("Yoruba"), null, null, null + ); + Query query = new Query(List.of(), List.of(), yorubaFilter, null, ResultType.COUNT, null, null); + Set yorubaIdList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(208, yorubaIdList.size()); + + PhenotypicFilter ageFilter = + new PhenotypicFilter(PhenotypicFilterType.REQUIRED, "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", null, null, null, null); + query = new Query(List.of(), List.of(), ageFilter, null, ResultType.COUNT, null, null); + Set ageIdList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(1126, ageIdList.size()); + + PhenotypicSubquery phenotypicSubquery = new PhenotypicSubquery(null, List.of(yorubaFilter, ageFilter), Operator.AND); + query = new Query(List.of(), List.of(), phenotypicSubquery, null, ResultType.COUNT, null, null); + Set bothIdList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(Sets.intersection(yorubaIdList, ageIdList), bothIdList); + } + + + @Test + public void getPatientSubsetForQuery_validPhenotypicQueryWithAuthorizationFilter() { + PhenotypicFilter finnishFilter = new PhenotypicFilter( + PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\POPULATION NAME\\", Set.of("Finnish"), null, null, null + ); + Query query = new Query(List.of(), List.of(), finnishFilter, null, ResultType.COUNT, null, null); + Set finnishIdList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(102, finnishIdList.size()); + + PhenotypicFilter femaleFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SEX\\", Set.of("female"), null, null, null); + query = new Query(List.of(), List.of(), femaleFilter, null, ResultType.COUNT, null, null); + Set femaleIdList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(2330, femaleIdList.size()); + + + AuthorizationFilter authorizationFilter = + new AuthorizationFilter("\\open_access-1000Genomes\\data\\POPULATION NAME\\", Set.of("Finnish")); + query = new Query(List.of(), List.of(authorizationFilter), femaleFilter, null, ResultType.COUNT, null, null); + Set bothIdList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(64, bothIdList.size()); + assertEquals(Sets.intersection(finnishIdList, femaleIdList), bothIdList); + } + + @Test + public void getPatientSubsetForQuery_validAnyRecordOfPhenotypicQuery_returnsPatients() { + Query query = new Query( + List.of(), List.of(), + new PhenotypicFilter(PhenotypicFilterType.ANY_RECORD_OF, "\\open_access-1000Genomes\\", null, null, null, null), null, + ResultType.COUNT, null, null + ); + + Set idList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(4978, idList.size()); + } + + @Test + public void getPatientSubsetForQuery_nonMatchingAnyRecordOfPhenotypicQuery_returnsNoPatients() { + Query query = new Query( + List.of(), List.of(), + new PhenotypicFilter(PhenotypicFilterType.ANY_RECORD_OF, "\\study-does-not-exist\\demographics\\", null, null, null, null), + null, ResultType.COUNT, null, null + ); + + Set idList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(0, idList.size()); + } + + @Test + public void getAllConceptPaths_validQuery_returnPaths() { + AuthorizationFilter authorizationFilter = new AuthorizationFilter("\\open_access-1000Genomes\\data\\AUTH_CONCEPT\\", Set.of("ABC")); + + PhenotypicFilter anyRecordOfFilter = + new PhenotypicFilter(PhenotypicFilterType.ANY_RECORD_OF, "\\open_access-1000Genomes\\data\\POPULATION", null, null, null, null); + PhenotypicFilter filterFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\AGE\\", null, null, null, null); + PhenotypicFilter requiredFilter = + new PhenotypicFilter(PhenotypicFilterType.REQUIRED, "\\open_access-1000Genomes\\data\\HEIGHT\\", null, null, null, null); + PhenotypicSubquery phenotypicClause = + new PhenotypicSubquery(null, List.of(anyRecordOfFilter, filterFilter, requiredFilter), Operator.AND); + Query query = new Query( + List.of("\\open_access-1000Genomes\\data\\SEX\\"), List.of(authorizationFilter), phenotypicClause, null, ResultType.COUNT, null, + null + ); + + SequencedSet allConceptPaths = queryExecutor.getAllConceptPaths(query); + assertTrue( + allConceptPaths.containsAll( + Set.of( + "\\open_access-1000Genomes\\data\\SEX\\", "\\open_access-1000Genomes\\data\\AGE\\", + "\\open_access-1000Genomes\\data\\HEIGHT\\", "\\open_access-1000Genomes\\data\\POPULATION CODE\\", + "\\open_access-1000Genomes\\data\\POPULATION NAME\\", "\\open_access-1000Genomes\\data\\POPULATION ELASTIC ID\\" + ) + ) + ); + assertFalse(allConceptPaths.contains("\\open_access-1000Genomes\\data\\AUTH_CONCEPT\\")); + assertEquals(6, allConceptPaths.size()); + } + + @Test + public void getAllConceptPaths_emptyQuery_returnEmpty() { + Query query = new Query(List.of(), List.of(), null, null, ResultType.COUNT, null, null); + + SequencedSet allConceptPaths = queryExecutor.getAllConceptPaths(query); + assertEquals(0, allConceptPaths.size()); + } + + @Test + public void getPatientSubsetForQuery_validLargeGenomicQuery() { + Query query = new Query( + List.of(), List.of(), + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", null, 35.0, 45.0, null), + List.of( + new GenomicFilter("Gene_with_variant", List.of("LOC102723996", "LOC101928576", "ABC1", "ABC2", "ABC3"), null, null), + new GenomicFilter( + "Variant_consequence_calculated", + List.of( + "splice_acceptor_variant", "splice_donor_variant", "stop_gained", "frameshift_variant", "stop_lost", "start_lost", + "inframe_insertion", "inframe_deletion", "missense_variant", "protein_altering_variant", "splice_region_variant", + "splice_donor_5th_base_variant", "splice_donor_region_variant", "splice_polypyrimidine_tract_variant", + "incomplete_terminal_codon_variant", "start_retained_variant", "stop_retained_variant", "synonymous_variant" + ), null, null + ) + ), ResultType.COUNT, null, null + ); + + Set idList = queryExecutor.getPatientSubsetForQuery(query); + assertEquals(14, idList.size()); + } + +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/TimeseriesProcessorIntegrationTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/TimeseriesProcessorIntegrationTest.java new file mode 100644 index 000000000..970d64123 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/TimeseriesProcessorIntegrationTest.java @@ -0,0 +1,85 @@ +package edu.harvard.hms.dbmi.avillach.hpds.test; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.processing.AsyncResult; +import edu.harvard.hms.dbmi.avillach.hpds.processing.io.CsvWriter; +import edu.harvard.hms.dbmi.avillach.hpds.processing.timeseries.TimeseriesProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.test.util.BuildIntegrationTestEnvironment; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.autoconfigure.EnableAutoConfiguration; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.ActiveProfiles; +import org.springframework.test.context.junit.jupiter.SpringExtension; + +import java.io.File; +import java.io.IOException; +import java.nio.file.Files; +import java.util.List; +import java.util.Map; + +import static org.junit.jupiter.api.Assertions.*; + +@ExtendWith(SpringExtension.class) +@EnableAutoConfiguration +@SpringBootTest(classes = edu.harvard.hms.dbmi.avillach.hpds.service.HpdsApplication.class) +@ActiveProfiles("integration-test") +public class TimeseriesProcessorIntegrationTest { + + @Autowired + private TimeseriesProcessor timeseriesProcessor; + + @BeforeAll + public static void beforeAll() { + BuildIntegrationTestEnvironment instance = BuildIntegrationTestEnvironment.INSTANCE; + } + + @Test + public void runQueryForTimestamp() throws IOException, InterruptedException { + Query query = new Query(); + query.setCrossCountFields(List.of()); + query.setCategoryFilters(Map.of("\\open_access-1000Genomes\\data\\SUPERPOPULATION NAME\\", new String[] {"American Ancestry"})); + query.setFields(List.of("\\open_access-1000Genomes\\data\\SUPERPOPULATION NAME\\")); + query.setExpectedResultType(ResultType.DATAFRAME_TIMESERIES); + + AsyncResult result = + new AsyncResult(query, timeseriesProcessor, new CsvWriter(File.createTempFile("result-" + System.nanoTime(), ".sstmp"))) + .setStatus(AsyncResult.Status.PENDING); + result.run(); + System.out.println(result.getStatus()); + Thread.sleep(1000); + File file = result.getStream().getFile(); + String csv = Files.readString(file.toPath()); + + csv.lines().skip(1).forEach(line -> { + String timestampValue = line.split(",", -1)[4]; + assertNotEquals("", timestampValue); + }); + } + + @Test + public void runQueryForNullTimestamp() throws IOException, InterruptedException { + Query query = new Query(); + query.setCrossCountFields(List.of()); + query.setCategoryFilters(Map.of("\\open_access-1000Genomes\\data\\SEX\\", new String[] {"male"})); + query.setFields(List.of("\\open_access-1000Genomes\\data\\SEX\\")); + query.setExpectedResultType(ResultType.DATAFRAME_TIMESERIES); + + AsyncResult result = + new AsyncResult(query, timeseriesProcessor, new CsvWriter(File.createTempFile("result-" + System.nanoTime(), ".sstmp"))) + .setStatus(AsyncResult.Status.PENDING); + result.run(); + System.out.println(result.getStatus()); + Thread.sleep(1000); + File file = result.getStream().getFile(); + String csv = Files.readString(file.toPath()); + + csv.lines().skip(1).forEach(line -> { + String timestampValue = line.split(",", -1)[4]; + assertEquals("", timestampValue); + }); + } +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/VariantListProcessorIntegrationTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/VariantListProcessorIntegrationTest.java new file mode 100644 index 000000000..b3b579dd5 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/VariantListProcessorIntegrationTest.java @@ -0,0 +1,216 @@ +package edu.harvard.hms.dbmi.avillach.hpds.test; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Filter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; +import edu.harvard.hms.dbmi.avillach.hpds.processing.VariantListProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.test.util.BuildIntegrationTestEnvironment; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.autoconfigure.EnableAutoConfiguration; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.ActiveProfiles; +import org.springframework.test.context.junit.jupiter.SpringExtension; + +import java.io.IOException; +import java.util.*; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; + +@ExtendWith(SpringExtension.class) +@EnableAutoConfiguration +@SpringBootTest(classes = edu.harvard.hms.dbmi.avillach.hpds.service.HpdsApplication.class) +@ActiveProfiles("integration-test") +public class VariantListProcessorIntegrationTest { + + private static final Logger log = LoggerFactory.getLogger(VariantListProcessorIntegrationTest.class); + + @Autowired + private VariantListProcessor variantListProcessor; + + @BeforeAll + public static void beforeAll() { + BuildIntegrationTestEnvironment instance = BuildIntegrationTestEnvironment.INSTANCE; + } + + @Test + public void runVcfExcerptQuery_validGeneWithVariantQuery() throws IOException { + Query query = new Query(); + List variantInfoFilters = new ArrayList<>(); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = Map.of("Gene_with_variant", new String[] {"LOC102723996"}); + variantInfoFilters.add(variantInfoFilter); + query.setVariantInfoFilters(variantInfoFilters); + + String vcfExerpt = variantListProcessor.runVcfExcerptQuery(query, true); + log.debug(vcfExerpt); + String[] vcfExcerptLines = vcfExerpt.split("\\n"); + + int totalExpectedPatients = 16; + int totalExpectedVariants = 4; + + // there should be a line per variant, plus one line for the header + assertEquals(totalExpectedVariants + 1, vcfExcerptLines.length); + List header = Arrays.asList(vcfExcerptLines[0].split("\\t")); + String[] variantLines = Arrays.copyOfRange(vcfExcerptLines, 1, vcfExcerptLines.length); + Arrays.stream(variantLines).forEach(line -> { + String[] columns = line.split("\\t"); + assertEquals("chr21", columns[0]); + int patientCount = 0; + for (String column : columns) { + if ("1/1".equals(column) || "0/1".equals(column)) patientCount++; + } + assertTrue(patientCount > 0); + assertEquals( + patientCount + "/" + totalExpectedPatients, getValueAtColumn(columns, header, "Patients with this variant in subset") + ); + assertEquals("LOC102723996", getValueAtColumn(columns, header, "Gene_with_variant")); + }); + } + + @Test + public void runVcfExcerptQuery_validGeneWithVariantQueryNoCall() throws IOException { + Query query = new Query(); + List variantInfoFilters = new ArrayList<>(); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = Map.of("Gene_with_variant", new String[] {"ABC1"}); + variantInfoFilters.add(variantInfoFilter); + query.setVariantInfoFilters(variantInfoFilters); + + String vcfExerpt = variantListProcessor.runVcfExcerptQuery(query, true); + log.debug(vcfExerpt); + String[] vcfExcerptLines = vcfExerpt.split("\\n"); + + int totalExpectedPatients = 16; + int totalExpectedVariants = 4; + + // there should be a line per variant, plus one line for the header + assertEquals(totalExpectedVariants + 1, vcfExcerptLines.length); + List header = Arrays.asList(vcfExcerptLines[0].split("\\t")); + String[] variantLines = Arrays.copyOfRange(vcfExcerptLines, 1, vcfExcerptLines.length); + Arrays.stream(variantLines).forEach(line -> { + String[] columns = line.split("\\t"); + assertEquals("chr20", columns[0]); + int patientCount = 0; + for (String column : columns) { + if ("1/1".equals(column) || "0/1".equals(column)) patientCount++; + } + assertTrue(patientCount > 0); + assertEquals( + patientCount + "/" + totalExpectedPatients, getValueAtColumn(columns, header, "Patients with this variant in subset") + ); + assertEquals("ABC1", getValueAtColumn(columns, header, "Gene_with_variant")); + }); + } + + + @Test + public void runVcfExcerptQuery_validGeneWithVariantAndPhenoQuery() throws IOException { + Query query = new Query(); + List variantInfoFilters = new ArrayList<>(); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = Map.of("Gene_with_variant", new String[] {"LOC102723996"}); + variantInfoFilters.add(variantInfoFilter); + query.setVariantInfoFilters(variantInfoFilters); + query.setNumericFilters(Map.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", new Filter.DoubleFilter(35.0, 45.0))); + + String vcfExerpt = variantListProcessor.runVcfExcerptQuery(query, true); + log.debug(vcfExerpt); + String[] vcfExcerptLines = vcfExerpt.split("\\n"); + + int totalExpectedPatients = 4; + int totalExpectedVariants = 2; + + // there should be a line per variant, plus one line for the header + assertEquals(totalExpectedVariants + 1, vcfExcerptLines.length); + List header = Arrays.asList(vcfExcerptLines[0].split("\\t")); + String[] variantLines = Arrays.copyOfRange(vcfExcerptLines, 1, vcfExcerptLines.length); + Arrays.stream(variantLines).forEach(line -> { + String[] columns = line.split("\\t"); + assertEquals("chr21", columns[0]); + int patientCount = 0; + for (String column : columns) { + if ("1/1".equals(column) || "0/1".equals(column)) patientCount++; + } + assertTrue(patientCount > 0); + assertEquals( + patientCount + "/" + totalExpectedPatients, getValueAtColumn(columns, header, "Patients with this variant in subset") + ); + assertEquals("LOC102723996", getValueAtColumn(columns, header, "Gene_with_variant")); + }); + } + + @Test + public void runVcfExcerptQuery_validGeneWithNoCallVariantAndPhenoQuery() throws IOException { + Query query = new Query(); + List variantInfoFilters = new ArrayList<>(); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = Map.of("Gene_with_variant", new String[] {"ABC1"}); + variantInfoFilters.add(variantInfoFilter); + query.setVariantInfoFilters(variantInfoFilters); + query.setNumericFilters(Map.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", new Filter.DoubleFilter(35.0, 45.0))); + + String vcfExerpt = variantListProcessor.runVcfExcerptQuery(query, true); + log.debug(vcfExerpt); + String[] vcfExcerptLines = vcfExerpt.split("\\n"); + + int totalExpectedPatients = 4; + int totalExpectedVariants = 2; + + // there should be a line per variant, plus one line for the header + assertEquals(totalExpectedVariants + 1, vcfExcerptLines.length); + List header = Arrays.asList(vcfExcerptLines[0].split("\\t")); + String[] variantLines = Arrays.copyOfRange(vcfExcerptLines, 1, vcfExcerptLines.length); + Arrays.stream(variantLines).forEach(line -> { + String[] columns = line.split("\\t"); + assertEquals("chr20", columns[0]); + int patientCount = 0; + for (String column : columns) { + if ("1/1".equals(column) || "0/1".equals(column)) patientCount++; + } + assertTrue(patientCount > 0); + assertEquals( + patientCount + "/" + totalExpectedPatients, getValueAtColumn(columns, header, "Patients with this variant in subset") + ); + assertEquals("ABC1", getValueAtColumn(columns, header, "Gene_with_variant")); + }); + } + + @Test + public void runVcfExcerptQuery_validQueryNoResults() throws IOException { + Query query = new Query(); + List variantInfoFilters = new ArrayList<>(); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = Map.of("Gene_with_variant", new String[] {"LOC102723996"}); + variantInfoFilters.add(variantInfoFilter); + query.setVariantInfoFilters(variantInfoFilters); + query.setNumericFilters(Map.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", new Filter.DoubleFilter(0.0, 1.0))); + + String vcfExerpt = variantListProcessor.runVcfExcerptQuery(query, true); + assertEquals("No Variants Found\n", vcfExerpt); + } + + @Test + public void runVariantListQuery_validQuery_returnVariants() { + Query query = new Query(); + List variantInfoFilters = new ArrayList<>(); + Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); + variantInfoFilter.categoryVariantInfoFilters = Map.of("Gene_with_variant", new String[] {"LOC102723996"}); + variantInfoFilters.add(variantInfoFilter); + query.setVariantInfoFilters(variantInfoFilters); + + String variantList = variantListProcessor.runVariantListQuery(query); + assertEquals( + "[chr21,5032061,A,G,LOC102723996,missense_variant, chr21,5033988,C,G,LOC102723996,synonymous_variant, chr21,5034028,C,T,LOC102723996,missense_variant, chr21,5033914,A,G,LOC102723996,missense_variant]", + variantList + ); + } + + private static String getValueAtColumn(String[] rowColumns, List header, String key) { + return rowColumns[header.indexOf(key)]; + } +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/VariantListV3ProcessorIntegrationTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/VariantListV3ProcessorIntegrationTest.java new file mode 100644 index 000000000..1bec45c72 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/VariantListV3ProcessorIntegrationTest.java @@ -0,0 +1,199 @@ +package edu.harvard.hms.dbmi.avillach.hpds.test; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.GenomicFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicFilterType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import edu.harvard.hms.dbmi.avillach.hpds.processing.v3.VariantListV3Processor; +import edu.harvard.hms.dbmi.avillach.hpds.test.util.BuildIntegrationTestEnvironment; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.autoconfigure.EnableAutoConfiguration; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.ActiveProfiles; +import org.springframework.test.context.junit.jupiter.SpringExtension; + +import java.util.Arrays; +import java.util.List; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; + +@ExtendWith(SpringExtension.class) +@EnableAutoConfiguration +@SpringBootTest(classes = edu.harvard.hms.dbmi.avillach.hpds.service.HpdsApplication.class) +@ActiveProfiles("integration-test") +public class VariantListV3ProcessorIntegrationTest { + + private static final Logger log = LoggerFactory.getLogger(VariantListV3ProcessorIntegrationTest.class); + + @Autowired + private VariantListV3Processor variantListProcessor; + + @BeforeAll + public static void beforeAll() { + BuildIntegrationTestEnvironment instance = BuildIntegrationTestEnvironment.INSTANCE; + } + + @Test + public void runVcfExcerptQuery_validGeneWithVariantQuery() { + GenomicFilter genomicFilter = new GenomicFilter("Gene_with_variant", List.of("LOC102723996"), null, null); + Query query = new Query(List.of(), List.of(), null, List.of(genomicFilter), ResultType.COUNT, null, null); + + String vcfExerpt = variantListProcessor.runVcfExcerptQuery(query, true); + log.debug(vcfExerpt); + String[] vcfExcerptLines = vcfExerpt.split("\\n"); + + int totalExpectedPatients = 16; + int totalExpectedVariants = 4; + + // there should be a line per variant, plus one line for the header + assertEquals(totalExpectedVariants + 1, vcfExcerptLines.length); + List header = Arrays.asList(vcfExcerptLines[0].split("\\t")); + String[] variantLines = Arrays.copyOfRange(vcfExcerptLines, 1, vcfExcerptLines.length); + Arrays.stream(variantLines).forEach(line -> { + String[] columns = line.split("\\t"); + assertEquals("chr21", columns[0]); + int patientCount = 0; + for (String column : columns) { + if ("1/1".equals(column) || "0/1".equals(column)) patientCount++; + } + assertTrue(patientCount > 0); + assertEquals( + patientCount + "/" + totalExpectedPatients, getValueAtColumn(columns, header, "Patients with this variant in subset") + ); + assertEquals("LOC102723996", getValueAtColumn(columns, header, "Gene_with_variant")); + }); + } + + @Test + public void runVcfExcerptQuery_validGeneWithVariantQueryNoCall() { + GenomicFilter genomicFilter = new GenomicFilter("Gene_with_variant", List.of("ABC1"), null, null); + Query query = new Query(List.of(), List.of(), null, List.of(genomicFilter), ResultType.COUNT, null, null); + + String vcfExerpt = variantListProcessor.runVcfExcerptQuery(query, true); + log.debug(vcfExerpt); + String[] vcfExcerptLines = vcfExerpt.split("\\n"); + + int totalExpectedPatients = 16; + int totalExpectedVariants = 4; + + // there should be a line per variant, plus one line for the header + assertEquals(totalExpectedVariants + 1, vcfExcerptLines.length); + List header = Arrays.asList(vcfExcerptLines[0].split("\\t")); + String[] variantLines = Arrays.copyOfRange(vcfExcerptLines, 1, vcfExcerptLines.length); + Arrays.stream(variantLines).forEach(line -> { + String[] columns = line.split("\\t"); + assertEquals("chr20", columns[0]); + int patientCount = 0; + for (String column : columns) { + if ("1/1".equals(column) || "0/1".equals(column)) patientCount++; + } + assertTrue(patientCount > 0); + assertEquals( + patientCount + "/" + totalExpectedPatients, getValueAtColumn(columns, header, "Patients with this variant in subset") + ); + assertEquals("ABC1", getValueAtColumn(columns, header, "Gene_with_variant")); + }); + } + + + @Test + public void runVcfExcerptQuery_validGeneWithVariantAndPhenoQuery() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", null, 35.0, 45.0, null); + GenomicFilter genomicFilter = new GenomicFilter("Gene_with_variant", List.of("LOC102723996"), null, null); + Query query = new Query(List.of(), List.of(), phenotypicFilter, List.of(genomicFilter), ResultType.COUNT, null, null); + + String vcfExerpt = variantListProcessor.runVcfExcerptQuery(query, true); + log.debug(vcfExerpt); + String[] vcfExcerptLines = vcfExerpt.split("\\n"); + + int totalExpectedPatients = 4; + int totalExpectedVariants = 2; + + // there should be a line per variant, plus one line for the header + assertEquals(totalExpectedVariants + 1, vcfExcerptLines.length); + List header = Arrays.asList(vcfExcerptLines[0].split("\\t")); + String[] variantLines = Arrays.copyOfRange(vcfExcerptLines, 1, vcfExcerptLines.length); + Arrays.stream(variantLines).forEach(line -> { + String[] columns = line.split("\\t"); + assertEquals("chr21", columns[0]); + int patientCount = 0; + for (String column : columns) { + if ("1/1".equals(column) || "0/1".equals(column)) patientCount++; + } + assertTrue(patientCount > 0); + assertEquals( + patientCount + "/" + totalExpectedPatients, getValueAtColumn(columns, header, "Patients with this variant in subset") + ); + assertEquals("LOC102723996", getValueAtColumn(columns, header, "Gene_with_variant")); + }); + } + + @Test + public void runVcfExcerptQuery_validGeneWithNoCallVariantAndPhenoQuery() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", null, 35.0, 45.0, null); + GenomicFilter genomicFilter = new GenomicFilter("Gene_with_variant", List.of("ABC1"), null, null); + Query query = new Query(List.of(), List.of(), phenotypicFilter, List.of(genomicFilter), ResultType.COUNT, null, null); + + String vcfExerpt = variantListProcessor.runVcfExcerptQuery(query, true); + log.debug(vcfExerpt); + String[] vcfExcerptLines = vcfExerpt.split("\\n"); + + int totalExpectedPatients = 4; + int totalExpectedVariants = 2; + + // there should be a line per variant, plus one line for the header + assertEquals(totalExpectedVariants + 1, vcfExcerptLines.length); + List header = Arrays.asList(vcfExcerptLines[0].split("\\t")); + String[] variantLines = Arrays.copyOfRange(vcfExcerptLines, 1, vcfExcerptLines.length); + Arrays.stream(variantLines).forEach(line -> { + String[] columns = line.split("\\t"); + assertEquals("chr20", columns[0]); + int patientCount = 0; + for (String column : columns) { + if ("1/1".equals(column) || "0/1".equals(column)) patientCount++; + } + assertTrue(patientCount > 0); + assertEquals( + patientCount + "/" + totalExpectedPatients, getValueAtColumn(columns, header, "Patients with this variant in subset") + ); + assertEquals("ABC1", getValueAtColumn(columns, header, "Gene_with_variant")); + }); + } + + + @Test + public void runVcfExcerptQuery_validQueryNoResults() { + PhenotypicFilter phenotypicFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", null, 0.0, 1.0, null); + GenomicFilter genomicFilter = new GenomicFilter("Gene_with_variant", List.of("LOC102723996"), null, null); + Query query = new Query(List.of(), List.of(), phenotypicFilter, List.of(genomicFilter), ResultType.COUNT, null, null); + + String vcfExerpt = variantListProcessor.runVcfExcerptQuery(query, true); + assertEquals("No Variants Found\n", vcfExerpt); + } + + @Test + public void runVariantListQuery_validQuery_returnVariants() { + GenomicFilter genomicFilter = new GenomicFilter("Gene_with_variant", List.of("LOC102723996"), null, null); + Query query = new Query(List.of(), List.of(), null, List.of(genomicFilter), ResultType.COUNT, null, null); + + String variantList = variantListProcessor.runVariantListQuery(query); + assertEquals( + "[chr21,5032061,A,G,LOC102723996,missense_variant, chr21,5033988,C,G,LOC102723996,synonymous_variant, chr21,5034028,C,T,LOC102723996,missense_variant, chr21,5033914,A,G,LOC102723996,missense_variant]", + variantList + ); + } + + private static String getValueAtColumn(String[] rowColumns, List header, String key) { + return rowColumns[header.indexOf(key)]; + } +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/VariantMetadataIndexTest.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/VariantMetadataIndexTest.java new file mode 100644 index 000000000..3284ff1cf --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/VariantMetadataIndexTest.java @@ -0,0 +1,189 @@ +package edu.harvard.hms.dbmi.avillach.hpds.test; + +import java.io.*; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.TreeMap; +import java.util.zip.GZIPInputStream; + +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMetadataIndex; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantSpec; +import edu.harvard.hms.dbmi.avillach.hpds.test.util.BuildIntegrationTestEnvironment; +import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.caching.VariantBucketHolder; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; + +import static org.junit.jupiter.api.Assertions.assertThrows; +import static org.springframework.test.util.AssertionErrors.assertEquals; +import static org.springframework.test.util.AssertionErrors.assertNotNull; + +public class VariantMetadataIndexTest { + + /** + * The metadataIndex is non-mutable (or should be) so we only need one object to test + */ + private static VariantMetadataIndex variantMetadataIndexChr4; + private static VariantMetadataIndex variantMetadataIndexChr21; + public static String chr4BinFile = "target/all/chr4/VariantMetadata.javabin"; + public static String chr21BinFile = "target/all/chr21/VariantMetadata.javabin"; + VariantBucketHolder bucketCache = new VariantBucketHolder(); + + // Some known variant specs from the input file. These have been designed for testing partially overlapping specs + private static final String spec1 = "chr4,9856624,CAAAAA,C,TVP23A,splice_acceptor_variant"; + private static final String spec1Info = + "Gene_with_variant=TVP23A;Variant_consequence_calculated=splice_acceptor_variant;AC=401;AF=8.00719e-02;NS=2504;AN=5008;EAS_AF=3.37000e-02;EUR_AF=4.97000e-02;AFR_AF=1.64100e-01;AMR_AF=3.75000e-02;SAS_AF=7.57000e-02;DP=18352;AA=G|||;VT=SNP"; + private static final String spec2 = "chr4,9856624,CAAA,C,TVP23A,splice_acceptor_variant"; + private static final String spec2Info = + "Gene_with_variant=TVP23A;Variant_consequence_calculated=splice_acceptor_variant;AC=62;AF=1.23802e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=4.54000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18328;AA=T|||;VT=SNP"; + private static final String spec3 = "chr4,9856624,CA,C,TVP23A,splice_acceptor_variant"; + private static final String spec3Info = + "Gene_with_variant=TVP23A;Variant_consequence_calculated=splice_acceptor_variant;AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18519;AA=T|||;VT=SNP"; + private static final String spec4 = "chr4,9856624,C,CA,TVP23A,splice_acceptor_variant"; + private static final String spec4Info = + "Gene_with_variant=TVP23A;Variant_consequence_calculated=splice_acceptor_variant;AC=75;AF=1.49760e-02;NS=2504;AN=5008;EAS_AF=3.27000e-02;EUR_AF=2.49000e-02;AFR_AF=6.80000e-03;AMR_AF=4.30000e-03;SAS_AF=5.10000e-03;DP=18008;AA=A|||;VT=SNP"; + private static final String spec5 = "chr4,9856624,CAAAAA,CA,TVP23A,splice_acceptor_variant"; + private static final String spec5Info = + "Gene_with_variant=TVP23A;Variant_consequence_calculated=splice_acceptor_variant;AC=3033;AF=6.05631e-01;NS=2504;AN=5008;EAS_AF=5.23800e-01;EUR_AF=7.54500e-01;AFR_AF=4.28900e-01;AMR_AF=7.82400e-01;SAS_AF=6.50300e-01;DP=20851;VT=INDEL"; + + + @BeforeAll + public static void initializeBinfiles() throws Exception { + BuildIntegrationTestEnvironment instance = BuildIntegrationTestEnvironment.INSTANCE; + if (new File(chr4BinFile).exists()) { + try (ObjectInputStream in = new ObjectInputStream(new GZIPInputStream(new FileInputStream(chr4BinFile)))) { + variantMetadataIndexChr4 = (VariantMetadataIndex) in.readObject(); + } catch (Exception e) { + e.printStackTrace(); + } + } + if (new File(chr21BinFile).exists()) { + try (ObjectInputStream in = new ObjectInputStream(new GZIPInputStream(new FileInputStream(chr21BinFile)))) { + variantMetadataIndexChr21 = (VariantMetadataIndex) in.readObject(); + } catch (Exception e) { + e.printStackTrace(); + } + } + } + + @Test + public void findByMultipleVariantSpec_invalidSpec() { + List variants = List.of("chr21,5032061,A,G,NOTAGENE,missense_variant"); + Map> expectedResult = Map.of(); + Map> data = variantMetadataIndexChr21.findByMultipleVariantSpec(variants); + + assertEquals("Wrong number of records in response.", 1, data.size()); + assertEquals("The expected values were not found.", Set.of(), data.get("chr21,5032061,A,G,NOTAGENE,missense_variant")); + } + + @Test + public void findByMultipleVariantSpec_validSpec() { + List variants = List.of("chr21,5032061,A,G,LOC102723996,missense_variant"); + Map> expectedResult = Map.of( + "chr21,5032061,A,G,LOC102723996,missense_variant", + Set.of( + "Gene_with_variant=LOC102723996;Variant_severity=MODERATE;Variant_consequence_calculated=missense_variant;Variant_class=SNV;Variant_frequency_in_gnomAD=0.0001346;Variant_frequency_as_text=Rare" + ) + ); + Map> data = variantMetadataIndexChr21.findByMultipleVariantSpec(variants); + + assertEquals("Wrong number of records in response.", data.size(), 1); + variants.stream().forEach(variant -> { + assertEquals("The expected values were not found.", expectedResult.get(variant), data.get(variant)); + }); + } + + @Test + public void findByMultipleVariantSpec_validSpecs() { + List variants = + List.of("chr21,5032061,A,G,LOC102723996,missense_variant", "chr21,5033914,A,G,LOC102723996,missense_variant"); + Map> expectedResult = Map.of( + "chr21,5032061,A,G,LOC102723996,missense_variant", + Set.of( + "Gene_with_variant=LOC102723996;Variant_severity=MODERATE;Variant_consequence_calculated=missense_variant;Variant_class=SNV;Variant_frequency_in_gnomAD=0.0001346;Variant_frequency_as_text=Rare" + ), "chr21,5033914,A,G,LOC102723996,missense_variant", + Set.of( + "Gene_with_variant=LOC102723996;Variant_severity=MODERATE;Variant_consequence_calculated=missense_variant;Variant_class=SNV;Variant_frequency_in_gnomAD=0.0009728;Variant_frequency_as_text=Rare" + ) + ); + Map> data = variantMetadataIndexChr21.findByMultipleVariantSpec(variants); + + assertEquals("Wrong number of records in response.", data.size(), 2); + variants.stream().forEach(variant -> { + assertEquals("The expected values were not found.", expectedResult.get(variant), data.get(variant)); + }); + } + + @Test + public void testMultipleVariantSpecSamePOS() { + + List variants = List.of(spec1, spec4); + Map> expectedResult = Map.of(spec1, Set.of(spec1Info), spec4, Set.of(spec4Info)); + Map> data = variantMetadataIndexChr4.findByMultipleVariantSpec(variants); + + assertEquals("Wrong number of records in response.", data.size(), 2); + variants.stream().forEach(variant -> { + assertEquals("The expected values were not found.", expectedResult.get(variant), data.get(variant)); + }); + } + + @Test + public void testMultipleVariantSpecSamePOSAndREF() { + List variants = List.of(spec1, spec5); + Map> expectedResult = Map.of(spec1, Set.of(spec1Info), spec5, Set.of(spec5Info)); + Map> data = variantMetadataIndexChr4.findByMultipleVariantSpec(variants); + + assertEquals("Wrong number of records in response.", data.size(), 2); + variants.stream().forEach(variant -> { + assertEquals("The expected values were not found.", expectedResult.get(variant), data.get(variant)); + }); + } + + @Test + public void testMultipleVariantSpecSamePOSAndALT() { + List variants = List.of(spec1, spec2); + Map> expectedResult = Map.of(spec1, Set.of(spec1Info), spec2, Set.of(spec2Info)); + Map> data = variantMetadataIndexChr4.findByMultipleVariantSpec(variants); + + assertEquals("Wrong number of records in response.", data.size(), 2); + variants.stream().forEach(variant -> { + assertEquals("The expected values were not found.", expectedResult.get(variant), data.get(variant)); + }); + } + + /** + * The google API that we use throws an IllegalStateException on duplicate entries + */ + @Test + public void testMultipleVariantSpecSameSpec() { + assertThrows(IllegalStateException.class, () -> { + List variants = List.of(spec1, spec1); + Map> expectedResult = Map.of(spec1, Set.of(spec1Info)); + Map> data = variantMetadataIndexChr4.findByMultipleVariantSpec(variants); + + assertEquals("Wrong number of records in response.", data.size(), 1); + variants.stream().forEach(variant -> { + assertEquals("The expected values were not found.", expectedResult.get(variant), data.get(variant)); + }); + }); + } + + @Test + public void testVariantSpecMapSorting() { + Map specMap = Map.of(spec1, new String[] {spec1Info}, spec2, new String[] {spec2Info}); + + TreeMap metadataSorted = new TreeMap<>((o1, o2) -> { + return new VariantSpec(o1).compareTo(new VariantSpec(o2)); + }); + metadataSorted.putAll(specMap); + + assertEquals("Wrong number of records in response.", metadataSorted.size(), 2); + assertNotNull("spec1 value not present in the sorted map", metadataSorted.get(spec1)); + assertEquals("Incorrect spec1 value in the sorted map", spec1Info, metadataSorted.get(spec1)[0]); + assertNotNull("spec2 value not present in the sorted map", metadataSorted.get(spec2)); + assertEquals("Incorrect spec2 value in the sorted map", spec2Info, metadataSorted.get(spec2)[0]); + } + + + +} diff --git a/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/util/BuildIntegrationTestEnvironment.java b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/util/BuildIntegrationTestEnvironment.java new file mode 100644 index 000000000..abeed4a8b --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/util/BuildIntegrationTestEnvironment.java @@ -0,0 +1,31 @@ +package edu.harvard.hms.dbmi.avillach.hpds.test.util; + +import edu.harvard.hms.dbmi.avillach.hpds.etl.genotype.*; +import edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.csv.CSVLoader; + +import java.io.IOException; + +public enum BuildIntegrationTestEnvironment { + INSTANCE; + + private static final String PHENOTYPIC_DATA_DIRECTORY = "target/test-classes/phenotypic/"; + private static final String VCF_INDEX_FILE = "./src/test/resources/test_vcfIndex.tsv"; + private static final String STORAGE_DIR = "./target/all/"; + private static final String MERGED_DIR = "./target/merged/"; + + BuildIntegrationTestEnvironment() { + try { + SplitChromosomeVcfLoader.main(new String[] {VCF_INDEX_FILE, STORAGE_DIR, MERGED_DIR}); + CSVLoader.main(new String[] {PHENOTYPIC_DATA_DIRECTORY}); + SplitChromosomeVariantMetadataLoader.main(new String[] {"./src/test/resources/test_vcfIndex.tsv", STORAGE_DIR}); + new GenomicDatasetFinalizer(STORAGE_DIR, 10).processDirectory(); + } catch (IOException e) { + throw new RuntimeException(e); + } + + } + + public static void main(String[] args) { + BuildIntegrationTestEnvironment instance = BuildIntegrationTestEnvironment.INSTANCE; + } +} diff --git a/services/pic-sure-hpds/service/src/test/resources/BucketIndexTestInput.vcf b/services/pic-sure-hpds/service/src/test/resources/BucketIndexTestInput.vcf new file mode 100644 index 000000000..bab60f9fe --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/resources/BucketIndexTestInput.vcf @@ -0,0 +1,2009 @@ +## +## Patient 1 - NO variants +## Patient 2 - ALL variants +## Patient 3 - NO CHR 14 variants, ALL CHR 4 variants +## Patient 4 - ALL CHR 14 variants, NO CHR 4 variants +## others mixed +## +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 HG00099 HG00100 HG00101 HG00102 HG00103 HG00105 HG00106 HG00107 +14 19000059 rs201622908 G T 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=5.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=2.00000e-03;DP=23196;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000060 rs28973059 C G 100 PASS AC=1536;AF=3.06709e-01;NS=2504;AN=5008;EAS_AF=3.91900e-01;EUR_AF=3.89700e-01;AFR_AF=1.20300e-01;AMR_AF=3.66000e-01;SAS_AF=3.43600e-01;DP=23505;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|0 1|0 0|1 0|1 1|0 +14 19000079 rs558975054 C A 100 PASS AC=23;AF=4.59265e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.74000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=29810;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000096 rs532880059 G C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=34132;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000105 rs28971053 A G 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.06000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35319;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000115 rs569534039 T G 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=6.00000e-03;AFR_AF=8.00000e-04;AMR_AF=2.90000e-03;SAS_AF=3.10000e-03;DP=36388;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000141 rs549268929 T C 100 PASS AC=65;AF=1.29792e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.92000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37540;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000152 rs567484204 C T 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=6.00000e-03;AFR_AF=8.00000e-04;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=37391;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000155 rs534769748 C A 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=8.90000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37450;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000161 rs554311888 G T 100 PASS AC=24;AF=4.79233e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.74000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37094;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000218 rs61973502 G A 100 PASS AC=40;AF=7.98722e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.80000e-02;AMR_AF=2.90000e-03;SAS_AF=1.00000e-03;DP=37318;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000224 rs201311189 G A 100 PASS AC=174;AF=3.47444e-02;NS=2504;AN=5008;EAS_AF=3.97000e-02;EUR_AF=1.99000e-02;AFR_AF=6.10000e-03;AMR_AF=8.21000e-02;SAS_AF=5.01000e-02;DP=37563;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000250 rs573896072 C T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=38030;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000259 rs541271558 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38140;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000268 rs559508913 G A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=38052;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000293 rs533080259 A T 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37556;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000328 rs563316563 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34879;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000367 rs549307377 A T 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=33172;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000368 rs374384267 C T 100 PASS AC=52;AF=1.03834e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.98000e-02;AFR_AF=0.00000e+00;AMR_AF=1.44000e-02;SAS_AF=1.23000e-02;DP=33480;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 0|0 0|0 0|0 0|0 0|0 +14 19000497 rs546858416 C T 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.80000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37797;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000498 rs372216337 G C 100 PASS AC=28;AF=5.59105e-03;NS=2504;AN=5008;EAS_AF=1.19000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.31000e-02;SAS_AF=0.00000e+00;DP=38119;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000515 rs539952297 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37800;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000541 rs570049776 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37713;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000552 rs28844105 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37462;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000571 rs574034644 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37259;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000572 rs541308805 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=37032;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000594 rs28834685 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38262;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000621 rs542692151 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=39804;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000632 rs560858949 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40484;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000636 rs528430882 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=40658;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000637 rs546897207 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40637;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000700 rs551865059 T G 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=42126;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000717 rs570094597 T C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=41821;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000720 rs537135209 T A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=41637;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000724 rs61973512 T C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=41522;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000727 rs567297966 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=41332;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000806 rs557528182 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=38157;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000827 rs575284448 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36983;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000858 rs528065999 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37265;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000881 rs372999416 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36430;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000889 rs564994953 C G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36829;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000929 rs530937749 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37132;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000950 rs549036376 T C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=37361;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19000968 rs567337119 A C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=38076;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001048 rs547273893 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37401;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001069 rs202011281 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=36568;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001098 rs575886516 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36883;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001116 rs536376785 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37075;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001160 rs572889065 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37065;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001170 rs74850277 C T 100 PASS AC=23;AF=4.59265e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.39000e-02;AFR_AF=2.30000e-03;AMR_AF=5.80000e-03;SAS_AF=2.00000e-03;DP=36766;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001179 rs535110682 C CA 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.10000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36794;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001211 rs544472365 T G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37227;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001230 rs562561406 C T 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36975;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001239 rs529804220 C T 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.06000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36876;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001261 rs369021247 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=37469;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001289 rs561001081 G A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37331;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001489 rs369942692 T A 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38756;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001490 rs573024917 G A 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38278;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001521 rs558294209 T C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=36327;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001669 rs541667778 C A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=36394;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001691 rs528598108 A G 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35905;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001741 rs565157506 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35978;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001757 rs551002244 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35383;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001770 rs569528200 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=34982;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001779 rs530417036 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35191;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001791 rs548831784 C A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=35888;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001797 rs567046418 A C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=36188;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001840 rs537464017 CTG C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38361;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001884 rs533669634 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37802;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001946 rs139189921 A T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35628;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001967 rs112767451 A G 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36503;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19001979 rs537800817 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37223;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002072 rs574432803 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35589;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002085 rs572178474 A G 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34835;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002107 rs540387233 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34468;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002264 rs532406891 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35854;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002298 rs562863926 A T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36182;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002403 rs546522736 A AT 100 PASS AC=36;AF=7.18850e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.57000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=35786;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002423 rs567084566 C G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34916;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002437 rs527844190 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35028;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002497 rs28854877 A G 100 PASS AC=3119;AF=6.22804e-01;NS=2504;AN=5008;EAS_AF=7.37100e-01;EUR_AF=5.50700e-01;AFR_AF=5.90800e-01;AMR_AF=6.32600e-01;SAS_AF=6.15500e-01;DP=36094;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|0 0|1 0|1 0|1 1|0 +14 19002679 rs572158426 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36424;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002727 rs577311413 C G 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=5.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35908;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002732 rs544693610 A G 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=5.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36006;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002775 rs574848914 A T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=35359;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002776 rs542547934 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35391;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002808 rs372181045 G C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=36433;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002826 rs552775981 G C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=36725;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002880 rs531463498 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37262;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002881 rs549438306 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37173;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002893 rs567735083 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37468;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002923 rs535044205 A T 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36916;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002979 rs566013436 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36892;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19002999 rs539345658 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36532;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003030 rs538355014 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36582;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003034 rs556652644 T C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36602;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003042 rs574887806 A G 100 PASS AC=41;AF=8.18690e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.03000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36249;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003096 rs564725001 G A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35083;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003149 rs531756358 T A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35281;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003156 rs561401073 T G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35334;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003285 rs551349590 C T 100 PASS AC=16;AF=3.19489e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.13000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37023;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003314 rs555596179 A G 100 PASS AC=51;AF=1.01837e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.86000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36760;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003352 rs575026280 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=38476;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003376 rs542143514 CTG C 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=6.10000e-03;DP=39744;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003383 rs554165999 T A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=38711;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003390 rs572322096 C T 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=6.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=1.00000e-03;DP=38555;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003461 rs546492087 A C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36359;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003495 rs576233756 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36569;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003497 rs543658259 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36629;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003498 rs561938192 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36661;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003509 rs540750076 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=37076;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003521 rs559313499 T C 100 PASS AC=20;AF=3.99361e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.51000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37297;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003564 rs551654593 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36777;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003618 rs530815112 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36697;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003640 rs567446878 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36436;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003660 rs28783708 T C 100 PASS AC=5006;AF=9.99601e-01;NS=2504;AN=5008;EAS_AF=1.00000e+00;EUR_AF=1.00000e+00;AFR_AF=9.98500e-01;AMR_AF=1.00000e+00;SAS_AF=1.00000e+00;DP=37118;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 +14 19003695 rs553941763 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=5.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38447;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003718 rs566076336 T A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39188;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003723 rs558121027 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=38951;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003732 rs576374048 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38730;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003740 rs543684799 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38950;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003794 rs573871306 G A 100 PASS AC=31;AF=6.19010e-03;NS=2504;AN=5008;EAS_AF=7.90000e-03;EUR_AF=1.00000e-03;AFR_AF=4.50000e-03;AMR_AF=2.02000e-02;SAS_AF=2.00000e-03;DP=37622;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003816 rs541127322 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37071;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003817 rs111251759 G A 100 PASS AC=16;AF=3.19489e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=3.00000e-03;AFR_AF=4.50000e-03;AMR_AF=5.80000e-03;SAS_AF=2.00000e-03;DP=36709;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003821 rs112176586 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37062;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003831 rs563253332 C A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=5.10000e-03;DP=37311;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003871 rs574063341 CA C 100 PASS AC=34;AF=6.78914e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.42000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=40028;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003889 rs530861140 C T 100 PASS AC=18;AF=3.59425e-03;NS=2504;AN=5008;EAS_AF=1.19000e-02;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=1.00000e-03;DP=39477;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|1 0|0 0|0 +14 19003918 rs567490561 A G 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38788;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003930 rs528226339 T C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39254;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19003985 rs547878277 G C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36634;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004018 rs149501549 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37748;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004023 rs569697306 T G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37728;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004024 rs537360555 G T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37557;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004062 rs573908596 G C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37474;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004161 rs577693707 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37756;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004209 rs545072557 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36736;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004243 rs199652137 C T 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=7.90000e-03;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=37130;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004249 rs111299063 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37357;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004271 rs561125785 A C 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37481;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004301 rs528376151 T A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37188;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004341 rs551424310 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35141;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004346 rs569721816 T C 100 PASS AC=51;AF=1.01837e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.78000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35079;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004400 rs567913058 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36472;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004418 rs578098141 C T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35813;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004419 rs538759751 A T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35909;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004475 rs573081707 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34516;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004493 rs564945277 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34189;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004559 rs563485075 G A 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=7.90000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36509;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004574 rs530911515 T G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36402;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004607 rs567636732 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36691;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004656 rs535023587 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=35264;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004664 rs376702146 A T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34857;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004680 rs368735792 G T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34874;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004686 rs371259263 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=34954;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004773 rs554300234 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36200;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004794 rs572761729 C T 100 PASS AC=29;AF=5.79073e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=1.49000e-02;AFR_AF=8.00000e-04;AMR_AF=1.01000e-02;SAS_AF=5.10000e-03;DP=35780;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004846 rs371730306 C T 100 PASS AC=28;AF=5.59105e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=1.89000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35707;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004897 rs377328711 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37488;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004898 rs577055970 A T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37524;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004912 rs370701389 ACT A 100 PASS AC=150;AF=2.99521e-02;NS=2504;AN=5008;EAS_AF=3.87000e-02;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.12500e-01;DP=37752;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004924 rs562322336 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36101;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004943 rs530947868 G A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35504;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004973 rs542678493 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35646;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004981 rs561148867 G C 100 PASS AC=28;AF=5.59105e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=1.89000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35529;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19004995 rs528440220 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=2.90000e-03;SAS_AF=1.00000e-03;DP=35404;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005003 rs546986364 G A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=34991;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005048 rs141842505 G A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=4.30000e-03;SAS_AF=1.00000e-03;DP=35975;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005081 rs536366538 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37048;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005117 rs566345687 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36910;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005118 rs533827934 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36838;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005144 rs558267474 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36539;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005164 rs544088158 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36273;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005172 rs555956890 A C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36496;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005225 rs561391954 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=38389;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005241 rs565112595 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39245;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005259 rs145745645 G A 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.10000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=39436;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005374 rs530268287 A C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=37203;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005378 rs371300164 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=37264;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005388 rs369029771 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37486;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005403 rs533631706 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37722;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005418 rs372380357 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=38020;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005503 rs537771872 G A 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.80000e-03;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=35672;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005507 rs28878025 T C 100 PASS AC=3772;AF=7.53195e-01;NS=2504;AN=5008;EAS_AF=8.38300e-01;EUR_AF=6.27200e-01;AFR_AF=8.37400e-01;AMR_AF=7.07500e-01;SAS_AF=7.13700e-01;DP=35701;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|0 1|0 0|1 1|0 1|0 +14 19005508 rs202025462 G T 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=9.90000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35630;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005530 rs553681366 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35355;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005532 rs573313835 A G 100 PASS AC=22;AF=4.39297e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.66000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35281;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005641 rs565293633 C T 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35924;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005688 rs577279789 C G 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34766;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005691 rs544921234 A C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=34954;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005716 rs548795475 G C 100 PASS AC=19;AF=3.79393e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.09000e-02;AFR_AF=0.00000e+00;AMR_AF=7.20000e-03;SAS_AF=3.10000e-03;DP=35704;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005739 rs527398619 A C 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=7.00000e-03;AFR_AF=8.00000e-04;AMR_AF=2.90000e-03;SAS_AF=1.00000e-03;DP=36390;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005743 rs551958713 T C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36559;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005750 rs570117594 T A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=3.10000e-03;DP=36793;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005760 rs537408026 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36897;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005761 rs549356918 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36920;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005904 rs572110462 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34461;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005935 rs559042750 C G 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35114;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005950 rs577316701 A C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=34920;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005953 rs544667163 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34631;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19005967 rs575113870 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=34643;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006007 rs542126377 A G 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.02000e-02;DP=33797;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006015 rs560761009 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=33555;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006108 rs563880604 A C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37319;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006209 rs549393538 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=35290;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006221 rs529202406 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35552;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006234 rs547344793 T C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=1.50000e-03;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=36477;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006311 rs565869433 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36936;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006326 rs539216112 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36587;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006391 rs570987988 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=36009;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006403 rs556614045 C A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=36169;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006404 rs28802366 G A 100 PASS AC=37;AF=7.38818e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.65000e-02;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=36121;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006417 rs542514645 G A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36412;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006459 rs28795095 A G 100 PASS AC=3809;AF=7.60583e-01;NS=2504;AN=5008;EAS_AF=8.43300e-01;EUR_AF=6.31200e-01;AFR_AF=8.43400e-01;AMR_AF=7.17600e-01;SAS_AF=7.27000e-01;DP=37005;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|0 1|0 0|1 1|0 1|0 +14 19006526 rs546035227 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37149;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006532 rs564317835 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37220;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006537 rs28883047 G A 100 PASS AC=24;AF=4.79233e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.74000e-02;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=36953;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006591 rs561743006 T C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=37578;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006697 rs533245224 C A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=35809;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006730 rs551638899 T G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=35488;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006770 rs568451888 G C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=36652;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006836 rs554133644 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37912;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006876 rs572677615 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34555;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006892 rs546072099 C T 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.06000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34505;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006893 rs557944005 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=34099;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006940 rs367799012 G A 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=1.19000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=36824;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006949 rs540714256 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37429;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006967 rs142170271 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37387;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19006994 rs533284955 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=36546;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007013 rs200799719 T A 100 PASS AC=154;AF=3.07508e-02;NS=2504;AN=5008;EAS_AF=3.47000e-02;EUR_AF=2.09000e-02;AFR_AF=8.00000e-04;AMR_AF=6.92000e-02;SAS_AF=5.01000e-02;DP=37355;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007014 rs201970796 C T 100 PASS AC=154;AF=3.07508e-02;NS=2504;AN=5008;EAS_AF=3.47000e-02;EUR_AF=2.09000e-02;AFR_AF=8.00000e-04;AMR_AF=6.92000e-02;SAS_AF=5.01000e-02;DP=36522;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007025 rs199917579 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36291;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007198 rs28838603 A T 100 PASS AC=28;AF=5.59105e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.29000e-02;AFR_AF=0.00000e+00;AMR_AF=5.80000e-03;SAS_AF=1.00000e-03;DP=37827;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007208 rs555923412 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=37547;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007222 rs573691447 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=37502;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007224 rs541088687 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37631;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007231 rs559111393 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=38414;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007233 rs577668411 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38262;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007253 rs545331681 A T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=39662;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007372 rs529383530 A T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38755;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007394 rs371581273 C T 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=7.20000e-03;DP=37955;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007395 rs28866192 G A 100 PASS AC=40;AF=7.98722e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=2.65000e-02;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=37746;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007520 rs545070094 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35855;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007590 rs556975253 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=35787;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007708 rs528242581 A C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35612;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007728 rs145104210 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35410;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007731 rs559457749 G C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35061;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007733 rs533246910 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35169;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 1|0 0|1 .|1 1|. +14 19007740 rs569683161 C A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=35098;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007741 rs531133411 G A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=5.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35312;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007761 rs369077250 G C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36024;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007803 rs535263136 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36418;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007834 rs571396389 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35103;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19007982 rs554808005 T A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=35739;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008010 rs200347442 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=35584;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008056 rs545073088 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=35462;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008080 rs563346538 C T 100 PASS AC=22;AF=4.39297e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.44000e-02;AMR_AF=1.40000e-03;SAS_AF=2.00000e-03;DP=35676;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008090 rs549102064 G A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35924;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008130 rs567997261 C G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37442;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008189 rs370744944 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36795;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008263 rs536283525 G C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=36152;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 1|0 0|0 +14 19008278 rs537395903 AC A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37698;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008386 rs372947446 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=36955;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008399 rs576583971 C T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37001;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008414 rs545109936 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=37278;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008435 rs563485025 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38377;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008453 rs575647443 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39371;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008504 rs28849738 T G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39270;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008511 rs547285526 A G 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38563;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008519 rs565480699 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=39203;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008584 rs192108471 G T 100 PASS AC=26;AF=5.19169e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.69000e-02;AFR_AF=0.00000e+00;AMR_AF=1.01000e-02;SAS_AF=2.00000e-03;DP=38455;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 1|0 0|0 0|0 +14 19008585 rs551185650 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38410;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008630 rs568978423 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40016;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008639 rs535941843 C G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40537;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008740 rs558392091 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=38556;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008749 rs576720136 C T 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=9.10000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=38204;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008756 rs537697535 C A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=6.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37813;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008768 rs150869471 C T 100 PASS AC=17;AF=3.39457e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=8.00000e-03;AFR_AF=3.00000e-03;AMR_AF=7.20000e-03;SAS_AF=0.00000e+00;DP=38412;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008777 rs184049796 A T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=38700;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008778 rs542722153 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=38917;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008805 rs573226441 C T 100 PASS AC=21;AF=4.19329e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=1.39000e-02;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=3.10000e-03;DP=39806;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008806 rs200665352 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39830;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008811 rs565617999 T G 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=8.90000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=40153;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|1 0|0 +14 19008924 rs529810758 G C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38539;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008931 rs547931176 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38729;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008937 rs372175346 C G 100 PASS AC=18;AF=3.59425e-03;NS=2504;AN=5008;EAS_AF=1.49000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=2.00000e-03;DP=39026;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008962 rs533586094 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=3.10000e-03;DP=40818;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19008997 rs570441593 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40694;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009012 rs28868990 C G 100 PASS AC=3804;AF=7.59585e-01;NS=2504;AN=5008;EAS_AF=8.38300e-01;EUR_AF=6.28200e-01;AFR_AF=8.54800e-01;AMR_AF=7.08900e-01;SAS_AF=7.20900e-01;DP=39990;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|0 1|0 0|1 1|0 1|0 +14 19009053 rs568135697 G A 100 PASS AC=37;AF=7.38818e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.65000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=38179;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009086 rs554724589 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=38032;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009104 rs61974089 G A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=5.00000e-03;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37396;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009105 rs577643947 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37529;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009142 rs563116556 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37598;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009166 rs559864015 A C 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=6.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=5.10000e-03;DP=37804;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009191 rs527365929 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36787;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009274 rs111924164 C T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36933;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009367 rs570079974 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37738;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009369 rs572111775 CAA C 100 PASS AC=263;AF=5.25160e-02;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=6.46000e-02;AFR_AF=7.11000e-02;AMR_AF=3.89000e-02;SAS_AF=7.57000e-02;DP=39090;VT=INDEL GT 0|0 1|1 0|0 1|1 0|1 0|0 0|0 0|0 0|0 0|0 +14 19009381 rs531523403 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=37518;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009420 rs568254310 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37220;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009447 rs76264538 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37236;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009547 rs559005050 A C 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=5.10000e-03;DP=37681;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009586 rs201038093 A T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=36304;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009602 rs137901365 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=35321;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009737 rs527401373 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37440;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009741 rs146904494 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37484;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009763 rs146520680 T A 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.09000e-02;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=36477;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 19009786 rs549740272 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36326;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009827 rs28870189 C T 100 PASS AC=3844;AF=7.67572e-01;NS=2504;AN=5008;EAS_AF=8.60100e-01;EUR_AF=6.45100e-01;AFR_AF=8.51000e-01;AMR_AF=7.17600e-01;SAS_AF=7.20900e-01;DP=36728;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 0|1 0|1 1|0 1|0 1|1 +14 19009858 rs183504744 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37154;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009874 rs28787113 A C 100 PASS AC=3852;AF=7.69169e-01;NS=2504;AN=5008;EAS_AF=8.61100e-01;EUR_AF=6.52100e-01;AFR_AF=8.46400e-01;AMR_AF=7.24800e-01;SAS_AF=7.21900e-01;DP=35859;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 0|1 0|1 1|0 1|0 1|1 +14 19009877 rs565842589 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35808;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19009914 rs552655968 T C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=35884;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010007 rs556502762 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36495;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010115 rs79863109 G A 100 PASS AC=20;AF=3.99361e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=1.44000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36907;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010139 rs545504700 T G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=37476;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010300 rs143313989 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35775;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010313 rs529187031 T C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35639;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010350 rs559590273 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=37365;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010375 rs533204520 G C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=6.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38052;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010414 rs570886777 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=38001;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010456 rs568414944 T G 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37688;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010559 rs576091423 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40842;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010562 rs149217092 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40818;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010566 rs573532344 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40615;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010567 rs541340677 A T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40657;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010663 rs550205187 C T 100 PASS AC=15;AF=2.99521e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.10000e-03;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=38296;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010714 rs547382941 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37623;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010718 rs566057756 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37223;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010765 rs555399607 G A 100 PASS AC=22;AF=4.39297e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.66000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38268;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010780 rs573652783 T C 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37625;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010809 rs552989409 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37208;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010814 rs578010610 C A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37247;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010837 rs535670659 CAA C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=6.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40722;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19010958 rs530693385 T C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37760;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011127 rs552004027 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=5.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37747;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011135 rs570163063 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37918;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011159 rs567404177 G A 100 PASS AC=55;AF=1.09824e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.16000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37238;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011168 rs534672527 C T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37436;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011187 rs545333656 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=37289;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011370 rs543548979 CT C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=38584;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011379 rs112400981 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38309;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011389 rs551474320 A G 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38731;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011444 rs531096230 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36801;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011469 rs534713155 T G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35488;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011477 rs77033728 GA G 100 PASS AC=1367;AF=2.72963e-01;NS=2504;AN=5008;EAS_AF=3.87900e-01;EUR_AF=1.79900e-01;AFR_AF=2.84400e-01;AMR_AF=2.49300e-01;SAS_AF=2.51500e-01;DP=35080;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 1|0 0|0 0|0 1|0 0|0 +14 19011568 rs538675818 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37310;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011584 rs556659460 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36628;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011608 rs536120514 T A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35972;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011648 rs572654674 T C 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35067;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011651 rs541136515 C A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35074;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011750 rs577711064 A C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36761;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011760 rs545421253 A C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36530;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011831 rs549365685 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36284;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011837 rs76682399 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36556;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011843 rs528738938 G T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36565;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011852 rs561910543 AC A 100 PASS AC=29;AF=5.79073e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.04000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=37189;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011893 rs571396490 T A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=38014;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011946 rs568729541 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37347;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011977 rs536548734 G T 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=37309;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011985 rs554402717 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37608;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19011999 rs533783349 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37242;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19012001 rs558307745 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37512;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19012036 rs575513463 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=39254;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19012037 rs543001697 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=39241;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19012057 rs528775482 A G 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40520;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19012229 rs568844496 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=42936;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19012367 rs566455907 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=44001;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19012414 rs533803420 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=43241;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19012416 rs28838588 T C 100 PASS AC=2502;AF=4.99601e-01;NS=2504;AN=5008;EAS_AF=5.02000e-01;EUR_AF=4.96000e-01;AFR_AF=5.00000e-01;AMR_AF=5.01400e-01;SAS_AF=4.99000e-01;DP=42419;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 0|1 0|1 1|0 1|0 1|0 +14 19012458 rs570506602 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=45402;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19012689 rs575693062 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=47020;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19012735 rs539845269 T TA 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=48150;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19012891 rs540898297 G C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40048;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19012914 rs565475946 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=39319;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013102 rs562490413 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36971;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013146 rs113934649 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37259;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013148 rs552012946 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37285;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013207 rs556302879 C A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36908;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013229 rs569289627 G C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=37934;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013283 rs555023916 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37973;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013284 rs573224590 A G 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37970;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013405 rs371166137 T A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=37256;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013463 rs59411215 C CA 100 PASS AC=3860;AF=7.70767e-01;NS=2504;AN=5008;EAS_AF=8.65100e-01;EUR_AF=6.36200e-01;AFR_AF=8.38100e-01;AMR_AF=7.30500e-01;SAS_AF=7.49500e-01;DP=35951;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|1 0|1 0|1 1|0 1|0 1|0 +14 19013468 rs576734940 A AG 100 PASS AC=22;AF=4.39297e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.51000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=34569;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013529 rs527328419 C T 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.06000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35775;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013549 rs552149768 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37642;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013588 rs564255135 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=39887;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013590 rs531620401 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40005;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013592 rs549727602 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=40032;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013647 rs201987889 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36872;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013804 rs538496244 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=41642;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013833 rs574652366 A C 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37370;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013841 rs542010326 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=35510;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013881 rs564077522 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34935;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013916 rs531528177 G C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36914;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013928 rs550000956 C A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37373;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19013970 rs529140291 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=36932;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014025 rs566999306 C G 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.80000e-03;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=34388;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014027 rs28797307 T G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34306;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014031 rs552303962 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=34258;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014038 rs570779216 A T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34323;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014042 rs538166735 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=34121;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014045 rs556856598 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34436;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014068 rs568411884 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35029;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014236 rs28835071 C T 100 PASS AC=3823;AF=7.63379e-01;NS=2504;AN=5008;EAS_AF=8.43300e-01;EUR_AF=6.40200e-01;AFR_AF=8.47200e-01;AMR_AF=7.14700e-01;SAS_AF=7.29000e-01;DP=36767;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|0 1|0 0|1 1|0 1|0 +14 19014248 rs557470091 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37451;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014250 rs575950645 A T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37508;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014294 rs562007004 C T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38372;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014296 rs529180262 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38168;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014374 rs541261924 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=34594;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014405 rs559554059 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=35182;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014474 rs28840207 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36135;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014488 rs531777957 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36175;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014562 rs561851380 CG C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=35882;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014611 rs565886823 G A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=8.20000e-03;DP=36004;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014623 rs539167229 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=36368;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014673 rs576051096 A G 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36850;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014674 rs28826949 T G 100 PASS AC=2505;AF=5.00200e-01;NS=2504;AN=5008;EAS_AF=5.04000e-01;EUR_AF=4.94000e-01;AFR_AF=4.97000e-01;AMR_AF=5.07200e-01;SAS_AF=5.02000e-01;DP=36100;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 0|0 1|0 1|0 1|0 1|0 +14 19014679 rs555386005 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36332;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014689 rs573998194 G C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=36103;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014715 rs541303773 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=36090;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014783 rs533193915 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=39434;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014842 rs531698212 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36652;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014925 rs529548697 G C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38148;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19014941 rs547641382 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38734;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015031 rs566229502 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=39340;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015069 rs569765512 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37834;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015092 rs555424521 T A 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.10000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37638;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015117 rs564621848 CA C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38597;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015163 rs577839703 C T 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38208;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015178 rs545223684 G C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38090;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015215 rs543467003 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=37094;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015282 rs529285299 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=38117;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015395 rs551965388 C A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37072;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015417 rs537146646 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36998;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015418 rs549141779 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=36783;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015466 rs552680016 G C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=37543;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015478 rs577887106 G C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37459;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015532 rs28891674 T C 100 PASS AC=20;AF=3.99361e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.51000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36046;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015546 rs575308158 T C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=5.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36004;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015555 rs542401807 A C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35861;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015575 rs149866623 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=36141;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015579 rs541059041 G C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35985;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015586 rs373718685 A C 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=1.09000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36182;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015587 rs533699083 G A 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=8.20000e-03;DP=36095;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015624 rs28805636 G T 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=7.90000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37470;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015634 rs140383373 A C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37797;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015678 rs531176497 A C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37267;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015773 rs567404320 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36053;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015876 rs528161200 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37483;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015912 rs546600104 C A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=6.10000e-03;DP=36056;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015920 rs571112296 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35925;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015950 rs538936283 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36540;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19015966 rs554325153 A T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37257;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016011 rs541136338 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=36994;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016087 rs545383089 C A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36522;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016108 rs531216699 A T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36179;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016263 rs546340304 G A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34856;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016274 rs532054401 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35719;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016280 rs372636264 A G 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=5.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36329;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016345 rs568844371 T A 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=7.60000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37540;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016419 rs554363985 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=1.00000e-03;DP=37045;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016445 rs535128787 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37396;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016470 rs578033513 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=37807;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016472 rs545106822 A G 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37900;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016473 rs557359479 A T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37991;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016495 rs561477652 C A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=38073;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016546 rs28838035 T C 100 PASS AC=3830;AF=7.64776e-01;NS=2504;AN=5008;EAS_AF=8.53200e-01;EUR_AF=6.48100e-01;AFR_AF=8.48000e-01;AMR_AF=7.16100e-01;SAS_AF=7.15700e-01;DP=38171;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 0|1 1|0 1|0 1|0 +14 19016618 rs550318561 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39023;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016655 rs548040378 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40750;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016662 rs533774866 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=40775;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016736 rs557397496 C G 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39696;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016812 rs573458823 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=39983;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19016899 rs540502513 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39454;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017016 rs565440074 G T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39587;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017031 rs562152316 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=38953;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017100 rs527547994 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=37296;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017179 rs570580236 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37615;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017242 rs569373030 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36233;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017246 rs536676109 T G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35888;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017247 rs554985129 G C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=35722;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017286 rs558886812 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=34268;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017315 rs577325925 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34367;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017334 rs28843138 G T 100 PASS AC=1617;AF=3.22883e-01;NS=2504;AN=5008;EAS_AF=4.08700e-01;EUR_AF=3.96600e-01;AFR_AF=1.46000e-01;AMR_AF=3.86200e-01;SAS_AF=3.52800e-01;DP=34545;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 0|0 1|0 1|0 1|0 0|1 +14 19017414 rs541441232 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36419;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017428 rs560067591 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36135;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017441 rs529531078 AT A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35835;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017460 rs527596096 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=1.00000e-03;DP=35147;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017687 rs549982336 C G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=38844;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017704 rs28819669 A G 100 PASS AC=25;AF=4.99201e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.82000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=38811;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017720 rs111635351 G A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38343;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017807 rs556305495 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37693;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017835 rs572050004 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37788;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017870 rs545480442 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=39344;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017873 rs564436169 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=39325;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017900 rs531624826 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39005;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017907 rs202007171 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39004;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19017980 rs548621398 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=36965;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018034 rs146358505 C T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=7.20000e-03;DP=37831;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018040 rs571139617 A G 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=5.10000e-03;DP=38103;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018138 rs535646258 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37801;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018144 rs572026350 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37590;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018154 rs545820665 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37791;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018184 rs557431445 A T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38418;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018225 rs576424331 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37970;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018235 rs28872628 T G 100 PASS AC=2497;AF=4.98602e-01;NS=2504;AN=5008;EAS_AF=5.01000e-01;EUR_AF=5.05000e-01;AFR_AF=4.92400e-01;AMR_AF=5.00000e-01;SAS_AF=4.96900e-01;DP=38553;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 0|1 0|1 1|0 1|0 1|0 +14 19018238 rs561871747 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36948;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018244 rs540864349 C G 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37220;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018274 rs560663419 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36530;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018290 rs527768429 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=36178;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018293 rs552563568 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36193;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018311 rs564094171 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=35925;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018313 rs531892906 G A 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.23000e-02;DP=35787;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018336 rs568413731 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35640;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018369 rs547663532 A C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=36920;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018419 rs557735560 C A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37107;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018422 rs576064666 A C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=37249;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018468 rs573960778 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37015;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018472 rs541254799 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37086;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018491 rs559254728 G A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=8.00000e-04;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=37009;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018557 rs564229870 C G 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=6.10000e-03;DP=37193;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018569 rs531638966 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=36946;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018590 rs547994802 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36276;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018689 rs555387723 A T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=36847;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018701 rs534566938 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=37362;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018731 rs545183005 A T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37454;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018750 rs557855819 C T 100 PASS AC=16;AF=3.19489e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=1.33000e-02;DP=36669;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018758 rs576110488 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=36740;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018854 rs28881254 A G 100 PASS AC=19;AF=3.79393e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.44000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37876;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018893 rs541325522 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=38971;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018924 rs533408359 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=39993;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19018993 rs549002912 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=37307;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019027 rs567109946 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37714;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019059 rs571494834 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=38925;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019074 rs202208641 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38749;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019076 rs576147401 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=4.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38299;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019093 rs543468649 A C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38502;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019200 rs28775893 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39504;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019224 rs559824535 C A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=6.10000e-03;DP=40633;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019260 rs28853679 T C 100 PASS AC=2502;AF=4.99601e-01;NS=2504;AN=5008;EAS_AF=4.99000e-01;EUR_AF=5.02000e-01;AFR_AF=4.95500e-01;AMR_AF=5.04300e-01;SAS_AF=5.00000e-01;DP=40187;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|0 1|0 0|1 0|1 0|1 +14 19019261 rs28851941 G A 100 PASS AC=60;AF=1.19808e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.54000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39222;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019265 rs563845387 A C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=6.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39704;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019287 rs201159773 T G 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=5.10000e-03;DP=40085;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019344 rs538514437 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40656;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019345 rs556737680 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=40237;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019404 rs555629716 G C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40196;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019428 rs534744031 A T 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=8.20000e-03;DP=39061;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019433 rs368498902 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39109;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019479 rs545676735 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=39826;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019548 rs543220565 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=39630;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019583 rs560852106 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=40486;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019621 rs528151845 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40709;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019637 rs546297460 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40829;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019662 rs532286240 T G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38937;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019760 rs567670950 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38498;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019841 rs575991609 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37958;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019846 rs112789397 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37699;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019882 rs561503018 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38467;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019889 rs572852041 G C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38562;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019949 rs564823908 T A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38402;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019992 rs532028611 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=5.80000e-03;SAS_AF=0.00000e+00;DP=38523;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19019993 rs550141494 A C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=5.80000e-03;SAS_AF=0.00000e+00;DP=37617;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020017 rs562478683 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37172;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020026 rs529905286 C T 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=7.20000e-03;DP=37155;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020036 rs548108052 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37220;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020040 rs201843075 G T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=37193;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020061 rs369148562 G C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=38131;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020069 rs571747017 A T 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=7.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=38419;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020098 rs539068329 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=39236;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020122 rs536901146 C A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=6.10000e-03;DP=38603;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020195 rs200145230 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36041;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020196 rs540469950 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35793;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020240 rs558260819 A C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=37077;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020249 rs28829342 A T 100 PASS AC=27;AF=5.39137e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.82000e-02;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=37510;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020273 rs376293501 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=5.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37123;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020310 rs542068092 C A 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35338;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020377 rs112834034 A C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36720;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020418 rs571783932 A C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37916;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020431 rs532620598 T C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=4.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37170;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020455 rs569231975 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36341;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020480 rs555293331 G T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=36121;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020534 rs71406421 G A 100 PASS AC=1619;AF=3.23283e-01;NS=2504;AN=5008;EAS_AF=3.97800e-01;EUR_AF=4.03600e-01;AFR_AF=1.42200e-01;AMR_AF=3.96300e-01;SAS_AF=3.56900e-01;DP=36355;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 0|1 0|1 1|0 0|1 0|1 +14 19020535 rs576553023 C T 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35973;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 1|0 0|0 0|0 0|0 +14 19020582 rs28861970 C T 100 PASS AC=3833;AF=7.65375e-01;NS=2504;AN=5008;EAS_AF=8.50200e-01;EUR_AF=6.43100e-01;AFR_AF=8.44200e-01;AMR_AF=7.19000e-01;SAS_AF=7.30100e-01;DP=36076;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|0 1|0 0|1 1|0 1|0 +14 19020615 rs112380113 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36852;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020682 rs560430368 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=35983;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020695 rs527556061 A G 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35600;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020696 rs201598404 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35690;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020703 rs551133753 A G 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=4.50000e-03;AMR_AF=1.40000e-03;SAS_AF=3.10000e-03;DP=35590;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020778 rs548275944 C A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=36303;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020853 rs535446689 C A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=4.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36184;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020860 rs553459698 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36018;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020918 rs556745417 TC T 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=8.90000e-03;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37105;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020936 rs564360310 A C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37097;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19020967 rs576348826 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37183;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 0|0 0|0 0|0 0|0 0|0 +14 19021111 rs560243396 T C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=38665;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021112 rs572911533 AT A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=7.20000e-03;DP=39035;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021128 rs552493061 G C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=38700;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021175 rs144904964 GT G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=38519;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021223 rs538082693 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38067;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021244 rs568169385 C A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39263;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021336 rs201291059 C G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39596;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021374 rs576391276 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=39321;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021427 rs574880890 T G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=39356;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021459 rs545776525 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=39315;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021507 rs564455970 C A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=39341;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021544 rs550351614 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39546;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021588 rs547219706 A G 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=6.10000e-03;DP=39714;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021652 rs539477363 T C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=40021;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021714 rs573795095 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39114;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021715 rs376655299 C T 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=39348;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021716 rs554003158 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=39142;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021747 rs545815246 G T 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=5.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=5.10000e-03;DP=39296;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021763 rs564092390 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39464;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021778 rs531890530 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39184;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021799 rs543799788 A T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39800;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021860 rs28771210 G T 100 PASS AC=2453;AF=4.89816e-01;NS=2504;AN=5008;EAS_AF=4.99000e-01;EUR_AF=4.87100e-01;AFR_AF=4.69700e-01;AMR_AF=5.02900e-01;SAS_AF=5.01000e-01;DP=38535;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 0|1 1|0 0|1 0|1 0|1 +14 19021862 rs529490288 A G 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37211;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19021945 rs533466235 AC A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=39770;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19022006 rs569630549 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=39492;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19022142 rs534533315 A T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=39207;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19022167 rs149880966 C G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=39120;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19022264 rs576071442 A T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39307;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19022292 rs533071279 C G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39744;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19022528 rs537068626 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=38681;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19022573 rs555706388 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=37001;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19022644 rs560078695 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38187;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 .|. 0|0 0|0 0|0 +14 19022646 rs578236664 A G 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=1.19000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37716;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 .|. 0|0 0|0 0|0 +14 19022771 rs546535172 C T 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=8.00000e-03;AFR_AF=0.00000e+00;AMR_AF=7.20000e-03;SAS_AF=0.00000e+00;DP=37062;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19022780 rs200760560 CA C 100 PASS AC=18;AF=3.59425e-03;NS=2504;AN=5008;EAS_AF=1.79000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37793;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19022841 rs538479269 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37020;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19022854 rs200070687 A C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=5.80000e-03;SAS_AF=0.00000e+00;DP=36953;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19022886 rs111904163 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36686;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19022887 rs555490457 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36733;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19022894 rs112607657 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36675;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19022909 rs535014755 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36583;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19022919 rs553731652 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36604;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19022948 rs557542249 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36480;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19022973 rs560815560 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37647;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023011 rs564849529 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=37758;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023016 rs532247556 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37786;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023038 rs568995118 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=37811;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023142 rs553369254 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=40386;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023154 rs571971690 G T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=5.10000e-03;DP=40786;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023158 rs539296751 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=40668;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023248 rs199588685 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=38723;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023251 rs564495662 T C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=38672;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023299 rs544143795 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40063;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023379 rs567765198 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39978;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023424 rs547024501 G T 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39168;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023435 rs539031294 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=39530;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023468 rs557660402 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=41070;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023482 rs569431837 T G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=41264;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023529 rs572609587 C A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=42444;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023551 rs533604561 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=42708;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023561 rs558223975 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=42772;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023623 rs527472959 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40593;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023678 rs532582496 T G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39162;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023738 rs536497220 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36418;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023762 rs548775057 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35104;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|1 0|0 0|0 0|0 +14 19023776 rs566766444 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34308;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023777 rs28811330 A G 100 PASS AC=3696;AF=7.38019e-01;NS=2504;AN=5008;EAS_AF=8.14500e-01;EUR_AF=6.30200e-01;AFR_AF=8.43400e-01;AMR_AF=6.58500e-01;SAS_AF=6.84000e-01;DP=33730;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|0 0|1 1|0 1|1 1|0 +14 19023812 rs576514849 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36204;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023864 rs537864114 C A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=39544;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023888 rs574680386 G C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=40078;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023914 rs560464603 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=38748;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023924 rs572297170 C A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=38270;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19023946 rs546005343 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37861;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 1|0 0|0 +14 19023958 rs551953236 TC T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38840;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024021 rs532470495 C T 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=38320;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024039 rs562700850 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=37277;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024117 rs113745977 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34727;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024123 rs534157582 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=34799;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024206 rs537497976 C A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=33948;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024254 rs553130602 T TCTAGAAGTTTCTAGAATACGG 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34061;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 1|0 0|0 0|0 +14 19024257 rs556212396 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=2.00000e-03;DP=34092;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024280 rs28876671 G A 100 PASS AC=2404;AF=4.80032e-01;NS=2504;AN=5008;EAS_AF=4.77200e-01;EUR_AF=4.83100e-01;AFR_AF=4.78100e-01;AMR_AF=4.78400e-01;SAS_AF=4.83600e-01;DP=34035;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 0|1 0|1 0|1 0|1 0|1 +14 19024405 rs546040231 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37624;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024458 rs557936642 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36011;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024459 rs577274846 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=35957;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024524 rs562999199 A C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37831;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024553 rs530069699 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=34960;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024577 rs183277728 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=5.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=33079;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024718 rs552357649 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34031;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024776 rs570917340 T A 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.87000e-02;SAS_AF=0.00000e+00;DP=33979;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024783 rs531928977 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=33937;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024795 rs549637334 C T 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.30000e-02;SAS_AF=2.00000e-03;DP=33783;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024806 rs568131437 C A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=5.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=34031;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024853 rs553772541 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36373;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024866 rs565980157 G T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=4.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36259;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19024984 rs556419645 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34631;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025070 rs146077897 A C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34648;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025106 rs199690628 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35267;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025175 rs374019579 G T 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=7.60000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35061;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025190 rs531844957 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35477;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025229 rs550314769 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35333;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025324 rs528947314 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36247;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025346 rs539439101 C T 100 PASS AC=25;AF=4.99201e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.89000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37266;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025347 rs551728766 G A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=37127;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025362 rs536868263 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37419;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025409 rs535518603 C T 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=37363;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025412 rs553841266 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=37335;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025413 rs572134321 G C 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=4.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=9.20000e-03;DP=37297;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025465 rs576645029 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35801;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025466 rs141748612 A AT 100 PASS AC=316;AF=6.30990e-02;NS=2504;AN=5008;EAS_AF=1.14100e-01;EUR_AF=7.65000e-02;AFR_AF=2.30000e-03;AMR_AF=5.19000e-02;SAS_AF=8.69000e-02;DP=35802;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025481 rs543657515 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35633;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025486 rs369368540 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=4.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35672;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025494 rs529499753 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=35949;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025516 rs547563546 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=2.00000e-03;DP=37062;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025525 rs559470726 A C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37314;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025547 rs551323350 A C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37641;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025556 rs569876428 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=37606;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025689 rs534486105 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38453;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025717 rs572171139 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39267;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025780 rs571082241 G GT 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=8.60000e-03;SAS_AF=0.00000e+00;DP=37424;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025814 rs558086018 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=36223;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025828 rs544134882 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35942;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025874 rs574313433 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37633;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025900 rs533031650 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37836;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19025997 rs61974792 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36449;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19026022 rs368452020 G C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=37458;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19026068 rs536791883 TC T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=38674;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19026081 rs546359412 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=37368;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19026086 rs565835953 A C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37200;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19026143 rs557960043 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=35326;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19026158 rs377142660 C A 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=1.39000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34826;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19026521 rs545131648 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35563;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19026617 rs111898644 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36670;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19026664 rs530560813 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=35291;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19026682 rs542222876 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=35289;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19026686 rs560867948 A T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35402;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19026728 rs374795811 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37000;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19026759 rs546398502 T C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36666;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19026786 rs532202573 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35762;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19026910 rs567963257 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=37143;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027011 rs578158456 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35816;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027018 rs545251798 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35953;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027019 rs557032976 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35911;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027032 rs575219828 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36529;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027053 rs542609286 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=37558;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027073 rs560505060 A G 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38182;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027099 rs528067714 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37707;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027217 rs200475939 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37069;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027261 rs550469505 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38588;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027272 rs563827178 G A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38084;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027280 rs530862155 A C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37847;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027301 rs535015113 G A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=6.10000e-03;DP=37581;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027360 rs539240573 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35039;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027361 rs557224893 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=34940;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027379 rs575304613 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=35583;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027432 rs535983088 C G 100 PASS AC=15;AF=2.99521e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.06000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37732;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027451 rs554239486 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36955;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027536 rs112923005 A C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35564;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027557 rs112571074 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36224;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027586 rs577035704 T A 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.33000e-02;DP=37680;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027702 rs562504524 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34188;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027758 rs529891773 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=6.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36196;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027823 rs528531488 T G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=35559;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027883 rs551243847 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=34191;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19027960 rs536425859 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=5.10000e-03;DP=36994;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028044 rs558220488 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=32350;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028065 rs577077791 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=31763;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028093 rs544223594 C T 100 PASS AC=41;AF=8.18690e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.03000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=31786;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028193 rs574714595 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34915;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028254 rs371218963 T C 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=4.10000e-03;DP=36088;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028287 rs565172662 G C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=36671;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028321 rs374718514 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=5.80000e-03;SAS_AF=0.00000e+00;DP=36224;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028359 rs368463829 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35541;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028468 rs548347864 T G 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=35812;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028477 rs566234813 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35790;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028508 rs533602485 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=35917;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028544 rs558610998 G C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=35070;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028553 rs147377084 C A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=4.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=34823;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028610 rs556221228 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36756;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028668 rs377438782 T C 100 PASS AC=388;AF=7.74760e-02;NS=2504;AN=5008;EAS_AF=1.36900e-01;EUR_AF=4.17000e-02;AFR_AF=4.50000e-03;AMR_AF=1.77200e-01;SAS_AF=8.08000e-02;DP=37254;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|1 0|0 1|0 +14 19028669 rs28795219 G C 100 PASS AC=1609;AF=3.21286e-01;NS=2504;AN=5008;EAS_AF=3.97800e-01;EUR_AF=3.99600e-01;AFR_AF=1.42200e-01;AMR_AF=3.97700e-01;SAS_AF=3.49700e-01;DP=36354;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|0 0|0 0|1 0|1 1|0 +14 19028693 rs200085407 C T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=7.20000e-03;DP=36322;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028732 rs530283757 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35951;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028752 rs548384785 C T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36690;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028913 rs539310810 GC G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38387;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028933 rs552017788 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37452;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028960 rs371634187 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37582;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028990 rs572629414 CA C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37030;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19028993 rs556075417 A T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36742;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029067 rs568371349 G A 100 PASS AC=26;AF=5.19169e-03;NS=2504;AN=5008;EAS_AF=1.29000e-02;EUR_AF=0.00000e+00;AFR_AF=7.60000e-03;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=36919;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029068 rs535785969 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37015;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029116 rs572297134 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=39033;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029120 rs545962974 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39311;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029130 rs558797026 A G 100 PASS AC=17;AF=3.39457e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=1.13000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39622;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029183 rs544283664 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=38487;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029276 rs542163527 A C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38134;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029345 rs560394237 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=6.10000e-03;DP=38218;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029352 rs527917516 T A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=38438;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029401 rs552705795 C T 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.73000e-02;SAS_AF=0.00000e+00;DP=36926;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029419 rs367638991 C A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=5.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36937;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029422 rs568107046 C A 100 PASS AC=20;AF=3.99361e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=1.21000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37229;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029429 rs535417498 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37657;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029576 rs557886763 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=36011;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029593 rs577276388 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36261;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029618 rs538378682 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36614;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029776 rs576925611 G GC 100 PASS AC=165;AF=3.29473e-02;NS=2504;AN=5008;EAS_AF=3.67000e-02;EUR_AF=2.09000e-02;AFR_AF=1.50000e-03;AMR_AF=7.93000e-02;SAS_AF=5.11000e-02;DP=37606;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029824 rs560430956 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39332;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029828 rs572672779 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=39049;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029829 rs181366258 G C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38982;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029874 rs564740784 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37760;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19029876 rs28847405 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37595;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030007 rs539680182 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=35427;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030021 rs28831154 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35008;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030052 rs569880093 T C 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=33846;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030084 rs536824429 C T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=33587;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030165 rs551228020 CT C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=37090;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 1|0 0|0 0|0 0|0 +14 19030286 rs553706260 C T 100 PASS AC=21;AF=4.19329e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.59000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=33002;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030308 rs572337711 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=33904;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030315 rs558144594 C A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34431;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030327 rs576607940 A C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=33963;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030413 rs528949403 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=6.10000e-03;DP=33734;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030420 rs541036856 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=34121;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030422 rs376377250 C T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34227;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030434 rs569835985 G A 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.09000e-02;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=34908;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030444 rs530636101 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35344;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030475 rs548742417 A T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36797;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030493 rs535591309 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37162;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030682 rs558441695 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36656;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030744 rs544033922 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35262;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030778 rs559163773 T A 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36166;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030839 rs563623406 G A 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=4.00000e-03;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38421;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030860 rs369691309 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37199;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030925 rs567167238 T C 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=8.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=35090;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19030958 rs528245927 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36363;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031006 rs547902801 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37377;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031031 rs376823899 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35943;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031131 rs570372656 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35452;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031204 rs371165736 C T 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=9.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34573;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031207 rs200177424 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=34818;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031225 rs553049138 T C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35570;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031227 rs577638553 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35775;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031228 rs544995630 G A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=35785;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031374 rs560831309 A C 100 PASS AC=26;AF=5.19169e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.97000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=32759;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031400 rs528283645 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=32231;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031461 rs533228541 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34257;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031480 rs570112427 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=35433;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031487 rs537421023 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=35938;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031500 rs549733303 T C 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=36166;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031524 rs567926442 G C 100 PASS AC=37;AF=7.38818e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.09000e-02;AFR_AF=1.50000e-03;AMR_AF=1.01000e-02;SAS_AF=7.20000e-03;DP=36556;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031540 rs535244570 T G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35868;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031571 rs111317542 A G 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=35153;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031876 rs560868080 G T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36457;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031890 rs572753026 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=35677;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19031930 rs540430082 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36482;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19032020 rs563756344 G C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35954;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19032036 rs549371042 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36407;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19032066 rs567965267 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36584;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19032225 rs571773199 G T 100 PASS AC=17;AF=3.39457e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.29000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36661;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19032226 rs539204563 A T 100 PASS AC=17;AF=3.39457e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.29000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35837;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19032240 rs556651650 A C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36297;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19032329 rs28788525 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36493;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19032656 rs199827876 A T 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35528;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19032756 rs561309387 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36917;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19032767 rs369154121 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36897;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19032796 rs571872495 A T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36294;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19032828 rs568619599 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=35912;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19032880 rs554239491 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37562;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19032897 rs566372488 A G 100 PASS AC=27;AF=5.39137e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.04000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37050;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19032978 rs558594826 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34131;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19032998 rs577039267 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=34566;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19033002 rs112180566 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34935;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19033021 rs556355335 T G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=35335;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19033120 rs543193728 T C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=33908;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19033137 rs561416043 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=33753;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19033151 rs540590553 T A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=5.10000e-03;DP=34328;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19033316 rs547916223 C A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=35911;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19033340 rs566528550 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35512;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19033365 rs552106635 T C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36179;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19033367 rs570666745 C G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=36241;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19033400 rs538185324 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37065;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19033564 rs535606892 A G 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36865;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19033627 rs540275682 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=36238;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19033651 rs565319824 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35691;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19033753 rs576822929 C A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=1.40000e-03;SAS_AF=2.00000e-03;DP=38542;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19033817 rs200227379 T G 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38571;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19033926 rs547272319 CTG C 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37700;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034000 rs570030028 CT C 100 PASS AC=47;AF=9.38498e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.40000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=36074;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034015 rs559994871 C A 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35817;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034044 rs527340446 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36148;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034124 rs537821898 G C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38345;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034194 rs28869799 C A 100 PASS AC=345;AF=6.88898e-02;NS=2504;AN=5008;EAS_AF=1.22000e-01;EUR_AF=2.78000e-02;AFR_AF=8.00000e-04;AMR_AF=4.03000e-02;SAS_AF=1.68700e-01;DP=37954;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034195 rs28795486 G A 100 PASS AC=345;AF=6.88898e-02;NS=2504;AN=5008;EAS_AF=1.22000e-01;EUR_AF=2.78000e-02;AFR_AF=8.00000e-04;AMR_AF=4.03000e-02;SAS_AF=1.68700e-01;DP=36851;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034239 rs553890060 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37822;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034253 rs534348958 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38886;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034335 rs558760086 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36239;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034370 rs576859915 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35488;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034375 rs544166389 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=7.20000e-03;SAS_AF=0.00000e+00;DP=35401;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034485 rs527879018 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=36302;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034527 rs545914517 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35654;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034528 rs113152421 G A 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=35592;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034536 rs531352071 C T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.01000e-02;SAS_AF=0.00000e+00;DP=35909;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034563 rs568371274 A C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36817;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034665 rs559024965 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37092;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 0|0 0|0 0|0 0|0 0|0 +14 19034727 rs570584453 A G 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37265;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034785 rs574484547 T A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=37263;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034805 rs542557966 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38003;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034819 rs554150720 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37596;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034833 rs572636459 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37497;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034862 rs201000470 G A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=7.90000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37169;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034864 rs28892951 A T 100 PASS AC=1739;AF=3.47244e-01;NS=2504;AN=5008;EAS_AF=4.12700e-01;EUR_AF=4.03600e-01;AFR_AF=2.13300e-01;AMR_AF=4.00600e-01;SAS_AF=3.65000e-01;DP=36718;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 0|1 0|0 0|1 0|1 0|1 +14 19034865 rs531402688 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=37064;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034887 rs367583388 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37871;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034890 rs565795997 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38015;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034930 rs533154105 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38758;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034933 rs551133206 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=38694;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19034958 rs570627342 G A 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=8.90000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38190;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035001 rs537981402 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37655;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035021 rs556215820 C A 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37565;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035036 rs568160939 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=5.80000e-03;SAS_AF=1.00000e-03;DP=37142;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035042 rs535469300 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=37366;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035059 rs558426734 A T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37525;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035062 rs576690416 T G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37656;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035069 rs543590991 T G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37515;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035161 rs559620720 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37055;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035189 rs530614619 T C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36725;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035198 rs200696510 G A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=6.10000e-03;DP=36312;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035217 rs568418499 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=35609;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035230 rs535841870 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35757;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035309 rs572770841 AC A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=8.20000e-03;DP=38337;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035328 rs566052089 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=37219;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035397 rs61974820 A G 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37191;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035398 rs537602915 T C 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37207;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035414 rs28858814 A C 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38144;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035433 rs541035768 C T 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=38831;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035467 rs544947201 T G 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.06000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37291;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035486 rs563231209 A T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36806;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035545 rs562229429 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36497;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035561 rs529404348 T G 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37412;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035586 rs539834707 G C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=6.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38490;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035735 rs542331610 AC A 100 PASS AC=184;AF=3.67412e-02;NS=2504;AN=5008;EAS_AF=4.07000e-02;EUR_AF=2.19000e-02;AFR_AF=6.80000e-03;AMR_AF=8.50000e-02;SAS_AF=5.42000e-02;DP=37876;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035764 rs555646209 T A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=5.10000e-03;DP=38802;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035823 rs534446750 A T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=39567;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035843 rs113666007 A T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=38979;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035846 rs577258017 T C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=38759;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035871 rs575165546 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=36902;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035940 rs528288192 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38106;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19035948 rs541208363 T C 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=7.60000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=38076;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19036091 rs544608649 CA C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=36649;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19036164 rs570961477 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37294;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19036179 rs538265561 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37071;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19036225 rs200011480 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=36323;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19036254 rs113200203 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=36854;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19036335 rs559613602 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=35488;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19036337 rs533431687 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=35457;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19036390 rs549451096 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=34608;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19036530 rs201463538 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37616;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19036626 rs556637456 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=37692;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19036654 rs554571948 T C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=38420;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19036720 rs533764809 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37711;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19036727 rs558822162 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37307;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19036728 rs75101722 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37272;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19036778 rs575557471 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36844;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19036805 rs561441944 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=37520;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19036919 rs528746468 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36279;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037021 rs535891948 C G 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36463;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037083 rs534122489 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=35805;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037125 rs558887790 G T 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36755;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037182 rs79797971 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=37338;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037245 rs575663151 C T 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36389;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037246 rs542669004 A T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36410;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037265 rs561365365 T G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=36216;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037311 rs573155296 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=37458;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037349 rs532573201 G T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36181;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037417 rs562259333 C A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=35681;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037516 rs566508795 T C 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=36059;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037546 rs533543728 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34630;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037557 rs552508438 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34742;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037588 rs570710347 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=34277;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037595 rs538059255 A C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34042;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037609 rs28861545 G A 100 PASS AC=3867;AF=7.72165e-01;NS=2504;AN=5008;EAS_AF=8.55200e-01;EUR_AF=6.58100e-01;AFR_AF=8.48700e-01;AMR_AF=7.33400e-01;SAS_AF=7.28000e-01;DP=35410;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|0 0|1 1|0 1|0 1|0 +14 19037613 rs568144038 C T 100 PASS AC=115;AF=2.29633e-02;NS=2504;AN=5008;EAS_AF=2.58000e-02;EUR_AF=1.09000e-02;AFR_AF=3.00000e-03;AMR_AF=5.62000e-02;SAS_AF=3.58000e-02;DP=33720;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037673 rs536802040 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=35535;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037690 rs554759418 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34530;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037746 rs544487948 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=35093;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037760 rs563126481 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=34893;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037770 rs530227932 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34756;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037776 rs112531044 A T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=34850;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037796 rs527285056 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34991;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037855 rs531667604 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34008;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037902 rs535257664 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=32836;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037928 rs555050279 G A 100 PASS AC=18;AF=3.59425e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=1.43000e-02;DP=33605;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037947 rs533948170 G T 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=34571;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19037973 rs544551089 G C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=36182;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19038102 rs542009975 T C 100 PASS AC=28;AF=5.59105e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.99000e-02;AFR_AF=1.50000e-03;AMR_AF=7.20000e-03;SAS_AF=1.00000e-03;DP=29216;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19038108 rs560212391 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=1.00000e-03;DP=28268;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19038132 rs560891083 AC A 100 PASS AC=303;AF=6.05032e-02;NS=2504;AN=5008;EAS_AF=1.05200e-01;EUR_AF=6.36000e-02;AFR_AF=2.30000e-03;AMR_AF=4.76000e-02;SAS_AF=9.92000e-02;DP=34917;AA=|||unknown(NO_COVERAGE);VT=INDEL GT 0|0 1|1 0|0 1|1 0|1 0|0 0|0 0|0 0|0 0|0 +14 19038256 rs545895367 C A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=2.00000e-03;DP=19053;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19038257 rs375909818 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=19478;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 19038291 rs550062154 C A 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.09000e-02;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=32694;AA=.|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21554855 rs74036591 G T 100 PASS AC=401;AF=8.00719e-02;NS=2504;AN=5008;EAS_AF=3.37000e-02;EUR_AF=4.97000e-02;AFR_AF=1.64100e-01;AMR_AF=3.75000e-02;SAS_AF=7.57000e-02;DP=18352;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21554860 rs56209647 T C 100 PASS AC=62;AF=1.23802e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=4.54000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18328;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21555035 rs146901485 T G 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18519;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21555063 rs7342537 A G 100 PASS AC=75;AF=1.49760e-02;NS=2504;AN=5008;EAS_AF=3.27000e-02;EUR_AF=2.49000e-02;AFR_AF=6.80000e-03;AMR_AF=4.30000e-03;SAS_AF=5.10000e-03;DP=18008;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21555087 rs145744937 AAATC A 100 PASS AC=3033;AF=6.05631e-01;NS=2504;AN=5008;EAS_AF=5.23800e-01;EUR_AF=7.54500e-01;AFR_AF=4.28900e-01;AMR_AF=7.82400e-01;SAS_AF=6.50300e-01;DP=20851;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 1|1 1|1 1|0 0|1 1|1 +14 21555238 rs78373354 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17048;AA=C|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21555322 rs553542471 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17169;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21555357 rs191129178 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16626;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21555367 rs549433318 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16603;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21555481 rs55901089 G A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=4.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=2.00000e-03;DP=13997;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21555574 rs75882726 C T 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=9.90000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16395;AA=C|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21555645 rs564666472 G C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17621;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21555659 rs75670895 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=1.00000e-03;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18140;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21555754 rs116011011 A G 100 PASS AC=86;AF=1.71725e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.28000e-02;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=19892;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21555756 rs190335871 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=19960;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21555817 rs143318804 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19384;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21555895 rs2274682 G T 100 PASS AC=249;AF=4.97204e-02;NS=2504;AN=5008;EAS_AF=6.05000e-02;EUR_AF=4.37000e-02;AFR_AF=7.72000e-02;AMR_AF=4.32000e-02;SAS_AF=1.23000e-02;DP=19016;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 0|0 0|0 0|0 1|0 0|0 +14 21555905 rs143638051 G C 100 PASS AC=27;AF=5.39137e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.89000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=18893;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21555917 rs182890854 A C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=18885;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21556005 rs111713440 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=8.00000e-04;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=19754;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21556167 rs2274683 A T 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=1.29000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15523;AA=A|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21556198 rs114151912 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15136;AA=C|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21556232 rs114938147 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16100;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21556447 rs369941900 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18136;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21556696 rs113694926 G C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15825;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21556699 rs375086014 G A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15841;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21556716 rs73589929 G A 100 PASS AC=150;AF=2.99521e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=1.10400e-01;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=15282;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21556846 rs560353259 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18033;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21556963 rs35186993 A AT 100 PASS AC=3305;AF=6.59944e-01;NS=2504;AN=5008;EAS_AF=5.66500e-01;EUR_AF=7.44500e-01;AFR_AF=5.80900e-01;AMR_AF=8.24200e-01;SAS_AF=6.59500e-01;DP=17907;AA=TT|TT|TTT|insertion;VT=INDEL;EX_TARGET GT 0|0 1|1 0|0 1|1 0|1 0|1 1|1 1|1 1|1 0|1 +14 21557021 rs74584322 G A 100 PASS AC=194;AF=3.87380e-02;NS=2504;AN=5008;EAS_AF=3.27000e-02;EUR_AF=4.77000e-02;AFR_AF=6.10000e-03;AMR_AF=2.16000e-02;SAS_AF=9.20000e-02;DP=18513;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21557063 rs534876124 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=6.10000e-03;DP=18109;AA=C|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21557089 rs141705468 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=5.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18338;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21557109 rs61978230 G A 100 PASS AC=193;AF=3.85383e-02;NS=2504;AN=5008;EAS_AF=3.27000e-02;EUR_AF=4.77000e-02;AFR_AF=6.10000e-03;AMR_AF=2.16000e-02;SAS_AF=9.10000e-02;DP=18884;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21557152 rs192765233 C T 100 PASS AC=20;AF=3.99361e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.51000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19402;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21557179 rs146244738 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19518;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21557430 rs184782434 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17141;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21557433 rs139383938 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17034;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21557487 rs144883695 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=5.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16312;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21557501 rs372534612 TCTC T 100 PASS AC=19;AF=3.79393e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=6.00000e-03;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=1.12000e-02;DP=16626;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21557529 rs114005868 C A 100 PASS AC=37;AF=7.38818e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.72000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=16000;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21557564 rs528395091 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18088;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21557652 rs73589932 A T 100 PASS AC=79;AF=1.57748e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.90000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19192;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21557737 rs191975607 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20838;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21557850 rs142111342 C G 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=6.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16555;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21557948 rs115687167 C T 100 PASS AC=45;AF=8.98562e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=3.33000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17262;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21557977 rs563198829 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18677;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21558012 rs151180024 G C 100 PASS AC=32;AF=6.38978e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=2.27000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19789;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21558103 rs181192302 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=22289;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21558159 rs74937678 T C 100 PASS AC=95;AF=1.89696e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.88000e-02;AMR_AF=5.80000e-03;SAS_AF=0.00000e+00;DP=20548;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21558270 rs115275386 G A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17953;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21558554 rs200238223 CCG C 100 PASS AC=90;AF=1.79712e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.73000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=16306;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21558558 rs6571653 G C 100 PASS AC=2004;AF=4.00160e-01;NS=2504;AN=5008;EAS_AF=3.76000e-01;EUR_AF=1.91800e-01;AFR_AF=7.73800e-01;AMR_AF=1.94500e-01;SAS_AF=2.80200e-01;DP=16023;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|0 0|0 0|0 0|0 1|1 +14 21558560 rs141238761 CTT C 100 PASS AC=90;AF=1.79712e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.73000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=16238;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21558588 rs574302373 G GA 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16191;AA=A|A|AA|insertion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21558679 rs200238072 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=13705;AA=c|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21558683 rs370670607 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=13657;AA=C|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21559119 rs28520010 G A 100 PASS AC=136;AF=2.71565e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=9.91000e-02;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=12558;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21559124 rs577616670 C G 100 PASS AC=23;AF=4.59265e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.35000e-02;DP=12562;AA=C|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21559170 rs569399756 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=12339;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21559195 rs186070988 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=11979;AA=C|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21559241 rs45524331 G C 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.09000e-02;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=13451;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21559311 rs34720103 G A 100 PASS AC=123;AF=2.45607e-02;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=5.27000e-02;AFR_AF=2.27000e-02;AMR_AF=4.32000e-02;SAS_AF=9.20000e-03;DP=14838;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 1|0 0|0 0|0 0|0 0|0 +14 21559317 rs553071051 G C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14785;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21559557 rs200418923 C A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17119;AA=C|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21559714 rs543425040 C T 100 PASS AC=20;AF=3.99361e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.04000e-02;DP=14777;AA=C|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21559815 rs150804235 C CGG 100 PASS AC=77;AF=1.53754e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.60000e-02;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=16649;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21559885 rs139176136 GAAAACAAAAC G 100 PASS AC=50;AF=9.98403e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.71000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19721;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21559930 rs74036595 G C 100 PASS AC=93;AF=1.85703e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=6.66000e-02;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=16505;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21559978 rs182015165 C G 100 PASS AC=25;AF=4.99201e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.74000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=13517;AA=C|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21559994 rs548889769 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=12562;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21560006 rs185810817 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=12763;AA=C|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21560007 rs77712292 G A 100 PASS AC=78;AF=1.55751e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=5.75000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=12703;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21560029 rs376640373 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=5.10000e-03;DP=12367;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21560048 rs115764390 G C 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=7.60000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=11755;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21560094 rs558471585 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=11325;AA=C|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21560162 rs150490488 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=11299;AA=C|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21560429 rs138145521 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=11401;AA=C|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21560455 rs199878395 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=11732;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21560706 rs1065496 C G 100 PASS AC=448;AF=8.94569e-02;NS=2504;AN=5008;EAS_AF=9.42000e-02;EUR_AF=7.85000e-02;AFR_AF=1.09700e-01;AMR_AF=4.90000e-02;SAS_AF=9.71000e-02;DP=11470;AA=C|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|1 0|0 0|0 0|0 1|0 0|0 +14 21560727 rs79837221 G A 100 PASS AC=34;AF=6.78914e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.29000e-02;AFR_AF=0.00000e+00;AMR_AF=5.80000e-03;SAS_AF=1.74000e-02;DP=11707;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|1 0|0 0|0 +14 21560752 rs3841049 GGAGGCT G 100 PASS AC=1230;AF=2.45607e-01;NS=2504;AN=5008;EAS_AF=1.25000e-01;EUR_AF=1.87900e-01;AFR_AF=2.54900e-01;AMR_AF=3.77500e-01;SAS_AF=3.23100e-01;DP=14407;VT=INDEL;EX_TARGET GT 0|0 1|1 0|0 1|1 0|1 0|0 0|0 0|1 1|0 0|0 +14 21560865 rs568724086 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14517;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21560882 rs528000807 C A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=7.20000e-03;DP=15083;AA=C|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21561030 rs116749937 G A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14194;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21561078 rs114931279 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14165;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21561165 rs61749060 C T 100 PASS AC=68;AF=1.35783e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.99000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=15197;AA=C|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21561300 rs11848574 T C 100 PASS AC=494;AF=9.86422e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.62300e-01;AMR_AF=2.16000e-02;SAS_AF=0.00000e+00;DP=15665;AA=T|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21561480 rs553746956 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=18422;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21561606 rs61488987 G A 100 PASS AC=82;AF=1.63738e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.13000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18152;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21561612 rs545964123 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=18240;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21561722 rs531715992 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=19258;AA=G|||;VT=SNP;EX_TARGET GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21561848 rs182870174 A C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20757;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21561879 rs527990791 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21013;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21561947 rs73589936 C T 100 PASS AC=77;AF=1.53754e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.75000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=20352;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21561999 rs114695976 T C 100 PASS AC=16;AF=3.19489e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.21000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19511;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21562288 rs539775181 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=20134;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21562387 rs376394244 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18727;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21562471 rs542391376 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16776;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21562476 rs545570275 AAG A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=5.10000e-03;DP=17047;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21562560 rs7149011 T C 100 PASS AC=2044;AF=4.08147e-01;NS=2504;AN=5008;EAS_AF=4.73200e-01;EUR_AF=6.43100e-01;AFR_AF=9.83000e-02;AMR_AF=4.98600e-01;SAS_AF=4.54000e-01;DP=14633;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|1 1|1 1|0 0|1 1|1 +14 21562590 rs541662863 C A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14058;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21562772 rs559682389 G A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=8.20000e-03;DP=12380;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21562814 rs528304945 C T 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=1.23000e-02;DP=10365;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21562894 rs562381632 G C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=4588;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21562929 rs142065766 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=7186;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21562989 rs567896891 A T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=11904;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21563066 rs59112788 CTTT C 100 PASS AC=4321;AF=8.62819e-01;NS=2504;AN=5008;EAS_AF=6.24000e-01;EUR_AF=8.97600e-01;AFR_AF=9.90900e-01;AMR_AF=9.51000e-01;SAS_AF=8.37400e-01;DP=12151;VT=INDEL GT 0|0 1|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 +14 21563106 rs533703772 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=10480;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21563300 rs532716578 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=16735;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21563319 rs182316452 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=17000;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21563350 rs73589940 T C 100 PASS AC=86;AF=1.71725e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.43000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=17792;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21563385 rs535939503 T C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18127;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21563535 rs371875091 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20639;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21563662 rs192465923 A C 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.15000e-02;SAS_AF=0.00000e+00;DP=20591;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21563796 rs543806026 G A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=1.00000e-03;DP=16805;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21563834 rs531239882 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16887;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21563929 rs528574310 GA G 100 PASS AC=51;AF=1.01837e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.78000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=15547;AA=AAAAAAA|AAAAAAA|AAAAAA|deletion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21563950 rs114879121 G C 100 PASS AC=28;AF=5.59105e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.12000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15582;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21564000 rs185011480 A G 100 PASS AC=23;AF=4.59265e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.49000e-02;AFR_AF=8.00000e-04;AMR_AF=1.01000e-02;SAS_AF=0.00000e+00;DP=14506;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 1|0 0|0 0|0 0|0 +14 21564203 rs113486825 G C 100 PASS AC=168;AF=3.35463e-02;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=2.19000e-02;AFR_AF=5.45000e-02;AMR_AF=2.16000e-02;SAS_AF=5.32000e-02;DP=6124;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21564338 rs566136417 A C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=12999;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21564407 rs534843836 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15357;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21564408 rs193169780 T C 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15349;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21564434 rs11629332 T A 100 PASS AC=1995;AF=3.98363e-01;NS=2504;AN=5008;EAS_AF=4.74200e-01;EUR_AF=6.14300e-01;AFR_AF=9.53000e-02;AMR_AF=4.81300e-01;SAS_AF=4.48900e-01;DP=15624;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|1 1|1 1|0 0|1 1|1 +14 21564474 rs141774012 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16063;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21564476 rs150600486 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16143;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21564588 rs115477880 A G 100 PASS AC=17;AF=3.39457e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.29000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18002;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21564730 rs367596561 C T 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.43000e-02;DP=19873;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21564731 rs149655923 G A 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=6.00000e-03;AFR_AF=0.00000e+00;AMR_AF=8.60000e-03;SAS_AF=0.00000e+00;DP=19763;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21564792 rs184585564 C G 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20317;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21564821 rs569921345 C T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19661;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21564827 rs181349159 C T 100 PASS AC=24;AF=4.79233e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=3.17000e-02;SAS_AF=0.00000e+00;DP=19540;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21564833 rs80159045 T C 100 PASS AC=53;AF=1.05831e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.86000e-02;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=19438;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21564859 rs66995536 G A 100 PASS AC=932;AF=1.86102e-01;NS=2504;AN=5008;EAS_AF=2.98000e-02;EUR_AF=1.35200e-01;AFR_AF=2.30000e-01;AMR_AF=3.47300e-01;SAS_AF=2.26000e-01;DP=19838;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|1 0|0 0|0 +14 21564958 rs115279178 G A 100 PASS AC=165;AF=3.29473e-02;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=2.19000e-02;AFR_AF=5.22000e-02;AMR_AF=2.16000e-02;SAS_AF=5.32000e-02;DP=20309;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21564971 rs557135862 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=20680;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21565146 rs2319625 C T 100 PASS AC=932;AF=1.86102e-01;NS=2504;AN=5008;EAS_AF=2.98000e-02;EUR_AF=1.35200e-01;AFR_AF=2.30000e-01;AMR_AF=3.47300e-01;SAS_AF=2.26000e-01;DP=20539;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|1 0|0 0|0 +14 21565149 rs2319626 G C 100 PASS AC=930;AF=1.85703e-01;NS=2504;AN=5008;EAS_AF=2.98000e-02;EUR_AF=1.34200e-01;AFR_AF=2.30000e-01;AMR_AF=3.47300e-01;SAS_AF=2.24900e-01;DP=20459;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|1 0|0 0|0 +14 21565173 rs145462239 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20481;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21565189 rs2319627 T C 100 PASS AC=933;AF=1.86302e-01;NS=2504;AN=5008;EAS_AF=2.98000e-02;EUR_AF=1.35200e-01;AFR_AF=2.30000e-01;AMR_AF=3.47300e-01;SAS_AF=2.27000e-01;DP=20653;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|1 0|0 0|0 +14 21565461 rs145168638 G A 100 PASS AC=17;AF=3.39457e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=9.90000e-03;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=4.10000e-03;DP=19592;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21565547 rs147924751 T C 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=5.10000e-03;DP=18756;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21565569 rs186358365 G C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=4.00000e-03;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=17873;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21565732 rs369793244 A C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=13304;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21566003 rs2771315 T C 100 PASS AC=4995;AF=9.97404e-01;NS=2504;AN=5008;EAS_AF=1.00000e+00;EUR_AF=9.91100e-01;AFR_AF=9.99200e-01;AMR_AF=1.00000e+00;SAS_AF=9.96900e-01;DP=5427;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 +14 21566030 rs573505502 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=5169;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21566642 rs534278641 C T 100 PASS AC=28;AF=5.59105e-03;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=1.89000e-02;AFR_AF=8.00000e-04;AMR_AF=4.30000e-03;SAS_AF=3.10000e-03;DP=1786;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21567072 rs191453915 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=14166;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21567165 rs528390137 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=16081;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21567333 rs12889457 C A 100 PASS AC=2338;AF=4.66853e-01;NS=2504;AN=5008;EAS_AF=5.30800e-01;EUR_AF=6.94800e-01;AFR_AF=1.15700e-01;AMR_AF=6.80100e-01;SAS_AF=4.89800e-01;DP=18921;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|1 1|1 1|0 1|1 1|1 +14 21567336 rs143814256 T C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=6.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18977;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21567489 rs1952512 G A 100 PASS AC=743;AF=1.48363e-01;NS=2504;AN=5008;EAS_AF=2.78000e-02;EUR_AF=8.75000e-02;AFR_AF=2.73100e-01;AMR_AF=1.75800e-01;SAS_AF=1.47200e-01;DP=18742;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|1 0|0 0|0 +14 21567587 rs117522219 G A 100 PASS AC=38;AF=7.58786e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.49000e-02;AFR_AF=0.00000e+00;AMR_AF=1.44000e-02;SAS_AF=3.10000e-03;DP=17485;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21567646 rs557462213 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=15398;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21567665 rs533236748 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=14991;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21567695 rs78148191 T C 100 PASS AC=34;AF=6.78914e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.34000e-02;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=17887;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21567705 rs573800499 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18159;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21567749 rs151106298 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19334;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21567755 rs141101171 C T 100 PASS AC=31;AF=6.19010e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.34000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19287;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21567816 rs150186336 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20370;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21567946 rs561001547 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18748;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21568099 rs532669148 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=19193;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21568128 rs552865411 A T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19628;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21568148 rs569464317 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=19750;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21568226 rs537014537 A C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=17543;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21568348 rs191417332 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=15017;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21568398 rs10149870 G A 100 PASS AC=15;AF=2.99521e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.06000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=13974;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21568399 rs573028165 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=14025;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21568759 rs140597115 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15881;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21568760 rs186693273 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=15906;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21568775 rs145719571 C T 100 PASS AC=16;AF=3.19489e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=9.90000e-03;AFR_AF=8.00000e-04;AMR_AF=2.90000e-03;SAS_AF=3.10000e-03;DP=15996;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21568899 rs115287685 G C 100 PASS AC=29;AF=5.79073e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.19000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17366;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21569041 rs189922989 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=22196;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21569114 rs149520287 C A 100 PASS AC=15;AF=2.99521e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=9.90000e-03;AFR_AF=0.00000e+00;AMR_AF=7.20000e-03;SAS_AF=0.00000e+00;DP=20293;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21569262 rs117857096 G A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=19093;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21569422 rs4982407 T C 100 PASS AC=159;AF=3.17492e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.29000e-02;AFR_AF=1.50000e-03;AMR_AF=1.65700e-01;SAS_AF=1.94000e-02;DP=24328;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21569454 rs144048367 G A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=24285;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21569504 rs114078341 T C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=23095;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21569591 rs74602443 G C 100 PASS AC=38;AF=7.58786e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.80000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19467;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21569615 rs544149989 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18845;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21569719 rs139486004 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21365;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21569806 rs574523579 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=24563;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21569817 rs145127867 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=24386;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21570157 rs79713019 G A 100 PASS AC=118;AF=2.35623e-02;NS=2504;AN=5008;EAS_AF=6.55000e-02;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=6.48000e-02;SAS_AF=3.10000e-03;DP=19863;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21570184 rs372143791 C T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=20055;AA=c|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21570257 rs183259006 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=19447;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21570273 rs745696 T C 100 PASS AC=3201;AF=6.39177e-01;NS=2504;AN=5008;EAS_AF=5.35700e-01;EUR_AF=7.15700e-01;AFR_AF=7.67000e-01;AMR_AF=5.89300e-01;SAS_AF=5.29700e-01;DP=22222;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|1 1|1 1|0 1|1 1|1 +14 21570287 rs535943725 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=22318;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21570614 rs4982408 A C 100 PASS AC=4009;AF=8.00519e-01;NS=2504;AN=5008;EAS_AF=6.01200e-01;EUR_AF=8.34000e-01;AFR_AF=9.38000e-01;AMR_AF=9.13500e-01;SAS_AF=7.05500e-01;DP=19579;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 +14 21570626 rs534149594 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=19698;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21570765 rs147177269 T A 100 PASS AC=18;AF=3.59425e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=8.00000e-03;AFR_AF=1.50000e-03;AMR_AF=1.01000e-02;SAS_AF=1.00000e-03;DP=21302;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21571119 rs12432043 A G 100 PASS AC=2647;AF=5.28554e-01;NS=2504;AN=5008;EAS_AF=4.67300e-01;EUR_AF=6.20300e-01;AFR_AF=5.76400e-01;AMR_AF=5.15900e-01;SAS_AF=4.41700e-01;DP=20546;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|1 1|1 1|0 0|1 0|1 +14 21571208 rs12880628 G T 100 PASS AC=1956;AF=3.90575e-01;NS=2504;AN=5008;EAS_AF=4.66300e-01;EUR_AF=6.00400e-01;AFR_AF=9.30000e-02;AMR_AF=4.78400e-01;SAS_AF=4.36600e-01;DP=19587;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|1 1|1 1|0 0|1 0|1 +14 21571223 rs57471121 G C 100 PASS AC=359;AF=7.16853e-02;NS=2504;AN=5008;EAS_AF=6.15000e-02;EUR_AF=7.26000e-02;AFR_AF=1.19500e-01;AMR_AF=5.33000e-02;SAS_AF=2.97000e-02;DP=19287;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 0|0 0|0 0|0 1|0 1|0 +14 21571257 rs368217898 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=5.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18821;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21571385 rs200993615 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17933;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21571556 rs150024369 A C 100 PASS AC=41;AF=8.18690e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.49000e-02;AFR_AF=0.00000e+00;AMR_AF=8.60000e-03;SAS_AF=2.04000e-02;DP=18678;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21571623 rs1057718 G C 100 PASS AC=2301;AF=4.59465e-01;NS=2504;AN=5008;EAS_AF=4.73200e-01;EUR_AF=6.18300e-01;AFR_AF=2.82900e-01;AMR_AF=4.97100e-01;SAS_AF=4.93900e-01;DP=20067;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|1 1|1 1|0 0|1 0|1 +14 21571649 rs145365080 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19889;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21571742 rs192809841 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18653;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21571779 rs142474306 C T 100 PASS AC=42;AF=8.38658e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.18000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18825;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21571794 rs11849129 C G 100 PASS AC=420;AF=8.38658e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.99000e-02;AFR_AF=2.83700e-01;AMR_AF=2.45000e-02;SAS_AF=8.20000e-03;DP=18653;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21571890 rs549304144 C G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=15686;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572020 rs115013601 C T 100 PASS AC=68;AF=1.35783e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.99000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=13900;AA=c|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572050 rs531314107 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14448;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572089 rs568209721 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=14396;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572092 rs58444293 C T 100 PASS AC=70;AF=1.39776e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=5.14000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=14361;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572107 rs61405772 G T 100 PASS AC=310;AF=6.19010e-02;NS=2504;AN=5008;EAS_AF=6.15000e-02;EUR_AF=7.16000e-02;AFR_AF=8.47000e-02;AMR_AF=5.04000e-02;SAS_AF=2.97000e-02;DP=15074;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 0|0 0|0 0|0 1|0 1|0 +14 21572117 rs539798742 G T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15458;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572259 rs74620539 G C 100 PASS AC=140;AF=2.79553e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.49000e-02;AFR_AF=1.50000e-03;AMR_AF=1.32600e-01;SAS_AF=2.15000e-02;DP=17015;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|1 0|0 0|0 +14 21572263 rs565989665 T G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=17100;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572308 rs572589358 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=11881;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572328 rs540088083 C CT 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=11817;AA=-|-|T|insertion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572329 rs541625767 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=11581;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572410 rs74036600 A G 100 PASS AC=416;AF=8.30671e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.99000e-02;AFR_AF=2.82900e-01;AMR_AF=2.45000e-02;SAS_AF=5.10000e-03;DP=15448;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572414 rs562184542 G C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=15642;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572496 rs145685170 G A 100 PASS AC=17;AF=3.39457e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.13000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=16810;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572506 rs74036601 C A 100 PASS AC=367;AF=7.32827e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=2.67000e-01;AMR_AF=1.87000e-02;SAS_AF=0.00000e+00;DP=16958;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572520 rs527467364 G T 100 PASS AC=21;AF=4.19329e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.59000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17665;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572543 rs73571904 A G 100 PASS AC=650;AF=1.29792e-01;NS=2504;AN=5008;EAS_AF=6.85000e-02;EUR_AF=9.44000e-02;AFR_AF=2.63200e-01;AMR_AF=8.21000e-02;SAS_AF=8.28000e-02;DP=18336;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 0|0 0|0 0|0 1|0 1|0 +14 21572573 rs115838908 G A 100 PASS AC=15;AF=2.99521e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.06000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18584;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572577 rs117105437 G A 100 PASS AC=40;AF=7.98722e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.49000e-02;AFR_AF=1.50000e-03;AMR_AF=1.87000e-02;SAS_AF=0.00000e+00;DP=18527;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 21572642 rs45515493 C G 100 PASS AC=772;AF=1.54153e-01;NS=2504;AN=5008;EAS_AF=6.45000e-02;EUR_AF=1.18300e-01;AFR_AF=1.38400e-01;AMR_AF=3.27100e-01;SAS_AF=1.82000e-01;DP=19812;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|1 0|0 0|0 +14 21572708 rs115178373 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20466;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572761 rs45566033 T G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=4.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19965;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572779 rs577906191 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20554;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572819 rs45543633 G T 100 PASS AC=185;AF=3.69409e-02;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=1.89000e-02;AFR_AF=7.19000e-02;AMR_AF=1.73000e-02;SAS_AF=5.32000e-02;DP=20650;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21572840 rs45486304 C T 100 PASS AC=773;AF=1.54353e-01;NS=2504;AN=5008;EAS_AF=6.45000e-02;EUR_AF=1.18300e-01;AFR_AF=1.39900e-01;AMR_AF=3.25600e-01;SAS_AF=1.82000e-01;DP=20177;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|1 0|0 0|0 +14 21572841 rs541831277 C A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=20195;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21573016 rs191353160 T A 100 PASS AC=17;AF=3.39457e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.13000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=20251;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21573051 rs73571905 A T 100 PASS AC=313;AF=6.25000e-02;NS=2504;AN=5008;EAS_AF=6.25000e-02;EUR_AF=7.26000e-02;AFR_AF=8.55000e-02;AMR_AF=5.04000e-02;SAS_AF=2.97000e-02;DP=20814;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 0|0 0|0 0|0 1|0 1|0 +14 21573082 rs8018832 A G 100 PASS AC=388;AF=7.74760e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.99000e-02;AFR_AF=2.61700e-01;AMR_AF=2.45000e-02;SAS_AF=5.10000e-03;DP=20910;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21573156 rs8023143 T C 100 PASS AC=388;AF=7.74760e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.99000e-02;AFR_AF=2.61700e-01;AMR_AF=2.45000e-02;SAS_AF=5.10000e-03;DP=20824;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21573177 rs140990837 G A 100 PASS AC=22;AF=4.39297e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.19000e-02;AFR_AF=8.00000e-04;AMR_AF=1.30000e-02;SAS_AF=0.00000e+00;DP=20713;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 1|0 0|0 0|0 0|0 +14 21573260 rs4982409 G A 100 PASS AC=1209;AF=2.41414e-01;NS=2504;AN=5008;EAS_AF=6.85000e-02;EUR_AF=1.10300e-01;AFR_AF=6.58100e-01;AMR_AF=1.05200e-01;SAS_AF=8.79000e-02;DP=19328;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 0|0 0|0 0|0 1|0 1|0 +14 21573408 rs150133071 C A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17348;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21573548 rs571334559 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=20168;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21573666 rs149318359 G A 100 PASS AC=29;AF=5.79073e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.12000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=17398;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21573784 rs147443525 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16350;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21573790 rs529210640 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16668;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21574039 rs547207988 C CA 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16019;AA=AAAAAAA|AAAAAAA|AAAAAAAA|insertion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21574200 rs115485245 G A 100 PASS AC=34;AF=6.78914e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.57000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16884;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21574320 rs28642891 A G 100 PASS AC=186;AF=3.71406e-02;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=1.89000e-02;AFR_AF=7.26000e-02;AMR_AF=1.73000e-02;SAS_AF=5.32000e-02;DP=18862;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21574577 rs56003716 A T 100 PASS AC=477;AF=9.52476e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.99000e-02;AFR_AF=3.25300e-01;AMR_AF=3.17000e-02;SAS_AF=5.10000e-03;DP=18682;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21574690 rs10872886 G T 100 PASS AC=4154;AF=8.29473e-01;NS=2504;AN=5008;EAS_AF=6.31000e-01;EUR_AF=8.48900e-01;AFR_AF=9.53900e-01;AMR_AF=9.19300e-01;SAS_AF=7.82200e-01;DP=20728;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 +14 21574697 rs77807471 T C 100 PASS AC=105;AF=2.09665e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=7.64000e-02;AMR_AF=1.40000e-03;SAS_AF=3.10000e-03;DP=20602;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21574712 rs114755408 A G 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20396;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21575008 rs12884034 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=20743;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21575049 rs150663643 T C 100 PASS AC=27;AF=5.39137e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.04000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21638;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21575330 rs28450772 A G 100 PASS AC=184;AF=3.67412e-02;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=1.89000e-02;AFR_AF=7.11000e-02;AMR_AF=1.73000e-02;SAS_AF=5.32000e-02;DP=18426;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21575419 rs573063533 C A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=16466;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21575440 rs544992123 T G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16896;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21575492 rs74037706 C T 100 PASS AC=477;AF=9.52476e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.99000e-02;AFR_AF=3.25300e-01;AMR_AF=3.17000e-02;SAS_AF=5.10000e-03;DP=19136;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21575523 rs28407152 C T 100 PASS AC=661;AF=1.31989e-01;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=3.88000e-02;AFR_AF=3.96400e-01;AMR_AF=4.90000e-02;SAS_AF=5.83000e-02;DP=20130;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21575607 rs4982410 A T 100 PASS AC=3158;AF=6.30591e-01;NS=2504;AN=5008;EAS_AF=5.33700e-01;EUR_AF=7.10700e-01;AFR_AF=7.48900e-01;AMR_AF=5.80700e-01;SAS_AF=5.23500e-01;DP=19129;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|1 1|1 1|0 1|1 1|1 +14 21575631 rs10133256 C T 100 PASS AC=184;AF=3.67412e-02;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=1.89000e-02;AFR_AF=7.11000e-02;AMR_AF=1.73000e-02;SAS_AF=5.32000e-02;DP=17893;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21575648 rs146889742 C A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17578;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21575697 rs186135997 C T 100 PASS AC=21;AF=4.19329e-03;NS=2504;AN=5008;EAS_AF=1.88000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=15781;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21575822 rs140721302 T A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14505;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21575908 rs115076727 G A 100 PASS AC=37;AF=7.38818e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.65000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=16648;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21575911 rs573089338 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=16499;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21575958 rs573436230 CAT C 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=4.00000e-03;AFR_AF=2.30000e-03;AMR_AF=7.20000e-03;SAS_AF=1.00000e-03;DP=15808;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21575963 rs4982411 G A 100 PASS AC=1010;AF=2.01677e-01;NS=2504;AN=5008;EAS_AF=7.04000e-02;EUR_AF=1.12300e-01;AFR_AF=5.04500e-01;AMR_AF=1.05200e-01;SAS_AF=8.79000e-02;DP=15506;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 0|0 0|0 0|0 1|0 1|0 +14 21575968 rs143672896 T TAC 100 PASS AC=844;AF=1.68530e-01;NS=2504;AN=5008;EAS_AF=6.94000e-02;EUR_AF=8.55000e-02;AFR_AF=4.47800e-01;AMR_AF=8.21000e-02;SAS_AF=3.99000e-02;DP=15465;VT=INDEL GT 0|0 1|1 0|0 1|1 0|1 0|0 0|0 0|0 1|0 1|0 +14 21575994 rs11628729 T C 100 PASS AC=777;AF=1.55152e-01;NS=2504;AN=5008;EAS_AF=6.45000e-02;EUR_AF=2.42500e-01;AFR_AF=1.73200e-01;AMR_AF=1.71500e-01;SAS_AF=1.22700e-01;DP=15037;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|0 1|0 0|0 1|0 0|1 +14 21575996 rs11628730 T C 100 PASS AC=663;AF=1.32388e-01;NS=2504;AN=5008;EAS_AF=3.37000e-02;EUR_AF=2.81300e-01;AFR_AF=6.43000e-02;AMR_AF=1.84400e-01;SAS_AF=1.36000e-01;DP=14918;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|0 1|0 0|0 0|0 0|1 +14 21576018 rs554337040 T TAC 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.80000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=14127;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21576022 rs144176911 C A 100 PASS AC=15;AF=2.99521e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.06000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=14065;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21576078 rs540814849 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=5.10000e-03;DP=14216;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21576134 rs201733465 C CA 100 PASS AC=44;AF=8.78594e-03;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=3.00000e-03;AFR_AF=2.27000e-02;AMR_AF=5.80000e-03;SAS_AF=5.10000e-03;DP=22252;AA=AAAAAAAAA|AAAAAAAAA|AAAAAAAAAA|insertion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21576194 rs536626644 GGAA G 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=5.10000e-03;DP=14190;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21576238 rs184043348 T C 100 PASS AC=16;AF=3.19489e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.43000e-02;DP=14816;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21576287 rs74525428 C T 100 PASS AC=45;AF=8.98562e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.33000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=15300;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21576314 rs557250114 T TA 100 PASS AC=17;AF=3.39457e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.13000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=16125;AA=A|A|AA|insertion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21576335 rs563191574 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=16510;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21576459 rs115068504 G C 100 PASS AC=47;AF=9.38498e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.48000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=17378;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21576681 rs367809266 C T 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=8.20000e-03;DP=17062;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21576715 rs538459766 C G 100 PASS AC=15;AF=2.99521e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.13000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16139;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21576745 rs575181029 G T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=15286;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21576867 rs187059238 A C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=16502;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21576974 rs143304923 C T 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=17252;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21577090 rs546442066 A G 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=5.10000e-03;DP=19046;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21577177 rs28645145 G A 100 PASS AC=477;AF=9.52476e-02;NS=2504;AN=5008;EAS_AF=6.75000e-02;EUR_AF=9.05000e-02;AFR_AF=1.42200e-01;AMR_AF=6.63000e-02;SAS_AF=8.59000e-02;DP=18146;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 0|0 0|0 0|0 1|0 1|0 +14 21577191 rs8005732 T C 100 PASS AC=486;AF=9.70447e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.99000e-02;AFR_AF=3.32800e-01;AMR_AF=3.03000e-02;SAS_AF=5.10000e-03;DP=18479;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21577526 rs117059543 T C 100 PASS AC=52;AF=1.03834e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.09000e-02;AFR_AF=0.00000e+00;AMR_AF=7.20000e-03;SAS_AF=2.66000e-02;DP=17711;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21577795 rs577419290 C G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=13213;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21577837 rs8006832 T G 100 PASS AC=995;AF=1.98682e-01;NS=2504;AN=5008;EAS_AF=6.75000e-02;EUR_AF=1.11300e-01;AFR_AF=4.91700e-01;AMR_AF=1.09500e-01;SAS_AF=9.10000e-02;DP=18559;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 0|0 0|0 0|0 1|0 1|0 +14 21577864 rs115205412 G A 100 PASS AC=39;AF=7.78754e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.87000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18776;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21577994 rs74037707 C T 100 PASS AC=75;AF=1.49760e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=5.52000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19591;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21578007 rs36100359 G A 100 PASS AC=769;AF=1.53554e-01;NS=2504;AN=5008;EAS_AF=6.65000e-02;EUR_AF=1.19300e-01;AFR_AF=1.31600e-01;AMR_AF=3.30000e-01;SAS_AF=1.83000e-01;DP=19039;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|1 0|0 0|0 +14 21578169 rs189345513 T C 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21702;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21578254 rs143755250 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21040;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21578353 rs568366040 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=20472;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21578420 rs115393001 G T 100 PASS AC=45;AF=8.98562e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.40000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19090;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21578421 rs115117352 A T 100 PASS AC=45;AF=8.98562e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.40000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18979;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21578433 rs146858306 TC T 100 PASS AC=43;AF=8.58626e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.25000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18942;AA=|||unknown(HR);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21578502 rs373546552 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=19646;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21578573 rs75766937 A G 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=7.60000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19835;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21578700 rs188924740 C A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19411;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21578701 rs10134413 T C 100 PASS AC=285;AF=5.69089e-02;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=2.09000e-02;AFR_AF=1.43700e-01;AMR_AF=2.02000e-02;SAS_AF=5.42000e-02;DP=19424;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21578740 rs181620369 A C 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19520;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21578772 rs145734763 T G 100 PASS AC=19;AF=3.79393e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.44000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19447;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21578790 rs562261203 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=19512;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21578837 rs73571913 G A 100 PASS AC=196;AF=3.91374e-02;NS=2504;AN=5008;EAS_AF=6.05000e-02;EUR_AF=5.96000e-02;AFR_AF=1.97000e-02;AMR_AF=4.03000e-02;SAS_AF=2.15000e-02;DP=19863;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 0|0 0|0 0|0 1|0 1|0 +14 21578864 rs78909204 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19593;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21579050 rs570893530 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19802;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21579072 rs76567489 G A 100 PASS AC=65;AF=1.29792e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=4.84000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20634;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21579099 rs28691757 A G 100 PASS AC=300;AF=5.99042e-02;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=1.99000e-02;AFR_AF=1.52000e-01;AMR_AF=2.74000e-02;SAS_AF=5.42000e-02;DP=21191;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21579161 rs570136288 T A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19966;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21579236 rs149264942 C T 100 PASS AC=40;AF=7.98722e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=1.00000e-03;AFR_AF=2.87000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20908;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21579357 rs148767540 C G 100 PASS AC=90;AF=1.79712e-02;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=1.79000e-02;AFR_AF=8.00000e-04;AMR_AF=1.59000e-02;SAS_AF=5.42000e-02;DP=18768;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21579426 rs142099668 A G 100 PASS AC=69;AF=1.37780e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.92000e-02;AMR_AF=5.80000e-03;SAS_AF=0.00000e+00;DP=18596;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21579580 rs185516868 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16707;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21579643 rs146365383 G A 100 PASS AC=20;AF=3.99361e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.44000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=16530;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21579666 rs139742938 A G 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=5.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16793;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21579702 rs11849908 G T 100 PASS AC=755;AF=1.50759e-01;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=3.98000e-02;AFR_AF=4.64400e-01;AMR_AF=5.19000e-02;SAS_AF=5.93000e-02;DP=17397;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21579757 rs564010756 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=16455;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21579839 rs547680844 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16360;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21579843 rs533317802 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=16321;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21579948 rs188663437 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=5.80000e-03;SAS_AF=0.00000e+00;DP=15106;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21579986 rs116616596 G A 100 PASS AC=39;AF=7.78754e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.87000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=16841;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21580055 rs151032188 A G 100 PASS AC=36;AF=7.18850e-03;NS=2504;AN=5008;EAS_AF=3.57000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19655;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21580161 rs181429309 T G 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20319;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21580214 rs80203169 A C 100 PASS AC=74;AF=1.47764e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.68000e-02;AFR_AF=8.00000e-04;AMR_AF=1.30000e-02;SAS_AF=3.78000e-02;DP=18412;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|1 0|0 +14 21580383 rs73571915 T G 100 PASS AC=154;AF=3.07508e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.14200e-01;AMR_AF=2.90000e-03;SAS_AF=1.00000e-03;DP=20496;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21580465 rs368048782 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=21567;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21580481 rs77231793 A G 100 PASS AC=19;AF=3.79393e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.36000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=21675;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21580671 rs8021387 A G 100 PASS AC=3996;AF=7.97923e-01;NS=2504;AN=5008;EAS_AF=6.01200e-01;EUR_AF=8.25000e-01;AFR_AF=9.36500e-01;AMR_AF=9.15000e-01;SAS_AF=7.02500e-01;DP=21042;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 +14 21580805 rs117069072 G A 100 PASS AC=128;AF=2.55591e-02;NS=2504;AN=5008;EAS_AF=3.37000e-02;EUR_AF=1.79000e-02;AFR_AF=1.50000e-03;AMR_AF=5.80000e-03;SAS_AF=7.16000e-02;DP=20090;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21580851 rs186018315 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19782;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21580857 rs190895018 G A 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19505;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21580864 rs76033072 G C 100 PASS AC=39;AF=7.78754e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.87000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19711;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21580938 rs551569646 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18842;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21580963 rs540903116 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=18612;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21581192 rs183945107 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19215;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21581529 rs145740608 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21460;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21581673 rs187270323 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=7.20000e-03;SAS_AF=0.00000e+00;DP=17684;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21581776 rs77108404 T C 100 PASS AC=132;AF=2.63578e-02;NS=2504;AN=5008;EAS_AF=1.29000e-01;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=19533;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21581976 rs545633298 CTTTTTTTTTT C 100 PASS AC=716;AF=1.42971e-01;NS=2504;AN=5008;EAS_AF=2.18000e-02;EUR_AF=6.36000e-02;AFR_AF=3.10900e-01;AMR_AF=1.75800e-01;SAS_AF=9.92000e-02;DP=18708;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|1 0|0 0|0 +14 21582110 rs10162361 A G 100 PASS AC=758;AF=1.51358e-01;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=4.08000e-02;AFR_AF=4.64400e-01;AMR_AF=5.48000e-02;SAS_AF=5.93000e-02;DP=15938;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21582143 rs190342116 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17206;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21582215 rs182905142 T G 100 PASS AC=137;AF=2.73562e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=6.00000e-03;AFR_AF=9.38000e-02;AMR_AF=8.60000e-03;SAS_AF=1.00000e-03;DP=17408;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21582223 rs11623521 T G 100 PASS AC=2763;AF=5.51717e-01;NS=2504;AN=5008;EAS_AF=5.71400e-01;EUR_AF=7.19700e-01;AFR_AF=3.22200e-01;AMR_AF=6.83000e-01;SAS_AF=5.75700e-01;DP=16831;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|1 1|1 1|0 1|1 1|1 +14 21582231 rs535388761 G T 100 PASS AC=93;AF=1.85703e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=6.81000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=16859;AA=-|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21582281 rs9322937 A C 100 PASS AC=928;AF=1.85304e-01;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=4.17000e-02;AFR_AF=5.90800e-01;AMR_AF=5.91000e-02;SAS_AF=5.83000e-02;DP=16092;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21582349 rs10145468 C T 100 PASS AC=15;AF=2.99521e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.06000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=16045;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21582375 rs557967283 C A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15314;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21582507 rs190077344 G A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14910;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21582517 rs111760315 C T 100 PASS AC=152;AF=3.03514e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.13500e-01;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=15220;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21582527 rs183110366 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15909;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21582751 rs150299226 G C 100 PASS AC=36;AF=7.18850e-03;NS=2504;AN=5008;EAS_AF=3.27000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=16970;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21583281 rs565059231 A G 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=7.20000e-03;DP=17578;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21583378 rs10400725 A T 100 PASS AC=1078;AF=2.15256e-01;NS=2504;AN=5008;EAS_AF=7.44000e-02;EUR_AF=1.41200e-01;AFR_AF=2.95800e-01;AMR_AF=3.45800e-01;SAS_AF=2.35200e-01;DP=17072;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|1 0|0 0|0 +14 21583457 rs142477911 G A 100 PASS AC=15;AF=2.99521e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.13000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19088;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21583611 rs537212273 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=15576;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21583647 rs139723612 C T 100 PASS AC=67;AF=1.33786e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.92000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=15072;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21583676 rs5807068 CA C 100 PASS AC=3880;AF=7.74760e-01;NS=2504;AN=5008;EAS_AF=5.97200e-01;EUR_AF=8.17100e-01;AFR_AF=8.73700e-01;AMR_AF=9.00600e-01;SAS_AF=6.91200e-01;DP=16362;AA=|||unknown(HR);VT=INDEL GT 0|0 1|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 +14 21583702 rs536183461 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=16821;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21583825 rs12893688 A G 100 PASS AC=3291;AF=6.57149e-01;NS=2504;AN=5008;EAS_AF=5.92300e-01;EUR_AF=8.05200e-01;AFR_AF=4.52300e-01;AMR_AF=8.74600e-01;SAS_AF=6.94300e-01;DP=17467;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 +14 21583896 rs143057962 G A 100 PASS AC=42;AF=8.38658e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.58000e-02;AFR_AF=8.00000e-04;AMR_AF=1.87000e-02;SAS_AF=2.00000e-03;DP=17510;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21584011 rs192373539 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=5.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14601;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21584158 rs10151757 C A 100 PASS AC=15;AF=2.99521e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.06000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=17131;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21584225 rs185515628 G A 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=6.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=7.20000e-03;DP=17677;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21584510 rs560790928 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=17625;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21584534 rs528046876 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=16546;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21584571 rs567759339 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=15030;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21584591 rs571358716 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=14184;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21584622 rs10151559 G A 100 PASS AC=15;AF=2.99521e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.06000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=13637;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21584657 rs536463500 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=14472;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21584836 rs148800167 A G 100 PASS AC=97;AF=1.93690e-02;NS=2504;AN=5008;EAS_AF=9.33000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=14739;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21584878 rs114816045 A G 100 PASS AC=65;AF=1.29792e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=4.84000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14624;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21584946 rs76742050 C T 100 PASS AC=41;AF=8.18690e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=2.95000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=15415;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21584971 rs555060251 G A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=6.10000e-03;DP=15531;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21585116 rs572674983 GT G 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18932;AA=|||unknown(STR4?);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21585143 rs181220073 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16661;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21585174 rs151254414 G A 100 PASS AC=16;AF=3.19489e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.13000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=16467;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21585203 rs139943383 G A 100 PASS AC=41;AF=8.18690e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=2.95000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=16445;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21585246 esv3633703 T 100 PASS CIEND=-29,29;CIPOS=-29,29;CS=DEL_union;END=21587390;SVTYPE=DEL;AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16300;VT=SV GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21585541 rs184868292 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20807;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21585583 rs116698985 T A 100 PASS AC=17;AF=3.39457e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.21000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18868;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21585586 rs558509882 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=18747;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21585622 rs538258139 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18496;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21585624 rs12884366 A G 100 PASS AC=1927;AF=3.84784e-01;NS=2504;AN=5008;EAS_AF=4.54400e-01;EUR_AF=6.07400e-01;AFR_AF=7.94000e-02;AMR_AF=4.75500e-01;SAS_AF=4.32500e-01;DP=18621;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|1 1|1 1|0 0|1 0|1 +14 21585684 rs142213900 G C 100 PASS AC=41;AF=8.18690e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=2.95000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=21636;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21585745 rs56969446 C T 100 PASS AC=473;AF=9.44489e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.99000e-02;AFR_AF=3.23000e-01;AMR_AF=3.03000e-02;SAS_AF=5.10000e-03;DP=21652;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21585791 rs8010018 A G 100 PASS AC=3971;AF=7.92931e-01;NS=2504;AN=5008;EAS_AF=5.93300e-01;EUR_AF=8.35000e-01;AFR_AF=9.07700e-01;AMR_AF=9.17900e-01;SAS_AF=7.11700e-01;DP=22377;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 +14 21585792 rs189320027 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=22424;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21585853 rs542324943 AGTTTG A 100 PASS AC=16;AF=3.19489e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.06000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=23161;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21585881 rs180895871 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20841;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21585986 rs61978232 G A 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=8.90000e-03;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=21789;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21585992 rs566361661 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21848;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21586052 rs78725179 G A 100 PASS AC=375;AF=7.48802e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.72300e-01;AMR_AF=2.16000e-02;SAS_AF=0.00000e+00;DP=20390;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21586100 rs148903235 T C 100 PASS AC=43;AF=8.58626e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=3.10000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=20167;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21586101 rs12887490 G A 100 PASS AC=2158;AF=4.30911e-01;NS=2504;AN=5008;EAS_AF=5.14900e-01;EUR_AF=6.64000e-01;AFR_AF=1.26300e-01;AMR_AF=5.20200e-01;SAS_AF=4.53000e-01;DP=20140;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|1 1|1 1|0 1|1 1|1 +14 21586142 rs75735264 C T 100 PASS AC=66;AF=1.31789e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.84000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=19874;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21586152 rs79279393 G T 100 PASS AC=71;AF=1.41773e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=5.22000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19530;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21586230 rs190891011 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19575;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21586332 rs147985152 C T 100 PASS AC=20;AF=3.99361e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=1.44000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21118;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21586457 rs185814874 G A 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.30000e-02;SAS_AF=0.00000e+00;DP=18018;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21586598 rs140887181 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=16462;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21586636 rs7151225 G A 100 PASS AC=2156;AF=4.30511e-01;NS=2504;AN=5008;EAS_AF=5.14900e-01;EUR_AF=6.65000e-01;AFR_AF=1.24100e-01;AMR_AF=5.18700e-01;SAS_AF=4.54000e-01;DP=17175;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|1 1|1 1|0 1|1 1|1 +14 21586734 rs71419104 A AAAAAC 100 PASS AC=835;AF=1.66733e-01;NS=2504;AN=5008;EAS_AF=9.23000e-02;EUR_AF=3.10100e-01;AFR_AF=1.08200e-01;AMR_AF=2.10400e-01;SAS_AF=1.44200e-01;DP=18994;VT=INDEL GT 0|0 1|1 0|0 1|1 0|1 1|0 0|0 0|0 1|0 1|0 +14 21586734 rs71419104 A AAAAACAAAAC 100 PASS AC=1216;AF=2.42812e-01;NS=2504;AN=5008;EAS_AF=3.93800e-01;EUR_AF=3.13100e-01;AFR_AF=1.36000e-02;AMR_AF=2.88200e-01;SAS_AF=2.92400e-01;DP=18994;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|1 1|1 1|0 0|1 0|1 +14 21586831 rs142914276 A C 100 PASS AC=38;AF=7.58786e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.80000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=17357;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21586876 rs11628703 A G 100 PASS AC=3901;AF=7.78954e-01;NS=2504;AN=5008;EAS_AF=5.91300e-01;EUR_AF=8.26000e-01;AFR_AF=8.75900e-01;AMR_AF=9.10700e-01;SAS_AF=6.99400e-01;DP=15330;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 +14 21586916 rs556762554 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14801;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21586957 rs188006386 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14318;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587072 rs143738147 A AT 100 PASS AC=262;AF=5.23163e-02;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=1.99000e-02;AFR_AF=1.24800e-01;AMR_AF=2.31000e-02;SAS_AF=5.52000e-02;DP=15059;AA=T|T|TT|insertion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587082 rs564842246 GT G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=16020;AA=TT|TT|T|deletion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587088 rs28585630 A G 100 PASS AC=265;AF=5.29153e-02;NS=2504;AN=5008;EAS_AF=6.90000e-03;EUR_AF=1.99000e-02;AFR_AF=1.27100e-01;AMR_AF=2.31000e-02;SAS_AF=5.52000e-02;DP=15119;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587269 rs11156853 T A 100 PASS AC=3927;AF=7.84145e-01;NS=2504;AN=5008;EAS_AF=5.85300e-01;EUR_AF=8.25000e-01;AFR_AF=8.98600e-01;AMR_AF=9.10700e-01;SAS_AF=7.02500e-01;DP=13797;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 +14 21587414 rs190838775 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=12810;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587478 rs531494913 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=15312;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587484 rs138929914 G A 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.29000e-02;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15298;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 0|0 0|0 0|0 0|0 0|0 +14 21587492 rs561984703 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15410;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587617 rs547822343 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19841;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587633 rs144671177 T A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19213;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587638 rs533424735 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18889;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587639 rs550091763 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=5.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18739;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587654 rs570195068 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=5.10000e-03;DP=17999;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587723 rs182557963 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=5.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15290;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587743 rs139905209 G A 100 PASS AC=41;AF=8.18690e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=2.95000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=14658;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587763 rs145448207 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14589;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587782 rs140824929 A C 100 PASS AC=19;AF=3.79393e-03;NS=2504;AN=5008;EAS_AF=1.79000e-02;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15222;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587797 rs545920792 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15643;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587807 rs142140955 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15790;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587834 rs151200811 T C 100 PASS AC=66;AF=1.31789e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.84000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=15336;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587858 rs140365620 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16040;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587865 rs12895726 C T 100 PASS AC=726;AF=1.44968e-01;NS=2504;AN=5008;EAS_AF=6.65000e-02;EUR_AF=1.10300e-01;AFR_AF=1.12000e-01;AMR_AF=3.24200e-01;SAS_AF=1.78900e-01;DP=16618;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|1 0|0 0|0 +14 21587898 rs114848533 G A 100 PASS AC=47;AF=9.38498e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.48000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18040;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21587921 rs10141637 C A 100 PASS AC=3986;AF=7.95927e-01;NS=2504;AN=5008;EAS_AF=6.13100e-01;EUR_AF=7.90300e-01;AFR_AF=9.21300e-01;AMR_AF=8.86200e-01;SAS_AF=7.56600e-01;DP=19024;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 +14 21587935 rs73571928 G C 100 PASS AC=103;AF=2.05671e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=7.72000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19355;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588001 rs570052758 T C 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.06000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20762;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588039 rs78119812 G A 100 PASS AC=47;AF=9.38498e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.48000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=20169;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588046 rs111861346 C G 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=7.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19986;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588050 rs535015797 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19774;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588051 rs553339695 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19728;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588175 rs201330985 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15204;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588204 rs149966035 C T 100 PASS AC=36;AF=7.18850e-03;NS=2504;AN=5008;EAS_AF=3.57000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15967;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588265 rs115080167 T C 100 PASS AC=63;AF=1.25799e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.69000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=16927;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588372 rs111813315 A C 100 PASS AC=188;AF=3.75399e-02;NS=2504;AN=5008;EAS_AF=3.77000e-02;EUR_AF=4.17000e-02;AFR_AF=8.30000e-03;AMR_AF=2.16000e-02;SAS_AF=8.38000e-02;DP=15850;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588379 rs572362335 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=15636;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588423 rs12434837 C T 100 PASS AC=703;AF=1.40375e-01;NS=2504;AN=5008;EAS_AF=6.75000e-02;EUR_AF=1.09300e-01;AFR_AF=1.00600e-01;AMR_AF=3.12700e-01;SAS_AF=1.78900e-01;DP=15682;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|1 0|0 0|0 +14 21588424 rs561104069 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=15613;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588486 rs199580273 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=13865;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588487 rs551630892 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=13705;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588521 rs7141678 G A 100 PASS AC=2247;AF=4.48682e-01;NS=2504;AN=5008;EAS_AF=5.23800e-01;EUR_AF=6.77900e-01;AFR_AF=1.58100e-01;AMR_AF=5.34600e-01;SAS_AF=4.67300e-01;DP=13139;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|1 1|1 1|0 1|1 1|1 +14 21588529 rs549553374 T C 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=13031;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588549 rs59110318 C T 100 PASS AC=50;AF=9.98403e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=3.63000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=13349;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588557 rs535578296 T C 100 PASS AC=26;AF=5.19169e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.89000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=13512;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588560 rs555516745 A G 100 PASS AC=25;AF=4.99201e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.82000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=13632;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588561 rs572241673 G A 100 PASS AC=25;AF=4.99201e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.82000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=13695;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588591 rs533675101 A AGGTTGC 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14221;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588593 rs557989323 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14179;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588605 rs565142291 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=14202;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588650 rs547265333 T TCC 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=13910;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588720 rs35737051 GA G 100 PASS AC=739;AF=1.47564e-01;NS=2504;AN=5008;EAS_AF=6.75000e-02;EUR_AF=1.10300e-01;AFR_AF=1.29300e-01;AMR_AF=3.08400e-01;SAS_AF=1.78900e-01;DP=15404;AA=AAAAAA|AAAAAA|AAAAA|deletion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|1 0|0 0|0 +14 21588779 rs12432623 T G 100 PASS AC=707;AF=1.41174e-01;NS=2504;AN=5008;EAS_AF=6.85000e-02;EUR_AF=1.12300e-01;AFR_AF=1.01400e-01;AMR_AF=3.06900e-01;SAS_AF=1.82000e-01;DP=15759;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|1 0|0 0|0 +14 21588818 rs187425542 G T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15792;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588873 rs376683573 C T 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.43000e-02;DP=14535;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21588994 rs184721723 A G 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=5.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17271;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589082 rs569513595 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18173;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589133 rs9671495 T C 100 PASS AC=41;AF=8.18690e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=5.00000e-03;AFR_AF=2.04000e-02;AMR_AF=4.30000e-03;SAS_AF=6.10000e-03;DP=17775;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|1 +14 21589148 rs568040368 C CT 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17573;AA=T|T|TT|insertion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589176 rs9671842 C T 100 PASS AC=2083;AF=4.15935e-01;NS=2504;AN=5008;EAS_AF=4.36500e-01;EUR_AF=2.86300e-01;AFR_AF=6.42200e-01;AMR_AF=3.87600e-01;SAS_AF=2.42300e-01;DP=17949;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 1|0 0|0 1|0 1|0 1|0 +14 21589202 rs189587660 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18210;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589208 rs181599742 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=18146;AA=c|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589209 rs564970094 G A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=8.20000e-03;DP=17987;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589266 rs530712200 T A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=19124;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589273 rs13379128 A T 100 PASS AC=22;AF=4.39297e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.59000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19343;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589309 rs377137978 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=19995;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589330 rs73571930 T A 100 PASS AC=105;AF=2.09665e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=7.72000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=19786;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589421 rs186313193 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17902;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589426 rs115162530 G A 100 PASS AC=20;AF=3.99361e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.51000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17794;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589462 rs191661732 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16934;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589562 rs537096496 A AT 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=15687;AA=TTTT|TTTT|TTTTT|insertion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589573 rs8011727 C T 100 PASS AC=350;AF=6.98882e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.56400e-01;AMR_AF=1.59000e-02;SAS_AF=0.00000e+00;DP=16579;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589575 rs200763830 TC T 100 PASS AC=37;AF=7.38818e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.65000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=17006;AA=C|C|-|deletion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589611 rs1243474 A G 100 PASS AC=551;AF=1.10024e-01;NS=2504;AN=5008;EAS_AF=1.07100e-01;EUR_AF=1.19000e-02;AFR_AF=2.86700e-01;AMR_AF=2.45000e-02;SAS_AF=3.58000e-02;DP=18212;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589622 rs537274323 T G 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=5.10000e-03;DP=18804;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589623 rs556929235 A T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=5.10000e-03;DP=18865;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589626 rs536239183 C A 100 PASS AC=16;AF=3.19489e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.64000e-02;DP=19043;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589630 rs8011753 C T 100 PASS AC=341;AF=6.80911e-02;NS=2504;AN=5008;EAS_AF=7.54000e-02;EUR_AF=1.59000e-02;AFR_AF=1.42200e-01;AMR_AF=5.62000e-02;SAS_AF=2.25000e-02;DP=19081;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589645 rs187156843 G C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18513;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589675 rs34247595 AT A 100 PASS AC=682;AF=1.36182e-01;NS=2504;AN=5008;EAS_AF=6.65000e-02;EUR_AF=1.61000e-01;AFR_AF=1.71000e-01;AMR_AF=1.51300e-01;SAS_AF=1.24700e-01;DP=18360;AA=|||unknown(HR);VT=INDEL GT 0|0 1|1 0|0 1|1 0|1 0|0 1|0 0|0 0|0 0|0 +14 21589775 rs559029518 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=13982;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589785 rs575698913 G C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=14840;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589813 rs191138740 G A 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=2.90000e-03;SAS_AF=3.10000e-03;DP=16949;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589882 rs75363289 G A 100 PASS AC=830;AF=1.65735e-01;NS=2504;AN=5008;EAS_AF=4.71200e-01;EUR_AF=7.65000e-02;AFR_AF=1.13000e-02;AMR_AF=1.67100e-01;SAS_AF=1.50300e-01;DP=15322;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|1 +14 21589931 rs542622435 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16949;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589964 rs143324629 G A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=5.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=18441;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21589977 rs1243475 C G 100 PASS AC=4147;AF=8.28075e-01;NS=2504;AN=5008;EAS_AF=9.08700e-01;EUR_AF=6.80900e-01;AFR_AF=8.93300e-01;AMR_AF=7.76700e-01;SAS_AF=8.44600e-01;DP=18563;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 1|1 0|0 1|1 1|0 1|1 +14 21590043 rs12879954 G A 100 PASS AC=1077;AF=2.15056e-01;NS=2504;AN=5008;EAS_AF=1.01200e-01;EUR_AF=2.84300e-01;AFR_AF=2.78400e-01;AMR_AF=2.29100e-01;SAS_AF=1.65600e-01;DP=19996;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 1|1 0|0 0|1 0|0 +14 21590138 rs1243476 T C 100 PASS AC=2789;AF=5.56909e-01;NS=2504;AN=5008;EAS_AF=7.35100e-01;EUR_AF=4.91100e-01;AFR_AF=3.80500e-01;AMR_AF=5.70600e-01;SAS_AF=6.69700e-01;DP=20928;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|1 1|0 0|0 0|0 0|1 +14 21590148 rs78094951 G C 100 PASS AC=270;AF=5.39137e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.98900e-01;AMR_AF=1.01000e-02;SAS_AF=0.00000e+00;DP=20279;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21590192 rs1243477 T C 100 PASS AC=2786;AF=5.56310e-01;NS=2504;AN=5008;EAS_AF=7.35100e-01;EUR_AF=4.91100e-01;AFR_AF=3.80500e-01;AMR_AF=5.69200e-01;SAS_AF=6.67700e-01;DP=19479;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|1 1|0 0|0 0|0 0|1 +14 21590413 rs143790158 C A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20504;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21590484 rs540896053 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21366;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21590671 rs140785259 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18656;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21590680 rs943993 G A 100 PASS AC=2782;AF=5.55511e-01;NS=2504;AN=5008;EAS_AF=7.36100e-01;EUR_AF=5.01000e-01;AFR_AF=3.63100e-01;AMR_AF=5.74900e-01;SAS_AF=6.71800e-01;DP=18683;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|1 1|0 0|0 0|0 0|1 +14 21590697 rs115534984 G A 100 PASS AC=23;AF=4.59265e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.74000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18786;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21590728 rs943994 A G 100 PASS AC=3297;AF=6.58347e-01;NS=2504;AN=5008;EAS_AF=8.13500e-01;EUR_AF=6.95800e-01;AFR_AF=3.99400e-01;AMR_AF=6.83000e-01;SAS_AF=7.92400e-01;DP=18827;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 1|1 1|0 0|0 1|0 0|1 +14 21590802 rs566765906 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20699;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21590816 rs943995 C T 100 PASS AC=2781;AF=5.55312e-01;NS=2504;AN=5008;EAS_AF=7.35100e-01;EUR_AF=5.01000e-01;AFR_AF=3.63100e-01;AMR_AF=5.74900e-01;SAS_AF=6.71800e-01;DP=21031;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|1 1|0 0|0 0|0 0|1 +14 21590855 rs149802271 T C 100 PASS AC=37;AF=7.38818e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.68000e-02;AFR_AF=8.00000e-04;AMR_AF=7.20000e-03;SAS_AF=4.10000e-03;DP=21469;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21590904 rs529256138 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=20673;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21590968 rs182799086 G A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=5.00000e-03;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18331;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21591040 rs943996 A G 100 PASS AC=2785;AF=5.56110e-01;NS=2504;AN=5008;EAS_AF=7.39100e-01;EUR_AF=5.01000e-01;AFR_AF=3.63100e-01;AMR_AF=5.73500e-01;SAS_AF=6.72800e-01;DP=18764;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|1 1|0 0|0 0|0 0|1 +14 21591070 rs111271502 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18933;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21591144 rs148462695 T G 100 PASS AC=25;AF=4.99201e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.82000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19369;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21591209 rs546427115 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=21431;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21591214 rs1268875 C G 100 PASS AC=1340;AF=2.67572e-01;NS=2504;AN=5008;EAS_AF=5.95200e-01;EUR_AF=1.67000e-01;AFR_AF=1.36000e-02;AMR_AF=3.44400e-01;SAS_AF=3.22100e-01;DP=21156;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 0|1 0|0 0|0 0|0 0|0 +14 21591347 rs4307864 G A 100 PASS AC=802;AF=1.60144e-01;NS=2504;AN=5008;EAS_AF=1.03200e-01;EUR_AF=2.27600e-01;AFR_AF=9.15000e-02;AMR_AF=1.61400e-01;SAS_AF=2.41300e-01;DP=19636;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|0 1|0 0|0 0|0 0|1 +14 21591351 rs11850177 A T 100 PASS AC=38;AF=7.58786e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.87000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19453;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21591653 rs139974221 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=23424;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21591667 rs716599 C A 100 PASS AC=2765;AF=5.52117e-01;NS=2504;AN=5008;EAS_AF=7.34100e-01;EUR_AF=5.01000e-01;AFR_AF=3.63100e-01;AMR_AF=5.60500e-01;SAS_AF=6.66700e-01;DP=23123;AA=c|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|1 1|0 0|0 0|0 0|1 +14 21591672 rs571037918 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=23077;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21591725 rs716598 C T 100 PASS AC=2768;AF=5.52716e-01;NS=2504;AN=5008;EAS_AF=7.34100e-01;EUR_AF=5.01000e-01;AFR_AF=3.63100e-01;AMR_AF=5.63400e-01;SAS_AF=6.67700e-01;DP=22423;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|1 1|0 0|0 0|0 0|1 +14 21591732 rs575128314 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=21899;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21591807 rs543811968 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19914;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21591876 rs554231188 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20436;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21592008 rs1243481 A C 100 PASS AC=2777;AF=5.54513e-01;NS=2504;AN=5008;EAS_AF=7.34100e-01;EUR_AF=5.02000e-01;AFR_AF=3.63100e-01;AMR_AF=5.73500e-01;SAS_AF=6.68700e-01;DP=20609;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|1 1|0 0|0 0|0 0|1 +14 21592009 rs560329042 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=20533;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21592012 rs60611772 G C 100 PASS AC=867;AF=1.73123e-01;NS=2504;AN=5008;EAS_AF=1.04200e-01;EUR_AF=2.61400e-01;AFR_AF=9.38000e-02;AMR_AF=1.81600e-01;SAS_AF=2.54600e-01;DP=20543;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|0 1|0 0|0 0|0 0|1 +14 21592024 rs546049082 A C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20167;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21592062 rs183266470 T C 100 PASS AC=15;AF=2.99521e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=1.00000e-03;AFR_AF=9.10000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19821;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21592103 rs568567236 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19802;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21592107 rs1312750 A C 100 PASS AC=2777;AF=5.54513e-01;NS=2504;AN=5008;EAS_AF=7.34100e-01;EUR_AF=5.02000e-01;AFR_AF=3.63100e-01;AMR_AF=5.73500e-01;SAS_AF=6.68700e-01;DP=19814;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|1 1|0 0|0 0|0 0|1 +14 21592130 rs187936456 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=19863;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21592146 rs117788320 C A 100 PASS AC=19;AF=3.79393e-03;NS=2504;AN=5008;EAS_AF=1.88000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19378;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21592194 rs1312751 G C 100 PASS AC=2765;AF=5.52117e-01;NS=2504;AN=5008;EAS_AF=7.34100e-01;EUR_AF=5.02000e-01;AFR_AF=3.57000e-01;AMR_AF=5.67700e-01;SAS_AF=6.68700e-01;DP=18088;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|1 1|0 0|0 0|0 0|1 +14 21592438 rs548915849 C T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=17294;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21592501 rs188827374 T C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16330;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21592524 rs34334298 TA T 100 PASS AC=2757;AF=5.50519e-01;NS=2504;AN=5008;EAS_AF=7.32100e-01;EUR_AF=5.02000e-01;AFR_AF=3.56300e-01;AMR_AF=5.62000e-01;SAS_AF=6.67700e-01;DP=16793;AA=|||unknown(LONG_INSERTION);VT=INDEL GT 0|0 1|1 0|0 1|1 1|0 1|1 1|0 0|0 0|0 0|1 +14 21592567 rs542225463 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=17702;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21592568 rs562101571 T C 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17732;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21592647 rs116244707 G A 100 PASS AC=22;AF=4.39297e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.66000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16813;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21592660 rs368037445 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17330;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21592752 rs1314325 C G 100 PASS AC=2763;AF=5.51717e-01;NS=2504;AN=5008;EAS_AF=7.35100e-01;EUR_AF=5.02000e-01;AFR_AF=3.55500e-01;AMR_AF=5.66300e-01;SAS_AF=6.68700e-01;DP=17505;AA=c|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|1 1|0 0|0 0|0 0|1 +14 21592879 rs146670756 G A 100 PASS AC=64;AF=1.27796e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=4.77000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17215;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21592903 rs184102740 G A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16383;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21592916 rs28463125 C T 100 PASS AC=93;AF=1.85703e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=6.96000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16040;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21592922 rs542113519 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=15766;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21592961 rs148992391 C T 100 PASS AC=76;AF=1.51757e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=5.30000e-02;AMR_AF=7.20000e-03;SAS_AF=0.00000e+00;DP=14857;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593013 rs572428189 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15960;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593058 rs112426866 A G 100 PASS AC=756;AF=1.50958e-01;NS=2504;AN=5008;EAS_AF=1.03200e-01;EUR_AF=2.59400e-01;AFR_AF=2.12000e-02;AMR_AF=1.74400e-01;SAS_AF=2.47400e-01;DP=13834;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|0 1|0 0|0 0|0 0|1 +14 21593061 rs10129576 A G 100 PASS AC=1351;AF=2.69768e-01;NS=2504;AN=5008;EAS_AF=1.04200e-01;EUR_AF=2.63400e-01;AFR_AF=4.55400e-01;AMR_AF=1.97400e-01;SAS_AF=2.47400e-01;DP=13651;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|0 1|0 0|0 0|0 0|1 +14 21593105 rs572735906 C CA 100 PASS AC=1607;AF=3.20887e-01;NS=2504;AN=5008;EAS_AF=5.69400e-01;EUR_AF=2.29600e-01;AFR_AF=1.35400e-01;AMR_AF=3.68900e-01;SAS_AF=3.75300e-01;DP=21717;AA=|||unknown(HR);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 21593186 rs112205918 T G 100 PASS AC=256;AF=5.11182e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.88400e-01;AMR_AF=1.01000e-02;SAS_AF=0.00000e+00;DP=19850;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593285 rs1312752 T C 100 PASS AC=1696;AF=3.38658e-01;NS=2504;AN=5008;EAS_AF=6.30000e-01;EUR_AF=2.38600e-01;AFR_AF=1.12700e-01;AMR_AF=3.80400e-01;SAS_AF=4.17200e-01;DP=17728;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 0|1 0|0 0|0 0|0 0|0 +14 21593300 rs370474774 CAAAAT C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18217;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593319 rs188005136 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=16930;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593335 rs570505646 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=16907;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593336 rs566053335 A G 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=7.20000e-03;DP=16879;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593381 rs191305634 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17682;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593424 rs76463842 G T 100 PASS AC=28;AF=5.59105e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.97000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=17829;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593438 rs555689287 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=17676;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593453 rs572295468 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=5.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17634;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593503 rs6571685 C G 100 PASS AC=859;AF=1.71526e-01;NS=2504;AN=5008;EAS_AF=1.04200e-01;EUR_AF=2.61400e-01;AFR_AF=9.30000e-02;AMR_AF=1.81600e-01;SAS_AF=2.47400e-01;DP=18452;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|0 1|0 0|0 0|0 0|1 +14 21593511 rs112909526 A AT 100 PASS AC=360;AF=7.18850e-02;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=6.00000e-03;AFR_AF=2.48900e-01;AMR_AF=2.45000e-02;SAS_AF=4.10000e-03;DP=18833;AA=TTTTTTTTT|TTTTTTTTT|TTTTTTTTTT|insertion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593521 rs563443089 A T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19118;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593549 rs529404825 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=20038;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593577 rs377021705 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21010;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593589 rs148307546 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21293;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593715 rs547356874 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=17779;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593744 rs150863554 G A 100 PASS AC=127;AF=2.53594e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=9.23000e-02;AMR_AF=5.80000e-03;SAS_AF=0.00000e+00;DP=17949;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593778 rs139142270 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17415;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593779 rs149497924 C G 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=5.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17439;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593843 rs111621053 A C 100 PASS AC=110;AF=2.19649e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=7.94000e-02;AMR_AF=5.80000e-03;SAS_AF=0.00000e+00;DP=16278;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593966 rs565947089 A G 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15964;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21593988 rs534578246 A C 100 PASS AC=64;AF=1.27796e-02;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=1.00000e-03;AFR_AF=4.61000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20995;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594048 rs543419980 T C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21442;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594069 rs182556938 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=21795;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594117 rs377521830 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=1181;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594217 rs1314371 C T 100 PASS AC=1678;AF=3.35064e-01;NS=2504;AN=5008;EAS_AF=6.24000e-01;EUR_AF=2.37600e-01;AFR_AF=1.12700e-01;AMR_AF=3.71800e-01;SAS_AF=4.12100e-01;DP=17896;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 0|1 0|0 0|0 0|0 0|0 +14 21594271 rs75102232 C T 100 PASS AC=123;AF=2.45607e-02;NS=2504;AN=5008;EAS_AF=3.47000e-02;EUR_AF=1.69000e-02;AFR_AF=1.97000e-02;AMR_AF=1.40000e-03;SAS_AF=4.50000e-02;DP=19866;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594313 rs112605653 G A 100 PASS AC=282;AF=5.63099e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.08000e-01;AMR_AF=1.01000e-02;SAS_AF=0.00000e+00;DP=20530;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594338 rs143520682 T A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20296;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594394 rs146659497 C T 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=3.10000e-03;DP=21771;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594419 rs1314659 C T 100 PASS AC=328;AF=6.54952e-02;NS=2504;AN=5008;EAS_AF=2.63900e-01;EUR_AF=1.39000e-02;AFR_AF=2.30000e-03;AMR_AF=5.62000e-02;SAS_AF=6.10000e-03;DP=22499;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594427 rs537044769 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=22534;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594474 rs76841263 G A 100 PASS AC=17;AF=3.39457e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.19000e-02;AFR_AF=0.00000e+00;AMR_AF=7.20000e-03;SAS_AF=0.00000e+00;DP=20695;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594515 rs553455935 C A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19214;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594577 rs117152095 A T 100 PASS AC=37;AF=7.38818e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.49000e-02;AFR_AF=8.00000e-04;AMR_AF=1.15000e-02;SAS_AF=3.10000e-03;DP=19486;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594581 rs80063119 A G 100 PASS AC=286;AF=5.71086e-02;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=2.07300e-01;AMR_AF=1.01000e-02;SAS_AF=3.10000e-03;DP=19423;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594586 rs565434567 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19529;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594591 rs78788976 A G 100 PASS AC=281;AF=5.61102e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.07300e-01;AMR_AF=1.01000e-02;SAS_AF=0.00000e+00;DP=19561;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594681 rs376141430 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=20584;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594795 rs370699428 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=19100;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594815 rs571429774 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19254;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594885 rs61978233 G A 100 PASS AC=42;AF=8.38658e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.29000e-02;AFR_AF=8.00000e-04;AMR_AF=2.16000e-02;SAS_AF=3.10000e-03;DP=18649;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|1 0|0 0|0 0|0 0|0 0|0 +14 21594916 rs150946136 G A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18937;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21594922 rs374071371 G C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=18862;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21595042 rs553154396 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18656;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21595090 rs112983377 A G 100 PASS AC=281;AF=5.61102e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.07300e-01;AMR_AF=1.01000e-02;SAS_AF=0.00000e+00;DP=19167;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21595099 rs147080449 C T 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19038;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21595130 rs147723123 G A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18475;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21595153 rs4981356 C A 100 PASS AC=715;AF=1.42772e-01;NS=2504;AN=5008;EAS_AF=1.07100e-01;EUR_AF=2.39600e-01;AFR_AF=1.82000e-02;AMR_AF=1.42700e-01;SAS_AF=2.48500e-01;DP=17961;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|0 1|0 0|0 0|0 0|1 +14 21595174 rs561569241 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17459;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21595210 rs181160398 G A 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=8.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=5.10000e-03;DP=16476;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21595254 rs368736541 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=17480;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21595255 rs142622196 G A 100 PASS AC=62;AF=1.23802e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=4.39000e-02;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=17442;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21595258 rs564705071 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17654;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21595350 rs372669240 A T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=19048;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21595435 rs550415521 T G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18834;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21595478 rs114974376 C G 100 PASS AC=65;AF=1.29792e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.84000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19665;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21595723 rs539087372 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15963;AA=c|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21595778 rs146911684 C T 100 PASS AC=78;AF=1.55751e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.75000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=17807;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21595932 rs544654550 TA T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19219;AA=AAAA|AAAA|AAA|deletion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21596003 rs570535226 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17187;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21596255 rs1313786 G A 100 PASS AC=248;AF=4.95208e-02;NS=2504;AN=5008;EAS_AF=2.25200e-01;EUR_AF=1.39000e-02;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=6.10000e-03;DP=16843;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21596304 rs72671131 T C 100 PASS AC=965;AF=1.92692e-01;NS=2504;AN=5008;EAS_AF=1.48800e-01;EUR_AF=2.66400e-01;AFR_AF=9.68000e-02;AMR_AF=2.34900e-01;SAS_AF=2.61800e-01;DP=16899;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|0 1|0 0|0 0|0 0|1 +14 21596559 rs182314478 G C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=15526;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21596576 rs368539383 ACT A 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15739;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21596645 rs149361421 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16789;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21596750 rs143657703 A C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16300;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21596893 rs114063431 G A 100 PASS AC=31;AF=6.19010e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=7.00000e-03;AFR_AF=1.13000e-02;AMR_AF=2.90000e-03;SAS_AF=7.20000e-03;DP=18310;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21596930 rs115091894 T A 100 PASS AC=239;AF=4.77236e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.75500e-01;AMR_AF=1.01000e-02;SAS_AF=0.00000e+00;DP=17838;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21597014 rs1271866 G T 100 PASS AC=2738;AF=5.46725e-01;NS=2504;AN=5008;EAS_AF=7.35100e-01;EUR_AF=5.02000e-01;AFR_AF=3.48000e-01;AMR_AF=5.54800e-01;SAS_AF=6.61600e-01;DP=17541;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|1 1|0 0|0 0|0 0|1 +14 21597106 rs186278517 A G 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15190;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21597185 rs144804260 C CT 100 PASS AC=39;AF=7.78754e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.39000e-02;AFR_AF=8.00000e-04;AMR_AF=1.30000e-02;SAS_AF=5.10000e-03;DP=17520;AA=TT|TT|TTT|insertion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21597200 rs77228434 C A 100 PASS AC=59;AF=1.17812e-02;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=1.59000e-02;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=4.19000e-02;DP=18022;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21597207 rs148106325 G A 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18244;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21597259 rs191942351 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=18890;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21597269 rs10130912 C T 100 PASS AC=25;AF=4.99201e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=1.66000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19252;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21597293 rs3118479 G A 100 PASS AC=2744;AF=5.47923e-01;NS=2504;AN=5008;EAS_AF=7.37100e-01;EUR_AF=5.02000e-01;AFR_AF=3.46400e-01;AMR_AF=5.51900e-01;SAS_AF=6.69700e-01;DP=19655;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|1 1|0 0|0 0|0 0|1 +14 21597402 rs552721878 C CTAACATCATACTCAA 100 PASS AC=19;AF=3.79393e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.94000e-02;DP=19079;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21597509 rs1271295 G A 100 PASS AC=2744;AF=5.47923e-01;NS=2504;AN=5008;EAS_AF=7.37100e-01;EUR_AF=5.02000e-01;AFR_AF=3.46400e-01;AMR_AF=5.51900e-01;SAS_AF=6.69700e-01;DP=17608;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|1 1|0 0|0 0|0 0|1 +14 21597642 rs145995338 G T 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.10000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18536;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21597900 rs117244244 T C 100 PASS AC=31;AF=6.19010e-03;NS=2504;AN=5008;EAS_AF=3.08000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16586;AA=N|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21597960 rs182385817 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18068;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21597966 rs112938898 G A 100 PASS AC=263;AF=5.25160e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.93600e-01;AMR_AF=1.01000e-02;SAS_AF=0.00000e+00;DP=18193;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21597967 rs187021538 G C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=18181;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21598022 rs373101221 A G 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=19623;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21598049 rs560391756 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18898;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21598067 rs139206600 A C 100 PASS AC=75;AF=1.49760e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=5.60000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18388;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21598332 rs191862436 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=17727;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21598333 rs149865234 G A 100 PASS AC=56;AF=1.11821e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.68000e-02;AFR_AF=8.00000e-04;AMR_AF=5.80000e-03;SAS_AF=2.45000e-02;DP=17658;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21598435 rs148628438 G A 100 PASS AC=18;AF=3.59425e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.36000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15728;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21598470 rs10133694 G A 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14713;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21598498 rs1268876 C T 100 PASS AC=2752;AF=5.49521e-01;NS=2504;AN=5008;EAS_AF=7.38100e-01;EUR_AF=5.03000e-01;AFR_AF=3.49500e-01;AMR_AF=5.54800e-01;SAS_AF=6.69700e-01;DP=14340;AA=c|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|1 1|0 0|0 0|0 0|1 +14 21598509 rs554638411 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14042;AA=c|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21598530 rs4981357 G A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=4.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=13336;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 1|0 0|0 0|0 0|0 +14 21598659 rs142583939 C A 100 PASS AC=19;AF=3.79393e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.36000e-02;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=12345;AA=c|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21598660 rs546092817 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=12224;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21598852 rs562774725 G A 100 PASS AC=447;AF=8.92572e-02;NS=2504;AN=5008;EAS_AF=4.66000e-02;EUR_AF=1.08300e-01;AFR_AF=1.31600e-01;AMR_AF=6.34000e-02;SAS_AF=7.46000e-02;DP=5725;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 1|0 0|1 1|0 +14 21598903 rs112545774 A G 100 PASS AC=2612;AF=5.21565e-01;NS=2504;AN=5008;EAS_AF=6.64700e-01;EUR_AF=4.90100e-01;AFR_AF=3.48700e-01;AMR_AF=5.46100e-01;SAS_AF=6.22700e-01;DP=10165;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 1|1 1|0 0|0 0|0 0|1 +14 21598958 rs75448094 T C 100 PASS AC=108;AF=2.15655e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=7.87000e-02;AMR_AF=5.80000e-03;SAS_AF=0.00000e+00;DP=13829;AA=t|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599045 rs562210890 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=13515;AA=c|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599068 rs557917508 GA G 100 PASS AC=72;AF=1.43770e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.09000e-02;AFR_AF=1.50000e-03;AMR_AF=5.80000e-03;SAS_AF=4.60000e-02;DP=14942;AA=AAAAAAAAA|AAAAAAAAA|AAAAAAAA|deletion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 1|1 0|0 1|0 +14 21599124 rs115201215 C T 100 PASS AC=255;AF=5.09185e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.87600e-01;AMR_AF=1.01000e-02;SAS_AF=0.00000e+00;DP=14847;AA=c|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599150 rs564490659 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=15405;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599235 rs150393811 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16623;AA=t|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599373 rs138169544 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=19105;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599452 rs113017333 G A 100 PASS AC=263;AF=5.25160e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.93600e-01;AMR_AF=1.01000e-02;SAS_AF=0.00000e+00;DP=17686;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599463 rs145082042 T C 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=5.00000e-03;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=17958;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599478 rs188667474 C A 100 PASS AC=19;AF=3.79393e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.09000e-02;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=5.10000e-03;DP=18095;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|1 +14 21599497 rs372429592 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=18490;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599515 rs138662462 G C 100 PASS AC=34;AF=6.78914e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.42000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=17866;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599527 rs181415312 A C 100 PASS AC=24;AF=4.79233e-03;NS=2504;AN=5008;EAS_AF=2.38000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17669;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599545 rs141705488 G A 100 PASS AC=62;AF=1.23802e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=4.61000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16898;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599590 rs144547894 G A 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=5.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=16216;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599597 rs185898687 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15646;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599602 rs191149819 G A 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=15036;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599645 rs148052387 C A 100 PASS AC=106;AF=2.11661e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=7.72000e-02;AMR_AF=5.80000e-03;SAS_AF=0.00000e+00;DP=15815;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599646 rs563615837 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=3.10000e-03;DP=15585;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599686 rs141794332 G A 100 PASS AC=18;AF=3.59425e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=5.00000e-03;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=1.02000e-02;DP=13105;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599726 rs576258415 CA C 100 PASS AC=4934;AF=9.85224e-01;NS=2504;AN=5008;EAS_AF=9.91100e-01;EUR_AF=9.96000e-01;AFR_AF=9.62900e-01;AMR_AF=9.89900e-01;SAS_AF=9.94900e-01;DP=22408;AA=|||unknown(HR);VT=INDEL GT 0|0 1|1 0|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 +14 21599737 rs202087833 A C 100 PASS AC=4934;AF=9.85224e-01;NS=2504;AN=5008;EAS_AF=9.91100e-01;EUR_AF=9.96000e-01;AFR_AF=9.62900e-01;AMR_AF=9.89900e-01;SAS_AF=9.94900e-01;DP=16829;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 +14 21599743 rs78231181 A C 100 PASS AC=4934;AF=9.85224e-01;NS=2504;AN=5008;EAS_AF=9.91100e-01;EUR_AF=9.96000e-01;AFR_AF=9.62900e-01;AMR_AF=9.89900e-01;SAS_AF=9.94900e-01;DP=17421;AA=a|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 +14 21599749 rs201199407 A C 100 PASS AC=954;AF=1.90495e-01;NS=2504;AN=5008;EAS_AF=1.59700e-01;EUR_AF=2.76300e-01;AFR_AF=8.09000e-02;AMR_AF=2.29100e-01;SAS_AF=2.54600e-01;DP=18051;AA=a|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|0 1|0 0|0 0|0 0|1 +14 21599766 rs570603338 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15793;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599770 rs539643385 C A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=15897;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21599817 rs113901462 T C 100 PASS AC=264;AF=5.27157e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.94400e-01;AMR_AF=1.01000e-02;SAS_AF=0.00000e+00;DP=18152;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21600000 rs111646240 G C 100 PASS AC=234;AF=4.67252e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.71700e-01;AMR_AF=1.01000e-02;SAS_AF=0.00000e+00;DP=18045;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21600012 rs541454012 T G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=17578;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21600092 rs1243482 T G 100 PASS AC=2743;AF=5.47724e-01;NS=2504;AN=5008;EAS_AF=7.37100e-01;EUR_AF=5.01000e-01;AFR_AF=3.46400e-01;AMR_AF=5.57600e-01;SAS_AF=6.65600e-01;DP=18717;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|1 1|0 0|0 0|0 0|1 +14 21600119 rs563504829 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19342;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21600183 rs1263873 G A 100 PASS AC=2711;AF=5.41334e-01;NS=2504;AN=5008;EAS_AF=7.37100e-01;EUR_AF=5.01000e-01;AFR_AF=3.25300e-01;AMR_AF=5.54800e-01;SAS_AF=6.63600e-01;DP=19452;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|1 1|0 0|0 0|0 0|1 +14 21600277 rs1243483 C G 100 PASS AC=1603;AF=3.20088e-01;NS=2504;AN=5008;EAS_AF=6.16100e-01;EUR_AF=2.22700e-01;AFR_AF=1.05900e-01;AMR_AF=3.17000e-01;SAS_AF=4.07000e-01;DP=20333;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 21600382 rs181995653 G A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21245;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21600433 rs371997964 A AGTGGG 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=23077;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21600434 rs147388966 G T 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=8.90000e-03;AFR_AF=0.00000e+00;AMR_AF=7.20000e-03;SAS_AF=0.00000e+00;DP=22207;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|0 0|0 0|0 0|0 0|0 +14 21600437 rs533096321 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=22049;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21600444 rs549920741 G C 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21996;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21600460 rs187420512 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21673;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21600503 rs113015651 A G 100 PASS AC=15;AF=2.99521e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.06000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=20317;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21600529 rs1243484 C T 100 PASS AC=2774;AF=5.53914e-01;NS=2504;AN=5008;EAS_AF=7.83700e-01;EUR_AF=5.01000e-01;AFR_AF=3.41100e-01;AMR_AF=5.51900e-01;SAS_AF=6.60500e-01;DP=19961;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|1 1|0 0|0 0|0 0|1 +14 21600586 rs557763551 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20866;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21600862 rs564027557 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=17135;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21600986 rs145822012 A G 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18122;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21601109 rs57282057 C T 100 PASS AC=900;AF=1.79712e-01;NS=2504;AN=5008;EAS_AF=1.11100e-01;EUR_AF=2.29600e-01;AFR_AF=1.64100e-01;AMR_AF=1.55600e-01;SAS_AF=2.37200e-01;DP=20495;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 1|0 1|0 0|0 0|0 0|1 +14 21601230 rs149003266 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21532;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21601292 rs537062946 A G 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20456;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21601322 rs557019443 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20426;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21601399 rs187498014 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21201;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21601411 rs142990872 G A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21464;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21601506 rs11624398 A G 100 PASS AC=574;AF=1.14617e-01;NS=2504;AN=5008;EAS_AF=6.45000e-02;EUR_AF=2.12700e-01;AFR_AF=1.21000e-02;AMR_AF=2.34900e-01;SAS_AF=1.18600e-01;DP=20192;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 0|0 0|1 0|0 0|1 0|0 +14 21601517 rs151036195 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20158;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21601654 rs74037713 A T 100 PASS AC=117;AF=2.33626e-02;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=8.47000e-02;AMR_AF=5.80000e-03;SAS_AF=0.00000e+00;DP=19531;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21601768 rs10150243 C A 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18357;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21601844 rs548814697 A T 100 PASS AC=18;AF=3.59425e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.36000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17766;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21601871 rs74037714 T G 100 PASS AC=151;AF=3.01518e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.11200e-01;AMR_AF=5.80000e-03;SAS_AF=0.00000e+00;DP=17747;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602061 rs141261856 A G 100 PASS AC=24;AF=4.79233e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.82000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18512;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602066 rs187509542 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18771;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602165 rs79723453 T C 100 PASS AC=64;AF=1.27796e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=4.77000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19144;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602172 rs192745839 A T 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.30000e-03;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=18900;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602265 rs145000006 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=16469;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602443 rs576056391 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16456;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602529 rs185404381 G C 100 PASS AC=25;AF=4.99201e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.89000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=10931;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602559 rs113069920 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=11984;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602584 rs573559712 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=13151;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602636 rs192695623 G A 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=8.90000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=12401;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602647 rs140620678 T C 100 PASS AC=182;AF=3.63419e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.34600e-01;AMR_AF=5.80000e-03;SAS_AF=0.00000e+00;DP=12441;AA=t|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602648 rs528255354 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=12397;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602654 rs150340354 C T 100 PASS AC=50;AF=9.98403e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.63000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=12411;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602702 rs564833915 G C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=11829;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602710 rs184501389 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=11520;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602783 rs537743932 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=12975;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602786 rs138051534 C T 100 PASS AC=19;AF=3.79393e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.36000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=13204;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602836 rs530059775 A T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=12026;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602875 rs562748955 CA C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14753;AA=AA|AA|A|deletion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602909 rs112150643 T C 100 PASS AC=42;AF=8.38658e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.03000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=15394;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21602959 rs115660704 T G 100 PASS AC=39;AF=7.78754e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=6.00000e-03;AFR_AF=2.19000e-02;AMR_AF=4.30000e-03;SAS_AF=1.00000e-03;DP=13728;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21603006 rs74037716 T C 100 PASS AC=180;AF=3.59425e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.33100e-01;AMR_AF=5.80000e-03;SAS_AF=0.00000e+00;DP=13640;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21603197 rs569483896 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16992;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21603279 rs143209695 C T 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.80000e-03;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=16686;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21603461 rs544792542 C A 100 PASS AC=22;AF=4.39297e-03;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=2.00000e-03;AFR_AF=1.06000e-02;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=18822;AA=-|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21603467 rs58324713 A AC 100 PASS AC=4609;AF=9.20327e-01;NS=2504;AN=5008;EAS_AF=9.25600e-01;EUR_AF=9.34400e-01;AFR_AF=8.86500e-01;AMR_AF=9.40900e-01;SAS_AF=9.31500e-01;DP=21993;AA=-|-|C|insertion;VT=INDEL GT 0|0 1|1 0|0 1|1 1|1 1|1 1|1 1|0 1|1 0|1 +14 21603469 rs564695065 A C 100 PASS AC=34;AF=6.78914e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.57000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19357;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21603477 rs60258396 A AC 100 PASS AC=4609;AF=9.20327e-01;NS=2504;AN=5008;EAS_AF=9.25600e-01;EUR_AF=9.34400e-01;AFR_AF=8.86500e-01;AMR_AF=9.40900e-01;SAS_AF=9.31500e-01;DP=19686;AA=|||unknown(HR);VT=INDEL GT 0|0 1|1 0|0 1|1 1|1 1|1 1|1 1|0 1|1 0|1 +14 21603497 rs117103034 A G 100 PASS AC=51;AF=1.01837e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.38000e-02;AFR_AF=1.50000e-03;AMR_AF=2.02000e-02;SAS_AF=1.00000e-03;DP=19105;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21603553 rs112982068 T C 100 PASS AC=59;AF=1.17812e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.31000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=19913;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21603557 rs11622020 G T 100 PASS AC=1046;AF=2.08866e-01;NS=2504;AN=5008;EAS_AF=7.24000e-02;EUR_AF=2.08700e-01;AFR_AF=3.31300e-01;AMR_AF=2.57900e-01;SAS_AF=1.49300e-01;DP=19727;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 0|0 0|1 0|0 0|1 0|0 +14 21603561 rs184984521 A G 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19675;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21603573 rs560561290 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=19284;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21603620 rs147353164 T C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=17886;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21603622 rs11622375 C G 100 PASS AC=1096;AF=2.18850e-01;NS=2504;AN=5008;EAS_AF=7.24000e-02;EUR_AF=2.08700e-01;AFR_AF=3.67600e-01;AMR_AF=2.60800e-01;SAS_AF=1.49300e-01;DP=17830;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 0|0 0|1 0|0 0|1 0|0 +14 21603656 rs548848652 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19230;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21603678 rs11627883 T C 100 PASS AC=1967;AF=3.92772e-01;NS=2504;AN=5008;EAS_AF=1.43800e-01;EUR_AF=4.52300e-01;AFR_AF=5.62800e-01;AMR_AF=4.03500e-01;SAS_AF=3.50700e-01;DP=19164;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|0 0|1 0|0 1|1 0|0 +14 21603775 rs111613881 C CT 100 PASS AC=140;AF=2.79553e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=9.98000e-02;AMR_AF=1.01000e-02;SAS_AF=0.00000e+00;DP=18271;AA=T|T|TT|insertion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21603798 rs189001479 C T 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=7.00000e-03;AFR_AF=8.00000e-04;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=18583;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21603800 rs138428678 A AC 100 PASS AC=32;AF=6.38978e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.34000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18715;AA=?|CCC|CCCC|unsure;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21603843 rs563597650 CCTT C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=20346;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604071 rs11623157 G A 100 PASS AC=1536;AF=3.06709e-01;NS=2504;AN=5008;EAS_AF=1.39900e-01;EUR_AF=4.13500e-01;AFR_AF=3.91100e-01;AMR_AF=3.58800e-01;SAS_AF=2.17800e-01;DP=19236;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|0 0|1 0|0 1|1 0|0 +14 21604329 rs186133786 T C 100 PASS AC=18;AF=3.59425e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.36000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18272;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604345 rs79710655 T C 100 PASS AC=114;AF=2.27636e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=8.17000e-02;AMR_AF=8.60000e-03;SAS_AF=0.00000e+00;DP=17773;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604375 rs374314923 G T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=17530;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604395 rs368123050 A C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17523;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604419 rs566102411 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=17573;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604511 rs538259480 T C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=14669;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604555 rs139524309 C T 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=14159;AA=t|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604589 rs10136872 C T 100 PASS AC=1016;AF=2.02875e-01;NS=2504;AN=5008;EAS_AF=8.73000e-02;EUR_AF=2.25600e-01;AFR_AF=2.54200e-01;AMR_AF=2.66600e-01;SAS_AF=1.84000e-01;DP=14468;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|0 0|0 1|1 0|0 0|1 0|0 +14 21604590 rs548260004 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=14471;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604635 rs141700983 G T 100 PASS AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.80000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=15634;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604721 rs577294185 A T 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=13293;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604759 rs150872433 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14063;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604789 rs10151385 T C 100 PASS AC=385;AF=7.68770e-02;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=3.00000e-03;AFR_AF=2.76100e-01;AMR_AF=2.16000e-02;SAS_AF=0.00000e+00;DP=14418;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604819 rs185775514 C G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=13609;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604876 rs11629128 A G 100 PASS AC=161;AF=3.21486e-02;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=4.57000e-02;AFR_AF=3.80000e-03;AMR_AF=2.59000e-02;SAS_AF=9.30000e-02;DP=12176;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604883 rs570841899 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=11874;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604884 rs1243485 A G 100 PASS AC=4415;AF=8.81589e-01;NS=2504;AN=5008;EAS_AF=8.96800e-01;EUR_AF=8.59800e-01;AFR_AF=9.10000e-01;AMR_AF=8.97700e-01;SAS_AF=8.38400e-01;DP=11896;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 +14 21604887 rs12434127 C T 100 PASS AC=76;AF=1.51757e-02;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=1.19000e-02;AFR_AF=3.00000e-03;AMR_AF=8.07000e-02;SAS_AF=3.10000e-03;DP=11893;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604888 rs568846818 G A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=6.10000e-03;DP=11774;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604895 rs554673192 G T 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=7.90000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=12059;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604897 rs28492014 T C 100 PASS AC=107;AF=2.13658e-02;NS=2504;AN=5008;EAS_AF=7.90000e-03;EUR_AF=1.39000e-02;AFR_AF=4.84000e-02;AMR_AF=8.60000e-03;SAS_AF=1.53000e-02;DP=12110;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604912 rs143561041 G A 100 PASS AC=268;AF=5.35144e-02;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=3.00000e-03;AFR_AF=1.91400e-01;AMR_AF=1.44000e-02;SAS_AF=0.00000e+00;DP=12625;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604931 rs546210731 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=13007;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604942 rs190597157 G A 100 PASS AC=34;AF=6.78914e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.99000e-02;AFR_AF=1.50000e-03;AMR_AF=1.73000e-02;SAS_AF=0.00000e+00;DP=13465;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 1|0 0|0 +14 21604947 rs562225199 A G 100 PASS AC=18;AF=3.59425e-03;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=2.00000e-03;AFR_AF=8.30000e-03;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=13454;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604972 rs12590860 A G 100 PASS AC=760;AF=1.51757e-01;NS=2504;AN=5008;EAS_AF=5.65000e-02;EUR_AF=6.46000e-02;AFR_AF=3.79700e-01;AMR_AF=5.19000e-02;SAS_AF=1.02200e-01;DP=14083;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604977 rs182846446 T C 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=7.00000e-03;AFR_AF=8.00000e-04;AMR_AF=2.90000e-03;SAS_AF=2.00000e-03;DP=14284;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604994 rs555270297 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14656;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21604996 rs140601350 C A 100 PASS AC=69;AF=1.37780e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.07000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=14857;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21605002 rs111815708 G A 100 PASS AC=98;AF=1.95687e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=7.26000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=15023;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21605113 rs10130905 T C 100 PASS AC=885;AF=1.76717e-01;NS=2504;AN=5008;EAS_AF=5.46000e-02;EUR_AF=6.46000e-02;AFR_AF=4.70500e-01;AMR_AF=6.20000e-02;SAS_AF=1.02200e-01;DP=19940;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21605132 rs562874248 CT C 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=4.00000e-03;AFR_AF=8.00000e-04;AMR_AF=5.80000e-03;SAS_AF=2.00000e-03;DP=19022;AA=T|T|-|deletion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21605282 rs80287944 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18500;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21605347 rs149299032 CTCA C 100 PASS AC=64;AF=1.27796e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.84000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19437;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21605505 rs71419106 A ATCTC 100 PASS AC=1144;AF=2.28435e-01;NS=2504;AN=5008;EAS_AF=1.30000e-01;EUR_AF=1.44100e-01;AFR_AF=4.67500e-01;AMR_AF=1.35400e-01;SAS_AF=1.59500e-01;DP=20865;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21605654 rs375795600 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21084;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21605661 rs564297115 C T 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21080;AA=c|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21605728 rs116269099 T G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=21560;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21605756 rs111938437 T C 100 PASS AC=135;AF=2.69569e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=9.68000e-02;AMR_AF=8.60000e-03;SAS_AF=0.00000e+00;DP=21947;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21605894 rs140852456 G C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20742;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21605922 rs185030263 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20313;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21605974 rs187430371 T G 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=4.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=19615;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21606010 rs572114048 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18985;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21606026 rs8007473 A G 100 PASS AC=1152;AF=2.30032e-01;NS=2504;AN=5008;EAS_AF=1.28000e-01;EUR_AF=1.45100e-01;AFR_AF=4.73500e-01;AMR_AF=1.35400e-01;SAS_AF=1.60500e-01;DP=18607;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21606128 rs544023475 T C 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16118;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21606147 rs8007044 C T 100 PASS AC=2773;AF=5.53714e-01;NS=2504;AN=5008;EAS_AF=4.96000e-01;EUR_AF=6.33200e-01;AFR_AF=4.07000e-01;AMR_AF=6.35400e-01;SAS_AF=6.71800e-01;DP=14314;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|1 1|1 1|1 1|0 +14 21606179 rs12432102 A G 100 PASS AC=1009;AF=2.01478e-01;NS=2504;AN=5008;EAS_AF=1.42900e-01;EUR_AF=1.76900e-01;AFR_AF=2.69300e-01;AMR_AF=2.17600e-01;SAS_AF=1.84000e-01;DP=12213;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|1 0|0 0|0 0|0 +14 21606186 rs8012221 T G 100 PASS AC=1579;AF=3.15296e-01;NS=2504;AN=5008;EAS_AF=3.51200e-01;EUR_AF=1.99800e-01;AFR_AF=3.01800e-01;AMR_AF=3.06900e-01;SAS_AF=4.21300e-01;DP=11589;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 21606193 rs371068935 CAAAAAAA C 100 PASS AC=2425;AF=4.84225e-01;NS=2504;AN=5008;EAS_AF=4.70200e-01;EUR_AF=3.33000e-01;AFR_AF=5.87000e-01;AMR_AF=4.56800e-01;SAS_AF=5.34800e-01;DP=17715;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 21606269 rs527303989 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15572;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21606284 rs528725974 G GTA 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=6.00000e-03;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=15795;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21606316 rs56077284 G A 100 PASS AC=1004;AF=2.00479e-01;NS=2504;AN=5008;EAS_AF=2.98600e-01;EUR_AF=1.39200e-01;AFR_AF=4.99000e-02;AMR_AF=2.62200e-01;SAS_AF=3.22100e-01;DP=13938;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 21606318 rs568533022 A G 100 PASS AC=15;AF=2.99521e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=8.00000e-04;AMR_AF=2.90000e-03;SAS_AF=1.02000e-02;DP=14129;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21606499 rs36115959 T C 100 PASS AC=453;AF=9.04553e-02;NS=2504;AN=5008;EAS_AF=7.54000e-02;EUR_AF=8.45000e-02;AFR_AF=1.31600e-01;AMR_AF=8.65000e-02;SAS_AF=5.93000e-02;DP=16586;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21606503 rs181428946 A G 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=7.60000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16667;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21606510 rs74748981 C T 100 PASS AC=29;AF=5.79073e-03;NS=2504;AN=5008;EAS_AF=2.38000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=5.80000e-03;SAS_AF=1.00000e-03;DP=16765;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21606644 rs56206931 A G 100 PASS AC=766;AF=1.52955e-01;NS=2504;AN=5008;EAS_AF=5.46000e-02;EUR_AF=3.16100e-01;AFR_AF=8.70000e-02;AMR_AF=1.55600e-01;SAS_AF=1.73800e-01;DP=18655;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|0 1|0 1|1 1|1 1|0 +14 21606707 rs111584132 A T 100 PASS AC=10;AF=1.99681e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=7.60000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16604;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21606729 rs35193384 C T 100 PASS AC=964;AF=1.92492e-01;NS=2504;AN=5008;EAS_AF=1.27000e-01;EUR_AF=1.32200e-01;AFR_AF=3.51000e-01;AMR_AF=1.21000e-01;SAS_AF=1.58500e-01;DP=16370;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21606733 rs35036745 C G 100 PASS AC=964;AF=1.92492e-01;NS=2504;AN=5008;EAS_AF=1.28000e-01;EUR_AF=1.32200e-01;AFR_AF=3.51000e-01;AMR_AF=1.21000e-01;SAS_AF=1.57500e-01;DP=16126;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21606735 rs533086491 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16131;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21606863 rs4981358 A G 100 PASS AC=2919;AF=5.82867e-01;NS=2504;AN=5008;EAS_AF=4.96000e-01;EUR_AF=6.33200e-01;AFR_AF=5.05300e-01;AMR_AF=6.48400e-01;SAS_AF=6.78900e-01;DP=18049;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|1 1|1 1|1 1|0 +14 21606938 rs184398111 T G 100 PASS AC=17;AF=3.39457e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.21000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19971;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21606946 rs4981359 G T 100 PASS AC=4016;AF=8.01917e-01;NS=2504;AN=5008;EAS_AF=6.24000e-01;EUR_AF=7.67400e-01;AFR_AF=9.55400e-01;AMR_AF=7.70900e-01;SAS_AF=8.35400e-01;DP=19967;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|1 1|1 1|1 1|0 +14 21606961 rs4981360 T C 100 PASS AC=2893;AF=5.77676e-01;NS=2504;AN=5008;EAS_AF=4.97000e-01;EUR_AF=6.33200e-01;AFR_AF=4.87100e-01;AMR_AF=6.47000e-01;SAS_AF=6.76900e-01;DP=20293;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|1 1|1 1|1 1|0 +14 21607052 rs573623492 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=16669;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607054 rs541016523 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=16437;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607092 rs557742893 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=14885;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607097 rs577590042 G A 100 PASS AC=16;AF=3.19489e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.21000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14203;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607121 rs113545971 C T 100 PASS AC=541;AF=1.08027e-01;NS=2504;AN=5008;EAS_AF=5.26000e-02;EUR_AF=4.87000e-02;AFR_AF=2.42800e-01;AMR_AF=3.31000e-02;SAS_AF=9.71000e-02;DP=11358;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607138 rs12887592 C A 100 PASS AC=4011;AF=8.00919e-01;NS=2504;AN=5008;EAS_AF=6.24000e-01;EUR_AF=7.68400e-01;AFR_AF=9.52300e-01;AMR_AF=7.70900e-01;SAS_AF=8.33300e-01;DP=11134;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|1 1|1 1|1 1|0 +14 21607139 rs12888235 A C 100 PASS AC=4013;AF=8.01318e-01;NS=2504;AN=5008;EAS_AF=6.24000e-01;EUR_AF=7.68400e-01;AFR_AF=9.53900e-01;AMR_AF=7.70900e-01;SAS_AF=8.33300e-01;DP=11368;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|1 1|1 1|1 1|0 +14 21607149 rs12887598 C A 100 PASS AC=705;AF=1.40775e-01;NS=2504;AN=5008;EAS_AF=7.54000e-02;EUR_AF=8.55000e-02;AFR_AF=3.15400e-01;AMR_AF=9.94000e-02;SAS_AF=5.83000e-02;DP=11512;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607153 rs559214127 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=11665;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607155 rs2771326 C T 100 PASS AC=4992;AF=9.96805e-01;NS=2504;AN=5008;EAS_AF=1.00000e+00;EUR_AF=9.86100e-01;AFR_AF=1.00000e+00;AMR_AF=9.98600e-01;SAS_AF=9.99000e-01;DP=11393;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 +14 21607170 rs551264709 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=11803;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607189 rs12887742 C G 100 PASS AC=4016;AF=8.01917e-01;NS=2504;AN=5008;EAS_AF=6.24000e-01;EUR_AF=7.66400e-01;AFR_AF=9.55400e-01;AMR_AF=7.70900e-01;SAS_AF=8.36400e-01;DP=11518;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|1 1|1 1|1 1|0 +14 21607199 rs186329575 G A 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=9.90000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=11381;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607272 rs188778543 G C 100 PASS AC=11;AF=2.19649e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=7.60000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=13866;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607325 rs140165545 T C 100 PASS AC=441;AF=8.80591e-02;NS=2504;AN=5008;EAS_AF=5.26000e-02;EUR_AF=4.77000e-02;AFR_AF=1.67200e-01;AMR_AF=3.17000e-02;SAS_AF=9.92000e-02;DP=13709;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607362 rs181933979 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14756;AA=t|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607399 rs369243138 T A 100 PASS AC=7;AF=1.39776e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=6.10000e-03;DP=16803;AA=t|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607407 rs143938576 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16502;AA=c|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607522 rs373919339 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=8456;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607647 rs559076273 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=10641;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607668 rs568705419 T TTTA 100 PASS AC=17;AF=3.39457e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.29000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=12110;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607687 rs530912133 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=13028;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607728 rs561422214 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=14514;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607780 rs567038292 G A 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16305;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607858 rs150007484 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18557;AA=c|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607913 rs573586649 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17076;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21607930 rs12893005 C T 100 PASS AC=3005;AF=6.00040e-01;NS=2504;AN=5008;EAS_AF=4.82100e-01;EUR_AF=5.90500e-01;AFR_AF=6.86800e-01;AMR_AF=5.56200e-01;SAS_AF=6.45200e-01;DP=17051;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|0 1|1 1|1 1|0 +14 21608023 rs12893824 A G 100 PASS AC=3056;AF=6.10224e-01;NS=2504;AN=5008;EAS_AF=4.87100e-01;EUR_AF=6.01400e-01;AFR_AF=7.08800e-01;AMR_AF=5.60500e-01;SAS_AF=6.48300e-01;DP=16248;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|0 1|1 1|1 1|0 +14 21608064 rs35390039 G A 100 PASS AC=952;AF=1.90096e-01;NS=2504;AN=5008;EAS_AF=3.02600e-01;EUR_AF=1.39200e-01;AFR_AF=7.60000e-03;AMR_AF=2.65100e-01;SAS_AF=3.20000e-01;DP=17267;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 21608183 rs561078487 G T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18305;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21608248 rs573962577 AT A 100 PASS AC=20;AF=3.99361e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.04000e-02;DP=19288;AA=TTT|TTT|TT|deletion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21608253 rs544351878 G T 100 PASS AC=20;AF=3.99361e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.04000e-02;DP=18493;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21608260 rs569443259 C A 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.23000e-02;DP=18435;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21608297 rs4982413 G C 100 PASS AC=3038;AF=6.06629e-01;NS=2504;AN=5008;EAS_AF=4.82100e-01;EUR_AF=6.08300e-01;AFR_AF=6.89100e-01;AMR_AF=5.63400e-01;SAS_AF=6.52400e-01;DP=18502;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|0 1|1 1|1 1|1 +14 21608334 rs117394160 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17808;AA=t|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21608347 rs186968552 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=17511;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21608418 rs191388474 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16367;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21608484 rs575397666 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16669;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21608584 rs28369245 G T 100 PASS AC=878;AF=1.75319e-01;NS=2504;AN=5008;EAS_AF=5.65000e-02;EUR_AF=3.16100e-01;AFR_AF=1.74000e-01;AMR_AF=1.58500e-01;SAS_AF=1.66700e-01;DP=16200;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|0 1|0 1|1 1|1 1|0 +14 21608609 rs114463447 T C 100 PASS AC=33;AF=6.58946e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.42000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=16429;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21608695 rs28628219 A G 100 PASS AC=779;AF=1.55551e-01;NS=2504;AN=5008;EAS_AF=5.46000e-02;EUR_AF=3.15100e-01;AFR_AF=9.91000e-02;AMR_AF=1.57100e-01;SAS_AF=1.70800e-01;DP=16826;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|0 1|0 1|1 1|1 1|0 +14 21608718 rs2319678 T G 100 PASS AC=2576;AF=5.14377e-01;NS=2504;AN=5008;EAS_AF=4.31500e-01;EUR_AF=5.41700e-01;AFR_AF=5.21900e-01;AMR_AF=5.25900e-01;SAS_AF=5.53200e-01;DP=16111;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|0 1|1 1|1 1|0 +14 21608802 rs2319679 T C 100 PASS AC=3063;AF=6.11621e-01;NS=2504;AN=5008;EAS_AF=4.83100e-01;EUR_AF=6.01400e-01;AFR_AF=7.11000e-01;AMR_AF=5.62000e-01;SAS_AF=6.55400e-01;DP=15156;AA=-|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|0 1|1 1|1 1|0 +14 21608803 rs546226906 C T 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=4.00000e-03;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15186;AA=-|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21608818 rs538306844 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15651;AA=-|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21608850 rs117389803 C T 100 PASS AC=59;AF=1.17812e-02;NS=2504;AN=5008;EAS_AF=5.85000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=12302;AA=-|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21608886 rs542625305 C G 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=8.20000e-03;DP=11524;AA=-|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21608978 rs12878595 C A 100 PASS AC=1540;AF=3.07508e-01;NS=2504;AN=5008;EAS_AF=3.83900e-01;EUR_AF=2.19700e-01;AFR_AF=2.37500e-01;AMR_AF=3.50100e-01;SAS_AF=3.83400e-01;DP=11078;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 21608986 rs8022689 G A 100 PASS AC=1581;AF=3.15695e-01;NS=2504;AN=5008;EAS_AF=1.32900e-01;EUR_AF=3.94600e-01;AFR_AF=4.93900e-01;AMR_AF=2.53600e-01;SAS_AF=2.26000e-01;DP=10691;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|0 1|0 1|1 1|1 1|0 +14 21609003 rs545943874 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=10156;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609020 rs11852130 G C 100 PASS AC=2353;AF=4.69848e-01;NS=2504;AN=5008;EAS_AF=4.38500e-01;EUR_AF=5.37800e-01;AFR_AF=3.58500e-01;AMR_AF=5.17300e-01;SAS_AF=5.49100e-01;DP=9781;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|0 1|1 1|1 1|0 +14 21609057 rs531789535 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=11988;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609098 rs185234871 A G 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=12440;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609143 rs137897463 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=14263;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609157 rs377211230 T G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14432;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609316 rs187941329 A G 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=1.50000e-03;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=12965;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609340 rs4982414 G A 100 PASS AC=974;AF=1.94489e-01;NS=2504;AN=5008;EAS_AF=3.07500e-01;EUR_AF=1.40200e-01;AFR_AF=1.66000e-02;AMR_AF=2.66600e-01;SAS_AF=3.23100e-01;DP=12942;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 21609378 rs140661600 G A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=12317;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609415 rs147507626 AT A 100 PASS AC=909;AF=1.81510e-01;NS=2504;AN=5008;EAS_AF=5.75000e-02;EUR_AF=3.24100e-01;AFR_AF=1.74000e-01;AMR_AF=1.70000e-01;SAS_AF=1.81000e-01;DP=13418;AA=?|TTT|TT|unsure;VT=INDEL GT 0|0 1|1 0|0 1|1 1|1 0|0 1|0 1|1 1|1 1|1 +14 21609420 rs554125643 A T 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=8.00000e-04;AMR_AF=1.01000e-02;SAS_AF=1.00000e-03;DP=12522;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609459 rs150087975 A T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=13983;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609475 rs550038751 G A 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=5.10000e-03;DP=14731;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609480 rs556378711 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14869;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609484 rs149276278 G T 100 PASS AC=25;AF=4.99201e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=9.90000e-03;AFR_AF=8.00000e-04;AMR_AF=1.44000e-02;SAS_AF=4.10000e-03;DP=14901;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609489 rs113417280 G A 100 PASS AC=113;AF=2.25639e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=7.94000e-02;AMR_AF=1.01000e-02;SAS_AF=0.00000e+00;DP=15176;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609529 rs112757282 G A 100 PASS AC=783;AF=1.56350e-01;NS=2504;AN=5008;EAS_AF=5.36000e-02;EUR_AF=3.27000e-01;AFR_AF=8.32000e-02;AMR_AF=1.65700e-01;SAS_AF=1.78900e-01;DP=15280;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|0 1|0 1|1 1|1 1|1 +14 21609561 rs138978795 C T 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15032;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609604 rs59690754 A AC 100 PASS AC=46;AF=9.18530e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.40000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=15572;AA=|||unknown(LONG_INSERTION);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609691 rs4982415 A G 100 PASS AC=2483;AF=4.95807e-01;NS=2504;AN=5008;EAS_AF=4.38500e-01;EUR_AF=5.52700e-01;AFR_AF=4.35700e-01;AMR_AF=5.21600e-01;SAS_AF=5.59300e-01;DP=14433;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|0 1|1 1|1 1|1 +14 21609715 rs562356892 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=14382;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609775 rs568227072 G A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=4.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15973;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609821 rs142244754 A G 100 PASS AC=45;AF=8.98562e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.33000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=17324;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609822 rs146406106 A G 100 PASS AC=45;AF=8.98562e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.33000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=17326;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609842 rs556480552 T A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=17271;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609883 rs193146179 A C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16958;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21609998 rs186677943 G A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=6.10000e-03;DP=13504;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21610075 rs183615582 T C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=15177;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21610436 rs7158576 C A 100 PASS AC=97;AF=1.93690e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=7.19000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=19611;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21610457 rs527479038 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18955;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21610630 rs547652370 A C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16649;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21610685 rs115529351 C T 100 PASS AC=22;AF=4.39297e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.59000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18883;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21610753 rs533203922 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19626;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21610897 rs71112552 TG T 100 PASS AC=1970;AF=3.93371e-01;NS=2504;AN=5008;EAS_AF=4.36500e-01;EUR_AF=2.47500e-01;AFR_AF=4.28100e-01;AMR_AF=3.90500e-01;SAS_AF=4.54000e-01;DP=14971;AA=?|G|-|unsure;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 21610898 rs76631114 G T 100 PASS AC=341;AF=6.80911e-02;NS=2504;AN=5008;EAS_AF=2.08000e-02;EUR_AF=1.99000e-02;AFR_AF=1.52000e-01;AMR_AF=7.78000e-02;SAS_AF=4.60000e-02;DP=14663;AA=t|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21610900 rs376581393 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14356;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21611033 rs35000518 G A 100 PASS AC=966;AF=1.92891e-01;NS=2504;AN=5008;EAS_AF=3.13500e-01;EUR_AF=1.37200e-01;AFR_AF=1.74000e-02;AMR_AF=2.65100e-01;SAS_AF=3.11900e-01;DP=13960;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 21611128 rs150620817 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=14488;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21611150 rs139761013 G A 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14164;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21611169 rs111251484 C A 100 PASS AC=15;AF=2.99521e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=9.90000e-03;AFR_AF=0.00000e+00;AMR_AF=5.80000e-03;SAS_AF=1.00000e-03;DP=13603;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21611186 rs116616025 T C 100 PASS AC=31;AF=6.19010e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.27000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=13164;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21611205 rs12879150 G A 100 PASS AC=399;AF=7.96725e-02;NS=2504;AN=5008;EAS_AF=6.55000e-02;EUR_AF=6.06000e-02;AFR_AF=1.33900e-01;AMR_AF=7.35000e-02;SAS_AF=4.50000e-02;DP=12087;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21611224 rs532995363 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=11726;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21611295 rs577339567 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=11941;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21611445 rs565739432 A G 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=3.10000e-03;DP=12528;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21611449 rs12885549 T A 100 PASS AC=1008;AF=2.01278e-01;NS=2504;AN=5008;EAS_AF=3.13500e-01;EUR_AF=1.37200e-01;AFR_AF=4.84000e-02;AMR_AF=2.66600e-01;SAS_AF=3.11900e-01;DP=12471;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 21611505 rs58824959 T G 100 PASS AC=96;AF=1.91693e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=7.11000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=12441;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21611598 rs141374518 G C 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=14373;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21611620 rs543351178 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14514;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21611669 rs145244025 C A 100 PASS AC=17;AF=3.39457e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.19000e-02;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=4.10000e-03;DP=16452;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21611759 rs1952513 T A 100 PASS AC=3553;AF=7.09465e-01;NS=2504;AN=5008;EAS_AF=5.71400e-01;EUR_AF=7.13700e-01;AFR_AF=7.83700e-01;AMR_AF=7.42100e-01;SAS_AF=7.23900e-01;DP=17683;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|1 1|1 1|1 1|1 +14 21611768 rs1952514 C T 100 PASS AC=3545;AF=7.07867e-01;NS=2504;AN=5008;EAS_AF=5.71400e-01;EUR_AF=7.13700e-01;AFR_AF=7.83700e-01;AMR_AF=7.39200e-01;SAS_AF=7.17800e-01;DP=17909;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|1 1|1 1|1 1|1 +14 21611835 rs529106274 T C 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18186;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21611895 rs114694059 G A 100 PASS AC=40;AF=7.98722e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.03000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17348;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21612109 rs149117026 T A 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15983;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21612114 rs7153865 T G 100 PASS AC=399;AF=7.96725e-02;NS=2504;AN=5008;EAS_AF=6.55000e-02;EUR_AF=6.06000e-02;AFR_AF=1.33900e-01;AMR_AF=7.35000e-02;SAS_AF=4.50000e-02;DP=16140;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21612170 rs550852835 T C 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15666;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21612218 rs564538367 TA T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=13971;AA=|||unknown(LONG_INSERTION);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21612251 rs118130230 T A 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=1.19000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14742;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21612348 rs75905949 TA T 100 PASS AC=2098;AF=4.18930e-01;NS=2504;AN=5008;EAS_AF=2.46000e-01;EUR_AF=5.06000e-01;AFR_AF=5.14400e-01;AMR_AF=4.09200e-01;SAS_AF=3.85500e-01;DP=14054;AA=|||unknown(LONG_INSERTION);VT=INDEL GT 0|0 1|1 0|0 1|1 1|1 0|0 0|1 1|1 1|1 1|1 +14 21612396 rs143007730 C A 100 PASS AC=18;AF=3.59425e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.09000e-02;AFR_AF=1.50000e-03;AMR_AF=4.30000e-03;SAS_AF=2.00000e-03;DP=12999;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21612464 rs559354545 G T 100 PASS AC=28;AF=5.59105e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.86000e-02;DP=14781;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21612504 rs577626089 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14209;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21612508 rs148203685 T A 100 PASS AC=41;AF=8.18690e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.03000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=14288;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21612573 rs57277470 C T 100 PASS AC=39;AF=7.78754e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.95000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15350;AA=c|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21612574 rs145398876 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15293;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21612676 rs528464248 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=15394;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21612878 rs567216668 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=15772;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21612968 rs184529457 T C 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.30000e-02;SAS_AF=0.00000e+00;DP=17370;AA=t|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21613056 rs190626771 A G 100 PASS AC=13;AF=2.59585e-03;NS=2504;AN=5008;EAS_AF=1.29000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18583;AA=a|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21613110 rs542463056 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19562;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21613148 rs12436265 G C 100 PASS AC=976;AF=1.94888e-01;NS=2504;AN=5008;EAS_AF=1.38900e-01;EUR_AF=1.78900e-01;AFR_AF=2.50400e-01;AMR_AF=2.17600e-01;SAS_AF=1.77900e-01;DP=20809;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|1 0|0 0|0 0|0 +14 21613164 rs573012179 T A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20817;AA=t|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21613165 rs71410264 C A 100 PASS AC=398;AF=7.94728e-02;NS=2504;AN=5008;EAS_AF=6.55000e-02;EUR_AF=5.96000e-02;AFR_AF=1.33900e-01;AMR_AF=7.35000e-02;SAS_AF=4.50000e-02;DP=20838;AA=c|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21613340 rs138959524 C T 100 PASS AC=25;AF=4.99201e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.89000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19538;AA=c|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21613420 rs7155274 C T 100 PASS AC=96;AF=1.91693e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=7.11000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18646;AA=c|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21613487 rs76615935 A G 100 PASS AC=80;AF=1.59744e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=5.90000e-02;AMR_AF=2.90000e-03;SAS_AF=0.00000e+00;DP=19280;AA=a|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21613621 rs556637443 G A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19750;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21613671 rs535952784 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=20266;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21613780 rs34731852 C T 100 PASS AC=402;AF=8.02716e-02;NS=2504;AN=5008;EAS_AF=6.55000e-02;EUR_AF=5.96000e-02;AFR_AF=1.36900e-01;AMR_AF=7.35000e-02;SAS_AF=4.50000e-02;DP=18183;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21613815 rs186908271 G A 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17949;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21613905 rs190106628 G A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=3.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17135;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21613908 rs149612923 GT G 100 PASS AC=802;AF=1.60144e-01;NS=2504;AN=5008;EAS_AF=1.37900e-01;EUR_AF=1.78900e-01;AFR_AF=1.26300e-01;AMR_AF=2.07500e-01;SAS_AF=1.75900e-01;DP=17322;AA=TTTT|TTTT|TTT|deletion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|1 0|0 0|0 0|0 +14 21614020 rs12897113 C A 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=13540;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21614093 rs4982416 T C 100 PASS AC=3429;AF=6.84704e-01;NS=2504;AN=5008;EAS_AF=5.70400e-01;EUR_AF=7.12700e-01;AFR_AF=7.01200e-01;AMR_AF=7.33400e-01;SAS_AF=7.16800e-01;DP=12804;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|1 1|1 1|1 1|1 +14 21614168 rs552576289 C T 100 PASS AC=23;AF=4.59265e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.09000e-02;AFR_AF=0.00000e+00;AMR_AF=1.30000e-02;SAS_AF=3.10000e-03;DP=10262;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21614185 rs200973757 G T 100 PASS AC=1521;AF=3.03714e-01;NS=2504;AN=5008;EAS_AF=3.81000e-01;EUR_AF=2.01800e-01;AFR_AF=2.57200e-01;AMR_AF=3.41500e-01;SAS_AF=3.65000e-01;DP=9167;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 21614193 rs200418344 T G 100 PASS AC=1457;AF=2.90935e-01;NS=2504;AN=5008;EAS_AF=3.78000e-01;EUR_AF=2.12700e-01;AFR_AF=2.08000e-01;AMR_AF=3.28500e-01;SAS_AF=3.67100e-01;DP=9475;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 21614213 rs566925113 T G 100 PASS AC=42;AF=8.38658e-03;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=2.27000e-02;AMR_AF=5.80000e-03;SAS_AF=4.10000e-03;DP=10511;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21614241 rs147472434 C A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=10118;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21614298 rs139979565 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=14708;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21614400 rs28880918 C T 100 PASS AC=537;AF=1.07228e-01;NS=2504;AN=5008;EAS_AF=6.55000e-02;EUR_AF=5.96000e-02;AFR_AF=2.36800e-01;AMR_AF=7.78000e-02;SAS_AF=4.50000e-02;DP=14662;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21614437 rs28830864 C T 100 PASS AC=21;AF=4.19329e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.59000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15093;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21614494 rs185772175 C T 100 PASS AC=5;AF=9.98403e-04;NS=2504;AN=5008;EAS_AF=5.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16143;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21614511 rs78811822 G A 100 PASS AC=15;AF=2.99521e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.80000e-03;AMR_AF=1.40000e-03;SAS_AF=1.00000e-03;DP=15834;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21614529 rs546420476 C G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15501;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21614539 rs140876207 C A 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=6.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=15591;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21614564 rs4982418 A C 100 PASS AC=1522;AF=3.03914e-01;NS=2504;AN=5008;EAS_AF=3.80000e-01;EUR_AF=2.01800e-01;AFR_AF=2.58700e-01;AMR_AF=3.42900e-01;SAS_AF=3.64000e-01;DP=15464;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 21614604 rs189702096 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=15976;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21614633 rs28775978 G C 100 PASS AC=24;AF=4.79233e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.82000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16925;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21614693 rs8008232 T C 100 PASS AC=4109;AF=8.20487e-01;NS=2504;AN=5008;EAS_AF=6.21000e-01;EUR_AF=8.04200e-01;AFR_AF=9.83400e-01;AMR_AF=7.92500e-01;SAS_AF=8.42500e-01;DP=16975;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|1 1|1 1|1 1|1 +14 21614703 rs551834317 C T 100 PASS AC=18;AF=3.59425e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.84000e-02;DP=16690;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21614704 rs140257461 G A 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.80000e-03;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=16609;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21614705 rs34997907 C T 100 PASS AC=398;AF=7.94728e-02;NS=2504;AN=5008;EAS_AF=6.55000e-02;EUR_AF=5.96000e-02;AFR_AF=1.33900e-01;AMR_AF=7.35000e-02;SAS_AF=4.50000e-02;DP=16714;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21614719 rs182277741 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=16707;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21614732 rs185462536 T C 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=3.00000e-03;AFR_AF=0.00000e+00;AMR_AF=2.90000e-03;SAS_AF=1.00000e-03;DP=16750;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21614884 rs534234692 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18455;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21615096 rs183998920 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17168;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21615161 rs562070395 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.00000e-03;DP=16590;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21615177 rs145253602 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=1.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=16243;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21615206 rs146440285 G A 100 PASS AC=18;AF=3.59425e-03;NS=2504;AN=5008;EAS_AF=1.79000e-02;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15590;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21615219 rs376146193 G C 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=4.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15490;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21615229 rs532185481 T A 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15272;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21615260 rs2182439 T G 100 PASS AC=1433;AF=2.86142e-01;NS=2504;AN=5008;EAS_AF=3.83900e-01;EUR_AF=2.00800e-01;AFR_AF=1.87600e-01;AMR_AF=3.42900e-01;SAS_AF=3.66100e-01;DP=16924;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 21615307 rs569059583 C T 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=2.00000e-03;DP=17165;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21615313 rs140927932 C T 100 PASS AC=24;AF=4.79233e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.74000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=16789;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21615355 rs12883729 A T 100 PASS AC=1955;AF=3.90375e-01;NS=2504;AN=5008;EAS_AF=3.88900e-01;EUR_AF=4.88100e-01;AFR_AF=2.03500e-01;AMR_AF=4.45200e-01;SAS_AF=5.05100e-01;DP=13776;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 1|1 0|1 1|0 1|1 1|1 1|1 +14 21615358 rs188544681 T A 100 PASS AC=9;AF=1.79712e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.80000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=13770;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21615392 rs12589796 T C 100 PASS AC=663;AF=1.32388e-01;NS=2504;AN=5008;EAS_AF=4.17000e-02;EUR_AF=9.15000e-02;AFR_AF=2.77600e-01;AMR_AF=6.20000e-02;SAS_AF=1.21700e-01;DP=14503;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21615601 rs570715845 AATAAC A 100 PASS AC=12;AF=2.39617e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=9.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15975;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21615617 rs12888690 T C 100 PASS AC=1041;AF=2.07867e-01;NS=2504;AN=5008;EAS_AF=3.16500e-01;EUR_AF=1.41200e-01;AFR_AF=6.05000e-02;AMR_AF=2.68000e-01;SAS_AF=3.21100e-01;DP=15328;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 21615674 rs560065523 C T 100 PASS AC=3;AF=5.99042e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.30000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=17118;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21615740 rs34753028 CA C 100 PASS AC=2418;AF=4.82827e-01;NS=2504;AN=5008;EAS_AF=4.35500e-01;EUR_AF=5.31800e-01;AFR_AF=4.31900e-01;AMR_AF=5.11500e-01;SAS_AF=5.29700e-01;DP=17308;AA=AAAAA|AAAAAA|AAAAA|insertion;VT=INDEL GT 0|0 1|1 0|0 1|1 1|1 0|1 1|0 1|1 1|1 1|1 +14 21615777 rs150281401 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=2.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18225;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21615794 rs78597440 T C 100 PASS AC=34;AF=6.78914e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.89000e-02;AFR_AF=1.50000e-03;AMR_AF=1.87000e-02;SAS_AF=0.00000e+00;DP=17980;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 1|0 0|0 +14 21615843 rs7151879 T G 100 PASS AC=1566;AF=3.12700e-01;NS=2504;AN=5008;EAS_AF=3.81000e-01;EUR_AF=2.01800e-01;AFR_AF=2.89700e-01;AMR_AF=3.42900e-01;SAS_AF=3.66100e-01;DP=17622;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|1 0|0 0|0 0|0 0|0 +14 21615917 rs146899232 T TA 100 PASS AC=31;AF=6.19010e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.27000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18601;AA=AAAAAAA|AAAAAAA|AAAAAAAA|insertion;VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21616020 rs71410265 C G 100 PASS AC=215;AF=4.29313e-02;NS=2504;AN=5008;EAS_AF=6.85000e-02;EUR_AF=5.67000e-02;AFR_AF=2.30000e-03;AMR_AF=6.05000e-02;SAS_AF=4.50000e-02;DP=16201;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21616035 rs375708715 T G 100 PASS AC=21;AF=4.19329e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=2.00000e-03;AFR_AF=0.00000e+00;AMR_AF=0.00000e+00;SAS_AF=1.94000e-02;DP=15451;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21616150 rs71419107 T TA 100 PASS AC=850;AF=1.69728e-01;NS=2504;AN=5008;EAS_AF=7.94000e-02;EUR_AF=1.20300e-01;AFR_AF=3.04100e-01;AMR_AF=1.11000e-01;SAS_AF=1.73800e-01;DP=13890;AA=|||unknown(HR);VT=INDEL GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21616226 rs183593495 T G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=13051;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21616281 rs142948623 G A 100 PASS AC=147;AF=2.93530e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.08200e-01;AMR_AF=5.80000e-03;SAS_AF=0.00000e+00;DP=15317;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21616298 rs535563155 A G 100 PASS AC=4;AF=7.98722e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.00000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=14923;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21616328 rs116941282 C T 100 PASS AC=28;AF=5.59105e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.99000e-02;AFR_AF=0.00000e+00;AMR_AF=5.80000e-03;SAS_AF=4.10000e-03;DP=14477;AA=C|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21616378 rs75854965 G A 100 PASS AC=51;AF=1.01837e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=3.86000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=15324;AA=g|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21616678 rs76561401 T G 100 PASS AC=31;AF=6.19010e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=2.27000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=17185;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21616807 rs193233280 T G 100 PASS AC=6;AF=1.19808e-03;NS=2504;AN=5008;EAS_AF=1.00000e-03;EUR_AF=0.00000e+00;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=2.00000e-03;DP=20278;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21616808 rs185647402 A C 100 PASS AC=16;AF=3.19489e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.21000e-02;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20258;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21616848 rs190114937 A G 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.50000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=20192;AA=A|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 +14 21616875 rs11156870 T C 100 PASS AC=1017;AF=2.03075e-01;NS=2504;AN=5008;EAS_AF=1.43800e-01;EUR_AF=1.78900e-01;AFR_AF=2.75300e-01;AMR_AF=2.20500e-01;SAS_AF=1.78900e-01;DP=19966;AA=T|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 0|1 0|0 .|0 0|. +14 21616876 rs549724318 G A 100 PASS AC=2;AF=3.99361e-04;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=8.00000e-04;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=19898;AA=G|||;VT=SNP GT 0|0 1|1 0|0 1|1 0|0 0|0 1|0 0|0 0|0 0|0 +4 9856624 test1 CAAAAA C 100 PASS AC=401;AF=8.00719e-02;NS=2504;AN=5008;EAS_AF=3.37000e-02;EUR_AF=4.97000e-02;AFR_AF=1.64100e-01;AMR_AF=3.75000e-02;SAS_AF=7.57000e-02;DP=18352;AA=G|||;VT=SNP GT 0|0 1|1 1|1 0|0 1|0 0|0 0|0 0|0 0|0 0|0 +4 9856624 test2 CAAA C 100 PASS AC=62;AF=1.23802e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=4.54000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18328;AA=T|||;VT=SNP GT 0|0 1|1 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 +4 9856624 test3 CA C 100 PASS AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18519;AA=T|||;VT=SNP GT 0|0 1|1 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 +4 9856624 test4 C CA 100 PASS AC=75;AF=1.49760e-02;NS=2504;AN=5008;EAS_AF=3.27000e-02;EUR_AF=2.49000e-02;AFR_AF=6.80000e-03;AMR_AF=4.30000e-03;SAS_AF=5.10000e-03;DP=18008;AA=A|||;VT=SNP GT 0|0 1|1 1|1 0|0 0|0 1|1 0|0 0|0 0|0 0|0 +4 9856624 test5 CAAAAA CA 100 PASS AC=3033;AF=6.05631e-01;NS=2504;AN=5008;EAS_AF=5.23800e-01;EUR_AF=7.54500e-01;AFR_AF=4.28900e-01;AMR_AF=7.82400e-01;SAS_AF=6.50300e-01;DP=20851;VT=INDEL GT 0|0 1|1 1|1 0|0 1|1 1|1 1|1 1|0 0|1 1|1 diff --git a/services/pic-sure-hpds/service/src/test/resources/bucketIndexBySampleTest_vcfIndex.tsv b/services/pic-sure-hpds/service/src/test/resources/bucketIndexBySampleTest_vcfIndex.tsv new file mode 100755 index 000000000..a5b9f5b70 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/resources/bucketIndexBySampleTest_vcfIndex.tsv @@ -0,0 +1,2 @@ +filename chromosome annotated gzip sample_ids patient_ids sample_relationship related_sample_ids +src/test/resources/BucketIndexTestInput.vcf ALL 1 0 "HG00096,HG00097,HG00099,HG00100,HG00101,HG00102,HG00103,HG00105,HG00106,HG00107" "1,2,3,4,5,6,7,8,9,10" diff --git a/services/pic-sure-hpds/service/src/test/resources/open_access-1000Genomes.chr20.annotated.vcf b/services/pic-sure-hpds/service/src/test/resources/open_access-1000Genomes.chr20.annotated.vcf new file mode 100644 index 000000000..19f1d0ea6 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/resources/open_access-1000Genomes.chr20.annotated.vcf @@ -0,0 +1,21 @@ +##fileformat=VCFv4.2 +## NOTE: this is not a real VCF file. It is a copy of chr20 but with no call data +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 HG00099 HG00100 HG00101 HG00102 HG00103 HG00105 HG00106 HG00107 HG00108 HG00109 HG00110 HG00111 HG00112 HG00113 HG00114 HG00115 HG00116 HG00117 HG00118 HG00119 HG00120 HG00121 HG00122 HG00123 HG00125 HG00126 HG00127 HG00128 HG00129 HG00130 HG00131 HG00132 HG00133 HG00136 HG00137 HG00138 HG00139 HG00140 HG00141 HG00142 HG00143 HG00145 HG00146 HG00148 HG00149 HG00150 HG00151 HG00154 HG00155 HG00157 HG00158 HG00159 HG00160 HG00171 HG00173 HG00174 HG00176 HG00177 HG00178 HG00179 HG00180 HG00181 HG00182 HG00183 HG00185 HG00186 HG00187 HG00188 HG00189 HG00190 HG00231 HG00232 HG00233 HG00234 HG00235 HG00236 HG00237 HG00238 HG00239 HG00240 HG00242 HG00243 HG00244 HG00245 HG00246 HG00250 HG00251 HG00252 HG00253 HG00254 HG00255 HG00256 HG00257 HG00258 HG00259 HG00260 HG00261 HG00262 HG00263 HG00264 HG00265 HG00266 HG00267 HG00268 HG00269 HG00271 HG00272 HG00273 HG00274 HG00275 HG00276 HG00277 HG00278 HG00280 HG00281 HG00282 HG00284 HG00285 HG00288 HG00290 HG00304 HG00306 HG00308 HG00309 HG00310 HG00311 HG00313 HG00315 HG00318 HG00319 HG00320 HG00321 HG00323 HG00324 HG00325 HG00326 HG00327 HG00328 HG00329 HG00330 HG00331 HG00332 HG00334 HG00335 HG00336 HG00337 HG00338 HG00339 HG00341 HG00342 HG00343 HG00344 HG00345 HG00346 HG00349 HG00350 HG00351 HG00353 HG00355 HG00356 HG00357 HG00358 HG00360 HG00361 HG00362 HG00364 HG00365 HG00366 HG00367 HG00368 HG00369 HG00371 HG00372 HG00373 HG00375 HG00376 HG00378 HG00379 HG00380 HG00381 HG00382 HG00383 HG00384 HG00403 HG00404 HG00405 HG00406 HG00407 HG00408 HG00409 HG00410 HG00418 HG00419 HG00420 HG00421 HG00422 HG00423 HG00427 HG00428 HG00429 HG00436 HG00437 HG00438 HG00442 HG00443 HG00444 HG00445 HG00446 HG00447 HG00448 HG00449 HG00450 HG00451 HG00452 HG00453 HG00457 HG00458 HG00459 HG00463 HG00464 HG00465 HG00472 HG00473 HG00474 HG00475 HG00476 HG00477 HG00478 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5033914 20:5033914:A:G A G . . 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diff --git a/services/pic-sure-hpds/service/src/test/resources/open_access-1000Genomes.chr4.annotated.vcf b/services/pic-sure-hpds/service/src/test/resources/open_access-1000Genomes.chr4.annotated.vcf new file mode 100644 index 000000000..06f640aaa --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/resources/open_access-1000Genomes.chr4.annotated.vcf @@ -0,0 +1,13 @@ +## +## THIS FILE IS FOR TESTING PURPOSES ONLY +## +## This file contains data inputs specifically modified to create certain scenarios +## during automated testing, and should not be used for others purpose +## +## +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 HG00099 HG00100 HG00101 HG00102 HG00103 HG00105 HG00106 HG00107 HG00108 HG00109 HG00110 HG00111 HG00112 HG00113 HG00114 HG00115 HG00116 HG00117 HG00118 HG00119 HG00120 HG00121 HG00122 HG00123 HG00125 HG00126 HG00127 HG00128 HG00129 HG00130 HG00131 HG00132 HG00133 HG00136 HG00137 HG00138 HG00139 HG00140 HG00141 HG00142 HG00143 HG00145 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C 100.00 PASS Gene_with_variant=TVP23A;Variant_consequence_calculated=splice_acceptor_variant;AC=62;AF=1.23802e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=4.54000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18328;AA=T|||;VT=SNP GT 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 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a/services/pic-sure-hpds/service/src/test/resources/phenotypic/encryption_key b/services/pic-sure-hpds/service/src/test/resources/phenotypic/encryption_key new file mode 100644 index 000000000..5aca1b5da --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/resources/phenotypic/encryption_key @@ -0,0 +1 @@ +1d3eb5177c06b2d19337fb7684429cda \ No newline at end of file diff --git a/services/pic-sure-hpds/service/src/test/resources/test_vcfIndex.tsv b/services/pic-sure-hpds/service/src/test/resources/test_vcfIndex.tsv new file mode 100755 index 000000000..f31827578 --- /dev/null +++ b/services/pic-sure-hpds/service/src/test/resources/test_vcfIndex.tsv @@ -0,0 +1,4 @@ +filename chromosome annotated gzip sample_ids patient_ids sample_relationship related_sample_ids +src/test/resources/open_access-1000Genomes.chr4.annotated.vcf 4 1 0 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\ No newline at end of file diff --git a/services/pic-sure-hpds/src/main/resources/.gitkeep b/services/pic-sure-hpds/src/main/resources/.gitkeep new file mode 100644 index 000000000..e69de29bb diff --git a/services/pic-sure-hpds/war/pom.xml b/services/pic-sure-hpds/war/pom.xml new file mode 100644 index 000000000..7d58bc818 --- /dev/null +++ b/services/pic-sure-hpds/war/pom.xml @@ -0,0 +1,44 @@ + + + 4.0.0 + + pic-sure-hpds + edu.harvard.hms.dbmi.avillach.hpds + ${revision} + + hpds-war + war + hpds-war + + + edu.harvard.hms.dbmi.avillach.hpds + service + + + + + + + org.apache.maven.plugins + maven-compiler-plugin + + 25 + + 3.15.0 + + + org.apache.maven.plugins + maven-eclipse-plugin + + [artifactId]-[version] + true + true + 2.0 + + + + + + diff --git a/services/pic-sure-hpds/war/src/main/webapp/META-INF/context.xml b/services/pic-sure-hpds/war/src/main/webapp/META-INF/context.xml new file mode 100644 index 000000000..d123dd3f8 --- /dev/null +++ b/services/pic-sure-hpds/war/src/main/webapp/META-INF/context.xml @@ -0,0 +1,2 @@ + + diff --git a/services/pic-sure-hpds/war/src/main/webapp/WEB-INF/web.xml b/services/pic-sure-hpds/war/src/main/webapp/WEB-INF/web.xml new file mode 100644 index 000000000..e2b7de9ff --- /dev/null +++ b/services/pic-sure-hpds/war/src/main/webapp/WEB-INF/web.xml @@ -0,0 +1,43 @@ + + + JAX-RS Simple Service + JAX-RS Simple Service + + contextConfigLocation + classpath*:jaxrs-context.xml + + + + org.springframework.web.context.ContextLoaderListener + + + + CXFServlet + + org.apache.cxf.transport.servlet.CXFServlet + + 1 + + + CXFServlet + /* + + + + + true + true + + + + 404 + /error-404.html + + + 500 + /error-500.html + + diff --git a/services/pic-sure-logging/.dockerignore b/services/pic-sure-logging/.dockerignore new file mode 100644 index 000000000..33021d9d2 --- /dev/null +++ b/services/pic-sure-logging/.dockerignore @@ -0,0 +1,11 @@ +.git +target/* +!target/pic-sure-logging-*.jar +*.md +docker-compose.yml +.idea/ +*.iml +.DS_Store +.claude/ +.env +.env.* diff --git a/services/pic-sure-logging/.env.example b/services/pic-sure-logging/.env.example new file mode 100644 index 000000000..5814ddbc6 --- /dev/null +++ b/services/pic-sure-logging/.env.example @@ -0,0 +1,24 @@ +# PIC-SURE Audit Logging Service Configuration +# Copy this file to .env and update the values for your environment. + +# REQUIRED: API key for authenticating POST /audit requests +LOGGING_API_KEY=change-me-to-a-secure-random-string + +# Application name included in audit log output +APP=pic-sure + +# Platform identifier included in audit log output +PLATFORM=avillach-lab + +# Deployment environment (e.g., local, dev, staging, production) +ENVIRONMENT=local + +# HTTP listen port +PORT=8080 + +# CORS allowed origin (* for any, or a specific origin like https://example.com) +ALLOWED_ORIGIN=* + +# JWT claim mapping (JSON object: JWT claim name -> output field name) +# Uncomment and customize to override the default mapping. +# JWT_CLAIM_MAPPING={"sub":"subject","email":"user_email","name":"user_name","roles":"roles","logged_in":"logged_in"} diff --git a/services/pic-sure-logging/.github/workflows/ci.yml b/services/pic-sure-logging/.github/workflows/ci.yml new file mode 100644 index 000000000..e2d2c2467 --- /dev/null +++ b/services/pic-sure-logging/.github/workflows/ci.yml @@ -0,0 +1,23 @@ +name: CI + +on: + push: + branches: [main] + pull_request: + branches: [main] + +jobs: + test: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Set up Java 21 + uses: actions/setup-java@v4 + with: + java-version: '21' + distribution: temurin + cache: maven + + - name: Run tests + run: mvn test diff --git a/services/pic-sure-logging/.gitignore b/services/pic-sure-logging/.gitignore new file mode 100644 index 000000000..163b6979b --- /dev/null +++ b/services/pic-sure-logging/.gitignore @@ -0,0 +1,15 @@ +target/ +*.class +*.jar +*.log +logs/ +.idea/ +*.iml +.settings/ +.project +.classpath +.DS_Store +*.swp +*.swo +.env +dependency-reduced-pom.xml \ No newline at end of file diff --git a/services/pic-sure-logging/.sdkmanrc b/services/pic-sure-logging/.sdkmanrc new file mode 100644 index 000000000..d2344323e --- /dev/null +++ b/services/pic-sure-logging/.sdkmanrc @@ -0,0 +1 @@ +java=25.0.3-tem diff --git a/services/pic-sure-logging/Dockerfile b/services/pic-sure-logging/Dockerfile new file mode 100644 index 000000000..30a8139d0 --- /dev/null +++ b/services/pic-sure-logging/Dockerfile @@ -0,0 +1,8 @@ +FROM eclipse-temurin:21-jre-alpine +WORKDIR /app +COPY target/pic-sure-logging-*.jar app.jar +RUN mkdir -p /app/logs +EXPOSE 80 +HEALTHCHECK --interval=30s --timeout=3s --start-period=10s --retries=3 \ + CMD wget --spider -q http://localhost:80/health || exit 1 +ENTRYPOINT ["java", "-jar", "app.jar"] diff --git a/services/pic-sure-logging/LICENSE b/services/pic-sure-logging/LICENSE new file mode 100644 index 000000000..d64569567 --- /dev/null +++ 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Designed to run as a Docker container on an internal network behind a reverse proxy. + +## Overview + +``` +Calling Service ──POST /audit──> Audit Logging Service ──JSON──> stdout & Log File ──> Splunk / ELK / etc. +``` + +The service is intentionally simple: it receives, enriches, and emits. It does not store data, manage state, or verify JWT signatures. Log shipping to your SIEM is handled at the infrastructure layer. + +## Quick Start + +### Docker Compose (recommended) + +```bash +docker compose up --build +``` + +This starts the service on port 8080 with a development API key. Test it: + +```bash +# Health check (no auth required) +curl http://localhost:8080/health + +# Send an audit event +curl -X POST http://localhost:8080/audit \ + -H "X-API-Key: dev-api-key-change-me" \ + -H "Content-Type: application/json" \ + -d '{"event_type": "QUERY", "action": "execute"}' +``` + +### Local Development + +Requires Java 21 and Maven 3.9+. + +```bash +# Build and run tests +mvn clean package + +# Run directly +LOGGING_API_KEY=my-secret-key java -jar target/pic-sure-logging-1.0-SNAPSHOT.jar +``` + +## API + +### POST /audit + +Accepts an audit event, enriches it with JWT claims and platform config, and writes a structured JSON log line to stdout and the audit log file. + +**Headers:** + +| Header | Required | Description | +|---|---|---| +| `X-API-Key` | Yes | Must match the configured `LOGGING_API_KEY` | +| `Content-Type` | Yes | Must be `application/json` | +| `Authorization` | No | `Bearer ` -- claims are extracted and included in the log | +| `X-Request-Id` | No | Fallback request ID if not provided in the body | + +**Request body:** + +```json +{ + "event_type": "QUERY", + "action": "execute", + "client_type": "web", + "request": { + "request_id": "abc-123", + "method": "POST", + "url": "/api/query", + "query_string": "limit=10", + "src_ip": "192.168.1.1", + "dest_ip": "10.0.0.5", + "dest_port": 8443, + "http_user_agent": "Mozilla/5.0", + "http_content_type": "application/json", + "status": 200, + "bytes": 1024, + "duration": 150, + "referrer": "https://example.com" + }, + "metadata": { + "queryId": "b93bbc83-19f6-478b-9e97-1b6dbe165a00", + "dataset": "phs000001" + }, + "error": { + "origin": "psama", + "message": "Internal error" + } +} +``` + +Only `event_type` is required. All other fields are optional. Unknown fields are silently ignored. + +**Responses:** + +| Status | Condition | +|---|---| +| `202 Accepted` | Event logged successfully | +| `400 Bad Request` | Invalid JSON or missing `event_type` | +| `401 Unauthorized` | Missing or invalid API key | +| `500 Internal Server Error` | Unexpected failure | + +### GET /health + +No authentication required. Returns `200 OK`: + +```json +{"status": "healthy"} +``` + +## Output Format + +Each audit event produces a single JSON line on both stdout and the rolling audit log file: + +```json +{ + "_time": "2025-01-15T14:30:00.123456Z", + "event_type": "QUERY", + "action": "execute", + "client_type": "web", + "subject": "user123", + "user_email": "user@example.com", + "user_name": "Jane Doe", + "roles": ["ADMIN", "USER"], + "logged_in": true, + "app": "pic-sure", + "platform": "avillach-lab", + "environment": "production", + "hostname": "audit-svc-7f8b9c", + "request_id": "abc-123", + "method": "POST", + "url": "/api/query", + "query_string": "limit=10", + "src_ip": "192.168.1.1", + "dest_ip": "10.0.0.5", + "dest_port": 8443, + "http_user_agent": "Mozilla/5.0", + "http_content_type": "application/json", + "status": 200, + "bytes": 1024, + "duration": 150, + "referrer": "https://example.com", + "metadata": {"queryId": "b93bbc83-19f6-478b-9e97-1b6dbe165a00", "dataset": "phs000001"}, + "error": {"code": "500", "message": "Internal error"} +} +``` + +**Key behaviors:** +- Null/missing fields are omitted entirely +- `metadata` and `error` are only included when non-empty +- `logged_in` is always present (`true` with a valid JWT, `false` without) +- `_time` is generated server-side in ISO-8601 format +- Request fields are flattened to the top level (not nested under `request`) +- Operational/application logs go to stderr as plain text, keeping stdout clean for log shippers + +## Configuration + +All configuration is via environment variables. + +| Variable | Required | Default | Description | +|---|---|---|---| +| `LOGGING_API_KEY` | **Yes** | -- | API key for `X-API-Key` authentication | +| `APP` | No | `unknown` | Application name included in log output | +| `PLATFORM` | No | `unknown` | Platform identifier included in log output | +| `ENVIRONMENT` | No | `unknown` | Deployment environment (e.g., `production`, `staging`) | +| `HOSTNAME` | No | System hostname | Container hostname (auto-set by Docker) | +| `PORT` | No | `8080` | HTTP listen port | +| `ALLOWED_ORIGIN` | No | `*` | CORS allowed origin (`*` for any) | +| `LOG_DIR` | No | `logs` | Directory for rolling log files (`audit.log`, `app.log`) | +| `JWT_CLAIM_MAPPING` | No | See below | JSON object mapping JWT claims to output field names | + +**Startup validation:** The service fails fast with a clear error message if `LOGGING_API_KEY` is missing, `PORT` is not a valid integer in range 1-65535, or `JWT_CLAIM_MAPPING` is not valid JSON. + +## JWT Claim Extraction + +The service decodes JWTs from the `Authorization: Bearer ` header to extract user context. **No signature verification is performed** -- the service trusts that the calling service or reverse proxy has already validated the token. + +### Configurable Claim Mapping + +The `JWT_CLAIM_MAPPING` environment variable controls which JWT claims are extracted and what they're named in the output. It's a JSON object where keys are JWT claim names and values are output field names: + +```bash +JWT_CLAIM_MAPPING='{"sub":"subject","email":"user_email","name":"user_name","roles":"roles"}' +``` + +**Default mapping** (used when `JWT_CLAIM_MAPPING` is not set): + +| JWT Claim | Output Field | +|---|---| +| `sub` | `subject` | +| `email` | `user_email` | +| `name` | `user_name` | +| `user_id` | `user_id` | +| `org` | `user_org` | +| `country_name` | `user_country_name` | +| `nih_ico` | `nih_ico` | +| `eRA_commons_id` | `eRA_commons_id` | +| `permission_group` | `user_permission_group` | +| `session_id` | `session_id` | +| `uuid` | `uuid` | +| `roles` | `roles` | +| `logged_in` | `logged_in` | +| `idp` | `user_id_provider` | +| `cadr_name` | `cadr_name` | + +### Type Handling + +- **`roles`** -- If the JWT claim is a JSON array, it is preserved as a list (e.g., `["ADMIN", "USER"]`), not flattened to a comma-separated string +- **`logged_in`** -- Boolean type is preserved +- **All other claims** -- Extracted as strings +- **Missing claims** -- Omitted from output (no nulls) + +### No JWT Present + +When no `Authorization` header is provided (or the token is blank/malformed), the output includes `"logged_in": false` and no other user fields. Malformed tokens log a warning to stderr but never cause request failures. + +## Request ID + +The service does not generate request IDs. It accepts them from: + +1. The `request.request_id` field in the POST body (takes priority) +2. The `X-Request-Id` HTTP header (fallback) + +If neither is present, the field is omitted from the output. Request IDs are expected to be generated by the reverse proxy or calling service. + +## Architecture + +``` +PIC-SURE-Logging/ +├── pom.xml # Maven build, Java 21, fat JAR via shade plugin +├── Dockerfile # Multi-stage: Maven build → JRE Alpine runtime +├── docker-compose.yml # Local development +└── src/main/java/edu/harvard/dbmi/avillach/logging/ + ├── App.java # Entry point, Javalin setup, route wiring + ├── config/ + │ └── AppConfig.java # Environment variable loading and validation + ├── handler/ + │ ├── AuditHandler.java # POST /audit — deserialize, validate, delegate + │ └── HealthHandler.java # GET /health — returns 200 + ├── middleware/ + │ └── ApiKeyAuthMiddleware.java # Constant-time API key comparison + ├── model/ + │ ├── AuditEvent.java # POST body record + │ └── RequestInfo.java # Nested request object record + └── service/ + ├── AuditLogService.java # Core logic: assemble fields, emit JSON + └── JwtDecodeService.java # JWT decode with configurable claim mapping +``` + +**Design decisions:** +- No dependency injection framework -- constructor injection, plain Java +- No database or persistent state -- pure log enrichment and forwarding +- JWT decode-only (no verification) -- trusts upstream authentication +- Constant-time API key comparison via `MessageDigest.isEqual()` to prevent timing attacks +- Logging failures never cause HTTP errors -- catch-all wraps the entire log assembly + +## Logging Architecture + +The service uses two separate log channels, each writing to both a console stream and an async rolling file: + +| Channel | Console | File | Format | Content | +|---|---|---|---|---| +| `AUDIT` logger | stdout | `${LOG_DIR}/audit.log` | Structured JSON (LogstashEncoder) | Audit event lines | +| Root logger | stderr | `${LOG_DIR}/app.log` | Plain text | Application/operational logs | + +File appenders use `SizeAndTimeBasedRollingPolicy` (rotates daily and at 50 MB, 30-day retention, 1 GB total cap for audit / 500 MB for app) and are wrapped in async appenders (`neverBlock=true`, `discardingThreshold=0`) so file I/O never blocks HTTP threads. + +This separation allows log shippers to capture clean JSON from stdout while operational noise goes to stderr. The rolling files provide a local fallback when stdout-based shipping is unavailable. + +## Docker + +### Building + +```bash +docker build -t pic-sure-logging . +``` + +The multi-stage Dockerfile: +1. **Build stage** -- Uses `maven:3.9-eclipse-temurin-21-alpine`, caches dependencies via `mvn dependency:go-offline` +2. **Runtime stage** -- Uses `eclipse-temurin:21-jre-alpine`, runs as non-root `appuser` + +### Running + +```bash +docker run -d \ + -p 8080:8080 \ + -e LOGGING_API_KEY=your-secret-key \ + -e APP=pic-sure \ + -e PLATFORM=avillach-lab \ + -e ENVIRONMENT=production \ + pic-sure-logging +``` + +The container includes a `HEALTHCHECK` that polls `GET /health` every 30 seconds. + +## Log Shipping + +The service writes JSON to both stdout and a rolling file (`${LOG_DIR}/audit.log`). Shipping logs to your SIEM is an infrastructure concern. Common approaches: + +### Docker Splunk Logging Driver + +```bash +docker run -d \ + --log-driver=splunk \ + --log-opt splunk-token=YOUR_HEC_TOKEN \ + --log-opt splunk-url=https://your-splunk:8088 \ + --log-opt splunk-format=json \ + --log-opt splunk-sourcetype=audit:picsure \ + -e LOGGING_API_KEY=your-key \ + pic-sure-logging +``` + +### OpenTelemetry Collector + +Use a `filelog` receiver to tail Docker JSON log files and forward to Splunk HEC, Elasticsearch, or any OTLP-compatible backend. + +### Fluentd / Fluent Bit + +Sidecar that reads Docker JSON log files and forwards to your destination. Well-documented for both Docker and Kubernetes deployments. + +### Splunk Compatibility + +- **`_time`** -- Recognized by Splunk as the event timestamp (configure `TIME_FORMAT = %Y-%m-%dT%H:%M:%S.%3NZ`) +- **Nested objects** (`metadata`, `error`) -- Auto-extracted via dot notation (e.g., `metadata.query_id`) +- **`hostname`** -- Does not conflict with Splunk's reserved `host` field +- **Array fields** (`roles`) -- Treated as multivalued fields, searchable with `roles=ADMIN` +- **Sourcetype** -- Use `_json` for automatic field extraction or a custom `audit:picsure` + +## Development + +### Prerequisites + +- Java 21 +- Maven 3.9+ +- Docker (for container builds) + +### Running Tests + +```bash +mvn test +``` + +The test suite includes: +- **Unit tests** -- `AppConfigTest`, `JwtDecodeServiceTest`, `AuditLogServiceTest`, `ApiKeyAuthMiddlewareTest`, `AuditHandlerTest` +- **Integration tests** -- `AppIntegrationTest` (full HTTP round-trips using javalin-testtools) + +Tests use a `ListAppender` on the `AUDIT` logger to capture and assert on structured log output, and a `TestJwtBuilder` helper to create JWTs signed with a test secret. + +### Building the Fat JAR + +```bash +mvn clean package +``` + +Produces `target/pic-sure-logging-1.0-SNAPSHOT.jar` (~9 MB) containing all dependencies. + +## Error Handling + +| Layer | Error | Behavior | +|---|---|---| +| Startup | Missing `LOGGING_API_KEY` | Exit with clear error message | +| Startup | Invalid `PORT` | Exit with clear error message | +| Startup | Invalid `JWT_CLAIM_MAPPING` | Exit with clear error message | +| HTTP | Missing/wrong API key | `401 Unauthorized` | +| HTTP | Malformed JSON body | `400 Bad Request` with detail | +| HTTP | Missing `event_type` | `400 Bad Request` | +| JWT | Null/blank/malformed token | Warning to stderr, `logged_in: false` in output | +| JWT | Missing individual claim | Omit that field | +| Logging | Any exception during log assembly | Catch-all logs error to stderr, HTTP still returns `202` | +| Global | Unexpected exception | `500 Internal Server Error` | + +## Deployment Requirements + +This service is designed to run behind a reverse proxy on an internal network. It does **not** handle TLS or JWT verification itself. + +| Requirement | Responsibility | Notes | +|---|---|---| +| **TLS termination** | Reverse proxy (e.g., Nginx, Traefik, ALB) | Service listens on plain HTTP | +| **JWT signature verification** | Upstream service or API gateway | Service decodes JWTs but does not verify signatures | +| **Request ID generation** | Reverse proxy or calling service | Service accepts `X-Request-Id` but does not generate IDs | + +### Resource Recommendations + +| Resource | Minimum | Recommended | +|---|---|---| +| Memory | 256 MB | 512 MB | +| CPU | 0.25 vCPU | 1 vCPU | +| Disk (logs) | 2 GB | 5 GB | + +The `docker-compose.yml` binds the port to `127.0.0.1` by default, which is appropriate when the service is only accessed through a local reverse proxy. Adjust the bind address if the reverse proxy runs on a separate host. + +## Security Considerations + +- **API key auth** -- All `/audit` requests require a valid `X-API-Key` header. The `/health` endpoint is unauthenticated. +- **Constant-time comparison** -- API key validation uses `MessageDigest.isEqual()` to prevent timing-based attacks. +- **No JWT verification** -- This service does not verify JWT signatures. It is designed to run on an internal network where tokens have already been validated by an upstream service or API gateway. +- **Non-root container** -- The Docker image runs as an unprivileged `appuser`. +- **Request size limit** -- HTTP request bodies are capped at 1 MB. +- **No secrets in logs** -- The raw JWT token is never written to the audit log; only extracted claims appear. + +## License + +Licensed under the Apache License, Version 2.0. See [LICENSE](LICENSE) for the full text. diff --git a/services/pic-sure-logging/docker-compose.yml b/services/pic-sure-logging/docker-compose.yml new file mode 100644 index 000000000..73ec4cfde --- /dev/null +++ b/services/pic-sure-logging/docker-compose.yml @@ -0,0 +1,15 @@ +services: + audit-logging: + build: . + env_file: + - .env + ports: + - "127.0.0.1:${PORT:-8080}:${PORT:-8080}" + volumes: + - ./logs:/app/logs + restart: unless-stopped + deploy: + resources: + limits: + memory: 512M + cpus: "1" diff --git a/services/pic-sure-logging/jenkinsfile b/services/pic-sure-logging/jenkinsfile new file mode 100644 index 000000000..07d0104a5 --- /dev/null +++ b/services/pic-sure-logging/jenkinsfile @@ -0,0 +1,99 @@ +pipeline { + agent any + + parameters { + string(name: 'git_hash', description: 'The Git hash to checkout', defaultValue: 'main') + string(name: 'DOCKER_REGISTRY', description: 'Docker registry URL (e.g., ECR URL)', defaultValue: 'hms-dbmi') + string(name: 'REPOSITORY_NAME', description: 'Docker repository name', defaultValue: 'pic-sure-logging') + choice(name: 'DEPLOY_METHOD', description: 'Deployment method', choices: ['docker', 's3', 'none']) + string(name: 'TARGET_STACK', description: 'Target stack for deployment (required for s3 deploy)', defaultValue: '') + string(name: 'STACK_S3_BUCKET', description: 'S3 bucket for image upload (required for s3 deploy)', defaultValue: '') + } + + stages { + stage('init') { + steps { + script { + env.GIT_BRANCH_SHORT = sh(script: 'echo "${GIT_BRANCH}" | awk -F/ \'{print $NF}\'', returnStdout: true).trim() + env.GIT_COMMIT_SHORT = sh(script: 'echo "${GIT_COMMIT}" | cut -c1-7', returnStdout: true).trim() + env.IMAGE_TAG = "${env.GIT_BRANCH_SHORT}_${env.GIT_COMMIT_SHORT}" + env.LATEST_TAG = params.DEPLOY_METHOD == 's3' ? 'latest' : 'LATEST' + env.IMAGE_NAME = "${params.DOCKER_REGISTRY}/${params.REPOSITORY_NAME}" + } + } + } + + stage('build jar (docker run)') { + steps { + sh ''' + set -euo pipefail + + # DOCKER_CONFIG_DIR is set in all-in-one but not BDC. + # In all-in-one the host path differs from the container path. + # In BDC the workspace mount is an identity map (host == container). + if [ -n "${DOCKER_CONFIG_DIR:-}" ]; then + MOUNT_PATH="$DOCKER_CONFIG_DIR/jenkins_home/workspace/$JOB_NAME" + else + MOUNT_PATH="/var/jenkins_home/workspace/${JOB_NAME}" + fi + + docker run --rm \ + -v "$MOUNT_PATH/:/app:Z" \ + -v maven_m2_cache:/root/.m2 \ + -w /app/services/pic-sure-logging \ + maven:3.9.9-amazoncorretto-24 \ + sh -lc "mvn clean install -B -T 1C -DskipTests" + + ls -lah services/pic-sure-logging/target || true + ''' + } + } + + stage('build image') { + steps { + sh ''' + set -euo pipefail + + PROXY_ARGS="" + if [ -n "${http_proxy:-}" ]; then + PROXY_ARGS="--build-arg http_proxy=$http_proxy --build-arg https_proxy=$http_proxy --build-arg HTTP_PROXY=$http_proxy --build-arg HTTPS_PROXY=$http_proxy" + fi + if [ -n "${no_proxy:-}" ]; then + PROXY_ARGS="$PROXY_ARGS --build-arg no_proxy=$no_proxy --build-arg NO_PROXY=$no_proxy" + fi + + docker build --load $PROXY_ARGS -t "${IMAGE_NAME}:${IMAGE_TAG}" services/pic-sure-logging + docker tag "${IMAGE_NAME}:${IMAGE_TAG}" "${IMAGE_NAME}:${LATEST_TAG}" + ''' + } + } + + stage('deploy') { + steps { + script { + if (params.DEPLOY_METHOD == 'docker') { + sh ''' + set +e + docker stop pic-sure-logging + docker rm pic-sure-logging + set -e + + docker run --name=pic-sure-logging --restart always \ + --network=picsure \ + --env-file /usr/local/docker-config/logging/logging.env \ + -v /usr/local/docker-config/log/logging-docker-logs/:/app/logs \ + -d "${IMAGE_NAME}:${IMAGE_TAG}" + ''' + } else if (params.DEPLOY_METHOD == 's3') { + sh ''' + docker save "${IMAGE_NAME}:${LATEST_TAG}" | gzip > pic-sure-logging.tar.gz + aws s3 --sse=AES256 cp pic-sure-logging.tar.gz "s3://${stack_s3_bucket}/${TARGET_STACK}/containers/pic-sure-logging.tar.gz" + ''' + } else { + echo "Deployment skipped." + } + } + } + } + } +} diff --git a/services/pic-sure-logging/pom.xml b/services/pic-sure-logging/pom.xml new file mode 100644 index 000000000..0a116638d --- /dev/null +++ b/services/pic-sure-logging/pom.xml @@ -0,0 +1,129 @@ + + + 4.0.0 + + edu.harvard.hms.dbmi.avillach + pic-sure-api + ${revision} + ../../pom.xml + + + edu.harvard.dbmi.avillach + pic-sure-logging + jar + + PIC-SURE Audit Logging Service + + + + 6.7.0 + 4.4.0 + + + + + + + org.eclipse.jetty + jetty-bom + 11.0.25 + pom + import + + + + + + + + io.javalin + javalin + ${javalin.version} + + + + + com.fasterxml.jackson.core + jackson-databind + + + + + com.auth0 + java-jwt + ${java-jwt.version} + + + + + org.slf4j + slf4j-api + + + ch.qos.logback + logback-classic + + + net.logstash.logback + logstash-logback-encoder + + + + + org.junit.jupiter + junit-jupiter + test + + + org.mockito + mockito-core + test + + + io.javalin + javalin-testtools + ${javalin.version} + test + + + + + + + org.apache.maven.plugins + maven-shade-plugin + 3.6.0 + + + package + + shade + + + + + edu.harvard.dbmi.avillach.logging.App + + + + + + *:* + + META-INF/*.SF + META-INF/*.DSA + META-INF/*.RSA + + + + + + + + + + diff --git a/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/App.java b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/App.java new file mode 100644 index 000000000..19f1343e8 --- /dev/null +++ b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/App.java @@ -0,0 +1,76 @@ +package edu.harvard.dbmi.avillach.logging; + +import edu.harvard.dbmi.avillach.logging.config.AppConfig; +import edu.harvard.dbmi.avillach.logging.handler.AuditHandler; +import edu.harvard.dbmi.avillach.logging.handler.HealthHandler; +import edu.harvard.dbmi.avillach.logging.handler.InfoHandler; +import edu.harvard.dbmi.avillach.logging.middleware.ApiKeyAuthMiddleware; +import edu.harvard.dbmi.avillach.logging.service.AuditLogService; +import edu.harvard.dbmi.avillach.logging.service.JwtDecodeService; +import io.javalin.Javalin; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.Map; +import java.util.concurrent.atomic.AtomicBoolean; + +public class App { + + private static final Logger log = LoggerFactory.getLogger(App.class); + + public static void main(String[] args) { + AppConfig config = AppConfig.fromEnvironment(); + AtomicBoolean readiness = new AtomicBoolean(false); + Javalin app = createApp(config, readiness); + app.start(config.port()); + readiness.set(true); + + Runtime.getRuntime().addShutdownHook(new Thread(() -> { + log.info("Shutting down..."); + readiness.set(false); + app.stop(); + })); + + log.info( + "Audit logging service started: app={}, platform={}, environment={}, hostname={}, port={}, allowedOrigin={}", config.app(), + config.platform(), config.environment(), config.hostname(), config.port(), config.allowedOrigin() + ); + } + + public static Javalin createApp(AppConfig config, AtomicBoolean readiness) { + JwtDecodeService jwtDecodeService = new JwtDecodeService(config.jwtClaimMapping()); + AuditLogService auditLogService = new AuditLogService(config, jwtDecodeService); + AuditHandler auditHandler = new AuditHandler(auditLogService); + HealthHandler healthHandler = new HealthHandler(readiness); + InfoHandler infoHandler = new InfoHandler(); + ApiKeyAuthMiddleware authMiddleware = new ApiKeyAuthMiddleware(config.auditApiKey()); + + Javalin app = Javalin.create(javalinConfig -> { + javalinConfig.showJavalinBanner = false; + javalinConfig.http.maxRequestSize = 1_048_576L; // 1MB + javalinConfig.bundledPlugins.enableCors(cors -> { + cors.addRule(rule -> { + if ("*".equals(config.allowedOrigin())) { + rule.anyHost(); + } else { + rule.allowHost(config.allowedOrigin()); + } + }); + }); + }); + + app.before("/audit", authMiddleware::authenticate); + + app.post("/audit", auditHandler::handle); + app.post("/info", infoHandler::handle); + app.get("/health", healthHandler::handle); + + app.exception(Exception.class, (e, ctx) -> { + log.error("Unhandled exception", e); + ctx.status(500); + ctx.json(Map.of("status", "error", "message", "Internal server error")); + }); + + return app; + } +} diff --git a/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/config/AppConfig.java b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/config/AppConfig.java new file mode 100644 index 000000000..b3555d5b8 --- /dev/null +++ b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/config/AppConfig.java @@ -0,0 +1,85 @@ +package edu.harvard.dbmi.avillach.logging.config; + +import com.fasterxml.jackson.core.type.TypeReference; +import com.fasterxml.jackson.databind.ObjectMapper; + +import java.net.InetAddress; +import java.util.Map; +import java.util.function.Function; + +public record AppConfig( + String auditApiKey, String app, String platform, String environment, String hostname, int port, String allowedOrigin, + Map jwtClaimMapping +) { + + private static final Map DEFAULT_JWT_CLAIM_MAPPING = Map.ofEntries( + Map.entry("sub", "subject"), Map.entry("email", "user_email"), Map.entry("name", "user_name"), Map.entry("userid", "user_id"), + Map.entry("preferred_username", "preferred_username"), Map.entry("org", "user_org"), Map.entry("country_name", "user_country_name"), + Map.entry("nih_ico", "nih_ico"), Map.entry("eRA_commons_id", "eRA_commons_id"), + Map.entry("user_permission_group", "user_permission_group"), Map.entry("uuid", "uuid"), Map.entry("roles", "roles"), + Map.entry("idp", "user_id_provider"), Map.entry("cadr_name", "cadr_name") + ); + + public static AppConfig fromEnvironment() { + return fromEnvironment(System::getenv); + } + + public static AppConfig fromEnvironment(Function env) { + String auditApiKey = env.apply("LOGGING_API_KEY"); + if (auditApiKey == null || auditApiKey.isBlank()) { + throw new IllegalStateException("LOGGING_API_KEY environment variable is required"); + } + + String app = getOrDefault(env, "APP", "unknown"); + String platform = getOrDefault(env, "PLATFORM", "unknown"); + String environment = getOrDefault(env, "ENVIRONMENT", "unknown"); + String hostname = getOrDefault(env, "HOSTNAME", getSystemHostname()); + String allowedOrigin = getOrDefault(env, "ALLOWED_ORIGIN", "*"); + + int port = parsePort(env.apply("PORT")); + + Map jwtClaimMapping = parseJwtClaimMapping(env.apply("JWT_CLAIM_MAPPING")); + + return new AppConfig(auditApiKey, app, platform, environment, hostname, port, allowedOrigin, jwtClaimMapping); + } + + private static String getOrDefault(Function env, String key, String defaultValue) { + String value = env.apply(key); + return (value != null && !value.isBlank()) ? value : defaultValue; + } + + private static int parsePort(String portStr) { + if (portStr == null || portStr.isBlank()) { + return 8080; + } + try { + int port = Integer.parseInt(portStr.trim()); + if (port < 1 || port > 65535) { + throw new IllegalStateException("PORT must be between 1 and 65535, got: " + port); + } + return port; + } catch (NumberFormatException e) { + throw new IllegalStateException("PORT must be a valid integer, got: " + portStr); + } + } + + private static Map parseJwtClaimMapping(String json) { + if (json == null || json.isBlank()) { + return DEFAULT_JWT_CLAIM_MAPPING; + } + try { + ObjectMapper mapper = new ObjectMapper(); + return mapper.readValue(json, new TypeReference>() {}); + } catch (Exception e) { + throw new IllegalStateException("JWT_CLAIM_MAPPING must be valid JSON object, got: " + json, e); + } + } + + private static String getSystemHostname() { + try { + return InetAddress.getLocalHost().getHostName(); + } catch (Exception e) { + return "unknown"; + } + } +} diff --git a/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/handler/AuditHandler.java b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/handler/AuditHandler.java new file mode 100644 index 000000000..8c85cd90c --- /dev/null +++ b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/handler/AuditHandler.java @@ -0,0 +1,56 @@ +package edu.harvard.dbmi.avillach.logging.handler; + +import com.fasterxml.jackson.core.StreamReadConstraints; +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.dbmi.avillach.logging.model.AuditEvent; +import edu.harvard.dbmi.avillach.logging.service.AuditLogService; +import io.javalin.http.BadRequestResponse; +import io.javalin.http.Context; + +import java.util.Map; + +public class AuditHandler { + + private final AuditLogService auditLogService; + private final ObjectMapper objectMapper; + + private static final int MAX_METADATA_KEYS = 50; + private static final int MAX_ERROR_KEYS = 20; + + public AuditHandler(AuditLogService auditLogService) { + this.auditLogService = auditLogService; + this.objectMapper = new ObjectMapper(); + objectMapper.getFactory().setStreamReadConstraints( + StreamReadConstraints.builder().maxNestingDepth(10).maxStringLength(10_240) // 10KB + .build() + ); + } + + public void handle(Context ctx) { + AuditEvent event; + try { + event = objectMapper.readValue(ctx.body(), AuditEvent.class); + } catch (Exception e) { + throw new BadRequestResponse("Invalid JSON: " + e.getMessage()); + } + + if (event.metadata() != null && event.metadata().size() > MAX_METADATA_KEYS) { + throw new BadRequestResponse("metadata must not exceed " + MAX_METADATA_KEYS + " keys"); + } + if (event.error() != null && event.error().size() > MAX_ERROR_KEYS) { + throw new BadRequestResponse("error must not exceed " + MAX_ERROR_KEYS + " keys"); + } + + if (event.eventType() == null || event.eventType().isBlank()) { + throw new BadRequestResponse("event_type is required"); + } + + String authHeader = ctx.header("Authorization"); + String requestIdHeader = ctx.header("X-Request-Id"); + + auditLogService.logEvent(event, authHeader, requestIdHeader); + + ctx.status(202); + ctx.json(Map.of("status", "accepted")); + } +} diff --git a/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/handler/HealthHandler.java b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/handler/HealthHandler.java new file mode 100644 index 000000000..fa3535655 --- /dev/null +++ b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/handler/HealthHandler.java @@ -0,0 +1,25 @@ +package edu.harvard.dbmi.avillach.logging.handler; + +import io.javalin.http.Context; + +import java.util.Map; +import java.util.concurrent.atomic.AtomicBoolean; + +public class HealthHandler { + + private final AtomicBoolean ready; + + public HealthHandler(AtomicBoolean ready) { + this.ready = ready; + } + + public void handle(Context ctx) { + if (ready.get()) { + ctx.status(200); + ctx.json(Map.of("status", "healthy")); + } else { + ctx.status(503); + ctx.json(Map.of("status", "starting")); + } + } +} diff --git a/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/handler/InfoHandler.java b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/handler/InfoHandler.java new file mode 100644 index 000000000..bbe818f78 --- /dev/null +++ b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/handler/InfoHandler.java @@ -0,0 +1,20 @@ +package edu.harvard.dbmi.avillach.logging.handler; + +import edu.harvard.dbmi.avillach.logging.model.InfoResponse; +import io.javalin.http.Context; + +import java.util.List; +import java.util.UUID; + +public class InfoHandler { + + private final InfoResponse response; + + public InfoHandler() { + this.response = new InfoResponse(UUID.nameUUIDFromBytes(":)".getBytes()), "Logging Service", List.of()); + } + + public void handle(Context ctx) { + ctx.json(response); + } +} diff --git a/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/middleware/ApiKeyAuthMiddleware.java b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/middleware/ApiKeyAuthMiddleware.java new file mode 100644 index 000000000..6a00e6fa8 --- /dev/null +++ b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/middleware/ApiKeyAuthMiddleware.java @@ -0,0 +1,28 @@ +package edu.harvard.dbmi.avillach.logging.middleware; + +import io.javalin.http.Context; +import io.javalin.http.UnauthorizedResponse; + +import java.nio.charset.StandardCharsets; +import java.security.MessageDigest; + +public class ApiKeyAuthMiddleware { + + private final byte[] expectedKeyBytes; + + public ApiKeyAuthMiddleware(String expectedApiKey) { + this.expectedKeyBytes = expectedApiKey.getBytes(StandardCharsets.UTF_8); + } + + public void authenticate(Context ctx) { + String provided = ctx.header("X-API-Key"); + if (provided == null || provided.isBlank()) { + throw new UnauthorizedResponse("Missing or invalid API key"); + } + + byte[] providedBytes = provided.getBytes(StandardCharsets.UTF_8); + if (!MessageDigest.isEqual(expectedKeyBytes, providedBytes)) { + throw new UnauthorizedResponse("Missing or invalid API key"); + } + } +} diff --git a/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/model/AuditEvent.java b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/model/AuditEvent.java new file mode 100644 index 000000000..64b2507d8 --- /dev/null +++ b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/model/AuditEvent.java @@ -0,0 +1,14 @@ +package edu.harvard.dbmi.avillach.logging.model; + +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; +import com.fasterxml.jackson.annotation.JsonProperty; + +import java.util.Map; + +@JsonIgnoreProperties(ignoreUnknown = true) +public record AuditEvent( + @JsonProperty("event_type") String eventType, @JsonProperty("action") String action, @JsonProperty("client_type") String clientType, + @JsonProperty("caller") String caller, @JsonProperty("session_id") String sessionId, @JsonProperty("request") RequestInfo request, + @JsonProperty("metadata") Map metadata, @JsonProperty("error") Map error +) { +} diff --git a/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/model/InfoResponse.java b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/model/InfoResponse.java new file mode 100644 index 000000000..3318e1e27 --- /dev/null +++ b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/model/InfoResponse.java @@ -0,0 +1,7 @@ +package edu.harvard.dbmi.avillach.logging.model; + +import java.util.List; +import java.util.UUID; + +public record InfoResponse(UUID id, String name, List queryFormats) { +} diff --git a/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/model/RequestInfo.java b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/model/RequestInfo.java new file mode 100644 index 000000000..53e6a54ed --- /dev/null +++ b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/model/RequestInfo.java @@ -0,0 +1,14 @@ +package edu.harvard.dbmi.avillach.logging.model; + +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; +import com.fasterxml.jackson.annotation.JsonProperty; + +@JsonIgnoreProperties(ignoreUnknown = true) +public record RequestInfo( + @JsonProperty("request_id") String requestId, @JsonProperty("method") String method, @JsonProperty("url") String url, + @JsonProperty("query_string") String queryString, @JsonProperty("src_ip") String srcIp, @JsonProperty("dest_ip") String destIp, + @JsonProperty("dest_port") Integer destPort, @JsonProperty("http_user_agent") String httpUserAgent, + @JsonProperty("http_content_type") String httpContentType, @JsonProperty("status") Integer status, @JsonProperty("bytes") Long bytes, + @JsonProperty("duration") Long duration, @JsonProperty("referrer") String referrer +) { +} diff --git a/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/service/AuditLogService.java b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/service/AuditLogService.java new file mode 100644 index 000000000..d8932a8ab --- /dev/null +++ b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/service/AuditLogService.java @@ -0,0 +1,140 @@ +package edu.harvard.dbmi.avillach.logging.service; + +import edu.harvard.dbmi.avillach.logging.config.AppConfig; +import edu.harvard.dbmi.avillach.logging.model.AuditEvent; +import edu.harvard.dbmi.avillach.logging.model.RequestInfo; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.time.Instant; +import java.util.LinkedHashMap; +import java.util.Map; + +import static net.logstash.logback.argument.StructuredArguments.entries; + +public class AuditLogService { + + private static final Logger auditLog = LoggerFactory.getLogger("AUDIT"); + private static final Logger appLog = LoggerFactory.getLogger(AuditLogService.class); + private static final int MAX_STRING_LENGTH = 2000; + + private final AppConfig config; + private final JwtDecodeService jwtDecodeService; + + public AuditLogService(AppConfig config, JwtDecodeService jwtDecodeService) { + this.config = config; + this.jwtDecodeService = jwtDecodeService; + } + + public void logEvent(AuditEvent event, String authorizationHeader, String requestIdHeader) { + if (event == null) { + appLog.warn("logEvent called with null event, ignoring"); + return; + } + try { + LinkedHashMap fields = new LinkedHashMap<>(); + + // 1. Timestamp + fields.put("_time", Instant.now().toString()); + + // 2. Event fields + putIfNotNull(fields, "event_type", event.eventType()); + putIfNotNull(fields, "action", event.action()); + putIfNotNull(fields, "client_type", event.clientType()); + + String caller = event.caller(); + if (caller != null && !caller.isBlank()) { + fields.put("caller", truncate(caller)); + } + + // 2b. Session ID: prefer top-level field, fall back to metadata for old clients + String sessionId = event.sessionId(); + if ((sessionId == null || sessionId.isBlank()) && event.metadata() != null) { + Object metaSessionId = event.metadata().get("session_id"); + if (metaSessionId != null) { + sessionId = metaSessionId.toString(); + } + } + if (sessionId != null && !sessionId.isBlank()) { + fields.put("session_id", truncate(sessionId)); + } + + // 3. User fields from JWT + Map userClaims = jwtDecodeService.extractClaims(authorizationHeader); + fields.putAll(userClaims); + + // 4. Platform fields + putIfNotNull(fields, "app", config.app()); + putIfNotNull(fields, "platform", config.platform()); + putIfNotNull(fields, "environment", config.environment()); + putIfNotNull(fields, "hostname", config.hostname()); + + // 5. Request fields + flattenRequest(fields, event.request(), requestIdHeader); + + // 6. Metadata and error (nested, only if non-empty) + if (event.metadata() != null && !event.metadata().isEmpty()) { + // Strip session_id from metadata since it is now a top-level field + LinkedHashMap filteredMetadata = new LinkedHashMap<>(event.metadata()); + filteredMetadata.remove("session_id"); + if (!filteredMetadata.isEmpty()) { + fields.put("metadata", filteredMetadata); + } + } + if (event.error() != null && !event.error().isEmpty()) { + fields.put("error", event.error()); + } + + auditLog.info("{}", entries(fields)); + } catch (Exception e) { + appLog.error("Failed to assemble audit log event", e); + } + } + + private void flattenRequest(LinkedHashMap fields, RequestInfo request, String requestIdHeader) { + if (request != null) { + // request_id from body takes priority + if (request.requestId() != null && !request.requestId().isBlank()) { + fields.put("request_id", truncate(request.requestId())); + } else if (requestIdHeader != null && !requestIdHeader.isBlank()) { + fields.put("request_id", truncate(requestIdHeader)); + } + + putIfNotNull(fields, "method", request.method()); + putIfNotNull(fields, "url", request.url()); + putIfNotNull(fields, "query_string", request.queryString()); + putIfNotNull(fields, "src_ip", request.srcIp()); + putIfNotNull(fields, "dest_ip", request.destIp()); + if (request.destPort() != null) { + fields.put("dest_port", request.destPort()); + } + putIfNotNull(fields, "http_user_agent", request.httpUserAgent()); + putIfNotNull(fields, "http_content_type", request.httpContentType()); + if (request.status() != null) { + fields.put("status", request.status()); + } + if (request.bytes() != null) { + fields.put("bytes", request.bytes()); + } + if (request.duration() != null) { + fields.put("duration", request.duration()); + } + putIfNotNull(fields, "referrer", request.referrer()); + } else if (requestIdHeader != null && !requestIdHeader.isBlank()) { + fields.put("request_id", truncate(requestIdHeader)); + } + } + + private void putIfNotNull(Map map, String key, String value) { + if (value != null) { + map.put(key, truncate(value)); + } + } + + private static String truncate(String value) { + if (value != null && value.length() > MAX_STRING_LENGTH) { + return value.substring(0, MAX_STRING_LENGTH); + } + return value; + } +} diff --git a/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/service/JwtDecodeService.java b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/service/JwtDecodeService.java new file mode 100644 index 000000000..56f5a188b --- /dev/null +++ b/services/pic-sure-logging/src/main/java/edu/harvard/dbmi/avillach/logging/service/JwtDecodeService.java @@ -0,0 +1,101 @@ +package edu.harvard.dbmi.avillach.logging.service; + +import com.auth0.jwt.JWT; +import com.auth0.jwt.interfaces.Claim; +import com.auth0.jwt.interfaces.DecodedJWT; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.*; + +public class JwtDecodeService { + + private static final Logger log = LoggerFactory.getLogger(JwtDecodeService.class); + private static final int MAX_TOKEN_BYTES = 16_384; // 16KB + + private final Map claimMapping; + + public JwtDecodeService(Map claimMapping) { + this.claimMapping = claimMapping; + } + + public Map extractClaims(String authorizationHeader) { + if (authorizationHeader == null || authorizationHeader.isBlank()) { + return Map.of("logged_in", false); + } + + String token = authorizationHeader.strip(); + if (token.regionMatches(true, 0, "Bearer ", 0, 7)) { + token = token.substring(7).strip(); + } + + if (token.isBlank()) { + return Map.of("logged_in", false); + } + + if (token.length() > MAX_TOKEN_BYTES) { + log.warn("JWT token exceeds maximum size of {} bytes (got {})", MAX_TOKEN_BYTES, token.length()); + return Map.of("logged_in", false); + } + + try { + DecodedJWT jwt = JWT.decode(token); + Map result = new LinkedHashMap<>(); + + for (Map.Entry entry : claimMapping.entrySet()) { + String claimName = entry.getKey(); + String outputField = entry.getValue(); + + Claim claim = jwt.getClaim(claimName); + if (claim.isMissing() || claim.isNull()) { + continue; + } + + Object value = extractClaimValue(claimName, claim); + if (value != null) { + result.put(outputField, value); + } + } + + // Always emit logged_in + String loggedInOutputField = claimMapping.get("logged_in"); + if (loggedInOutputField != null && !result.containsKey(loggedInOutputField)) { + result.put(loggedInOutputField, true); + } else if (loggedInOutputField == null) { + result.put("logged_in", true); + } + + return result; + } catch (Exception e) { + log.warn("Failed to decode JWT: {}", e.getMessage()); + return Map.of("logged_in", false); + } + } + + private Object extractClaimValue(String claimName, Claim claim) { + // roles → keep as List + if ("roles".equals(claimName)) { + try { + List list = claim.asList(String.class); + if (list != null) { + return list; + } + } catch (Exception ignored) { + // fall through to string + } + return claim.asString(); + } + + // logged_in → preserve boolean + if ("logged_in".equals(claimName)) { + Boolean boolVal = claim.asBoolean(); + if (boolVal != null) { + return boolVal; + } + return claim.asString(); + } + + // All others → string + return claim.asString(); + } +} diff --git a/services/pic-sure-logging/src/main/resources/logback.xml b/services/pic-sure-logging/src/main/resources/logback.xml new file mode 100644 index 000000000..13d127f8e --- /dev/null +++ b/services/pic-sure-logging/src/main/resources/logback.xml @@ -0,0 +1,102 @@ + + + + + + + + System.out + + + [ignore] + [ignore] + [ignore] + [ignore] + [ignore] + [ignore] + [ignore] + + + + + + + + System.err + + %d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n + + + + + + + + ${LOG_DIR:-logs}/audit.log + + ${LOG_DIR:-logs}/audit.%d{yyyy-MM-dd}.%i.log + 50MB + 30 + 1GB + + + + [ignore] + [ignore] + [ignore] + [ignore] + [ignore] + [ignore] + [ignore] + + + + + + + + ${LOG_DIR:-logs}/app.log + + ${LOG_DIR:-logs}/app.%d{yyyy-MM-dd}.%i.log + 50MB + 30 + 500MB + + + %d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n + + + + + + + + 1024 + 0 + true + + + + + + 512 + 0 + true + + + + + + + + + + + + + + + + + + diff --git a/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/AppIntegrationTest.java b/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/AppIntegrationTest.java new file mode 100644 index 000000000..26e8fd284 --- /dev/null +++ b/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/AppIntegrationTest.java @@ -0,0 +1,201 @@ +package edu.harvard.dbmi.avillach.logging; + +import ch.qos.logback.classic.Logger; +import ch.qos.logback.classic.spi.ILoggingEvent; +import ch.qos.logback.core.read.ListAppender; +import edu.harvard.dbmi.avillach.logging.config.AppConfig; +import io.javalin.Javalin; +import io.javalin.testtools.JavalinTest; +import okhttp3.MediaType; +import okhttp3.RequestBody; +import okhttp3.Response; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.slf4j.LoggerFactory; + +import java.util.Map; +import java.util.concurrent.atomic.AtomicBoolean; + +import static org.junit.jupiter.api.Assertions.*; + +class AppIntegrationTest { + + private static final String API_KEY = "integration-test-key"; + private static final MediaType JSON = MediaType.get("application/json"); + + private ListAppender listAppender; + private Logger auditLogger; + + private AppConfig createTestConfig() { + return new AppConfig( + API_KEY, "testapp", "testplatform", "test", "testhost", 0, "*", + Map.of("sub", "subject", "email", "user_email", "roles", "roles", "logged_in", "logged_in") + ); + } + + @BeforeEach + void setUp() { + auditLogger = (Logger) LoggerFactory.getLogger("AUDIT"); + listAppender = new ListAppender<>(); + listAppender.start(); + auditLogger.addAppender(listAppender); + } + + @AfterEach + void tearDown() { + auditLogger.detachAppender(listAppender); + } + + @Test + void validRequestReturns202() { + Javalin app = App.createApp(createTestConfig(), new AtomicBoolean(true)); + JavalinTest.test(app, (server, client) -> { + RequestBody body = RequestBody.create("{\"event_type\":\"QUERY\",\"action\":\"execute\"}", JSON); + Response response = client + .request("/audit", builder -> builder.post(body).header("X-API-Key", API_KEY).header("Content-Type", "application/json")); + + assertEquals(202, response.code()); + assertTrue(response.body().string().contains("accepted")); + assertEquals(1, listAppender.list.size()); + }); + } + + @Test + void missingApiKeyReturns401() { + Javalin app = App.createApp(createTestConfig(), new AtomicBoolean(true)); + JavalinTest.test(app, (server, client) -> { + RequestBody body = RequestBody.create("{\"event_type\":\"QUERY\"}", JSON); + Response response = client.request("/audit", builder -> builder.post(body).header("Content-Type", "application/json")); + + assertEquals(401, response.code()); + }); + } + + @Test + void wrongApiKeyReturns401() { + Javalin app = App.createApp(createTestConfig(), new AtomicBoolean(true)); + JavalinTest.test(app, (server, client) -> { + RequestBody body = RequestBody.create("{\"event_type\":\"QUERY\"}", JSON); + Response response = client.request( + "/audit", builder -> builder.post(body).header("X-API-Key", "wrong-key").header("Content-Type", "application/json") + ); + + assertEquals(401, response.code()); + }); + } + + @Test + void badJsonReturns400() { + Javalin app = App.createApp(createTestConfig(), new AtomicBoolean(true)); + JavalinTest.test(app, (server, client) -> { + RequestBody body = RequestBody.create("not-json", JSON); + Response response = client + .request("/audit", builder -> builder.post(body).header("X-API-Key", API_KEY).header("Content-Type", "application/json")); + + assertEquals(400, response.code()); + }); + } + + @Test + void missingEventTypeReturns400() { + Javalin app = App.createApp(createTestConfig(), new AtomicBoolean(true)); + JavalinTest.test(app, (server, client) -> { + RequestBody body = RequestBody.create("{\"action\":\"execute\"}", JSON); + Response response = client + .request("/audit", builder -> builder.post(body).header("X-API-Key", API_KEY).header("Content-Type", "application/json")); + + assertEquals(400, response.code()); + }); + } + + @Test + void healthReturns200WithoutAuth() { + Javalin app = App.createApp(createTestConfig(), new AtomicBoolean(true)); + JavalinTest.test(app, (server, client) -> { + Response response = client.get("/health"); + + assertEquals(200, response.code()); + assertTrue(response.body().string().contains("healthy")); + }); + } + + @Test + void jwtClaimsAppearInLog() { + Javalin app = App.createApp(createTestConfig(), new AtomicBoolean(true)); + JavalinTest.test(app, (server, client) -> { + String token = TestJwtBuilder.buildToken(Map.of("sub", "user123", "email", "user@example.com")); + + RequestBody body = RequestBody.create("{\"event_type\":\"QUERY\"}", JSON); + Response response = client.request( + "/audit", + builder -> builder.post(body).header("X-API-Key", API_KEY).header("Authorization", "Bearer " + token) + .header("Content-Type", "application/json") + ); + + assertEquals(202, response.code()); + assertEquals(1, listAppender.list.size()); + String logMessage = listAppender.list.get(0).getFormattedMessage(); + assertTrue(logMessage.contains("subject=user123")); + assertTrue(logMessage.contains("user_email=user@example.com")); + }); + } + + @Test + void requestIdFromHeaderAppearsInLog() { + Javalin app = App.createApp(createTestConfig(), new AtomicBoolean(true)); + JavalinTest.test(app, (server, client) -> { + RequestBody body = RequestBody.create("{\"event_type\":\"QUERY\"}", JSON); + Response response = client.request( + "/audit", + builder -> builder.post(body).header("X-API-Key", API_KEY).header("X-Request-Id", "req-abc-123") + .header("Content-Type", "application/json") + ); + + assertEquals(202, response.code()); + assertEquals(1, listAppender.list.size()); + String logMessage = listAppender.list.get(0).getFormattedMessage(); + assertTrue(logMessage.contains("request_id=req-abc-123")); + }); + } + + // --- Health check readiness tests (Change 6) --- + + @Test + void healthReturns503WhenNotReady() { + AtomicBoolean readiness = new AtomicBoolean(false); + Javalin app = App.createApp(createTestConfig(), readiness); + JavalinTest.test(app, (server, client) -> { + Response response = client.get("/health"); + + assertEquals(503, response.code()); + assertTrue(response.body().string().contains("starting")); + }); + } + + @Test + void infoReturns200WithoutAuth() { + Javalin app = App.createApp(createTestConfig(), new AtomicBoolean(true)); + JavalinTest.test(app, (server, client) -> { + RequestBody body = RequestBody.create("{}", JSON); + Response response = client.request("/info", builder -> builder.post(body).header("Content-Type", "application/json")); + + assertEquals(200, response.code()); + String responseBody = response.body().string(); + assertTrue(responseBody.contains("Logging Service")); + assertTrue(responseBody.contains("queryFormats")); + }); + } + + @Test + void healthReturns200WhenReady() { + AtomicBoolean readiness = new AtomicBoolean(true); + Javalin app = App.createApp(createTestConfig(), readiness); + JavalinTest.test(app, (server, client) -> { + Response response = client.get("/health"); + + assertEquals(200, response.code()); + assertTrue(response.body().string().contains("healthy")); + }); + } +} diff --git a/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/HealthRouteTest.java b/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/HealthRouteTest.java new file mode 100644 index 000000000..74ef1b1fe --- /dev/null +++ b/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/HealthRouteTest.java @@ -0,0 +1,51 @@ +package edu.harvard.dbmi.avillach.logging; + +import edu.harvard.dbmi.avillach.logging.config.AppConfig; +import io.javalin.Javalin; +import io.javalin.testtools.JavalinTest; + +import java.util.Map; +import java.util.concurrent.atomic.AtomicBoolean; + +import org.junit.jupiter.api.Test; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; + +/** + * Contract pin for the Javalin-native {@code GET /health} route (Phase 3 Task 8). + * + *

    The gateway's system-status aggregation probes this endpoint directly (this service is Javalin, not Spring Boot, so there is no + * Actuator {@code status:UP} body here). The contract being pinned is: {@code 200 {"status":"healthy"}} when ready, {@code 503 + * {"status":"starting"}} otherwise. This test exists so a future refactor of {@code App}/{@code HealthHandler} cannot silently change that + * contract without a test failing. + */ +class HealthRouteTest { + + private static AppConfig testConfig() { + return new AppConfig( + "test-api-key", "testapp", "testplatform", "test", "testhost", 0, "*", + Map.of("sub", "subject", "email", "user_email", "roles", "roles", "logged_in", "logged_in") + ); + } + + @Test + void healthReturns200HealthyWhenReady() { + Javalin app = App.createApp(testConfig(), new AtomicBoolean(true)); + JavalinTest.test(app, (server, client) -> { + var resp = client.get("/health"); + assertEquals(200, resp.code()); + assertTrue(resp.body().string().contains("healthy")); + }); + } + + @Test + void healthReturns503StartingWhenNotReady() { + Javalin app = App.createApp(testConfig(), new AtomicBoolean(false)); + JavalinTest.test(app, (server, client) -> { + var resp = client.get("/health"); + assertEquals(503, resp.code()); + assertTrue(resp.body().string().contains("starting")); + }); + } +} diff --git a/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/LogbackConfigTest.java b/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/LogbackConfigTest.java new file mode 100644 index 000000000..0d315e9ab --- /dev/null +++ b/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/LogbackConfigTest.java @@ -0,0 +1,286 @@ +package edu.harvard.dbmi.avillach.logging; + +import ch.qos.logback.classic.AsyncAppender; +import ch.qos.logback.classic.Logger; +import ch.qos.logback.classic.LoggerContext; +import ch.qos.logback.classic.joran.JoranConfigurator; +import ch.qos.logback.classic.spi.ILoggingEvent; +import ch.qos.logback.core.Appender; +import ch.qos.logback.core.rolling.RollingFileAppender; +import ch.qos.logback.core.rolling.SizeAndTimeBasedRollingPolicy; +import ch.qos.logback.core.status.Status; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.io.TempDir; + +import java.io.InputStream; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.Iterator; +import java.util.List; + +import static org.junit.jupiter.api.Assertions.*; + +class LogbackConfigTest { + + @TempDir + Path tempDir; + + private LoggerContext context; + + @BeforeEach + void setUp() throws Exception { + context = new LoggerContext(); + context.putProperty("LOG_DIR", tempDir.toString()); + + JoranConfigurator configurator = new JoranConfigurator(); + configurator.setContext(context); + + try (InputStream is = getClass().getResourceAsStream("/logback.xml")) { + assertNotNull(is, "logback.xml must be on the classpath"); + configurator.doConfigure(is); + } + context.start(); + } + + @Test + void configurationLoadsWithoutErrors() { + List statusList = context.getStatusManager().getCopyOfStatusList(); + List errors = statusList.stream().filter(s -> s.getLevel() == Status.ERROR).toList(); + assertTrue(errors.isEmpty(), "Logback config should load without errors, but got: " + errors); + } + + @Test + void configurationLoadsWithoutWarnings() { + List statusList = context.getStatusManager().getCopyOfStatusList(); + List warnings = statusList.stream().filter(s -> s.getLevel() == Status.WARN).toList(); + assertTrue(warnings.isEmpty(), "Logback config should load without warnings, but got: " + warnings); + } + + // --- AUDIT logger appender tests --- + + @Test + void auditLoggerHasAsyncFileAppender() { + Logger auditLogger = context.getLogger("AUDIT"); + AsyncAppender appender = findAppender(auditLogger, "ASYNC_AUDIT_FILE"); + assertNotNull(appender, "AUDIT logger should have ASYNC_AUDIT_FILE appender"); + } + + @Test + void auditAsyncAppenderWrapsFileAppender() { + Logger auditLogger = context.getLogger("AUDIT"); + AsyncAppender asyncAppender = findAppender(auditLogger, "ASYNC_AUDIT_FILE"); + // The async appender should delegate to the underlying AUDIT_FILE + Appender delegate = asyncAppender.getAppender("AUDIT_FILE"); + assertNotNull(delegate, "ASYNC_AUDIT_FILE should wrap AUDIT_FILE"); + assertInstanceOf(RollingFileAppender.class, delegate); + } + + @Test + void auditFileAppenderTargetsCorrectFile() { + Logger auditLogger = context.getLogger("AUDIT"); + AsyncAppender asyncAppender = findAppender(auditLogger, "ASYNC_AUDIT_FILE"); + RollingFileAppender fileAppender = (RollingFileAppender) asyncAppender.getAppender("AUDIT_FILE"); + assertEquals(tempDir.resolve("audit.log").toString(), fileAppender.getFile()); + } + + @Test + void auditFileAppenderUsesSizeAndTimeRollingPolicy() { + Logger auditLogger = context.getLogger("AUDIT"); + AsyncAppender asyncAppender = findAppender(auditLogger, "ASYNC_AUDIT_FILE"); + RollingFileAppender fileAppender = (RollingFileAppender) asyncAppender.getAppender("AUDIT_FILE"); + assertInstanceOf(SizeAndTimeBasedRollingPolicy.class, fileAppender.getRollingPolicy()); + } + + @Test + void auditFileAppenderHasCorrectMaxHistory() { + Logger auditLogger = context.getLogger("AUDIT"); + AsyncAppender asyncAppender = findAppender(auditLogger, "ASYNC_AUDIT_FILE"); + RollingFileAppender fileAppender = (RollingFileAppender) asyncAppender.getAppender("AUDIT_FILE"); + SizeAndTimeBasedRollingPolicy policy = (SizeAndTimeBasedRollingPolicy) fileAppender.getRollingPolicy(); + assertEquals(30, policy.getMaxHistory()); + } + + @Test + void auditFileAppenderHasDateAndIndexInPattern() { + Logger auditLogger = context.getLogger("AUDIT"); + AsyncAppender asyncAppender = findAppender(auditLogger, "ASYNC_AUDIT_FILE"); + RollingFileAppender fileAppender = (RollingFileAppender) asyncAppender.getAppender("AUDIT_FILE"); + SizeAndTimeBasedRollingPolicy policy = (SizeAndTimeBasedRollingPolicy) fileAppender.getRollingPolicy(); + String pattern = policy.getFileNamePattern(); + assertTrue(pattern.contains("audit.%d{yyyy-MM-dd}.%i.log"), "Rolling pattern should include date and index for size+time rotation"); + } + + // --- APP (root) logger appender tests --- + + @Test + void rootLoggerHasAsyncFileAppender() { + Logger rootLogger = context.getLogger(Logger.ROOT_LOGGER_NAME); + AsyncAppender appender = findAppender(rootLogger, "ASYNC_APP_FILE"); + assertNotNull(appender, "Root logger should have ASYNC_APP_FILE appender"); + } + + @Test + void appAsyncAppenderWrapsFileAppender() { + Logger rootLogger = context.getLogger(Logger.ROOT_LOGGER_NAME); + AsyncAppender asyncAppender = findAppender(rootLogger, "ASYNC_APP_FILE"); + Appender delegate = asyncAppender.getAppender("APP_FILE"); + assertNotNull(delegate, "ASYNC_APP_FILE should wrap APP_FILE"); + assertInstanceOf(RollingFileAppender.class, delegate); + } + + @Test + void appFileAppenderTargetsCorrectFile() { + Logger rootLogger = context.getLogger(Logger.ROOT_LOGGER_NAME); + AsyncAppender asyncAppender = findAppender(rootLogger, "ASYNC_APP_FILE"); + RollingFileAppender fileAppender = (RollingFileAppender) asyncAppender.getAppender("APP_FILE"); + assertEquals(tempDir.resolve("app.log").toString(), fileAppender.getFile()); + } + + @Test + void appFileAppenderUsesSizeAndTimeRollingPolicy() { + Logger rootLogger = context.getLogger(Logger.ROOT_LOGGER_NAME); + AsyncAppender asyncAppender = findAppender(rootLogger, "ASYNC_APP_FILE"); + RollingFileAppender fileAppender = (RollingFileAppender) asyncAppender.getAppender("APP_FILE"); + assertInstanceOf(SizeAndTimeBasedRollingPolicy.class, fileAppender.getRollingPolicy()); + } + + @Test + void appFileAppenderHasCorrectMaxHistory() { + Logger rootLogger = context.getLogger(Logger.ROOT_LOGGER_NAME); + AsyncAppender asyncAppender = findAppender(rootLogger, "ASYNC_APP_FILE"); + RollingFileAppender fileAppender = (RollingFileAppender) asyncAppender.getAppender("APP_FILE"); + SizeAndTimeBasedRollingPolicy policy = (SizeAndTimeBasedRollingPolicy) fileAppender.getRollingPolicy(); + assertEquals(30, policy.getMaxHistory()); + } + + @Test + void appFileAppenderHasDateAndIndexInPattern() { + Logger rootLogger = context.getLogger(Logger.ROOT_LOGGER_NAME); + AsyncAppender asyncAppender = findAppender(rootLogger, "ASYNC_APP_FILE"); + RollingFileAppender fileAppender = (RollingFileAppender) asyncAppender.getAppender("APP_FILE"); + SizeAndTimeBasedRollingPolicy policy = (SizeAndTimeBasedRollingPolicy) fileAppender.getRollingPolicy(); + String pattern = policy.getFileNamePattern(); + assertTrue(pattern.contains("app.%d{yyyy-MM-dd}.%i.log"), "Rolling pattern should include date and index for size+time rotation"); + } + + // --- Functional tests: logs actually get written to files --- + + @Test + void rollingFileAppenderWritesToDisk() throws Exception { + LoggerContext defaultContext = (LoggerContext) org.slf4j.LoggerFactory.getILoggerFactory(); + + RollingFileAppender appender = new RollingFileAppender<>(); + appender.setContext(defaultContext); + appender.setFile(tempDir.resolve("rolling-test.log").toString()); + + SizeAndTimeBasedRollingPolicy policy = new SizeAndTimeBasedRollingPolicy<>(); + policy.setContext(defaultContext); + policy.setParent(appender); + policy.setFileNamePattern(tempDir.resolve("rolling-test.%d{yyyy-MM-dd}.%i.log").toString()); + policy.setMaxFileSize(new ch.qos.logback.core.util.FileSize(50 * ch.qos.logback.core.util.FileSize.MB_COEFFICIENT)); + policy.setMaxHistory(30); + policy.setTotalSizeCap(new ch.qos.logback.core.util.FileSize(500 * ch.qos.logback.core.util.FileSize.MB_COEFFICIENT)); + policy.start(); + appender.setRollingPolicy(policy); + + ch.qos.logback.classic.encoder.PatternLayoutEncoder encoder = new ch.qos.logback.classic.encoder.PatternLayoutEncoder(); + encoder.setContext(defaultContext); + encoder.setPattern("%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n"); + encoder.start(); + appender.setEncoder(encoder); + appender.start(); + + Logger testLogger = defaultContext.getLogger("ROLLING_FILE_TEST"); + testLogger.setAdditive(false); + testLogger.addAppender(appender); + + testLogger.info("rolling file test event"); + appender.stop(); + testLogger.detachAppender(appender); + + Path testLog = tempDir.resolve("rolling-test.log"); + assertTrue(Files.exists(testLog), "rolling-test.log should be created"); + String content = Files.readString(testLog); + assertTrue( + content.contains("rolling file test event"), + "RollingFileAppender with SizeAndTimeBasedRollingPolicy should write events to disk" + ); + } + + @Test + void auditLoggerDoesNotPropagateToRoot() { + Logger auditLogger = context.getLogger("AUDIT"); + assertFalse(auditLogger.isAdditive(), "AUDIT logger should have additivity=false"); + } + + @Test + void auditEventsDoNotAppearInAppLog() throws Exception { + Logger auditLogger = context.getLogger("AUDIT"); + auditLogger.info("secret audit data"); + + Path appLog = tempDir.resolve("app.log"); + if (Files.exists(appLog)) { + String content = Files.readString(appLog); + assertFalse(content.contains("secret audit data"), "Audit events should not leak into app.log"); + } + } + + // --- Async appender configuration tests --- + + @Test + void auditAsyncAppenderHasCorrectQueueSize() { + Logger auditLogger = context.getLogger("AUDIT"); + AsyncAppender asyncAppender = findAppender(auditLogger, "ASYNC_AUDIT_FILE"); + assertEquals(1024, asyncAppender.getQueueSize()); + } + + @Test + void appAsyncAppenderHasCorrectQueueSize() { + Logger rootLogger = context.getLogger(Logger.ROOT_LOGGER_NAME); + AsyncAppender asyncAppender = findAppender(rootLogger, "ASYNC_APP_FILE"); + assertEquals(512, asyncAppender.getQueueSize()); + } + + @Test + void auditAsyncAppenderNeverDiscards() { + Logger auditLogger = context.getLogger("AUDIT"); + AsyncAppender asyncAppender = findAppender(auditLogger, "ASYNC_AUDIT_FILE"); + assertEquals(0, asyncAppender.getDiscardingThreshold()); + } + + @Test + void appAsyncAppenderNeverDiscards() { + Logger rootLogger = context.getLogger(Logger.ROOT_LOGGER_NAME); + AsyncAppender asyncAppender = findAppender(rootLogger, "ASYNC_APP_FILE"); + assertEquals(0, asyncAppender.getDiscardingThreshold()); + } + + @Test + void auditAsyncAppenderNeverBlocks() { + Logger auditLogger = context.getLogger("AUDIT"); + AsyncAppender asyncAppender = findAppender(auditLogger, "ASYNC_AUDIT_FILE"); + assertTrue(asyncAppender.isNeverBlock()); + } + + @Test + void appAsyncAppenderNeverBlocks() { + Logger rootLogger = context.getLogger(Logger.ROOT_LOGGER_NAME); + AsyncAppender asyncAppender = findAppender(rootLogger, "ASYNC_APP_FILE"); + assertTrue(asyncAppender.isNeverBlock()); + } + + // --- Helper --- + + @SuppressWarnings("unchecked") + private > T findAppender(Logger logger, String name) { + Iterator> it = logger.iteratorForAppenders(); + while (it.hasNext()) { + Appender appender = it.next(); + if (name.equals(appender.getName())) { + return (T) appender; + } + } + return null; + } +} diff --git a/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/TestJwtBuilder.java b/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/TestJwtBuilder.java new file mode 100644 index 000000000..bb5856637 --- /dev/null +++ b/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/TestJwtBuilder.java @@ -0,0 +1,54 @@ +package edu.harvard.dbmi.avillach.logging; + +import com.auth0.jwt.JWT; +import com.auth0.jwt.algorithms.Algorithm; + +import java.time.Instant; +import java.util.Date; +import java.util.List; +import java.util.Map; + +public class TestJwtBuilder { + + private static final Algorithm ALGORITHM = Algorithm.HMAC256("test-secret"); + + public static String buildToken(Map claims) { + var builder = JWT.create(); + for (Map.Entry entry : claims.entrySet()) { + String key = entry.getKey(); + Object value = entry.getValue(); + if (value instanceof String s) { + builder.withClaim(key, s); + } else if (value instanceof Boolean b) { + builder.withClaim(key, b); + } else if (value instanceof Integer i) { + builder.withClaim(key, i); + } else if (value instanceof Long l) { + builder.withClaim(key, l); + } else if (value instanceof List list) { + @SuppressWarnings("unchecked") + List stringList = (List) list; + builder.withClaim(key, stringList); + } + } + return builder.sign(ALGORITHM); + } + + public static String buildExpiredToken(Map claims) { + var builder = JWT.create().withExpiresAt(Date.from(Instant.now().minusSeconds(3600))); + for (Map.Entry entry : claims.entrySet()) { + String key = entry.getKey(); + Object value = entry.getValue(); + if (value instanceof String s) { + builder.withClaim(key, s); + } else if (value instanceof Boolean b) { + builder.withClaim(key, b); + } else if (value instanceof List list) { + @SuppressWarnings("unchecked") + List stringList = (List) list; + builder.withClaim(key, stringList); + } + } + return builder.sign(ALGORITHM); + } +} diff --git a/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/config/AppConfigTest.java b/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/config/AppConfigTest.java new file mode 100644 index 000000000..e61c4a662 --- /dev/null +++ b/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/config/AppConfigTest.java @@ -0,0 +1,125 @@ +package edu.harvard.dbmi.avillach.logging.config; + +import org.junit.jupiter.api.Test; + +import java.util.HashMap; +import java.util.Map; +import java.util.function.Function; + +import static org.junit.jupiter.api.Assertions.*; + +class AppConfigTest { + + private Function envWith(Map vars) { + return vars::get; + } + + @Test + void allVarsSet() { + Map env = new HashMap<>(); + env.put("LOGGING_API_KEY", "test-key"); + env.put("APP", "myapp"); + env.put("PLATFORM", "myplatform"); + env.put("ENVIRONMENT", "staging"); + env.put("HOSTNAME", "myhost"); + env.put("PORT", "9090"); + env.put("ALLOWED_ORIGIN", "https://example.com"); + env.put("JWT_CLAIM_MAPPING", "{\"sub\":\"subject\",\"email\":\"mail\"}"); + + AppConfig config = AppConfig.fromEnvironment(envWith(env)); + + assertEquals("test-key", config.auditApiKey()); + assertEquals("myapp", config.app()); + assertEquals("myplatform", config.platform()); + assertEquals("staging", config.environment()); + assertEquals("myhost", config.hostname()); + assertEquals(9090, config.port()); + assertEquals("https://example.com", config.allowedOrigin()); + assertEquals(Map.of("sub", "subject", "email", "mail"), config.jwtClaimMapping()); + } + + @Test + void missingApiKeyFails() { + Map env = new HashMap<>(); + IllegalStateException ex = assertThrows(IllegalStateException.class, () -> AppConfig.fromEnvironment(envWith(env))); + assertTrue(ex.getMessage().contains("LOGGING_API_KEY")); + } + + @Test + void blankApiKeyFails() { + Map env = new HashMap<>(); + env.put("LOGGING_API_KEY", " "); + IllegalStateException ex = assertThrows(IllegalStateException.class, () -> AppConfig.fromEnvironment(envWith(env))); + assertTrue(ex.getMessage().contains("LOGGING_API_KEY")); + } + + @Test + void invalidPortFails() { + Map env = new HashMap<>(); + env.put("LOGGING_API_KEY", "test-key"); + env.put("PORT", "not-a-number"); + IllegalStateException ex = assertThrows(IllegalStateException.class, () -> AppConfig.fromEnvironment(envWith(env))); + assertTrue(ex.getMessage().contains("PORT")); + } + + @Test + void portOutOfRangeFails() { + Map env = new HashMap<>(); + env.put("LOGGING_API_KEY", "test-key"); + env.put("PORT", "99999"); + IllegalStateException ex = assertThrows(IllegalStateException.class, () -> AppConfig.fromEnvironment(envWith(env))); + assertTrue(ex.getMessage().contains("PORT")); + } + + @Test + void defaultsUsedWhenVarsNotSet() { + Map env = new HashMap<>(); + env.put("LOGGING_API_KEY", "test-key"); + + AppConfig config = AppConfig.fromEnvironment(envWith(env)); + + assertEquals("unknown", config.app()); + assertEquals("unknown", config.platform()); + assertEquals("unknown", config.environment()); + assertEquals(8080, config.port()); + assertEquals("*", config.allowedOrigin()); + assertNotNull(config.hostname()); + assertFalse(config.jwtClaimMapping().isEmpty()); + } + + @Test + void defaultJwtClaimMappingUsed() { + Map env = new HashMap<>(); + env.put("LOGGING_API_KEY", "test-key"); + + AppConfig config = AppConfig.fromEnvironment(envWith(env)); + + assertEquals("subject", config.jwtClaimMapping().get("sub")); + assertEquals("user_email", config.jwtClaimMapping().get("email")); + assertEquals("roles", config.jwtClaimMapping().get("roles")); + assertEquals("user_id", config.jwtClaimMapping().get("userid")); + assertEquals("preferred_username", config.jwtClaimMapping().get("preferred_username")); + assertEquals("user_permission_group", config.jwtClaimMapping().get("user_permission_group")); + } + + @Test + void customJwtClaimMappingParsed() { + Map env = new HashMap<>(); + env.put("LOGGING_API_KEY", "test-key"); + env.put("JWT_CLAIM_MAPPING", "{\"custom_claim\":\"output_field\"}"); + + AppConfig config = AppConfig.fromEnvironment(envWith(env)); + + assertEquals(Map.of("custom_claim", "output_field"), config.jwtClaimMapping()); + } + + @Test + void invalidJwtClaimMappingFails() { + Map env = new HashMap<>(); + env.put("LOGGING_API_KEY", "test-key"); + env.put("JWT_CLAIM_MAPPING", "not-json"); + + IllegalStateException ex = assertThrows(IllegalStateException.class, () -> AppConfig.fromEnvironment(envWith(env))); + assertTrue(ex.getMessage().contains("JWT_CLAIM_MAPPING")); + } +} diff --git a/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/handler/AuditHandlerTest.java b/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/handler/AuditHandlerTest.java new file mode 100644 index 000000000..726f5d5f9 --- /dev/null +++ b/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/handler/AuditHandlerTest.java @@ -0,0 +1,204 @@ +package edu.harvard.dbmi.avillach.logging.handler; + +import edu.harvard.dbmi.avillach.logging.model.AuditEvent; +import edu.harvard.dbmi.avillach.logging.service.AuditLogService; +import io.javalin.http.BadRequestResponse; +import io.javalin.http.Context; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.ArgumentCaptor; + +import java.util.HashMap; +import java.util.Map; +import java.util.stream.Collectors; +import java.util.stream.IntStream; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + +class AuditHandlerTest { + + private AuditLogService auditLogService; + private AuditHandler handler; + + @BeforeEach + void setUp() { + auditLogService = mock(AuditLogService.class); + handler = new AuditHandler(auditLogService); + } + + @Test + void validRequestReturns202() { + Context ctx = mock(Context.class); + when(ctx.body()).thenReturn("{\"event_type\":\"QUERY\",\"action\":\"execute\"}"); + when(ctx.header("Authorization")).thenReturn("Bearer token"); + when(ctx.header("X-Request-Id")).thenReturn("req-123"); + when(ctx.status(202)).thenReturn(ctx); + + handler.handle(ctx); + + verify(ctx).status(202); + ArgumentCaptor captor = ArgumentCaptor.forClass(AuditEvent.class); + verify(auditLogService).logEvent(captor.capture(), eq("Bearer token"), eq("req-123")); + assertEquals("QUERY", captor.getValue().eventType()); + assertEquals("execute", captor.getValue().action()); + } + + @Test + void invalidJsonThrows400() { + Context ctx = mock(Context.class); + when(ctx.body()).thenReturn("not-json"); + + assertThrows(BadRequestResponse.class, () -> handler.handle(ctx)); + } + + @Test + void missingEventTypeThrows400() { + Context ctx = mock(Context.class); + when(ctx.body()).thenReturn("{\"action\":\"execute\"}"); + + assertThrows(BadRequestResponse.class, () -> handler.handle(ctx)); + } + + @Test + void blankEventTypeThrows400() { + Context ctx = mock(Context.class); + when(ctx.body()).thenReturn("{\"event_type\":\" \"}"); + + assertThrows(BadRequestResponse.class, () -> handler.handle(ctx)); + } + + @Test + void unknownFieldsIgnored() { + Context ctx = mock(Context.class); + when(ctx.body()).thenReturn("{\"event_type\":\"TEST\",\"unknown_field\":\"value\"}"); + when(ctx.status(202)).thenReturn(ctx); + + assertDoesNotThrow(() -> handler.handle(ctx)); + verify(auditLogService).logEvent(any(), any(), any()); + } + + // --- ObjectMapper hardening tests (Change 1) --- + + @Test + void deeplyNestedJsonRejected() { + // Build JSON nested beyond depth 10 + StringBuilder json = new StringBuilder(); + json.append("{\"event_type\":\"TEST\",\"metadata\":"); + for (int i = 0; i < 15; i++) { + json.append("{\"k\":"); + } + json.append("\"v\""); + for (int i = 0; i < 15; i++) { + json.append("}"); + } + json.append("}"); + + Context ctx = mock(Context.class); + when(ctx.body()).thenReturn(json.toString()); + + assertThrows(BadRequestResponse.class, () -> handler.handle(ctx)); + } + + @Test + void oversizedStringRejected() { + // Build a string longer than 10KB + String bigValue = "x".repeat(11_000); + String json = "{\"event_type\":\"TEST\",\"action\":\"" + bigValue + "\"}"; + + Context ctx = mock(Context.class); + when(ctx.body()).thenReturn(json); + + assertThrows(BadRequestResponse.class, () -> handler.handle(ctx)); + } + + // --- Metadata/error key limit tests (Change 2) --- + + @Test + void metadataExceeding50KeysRejected() { + Map metadata = IntStream.rangeClosed(1, 51).boxed().collect(Collectors.toMap(i -> "key" + i, i -> "val" + i)); + String metadataJson = mapToJson(metadata); + String json = "{\"event_type\":\"TEST\",\"metadata\":" + metadataJson + "}"; + + Context ctx = mock(Context.class); + when(ctx.body()).thenReturn(json); + + BadRequestResponse ex = assertThrows(BadRequestResponse.class, () -> handler.handle(ctx)); + assertTrue(ex.getMessage().contains("metadata")); + } + + @Test + void errorExceeding20KeysRejected() { + Map error = IntStream.rangeClosed(1, 21).boxed().collect(Collectors.toMap(i -> "key" + i, i -> "val" + i)); + String errorJson = mapToJson(error); + String json = "{\"event_type\":\"TEST\",\"error\":" + errorJson + "}"; + + Context ctx = mock(Context.class); + when(ctx.body()).thenReturn(json); + + BadRequestResponse ex = assertThrows(BadRequestResponse.class, () -> handler.handle(ctx)); + assertTrue(ex.getMessage().contains("error")); + } + + @Test + void metadataAtExactly50KeysAccepted() { + Map metadata = IntStream.rangeClosed(1, 50).boxed().collect(Collectors.toMap(i -> "key" + i, i -> "val" + i)); + String metadataJson = mapToJson(metadata); + String json = "{\"event_type\":\"TEST\",\"metadata\":" + metadataJson + "}"; + + Context ctx = mock(Context.class); + when(ctx.body()).thenReturn(json); + when(ctx.status(202)).thenReturn(ctx); + + assertDoesNotThrow(() -> handler.handle(ctx)); + verify(auditLogService).logEvent(any(), any(), any()); + } + + @Test + void errorAtExactly20KeysAccepted() { + Map error = IntStream.rangeClosed(1, 20).boxed().collect(Collectors.toMap(i -> "key" + i, i -> "val" + i)); + String errorJson = mapToJson(error); + String json = "{\"event_type\":\"TEST\",\"error\":" + errorJson + "}"; + + Context ctx = mock(Context.class); + when(ctx.body()).thenReturn(json); + when(ctx.status(202)).thenReturn(ctx); + + assertDoesNotThrow(() -> handler.handle(ctx)); + verify(auditLogService).logEvent(any(), any(), any()); + } + + @Test + void nestingAtDepth10Accepted() { + // Build JSON nested exactly to depth 10 (object with metadata containing nested objects) + // event_type field + metadata with 8 levels of nesting (root object = 1, metadata object = 2, so 8 more = 10) + StringBuilder json = new StringBuilder(); + json.append("{\"event_type\":\"TEST\",\"metadata\":"); + for (int i = 0; i < 8; i++) { + json.append("{\"k\":"); + } + json.append("\"v\""); + for (int i = 0; i < 8; i++) { + json.append("}"); + } + json.append("}"); + + Context ctx = mock(Context.class); + when(ctx.body()).thenReturn(json.toString()); + when(ctx.status(202)).thenReturn(ctx); + + assertDoesNotThrow(() -> handler.handle(ctx)); + } + + private String mapToJson(Map map) { + StringBuilder sb = new StringBuilder("{"); + boolean first = true; + for (Map.Entry entry : map.entrySet()) { + if (!first) sb.append(","); + sb.append("\"").append(entry.getKey()).append("\":\"").append(entry.getValue()).append("\""); + first = false; + } + sb.append("}"); + return sb.toString(); + } +} diff --git a/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/middleware/ApiKeyAuthMiddlewareTest.java b/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/middleware/ApiKeyAuthMiddlewareTest.java new file mode 100644 index 000000000..32d3cd08f --- /dev/null +++ b/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/middleware/ApiKeyAuthMiddlewareTest.java @@ -0,0 +1,51 @@ +package edu.harvard.dbmi.avillach.logging.middleware; + +import io.javalin.http.Context; +import io.javalin.http.UnauthorizedResponse; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + +class ApiKeyAuthMiddlewareTest { + + private ApiKeyAuthMiddleware middleware; + + @BeforeEach + void setUp() { + middleware = new ApiKeyAuthMiddleware("test-api-key"); + } + + @Test + void validKeyPasses() { + Context ctx = mock(Context.class); + when(ctx.header("X-API-Key")).thenReturn("test-api-key"); + + assertDoesNotThrow(() -> middleware.authenticate(ctx)); + } + + @Test + void missingHeaderThrows401() { + Context ctx = mock(Context.class); + when(ctx.header("X-API-Key")).thenReturn(null); + + assertThrows(UnauthorizedResponse.class, () -> middleware.authenticate(ctx)); + } + + @Test + void blankHeaderThrows401() { + Context ctx = mock(Context.class); + when(ctx.header("X-API-Key")).thenReturn(" "); + + assertThrows(UnauthorizedResponse.class, () -> middleware.authenticate(ctx)); + } + + @Test + void wrongKeyThrows401() { + Context ctx = mock(Context.class); + when(ctx.header("X-API-Key")).thenReturn("wrong-key"); + + assertThrows(UnauthorizedResponse.class, () -> middleware.authenticate(ctx)); + } +} diff --git a/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/service/AuditLogServiceTest.java b/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/service/AuditLogServiceTest.java new file mode 100644 index 000000000..212797caa --- /dev/null +++ b/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/service/AuditLogServiceTest.java @@ -0,0 +1,288 @@ +package edu.harvard.dbmi.avillach.logging.service; + +import ch.qos.logback.classic.Logger; +import ch.qos.logback.classic.spi.ILoggingEvent; +import ch.qos.logback.core.read.ListAppender; +import edu.harvard.dbmi.avillach.logging.TestJwtBuilder; +import edu.harvard.dbmi.avillach.logging.config.AppConfig; +import edu.harvard.dbmi.avillach.logging.model.AuditEvent; +import edu.harvard.dbmi.avillach.logging.model.RequestInfo; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.slf4j.LoggerFactory; + +import java.util.Map; + +import static org.junit.jupiter.api.Assertions.*; + +class AuditLogServiceTest { + + private AuditLogService service; + private ListAppender listAppender; + private Logger auditLogger; + + @BeforeEach + void setUp() { + AppConfig config = new AppConfig( + "test-key", "myapp", "myplatform", "staging", "myhost", 8080, "*", + Map.of("sub", "subject", "email", "user_email", "roles", "roles", "logged_in", "logged_in") + ); + JwtDecodeService jwtService = new JwtDecodeService(config.jwtClaimMapping()); + service = new AuditLogService(config, jwtService); + + auditLogger = (Logger) LoggerFactory.getLogger("AUDIT"); + listAppender = new ListAppender<>(); + listAppender.start(); + auditLogger.addAppender(listAppender); + } + + @AfterEach + void tearDown() { + auditLogger.detachAppender(listAppender); + } + + @Test + void fullEventWithAllFields() { + RequestInfo request = new RequestInfo( + "req-123", "POST", "/api/query", "limit=10", "192.168.1.1", "10.0.0.5", 8443, "Mozilla/5.0", "application/json", 200, 1024L, + 150L, "https://example.com" + ); + AuditEvent event = new AuditEvent( + "QUERY", "execute", "web", null, null, request, Map.of("query_id", "q1"), Map.of("code", "500", "message", "Internal error") + ); + + String token = TestJwtBuilder.buildToken(Map.of("sub", "user123", "email", "user@example.com")); + + service.logEvent(event, "Bearer " + token, null); + + assertEquals(1, listAppender.list.size()); + String message = listAppender.list.get(0).getFormattedMessage(); + assertTrue(message.contains("event_type=QUERY")); + assertTrue(message.contains("action=execute")); + assertTrue(message.contains("request_id=req-123")); + assertTrue(message.contains("app=myapp")); + } + + @Test + void nullRequestHandled() { + AuditEvent event = new AuditEvent("LOGIN", null, null, null, null, null, null, null); + + service.logEvent(event, null, null); + + assertEquals(1, listAppender.list.size()); + String message = listAppender.list.get(0).getFormattedMessage(); + assertTrue(message.contains("event_type=LOGIN")); + assertTrue(message.contains("logged_in=false")); + } + + @Test + void emptyMetadataAndErrorOmitted() { + AuditEvent event = new AuditEvent("LOGIN", null, null, null, null, null, Map.of(), Map.of()); + + service.logEvent(event, null, null); + + assertEquals(1, listAppender.list.size()); + String message = listAppender.list.get(0).getFormattedMessage(); + assertFalse(message.contains("metadata")); + assertFalse(message.contains("error")); + } + + @Test + void noJwtSetsLoggedInFalse() { + AuditEvent event = new AuditEvent("PAGE_VIEW", null, null, null, null, null, null, null); + + service.logEvent(event, null, null); + + assertEquals(1, listAppender.list.size()); + String message = listAppender.list.get(0).getFormattedMessage(); + assertTrue(message.contains("logged_in=false")); + } + + @Test + void requestIdFromBody() { + RequestInfo request = new RequestInfo("body-id", null, null, null, null, null, null, null, null, null, null, null, null); + AuditEvent event = new AuditEvent("TEST", null, null, null, null, request, null, null); + + service.logEvent(event, null, "header-id"); + + assertEquals(1, listAppender.list.size()); + String message = listAppender.list.get(0).getFormattedMessage(); + assertTrue(message.contains("request_id=body-id")); + } + + @Test + void requestIdFromHeaderFallback() { + AuditEvent event = new AuditEvent("TEST", null, null, null, null, null, null, null); + + service.logEvent(event, null, "header-id"); + + assertEquals(1, listAppender.list.size()); + String message = listAppender.list.get(0).getFormattedMessage(); + assertTrue(message.contains("request_id=header-id")); + } + + @Test + void requestIdFromHeaderFallbackWhenBodyRequestIdBlank() { + RequestInfo request = new RequestInfo(" ", null, null, null, null, null, null, null, null, null, null, null, null); + AuditEvent event = new AuditEvent("TEST", null, null, null, null, request, null, null); + + service.logEvent(event, null, "header-id"); + + assertEquals(1, listAppender.list.size()); + String message = listAppender.list.get(0).getFormattedMessage(); + assertTrue(message.contains("request_id=header-id")); + } + + @Test + void timestampFormatIsISO8601() { + AuditEvent event = new AuditEvent("TEST", null, null, null, null, null, null, null); + + service.logEvent(event, null, null); + + assertEquals(1, listAppender.list.size()); + String message = listAppender.list.get(0).getFormattedMessage(); + // ISO-8601 format contains 'T' between date and time + assertTrue(message.contains("_time=")); + } + + @Test + void platformFieldsPresent() { + AuditEvent event = new AuditEvent("TEST", null, null, null, null, null, null, null); + + service.logEvent(event, null, null); + + assertEquals(1, listAppender.list.size()); + String message = listAppender.list.get(0).getFormattedMessage(); + assertTrue(message.contains("app=myapp")); + assertTrue(message.contains("platform=myplatform")); + assertTrue(message.contains("environment=staging")); + assertTrue(message.contains("hostname=myhost")); + } + + @Test + void exceptionSafety() { + // Service should never throw, even with a null event + assertDoesNotThrow(() -> service.logEvent(null, null, null)); + } + + // --- String truncation tests (Change 3) --- + + @Test + void longUrlTruncatedTo2000() { + String longUrl = "x".repeat(3000); + RequestInfo request = new RequestInfo(null, "GET", longUrl, null, null, null, null, null, null, null, null, null, null); + AuditEvent event = new AuditEvent("TEST", null, null, null, null, request, null, null); + + service.logEvent(event, null, null); + + assertEquals(1, listAppender.list.size()); + String message = listAppender.list.get(0).getFormattedMessage(); + // The truncated URL should be exactly 2000 chars of 'x' + String expected = "x".repeat(2000); + assertTrue(message.contains("url=" + expected)); + // Should NOT contain the full 3000-char value + assertFalse(message.contains("x".repeat(2001))); + } + + @Test + void exact2000CharStringNotTruncated() { + String exactUrl = "y".repeat(2000); + RequestInfo request = new RequestInfo(null, "GET", exactUrl, null, null, null, null, null, null, null, null, null, null); + AuditEvent event = new AuditEvent("TEST", null, null, null, null, request, null, null); + + service.logEvent(event, null, null); + + assertEquals(1, listAppender.list.size()); + String message = listAppender.list.get(0).getFormattedMessage(); + assertTrue(message.contains("url=" + exactUrl)); + } + + @Test + void longRequestIdFromHeaderTruncated() { + String longRequestId = "r".repeat(3000); + AuditEvent event = new AuditEvent("TEST", null, null, null, null, null, null, null); + + service.logEvent(event, null, longRequestId); + + assertEquals(1, listAppender.list.size()); + String message = listAppender.list.get(0).getFormattedMessage(); + String expected = "r".repeat(2000); + assertTrue(message.contains("request_id=" + expected)); + assertFalse(message.contains("r".repeat(2001))); + } + + // --- Session ID tests --- + + @Test + void sessionIdFromTopLevelField() { + AuditEvent event = new AuditEvent("TEST", null, null, null, "sess-abc", null, null, null); + + service.logEvent(event, null, null); + + assertEquals(1, listAppender.list.size()); + String message = listAppender.list.get(0).getFormattedMessage(); + assertTrue(message.contains("session_id=sess-abc")); + } + + @Test + void sessionIdFallbackFromMetadata() { + AuditEvent event = new AuditEvent("TEST", null, null, null, null, null, Map.of("session_id", "meta-xyz"), null); + + service.logEvent(event, null, null); + + assertEquals(1, listAppender.list.size()); + String message = listAppender.list.get(0).getFormattedMessage(); + assertTrue(message.contains("session_id=meta-xyz")); + } + + @Test + void sessionIdTopLevelTakesPrecedenceOverMetadata() { + AuditEvent event = new AuditEvent("TEST", null, null, null, "top-level", null, Map.of("session_id", "from-meta"), null); + + service.logEvent(event, null, null); + + assertEquals(1, listAppender.list.size()); + String message = listAppender.list.get(0).getFormattedMessage(); + assertTrue(message.contains("session_id=top-level")); + assertFalse(message.contains("session_id=from-meta")); + } + + @Test + void sessionIdStrippedFromMetadataInOutput() { + AuditEvent event = new AuditEvent("TEST", null, null, null, null, null, Map.of("session_id", "sid", "other_key", "val"), null); + + service.logEvent(event, null, null); + + assertEquals(1, listAppender.list.size()); + String message = listAppender.list.get(0).getFormattedMessage(); + // session_id should appear at top level + assertTrue(message.contains("session_id=sid")); + // other_key should still be in metadata + assertTrue(message.contains("other_key=val")); + } + + @Test + void metadataWithOnlySessionIdProducesNoMetadataField() { + AuditEvent event = new AuditEvent("TEST", null, null, null, null, null, Map.of("session_id", "only-sid"), null); + + service.logEvent(event, null, null); + + assertEquals(1, listAppender.list.size()); + String message = listAppender.list.get(0).getFormattedMessage(); + assertTrue(message.contains("session_id=only-sid")); + // metadata map should be omitted since it's empty after removing session_id + assertFalse(message.contains("metadata=")); + } + + @Test + void callerFromTopLevelField() { + AuditEvent event = new AuditEvent("TEST", null, null, "PYTHON_ADAPTER", null, null, null, null); + + service.logEvent(event, null, null); + + assertEquals(1, listAppender.list.size()); + String message = listAppender.list.get(0).getFormattedMessage(); + assertTrue(message.contains("caller=PYTHON_ADAPTER")); + } +} diff --git a/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/service/JwtDecodeServiceTest.java b/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/service/JwtDecodeServiceTest.java new file mode 100644 index 000000000..c6ec45b94 --- /dev/null +++ b/services/pic-sure-logging/src/test/java/edu/harvard/dbmi/avillach/logging/service/JwtDecodeServiceTest.java @@ -0,0 +1,137 @@ +package edu.harvard.dbmi.avillach.logging.service; + +import edu.harvard.dbmi.avillach.logging.TestJwtBuilder; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +import java.util.List; +import java.util.Map; + +import static org.junit.jupiter.api.Assertions.*; + +class JwtDecodeServiceTest { + + private static final Map DEFAULT_MAPPING = + Map.of("sub", "subject", "email", "user_email", "name", "user_name", "roles", "roles", "logged_in", "logged_in"); + + private JwtDecodeService service; + + @BeforeEach + void setUp() { + service = new JwtDecodeService(DEFAULT_MAPPING); + } + + @Test + void validTokenExtractsClaims() { + String token = TestJwtBuilder.buildToken(Map.of("sub", "user123", "email", "user@example.com", "name", "John Doe")); + + Map result = service.extractClaims("Bearer " + token); + + assertEquals("user123", result.get("subject")); + assertEquals("user@example.com", result.get("user_email")); + assertEquals("John Doe", result.get("user_name")); + assertEquals(true, result.get("logged_in")); + } + + @Test + void nullTokenReturnsLoggedInFalse() { + Map result = service.extractClaims(null); + assertEquals(false, result.get("logged_in")); + assertEquals(1, result.size()); + } + + @Test + void blankTokenReturnsLoggedInFalse() { + Map result = service.extractClaims(" "); + assertEquals(false, result.get("logged_in")); + } + + @Test + void bearerPrefixOnlyReturnsLoggedInFalse() { + Map result = service.extractClaims("Bearer "); + assertEquals(false, result.get("logged_in")); + } + + @Test + void malformedTokenReturnsLoggedInFalse() { + Map result = service.extractClaims("Bearer not.a.jwt"); + assertEquals(false, result.get("logged_in")); + } + + @Test + void tokenWithoutBearerPrefix() { + String token = TestJwtBuilder.buildToken(Map.of("sub", "user123")); + Map result = service.extractClaims(token); + assertEquals("user123", result.get("subject")); + } + + @Test + void missingClaimsAreOmitted() { + String token = TestJwtBuilder.buildToken(Map.of("sub", "user123")); + Map result = service.extractClaims("Bearer " + token); + + assertEquals("user123", result.get("subject")); + assertNull(result.get("user_email")); + assertNull(result.get("user_name")); + } + + @Test + void arrayRolesPreservedAsList() { + String token = TestJwtBuilder.buildToken(Map.of("roles", List.of("ADMIN", "USER"))); + + Map result = service.extractClaims("Bearer " + token); + + Object roles = result.get("roles"); + assertInstanceOf(List.class, roles); + assertEquals(List.of("ADMIN", "USER"), roles); + } + + @Test + void booleanLoggedInPreserved() { + String token = TestJwtBuilder.buildToken(Map.of("logged_in", true)); + + Map result = service.extractClaims("Bearer " + token); + assertEquals(true, result.get("logged_in")); + } + + @Test + void expiredTokenStillDecodes() { + String token = TestJwtBuilder.buildExpiredToken(Map.of("sub", "user123", "email", "user@example.com")); + + Map result = service.extractClaims("Bearer " + token); + assertEquals("user123", result.get("subject")); + assertEquals("user@example.com", result.get("user_email")); + } + + @Test + void customClaimMapping() { + JwtDecodeService customService = new JwtDecodeService(Map.of("custom_id", "my_id", "custom_email", "my_email")); + + String token = TestJwtBuilder.buildToken(Map.of("custom_id", "abc", "custom_email", "test@test.com")); + + Map result = customService.extractClaims("Bearer " + token); + assertEquals("abc", result.get("my_id")); + assertEquals("test@test.com", result.get("my_email")); + } + + // --- JWT size check tests (Change 4) --- + + @Test + void oversizedTokenReturnsLoggedInFalse() { + // Build a token string larger than 16KB + String bigToken = "Bearer " + "a".repeat(17_000); + Map result = service.extractClaims(bigToken); + assertEquals(false, result.get("logged_in")); + assertEquals(1, result.size()); + } + + @Test + void tokenUnderSizeLimitStillWorks() { + String token = TestJwtBuilder.buildToken(Map.of("sub", "user123")); + // Normal tokens are well under 16KB + assertTrue(token.length() < 16_384); + Map result = service.extractClaims("Bearer " + token); + assertEquals("user123", result.get("subject")); + assertEquals(true, result.get("logged_in")); + } +} diff --git a/services/pic-sure-operations-service/Dockerfile b/services/pic-sure-operations-service/Dockerfile new file mode 100644 index 000000000..cc254930e --- /dev/null +++ b/services/pic-sure-operations-service/Dockerfile @@ -0,0 +1,5 @@ +FROM amazoncorretto:25 +WORKDIR /app +COPY target/pic-sure-operations-service-*.jar /app/app.jar +EXPOSE 8080 +ENTRYPOINT ["sh", "-c", "java ${JAVA_OPTS} -jar /app/app.jar"] diff --git a/services/pic-sure-operations-service/pom.xml b/services/pic-sure-operations-service/pom.xml new file mode 100644 index 000000000..a2658d9cf --- /dev/null +++ b/services/pic-sure-operations-service/pom.xml @@ -0,0 +1,106 @@ + + + 4.0.0 + + + edu.harvard.hms.dbmi.avillach + pic-sure-api + ${revision} + ../../pom.xml + + + pic-sure-operations-service + ${revision} + jar + + pic-sure-operations-service + Sole pic-sure-DB owner: Configuration + NamedDataset + Query, exposing /configuration/**, /dataset/**, and (later) an + internal query API. Trusts the gateway's X-User-* headers; performs no JWT validation locally. + + + + org.springframework.boot + spring-boot-starter-web + + + org.springframework.boot + spring-boot-starter-data-jpa + + + org.springframework.boot + spring-boot-starter-validation + + + org.springframework.boot + spring-boot-starter-actuator + + + + io.micrometer + micrometer-registry-prometheus + + + org.springframework.boot + spring-boot-starter-security + + + + + edu.harvard.hms.dbmi.avillach + pic-sure-spring-commons + + + + edu.harvard.hms.dbmi.avillach + pic-sure-api-model + + + + com.mysql + mysql-connector-j + runtime + + + + org.springframework.boot + spring-boot-starter-test + test + + + org.springframework.security + spring-security-test + test + + + com.h2database + h2 + test + + + + + + + org.springframework.boot + spring-boot-maven-plugin + + + + repackage + + + + + + + + + + github + GitHub HMS-DBMI Apache Maven Packages + https://maven.pkg.github.com/hms-dbmi/pic-sure + + + diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/OperationsApplication.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/OperationsApplication.java new file mode 100644 index 000000000..86b2bc2d3 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/OperationsApplication.java @@ -0,0 +1,27 @@ +package edu.harvard.hms.dbmi.avillach.operations; + +import org.springframework.boot.SpringApplication; +import org.springframework.boot.autoconfigure.SpringBootApplication; +import org.springframework.context.annotation.Import; + +import edu.harvard.hms.dbmi.avillach.commons.error.GatewayExceptionAdvice; + +/** + * Entry point for pic-sure-operations-service: the sole owner of the pic-sure MySQL {@code Configuration}, {@code NamedDataset}, and + * {@code Query} tables. Exposes {@code /configuration/**}, {@code /dataset/**}, and (later) an internal query API. + * + *

    The JPA entities and repositories live under this application's own base package ({@code edu.harvard.hms.dbmi.avillach.operations}, + * co-located with each feature's service/mapper), so Spring Boot's default same-package {@code @EntityScan}/repository auto-detection finds + * them without any explicit scan configuration. + * + *

    {@link GatewayExceptionAdvice} (from {@code pic-sure-spring-commons}) is imported explicitly because it lives outside this + * application's base package, so component scanning alone would not pick it up. + */ +@SpringBootApplication +@Import(GatewayExceptionAdvice.class) +public class OperationsApplication { + + public static void main(String[] args) { + SpringApplication.run(OperationsApplication.class, args); + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/ActuatorSecurityConfig.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/ActuatorSecurityConfig.java new file mode 100644 index 000000000..e589d2853 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/ActuatorSecurityConfig.java @@ -0,0 +1,28 @@ +package edu.harvard.hms.dbmi.avillach.operations.config; + +import org.springframework.boot.context.properties.EnableConfigurationProperties; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.core.annotation.Order; +import org.springframework.security.config.annotation.web.builders.HttpSecurity; +import org.springframework.security.web.SecurityFilterChain; + +import edu.harvard.hms.dbmi.avillach.commons.security.ActuatorSecurityHelper; +import edu.harvard.hms.dbmi.avillach.commons.security.ActuatorTokenProperties; + +/** + * Gates {@code /actuator/**} behind {@code X-Application-Token} via the shared {@link ActuatorSecurityHelper}. Registered at + * {@code @Order(0)} so it wins over {@link WebSecurityConfig}'s gateway-header-trust main chain ({@code @Order(10)}) for actuator paths -- + * the two chains never compete because {@code EndpointRequest.toAnyEndpoint()} scopes this chain to {@code /actuator/**} only, leaving + * {@code /configuration/admin/**}, {@code /dataset/**}, and {@code /internal/**} governed exactly as {@link WebSecurityConfig} defines. + */ +@Configuration +@EnableConfigurationProperties(ActuatorTokenProperties.class) +public class ActuatorSecurityConfig { + + @Bean + @Order(0) + SecurityFilterChain actuatorChain(HttpSecurity http, ActuatorTokenProperties props) throws Exception { + return ActuatorSecurityHelper.actuatorChain(http, props); + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/GatewayPrivilegesFilter.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/GatewayPrivilegesFilter.java new file mode 100644 index 000000000..a37834008 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/GatewayPrivilegesFilter.java @@ -0,0 +1,40 @@ +package edu.harvard.hms.dbmi.avillach.operations.config; + +import java.io.IOException; +import java.util.List; + +import org.springframework.security.authentication.UsernamePasswordAuthenticationToken; +import org.springframework.security.core.authority.SimpleGrantedAuthority; +import org.springframework.security.core.context.SecurityContextHolder; +import org.springframework.web.filter.OncePerRequestFilter; + +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUser; +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +/** + * Maps the gateway-set {@code X-User-Privileges} header into Spring {@link SimpleGrantedAuthority}s so {@code /configuration/admin/**} can + * require {@code SUPER_ADMIN} and {@code /dataset/**} can require an authenticated caller. The gateway is the only entity that talks to + * PSAMA; this service trusts the header (network ACLs prevent direct access) and performs no JWT validation of its own. + * + *

    Delegates to {@link GatewayUserResolver#resolve(HttpServletRequest)}: when {@code X-User-Id} is absent, {@code resolve} yields + * {@link java.util.Optional#empty()} and this filter leaves the {@code SecurityContext} untouched -- the request stays anonymous. + */ +public class GatewayPrivilegesFilter extends OncePerRequestFilter { + + @Override + protected void doFilterInternal(HttpServletRequest request, HttpServletResponse response, FilterChain filterChain) + throws ServletException, IOException { + GatewayUserResolver.resolve(request).ifPresent(this::authenticate); + filterChain.doFilter(request, response); + } + + private void authenticate(GatewayUser user) { + List authorities = user.getPrivileges().stream().map(SimpleGrantedAuthority::new).toList(); + var authentication = new UsernamePasswordAuthenticationToken(user.getUserId(), "N/A", authorities); + SecurityContextHolder.getContext().setAuthentication(authentication); + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/GatewayUserArgumentResolver.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/GatewayUserArgumentResolver.java new file mode 100644 index 000000000..514f539d7 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/GatewayUserArgumentResolver.java @@ -0,0 +1,32 @@ +package edu.harvard.hms.dbmi.avillach.operations.config; + +import org.springframework.core.MethodParameter; +import org.springframework.web.bind.support.WebDataBinderFactory; +import org.springframework.web.context.request.NativeWebRequest; +import org.springframework.web.method.support.HandlerMethodArgumentResolver; +import org.springframework.web.method.support.ModelAndViewContainer; + +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUser; +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import jakarta.servlet.http.HttpServletRequest; + +/** + * Resolves a {@link GatewayUser} controller argument by re-deriving it from the gateway's {@code X-User-*} headers via + * {@link GatewayUserResolver#resolve(HttpServletRequest)}. Yields {@code null} when the gateway supplied no identity (no {@code X-User-Id} + * header) -- controllers that require an identity must null-check and reject accordingly. + */ +public class GatewayUserArgumentResolver implements HandlerMethodArgumentResolver { + + @Override + public boolean supportsParameter(MethodParameter parameter) { + return GatewayUser.class.equals(parameter.getParameterType()); + } + + @Override + public Object resolveArgument( + MethodParameter parameter, ModelAndViewContainer mavContainer, NativeWebRequest webRequest, WebDataBinderFactory binderFactory + ) { + HttpServletRequest request = (HttpServletRequest) webRequest.getNativeRequest(); + return GatewayUserResolver.resolve(request).orElse(null); + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/InternalTokenFilterConfig.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/InternalTokenFilterConfig.java new file mode 100644 index 000000000..149630f17 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/InternalTokenFilterConfig.java @@ -0,0 +1,33 @@ +package edu.harvard.hms.dbmi.avillach.operations.config; + +import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.web.servlet.FilterRegistrationBean; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; + +import edu.harvard.hms.dbmi.avillach.operations.query.InternalTokenFilter; + +/** + * Registers {@link InternalTokenFilter} exactly once, scoped at the container level to {@code /internal/*} via + * {@link FilterRegistrationBean#addUrlPatterns(String...)}. Servlet URL-pattern matching is normalized and context-path-relative -- the + * same routing the {@code DispatcherServlet} uses to reach {@code InternalQueryController} -- so this registration can never disagree with + * "is this request actually going to the internal controller?" the way a hand-rolled {@code request.getRequestURI().startsWith(...)} check + * could (e.g. under a non-empty {@code server.servlet.context-path}). + * + *

    {@link InternalTokenFilter} is deliberately NOT a {@code @Component}: it is constructed here, directly, from the same + * {@code picsure.operations.internal-token} property it always used. If it were also annotated {@code @Component}, Spring Boot's own + * filter-bean auto-registration would additionally wire it in a second time (with the default {@code /*} mapping), which is exactly the + * double-registration this class exists to avoid. + */ +@Configuration +public class InternalTokenFilterConfig { + + @Bean + public FilterRegistrationBean internalTokenFilter( + @Value("${picsure.operations.internal-token:}") String expectedToken + ) { + FilterRegistrationBean registration = new FilterRegistrationBean<>(new InternalTokenFilter(expectedToken)); + registration.addUrlPatterns("/internal/*"); + return registration; + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/RequestConfig.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/RequestConfig.java new file mode 100644 index 000000000..c4330988f --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/RequestConfig.java @@ -0,0 +1,24 @@ +package edu.harvard.hms.dbmi.avillach.operations.config; + +import org.springframework.boot.web.servlet.FilterRegistrationBean; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.core.Ordered; + +import edu.harvard.hms.dbmi.avillach.commons.request.RequestIdFilter; + +/** + * Registers the commons {@link RequestIdFilter} (mirrors {@code pic-sure-gateway}'s {@code ObservabilityConfig}) so every request/response + * carries {@code X-Request-Id} and every log line + {@link edu.harvard.hms.dbmi.avillach.commons.error.GatewayExceptionAdvice} error body + * on this service is tagged with it. + */ +@Configuration +public class RequestConfig { + + @Bean + public FilterRegistrationBean requestIdFilter() { + FilterRegistrationBean registration = new FilterRegistrationBean<>(new RequestIdFilter()); + registration.setOrder(Ordered.HIGHEST_PRECEDENCE); + return registration; + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/WebMvcConfig.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/WebMvcConfig.java new file mode 100644 index 000000000..f43b36715 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/WebMvcConfig.java @@ -0,0 +1,21 @@ +package edu.harvard.hms.dbmi.avillach.operations.config; + +import java.util.List; + +import org.springframework.context.annotation.Configuration; +import org.springframework.web.method.support.HandlerMethodArgumentResolver; +import org.springframework.web.servlet.config.annotation.WebMvcConfigurer; + +/** + * Registers {@link GatewayUserArgumentResolver} so later controllers (config/dataset/query) can declare a + * {@code edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUser} method parameter and receive the caller's identity, re-derived from + * the gateway's {@code X-User-*} headers. + */ +@Configuration +public class WebMvcConfig implements WebMvcConfigurer { + + @Override + public void addArgumentResolvers(List resolvers) { + resolvers.add(new GatewayUserArgumentResolver()); + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/WebSecurityConfig.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/WebSecurityConfig.java new file mode 100644 index 000000000..e06fc1be1 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/config/WebSecurityConfig.java @@ -0,0 +1,56 @@ +package edu.harvard.hms.dbmi.avillach.operations.config; + +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.core.annotation.Order; +import org.springframework.http.HttpMethod; +import org.springframework.security.config.annotation.web.builders.HttpSecurity; +import org.springframework.security.config.http.SessionCreationPolicy; +import org.springframework.security.web.SecurityFilterChain; +import org.springframework.security.web.access.intercept.AuthorizationFilter; + +/** + * Security posture for the sole pic-sure-DB owner. This service performs NO JWT validation of its own -- the gateway is the sole PSAMA + * client and has already authorized the request; {@link GatewayPrivilegesFilter} rebuilds a {@code SecurityContext} from the gateway's + * {@code X-User-*} headers purely so the rules below can be expressed declaratively. Network ACLs (not this filter chain) are what actually + * stop a client from reaching this service directly and forging the headers. + * + *

    Path rules, in the order they are declared (first match wins):

    1. {@code /actuator/health}, {@code /actuator/info}, + * {@code /v3/api-docs/**}, {@code /swagger-ui/**}, {@code /openapi/**} -- unauthenticated (ops/tooling surfaces, never gated behind caller + * identity).
    2. {@code /configuration/admin/**} -- requires the {@code SUPER_ADMIN} authority. Declared before the broader + * public-read rule below so it wins for every HTTP method, including {@code GET}.
    3. {@code GET /configuration} and + * {@code GET /configuration/*} -- public, UNAUTHENTICATED reads (slash-less, matching the controller's mappings). The gateway allow-lists + * these paths at its introspection layer, so they arrive with NO {@code X-User-*} headers at all; security here must not require an + * identity that will never be present.
    4. {@code /internal/**} -- explicitly {@code permitAll()} at THIS layer (belt-and-suspenders, + * redundant with the catch-all rule below). Spring Security performs no authentication/authorization for these paths because it isn't the + * real gate: {@code edu.harvard.hms.dbmi.avillach.operations.query.InternalTokenFilter}, registered by {@code InternalTokenFilterConfig} + * against the exact same {@code /internal/*} URL pattern, is what actually enforces the shared-secret check on every request the container + * routes here.
    5. {@code /dataset/**} -- requires an authenticated caller, i.e. the gateway supplied {@code X-User-Id}. Spring + * Security's {@code authenticated()} already excludes the default anonymous principal (see {@code AuthenticatedAuthorizationManager}), so a + * request with no identity is correctly rejected rather than silently treated as authenticated.
    6. Everything else is permitted at + * this layer; the config/dataset controllers built in later tasks enforce any remaining per-endpoint rules themselves (e.g. the + * {@code NamedDataset} owner-email check).
    + * + *

    CSRF is disabled and sessions are stateless: every request carries its own trust via headers, there is no browser session to protect + * and nothing is stored server-side between requests. + */ +@Configuration +public class WebSecurityConfig { + + static final String SUPER_ADMIN = "SUPER_ADMIN"; + + @Bean + @Order(10) // yields /actuator/** to ActuatorSecurityConfig's @Order(0) chain. + SecurityFilterChain filterChain(HttpSecurity http) throws Exception { + return http.csrf(csrf -> csrf.disable()) + .sessionManagement(session -> session.sessionCreationPolicy(SessionCreationPolicy.STATELESS)) + // Populate the SecurityContext from X-User-Privileges BEFORE authorization runs. + .addFilterBefore(new GatewayPrivilegesFilter(), AuthorizationFilter.class) + .authorizeHttpRequests( + auth -> auth.requestMatchers("/actuator/health", "/actuator/info", "/v3/api-docs/**", "/swagger-ui/**", "/openapi/**") + .permitAll().requestMatchers("/configuration/admin/**").hasAuthority(SUPER_ADMIN) + .requestMatchers(HttpMethod.GET, "/configuration", "/configuration/*").permitAll().requestMatchers("/internal/**") + .permitAll().requestMatchers("/dataset/**").authenticated().anyRequest().permitAll() + ).build(); + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/Configuration.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/Configuration.java new file mode 100644 index 000000000..bccb9e21b --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/Configuration.java @@ -0,0 +1,136 @@ +package edu.harvard.hms.dbmi.avillach.operations.configuration; + +import java.util.Objects; +import java.util.UUID; + +import io.swagger.v3.oas.annotations.media.Schema; + +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.GeneratedValue; +import jakarta.persistence.Id; +import jakarta.persistence.Lob; +import jakarta.persistence.Table; +import jakarta.persistence.UniqueConstraint; + +/** + * Ported from the legacy {@code edu.harvard.dbmi.avillach.data.entity.Configuration} (javax/CDI). The + * {@code patch(ConfigurationRequest)}/{@code fromRequest(ConfigurationRequest)}/ {@code toString()} convenience methods were intentionally + * dropped: they depended on the javax {@code ConfigurationRequest} DTO (not ported — out of scope, see task description) and on the JSON-P + * ({@code javax.json}) API, neither of which is needed by the persistence layer. Downstream services define their own request/response DTOs + * and mappers. + */ +@Schema(description = "A Configuration object containing name, kind, enabled status, and description.") +@Entity(name = "configuration") +@Table( + name = "configuration", + uniqueConstraints = {@UniqueConstraint(name = "unique_uuid", columnNames = {"uuid"}), + @UniqueConstraint(name = "unique_name_kind", columnNames = {"name", "kind"})} +) +public class Configuration { + + // Hibernate 6+: a UUID-typed id with a bare @GeneratedValue (AUTO strategy) is generated via + // the built-in random UUID generator. This replaces the legacy javax + // `@GenericGenerator(strategy = "org.hibernate.id.UUIDGenerator")`, which Hibernate 6 removed; + // both produce a random UUID, so the persisted values and BINARY(16) column are unaffected. + @Id + @GeneratedValue + @Column(columnDefinition = "BINARY(16)") + private UUID uuid; + + @Schema(description = "The configuration name") + @Column(length = 255) + private String name; + + @Schema(description = "The configuration kind/type") + @Column(length = 255) + private String kind; + + // Quoted: VALUE is a reserved word in H2 (not in MySQL, where legacy leaves it unquoted); see + // the equivalent note on NamedDataset.user. + @Schema(description = "The configuration value") + @Lob + @Column(name = "\"value\"", columnDefinition = "TEXT") + private String value; + + @Schema(description = "The configuration description") + @Column(length = 255) + private String description; + + @Schema(description = "This configuration is flagged for deletion") + private Boolean markForDelete = false; + + public UUID getUuid() { + return uuid; + } + + public void setUuid(UUID uuid) { + this.uuid = uuid; + } + + public Configuration setName(String name) { + this.name = name; + return this; + } + + public String getName() { + return name; + } + + public Configuration setKind(String kind) { + this.kind = kind; + return this; + } + + public String getKind() { + return kind; + } + + public Configuration setValue(String value) { + this.value = value; + return this; + } + + public String getValue() { + return value; + } + + public Configuration setDescription(String description) { + this.description = description; + return this; + } + + public String getDescription() { + return description; + } + + public Configuration setMarkForDelete(Boolean markForDelete) { + this.markForDelete = markForDelete; + return this; + } + + public Boolean getMarkForDelete() { + return markForDelete; + } + + @Override + public int hashCode() { + return Objects.hash(uuid); + } + + @Override + public boolean equals(Object obj) { + if (obj == this) { + return true; + } + if (!(obj instanceof Configuration other)) { + return false; + } + return this.uuid != null && this.uuid.equals(other.uuid); + } + + @Override + public String toString() { + return this.uuid != null ? this.uuid.toString() : super.toString(); + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationController.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationController.java new file mode 100644 index 000000000..e4f4b356c --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationController.java @@ -0,0 +1,71 @@ +package edu.harvard.hms.dbmi.avillach.operations.configuration; + +import java.util.List; +import java.util.UUID; + +import org.springframework.http.HttpStatus; +import org.springframework.web.bind.annotation.DeleteMapping; +import org.springframework.web.bind.annotation.GetMapping; +import org.springframework.web.bind.annotation.PatchMapping; +import org.springframework.web.bind.annotation.PathVariable; +import org.springframework.web.bind.annotation.PostMapping; +import org.springframework.web.bind.annotation.RequestBody; +import org.springframework.web.bind.annotation.RequestMapping; +import org.springframework.web.bind.annotation.RequestParam; +import org.springframework.web.bind.annotation.RestController; + +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; +import jakarta.validation.Valid; + +/** + * Ports the legacy WildFly {@code ConfigurationRS}. Mappings are slash-less on purpose: Spring 6 -- unlike the legacy JAX-RS runtime, which + * matched both forms -- serves EXACTLY the declared form, and PIC-SURE clients call slash-less URLs. Authorization is enforced entirely by + * {@link edu.harvard.hms.dbmi.avillach.operations.config.WebSecurityConfig} ({@code /configuration/admin/**} requires {@code SUPER_ADMIN}; + * the two plain {@code GET}s below are public) -- this controller carries no auth code of its own, and its mappings must match those + * security-layer paths exactly. + * + *

    Admin writes return {@code 200 + entity body} (matching the WAR's documented {@code 200} response and {@code PICSUREResponse.success}, + * including DELETE returning the deleted configuration) -- a deliberate divergence from other surfaces' {@code 201} create, kept to + * preserve the documented config contract. + */ +@RestController +@RequestMapping("/configuration") +public class ConfigurationController { + + private final ConfigurationService service; + + public ConfigurationController(ConfigurationService service) { + this.service = service; + } + + @GetMapping("") + public List getConfigurations(@RequestParam(name = "kind", required = false) String kind) { + return service.getConfigurations(kind); + } + + @GetMapping("/{identifier}") + public ConfigurationDto getConfigurationById(@PathVariable("identifier") String identifier) { + return service.getByIdentifier(identifier); + } + + @PostMapping("/admin") + public ConfigurationDto addConfiguration(@Valid @RequestBody ConfigurationRequestDto request) { + if (request.name() == null || request.kind() == null || request.value() == null) { + throw new PicsureException(HttpStatus.BAD_REQUEST, "bad_request", "Name, Kind, and Value properties must not be null"); + } + return service.create(request); + } + + @PatchMapping("/admin/{id}") + public ConfigurationDto updateConfiguration(@PathVariable("id") UUID id, @Valid @RequestBody ConfigurationRequestDto request) { + if (request.uuid() != null && !id.equals(request.uuid())) { + throw new PicsureException(HttpStatus.BAD_REQUEST, "bad_request", "UUID cannot be changed"); + } + return service.update(id, request); + } + + @DeleteMapping("/admin/{id}") + public ConfigurationDto deleteConfiguration(@PathVariable("id") UUID id) { + return service.delete(id); + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationDto.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationDto.java new file mode 100644 index 000000000..7549d026a --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationDto.java @@ -0,0 +1,10 @@ +package edu.harvard.hms.dbmi.avillach.operations.configuration; + +import java.util.UUID; + +/** + * Public JSON shape for a {@code Configuration}, mirroring exactly what the legacy WildFly {@code ConfigurationRS} serialized. Kept + * separate from the {@code pic-sure-api-data} JPA entity so the persistence model never leaks directly onto the wire. + */ +public record ConfigurationDto(UUID uuid, String name, String kind, String value, String description, Boolean markForDelete) { +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationMapper.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationMapper.java new file mode 100644 index 000000000..af4a42047 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationMapper.java @@ -0,0 +1,42 @@ +package edu.harvard.hms.dbmi.avillach.operations.configuration; + +import org.springframework.stereotype.Component; + + +/** + * Translates between the {@code pic-sure-api-data} {@link Configuration} entity and this service's DTOs. Replicates the partial-update + * semantics of the legacy entity's {@code fromRequest}/{@code patch} helpers, which were intentionally dropped from the ported entity (they + * depended on the javax {@code ConfigurationRequest} DTO and the JSON-P API). + */ +@Component +public class ConfigurationMapper { + + public ConfigurationDto toDto(Configuration c) { + return new ConfigurationDto(c.getUuid(), c.getName(), c.getKind(), c.getValue(), c.getDescription(), c.getMarkForDelete()); + } + + /** Build a fresh entity from a create request (mirrors the legacy {@code Configuration.fromRequest}). */ + public Configuration toEntity(ConfigurationRequestDto req) { + return applyPatch(new Configuration(), req); + } + + /** Apply only the non-null fields (mirrors the legacy {@code Configuration.patch} -- PATCH semantics). */ + public Configuration applyPatch(Configuration c, ConfigurationRequestDto req) { + if (req.name() != null) { + c.setName(req.name()); + } + if (req.kind() != null) { + c.setKind(req.kind()); + } + if (req.value() != null) { + c.setValue(req.value()); + } + if (req.description() != null) { + c.setDescription(req.description()); + } + if (req.markForDelete() != null) { + c.setMarkForDelete(req.markForDelete()); + } + return c; + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationRepository.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationRepository.java new file mode 100644 index 000000000..60d1a6dc3 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationRepository.java @@ -0,0 +1,28 @@ +package edu.harvard.hms.dbmi.avillach.operations.configuration; + +import java.util.List; +import java.util.Optional; +import java.util.UUID; + +import org.springframework.data.jpa.repository.JpaRepository; + + +/** + * Ported from the legacy {@code edu.harvard.dbmi.avillach.data.repository.ConfigurationRepository} (CDI/{@code BaseRepository}). + * {@code findById}/{@code findAll}/{@code save}/{@code delete} are inherited from {@link JpaRepository}; the derived queries below replace + * the legacy {@code BaseRepository.getByColumn}/{@code getByColumns} calls used by {@code ConfigurationService}. + */ +public interface ConfigurationRepository extends JpaRepository { + + /** Replaces {@code getByColumn("kind", kind)} -- the kind filter on the list endpoint. */ + List findByKind(String kind); + + /** Replaces {@code getByColumn("name", name)} -- the name-based identifier lookup. */ + List findByName(String name); + + /** + * Replaces {@code getByColumns({name, kind})} for the uniqueness check. The unique constraint {@code unique_name_kind} guarantees at + * most one match. + */ + Optional findByNameAndKind(String name, String kind); +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationRequestDto.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationRequestDto.java new file mode 100644 index 000000000..4b9f195dc --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationRequestDto.java @@ -0,0 +1,21 @@ +package edu.harvard.hms.dbmi.avillach.operations.configuration; + +import java.util.UUID; + +import jakarta.validation.constraints.Pattern; +import jakarta.validation.constraints.Size; + +/** + * Create/update request body for {@code /configuration/admin/**}. Mirrors {@code pic-sure-api-data}'s javax-validated + * {@code ConfigurationRequest} verbatim, in the jakarta namespace, so this service stays self-contained. + * + *

    No {@code @NotNull}: the legacy {@code ConfigurationRS} did manual null checks for {@code name}/{@code kind}/{@code value} on create + * (reproduced in {@link ConfigurationController}), and PATCH treats every field as optional (partial update). {@code uuid} is accepted only + * to honor the "UUID cannot be changed" guard on PATCH. + */ +public record ConfigurationRequestDto( + UUID uuid, @Pattern(regexp = "^[\\w\\d\\-?\\[\\].():]+$") @Size(max = 255) String name, + @Pattern(regexp = "^[\\w\\d\\-?\\[\\].():]+$") @Size(max = 255) String kind, String value, @Size(max = 255) String description, + Boolean markForDelete +) { +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationService.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationService.java new file mode 100644 index 000000000..52fc12e6f --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationService.java @@ -0,0 +1,119 @@ +package edu.harvard.hms.dbmi.avillach.operations.configuration; + +import java.util.List; +import java.util.Optional; +import java.util.UUID; + +import org.springframework.dao.DataIntegrityViolationException; +import org.springframework.http.HttpStatus; +import org.springframework.stereotype.Service; +import org.springframework.transaction.annotation.Transactional; + +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; + +/** + * Ports the legacy WildFly {@code ConfigurationService}. Preserved behaviors: (1) UUID-or-name lookup ({@link #getByIdentifier(String)}) -- + * try {@link UUID#fromString}; if valid, look up by id; if absent (or if the identifier is not a valid UUID at all), fall back to the first + * {@code findByName} match. (2) name+kind uniqueness on create and update via {@code findByNameAndKind}, excluding the row being updated. + * (3) partial PATCH via {@link ConfigurationMapper#applyPatch}. + * + *

    Behavior upgrades to honest statuses: not-found -> 404, duplicate name+kind -> 409. Both are expressed as {@link PicsureException} -- + * the actual {@code pic-sure-spring-commons} built for this monorepo ships only that one public error class (no + * {@code PicsureNotFoundException} subclass), so 404 is carried the same way as 409: via the status code on {@link PicsureException}, not + * the exception's Java type. + * + *

    {@code Configuration} carries a DB-level unique constraint on {@code (name, kind)}. The {@code findByNameAndKind} pre-check above + * handles the common case, but a check-then-save is inherently racy under concurrent writers (two SUPER_ADMIN requests, or a residual + * WildFly writer during migration). {@link #create} and {@link #update} therefore also use {@code saveAndFlush} inside a try/catch so a + * constraint violation that slips past the pre-check is translated to {@code 409 CONFLICT} via {@link PicsureException}, mirroring + * {@code NamedDatasetService.saveOrConflict}. + */ +@Service +public class ConfigurationService { + + private final ConfigurationRepository repo; + private final ConfigurationMapper mapper; + + public ConfigurationService(ConfigurationRepository repo, ConfigurationMapper mapper) { + this.repo = repo; + this.mapper = mapper; + } + + @Transactional(readOnly = true) + public List getConfigurations(String kind) { + List configs = (kind != null) ? repo.findByKind(kind) : repo.findAll(); + return configs.stream().map(mapper::toDto).toList(); + } + + /** UUID-or-name lookup, preserving the legacy {@code ConfigurationService.getConfigurationByIdentifier}. */ + @Transactional(readOnly = true) + public ConfigurationDto getByIdentifier(String identifier) { + return findEntityByIdentifier(identifier).map(mapper::toDto).orElseThrow(() -> notFound(identifier)); + } + + @Transactional + public ConfigurationDto create(ConfigurationRequestDto req) { + Configuration config = mapper.toEntity(req); + if (repo.findByNameAndKind(config.getName(), config.getKind()).isPresent()) { + throw conflict(config.getName(), config.getKind()); + } + return mapper.toDto(saveOrConflict(config, config.getName(), config.getKind())); + } + + @Transactional + public ConfigurationDto update(UUID id, ConfigurationRequestDto req) { + Configuration existing = repo.findById(id).orElseThrow(() -> notFound(id.toString())); + String proposedName = req.name() != null ? req.name() : existing.getName(); + String proposedKind = req.kind() != null ? req.kind() : existing.getKind(); + boolean clash = repo.findByNameAndKind(proposedName, proposedKind).filter(other -> !other.getUuid().equals(id)).isPresent(); + if (clash) { + throw conflict(proposedName, proposedKind); + } + mapper.applyPatch(existing, req); + return mapper.toDto(saveOrConflict(existing, proposedName, proposedKind)); + } + + @Transactional + public ConfigurationDto delete(UUID id) { + Configuration existing = repo.findById(id).orElseThrow(() -> notFound(id.toString())); + repo.delete(existing); + return mapper.toDto(existing); + } + + /** + * {@code saveAndFlush} (not {@code save}) so the {@code unique_name_kind} constraint violation -- if any -- is raised by the database + * and thrown here, inside the try/catch, rather than deferred to end-of-transaction flush where it could no longer be translated into a + * 409. On {@link #update}, a violation here means the proposed {@code (name,kind)} collides with a different row that was created + * concurrently after the pre-check ran -- same 409 as the create-path race. + */ + private Configuration saveOrConflict(Configuration entity, String name, String kind) { + try { + return repo.saveAndFlush(entity); + } catch (DataIntegrityViolationException e) { + throw conflict(name, kind); + } + } + + private Optional findEntityByIdentifier(String identifier) { + try { + UUID uuid = UUID.fromString(identifier); + Optional byId = repo.findById(uuid); + if (byId.isPresent()) { + return byId; + } + } catch (IllegalArgumentException notAUuid) { + // fall through to name lookup + } + return repo.findByName(identifier).stream().findFirst(); + } + + private static PicsureException notFound(String identifier) { + return new PicsureException(HttpStatus.NOT_FOUND, "not_found", "Configuration " + identifier + " not found"); + } + + private static PicsureException conflict(String name, String kind) { + return new PicsureException( + HttpStatus.CONFLICT, "conflict", "A configuration with name '" + name + "' and kind '" + kind + "' already exists" + ); + } +} diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/convert/JsonConverter.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/JsonConverter.java similarity index 82% rename from pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/convert/JsonConverter.java rename to services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/JsonConverter.java index 77d7deccf..f5b4b49e7 100644 --- a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/convert/JsonConverter.java +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/JsonConverter.java @@ -1,10 +1,10 @@ -package edu.harvard.dbmi.avillach.data.entity.convert; +package edu.harvard.hms.dbmi.avillach.operations.dataset; import java.io.IOException; import java.util.HashMap; import java.util.Map; -import javax.persistence.AttributeConverter; +import jakarta.persistence.AttributeConverter; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -13,6 +13,10 @@ import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; +/** + * Ported from the legacy {@code edu.harvard.dbmi.avillach.data.entity.convert.JsonConverter} (javax) verbatim other than the + * {@code jakarta.persistence.AttributeConverter} import. + */ public class JsonConverter implements AttributeConverter, String> { private final Logger logger = LoggerFactory.getLogger(JsonConverter.class); @@ -47,4 +51,4 @@ public Map convertToEntityAttribute(String jsonData) { return objectData; } -} \ No newline at end of file +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDataset.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDataset.java new file mode 100644 index 000000000..5e9de2422 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDataset.java @@ -0,0 +1,138 @@ +package edu.harvard.hms.dbmi.avillach.operations.dataset; + +import java.util.Map; +import java.util.Objects; +import java.util.UUID; + +import io.swagger.v3.oas.annotations.media.Schema; + +import jakarta.persistence.Column; +import jakarta.persistence.Convert; +import jakarta.persistence.Entity; +import jakarta.persistence.GeneratedValue; +import jakarta.persistence.Id; +import jakarta.persistence.JoinColumn; +import jakarta.persistence.OneToOne; +import jakarta.persistence.Table; +import jakarta.persistence.UniqueConstraint; + +import edu.harvard.hms.dbmi.avillach.operations.query.Query; + +/** + * Ported from the legacy {@code edu.harvard.dbmi.avillach.data.entity.NamedDataset} (javax/CDI). The JSON-P-based {@code toString()} + * override was intentionally dropped (not needed by the persistence layer; would otherwise pull in the + * {@code javax.json}/{@code jakarta.json} API for no functional benefit). + */ +@Schema(description = "A NamedDataset object containing query, name, user, and archived status.") +@Entity(name = "named_dataset") +@Table(uniqueConstraints = {@UniqueConstraint(name = "unique_queryId_user", columnNames = {"queryId", "\"user\""})}) +public class NamedDataset { + + // Hibernate 6+: a UUID-typed id with a bare @GeneratedValue (AUTO strategy) is generated via + // the built-in random UUID generator. This replaces the legacy javax + // `@GenericGenerator(strategy = "org.hibernate.id.UUIDGenerator")`, which Hibernate 6 removed; + // both produce a random UUID, so the persisted values and BINARY(16) column are unaffected. + @Id + @GeneratedValue + @Column(columnDefinition = "BINARY(16)") + private UUID uuid; + + @Schema(description = "The associated Query") + @OneToOne + @JoinColumn(name = "queryId") + private Query query; + + // Quoted so Hibernate emits a properly escaped identifier: `user` is not a real reserved word + // in MySQL (legacy's V5 migration backtick-quotes it defensively anyway) but H2 does reserve + // it, and the quoting is honored per-dialect (backticks on MySQL, double quotes on H2) rather + // than changing the physical column name. + @Schema(description = "The user identifier") + @Column(name = "\"user\"", length = 255) + private String user; + + @Schema(description = "The name user has assigned to this dataset") + @Column(length = 255) + private String name; + + @Schema(description = "The archived state") + private Boolean archived = false; + + @Schema(description = "A json string object containing override specific values") + @Column(length = 8192) + @Convert(converter = JsonConverter.class) + private Map metadata; + + public UUID getUuid() { + return uuid; + } + + public void setUuid(UUID uuid) { + this.uuid = uuid; + } + + public NamedDataset setName(String name) { + this.name = name; + return this; + } + + public String getName() { + return name; + } + + public NamedDataset setArchived(Boolean archived) { + this.archived = archived; + return this; + } + + public Boolean getArchived() { + return archived; + } + + public NamedDataset setQuery(Query query) { + this.query = query; + return this; + } + + public Query getQuery() { + return query; + } + + public NamedDataset setUser(String user) { + this.user = user; + return this; + } + + public String getUser() { + return user; + } + + public Map getMetadata() { + return metadata; + } + + public NamedDataset setMetadata(Map metadata) { + this.metadata = metadata; + return this; + } + + @Override + public int hashCode() { + return Objects.hash(uuid); + } + + @Override + public boolean equals(Object obj) { + if (obj == this) { + return true; + } + if (!(obj instanceof NamedDataset other)) { + return false; + } + return this.uuid != null && this.uuid.equals(other.uuid); + } + + @Override + public String toString() { + return this.uuid != null ? this.uuid.toString() : super.toString(); + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetController.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetController.java new file mode 100644 index 000000000..fdae86295 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetController.java @@ -0,0 +1,79 @@ +package edu.harvard.hms.dbmi.avillach.operations.dataset; + +import java.util.List; +import java.util.UUID; + +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.web.bind.annotation.DeleteMapping; +import org.springframework.web.bind.annotation.GetMapping; +import org.springframework.web.bind.annotation.PathVariable; +import org.springframework.web.bind.annotation.PostMapping; +import org.springframework.web.bind.annotation.PutMapping; +import org.springframework.web.bind.annotation.RequestBody; +import org.springframework.web.bind.annotation.RequestMapping; +import org.springframework.web.bind.annotation.RestController; + +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUser; +import jakarta.validation.Valid; + +/** + * Ports the legacy WildFly {@code NamedDatasetRS}: {@code GET/POST /dataset/named} and {@code GET/PUT/DELETE /dataset/named/{id}}. Mappings + * are slash-less on purpose: the frontend calls the slash-less form, and Spring 6 -- unlike the legacy JAX-RS runtime, which matched both + * -- serves EXACTLY the declared form (a trailing-slash mapping 404s the slash-less request). Authorization is enforced in two layers: + * {@code WebSecurityConfig} requires an authenticated caller for all of {@code /dataset/**} (the gateway must have supplied + * {@code X-User-Id}); this controller then email-scopes every operation via {@link NamedDatasetService}, whose repository lookups are keyed + * on the caller's email ({@code GatewayUser#getEmail()}), never {@code userId}. + * + *

    DELETE is net-new relative to the legacy {@code NamedDatasetRS} (which had no delete endpoint) -- added here per the migration plan. + */ +@RestController +@RequestMapping("/dataset/named") +public class NamedDatasetController { + + private final NamedDatasetService service; + + public NamedDatasetController(NamedDatasetService service) { + this.service = service; + } + + @GetMapping("") + public List list(GatewayUser user) { + return service.listForUser(requireEmail(user)); + } + + @PostMapping("") + public ResponseEntity create(GatewayUser user, @Valid @RequestBody NamedDatasetRequestDto req) { + NamedDatasetDto created = service.create(requireEmail(user), req); + return ResponseEntity.status(HttpStatus.CREATED).body(created); + } + + @GetMapping("/{id}") + public NamedDatasetDto get(GatewayUser user, @PathVariable("id") UUID id) { + return service.getForUser(requireEmail(user), id); + } + + @PutMapping("/{id}") + public NamedDatasetDto update(GatewayUser user, @PathVariable("id") UUID id, @Valid @RequestBody NamedDatasetRequestDto req) { + return service.update(requireEmail(user), id, req); + } + + @DeleteMapping("/{id}") + public ResponseEntity delete(GatewayUser user, @PathVariable("id") UUID id) { + service.delete(requireEmail(user), id); + return ResponseEntity.noContent().build(); + } + + /** + * Returns the caller's email owner key. {@code WebSecurityConfig} already rejects unauthenticated requests to {@code /dataset/**} + * before this method runs, so this is a defensive guard against a gateway that authenticated the caller (sent {@code X-User-Id}) but + * omitted {@code X-User-Email} -- not the primary auth gate. + */ + private String requireEmail(GatewayUser user) { + if (user == null || user.getEmail() == null || user.getEmail().isBlank()) { + throw new PicsureException(HttpStatus.UNAUTHORIZED, "unauthorized", "User identity (email) not present in request"); + } + return user.getEmail(); + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetDto.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetDto.java new file mode 100644 index 000000000..ba352e2b5 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetDto.java @@ -0,0 +1,12 @@ +package edu.harvard.hms.dbmi.avillach.operations.dataset; + +import java.util.Map; +import java.util.UUID; + +/** + * Public JSON shape for a {@code NamedDataset}, mirroring the legacy {@code NamedDatasetRS} wire shape. Kept separate from the + * {@code pic-sure-api-data} JPA entity so the persistence model (and the gzip-compressed {@code Query} blob it references) never leaks + * directly onto the wire -- {@code queryId} is the referenced {@code Query}'s uuid, not the query body itself. + */ +public record NamedDatasetDto(UUID uuid, String name, UUID queryId, Boolean archived, Map metadata) { +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetMapper.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetMapper.java new file mode 100644 index 000000000..f1832fe46 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetMapper.java @@ -0,0 +1,25 @@ +package edu.harvard.hms.dbmi.avillach.operations.dataset; + +import org.springframework.stereotype.Component; + +import edu.harvard.hms.dbmi.avillach.operations.query.Query; + +/** + * Translates between the {@code pic-sure-api-data} {@link NamedDataset} entity and this service's DTOs. Pure field mapping -- the + * {@code Query} referenced by {@code queryId} is resolved/persisted by {@link NamedDatasetService} (via {@code QueryRepository}) and handed + * in already-loaded, mirroring the legacy WAR's {@code NamedDatasetService}. + */ +@Component +public class NamedDatasetMapper { + + public NamedDatasetDto toDto(NamedDataset e) { + return new NamedDatasetDto( + e.getUuid(), e.getName(), e.getQuery() == null ? null : e.getQuery().getUuid(), e.getArchived(), e.getMetadata() + ); + } + + /** {@code user} is the caller's EMAIL (owner key); {@code query} is pre-resolved by the service. */ + public NamedDataset toEntity(String user, Query query, NamedDatasetRequestDto req) { + return new NamedDataset().setUser(user).setQuery(query).setName(req.name()).setArchived(req.archived()).setMetadata(req.metadata()); + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetRepository.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetRepository.java new file mode 100644 index 000000000..36ee9c91e --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetRepository.java @@ -0,0 +1,23 @@ +package edu.harvard.hms.dbmi.avillach.operations.dataset; + +import java.util.List; +import java.util.Optional; +import java.util.UUID; + +import org.springframework.data.jpa.repository.JpaRepository; + + +/** + * Ported from the legacy {@code edu.harvard.dbmi.avillach.data.repository.NamedDatasetRepository} (CDI/{@code BaseRepository}), which had + * no custom finder methods beyond generic CRUD. + * + *

    {@code findByUser}/{@code findByUuidAndUser} are added proactively (not present in legacy) because the downstream platform service + * expects them from this foundational module, replacing the WAR's in-Java owner check with SQL-level user scoping. They are simple derived + * queries on existing columns ({@code uuid}, {@code user}) and carry no risk to the entities/mappings this unit is responsible for. + */ +public interface NamedDatasetRepository extends JpaRepository { + + List findByUser(String user); + + Optional findByUuidAndUser(UUID uuid, String user); +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetRequestDto.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetRequestDto.java new file mode 100644 index 000000000..fc25a5378 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetRequestDto.java @@ -0,0 +1,27 @@ +package edu.harvard.hms.dbmi.avillach.operations.dataset; + +import java.util.HashMap; +import java.util.Map; +import java.util.UUID; + +import jakarta.validation.constraints.NotNull; +import jakarta.validation.constraints.Pattern; + +/** + * Create/update request body for {@code /dataset/named/**}. Mirrors {@code pic-sure-api-data}'s javax-validated {@code NamedDatasetRequest} + * verbatim (the {@code @Pattern} on {@code name} is copied byte-for-byte), in the jakarta namespace, so this service stays self-contained. + * {@code queryId} is resolved to a persisted {@code Query} by the service -- it is not a column on {@code NamedDataset} itself. + */ +public record NamedDatasetRequestDto( + @NotNull UUID queryId, @NotNull @Pattern(regexp = "^[\\w\\d \\-\\\\/?+=\\[\\].():\"']+$") String name, Boolean archived, + Map metadata +) { + public NamedDatasetRequestDto { + if (archived == null) { + archived = false; + } + if (metadata == null) { + metadata = new HashMap<>(); + } + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetService.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetService.java new file mode 100644 index 000000000..05835cba5 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetService.java @@ -0,0 +1,106 @@ +package edu.harvard.hms.dbmi.avillach.operations.dataset; + +import java.util.List; +import java.util.UUID; + +import org.springframework.dao.DataIntegrityViolationException; +import org.springframework.http.HttpStatus; +import org.springframework.stereotype.Service; +import org.springframework.transaction.annotation.Transactional; + +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; +import edu.harvard.hms.dbmi.avillach.operations.query.Query; +import edu.harvard.hms.dbmi.avillach.operations.query.QueryRepository; + +/** + * Ports the legacy WildFly {@code NamedDatasetService}. User-scoping is pushed into SQL via {@code NamedDatasetRepository}'s + * {@code findByUser}/{@code findByUuidAndUser}, replacing the WAR's in-Java owner check; the owner key is the caller's EMAIL. Because the + * lookup is scoped at the SQL layer, a caller reading/mutating another user's dataset gets exactly the same 404 as a genuinely-missing uuid + * -- there is no separate 403 branch, and existence is never leaked to a non-owning caller (same posture as {@code ConfigurationService}'s + * not-found handling). + * + *

    {@code archived} is not a list filter -- {@code findByUser} returns archived and non-archived rows alike; there is no soft-delete. + * + *

    {@code queryId} is resolved to a persisted {@code Query} via {@code QueryRepository.findById}, 404 when absent (preserving the WAR's + * "query not found" branch). + * + *

    {@code NamedDataset} carries a DB-level unique constraint on {@code (queryId, user)}. Rather than a check-then-save pre-check (which + * would race under concurrent requests), {@link #create} and {@link #update} (when it repoints the query) use {@code saveAndFlush} inside a + * try/catch so the constraint violation surfaces synchronously and is translated to {@code 409 CONFLICT} via {@link PicsureException}, + * mirroring how {@code ConfigurationService} handles its name+kind conflict. + */ +@Service +public class NamedDatasetService { + + private final NamedDatasetRepository repo; + private final QueryRepository queryRepo; + private final NamedDatasetMapper mapper; + + public NamedDatasetService(NamedDatasetRepository repo, QueryRepository queryRepo, NamedDatasetMapper mapper) { + this.repo = repo; + this.queryRepo = queryRepo; + this.mapper = mapper; + } + + @Transactional(readOnly = true) + public List listForUser(String user) { + return repo.findByUser(user).stream().map(mapper::toDto).toList(); + } + + @Transactional(readOnly = true) + public NamedDatasetDto getForUser(String user, UUID id) { + NamedDataset e = repo.findByUuidAndUser(id, user).orElseThrow(() -> notFound(id)); + return mapper.toDto(e); + } + + @Transactional + public NamedDatasetDto create(String user, NamedDatasetRequestDto req) { + Query query = resolveQuery(req.queryId()); + NamedDataset saved = saveOrConflict(mapper.toEntity(user, query, req), req.queryId(), user); + return mapper.toDto(saved); + } + + @Transactional + public NamedDatasetDto update(String user, UUID id, NamedDatasetRequestDto req) { + NamedDataset existing = repo.findByUuidAndUser(id, user).orElseThrow(() -> notFound(id)); + if (existing.getQuery() == null || !existing.getQuery().getUuid().equals(req.queryId())) { + existing.setQuery(resolveQuery(req.queryId())); + } + existing.setName(req.name()).setArchived(req.archived()).setMetadata(req.metadata()); + return mapper.toDto(saveOrConflict(existing, req.queryId(), user)); + } + + @Transactional + public void delete(String user, UUID id) { + NamedDataset existing = repo.findByUuidAndUser(id, user).orElseThrow(() -> notFound(id)); + repo.delete(existing); + } + + private Query resolveQuery(UUID queryId) { + return queryRepo.findById(queryId) + .orElseThrow(() -> new PicsureException(HttpStatus.NOT_FOUND, "not_found", "Query " + queryId + " not found")); + } + + /** + * {@code saveAndFlush} (not {@code save}) so the {@code unique_queryId_user} constraint violation -- if any -- is raised by the + * database and thrown here, inside the try/catch, rather than deferred to end-of-transaction flush where it could no longer be + * translated into a 409. + */ + private NamedDataset saveOrConflict(NamedDataset entity, UUID queryId, String user) { + try { + return repo.saveAndFlush(entity); + } catch (DataIntegrityViolationException e) { + throw conflict(queryId, user); + } + } + + private static PicsureException notFound(UUID id) { + return new PicsureException(HttpStatus.NOT_FOUND, "not_found", "NamedDataset " + id + " not found"); + } + + private static PicsureException conflict(UUID queryId, String user) { + return new PicsureException( + HttpStatus.CONFLICT, "conflict", "A NamedDataset for query " + queryId + " and user '" + user + "' already exists" + ); + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/InternalQueryController.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/InternalQueryController.java new file mode 100644 index 000000000..f176e18e3 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/InternalQueryController.java @@ -0,0 +1,67 @@ +package edu.harvard.hms.dbmi.avillach.operations.query; + +import java.util.LinkedHashMap; +import java.util.Map; +import java.util.UUID; + +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.web.bind.annotation.GetMapping; +import org.springframework.web.bind.annotation.PatchMapping; +import org.springframework.web.bind.annotation.PathVariable; +import org.springframework.web.bind.annotation.PostMapping; +import org.springframework.web.bind.annotation.RequestBody; +import org.springframework.web.bind.annotation.RequestMapping; +import org.springframework.web.bind.annotation.RestController; + +/** + * The internal query API: the token-gated boundary the hpds-query-service and the gateway both call. {@code /internal/**} passes + * {@code WebSecurityConfig}'s {@code anyRequest().permitAll()} unauthenticated -- it is {@link InternalTokenFilter} (a plain servlet + * filter, not this controller) that actually gates every request here on {@code X-PIC-SURE-INTERNAL-TOKEN}, and network isolation (out of + * this service's hands) that keeps it unreachable from outside the cluster. + * + *

    {@code GET /{picsureId}/dispatch} is the one FIXED external contract: the gateway's dormant {@code QueryAuthFetcher} already calls + * {@code GET {base}/internal/queries/{id}/dispatch} expecting exactly {@code {"queryJson": ""}} (deserialized as + * {@code record DispatchResponse(String queryJson)}), 404 for an unknown id, 403 for a bad/missing token -- the key name, and that its + * value is a JSON string (not a nested object), are load-bearing. + */ +@RestController +@RequestMapping("/internal/queries") +public class InternalQueryController { + + private final QueryPersistenceService service; + + public InternalQueryController(QueryPersistenceService service) { + this.service = service; + } + + @PostMapping("") + public ResponseEntity> save(@RequestBody SaveQueryRequest req) { + UUID picsureId = service.save(req); + Map body = new LinkedHashMap<>(); + body.put("picsureId", picsureId); + return ResponseEntity.status(HttpStatus.CREATED).body(body); + } + + @GetMapping("/{picsureId}") + public StoredQuery get(@PathVariable("picsureId") UUID picsureId) { + return service.get(picsureId); + } + + @PatchMapping("/{picsureId}") + public ResponseEntity update(@PathVariable("picsureId") UUID picsureId, @RequestBody UpdateQueryRequest req) { + service.update(picsureId, req); + return ResponseEntity.noContent().build(); + } + + /** + * MUST match the gateway's {@code QueryAuthFetcher} contract exactly: {@code {"queryJson": ""}}, the stored query JSON + * re-serialized as a string with {@code resourceCredentials} stripped (or {@code null} for a blank stored query). + */ + @GetMapping("/{picsureId}/dispatch") + public Map dispatch(@PathVariable("picsureId") UUID picsureId) { + Map body = new LinkedHashMap<>(); + body.put("queryJson", service.dispatchQueryJson(picsureId)); + return body; + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/InternalTokenFilter.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/InternalTokenFilter.java new file mode 100644 index 000000000..5b7c4f386 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/InternalTokenFilter.java @@ -0,0 +1,100 @@ +package edu.harvard.hms.dbmi.avillach.operations.query; + +import java.io.IOException; +import java.nio.charset.StandardCharsets; +import java.security.MessageDigest; +import java.util.LinkedHashMap; +import java.util.Map; + +import org.slf4j.MDC; +import org.springframework.http.HttpStatus; +import org.springframework.http.MediaType; +import org.springframework.web.filter.OncePerRequestFilter; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import edu.harvard.hms.dbmi.avillach.commons.request.RequestIdFilter; +import edu.harvard.hms.dbmi.avillach.operations.config.InternalTokenFilterConfig; +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +/** + * Defense-in-depth gate for {@code /internal/**}: network isolation (not this class's job) PLUS a mandatory shared secret. Validates + * {@code X-PIC-SURE-INTERNAL-TOKEN} against the configured {@code picsure.operations.internal-token} (env + * {@code QUERY_SERVICE_INTERNAL_TOKEN}); missing/mismatched token -> 403 with {@code {errorType:"FORBIDDEN", message:"Forbidden", + * requestId}}. Fail-closed: if the configured token is blank/unset, EVERY {@code /internal/**} call is rejected, including one that + * happens to present a matching-looking header -- there is deliberately no way to satisfy this filter when the secret is unconfigured. + * + *

    NOT a {@code @Component}: it is registered exactly once, by {@link InternalTokenFilterConfig}, via a + * {@code FilterRegistrationBean} with {@code addUrlPatterns("/internal/*")}. That container-level URL-pattern match is + * normalized/authoritative and (per the servlet spec) is always evaluated relative to the context path -- accounting for any servlet + * context path and path normalization the same way the {@code DispatcherServlet} routing to {@link InternalQueryController} does, so the + * two can never disagree about which requests are "internal". + * + *

    {@link #shouldNotFilter(HttpServletRequest)} is a second, redundant guard on top of that container-level mapping + * (belt-and-suspenders), not the primary gate -- but it MUST agree with the container's context-relative matching. It therefore strips + * {@link HttpServletRequest#getContextPath()} off {@link HttpServletRequest#getRequestURI()} before comparing, rather than testing the raw + * URI directly: {@code getRequestURI()} INCLUDES any context path, so under a non-empty {@code server.servlet.context-path} the raw URI + * would never start with the literal string {@code "/internal/"} even for a request the container correctly dispatches to + * {@link InternalQueryController} -- which used to make this exact check silently skip the token gate. (Deliberately not + * {@code getServletPath()}: that is populated per the target servlet's own mapping style -- e.g. empty in some test/mock harnesses -- + * whereas context-path-stripping only ever depends on {@code getContextPath()}, which is reliable in both real containers and MockMvc.) + * + *

    Runs independently of (and does not need to be woven into) {@link edu.harvard.hms.dbmi.avillach.operations.config.WebSecurityConfig}'s + * Spring Security chain, which already {@code permitAll()}s these paths at that layer -- this filter is what actually gates them. + */ +public class InternalTokenFilter extends OncePerRequestFilter { + + public static final String HEADER = "X-PIC-SURE-INTERNAL-TOKEN"; + + private static final ObjectMapper MAPPER = new ObjectMapper(); + + private final String expectedToken; + + public InternalTokenFilter(String expectedToken) { + this.expectedToken = expectedToken; + } + + @Override + protected boolean shouldNotFilter(HttpServletRequest request) { + return !contextRelativePath(request).startsWith("/internal/"); + } + + /** {@code request.getRequestURI()} with any {@code request.getContextPath()} prefix stripped off. */ + private static String contextRelativePath(HttpServletRequest request) { + String uri = request.getRequestURI(); + String contextPath = request.getContextPath(); + if (contextPath != null && !contextPath.isEmpty() && uri.startsWith(contextPath)) { + return uri.substring(contextPath.length()); + } + return uri; + } + + @Override + protected void doFilterInternal(HttpServletRequest req, HttpServletResponse res, FilterChain chain) + throws ServletException, IOException { + String provided = req.getHeader(HEADER); + if (expectedToken == null || expectedToken.isBlank() || provided == null || !constantTimeEquals(expectedToken, provided)) { + forbidden(res); + return; + } + chain.doFilter(req, res); + } + + private void forbidden(HttpServletResponse res) throws IOException { + res.setStatus(HttpStatus.FORBIDDEN.value()); + res.setContentType(MediaType.APPLICATION_JSON_VALUE); + String requestId = MDC.get(RequestIdFilter.MDC_KEY); + Map body = new LinkedHashMap<>(); + body.put("errorType", "FORBIDDEN"); + body.put("message", "Forbidden"); + body.put("requestId", requestId == null ? "" : requestId); + MAPPER.writeValue(res.getWriter(), body); + } + + private static boolean constantTimeEquals(String a, String b) { + return MessageDigest.isEqual(a.getBytes(StandardCharsets.UTF_8), b.getBytes(StandardCharsets.UTF_8)); + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/Query.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/Query.java new file mode 100644 index 000000000..f2caf14a9 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/Query.java @@ -0,0 +1,178 @@ +package edu.harvard.hms.dbmi.avillach.operations.query; + +import java.io.BufferedReader; +import java.io.ByteArrayInputStream; +import java.io.ByteArrayOutputStream; +import java.io.IOException; +import java.io.InputStreamReader; +import java.io.UncheckedIOException; +import java.nio.charset.StandardCharsets; +import java.sql.Date; +import java.util.Objects; +import java.util.UUID; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; + +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.EnumType; +import jakarta.persistence.Enumerated; +import jakarta.persistence.GeneratedValue; +import jakarta.persistence.Id; +import jakarta.persistence.Lob; + +import edu.harvard.dbmi.avillach.domain.PicSureStatus; + +/** + * Ported from the legacy {@code edu.harvard.dbmi.avillach.data.entity.Query} (javax/CDI). The {@code resourceId} FK / + * {@code @ManyToOne Resource resource} association is intentionally dropped: the {@code resource} registry table/entity is being removed in + * this migration, the {@code query.resourceId} column is nullable (see legacy V1__CREATE_PICSURE_INITIAL.sql), and the platform services do + * not read or write it (new rows simply leave it NULL until the column itself is dropped). + */ +@Entity(name = "query") +public class Query { + + // Hibernate 6+: a UUID-typed id with a bare @GeneratedValue (AUTO strategy) is generated via + // the built-in random UUID generator. This replaces the legacy javax + // `@GenericGenerator(strategy = "org.hibernate.id.UUIDGenerator")`, which Hibernate 6 removed; + // both produce a random UUID, so the persisted values and BINARY(16) column are unaffected. + @Id + @GeneratedValue + @Column(columnDefinition = "BINARY(16)") + private UUID uuid; + + private Date startTime; + + private Date readyTime; + + // Resource is responsible for mapping internal status to picsurestatus. + // No @Enumerated annotation in the legacy entity -> default JPA enum mapping is ORDINAL; + // made explicit here to preserve that mapping unambiguously. + @Enumerated(EnumType.ORDINAL) + private PicSureStatus status; + + private String resourceResultId; + + // Original query request, gzip-compressed. + @Lob + @Column(columnDefinition = "BLOB") + private byte[] query; + + @Column(length = 8192) + private byte[] metadata; + + private String version; + + public UUID getUuid() { + return uuid; + } + + public void setUuid(UUID uuid) { + this.uuid = uuid; + } + + public String getResourceResultId() { + return resourceResultId; + } + + public void setResourceResultId(String resourceResultId) { + this.resourceResultId = resourceResultId; + } + + public void setStartTime(Date startTime) { + this.startTime = startTime; + } + + public Date getStartTime() { + return startTime; + } + + public Date getReadyTime() { + return readyTime; + } + + public PicSureStatus getStatus() { + return status; + } + + public void setReadyTime(Date readyTime) { + this.readyTime = readyTime; + } + + public void setStatus(PicSureStatus status) { + this.status = status; + } + + public String getVersion() { + return version; + } + + public Query setVersion(String version) { + this.version = version; + return this; + } + + public String getQuery() { + if (this.query == null || this.query.length == 0) { + return ""; + } + + StringBuilder outStr = new StringBuilder(); + try ( + GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream(this.query)); BufferedReader bf = + new BufferedReader(new InputStreamReader(gis, StandardCharsets.UTF_8)) + ) { + String line; + while ((line = bf.readLine()) != null) { + outStr.append(line); + } + } catch (IOException e) { + throw new UncheckedIOException(e); + } + return outStr.toString(); + } + + public void setQuery(String queryStr) { + if (queryStr == null || queryStr.length() == 0) { + this.query = new byte[0]; + return; + } + + try (ByteArrayOutputStream obj = new ByteArrayOutputStream(); GZIPOutputStream gzip = new GZIPOutputStream(obj)) { + gzip.write(queryStr.getBytes(StandardCharsets.UTF_8)); + gzip.close(); + this.query = obj.toByteArray(); + } catch (IOException e) { + throw new UncheckedIOException(e); + } + } + + public byte[] getMetadata() { + return metadata; + } + + public void setMetadata(byte[] metadata) { + this.metadata = metadata; + } + + @Override + public int hashCode() { + return Objects.hash(uuid); + } + + @Override + public boolean equals(Object obj) { + if (obj == this) { + return true; + } + if (!(obj instanceof Query other)) { + return false; + } + return this.uuid != null && this.uuid.equals(other.uuid); + } + + @Override + public String toString() { + return this.uuid != null ? this.uuid.toString() : super.toString(); + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/QueryPersistenceService.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/QueryPersistenceService.java new file mode 100644 index 000000000..2d0753ef3 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/QueryPersistenceService.java @@ -0,0 +1,136 @@ +package edu.harvard.hms.dbmi.avillach.operations.query; + +import java.util.Base64; +import java.util.UUID; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.http.HttpStatus; +import org.springframework.stereotype.Service; +import org.springframework.transaction.annotation.Transactional; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.node.ObjectNode; + +import edu.harvard.dbmi.avillach.domain.PicSureStatus; +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; + +/** + * The sole read/write path onto the {@code query} table for the internal query API ({@link InternalQueryController}). + * Persists/loads/updates {@link Query} rows and produces the gateway-only dispatch payload -- the stored query JSON with + * {@code resourceCredentials} stripped, per the fixed {@code QueryAuthFetcher} contract ({@code {queryJson: ""}}). + * + *

    {@code status} travels on the wire as the {@link PicSureStatus} enum NAME, never its ordinal, so callers never need the enum type; an + * unrecognized name is a caller error (400), not a 500. {@code metadata} travels as base64-encoded bytes, matching the entity's raw + * {@code byte[]} column; malformed base64 is likewise a caller error (400), not a 500. + */ +@Service +public class QueryPersistenceService { + + private static final Logger LOG = LoggerFactory.getLogger(QueryPersistenceService.class); + private static final ObjectMapper MAPPER = new ObjectMapper(); + + private final QueryRepository repo; + + public QueryPersistenceService(QueryRepository repo) { + this.repo = repo; + } + + @Transactional + public UUID save(SaveQueryRequest req) { + Query entity = new Query(); + entity.setQuery(req.query()); + entity.setResourceResultId(req.resourceResultId()); + entity.setStatus(parseStatus(req.status())); + entity.setVersion(req.version()); + entity.setMetadata(decodeMetadata(req.metadata())); + return repo.save(entity).getUuid(); + } + + @Transactional(readOnly = true) + public StoredQuery get(UUID picsureId) { + return toDto(load(picsureId)); + } + + @Transactional + public void update(UUID picsureId, UpdateQueryRequest req) { + Query entity = load(picsureId); + if (req.status() != null) { + entity.setStatus(parseStatus(req.status())); + } + if (req.resourceResultId() != null) { + entity.setResourceResultId(req.resourceResultId()); + } + if (req.metadata() != null) { + entity.setMetadata(decodeMetadata(req.metadata())); + } + repo.save(entity); + } + + /** + * Gateway-only auth-fetch payload: the stored query JSON, re-serialized as a STRING with {@code resourceCredentials} removed. 404 when + * the row is absent (the gateway's {@code QueryAuthFetcher} fails closed on that). A blank/absent stored query body yields {@code null} + * (never a 500) -- malformed JSON is logged and also yields {@code null} rather than leaking the raw unparsed body. + */ + @Transactional(readOnly = true) + public String dispatchQueryJson(UUID picsureId) { + Query entity = load(picsureId); + String json = entity.getQuery(); + if (json == null || json.isBlank()) { + return null; + } + try { + JsonNode node = MAPPER.readTree(json); + if (node instanceof ObjectNode obj) { + obj.remove("resourceCredentials"); // SECURITY: never return stored credentials + } + return MAPPER.writeValueAsString(node); + } catch (JsonProcessingException e) { + LOG.warn("Stored query for {} is not valid JSON", picsureId, e); + return null; + } + } + + private Query load(UUID picsureId) { + return repo.findById(picsureId).orElseThrow(() -> notFound(picsureId)); + } + + private static StoredQuery toDto(Query entity) { + return new StoredQuery( + entity.getUuid(), entity.getQuery(), entity.getResourceResultId(), + entity.getStatus() == null ? null : entity.getStatus().name(), entity.getVersion(), encodeMetadata(entity.getMetadata()) + ); + } + + private static PicSureStatus parseStatus(String status) { + if (status == null) { + return null; + } + try { + return PicSureStatus.valueOf(status); + } catch (IllegalArgumentException e) { + throw new PicsureException(HttpStatus.BAD_REQUEST, "invalid_status", "Unknown status: " + status); + } + } + + private static byte[] decodeMetadata(String metadata) { + if (metadata == null) { + return null; + } + try { + return Base64.getDecoder().decode(metadata); + } catch (IllegalArgumentException e) { + throw new PicsureException(HttpStatus.BAD_REQUEST, "invalid_metadata", "metadata is not valid base64"); + } + } + + private static String encodeMetadata(byte[] metadata) { + return metadata == null ? null : Base64.getEncoder().encodeToString(metadata); + } + + private static PicsureException notFound(UUID id) { + return new PicsureException(HttpStatus.NOT_FOUND, "not_found", "Query " + id + " not found"); + } +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/QueryRepository.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/QueryRepository.java new file mode 100644 index 000000000..5d4c669e9 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/QueryRepository.java @@ -0,0 +1,12 @@ +package edu.harvard.hms.dbmi.avillach.operations.query; + +import java.util.UUID; + +import org.springframework.data.jpa.repository.JpaRepository; + +/** + * Ported from the legacy {@code edu.harvard.dbmi.avillach.data.repository.QueryRepository} (CDI/{@code BaseRepository}) to a Spring Data + * JPA interface. {@code findById}/{@code save} are inherited from {@link JpaRepository}. + */ +public interface QueryRepository extends JpaRepository { +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/SaveQueryRequest.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/SaveQueryRequest.java new file mode 100644 index 000000000..bf0dcbe97 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/SaveQueryRequest.java @@ -0,0 +1,10 @@ +package edu.harvard.hms.dbmi.avillach.operations.query; + +/** + * Request body for {@code POST /internal/queries}: the caller (hpds-query-service) hands over the full query it wants persisted. + * {@code status} is the {@link edu.harvard.dbmi.avillach.domain.PicSureStatus} enum NAME (e.g. {@code "QUEUED"}), not its ordinal -- kept + * as a plain string on the wire so callers never need the enum type. {@code metadata} is base64-encoded bytes (mirrors the {@code Query} + * entity's {@code byte[] metadata} column), or {@code null} when there is none. + */ +public record SaveQueryRequest(String query, String resourceResultId, String status, String version, String metadata) { +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/StoredQuery.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/StoredQuery.java new file mode 100644 index 000000000..8ece9efed --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/StoredQuery.java @@ -0,0 +1,14 @@ +package edu.harvard.hms.dbmi.avillach.operations.query; + +import java.util.UUID; + +/** + * Public JSON shape returned by {@code GET /internal/queries/{picsureId}}: the full persisted {@code Query} row, minus the gzip-blob/entity + * plumbing. {@code status} is the {@link edu.harvard.dbmi.avillach.domain.PicSureStatus} enum NAME (or {@code null} if unset). + * {@code metadata} is base64-encoded bytes (or {@code null} if unset) -- callers that need the raw JSON therein decode it themselves. + * + *

    Deliberately distinct from the gateway-only dispatch payload ({@code {queryJson: "..."}}), which excludes everything here except the + * (auth-mutated) query body -- see {@code InternalQueryController#dispatch}. + */ +public record StoredQuery(UUID picsureId, String query, String resourceResultId, String status, String version, String metadata) { +} diff --git a/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/UpdateQueryRequest.java b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/UpdateQueryRequest.java new file mode 100644 index 000000000..b0b2c9d81 --- /dev/null +++ b/services/pic-sure-operations-service/src/main/java/edu/harvard/hms/dbmi/avillach/operations/query/UpdateQueryRequest.java @@ -0,0 +1,10 @@ +package edu.harvard.hms.dbmi.avillach.operations.query; + +/** + * Request body for {@code PATCH /internal/queries/{picsureId}}: every field is nullable and means "leave unchanged" when absent, so callers + * can update just the one field they care about (typically {@code status} as a dispatch completes, or {@code resourceResultId} once HPDS + * assigns one) without re-sending the whole row. {@code status} is the {@link edu.harvard.dbmi.avillach.domain.PicSureStatus} enum NAME; + * {@code metadata} is base64-encoded bytes. + */ +public record UpdateQueryRequest(String status, String resourceResultId, String metadata) { +} diff --git a/services/pic-sure-operations-service/src/main/resources/application.yml b/services/pic-sure-operations-service/src/main/resources/application.yml new file mode 100644 index 000000000..cd2cda83d --- /dev/null +++ b/services/pic-sure-operations-service/src/main/resources/application.yml @@ -0,0 +1,71 @@ +spring: + application: + name: pic-sure-operations-service + datasource: + url: ${SPRING_DATASOURCE_URL:jdbc:mysql://picsure-db:3306/picsure?useUnicode=true&characterEncoding=UTF-8&autoReconnect=true&autoReconnectForPools=true&serverTimezone=UTC} + username: ${SPRING_DATASOURCE_USERNAME:picsure} + password: ${SPRING_DATASOURCE_PASSWORD:} + driver-class-name: com.mysql.cj.jdbc.Driver + jpa: + open-in-view: false + hibernate: + # The pic-sure MySQL schema (Configuration/NamedDataset/Query) already exists and is owned by the legacy Flyway + # migrations -- this service must never generate or alter DDL against it. + ddl-auto: none + naming: + # CRITICAL / LOAD-BEARING: Spring Boot's default SpringPhysicalNamingStrategy snake_cases identifiers even when + # the JPA entities give an explicit camelCase @Column/@JoinColumn name (e.g. "queryId" -> "query_id", + # "resourceResultId" -> "resource_result_id"). The real production schema is camelCase throughout, not snake_case. + # Without this override, Hibernate silently generates SQL that references columns which do not exist -- every query + # against the real database breaks. Hibernate's own PhysicalNamingStrategyStandardImpl passes names through + # unchanged, matching the schema exactly. + physical-strategy: org.hibernate.boot.model.naming.PhysicalNamingStrategyStandardImpl + +picsure: + operations: + # Shared secret enforced by InternalTokenFilter on /internal/** (the gateway's QueryAuthFetcher dispatch calls, + # and any future hpds-query-service caller). Fail-closed: left blank, InternalTokenFilter rejects every + # /internal/** request rather than treating an unconfigured secret as "wide open". + internal-token: ${QUERY_SERVICE_INTERNAL_TOKEN:} + # The X-Application-Token gate for /actuator/** (ActuatorSecurityConfig + the shared + # ActuatorSecurityHelper in pic-sure-spring-commons). Shallow health/liveness/readiness stay open regardless. + actuator: + require-token: ${PICSURE_ACTUATOR_REQUIRE_TOKEN:true} + token: ${PICSURE_APPLICATION_TOKEN:} + header-name: X-Application-Token + +server: + port: ${SERVER_PORT:8080} + servlet: + context-path: /operations + +management: + endpoints: + web: + exposure: + # OFF BY DEFAULT: 'none' is a sentinel that matches no endpoint, so /actuator/** is 404. (An EMPTY include is + # NOT off -- Spring Boot then falls back to exposing health.) AIO enables it via PICSURE_ACTUATOR_EXPOSURE; + # prometheus/metrics are added via the same var in the monitoring (M2) rollout. + include: ${PICSURE_ACTUATOR_EXPOSURE:none} + endpoint: + health: + show-details: ${PICSURE_ACTUATOR_DETAILS:never} # default never; when_authorized (AIO) gates detail behind picsure.actuator.token + probes: + enabled: true # /actuator/health/liveness stays shallow-open + group: + # Explicit liveness group (mirrors the gateway's) -- pins /actuator/health/liveness to the app's + # own process state so it never depends on the datasource or auto-registration nuances of probes.enabled. + liveness: + include: livenessState + # Deep health: readiness is only reported UP once the datasource is actually reachable, not merely once the + # process is running (mirrors the gateway's liveness/readiness split, adapted here for a service that -- + # unlike the gateway -- owns a real database dependency). + readiness: + include: readinessState,db + health: + defaults: + enabled: true + prometheus: + metrics: + export: + enabled: true diff --git a/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/OperationsApplicationTest.java b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/OperationsApplicationTest.java new file mode 100644 index 000000000..e1eb2a60c --- /dev/null +++ b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/OperationsApplicationTest.java @@ -0,0 +1,56 @@ +package edu.harvard.hms.dbmi.avillach.operations; + +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.UUID; + +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.transaction.annotation.Transactional; + +import edu.harvard.hms.dbmi.avillach.operations.configuration.Configuration; +import edu.harvard.hms.dbmi.avillach.operations.configuration.ConfigurationRepository; +import edu.harvard.hms.dbmi.avillach.operations.dataset.NamedDatasetRepository; +import edu.harvard.hms.dbmi.avillach.operations.query.QueryRepository; + +/** + * Smoke test: boots the full Spring context against H2 (see src/test/resources/application.yml) and proves that (1) the application context + * loads at all -- including the security configuration (WebSecurityConfig, GatewayPrivilegesFilter) and the web MVC configuration + * (GatewayUserArgumentResolver) -- and (2) the JPA entities and repositories, co-located under this application's base package, are + * correctly detected and wired. + */ +@SpringBootTest +class OperationsApplicationTest { + + @Autowired + private ConfigurationRepository configurationRepository; + + @Autowired + private NamedDatasetRepository namedDatasetRepository; + + @Autowired + private QueryRepository queryRepository; + + @Test + void contextLoadsWithApiDataRepositoriesWired() { + assertThat(configurationRepository).isNotNull(); + assertThat(namedDatasetRepository).isNotNull(); + assertThat(queryRepository).isNotNull(); + } + + @Test + @Transactional + void apiDataRepositoriesCanRoundTripAgainstTheRealEntityTables() { + // A real save -> reload round trip (not just a non-null bean / always-true count check) -- proves the + // naming-strategy override and entity scan actually produced a working JPA mapping against the H2-backed + // schema, not merely that Spring wired *some* proxy. + String uniqueName = "smoke-test-" + UUID.randomUUID(); + Configuration saved = configurationRepository.save(new Configuration().setName(uniqueName).setKind("smoke-test")); + + Configuration reloaded = configurationRepository.findById(saved.getUuid()).orElseThrow(); + + assertThat(reloaded.getName()).isEqualTo(uniqueName); + assertThat(reloaded.getKind()).isEqualTo("smoke-test"); + } +} diff --git a/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/config/ActuatorSecurityConfigTest.java b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/config/ActuatorSecurityConfigTest.java new file mode 100644 index 000000000..65e01b83b --- /dev/null +++ b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/config/ActuatorSecurityConfigTest.java @@ -0,0 +1,86 @@ +package edu.harvard.hms.dbmi.avillach.operations.config; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status; + +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.actuate.observability.AutoConfigureObservability; +import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.MediaType; +import org.springframework.test.context.TestPropertySource; +import org.springframework.test.web.servlet.MockMvc; +import org.springframework.test.web.servlet.MvcResult; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; + +/** + * Proves the {@code ActuatorSecurityConfig} chain (order 0) and the pre-existing {@link WebSecurityConfig} main chain (order 10) coexist on + * operations-service: the actuator chain owns {@code /actuator/**} (shallow health open, detail/prometheus gated by + * {@code X-Application-Token}) while the main chain's {@code SUPER_ADMIN} rule on {@code /configuration/admin/**} is untouched. + * + *

    {@code src/test/resources/application.yml} is a self-contained test config (H2 datasource, etc.) that Spring Boot's classpath config + * loading resolves INSTEAD OF (not merged with) {@code src/main/resources/application.yml} -- test-classes precedes classes on the Surefire + * classpath, and {@code classpath:/application.yml} resolves to a single resource. The production {@code management.*}/ + * {@code picsure.actuator.*} block therefore never reaches this test context, so this class supplies the equivalent settings itself via + * {@code @TestPropertySource} rather than relying on the (shadowed) main resource file. + */ +@SpringBootTest +@AutoConfigureMockMvc +@AutoConfigureObservability // prometheus export is disabled by default in @SpringBootTest contexts +@TestPropertySource( + properties = {"picsure.actuator.require-token=true", "picsure.actuator.token=ops-secret", + "management.endpoints.web.exposure.include=health,info,prometheus,metrics", + "management.endpoint.health.show-details=when_authorized", "management.endpoint.health.probes.enabled=true", + "management.endpoint.health.group.liveness.include=livenessState", + "management.endpoint.health.group.readiness.include=readinessState,db"} +) +class ActuatorSecurityConfigTest { + + @Autowired + private MockMvc mockMvc; + + private final ObjectMapper json = new ObjectMapper(); + + @Test + void healthIsOpenAndShallowWithoutToken() throws Exception { + MvcResult res = mockMvc.perform(get("/actuator/health")).andExpect(status().isOk()).andReturn(); + JsonNode body = json.readTree(res.getResponse().getContentAsString()); + assertThat(body.has("status")).isTrue(); + assertThat(body.has("components")).isFalse(); + } + + @Test + void livenessIsOpenWithoutToken() throws Exception { + mockMvc.perform(get("/actuator/health/liveness")).andExpect(status().isOk()); + } + + @Test + void healthRevealsComponentDetailWithValidToken() throws Exception { + MvcResult res = + mockMvc.perform(get("/actuator/health").header("X-Application-Token", "ops-secret")).andExpect(status().isOk()).andReturn(); + JsonNode body = json.readTree(res.getResponse().getContentAsString()); + assertThat(body.has("components")).isTrue(); + } + + @Test + void prometheusRejectedWithoutToken() throws Exception { + mockMvc.perform(get("/actuator/prometheus")).andExpect(status().isUnauthorized()); + } + + @Test + void prometheusOkWithToken() throws Exception { + mockMvc.perform(get("/actuator/prometheus").header("X-Application-Token", "ops-secret")).andExpect(status().isOk()); + } + + /** Coexistence: the main chain's SUPER_ADMIN gate on /configuration/admin/** must be unaffected by the actuator chain. */ + @Test + void adminEndpointStillRequiresSuperAdminAlongsideActuatorChain() throws Exception { + mockMvc.perform(post("/configuration/admin").contentType(MediaType.APPLICATION_JSON).content("{}")) + .andExpect(status().isForbidden()); + } +} diff --git a/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/config/GatewayPrivilegesFilterTest.java b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/config/GatewayPrivilegesFilterTest.java new file mode 100644 index 000000000..649efa7c9 --- /dev/null +++ b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/config/GatewayPrivilegesFilterTest.java @@ -0,0 +1,69 @@ +package edu.harvard.hms.dbmi.avillach.operations.config; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.verify; +import static org.mockito.Mockito.when; + +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.Test; +import org.springframework.security.core.Authentication; +import org.springframework.security.core.context.SecurityContextHolder; + +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import jakarta.servlet.FilterChain; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +class GatewayPrivilegesFilterTest { + + private final GatewayPrivilegesFilter filter = new GatewayPrivilegesFilter(); + + @AfterEach + void clear() { + SecurityContextHolder.clearContext(); + } + + @Test + void mapsPrivilegesHeaderToAuthoritiesWhenUserIdPresent() throws Exception { + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getHeader(GatewayUserResolver.HEADER_USER_ID)).thenReturn("auth0|abc123"); + when(req.getHeader(GatewayUserResolver.HEADER_USER_PRIVILEGES)).thenReturn("SUPER_ADMIN,USER"); + FilterChain chain = mock(FilterChain.class); + + filter.doFilter(req, mock(HttpServletResponse.class), chain); + + Authentication auth = SecurityContextHolder.getContext().getAuthentication(); + assertThat(auth).isNotNull(); + assertThat(auth.isAuthenticated()).isTrue(); + assertThat(auth.getName()).isEqualTo("auth0|abc123"); + assertThat(auth.getAuthorities()).extracting("authority").containsExactlyInAnyOrder("SUPER_ADMIN", "USER"); + verify(chain).doFilter(any(), any()); + } + + @Test + void noPrivilegesHeaderStillAuthenticatesWithNoAuthoritiesWhenUserIdPresent() throws Exception { + HttpServletRequest req = mock(HttpServletRequest.class); + when(req.getHeader(GatewayUserResolver.HEADER_USER_ID)).thenReturn("auth0|abc123"); + FilterChain chain = mock(FilterChain.class); + + filter.doFilter(req, mock(HttpServletResponse.class), chain); + + Authentication auth = SecurityContextHolder.getContext().getAuthentication(); + assertThat(auth).isNotNull(); + assertThat(auth.getAuthorities()).isEmpty(); + verify(chain).doFilter(any(), any()); + } + + @Test + void noUserIdHeaderLeavesContextAnonymous() throws Exception { + HttpServletRequest req = mock(HttpServletRequest.class); + FilterChain chain = mock(FilterChain.class); + + filter.doFilter(req, mock(HttpServletResponse.class), chain); + + assertThat(SecurityContextHolder.getContext().getAuthentication()).isNull(); + verify(chain).doFilter(any(), any()); + } +} diff --git a/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/config/InternalTokenFilterConfigTest.java b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/config/InternalTokenFilterConfigTest.java new file mode 100644 index 000000000..dbfc95e64 --- /dev/null +++ b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/config/InternalTokenFilterConfigTest.java @@ -0,0 +1,26 @@ +package edu.harvard.hms.dbmi.avillach.operations.config; + +import static org.assertj.core.api.Assertions.assertThat; + +import org.junit.jupiter.api.Test; +import org.springframework.boot.web.servlet.FilterRegistrationBean; + +import edu.harvard.hms.dbmi.avillach.operations.query.InternalTokenFilter; + +/** + * Pure unit test for the {@link InternalTokenFilterConfig} bean method itself: proves the registration is scoped to the container-level + * {@code /internal/*} URL pattern (not the default {@code /*}), which is the actual fix for path-gating that used to rely solely on + * {@code InternalTokenFilter#shouldNotFilter} comparing the raw request URI. + */ +class InternalTokenFilterConfigTest { + + @Test + void registersTheFilterScopedToInternalUrlPatternOnly() { + InternalTokenFilterConfig config = new InternalTokenFilterConfig(); + + FilterRegistrationBean registration = config.internalTokenFilter("secret"); + + assertThat(registration.getUrlPatterns()).containsExactly("/internal/*"); + assertThat(registration.getFilter()).isInstanceOf(InternalTokenFilter.class); + } +} diff --git a/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationControllerTest.java b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationControllerTest.java new file mode 100644 index 000000000..65791b31e --- /dev/null +++ b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationControllerTest.java @@ -0,0 +1,182 @@ +package edu.harvard.hms.dbmi.avillach.operations.configuration; + +import static org.hamcrest.Matchers.hasSize; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.delete; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.patch; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.jsonPath; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status; + +import java.util.UUID; + +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.MediaType; +import org.springframework.test.web.servlet.MockMvc; +import org.springframework.transaction.annotation.Transactional; + +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; + +/** + * Full-context MockMvc test: exercises the real {@link edu.harvard.hms.dbmi.avillach.operations.config.WebSecurityConfig} filter chain (not + * a mocked security layer), so SUPER_ADMIN enforcement is proven end-to-end. Requests simulate the gateway by setting the {@code X-User-*} + * headers {@link GatewayUserResolver} reads -- there is no login/session in this service. + * + *

    {@code @Transactional} wraps each test method (and the in-thread MockMvc dispatch) in a transaction rolled back afterward, so + * configuration rows created by one test don't leak into the next. + */ +@SpringBootTest +@AutoConfigureMockMvc +@Transactional +class ConfigurationControllerTest { + + @Autowired + private MockMvc mockMvc; + + @Autowired + private ConfigurationRepository repo; + + @Test + void publicListWorksUnauthenticated() throws Exception { + repo.save(new Configuration().setName("feature-x").setKind("ui")); + + mockMvc.perform(get("/configuration")).andExpect(status().isOk()).andExpect(jsonPath("$", hasSize(1))) + .andExpect(jsonPath("$[0].name").value("feature-x")); + } + + @Test + void publicListFiltersByKind() throws Exception { + repo.save(new Configuration().setName("feature-x").setKind("ui")); + repo.save(new Configuration().setName("feature-y").setKind("backend")); + + mockMvc.perform(get("/configuration").param("kind", "ui")).andExpect(status().isOk()).andExpect(jsonPath("$", hasSize(1))) + .andExpect(jsonPath("$[0].kind").value("ui")); + } + + @Test + void publicGetByUuidWorksUnauthenticated() throws Exception { + Configuration saved = repo.save(new Configuration().setName("feature-x").setKind("ui")); + + mockMvc.perform(get("/configuration/{id}", saved.getUuid())).andExpect(status().isOk()) + .andExpect(jsonPath("$.name").value("feature-x")); + } + + @Test + void publicGetByNameWorksUnauthenticated() throws Exception { + repo.save(new Configuration().setName("feature-x").setKind("ui")); + + mockMvc.perform(get("/configuration/{id}", "feature-x")).andExpect(status().isOk()).andExpect(jsonPath("$.kind").value("ui")); + } + + @Test + void publicGetUnknownIdentifierReturns404() throws Exception { + mockMvc.perform(get("/configuration/{id}", "does-not-exist")).andExpect(status().isNotFound()) + .andExpect(jsonPath("$.errorType").value("not_found")); + } + + @Test + void adminCreateWithoutSuperAdminIsForbidden() throws Exception { + mockMvc.perform( + post("/configuration/admin").contentType(MediaType.APPLICATION_JSON) + .content("{\"name\":\"A\",\"kind\":\"ui\",\"value\":\"true\"}") + ).andExpect(status().isForbidden()); + } + + @Test + void adminCreateAsPlainAuthenticatedUserIsForbidden() throws Exception { + mockMvc.perform( + post("/configuration/admin").header(GatewayUserResolver.HEADER_USER_ID, "auth0|abc") + .header(GatewayUserResolver.HEADER_USER_PRIVILEGES, "USER").contentType(MediaType.APPLICATION_JSON) + .content("{\"name\":\"A\",\"kind\":\"ui\",\"value\":\"true\"}") + ).andExpect(status().isForbidden()); + } + + @Test + void adminCreateAsSuperAdminSucceedsWith200AndBody() throws Exception { + mockMvc.perform( + post("/configuration/admin").header(GatewayUserResolver.HEADER_USER_ID, "auth0|abc") + .header(GatewayUserResolver.HEADER_USER_PRIVILEGES, "SUPER_ADMIN").contentType(MediaType.APPLICATION_JSON) + .content("{\"name\":\"A\",\"kind\":\"ui\",\"value\":\"true\",\"description\":\"desc\"}") + ).andExpect(status().isOk()).andExpect(jsonPath("$.name").value("A")).andExpect(jsonPath("$.uuid").exists()); + } + + @Test + void adminCreateMissingRequiredFieldReturns400() throws Exception { + mockMvc.perform( + post("/configuration/admin").header(GatewayUserResolver.HEADER_USER_ID, "auth0|abc") + .header(GatewayUserResolver.HEADER_USER_PRIVILEGES, "SUPER_ADMIN").contentType(MediaType.APPLICATION_JSON) + .content("{\"name\":\"A\",\"kind\":\"ui\"}") + ).andExpect(status().isBadRequest()); + } + + @Test + void adminCreateDuplicateNameKindReturns409() throws Exception { + repo.save(new Configuration().setName("A").setKind("ui").setValue("true")); + + mockMvc.perform( + post("/configuration/admin").header(GatewayUserResolver.HEADER_USER_ID, "auth0|abc") + .header(GatewayUserResolver.HEADER_USER_PRIVILEGES, "SUPER_ADMIN").contentType(MediaType.APPLICATION_JSON) + .content("{\"name\":\"A\",\"kind\":\"ui\",\"value\":\"false\"}") + ).andExpect(status().isConflict()).andExpect(jsonPath("$.errorType").value("conflict")); + } + + @Test + void adminUpdateWithoutSuperAdminIsForbidden() throws Exception { + Configuration saved = repo.save(new Configuration().setName("A").setKind("ui").setValue("true")); + + mockMvc.perform( + patch("/configuration/admin/{id}", saved.getUuid()).contentType(MediaType.APPLICATION_JSON).content("{\"value\":\"false\"}") + ).andExpect(status().isForbidden()); + } + + @Test + void adminUpdateAsSuperAdminAppliesPartialPatch() throws Exception { + Configuration saved = repo.save(new Configuration().setName("A").setKind("ui").setValue("true").setDescription("old")); + + mockMvc.perform( + patch("/configuration/admin/{id}", saved.getUuid()).header(GatewayUserResolver.HEADER_USER_ID, "auth0|abc") + .header(GatewayUserResolver.HEADER_USER_PRIVILEGES, "SUPER_ADMIN").contentType(MediaType.APPLICATION_JSON) + .content("{\"value\":\"false\"}") + ).andExpect(status().isOk()).andExpect(jsonPath("$.value").value("false")).andExpect(jsonPath("$.description").value("old")); + } + + @Test + void adminUpdateWithMismatchedBodyUuidReturns400() throws Exception { + Configuration saved = repo.save(new Configuration().setName("A").setKind("ui").setValue("true")); + + mockMvc.perform( + patch("/configuration/admin/{id}", saved.getUuid()).header(GatewayUserResolver.HEADER_USER_ID, "auth0|abc") + .header(GatewayUserResolver.HEADER_USER_PRIVILEGES, "SUPER_ADMIN").contentType(MediaType.APPLICATION_JSON) + .content("{\"uuid\":\"" + UUID.randomUUID() + "\",\"value\":\"false\"}") + ).andExpect(status().isBadRequest()); + } + + @Test + void adminUpdateMissingReturns404() throws Exception { + mockMvc.perform( + patch("/configuration/admin/{id}", UUID.randomUUID()).header(GatewayUserResolver.HEADER_USER_ID, "auth0|abc") + .header(GatewayUserResolver.HEADER_USER_PRIVILEGES, "SUPER_ADMIN").contentType(MediaType.APPLICATION_JSON) + .content("{\"value\":\"false\"}") + ).andExpect(status().isNotFound()); + } + + @Test + void adminDeleteWithoutSuperAdminIsForbidden() throws Exception { + Configuration saved = repo.save(new Configuration().setName("A").setKind("ui").setValue("true")); + + mockMvc.perform(delete("/configuration/admin/{id}", saved.getUuid())).andExpect(status().isForbidden()); + } + + @Test + void adminDeleteAsSuperAdminReturns200WithDeletedBody() throws Exception { + Configuration saved = repo.save(new Configuration().setName("A").setKind("ui").setValue("true")); + + mockMvc.perform( + delete("/configuration/admin/{id}", saved.getUuid()).header(GatewayUserResolver.HEADER_USER_ID, "auth0|abc") + .header(GatewayUserResolver.HEADER_USER_PRIVILEGES, "SUPER_ADMIN") + ).andExpect(status().isOk()).andExpect(jsonPath("$.name").value("A")); + } +} diff --git a/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationMapperTest.java b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationMapperTest.java new file mode 100644 index 000000000..32e67a005 --- /dev/null +++ b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationMapperTest.java @@ -0,0 +1,58 @@ +package edu.harvard.hms.dbmi.avillach.operations.configuration; + +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.UUID; + +import org.junit.jupiter.api.Test; + + +class ConfigurationMapperTest { + + private final ConfigurationMapper mapper = new ConfigurationMapper(); + + @Test + void toDtoCopiesAllFields() { + UUID id = UUID.randomUUID(); + Configuration config = + new Configuration().setName("A").setKind("ui").setValue("true").setDescription("desc").setMarkForDelete(true); + config.setUuid(id); + + ConfigurationDto dto = mapper.toDto(config); + + assertThat(dto.uuid()).isEqualTo(id); + assertThat(dto.name()).isEqualTo("A"); + assertThat(dto.kind()).isEqualTo("ui"); + assertThat(dto.value()).isEqualTo("true"); + assertThat(dto.description()).isEqualTo("desc"); + assertThat(dto.markForDelete()).isTrue(); + } + + @Test + void toEntityBuildsFreshEntityFromRequest() { + ConfigurationRequestDto req = new ConfigurationRequestDto(null, "A", "ui", "true", "desc", false); + + Configuration config = mapper.toEntity(req); + + assertThat(config.getName()).isEqualTo("A"); + assertThat(config.getKind()).isEqualTo("ui"); + assertThat(config.getValue()).isEqualTo("true"); + assertThat(config.getDescription()).isEqualTo("desc"); + assertThat(config.getMarkForDelete()).isFalse(); + } + + @Test + void applyPatchOnlyChangesNonNullFields() { + Configuration existing = + new Configuration().setName("A").setKind("ui").setValue("old").setDescription("old-desc").setMarkForDelete(false); + + ConfigurationRequestDto patch = new ConfigurationRequestDto(null, null, null, "new-value", null, null); + mapper.applyPatch(existing, patch); + + assertThat(existing.getName()).isEqualTo("A"); + assertThat(existing.getKind()).isEqualTo("ui"); + assertThat(existing.getValue()).isEqualTo("new-value"); + assertThat(existing.getDescription()).isEqualTo("old-desc"); + assertThat(existing.getMarkForDelete()).isFalse(); + } +} diff --git a/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationServiceTest.java b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationServiceTest.java new file mode 100644 index 000000000..7c6214153 --- /dev/null +++ b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/configuration/ConfigurationServiceTest.java @@ -0,0 +1,179 @@ +package edu.harvard.hms.dbmi.avillach.operations.configuration; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.junit.jupiter.api.Assertions.assertThrows; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.never; +import static org.mockito.Mockito.verify; +import static org.mockito.Mockito.when; + +import java.util.List; +import java.util.Optional; +import java.util.UUID; + +import org.junit.jupiter.api.Test; +import org.springframework.dao.DataIntegrityViolationException; +import org.springframework.http.HttpStatus; + +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; + +/** + * Note: the plan brief this task was ported from assumed a {@code PicsureNotFoundException} subclass and an {@code ex.status()}-style + * accessor. Neither exists in the actual {@code pic-sure-spring-commons} built for this monorepo (it ships only the single public + * {@link PicsureException}, carrying status via {@code getStatus()}) -- so every not-found case here asserts {@code PicsureException} with + * {@code HttpStatus.NOT_FOUND}, consistent with how the 409 duplicate case is already expressed. + */ +class ConfigurationServiceTest { + + ConfigurationRepository repo = mock(ConfigurationRepository.class); + ConfigurationMapper mapper = new ConfigurationMapper(); + ConfigurationService service = new ConfigurationService(repo, mapper); + + @Test + void listAllWhenNoKind() { + Configuration c = new Configuration().setName("A").setKind("ui"); + c.setUuid(UUID.randomUUID()); + when(repo.findAll()).thenReturn(List.of(c)); + assertThat(service.getConfigurations(null)).hasSize(1); + verify(repo).findAll(); + verify(repo, never()).findByKind(any()); + } + + @Test + void listByKindWhenKindGiven() { + when(repo.findByKind("ui")).thenReturn(List.of()); + service.getConfigurations("ui"); + verify(repo).findByKind("ui"); + } + + @Test + void getByIdentifierResolvesUuid() { + UUID id = UUID.randomUUID(); + Configuration c = new Configuration().setName("A").setKind("ui"); + c.setUuid(id); + when(repo.findById(id)).thenReturn(Optional.of(c)); + assertThat(service.getByIdentifier(id.toString()).uuid()).isEqualTo(id); + } + + @Test + void getByIdentifierFallsBackToName() { + when(repo.findByName("FEATURE_X")).thenReturn(List.of(new Configuration().setName("FEATURE_X").setKind("ui"))); + assertThat(service.getByIdentifier("FEATURE_X").name()).isEqualTo("FEATURE_X"); + } + + @Test + void getByIdentifierNotFoundThrows404() { + when(repo.findByName("nope")).thenReturn(List.of()); + PicsureException ex = assertThrows(PicsureException.class, () -> service.getByIdentifier("nope")); + assertThat(ex.getStatus()).isEqualTo(HttpStatus.NOT_FOUND); + } + + @Test + void createRejectsDuplicateNameKind() { + when(repo.findByNameAndKind("A", "ui")).thenReturn(Optional.of(new Configuration().setName("A").setKind("ui"))); + ConfigurationRequestDto req = new ConfigurationRequestDto(null, "A", "ui", "true", null, null); + PicsureException ex = assertThrows(PicsureException.class, () -> service.create(req)); + assertThat(ex.getStatus()).isEqualTo(HttpStatus.CONFLICT); + } + + @Test + void createPersistsAndReturnsDto() { + when(repo.findByNameAndKind("A", "ui")).thenReturn(Optional.empty()); + when(repo.saveAndFlush(any())).thenAnswer(inv -> { + Configuration c = inv.getArgument(0); + c.setUuid(UUID.randomUUID()); + return c; + }); + ConfigurationRequestDto req = new ConfigurationRequestDto(null, "A", "ui", "true", "desc", false); + ConfigurationDto dto = service.create(req); + assertThat(dto.name()).isEqualTo("A"); + assertThat(dto.value()).isEqualTo("true"); + } + + @Test + void createRaceLostToConcurrentDuplicateThrows409() { + when(repo.findByNameAndKind("A", "ui")).thenReturn(Optional.empty()); + when(repo.saveAndFlush(any())).thenThrow(new DataIntegrityViolationException("unique_name_kind")); + + ConfigurationRequestDto req = new ConfigurationRequestDto(null, "A", "ui", "true", null, null); + PicsureException ex = assertThrows(PicsureException.class, () -> service.create(req)); + + assertThat(ex.getStatus()).isEqualTo(HttpStatus.CONFLICT); + } + + @Test + void updateMissingThrows404() { + UUID id = UUID.randomUUID(); + when(repo.findById(id)).thenReturn(Optional.empty()); + PicsureException ex = + assertThrows(PicsureException.class, () -> service.update(id, new ConfigurationRequestDto(null, "A", "ui", "v", null, null))); + assertThat(ex.getStatus()).isEqualTo(HttpStatus.NOT_FOUND); + } + + @Test + void updateRejectsClashWithAnotherRow() { + UUID id = UUID.randomUUID(); + UUID otherId = UUID.randomUUID(); + Configuration existing = new Configuration().setName("A").setKind("ui"); + existing.setUuid(id); + Configuration other = new Configuration().setName("B").setKind("ui"); + other.setUuid(otherId); + when(repo.findById(id)).thenReturn(Optional.of(existing)); + when(repo.findByNameAndKind("B", "ui")).thenReturn(Optional.of(other)); + + PicsureException ex = + assertThrows(PicsureException.class, () -> service.update(id, new ConfigurationRequestDto(null, "B", "ui", null, null, null))); + assertThat(ex.getStatus()).isEqualTo(HttpStatus.CONFLICT); + } + + @Test + void updateRaceLostToConcurrentDuplicateThrows409() { + UUID id = UUID.randomUUID(); + Configuration existing = new Configuration().setName("A").setKind("ui"); + existing.setUuid(id); + when(repo.findById(id)).thenReturn(Optional.of(existing)); + when(repo.findByNameAndKind("B", "ui")).thenReturn(Optional.empty()); + when(repo.saveAndFlush(any())).thenThrow(new DataIntegrityViolationException("unique_name_kind")); + + PicsureException ex = + assertThrows(PicsureException.class, () -> service.update(id, new ConfigurationRequestDto(null, "B", "ui", null, null, null))); + + assertThat(ex.getStatus()).isEqualTo(HttpStatus.CONFLICT); + } + + @Test + void updateAllowsKeepingItsOwnNameAndKind() { + UUID id = UUID.randomUUID(); + Configuration existing = new Configuration().setName("A").setKind("ui").setValue("old"); + existing.setUuid(id); + when(repo.findById(id)).thenReturn(Optional.of(existing)); + when(repo.findByNameAndKind("A", "ui")).thenReturn(Optional.of(existing)); + when(repo.saveAndFlush(any())).thenAnswer(inv -> inv.getArgument(0)); + + ConfigurationDto dto = service.update(id, new ConfigurationRequestDto(null, "A", "ui", "new", null, null)); + + assertThat(dto.value()).isEqualTo("new"); + } + + @Test + void deleteMissingThrows404() { + UUID id = UUID.randomUUID(); + when(repo.findById(id)).thenReturn(Optional.empty()); + PicsureException ex = assertThrows(PicsureException.class, () -> service.delete(id)); + assertThat(ex.getStatus()).isEqualTo(HttpStatus.NOT_FOUND); + } + + @Test + void deleteReturnsDeletedConfiguration() { + UUID id = UUID.randomUUID(); + Configuration existing = new Configuration().setName("A").setKind("ui"); + existing.setUuid(id); + when(repo.findById(id)).thenReturn(Optional.of(existing)); + + ConfigurationDto dto = service.delete(id); + + assertThat(dto.uuid()).isEqualTo(id); + verify(repo).delete(existing); + } +} diff --git a/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetControllerTest.java b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetControllerTest.java new file mode 100644 index 000000000..db04e8f6c --- /dev/null +++ b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetControllerTest.java @@ -0,0 +1,199 @@ +package edu.harvard.hms.dbmi.avillach.operations.dataset; + +import static org.hamcrest.Matchers.hasSize; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.delete; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.put; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.jsonPath; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status; + +import java.util.UUID; + +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.MediaType; +import org.springframework.test.web.servlet.MockMvc; +import org.springframework.transaction.annotation.Transactional; + +import edu.harvard.hms.dbmi.avillach.commons.identity.GatewayUserResolver; +import edu.harvard.hms.dbmi.avillach.operations.query.Query; +import edu.harvard.hms.dbmi.avillach.operations.query.QueryRepository; + +/** + * Full-context MockMvc test: exercises the real {@link edu.harvard.hms.dbmi.avillach.operations.config.WebSecurityConfig} filter chain (not + * a mocked security layer), so the "/dataset/** requires an authenticated caller" rule is proven end-to-end, same style as + * {@code ConfigurationControllerTest}. Requests simulate the gateway by setting the {@code X-User-*} headers {@link GatewayUserResolver} + * reads -- there is no login/session in this service. Email is the owner key throughout, never userId. + */ +@SpringBootTest +@AutoConfigureMockMvc +@Transactional +class NamedDatasetControllerTest { + + private static final String ALICE = "alice@example.com"; + private static final String BOB = "bob@example.com"; + + @Autowired + private MockMvc mockMvc; + + @Autowired + private NamedDatasetRepository namedDatasetRepo; + + @Autowired + private QueryRepository queryRepo; + + @Test + void listWithoutIdentityIsForbidden() throws Exception { + mockMvc.perform(get("/dataset/named")).andExpect(status().isForbidden()); + } + + @Test + void listReturnsOnlyCallersDatasets() throws Exception { + Query aliceQuery = queryRepo.save(new Query()); + Query bobQuery = queryRepo.save(new Query()); + namedDatasetRepo.save(new NamedDataset().setUser(ALICE).setName("alice-1").setQuery(aliceQuery)); + namedDatasetRepo.save(new NamedDataset().setUser(BOB).setName("bob-1").setQuery(bobQuery)); + + mockMvc.perform( + get("/dataset/named").header(GatewayUserResolver.HEADER_USER_ID, "auth0|alice") + .header(GatewayUserResolver.HEADER_USER_EMAIL, ALICE) + ).andExpect(status().isOk()).andExpect(jsonPath("$", hasSize(1))).andExpect(jsonPath("$[0].name").value("alice-1")); + } + + @Test + void createPersistsUnderCallersEmailAndReturns201() throws Exception { + Query query = queryRepo.save(new Query()); + + mockMvc + .perform( + post("/dataset/named").header(GatewayUserResolver.HEADER_USER_ID, "auth0|alice") + .header(GatewayUserResolver.HEADER_USER_EMAIL, ALICE).contentType(MediaType.APPLICATION_JSON) + .content("{\"queryId\":\"" + query.getUuid() + "\",\"name\":\"my dataset\"}") + ).andExpect(status().isCreated()).andExpect(jsonPath("$.name").value("my dataset")).andExpect(jsonPath("$.uuid").exists()) + .andExpect(jsonPath("$.queryId").value(query.getUuid().toString())); + } + + @Test + void createWithUnknownQueryReturns404() throws Exception { + mockMvc.perform( + post("/dataset/named").header(GatewayUserResolver.HEADER_USER_ID, "auth0|alice") + .header(GatewayUserResolver.HEADER_USER_EMAIL, ALICE).contentType(MediaType.APPLICATION_JSON) + .content("{\"queryId\":\"" + UUID.randomUUID() + "\",\"name\":\"my dataset\"}") + ).andExpect(status().isNotFound()); + } + + @Test + void createSecondDatasetOverSameQueryAndUserReturns409() throws Exception { + Query query = queryRepo.save(new Query()); + + mockMvc.perform( + post("/dataset/named").header(GatewayUserResolver.HEADER_USER_ID, "auth0|alice") + .header(GatewayUserResolver.HEADER_USER_EMAIL, ALICE).contentType(MediaType.APPLICATION_JSON) + .content("{\"queryId\":\"" + query.getUuid() + "\",\"name\":\"first\"}") + ).andExpect(status().isCreated()); + + mockMvc.perform( + post("/dataset/named").header(GatewayUserResolver.HEADER_USER_ID, "auth0|alice") + .header(GatewayUserResolver.HEADER_USER_EMAIL, ALICE).contentType(MediaType.APPLICATION_JSON) + .content("{\"queryId\":\"" + query.getUuid() + "\",\"name\":\"second\"}") + ).andExpect(status().isConflict()); + } + + @Test + void createWithMissingNameReturns400() throws Exception { + Query query = queryRepo.save(new Query()); + + mockMvc.perform( + post("/dataset/named").header(GatewayUserResolver.HEADER_USER_ID, "auth0|alice") + .header(GatewayUserResolver.HEADER_USER_EMAIL, ALICE).contentType(MediaType.APPLICATION_JSON) + .content("{\"queryId\":\"" + query.getUuid() + "\"}") + ).andExpect(status().isBadRequest()); + } + + @Test + void getOwnDatasetSucceeds() throws Exception { + Query query = queryRepo.save(new Query()); + NamedDataset saved = namedDatasetRepo.save(new NamedDataset().setUser(ALICE).setName("mine").setQuery(query)); + + mockMvc.perform( + get("/dataset/named/{id}", saved.getUuid()).header(GatewayUserResolver.HEADER_USER_ID, "auth0|alice") + .header(GatewayUserResolver.HEADER_USER_EMAIL, ALICE) + ).andExpect(status().isOk()).andExpect(jsonPath("$.name").value("mine")); + } + + @Test + void getAnotherUsersDatasetReturns404() throws Exception { + Query query = queryRepo.save(new Query()); + NamedDataset saved = namedDatasetRepo.save(new NamedDataset().setUser(BOB).setName("bobs").setQuery(query)); + + mockMvc.perform( + get("/dataset/named/{id}", saved.getUuid()).header(GatewayUserResolver.HEADER_USER_ID, "auth0|alice") + .header(GatewayUserResolver.HEADER_USER_EMAIL, ALICE) + ).andExpect(status().isNotFound()); + } + + @Test + void updateOwnDatasetSucceeds() throws Exception { + Query query = queryRepo.save(new Query()); + NamedDataset saved = namedDatasetRepo.save(new NamedDataset().setUser(ALICE).setName("old").setQuery(query)); + + mockMvc.perform( + put("/dataset/named/{id}", saved.getUuid()).header(GatewayUserResolver.HEADER_USER_ID, "auth0|alice") + .header(GatewayUserResolver.HEADER_USER_EMAIL, ALICE).contentType(MediaType.APPLICATION_JSON) + .content("{\"queryId\":\"" + query.getUuid() + "\",\"name\":\"new-name\",\"archived\":true}") + ).andExpect(status().isOk()).andExpect(jsonPath("$.name").value("new-name")).andExpect(jsonPath("$.archived").value(true)); + } + + @Test + void updateAnotherUsersDatasetReturns404() throws Exception { + Query query = queryRepo.save(new Query()); + NamedDataset saved = namedDatasetRepo.save(new NamedDataset().setUser(BOB).setName("bobs").setQuery(query)); + + mockMvc.perform( + put("/dataset/named/{id}", saved.getUuid()).header(GatewayUserResolver.HEADER_USER_ID, "auth0|alice") + .header(GatewayUserResolver.HEADER_USER_EMAIL, ALICE).contentType(MediaType.APPLICATION_JSON) + .content("{\"queryId\":\"" + query.getUuid() + "\",\"name\":\"hijacked\"}") + ).andExpect(status().isNotFound()); + } + + @Test + void deleteOwnDatasetReturns204() throws Exception { + Query query = queryRepo.save(new Query()); + NamedDataset saved = namedDatasetRepo.save(new NamedDataset().setUser(ALICE).setName("mine").setQuery(query)); + + mockMvc.perform( + delete("/dataset/named/{id}", saved.getUuid()).header(GatewayUserResolver.HEADER_USER_ID, "auth0|alice") + .header(GatewayUserResolver.HEADER_USER_EMAIL, ALICE) + ).andExpect(status().isNoContent()); + } + + @Test + void deleteAnotherUsersDatasetReturns404() throws Exception { + Query query = queryRepo.save(new Query()); + NamedDataset saved = namedDatasetRepo.save(new NamedDataset().setUser(BOB).setName("bobs").setQuery(query)); + + mockMvc.perform( + delete("/dataset/named/{id}", saved.getUuid()).header(GatewayUserResolver.HEADER_USER_ID, "auth0|alice") + .header(GatewayUserResolver.HEADER_USER_EMAIL, ALICE) + ).andExpect(status().isNotFound()); + } + + @Test + void queryBlobRoundTripsThroughTheLinkedNamedDataset() throws Exception { + Query query = new Query(); + query.setQuery("{\"consentGroups\":[\"phs000001\"]}"); + query = queryRepo.save(query); + NamedDataset saved = namedDatasetRepo.save(new NamedDataset().setUser(ALICE).setName("with-query").setQuery(query)); + + mockMvc.perform( + get("/dataset/named/{id}", saved.getUuid()).header(GatewayUserResolver.HEADER_USER_ID, "auth0|alice") + .header(GatewayUserResolver.HEADER_USER_EMAIL, ALICE) + ).andExpect(status().isOk()).andExpect(jsonPath("$.queryId").value(query.getUuid().toString())); + + Query reloaded = queryRepo.findById(query.getUuid()).orElseThrow(); + org.assertj.core.api.Assertions.assertThat(reloaded.getQuery()).isEqualTo("{\"consentGroups\":[\"phs000001\"]}"); + } +} diff --git a/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetMapperTest.java b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetMapperTest.java new file mode 100644 index 000000000..48026bd85 --- /dev/null +++ b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetMapperTest.java @@ -0,0 +1,60 @@ +package edu.harvard.hms.dbmi.avillach.operations.dataset; + +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.Map; +import java.util.UUID; + +import org.junit.jupiter.api.Test; + +import edu.harvard.hms.dbmi.avillach.operations.query.Query; + +class NamedDatasetMapperTest { + + private final NamedDatasetMapper mapper = new NamedDatasetMapper(); + + @Test + void toDtoCopiesAllFieldsIncludingQueryId() { + UUID datasetId = UUID.randomUUID(); + UUID queryId = UUID.randomUUID(); + Query query = new Query(); + query.setUuid(queryId); + NamedDataset entity = + new NamedDataset().setUser("alice@example.com").setName("d1").setQuery(query).setArchived(true).setMetadata(Map.of("k", "v")); + entity.setUuid(datasetId); + + NamedDatasetDto dto = mapper.toDto(entity); + + assertThat(dto.uuid()).isEqualTo(datasetId); + assertThat(dto.name()).isEqualTo("d1"); + assertThat(dto.queryId()).isEqualTo(queryId); + assertThat(dto.archived()).isTrue(); + assertThat(dto.metadata()).containsEntry("k", "v"); + } + + @Test + void toDtoHandlesNullQuery() { + NamedDataset entity = new NamedDataset().setUser("alice@example.com").setName("d1").setArchived(false); + entity.setUuid(UUID.randomUUID()); + + NamedDatasetDto dto = mapper.toDto(entity); + + assertThat(dto.queryId()).isNull(); + } + + @Test + void toEntityBuildsEntityFromRequestWithResolvedQueryAndUser() { + UUID queryId = UUID.randomUUID(); + Query query = new Query(); + query.setUuid(queryId); + NamedDatasetRequestDto req = new NamedDatasetRequestDto(queryId, "d2", true, Map.of("a", 1)); + + NamedDataset entity = mapper.toEntity("bob@example.com", query, req); + + assertThat(entity.getUser()).isEqualTo("bob@example.com"); + assertThat(entity.getQuery()).isSameAs(query); + assertThat(entity.getName()).isEqualTo("d2"); + assertThat(entity.getArchived()).isTrue(); + assertThat(entity.getMetadata()).containsEntry("a", 1); + } +} diff --git a/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetServiceTest.java b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetServiceTest.java new file mode 100644 index 000000000..f5ecd0d56 --- /dev/null +++ b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/dataset/NamedDatasetServiceTest.java @@ -0,0 +1,210 @@ +package edu.harvard.hms.dbmi.avillach.operations.dataset; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.junit.jupiter.api.Assertions.assertThrows; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.verify; +import static org.mockito.Mockito.when; + +import java.util.List; +import java.util.Optional; +import java.util.UUID; + +import org.junit.jupiter.api.Test; +import org.springframework.dao.DataIntegrityViolationException; +import org.springframework.http.HttpStatus; + +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; +import edu.harvard.hms.dbmi.avillach.operations.query.Query; +import edu.harvard.hms.dbmi.avillach.operations.query.QueryRepository; + +/** + * Note: a dedicated {@code PicsureNotFoundException} subclass might be expected here, but none exists in the actual + * {@code pic-sure-spring-commons} built for this monorepo (it ships only the single public {@link PicsureException}, carrying status via + * {@code getStatus()}) -- so every not-found case here asserts {@code PicsureException} with {@code HttpStatus.NOT_FOUND}, consistent with + * how {@code ConfigurationService} already expresses its not-found cases. + * + *

    Cross-user access: {@code findByUuidAndUser} scopes the lookup at the SQL layer, so a caller reading/mutating another user's dataset + * gets exactly the same {@code PicsureException(NOT_FOUND)} as a genuinely-missing uuid -- there is no separate 403 branch, and existence + * is never leaked to a non-owning caller. + */ +class NamedDatasetServiceTest { + + NamedDatasetRepository repo = mock(NamedDatasetRepository.class); + QueryRepository queryRepo = mock(QueryRepository.class); + NamedDatasetMapper mapper = new NamedDatasetMapper(); + NamedDatasetService service = new NamedDatasetService(repo, queryRepo, mapper); + + @Test + void listsByUserEmail() { + Query q = new Query(); + q.setUuid(UUID.randomUUID()); + NamedDataset e = new NamedDataset().setUser("alice@example.com").setName("d1").setQuery(q); + e.setUuid(UUID.randomUUID()); + when(repo.findByUser("alice@example.com")).thenReturn(List.of(e)); + + List result = service.listForUser("alice@example.com"); + + assertThat(result).hasSize(1).extracting(NamedDatasetDto::name).containsExactly("d1"); + } + + @Test + void findByIdScopedToUserThrows404WhenAbsentOrNotOwned() { + UUID id = UUID.randomUUID(); + when(repo.findByUuidAndUser(id, "alice@example.com")).thenReturn(Optional.empty()); + + PicsureException ex = assertThrows(PicsureException.class, () -> service.getForUser("alice@example.com", id)); + + assertThat(ex.getStatus()).isEqualTo(HttpStatus.NOT_FOUND); + } + + @Test + void getForUserReturnsDtoWhenOwned() { + UUID id = UUID.randomUUID(); + NamedDataset e = new NamedDataset().setUser("alice@example.com").setName("d1"); + e.setUuid(id); + when(repo.findByUuidAndUser(id, "alice@example.com")).thenReturn(Optional.of(e)); + + NamedDatasetDto dto = service.getForUser("alice@example.com", id); + + assertThat(dto.name()).isEqualTo("d1"); + } + + @Test + void createResolvesQueryAndReturnsDto() { + UUID queryId = UUID.randomUUID(); + Query q = new Query(); + q.setUuid(queryId); + when(queryRepo.findById(queryId)).thenReturn(Optional.of(q)); + when(repo.saveAndFlush(any())).thenAnswer(inv -> { + NamedDataset e = inv.getArgument(0); + e.setUuid(UUID.randomUUID()); + return e; + }); + + NamedDatasetRequestDto req = new NamedDatasetRequestDto(queryId, "d2", false, null); + NamedDatasetDto dto = service.create("alice@example.com", req); + + assertThat(dto.name()).isEqualTo("d2"); + assertThat(dto.queryId()).isEqualTo(queryId); + } + + @Test + void createDuplicateQueryAndUserThrows409() { + UUID queryId = UUID.randomUUID(); + Query q = new Query(); + q.setUuid(queryId); + when(queryRepo.findById(queryId)).thenReturn(Optional.of(q)); + when(repo.saveAndFlush(any())).thenThrow(new DataIntegrityViolationException("unique_queryId_user")); + + NamedDatasetRequestDto req = new NamedDatasetRequestDto(queryId, "dup", false, null); + PicsureException ex = assertThrows(PicsureException.class, () -> service.create("alice@example.com", req)); + + assertThat(ex.getStatus()).isEqualTo(HttpStatus.CONFLICT); + } + + @Test + void createWithMissingQueryThrows404() { + UUID queryId = UUID.randomUUID(); + when(queryRepo.findById(queryId)).thenReturn(Optional.empty()); + NamedDatasetRequestDto req = new NamedDatasetRequestDto(queryId, "d3", false, null); + + PicsureException ex = assertThrows(PicsureException.class, () -> service.create("alice@example.com", req)); + + assertThat(ex.getStatus()).isEqualTo(HttpStatus.NOT_FOUND); + } + + @Test + void updateScopedToUserThrows404WhenNotOwned() { + UUID id = UUID.randomUUID(); + when(repo.findByUuidAndUser(id, "alice@example.com")).thenReturn(Optional.empty()); + NamedDatasetRequestDto req = new NamedDatasetRequestDto(UUID.randomUUID(), "renamed", false, null); + + PicsureException ex = assertThrows(PicsureException.class, () -> service.update("alice@example.com", id, req)); + + assertThat(ex.getStatus()).isEqualTo(HttpStatus.NOT_FOUND); + } + + @Test + void updateAppliesNameArchivedAndMetadata() { + UUID id = UUID.randomUUID(); + UUID queryId = UUID.randomUUID(); + Query q = new Query(); + q.setUuid(queryId); + NamedDataset existing = new NamedDataset().setUser("alice@example.com").setName("old").setQuery(q).setArchived(false); + existing.setUuid(id); + when(repo.findByUuidAndUser(id, "alice@example.com")).thenReturn(Optional.of(existing)); + when(repo.saveAndFlush(any())).thenAnswer(inv -> inv.getArgument(0)); + + NamedDatasetRequestDto req = new NamedDatasetRequestDto(queryId, "renamed", true, null); + NamedDatasetDto dto = service.update("alice@example.com", id, req); + + assertThat(dto.name()).isEqualTo("renamed"); + assertThat(dto.archived()).isTrue(); + } + + @Test + void updateResolvesNewQueryWhenQueryIdChanges() { + UUID id = UUID.randomUUID(); + UUID oldQueryId = UUID.randomUUID(); + UUID newQueryId = UUID.randomUUID(); + Query oldQuery = new Query(); + oldQuery.setUuid(oldQueryId); + Query newQuery = new Query(); + newQuery.setUuid(newQueryId); + NamedDataset existing = new NamedDataset().setUser("alice@example.com").setName("d1").setQuery(oldQuery); + existing.setUuid(id); + when(repo.findByUuidAndUser(id, "alice@example.com")).thenReturn(Optional.of(existing)); + when(queryRepo.findById(newQueryId)).thenReturn(Optional.of(newQuery)); + when(repo.saveAndFlush(any())).thenAnswer(inv -> inv.getArgument(0)); + + NamedDatasetRequestDto req = new NamedDatasetRequestDto(newQueryId, "d1", false, null); + NamedDatasetDto dto = service.update("alice@example.com", id, req); + + assertThat(dto.queryId()).isEqualTo(newQueryId); + } + + @Test + void updateRepointingToADuplicateQueryAndUserThrows409() { + UUID id = UUID.randomUUID(); + UUID oldQueryId = UUID.randomUUID(); + UUID newQueryId = UUID.randomUUID(); + Query oldQuery = new Query(); + oldQuery.setUuid(oldQueryId); + Query newQuery = new Query(); + newQuery.setUuid(newQueryId); + NamedDataset existing = new NamedDataset().setUser("alice@example.com").setName("d1").setQuery(oldQuery); + existing.setUuid(id); + when(repo.findByUuidAndUser(id, "alice@example.com")).thenReturn(Optional.of(existing)); + when(queryRepo.findById(newQueryId)).thenReturn(Optional.of(newQuery)); + when(repo.saveAndFlush(any())).thenThrow(new DataIntegrityViolationException("unique_queryId_user")); + + NamedDatasetRequestDto req = new NamedDatasetRequestDto(newQueryId, "d1", false, null); + PicsureException ex = assertThrows(PicsureException.class, () -> service.update("alice@example.com", id, req)); + + assertThat(ex.getStatus()).isEqualTo(HttpStatus.CONFLICT); + } + + @Test + void deleteScopedToUserThrows404WhenNotOwned() { + UUID id = UUID.randomUUID(); + when(repo.findByUuidAndUser(id, "alice@example.com")).thenReturn(Optional.empty()); + + PicsureException ex = assertThrows(PicsureException.class, () -> service.delete("alice@example.com", id)); + + assertThat(ex.getStatus()).isEqualTo(HttpStatus.NOT_FOUND); + } + + @Test + void deleteRemovesOwnedDataset() { + UUID id = UUID.randomUUID(); + NamedDataset existing = new NamedDataset().setUser("alice@example.com").setName("d1"); + existing.setUuid(id); + when(repo.findByUuidAndUser(id, "alice@example.com")).thenReturn(Optional.of(existing)); + + service.delete("alice@example.com", id); + + verify(repo).delete(existing); + } +} diff --git a/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/query/InternalQueryControllerTest.java b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/query/InternalQueryControllerTest.java new file mode 100644 index 000000000..31544f77f --- /dev/null +++ b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/query/InternalQueryControllerTest.java @@ -0,0 +1,158 @@ +package edu.harvard.hms.dbmi.avillach.operations.query; + +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.patch; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.jsonPath; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status; + +import java.util.UUID; + +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.MediaType; +import org.springframework.test.web.servlet.MockMvc; +import org.springframework.transaction.annotation.Transactional; + +import com.fasterxml.jackson.databind.ObjectMapper; + + +/** + * Full-context MockMvc test exercising the real {@code InternalTokenFilter} (registered by {@code InternalTokenFilterConfig} as a + * {@code FilterRegistrationBean} scoped to the {@code /internal/*} URL pattern) together with {@link InternalQueryController}, same posture + * as {@code NamedDatasetControllerTest}: no mocked security layer. {@code picsure.operations.internal-token} is set in + * {@code src/test/resources/application.yml}, so the "unconfigured token fail-closed" behavior itself is covered by the dedicated pure-unit + * {@code InternalTokenFilterTest} (constructing the filter directly with a blank token) rather than here. The context-path-robustness of + * the URL-pattern-based registration itself is covered separately by {@code InternalTokenFilterContextPathTest}. + */ +@SpringBootTest +@AutoConfigureMockMvc +@Transactional +class InternalQueryControllerTest { + + @Autowired + private MockMvc mockMvc; + + @Autowired + private QueryRepository queryRepo; + + @Value("${picsure.operations.internal-token}") + private String validToken; + + private static final ObjectMapper MAPPER = new ObjectMapper(); + + @Test + void missingTokenIsForbiddenWithTheExactErrorBody() throws Exception { + mockMvc.perform(get("/internal/queries/{id}", UUID.randomUUID())).andExpect(status().isForbidden()) + .andExpect(jsonPath("$.errorType").value("FORBIDDEN")).andExpect(jsonPath("$.message").value("Forbidden")) + .andExpect(jsonPath("$.requestId").exists()); + } + + @Test + void wrongTokenIsForbidden() throws Exception { + mockMvc.perform(get("/internal/queries/{id}", UUID.randomUUID()).header(InternalTokenFilter.HEADER, "wrong-token")) + .andExpect(status().isForbidden()); + } + + @Test + void saveWithValidTokenReturns201WithPicsureId() throws Exception { + mockMvc.perform( + post("/internal/queries").header(InternalTokenFilter.HEADER, validToken).contentType(MediaType.APPLICATION_JSON) + .content("{\"query\":\"{\\\"q\\\":1}\",\"status\":\"QUEUED\"}") + ).andExpect(status().isCreated()).andExpect(jsonPath("$.picsureId").exists()); + } + + @Test + void saveWithMalformedBase64MetadataReturns400() throws Exception { + mockMvc.perform( + post("/internal/queries").header(InternalTokenFilter.HEADER, validToken).contentType(MediaType.APPLICATION_JSON) + .content("{\"query\":\"{\\\"q\\\":1}\",\"status\":\"QUEUED\",\"metadata\":\"not-valid-base64!!!\"}") + ).andExpect(status().isBadRequest()); + } + + @Test + void saveThenGetRoundTripsWithValidToken() throws Exception { + String body = mockMvc.perform( + post("/internal/queries").header(InternalTokenFilter.HEADER, validToken).contentType(MediaType.APPLICATION_JSON) + .content("{\"query\":\"{\\\"q\\\":1}\",\"resourceResultId\":\"rr-1\",\"status\":\"QUEUED\",\"version\":\"7\"}") + ).andExpect(status().isCreated()).andReturn().getResponse().getContentAsString(); + + String picsureId = MAPPER.readTree(body).get("picsureId").asText(); + + mockMvc.perform(get("/internal/queries/{picsureId}", picsureId).header(InternalTokenFilter.HEADER, validToken)) + .andExpect(status().isOk()).andExpect(jsonPath("$.picsureId").value(picsureId)) + .andExpect(jsonPath("$.query").value("{\"q\":1}")).andExpect(jsonPath("$.resourceResultId").value("rr-1")) + .andExpect(jsonPath("$.status").value("QUEUED")).andExpect(jsonPath("$.version").value("7")); + } + + @Test + void getUnknownIdReturns404() throws Exception { + mockMvc.perform(get("/internal/queries/{id}", UUID.randomUUID()).header(InternalTokenFilter.HEADER, validToken)) + .andExpect(status().isNotFound()); + } + + @Test + void patchUpdatesStatusAndResultId() throws Exception { + Query saved = queryRepo.save(new Query()); + + mockMvc.perform( + patch("/internal/queries/{picsureId}", saved.getUuid()).header(InternalTokenFilter.HEADER, validToken) + .contentType(MediaType.APPLICATION_JSON).content("{\"status\":\"AVAILABLE\",\"resourceResultId\":\"rr-9\"}") + ).andExpect(status().is2xxSuccessful()); + + mockMvc.perform(get("/internal/queries/{picsureId}", saved.getUuid()).header(InternalTokenFilter.HEADER, validToken)) + .andExpect(jsonPath("$.status").value("AVAILABLE")).andExpect(jsonPath("$.resourceResultId").value("rr-9")); + } + + @Test + void patchUnknownIdReturns404() throws Exception { + mockMvc.perform( + patch("/internal/queries/{id}", UUID.randomUUID()).header(InternalTokenFilter.HEADER, validToken) + .contentType(MediaType.APPLICATION_JSON).content("{\"status\":\"AVAILABLE\"}") + ).andExpect(status().isNotFound()); + } + + @Test + void dispatchReturnsQueryJsonWithResourceCredentialsStripped() throws Exception { + Query saved = new Query(); + saved.setQuery("{\"resourceUUID\":\"r\",\"resourceCredentials\":{\"BEARER_TOKEN\":\"secret\"},\"query\":\"q\"}"); + saved = queryRepo.save(saved); + + mockMvc.perform(get("/internal/queries/{picsureId}/dispatch", saved.getUuid()).header(InternalTokenFilter.HEADER, validToken)) + .andExpect(status().isOk()).andExpect(jsonPath("$.queryJson").isString()).andExpect( + result -> org.assertj.core.api.Assertions.assertThat(result.getResponse().getContentAsString()).doesNotContain("secret") + .doesNotContain("resourceCredentials") + ); + } + + @Test + void dispatchUnknownIdReturns404() throws Exception { + mockMvc.perform(get("/internal/queries/{id}/dispatch", UUID.randomUUID()).header(InternalTokenFilter.HEADER, validToken)) + .andExpect(status().isNotFound()); + } + + @Test + void dispatchWithoutTokenIsForbidden() throws Exception { + Query saved = queryRepo.save(new Query()); + mockMvc.perform(get("/internal/queries/{picsureId}/dispatch", saved.getUuid())).andExpect(status().isForbidden()); + } + + // --- the federated/GIC surface is gone; these endpoints must stay gone --- + // A 404 here is the contract: it guards against someone reintroducing the routes while wiring something + // unrelated. + + @Test + void byCommonAreaIsGone() throws Exception { + mockMvc.perform(get("/internal/queries/by-common-area/{id}", UUID.randomUUID()).header(InternalTokenFilter.HEADER, validToken)) + .andExpect(status().isNotFound()); + } + + @Test + void sitesByDomainIsGone() throws Exception { + mockMvc.perform(get("/internal/sites/by-domain/{domain}", "harvard.edu").header(InternalTokenFilter.HEADER, validToken)) + .andExpect(status().isNotFound()); + } +} diff --git a/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/query/InternalTokenFilterContextPathTest.java b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/query/InternalTokenFilterContextPathTest.java new file mode 100644 index 000000000..c255a5d2d --- /dev/null +++ b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/query/InternalTokenFilterContextPathTest.java @@ -0,0 +1,70 @@ +package edu.harvard.hms.dbmi.avillach.operations.query; + +import static org.assertj.core.api.Assertions.assertThat; + +import java.util.UUID; + +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.web.client.TestRestTemplate; +import org.springframework.http.HttpEntity; +import org.springframework.http.HttpHeaders; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; + +/** + * Regression test for the finding that {@link InternalTokenFilter} used to gate {@code /internal/**} by checking + * {@code request.getRequestURI().startsWith("/internal/")} directly -- which silently breaks under a non-empty + * {@code server.servlet.context-path}, because {@code getRequestURI()} includes the context path prefix (e.g. + * {@code /ops/internal/queries/...}), so it never starts with the literal string {@code "/internal/"} even though the + * {@code DispatcherServlet} still routes the request straight to {@link InternalQueryController}. + * + *

    Boots the full application under {@code server.servlet.context-path=/ops} and proves the filter -- now registered via + * {@code InternalTokenFilterConfig} as a {@code FilterRegistrationBean} with a container-level + * {@code addUrlPatterns("/internal/*")} (matched relative to the context path, exactly like the servlet mapping that dispatches to the + * controller) -- still runs and still gates the request under that context path. + * + *

    Requests below use the CONTEXT-RELATIVE path ({@code /internal/queries/...}), not the {@code /ops}-prefixed one: + * {@link TestRestTemplate}'s root URI already incorporates {@code server.servlet.context-path} (see {@code LocalHostUriTemplateHandler}), + * so prefixing it again here would double it up. + */ +@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT) +class InternalTokenFilterContextPathTest { + + @DynamicPropertySource + static void contextPath(DynamicPropertyRegistry registry) { + registry.add("server.servlet.context-path", () -> "/ops"); + } + + @Autowired + private TestRestTemplate restTemplate; + + @Value("${picsure.operations.internal-token}") + private String validToken; + + @Test + void missingTokenIsForbiddenUnderAContextPath() { + ResponseEntity response = restTemplate.getForEntity("/internal/queries/{id}", String.class, UUID.randomUUID()); + + assertThat(response.getStatusCode()).isEqualTo(HttpStatus.FORBIDDEN); + assertThat(response.getBody()).contains("\"errorType\":\"FORBIDDEN\""); + } + + @Test + void validTokenReachesTheControllerUnderAContextPath() { + HttpHeaders headers = new HttpHeaders(); + headers.add(InternalTokenFilter.HEADER, validToken); + + ResponseEntity response = restTemplate.exchange( + "/internal/queries/{id}", org.springframework.http.HttpMethod.GET, new HttpEntity<>(headers), String.class, UUID.randomUUID() + ); + + // Token accepted -> request actually reaches InternalQueryController, which 404s on an unknown id. + // (A 403 here would mean the filter never ran under the context path -- the exact bug being regression-tested.) + assertThat(response.getStatusCode()).isEqualTo(HttpStatus.NOT_FOUND); + } +} diff --git a/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/query/InternalTokenFilterTest.java b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/query/InternalTokenFilterTest.java new file mode 100644 index 000000000..5ea2972e2 --- /dev/null +++ b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/query/InternalTokenFilterTest.java @@ -0,0 +1,130 @@ +package edu.harvard.hms.dbmi.avillach.operations.query; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.never; +import static org.mockito.Mockito.verify; + +import org.junit.jupiter.api.Test; +import org.springframework.mock.web.MockHttpServletRequest; +import org.springframework.mock.web.MockHttpServletResponse; + +import jakarta.servlet.FilterChain; + +/** + * Pure unit tests for {@link InternalTokenFilter}: no Spring context, direct {@code doFilter} calls, matching the pattern used by + * {@code GatewayPrivilegesFilterTest}. + */ +class InternalTokenFilterTest { + + private final InternalTokenFilter filter = new InternalTokenFilter("secret"); + + private MockHttpServletRequest internalReq() { + MockHttpServletRequest r = new MockHttpServletRequest(); + r.setRequestURI("/internal/queries/abc/dispatch"); + return r; + } + + @Test + void validTokenPassesThrough() throws Exception { + MockHttpServletRequest req = internalReq(); + req.addHeader(InternalTokenFilter.HEADER, "secret"); + MockHttpServletResponse res = new MockHttpServletResponse(); + FilterChain chain = mock(FilterChain.class); + + filter.doFilter(req, res, chain); + + verify(chain).doFilter(req, res); + assertThat(res.getStatus()).isEqualTo(200); // chain proceeds; the real controller would set the actual body/status + } + + @Test + void missingTokenForbidden() throws Exception { + MockHttpServletRequest req = internalReq(); + MockHttpServletResponse res = new MockHttpServletResponse(); + FilterChain chain = mock(FilterChain.class); + + filter.doFilter(req, res, chain); + + verify(chain, never()).doFilter(any(), any()); + assertThat(res.getStatus()).isEqualTo(403); + assertThat(res.getContentAsString()).contains("\"errorType\":\"FORBIDDEN\"").contains("\"message\":\"Forbidden\"") + .contains("requestId"); + } + + @Test + void wrongTokenForbidden() throws Exception { + MockHttpServletRequest req = internalReq(); + req.addHeader(InternalTokenFilter.HEADER, "nope"); + MockHttpServletResponse res = new MockHttpServletResponse(); + FilterChain chain = mock(FilterChain.class); + + filter.doFilter(req, res, chain); + + verify(chain, never()).doFilter(any(), any()); + assertThat(res.getStatus()).isEqualTo(403); + } + + @Test + void unconfiguredTokenRejectsEvenAValidLookingCall() throws Exception { + InternalTokenFilter unconfigured = new InternalTokenFilter(""); + MockHttpServletRequest req = internalReq(); + req.addHeader(InternalTokenFilter.HEADER, "anything"); + MockHttpServletResponse res = new MockHttpServletResponse(); + FilterChain chain = mock(FilterChain.class); + + unconfigured.doFilter(req, res, chain); + + verify(chain, never()).doFilter(any(), any()); + assertThat(res.getStatus()).isEqualTo(403); + } + + @Test + void nonInternalPathSkipped() throws Exception { + MockHttpServletRequest req = new MockHttpServletRequest(); + req.setRequestURI("/configuration/"); + MockHttpServletResponse res = new MockHttpServletResponse(); + FilterChain chain = mock(FilterChain.class); + + filter.doFilter(req, res, chain); + + verify(chain).doFilter(req, res); + } + + /** + * Regression test for the finding this filter was hardened against: gating {@code /internal/**} by checking + * {@code request.getRequestURI().startsWith("/internal/")} DIRECTLY breaks under a non-empty {@code server.servlet.context-path}, + * because {@code getRequestURI()} includes the context path prefix (here, {@code /ops}) and so never starts with the literal string + * {@code "/internal/"} -- even though the container would still dispatch this exact request to {@code InternalQueryController} per the + * {@code addUrlPatterns("/internal/*")} registration. {@link InternalTokenFilter} now strips {@code getContextPath()} off first, so it + * agrees with the container's own routing decision regardless of context path. + */ + @Test + void tokenStillEnforcedUnderANonEmptyContextPath() throws Exception { + MockHttpServletRequest req = new MockHttpServletRequest(); + req.setContextPath("/ops"); + req.setRequestURI("/ops/internal/queries/abc/dispatch"); + MockHttpServletResponse res = new MockHttpServletResponse(); + FilterChain chain = mock(FilterChain.class); + + filter.doFilter(req, res, chain); + + verify(chain, never()).doFilter(any(), any()); + assertThat(res.getStatus()).isEqualTo(403); + } + + @Test + void validTokenPassesThroughUnderANonEmptyContextPath() throws Exception { + MockHttpServletRequest req = new MockHttpServletRequest(); + req.setContextPath("/ops"); + req.setRequestURI("/ops/internal/queries/abc/dispatch"); + req.addHeader(InternalTokenFilter.HEADER, "secret"); + MockHttpServletResponse res = new MockHttpServletResponse(); + FilterChain chain = mock(FilterChain.class); + + filter.doFilter(req, res, chain); + + verify(chain).doFilter(req, res); + } +} diff --git a/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/query/QueryPersistenceServiceTest.java b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/query/QueryPersistenceServiceTest.java new file mode 100644 index 000000000..0df756037 --- /dev/null +++ b/services/pic-sure-operations-service/src/test/java/edu/harvard/hms/dbmi/avillach/operations/query/QueryPersistenceServiceTest.java @@ -0,0 +1,154 @@ +package edu.harvard.hms.dbmi.avillach.operations.query; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.assertj.core.api.Assertions.assertThatThrownBy; + +import java.util.Base64; +import java.util.UUID; + +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase.Replace; +import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest; +import org.springframework.boot.test.autoconfigure.orm.jpa.TestEntityManager; +import org.springframework.context.annotation.Import; + +import edu.harvard.dbmi.avillach.domain.PicSureStatus; +import edu.harvard.hms.dbmi.avillach.commons.error.PicsureException; + +/** + * Boots a real (H2) JPA context so save/get/update/dispatch are proven against an actual repository, not a mock. + */ +@DataJpaTest +@AutoConfigureTestDatabase(replace = Replace.NONE) +@Import(QueryPersistenceService.class) +class QueryPersistenceServiceTest { + + @Autowired + private QueryPersistenceService service; + + @Autowired + private QueryRepository repo; + + @Autowired + private TestEntityManager entityManager; + + @Test + void saveThenGetRoundTripsTheGzipQueryStatusAndVersion() { + SaveQueryRequest req = new SaveQueryRequest( + "{\"select\":[\"foo\"]}", "resource-result-1", "QUEUED", "3", Base64.getEncoder().encodeToString("meta".getBytes()) + ); + + UUID picsureId = service.save(req); + entityManager.flush(); + entityManager.clear(); + + StoredQuery stored = service.get(picsureId); + assertThat(stored.picsureId()).isEqualTo(picsureId); + assertThat(stored.query()).isEqualTo("{\"select\":[\"foo\"]}"); + assertThat(stored.resourceResultId()).isEqualTo("resource-result-1"); + assertThat(stored.status()).isEqualTo("QUEUED"); + assertThat(stored.version()).isEqualTo("3"); + assertThat(new String(Base64.getDecoder().decode(stored.metadata()))).isEqualTo("meta"); + } + + @Test + void getUnknownIdThrowsNotFound() { + UUID unknown = UUID.randomUUID(); + assertThatThrownBy(() -> service.get(unknown)).isInstanceOf(PicsureException.class) + .satisfies(e -> assertThat(((PicsureException) e).getStatus().value()).isEqualTo(404)); + } + + @Test + void updateChangesOnlyThePresentFields() { + UUID picsureId = service.save(new SaveQueryRequest("{\"q\":1}", "orig-result-id", "QUEUED", "1", null)); + entityManager.flush(); + entityManager.clear(); + + service.update(picsureId, new UpdateQueryRequest("AVAILABLE", null, null)); + entityManager.flush(); + entityManager.clear(); + + StoredQuery stored = service.get(picsureId); + assertThat(stored.status()).isEqualTo("AVAILABLE"); + // resourceResultId/metadata were not part of the update -> unchanged. + assertThat(stored.resourceResultId()).isEqualTo("orig-result-id"); + assertThat(stored.version()).isEqualTo("1"); + } + + @Test + void updateUnknownIdThrowsNotFound() { + UUID unknown = UUID.randomUUID(); + UpdateQueryRequest req = new UpdateQueryRequest("AVAILABLE", null, null); + assertThatThrownBy(() -> service.update(unknown, req)).isInstanceOf(PicsureException.class) + .satisfies(e -> assertThat(((PicsureException) e).getStatus().value()).isEqualTo(404)); + } + + @Test + void dispatchStripsResourceCredentialsAndReturnsAString() { + UUID picsureId = service.save( + new SaveQueryRequest( + "{\"resourceUUID\":\"r\",\"resourceCredentials\":{\"BEARER_TOKEN\":\"secret\"},\"query\":\"q\"}", null, "QUEUED", null, null + ) + ); + entityManager.flush(); + entityManager.clear(); + + String dispatchJson = service.dispatchQueryJson(picsureId); + + assertThat(dispatchJson).doesNotContain("resourceCredentials").doesNotContain("secret").contains("\"query\":\"q\""); + } + + @Test + void dispatchUnknownIdThrowsNotFound() { + UUID unknown = UUID.randomUUID(); + assertThatThrownBy(() -> service.dispatchQueryJson(unknown)).isInstanceOf(PicsureException.class) + .satisfies(e -> assertThat(((PicsureException) e).getStatus().value()).isEqualTo(404)); + } + + @Test + void dispatchOfBlankStoredQueryReturnsNull() { + UUID picsureId = service.save(new SaveQueryRequest(null, null, "QUEUED", null, null)); + entityManager.flush(); + entityManager.clear(); + + assertThat(service.dispatchQueryJson(picsureId)).isNull(); + } + + @Test + void invalidStatusOnSaveThrowsBadRequest() { + SaveQueryRequest req = new SaveQueryRequest("{}", null, "NOT_A_REAL_STATUS", null, null); + assertThatThrownBy(() -> service.save(req)).isInstanceOf(PicsureException.class) + .satisfies(e -> assertThat(((PicsureException) e).getStatus().value()).isEqualTo(400)); + } + + @Test + void invalidBase64MetadataOnSaveThrowsBadRequest() { + SaveQueryRequest req = new SaveQueryRequest("{}", null, "QUEUED", null, "not-valid-base64!!!"); + assertThatThrownBy(() -> service.save(req)).isInstanceOf(PicsureException.class) + .satisfies(e -> assertThat(((PicsureException) e).getStatus().value()).isEqualTo(400)); + } + + @Test + void invalidBase64MetadataOnUpdateThrowsBadRequest() { + UUID picsureId = service.save(new SaveQueryRequest("{}", null, "QUEUED", null, null)); + entityManager.flush(); + entityManager.clear(); + + UpdateQueryRequest req = new UpdateQueryRequest(null, null, "not-valid-base64!!!"); + assertThatThrownBy(() -> service.update(picsureId, req)).isInstanceOf(PicsureException.class) + .satisfies(e -> assertThat(((PicsureException) e).getStatus().value()).isEqualTo(400)); + } + + @Test + void savedStatusEnumRoundTripsThroughOrdinalMapping() { + for (PicSureStatus status : PicSureStatus.values()) { + UUID picsureId = service.save(new SaveQueryRequest("{}", null, status.name(), null, null)); + entityManager.flush(); + entityManager.clear(); + + assertThat(service.get(picsureId).status()).isEqualTo(status.name()); + } + } +} diff --git a/services/pic-sure-operations-service/src/test/resources/application.yml b/services/pic-sure-operations-service/src/test/resources/application.yml new file mode 100644 index 000000000..156462a45 --- /dev/null +++ b/services/pic-sure-operations-service/src/test/resources/application.yml @@ -0,0 +1,23 @@ +spring: + datasource: + url: jdbc:h2:mem:ops;MODE=MySQL;DB_CLOSE_DELAY=-1 + driver-class-name: org.h2.Driver + username: sa + password: + jpa: + # Test-only: H2 has no pre-existing schema to preserve, so let Hibernate build the api-data tables from the + # entities themselves to prove they bind cleanly. NEVER set this to anything but "none" against the real MySQL + # schema (see the load-bearing comment in src/main/resources/application.yml). + hibernate: + ddl-auto: create-drop + naming: + physical-strategy: org.hibernate.boot.model.naming.PhysicalNamingStrategyStandardImpl + properties: + hibernate: + dialect: org.hibernate.dialect.H2Dialect + +picsure: + operations: + # Test-only shared secret for InternalTokenFilter (/internal/**). NEVER commit a real production value here -- + # the real deployment sources this from the QUERY_SERVICE_INTERNAL_TOKEN env var (see src/main/resources/application.yml). + internal-token: test-internal-secret diff --git a/services/pic-sure-services/.env b/services/pic-sure-services/.env new file mode 100644 index 000000000..e69de29bb diff --git a/services/pic-sure-services/.github/release.yml b/services/pic-sure-services/.github/release.yml new file mode 100644 index 000000000..0db6cd02d --- /dev/null +++ b/services/pic-sure-services/.github/release.yml @@ -0,0 +1,20 @@ +changelog: + exclude: + labels: + - ignore-for-release + categories: + - title: Breaking Changes + labels: + - breaking-change + - title: Features + labels: + - feature + - title: Enhancements + labels: + - enhancement + - title: Bug Fixes + labels: + - bug + - title: Other Changes + labels: + - "*" diff --git a/services/pic-sure-services/.github/sync_release.yml b/services/pic-sure-services/.github/sync_release.yml new file mode 100644 index 000000000..889579be2 --- /dev/null +++ b/services/pic-sure-services/.github/sync_release.yml @@ -0,0 +1,32 @@ +name: Update Test Branch + +on: + push: + branches: [main] + +permissions: write-all + +jobs: + sync: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v3 + with: + ssh-key: ${{secrets.SECRET_KEY}} + fetch-depth: 0 + + - name: Setup Git User + run: | + git config user.name "Luke Sikina" + git config user.email "lucas.sikina@gmail.com" + + - name: Update Test Branch + run: | + git checkout main + git fetch origin + git checkout release + git pull + git rebase origin/main + git push origin release --force + diff --git a/services/pic-sure-services/.github/workflows/label-checker.yml b/services/pic-sure-services/.github/workflows/label-checker.yml new file mode 100644 index 000000000..2bd9019bf --- /dev/null +++ b/services/pic-sure-services/.github/workflows/label-checker.yml @@ -0,0 +1,21 @@ +name: Label Checker +on: + pull_request: + types: + - opened + - synchronize + - reopened + - labeled + - unlabeled + +jobs: + + check_labels: + name: Check labels + runs-on: ubuntu-latest + steps: + - uses: docker://agilepathway/pull-request-label-checker:latest + with: + one_of: breaking-change,enhancement,bug,documentation,ignore-for-release,dependencies + repo_token: ${{ secrets.GITHUB_TOKEN }} + diff --git a/services/pic-sure-services/.github/workflows/sync_release.yml b/services/pic-sure-services/.github/workflows/sync_release.yml new file mode 100644 index 000000000..889579be2 --- /dev/null +++ b/services/pic-sure-services/.github/workflows/sync_release.yml @@ -0,0 +1,32 @@ +name: Update Test Branch + +on: + push: + branches: [main] + +permissions: write-all + +jobs: + sync: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v3 + with: + ssh-key: ${{secrets.SECRET_KEY}} + fetch-depth: 0 + + - name: Setup Git User + run: | + git config user.name "Luke Sikina" + git config user.email "lucas.sikina@gmail.com" + + - name: Update Test Branch + run: | + git checkout main + git fetch origin + git checkout release + git pull + git rebase origin/main + git push origin release --force + diff --git a/services/pic-sure-services/.github/workflows/test-runner.yml b/services/pic-sure-services/.github/workflows/test-runner.yml new file mode 100644 index 000000000..8f1102164 --- /dev/null +++ b/services/pic-sure-services/.github/workflows/test-runner.yml @@ -0,0 +1,24 @@ +name: Java CI with Maven + +on: + push: + branches: [ "main", "release" ] + pull_request: + branches: [ "*" ] + +jobs: + build: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v3 + - name: Set up JDK 21 + uses: actions/setup-java@v3 + with: + java-version: '21' + distribution: 'corretto' + cache: maven + - name: Build with Maven + run: "for dir in 'uploader' 'info-service'; do cd $dir; mvn verify; cd ..; done" + diff --git a/services/pic-sure-services/.gitignore b/services/pic-sure-services/.gitignore new file mode 100644 index 000000000..1727df886 --- /dev/null +++ b/services/pic-sure-services/.gitignore @@ -0,0 +1,53 @@ +### Java template +# Compiled class file +*.class + +# Log file +*.log + +# BlueJ files +*.ctxt + +# Mobile Tools for Java (J2ME) +.mtj.tmp/ + +# Package Files # +*.jar +*.war +*.nar +*.ear +*.zip +*.tar.gz +*.rar + +# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml +hs_err_pid* +replay_pid* + +### Maven template +target/ +pom.xml.tag +pom.xml.releaseBackup +pom.xml.versionsBackup +pom.xml.next +release.properties +dependency-reduced-pom.xml +buildNumber.properties +.mvn/timing.properties +# https://github.com/takari/maven-wrapper#usage-without-binary-jar +.mvn/wrapper/maven-wrapper.jar + +# Eclipse m2e generated files +# Eclipse Core +.project +# JDT-specific (Eclipse Java Development Tools) +.classpath + +### Example user template template +### Example user template + +# IntelliJ project files +.idea +*.iml +out +gen diff --git a/services/pic-sure-services/.sdkmanrc b/services/pic-sure-services/.sdkmanrc new file mode 100644 index 000000000..38b733ba0 --- /dev/null +++ b/services/pic-sure-services/.sdkmanrc @@ -0,0 +1 @@ +java=21.0.10-tem diff --git a/services/pic-sure-services/LICENSE b/services/pic-sure-services/LICENSE new file mode 100644 index 000000000..261eeb9e9 --- /dev/null +++ b/services/pic-sure-services/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/services/pic-sure-services/README.md b/services/pic-sure-services/README.md new file mode 100644 index 000000000..edd57470b --- /dev/null +++ b/services/pic-sure-services/README.md @@ -0,0 +1,62 @@ +# PIC-SURE Services + +This is a collection of microservices. You can deploy any number of these microservices +to a PIC-SURE environment and access their respective APIs via the /proxy/ endpoint. +Every directory in this repo is a separate microservice. + +## Deploying a Service + +1. Pick a tag in this repo +2. On the server you wish to deploy to, run the Build and Deploy Microservice job + - If the service requires an .env file, figure that out + - The name the job asks for is the name of the service directory in this repo + - I do not care what you put for the description +3. The auth logic needed to permit roles access to your API is on you. Those migrations +belong in the custom UI repo for your environment. +4. That's it. You don't need to restart PIC-SURE or anything. + +## Using a Service + +You can hit your API through PIC-SURE via the proxy endpoint. Requests to +`/proxy/service-name` will be routed to your container. The service name is determined +by the `container_name` attribute in your `*-docker-compose.yml` file. + +## Creating a Service + +Your service should be a REST API, and should implement the `/info` endpoint as +implemented in PIC-SURE. If you want to implement your service in a language other +than Java, you're on your own. For java, you can look at the example `infoservice`. +One note: pulling in that ResourceInfo class was tricky. I used jitpack because +relying on the `.m2` cache leads to docker images with nasty builds. You can +pull in the artifact by including the following in your pom: + +```xml + + + jitpack.io + https://jitpack.io + + +``` +... +```xml + +com.github.hms-dbmi +pic-sure +e421ae9caff5ed02e9cd27812edfe24ec455281c + + + + org.slf4j + * + + + +``` + +:) + + +When implementing the info endpoint, you can assume your service's resource ID will +be available inside your container via the environment variable `RESOURCE_UUID` + diff --git a/services/pic-sure-services/docker-compose.yml b/services/pic-sure-services/docker-compose.yml new file mode 100644 index 000000000..9e42d4eaa --- /dev/null +++ b/services/pic-sure-services/docker-compose.yml @@ -0,0 +1,9 @@ +--- +version: '3' + +networks: + picsure: + external: true + hpdsNet: + external: true + diff --git a/services/pic-sure-services/info-service/.env b/services/pic-sure-services/info-service/.env new file mode 100644 index 000000000..4ff9abf15 --- /dev/null +++ b/services/pic-sure-services/info-service/.env @@ -0,0 +1 @@ +RESOURCE_UUID=123e4567-e89b-42d3-a456-556642440000 \ No newline at end of file diff --git a/services/pic-sure-services/info-service/.gitignore b/services/pic-sure-services/info-service/.gitignore new file mode 100644 index 000000000..549e00a2a --- /dev/null +++ b/services/pic-sure-services/info-service/.gitignore @@ -0,0 +1,33 @@ +HELP.md +target/ +!.mvn/wrapper/maven-wrapper.jar +!**/src/main/**/target/ +!**/src/test/**/target/ + +### STS ### +.apt_generated +.classpath +.factorypath +.project +.settings +.springBeans +.sts4-cache + +### IntelliJ IDEA ### +.idea +*.iws +*.iml +*.ipr + +### NetBeans ### +/nbproject/private/ +/nbbuild/ +/dist/ +/nbdist/ +/.nb-gradle/ +build/ +!**/src/main/**/build/ +!**/src/test/**/build/ + +### VS Code ### +.vscode/ diff --git a/services/pic-sure-services/info-service/.sdkmanrc b/services/pic-sure-services/info-service/.sdkmanrc new file mode 100644 index 000000000..d2344323e --- /dev/null +++ b/services/pic-sure-services/info-service/.sdkmanrc @@ -0,0 +1 @@ +java=25.0.3-tem diff --git a/services/pic-sure-services/info-service/Dockerfile b/services/pic-sure-services/info-service/Dockerfile new file mode 100644 index 000000000..90118c769 --- /dev/null +++ b/services/pic-sure-services/info-service/Dockerfile @@ -0,0 +1,11 @@ +FROM amazoncorretto:25 + +# Runtime-only image (reactor convention): build the jar first with +# mvn -pl services/pic-sure-services/info-service -am package +# from the monorepo root, then build this image from the module directory. +COPY target/infoservice-*.jar /service.jar + +# Time zone +ENV TZ="US/Eastern" + +ENTRYPOINT ["java", "-Xmx8192m", "-jar", "/service.jar"] diff --git a/services/pic-sure-services/info-service/env-proto b/services/pic-sure-services/info-service/env-proto new file mode 100644 index 000000000..66196333d --- /dev/null +++ b/services/pic-sure-services/info-service/env-proto @@ -0,0 +1 @@ +RESOURCE_UUID= \ No newline at end of file diff --git a/services/pic-sure-services/info-service/info-service-docker-compose.yml b/services/pic-sure-services/info-service/info-service-docker-compose.yml new file mode 100644 index 000000000..cb78711ea --- /dev/null +++ b/services/pic-sure-services/info-service/info-service-docker-compose.yml @@ -0,0 +1,11 @@ +--- +version: '3' +services: + info-service: + image: info-service:latest + container_name: info-service + build: info-service/ + env_file: + - info-service/.env + networks: + - picsure diff --git a/services/pic-sure-services/info-service/pom.xml b/services/pic-sure-services/info-service/pom.xml new file mode 100644 index 000000000..884bc1c0c --- /dev/null +++ b/services/pic-sure-services/info-service/pom.xml @@ -0,0 +1,45 @@ + + + 4.0.0 + + edu.harvard.hms.dbmi.avillach + pic-sure-api + ${revision} + ../../../pom.xml + + edu.harvard.dbmi.avillach + infoservice + Info Service + Info Service API + + + edu.harvard.hms.dbmi.avillach + pic-sure-api-model + + + org.springframework.boot + spring-boot-starter-web + + + org.springframework.boot + spring-boot-starter + + + + org.springframework.boot + spring-boot-starter-test + test + + + + + + + org.springframework.boot + spring-boot-maven-plugin + + + + + diff --git a/services/pic-sure-services/info-service/src/main/java/edu/harvard/dbmi/avillach/infoservice/InfoController.java b/services/pic-sure-services/info-service/src/main/java/edu/harvard/dbmi/avillach/infoservice/InfoController.java new file mode 100644 index 000000000..88eea82c3 --- /dev/null +++ b/services/pic-sure-services/info-service/src/main/java/edu/harvard/dbmi/avillach/infoservice/InfoController.java @@ -0,0 +1,28 @@ +package edu.harvard.dbmi.avillach.infoservice; + +import edu.harvard.dbmi.avillach.domain.ResourceInfo; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.PostMapping; +import org.springframework.web.bind.annotation.RequestBody; + +import java.util.List; +import java.util.UUID; + +@Controller +public class InfoController { + + @Value("${pic-sure-resource-uuid}") + private UUID uuid; + + @PostMapping("/info") + public ResponseEntity healthCheck(@RequestBody Object ignored) { + ResourceInfo info = new ResourceInfo(); + info.setName("Info Service"); + info.setId(uuid); + info.setQueryFormats(List.of()); + return new ResponseEntity<>(info, HttpStatus.OK); + } +} diff --git a/services/pic-sure-services/info-service/src/main/java/edu/harvard/dbmi/avillach/infoservice/InfoServiceApplication.java b/services/pic-sure-services/info-service/src/main/java/edu/harvard/dbmi/avillach/infoservice/InfoServiceApplication.java new file mode 100644 index 000000000..cde4e5f78 --- /dev/null +++ b/services/pic-sure-services/info-service/src/main/java/edu/harvard/dbmi/avillach/infoservice/InfoServiceApplication.java @@ -0,0 +1,13 @@ +package edu.harvard.dbmi.avillach.infoservice; + +import org.springframework.boot.SpringApplication; +import org.springframework.boot.autoconfigure.SpringBootApplication; + +@SpringBootApplication +public class InfoServiceApplication { + + public static void main(String[] args) { + SpringApplication.run(InfoServiceApplication.class, args); + } + +} diff --git a/services/pic-sure-services/info-service/src/main/resources/application.properties b/services/pic-sure-services/info-service/src/main/resources/application.properties new file mode 100644 index 000000000..9ce29f2f3 --- /dev/null +++ b/services/pic-sure-services/info-service/src/main/resources/application.properties @@ -0,0 +1,2 @@ +pic-sure-resource-uuid=${RESOURCE_UUID} +server.port=80 \ No newline at end of file diff --git a/services/pic-sure-services/info-service/src/test/java/edu/harvard/dbmi/avillach/infoservice/InfoControllerTest.java b/services/pic-sure-services/info-service/src/test/java/edu/harvard/dbmi/avillach/infoservice/InfoControllerTest.java new file mode 100644 index 000000000..cda2511f2 --- /dev/null +++ b/services/pic-sure-services/info-service/src/test/java/edu/harvard/dbmi/avillach/infoservice/InfoControllerTest.java @@ -0,0 +1,35 @@ +package edu.harvard.dbmi.avillach.infoservice; + +import edu.harvard.dbmi.avillach.domain.ResourceInfo; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; + +import java.util.List; +import java.util.UUID; + +@SpringBootTest +class InfoControllerTest { + + @Autowired + InfoController infoController; + + @SuppressWarnings("DataFlowIssue") + @Test + void shouldDoHealthCheck() { + ResponseEntity actual = infoController.healthCheck(null); + + ResourceInfo expected = new ResourceInfo(); + expected.setName("Info Service"); + expected.setId(UUID.fromString("123e4567-e89b-42d3-a456-556642440000")); // from application.properties + expected.setQueryFormats(List.of()); + + Assertions.assertEquals(HttpStatus.OK, actual.getStatusCode()); + Assertions.assertEquals(expected.getName(), actual.getBody().getName()); + Assertions.assertEquals(expected.getId(), actual.getBody().getId()); + Assertions.assertEquals(expected.getQueryFormats(), actual.getBody().getQueryFormats()); + } +} diff --git a/services/pic-sure-services/info-service/src/test/java/edu/harvard/dbmi/avillach/infoservice/InfoServiceApplicationTests.java b/services/pic-sure-services/info-service/src/test/java/edu/harvard/dbmi/avillach/infoservice/InfoServiceApplicationTests.java new file mode 100644 index 000000000..005ea62dc --- /dev/null +++ b/services/pic-sure-services/info-service/src/test/java/edu/harvard/dbmi/avillach/infoservice/InfoServiceApplicationTests.java @@ -0,0 +1,12 @@ +package edu.harvard.dbmi.avillach.infoservice; + +import org.junit.jupiter.api.Test; +import org.springframework.boot.test.context.SpringBootTest; + +@SpringBootTest +class InfoServiceApplicationTests { + + @Test + void contextLoads() {} + +} diff --git a/services/pic-sure-services/info-service/src/test/resources/application.properties b/services/pic-sure-services/info-service/src/test/resources/application.properties new file mode 100644 index 000000000..10755cbdc --- /dev/null +++ b/services/pic-sure-services/info-service/src/test/resources/application.properties @@ -0,0 +1 @@ +pic-sure-resource-uuid=123e4567-e89b-42d3-a456-556642440000 diff --git a/services/pic-sure-services/uploader/.gitignore b/services/pic-sure-services/uploader/.gitignore new file mode 100644 index 000000000..8b3677510 --- /dev/null +++ b/services/pic-sure-services/uploader/.gitignore @@ -0,0 +1,34 @@ +HELP.md +.env +.mvn +target/ +!**/src/main/**/target/ +!**/src/test/**/target/ + +### STS ### +.apt_generated +.classpath +.factorypath +.project +.settings +.springBeans +.sts4-cache + +### IntelliJ IDEA ### +.idea +*.iws +*.iml +*.ipr + +### NetBeans ### +/nbproject/private/ +/nbbuild/ +/dist/ +/nbdist/ +/.nb-gradle/ +build/ +!**/src/main/**/build/ +!**/src/test/**/build/ + +### VS Code ### +.vscode/ diff --git a/services/pic-sure-services/uploader/.sdkmanrc b/services/pic-sure-services/uploader/.sdkmanrc new file mode 100644 index 000000000..d2344323e --- /dev/null +++ b/services/pic-sure-services/uploader/.sdkmanrc @@ -0,0 +1 @@ +java=25.0.3-tem diff --git a/services/pic-sure-services/uploader/Dockerfile b/services/pic-sure-services/uploader/Dockerfile new file mode 100644 index 000000000..3c15162f9 --- /dev/null +++ b/services/pic-sure-services/uploader/Dockerfile @@ -0,0 +1,11 @@ +FROM amazoncorretto:25 + +# Runtime-only image (reactor convention): build the jar first with +# mvn -pl services/pic-sure-services/uploader -am package +# from the monorepo root, then build this image from the module directory. +COPY target/uploader-*.jar /dataupload.jar + +# Time zone +ENV TZ="US/Eastern" + +ENTRYPOINT java $DEBUG_VARS $PROXY_VARS -Xmx8192m -jar /dataupload.jar diff --git a/services/pic-sure-services/uploader/LICENSE b/services/pic-sure-services/uploader/LICENSE new file mode 100644 index 000000000..261eeb9e9 --- /dev/null +++ b/services/pic-sure-services/uploader/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/services/pic-sure-services/uploader/README.md b/services/pic-sure-services/uploader/README.md new file mode 100644 index 000000000..6df394512 --- /dev/null +++ b/services/pic-sure-services/uploader/README.md @@ -0,0 +1,84 @@ +# GIC S3 Data Sharing Solution + +## Overview + +This repository is a data sharing solution for GIC. It creates an S3 bucket with +server side encryption, as well as the keys, roles, and policies needed to permit +third party users write / delete access, but not read access to the bucket. It also +contains the source code for a Java application that can authenticate with AWS, +assume the uploader role, and then upload / delete data. + +This repository is structured as follows: +`aws`: Cloud formation template, any other AWS specific resources +`src`: Java source code for Data Uploader +`env-proto`: a template file for creating your .env file +`pom.xml`: Java dependencies +`Dockerfile`: Build specification for the docker image + +## Usage + +1. Configure Dependencies + +You will need at least one AWS to run this application, and preferably two if you +want to properly demonstrate third party uploading. You will also need `docker` +installed to run the data uploader. For development, please install `maven` and +the Java 21 JDK. + +2. Build Docker Image + +In the root of this repo, run `docker build . -t gic-data-uploader`. This builds +the Data Uploader application, and tags (names) it `gic-data-uploader`. + +3. Provision AWS Resources + +In the AWS console of the account you would like to provision an S3 bucket for, +go to AWS Cloud Formation Template and create a new stack using the template in +`aws/s3-bucket.yml`. You must specify at least 1 account for the +`UploaderAccountIds` parameter. When you get a stack status of `UPDATE_COMPLETE`, +continue to the next step. + +4. Set Up Environment File + +Run the following command to start setting up your env file. `cp env-proto .env` +This file `.env` is not versioned because it contains secret AWS credentials that +you should not share. Fill out the empty environment variables in your new `.env` +file using resources in your new AWS cloud stack and the authentication credentials +that Amazon provides you. + +5. Run + +Run `docker compose --profile production up -d `. Here is an example of a +successful output, with logging prefixes omitted: + +``` + . ____ _ __ _ _ + /\\ / ___'_ __ _ _(_)_ __ __ _ \ \ \ \ +( ( )\___ | '_ | '_| | '_ \/ _` | \ \ \ \ + \\/ ___)| |_)| | | | | || (_| | ) ) ) ) + ' |____| .__|_| |_|_| |_\__, | / / / / + =========|_|==============|___/=/_/_/_/ + :: Spring Boot :: (v3.1.4) + +Starting DatauploadApplication v0.0.1-SNAPSHOT using Java 21.0.1 with PID 1 (/dataupload.jar started by root in /) +No active profile set, falling back to 1 default profile: "default" +Tomcat initialized with port(s): 8080 (http) +Starting service [Tomcat] +Starting Servlet engine: [Apache Tomcat/10.1.13] +Initializing Spring embedded WebApplicationContext +Root WebApplicationContext: initialization completed in 1218 ms +Locking s3 client while refreshing session +Attempting to assume data uploader role +Successfully assumed role, using credentials to create new S3 client +Unlocking s3 client. Session refreshed +Checking S3 connection... +Next refresh will be at 2023-10-22T15:33:13Z +Verifying upload capabilities +Tomcat started on port(s): 8080 (http) with context path '' +Started DatauploadApplication in 3.342 seconds (process running for 3.824) +Verifying delete capabilities +S3 connection verified. +``` + +6. Run Migrations + +`docker compose --profile migrate up -d` \ No newline at end of file diff --git a/services/pic-sure-services/uploader/aws/user-based-aws-resources.yml b/services/pic-sure-services/uploader/aws/user-based-aws-resources.yml new file mode 100644 index 000000000..e95a03d3e --- /dev/null +++ b/services/pic-sure-services/uploader/aws/user-based-aws-resources.yml @@ -0,0 +1,363 @@ +Description: S3 Bucket for GIC Data Access + +Parameters: + InstitutionName: + Type: String + Description: The short name of your institution + Default: prototype + ExternalId: + Type: String + Description: External ID to be shared with uploaders + Default: 12345 + # 3rd party accounts can successfully assume our role, but users created by + # that account cannot, regardless of if we add them to the trust policy + # Hence why we're using account roots rather than iam users. + UploaderAccountIds: + Type: List + Description: 'A comma delimited list of AWS account roots. Ex: arn:aws:iam::762503070141:root,arn:aws:iam::2222222222222:root' + Default: '' + AllRoleArns: + Type: List + Description: 'A comma delimited list of role ARNS that we want to be able to assume.' + Default: '' + +Resources: +#------------------------------------------------------------------------------- +# Users & Access Keys +#------------------------------------------------------------------------------- + DataUploadUser: + # make dep on policy + Type: AWS::IAM::User + Properties: + Path: "/data-upload-user/" + Policies: + - PolicyName: DataUploadUserKeyPolicy + PolicyDocument: + Statement: + - Effect: Allow + Resource: + - !GetAtt BucketKMSKey.Arn + Action: + - 'kms:GetPublicKey' + - 'kms:Decrypt' + - 'kms:ListKeyPolicies' + - 'kms:GetKeyPolicy' + - 'kms:GenerateDataKeyWithoutPlaintext' + - 'kms:ListResourceTags' + - 'kms:GenerateDataKeyPairWithoutPlaintext' + - 'kms:GenerateDataKeyPair' + - 'kms:ReEncryptFrom' + - 'kms:ListGrants' + - 'kms:GetParametersForImport' + - 'kms:Encrypt' + - 'kms:GetKeyRotationStatus' + - 'kms:GenerateDataKey' + - 'kms:ReEncryptTo' + - 'kms:DescribeKey' + - PolicyName: DataUploadUserKMSPolicy + PolicyDocument: + Statement: + - Effect: Allow + Resource: + - !GetAtt BucketKMSKey.Arn + Action: + - 'kms:DescribeCustomKeyStores' + - 'kms:ListKeys' + - 'kms:ListRetirableGrants' + - 'kms:ListAliases' + - PolicyName: DataUploadUserSTSPolicy + PolicyDocument: + Statement: + - Effect: Allow + Resource: !Ref AllRoleArns + Action: + - 'sts:AssumeRole' + + DataUploadUserAccessKey: + Type: AWS::IAM::AccessKey + Properties: + UserName: + !Ref DataUploadUser + + DataUploadUserSecret: + Type: AWS::SecretsManager::Secret + Properties: + Name: !Join ['-', [!Ref InstitutionName, data-upload-user-secret]] + Description: Access Key secret for Data Upload User + SecretString: !GetAtt DataUploadUserAccessKey.SecretAccessKey +#------------------------------------------------------------------------------- +# Roles & Policies +#------------------------------------------------------------------------------- + PicSureUploadPolicy: + Type: AWS::IAM::ManagedPolicy + Properties: + Roles: + - !Ref PicSureDataUploader + PolicyDocument: + Version: '2012-10-17' + Statement: + - Effect: Allow + Action: + - s3:DeleteObject + - s3:GetObject + - s3:PutObject + - s3:ListBucket + - s3:PutObjectTagging + - s3:PutObjectVersionTagging + - s3:GetObjectTagging + - s3:GetObjectVersionTagging + - s3:DeleteObjectTagging + - s3:DeleteObjectVersionTagging + - s3:GetObjectVersion + - s3:ListBucketVersions + - s3:DeleteObjectVersion + Resource: + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}/*' + + # Uploaders need to be able to encrypt their data prior to upload + PicSureDataUploaderKMSPolicy: + Type: AWS::IAM::Policy + Properties: + PolicyName: UploaderKMSPolicy + PolicyDocument: + Version: '2012-10-17' + Statement: + - Effect: Allow + Action: + - 'kms:DescribeKey' + - 'kms:Encrypt' + - 'kms:Decrypt' + - 'kms:ReEncrypt*' + - 'kms:GenerateDataKey' + - 'kms:GenerateDataKeyWithoutPlaintext' + Resource: !GetAtt BucketKMSKey.Arn + Roles: + - !Ref PicSureDataUploader + + # Uploaders need PUT access to the S3 bucket, but nothing else + # Each institution has a single uploader, tied to their PIC-SURE node + PicSureDataUploader: + Type: AWS::IAM::Role + Properties: + RoleName: PicSureDataUploaderRole + Path: '/' + # unit = seconds. 12 hours + MaxSessionDuration: 43200 + AssumeRolePolicyDocument: + Version: '2012-10-17' + Statement: + - Effect: 'Allow' + Principal: + AWS: !Ref UploaderAccountIds + Action: + - 'sts:AssumeRole' + Condition: + StringEquals: + sts:ExternalId: !Ref ExternalId + Policies: [] + + # The site owner runs a Service Workbench instance that has full access to the + # S3 bucket + ServiceWorkbenchClient: + Type: AWS::IAM::Role + Properties: + # unit seconds. 12 hours + MaxSessionDuration: 43200 + RoleName: ServiceWorkbenchRole + AssumeRolePolicyDocument: + Version: '2012-10-17' + Statement: + - Effect: 'Allow' + Principal: + AWS: !Ref 'AWS::AccountId' + Action: + - 'sts:AssumeRole' + Policies: + - PolicyName: PicSureUploadPolicy + PolicyDocument: + Statement: + - Effect: Allow + Resource: + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}/*' + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}' + Action: + - s3:* + +#------------------------------------------------------------------------------- +# Encryption Key +#------------------------------------------------------------------------------- + BucketKMSKey: + Type: 'AWS::KMS::Key' + Properties: + Description: Symmetric encryption KMS key for bucket + EnableKeyRotation: true + PendingWindowInDays: 20 + KeyPolicy: + Version: 2012-10-17 + Id: key-default-1 + Statement: + - Sid: Enable IAM User Permissions + Effect: Allow + Principal: + AWS: !Sub 'arn:aws:iam::${AWS::AccountId}:root' + Action: 'kms:*' + Resource: '*' + - Sid: Allow use of the key + Effect: Allow + Principal: + AWS: !Ref UploaderAccountIds + Action: + - 'kms:DescribeKey' + - 'kms:Encrypt' + - 'kms:Decrypt' + - 'kms:ReEncrypt*' + - 'kms:GenerateDataKey' + - 'kms:GenerateDataKeyWithoutPlaintext' + Resource: '*' + BucketKMSKeyAlias: + Type: AWS::KMS::Alias + Properties: + AliasName: alias/s3gic + TargetKeyId: + Ref: BucketKMSKey + +#------------------------------------------------------------------------------- +# Buckets & Policies +#------------------------------------------------------------------------------- + +# Define logging bucket and logging bucket policy first + PicSureLoggingBucket: + Type: AWS::S3::Bucket + Properties: + BucketName: !Join [ '-', [ 'pic-sure-data-sharing-bucket-access-logs', !Ref InstitutionName ] ] + AccessControl: LogDeliveryWrite + PublicAccessBlockConfiguration: + BlockPublicAcls: true + BlockPublicPolicy: true + IgnorePublicAcls: true + RestrictPublicBuckets: true + VersioningConfiguration: + Status: Enabled + OwnershipControls: + Rules: + - ObjectOwnership: ObjectWriter + BucketEncryption: + ServerSideEncryptionConfiguration: + - ServerSideEncryptionByDefault: + SSEAlgorithm: 'AES256' + + PicSureLoggingBucketPolicy: + Type: AWS::S3::BucketPolicy + DependsOn: + - PicSureLoggingBucket + Properties: + Bucket: !Join [ '-', [ 'pic-sure-data-sharing-bucket-access-logs', !Ref InstitutionName ] ] + PolicyDocument: + Statement: + - Sid: Allow this account access + Effect: Allow + Principal: + AWS: + - !Sub arn:aws:iam::${AWS::AccountId}:root + Action: s3:* + Resource: + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-access-logs-${InstitutionName}/*' + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-access-logs-${InstitutionName}' + + PicSureStudyBucket: + Type: AWS::S3::Bucket + Properties: + BucketName: !Join ['-', ['pic-sure-data-sharing-bucket', !Ref InstitutionName]] + LoggingConfiguration: + DestinationBucketName: !Ref PicSureLoggingBucket + PublicAccessBlockConfiguration: + BlockPublicAcls: true + BlockPublicPolicy: true + IgnorePublicAcls: true + RestrictPublicBuckets: true + VersioningConfiguration: + Status: Enabled + OwnershipControls: + Rules: + - ObjectOwnership: ObjectWriter + BucketEncryption: + ServerSideEncryptionConfiguration: + - ServerSideEncryptionByDefault: + KMSMasterKeyID: !Sub 'arn:aws:kms:${AWS::Region}:${AWS::AccountId}:${BucketKMSKeyAlias}' + SSEAlgorithm: 'aws:kms' + + PicSureStudyBucketPolicy: + Type: AWS::S3::BucketPolicy + DependsOn: + - PicSureDataUploader + - ServiceWorkbenchClient + - PicSureStudyBucket + - PicSureLoggingBucket + - PicSureLoggingBucketPolicy + Properties: + Bucket: !Join [ '-', [ 'pic-sure-data-sharing-bucket', !Ref InstitutionName ] ] + PolicyDocument: + Statement: + - Sid: Deny requests that do not use TLS/HTTPS + Effect: Deny + Principal: '*' + Action: s3:* + Resource: + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}/*' + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}' + Condition: + Bool: + aws:SecureTransport: false + - Sid: Allow PIC-SURE clients with uploader role + Effect: Allow + Principal: + AWS: + - !Sub 'arn:aws:iam::${AWS::AccountId}:role/PicSureDataUploaderRole' + Action: + - s3:DeleteObject + - s3:GetObject + - s3:PutObject + - s3:ListBucket + - s3:PutObjectTagging + - s3:PutObjectVersionTagging + - s3:GetObjectTagging + - s3:GetObjectVersionTagging + - s3:DeleteObjectTagging + - s3:DeleteObjectVersionTagging + - s3:GetObjectVersion + - s3:ListBucketVersions + - s3:DeleteObjectVersion + Resource: + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}/*' + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}' + - Sid: Allow SWB clients with everything role + Effect: Allow + Principal: + AWS: + - !Sub arn:aws:iam::${AWS::AccountId}:role/ServiceWorkbenchRole + Action: s3:* + Resource: + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}/*' + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}' + - Sid: Deny unencrypted object uploads + Effect: Deny + Principal: '*' + Action: + - s3:PutObject* + Resource: + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}/*' + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}' + Condition: + StringNotEquals: + s3:x-amz-server-side-encryption: 'aws:kms' + - Sid: Deny Wrong KMS Key + Effect: Deny + Principal: '*' + Action: + - s3:PutObject* + Resource: + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}/*' + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}' + Condition: + StringNotEqualsIfExists: + s3:x-amz-server-side-encryption-aws-kms-key-id: !GetAtt BucketKMSKey.Arn diff --git a/services/pic-sure-services/uploader/aws/userless-aws-resources.yml b/services/pic-sure-services/uploader/aws/userless-aws-resources.yml new file mode 100644 index 000000000..9a87fa41f --- /dev/null +++ b/services/pic-sure-services/uploader/aws/userless-aws-resources.yml @@ -0,0 +1,300 @@ +Description: S3 Bucket for GIC Data Access + +Parameters: + InstitutionName: + Type: String + Description: The short name of your institution + Default: prototype + ExternalId: + Type: String + Description: External ID to be shared with uploaders + Default: 12345 + UploaderAccountIds: + Type: List + Description: 'A comma delimited list of arns. Ex: arn:aws:iam::762503070141:root,arn:aws:iam::2222222222222:root' + Default: '' + +Resources: +#------------------------------------------------------------------------------- +# Users & Access Keys +#------------------------------------------------------------------------------- + +# This template assumes you're using an Instance Profile to authenticate. As a +# result, we don't provision a user. + +#------------------------------------------------------------------------------- +# Roles & Policies +#------------------------------------------------------------------------------- + PicSureUploadPolicy: + Type: AWS::IAM::ManagedPolicy + Properties: + Roles: + - !Ref PicSureDataUploader + PolicyDocument: + Version: '2012-10-17' + Statement: + - Effect: Allow + Action: + - s3:DeleteObject + - s3:GetObject + - s3:PutObject + - s3:ListBucket + - s3:PutObjectTagging + - s3:PutObjectVersionTagging + - s3:GetObjectTagging + - s3:GetObjectVersionTagging + - s3:DeleteObjectTagging + - s3:DeleteObjectVersionTagging + - s3:GetObjectVersion + - s3:ListBucketVersions + - s3:DeleteObjectVersion + Resource: + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}/*' + + # Uploaders need to be able to encrypt their data prior to upload + PicSureDataUploaderKMSPolicy: + Type: AWS::IAM::Policy + Properties: + PolicyName: UploaderKMSPolicy + PolicyDocument: + Version: '2012-10-17' + Statement: + - Effect: Allow + Action: + - 'kms:DescribeKey' + - 'kms:Encrypt' + - 'kms:Decrypt' + - 'kms:ReEncrypt*' + - 'kms:GenerateDataKey' + - 'kms:GenerateDataKeyWithoutPlaintext' + Resource: !GetAtt BucketKMSKey.Arn + Roles: + - !Ref PicSureDataUploader + + # Uploaders need PUT access to the S3 bucket, but nothing else + # Each institution has a single uploader, tied to their PIC-SURE node + PicSureDataUploader: + Type: AWS::IAM::Role + Properties: + RoleName: PicSureDataUploaderRole + Path: '/' + # unit = seconds. 12 hours + MaxSessionDuration: 43200 + AssumeRolePolicyDocument: + Version: '2012-10-17' + Statement: + - Effect: 'Allow' + Principal: + AWS: !Ref UploaderAccountIds + Action: + - 'sts:AssumeRole' + Condition: + StringEquals: + sts:ExternalId: !Ref ExternalId + Policies: [] + + # The site owner runs a Service Workbench instance that has full access to the + # S3 bucket + ServiceWorkbenchClient: + Type: AWS::IAM::Role + Properties: + # unit seconds. 12 hours + MaxSessionDuration: 43200 + RoleName: ServiceWorkbenchRole + AssumeRolePolicyDocument: + Version: '2012-10-17' + Statement: + - Effect: 'Allow' + Principal: + AWS: !Ref 'AWS::AccountId' + Action: + - 'sts:AssumeRole' + Policies: + - PolicyName: PicSureUploadPolicy + PolicyDocument: + Statement: + - Effect: Allow + Resource: + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}/*' + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}' + Action: + - s3:* + +#------------------------------------------------------------------------------- +# Encryption Key +#------------------------------------------------------------------------------- + BucketKMSKey: + Type: 'AWS::KMS::Key' + Properties: + Description: Symmetric encryption KMS key for bucket + EnableKeyRotation: true + PendingWindowInDays: 20 + KeyPolicy: + Version: 2012-10-17 + Id: key-default-1 + Statement: + - Sid: Enable IAM User Permissions + Effect: Allow + Principal: + AWS: !Sub 'arn:aws:iam::${AWS::AccountId}:root' + Action: 'kms:*' + Resource: '*' + - Sid: Allow use of the key + Effect: Allow + Principal: + AWS: !Ref UploaderAccountIds + Action: + - 'kms:DescribeKey' + - 'kms:Encrypt' + - 'kms:Decrypt' + - 'kms:ReEncrypt*' + - 'kms:GenerateDataKey' + - 'kms:GenerateDataKeyWithoutPlaintext' + Resource: '*' + BucketKMSKeyAlias: + Type: AWS::KMS::Alias + Properties: + AliasName: alias/s3gic + TargetKeyId: + Ref: BucketKMSKey + +#------------------------------------------------------------------------------- +# Buckets & Policies +#------------------------------------------------------------------------------- + +# Define logging bucket and logging bucket policy first + PicSureLoggingBucket: + Type: AWS::S3::Bucket + Properties: + BucketName: !Join [ '-', [ 'pic-sure-data-sharing-bucket-access-logs', !Ref InstitutionName ] ] + AccessControl: LogDeliveryWrite + PublicAccessBlockConfiguration: + BlockPublicAcls: true + BlockPublicPolicy: true + IgnorePublicAcls: true + RestrictPublicBuckets: true + VersioningConfiguration: + Status: Enabled + OwnershipControls: + Rules: + - ObjectOwnership: ObjectWriter + BucketEncryption: + ServerSideEncryptionConfiguration: + - ServerSideEncryptionByDefault: + SSEAlgorithm: 'AES256' + + PicSureLoggingBucketPolicy: + Type: AWS::S3::BucketPolicy + DependsOn: + - PicSureLoggingBucket + Properties: + Bucket: !Join [ '-', [ 'pic-sure-data-sharing-bucket-access-logs', !Ref InstitutionName ] ] + PolicyDocument: + Statement: + - Sid: Allow this account access + Effect: Allow + Principal: + AWS: + - !Sub arn:aws:iam::${AWS::AccountId}:root + Action: s3:* + Resource: + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-access-logs-${InstitutionName}/*' + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-access-logs-${InstitutionName}' + + PicSureStudyBucket: + Type: AWS::S3::Bucket + Properties: + BucketName: !Join ['-', ['pic-sure-data-sharing-bucket', !Ref InstitutionName]] + LoggingConfiguration: + DestinationBucketName: !Ref PicSureLoggingBucket + PublicAccessBlockConfiguration: + BlockPublicAcls: true + BlockPublicPolicy: true + IgnorePublicAcls: true + RestrictPublicBuckets: true + VersioningConfiguration: + Status: Enabled + OwnershipControls: + Rules: + - ObjectOwnership: ObjectWriter + BucketEncryption: + ServerSideEncryptionConfiguration: + - ServerSideEncryptionByDefault: + KMSMasterKeyID: !Sub 'arn:aws:kms:${AWS::Region}:${AWS::AccountId}:${BucketKMSKeyAlias}' + SSEAlgorithm: 'aws:kms' + + PicSureStudyBucketPolicy: + Type: AWS::S3::BucketPolicy + DependsOn: + - PicSureDataUploader + - ServiceWorkbenchClient + - PicSureStudyBucket + - PicSureLoggingBucket + - PicSureLoggingBucketPolicy + Properties: + Bucket: !Join [ '-', [ 'pic-sure-data-sharing-bucket', !Ref InstitutionName ] ] + PolicyDocument: + Statement: + - Sid: Deny requests that do not use TLS/HTTPS + Effect: Deny + Principal: '*' + Action: s3:* + Resource: + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}/*' + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}' + Condition: + Bool: + aws:SecureTransport: false + - Sid: Allow PIC-SURE clients with uploader role + Effect: Allow + Principal: + AWS: + - !Sub 'arn:aws:iam::${AWS::AccountId}:role/PicSureDataUploaderRole' + Action: + - s3:DeleteObject + - s3:GetObject + - s3:PutObject + - s3:ListBucket + - s3:PutObjectTagging + - s3:PutObjectVersionTagging + - s3:GetObjectTagging + - s3:GetObjectVersionTagging + - s3:DeleteObjectTagging + - s3:DeleteObjectVersionTagging + - s3:GetObjectVersion + - s3:ListBucketVersions + - s3:DeleteObjectVersion + Resource: + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}/*' + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}' + - Sid: Allow SWB clients with everything role + Effect: Allow + Principal: + AWS: + - !Sub arn:aws:iam::${AWS::AccountId}:role/ServiceWorkbenchRole + Action: s3:* + Resource: + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}/*' + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}' + - Sid: Deny unencrypted object uploads + Effect: Deny + Principal: '*' + Action: + - s3:PutObject* + Resource: + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}/*' + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}' + Condition: + StringNotEquals: + s3:x-amz-server-side-encryption: 'aws:kms' + - Sid: Deny Wrong KMS Key + Effect: Deny + Principal: '*' + Action: + - s3:PutObject* + Resource: + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}/*' + - !Sub 'arn:aws:s3:::pic-sure-data-sharing-bucket-${InstitutionName}' + Condition: + StringNotEqualsIfExists: + s3:x-amz-server-side-encryption-aws-kms-key-id: !GetAtt BucketKMSKey.Arn diff --git a/services/pic-sure-services/uploader/data/seed.sql b/services/pic-sure-services/uploader/data/seed.sql new file mode 100644 index 000000000..48056ed72 --- /dev/null +++ b/services/pic-sure-services/uploader/data/seed.sql @@ -0,0 +1,10 @@ +DROP TABLE IF EXISTS `query_status`; + +CREATE TABLE `query_status` ( + QUERY BINARY(16) NOT NULL, + GENOMIC_STATUS VARCHAR(64) NOT NULL DEFAULT 'Unsent', + PHENOTYPIC_STATUS VARCHAR(64) NOT NULL DEFAULT 'Unsent', + APPROVED DATETIME, + SITE VARCHAR(64) NOT NULL DEFAULT '', + PRIMARY KEY (`QUERY`) +); diff --git a/services/pic-sure-services/uploader/docker-compose.yml b/services/pic-sure-services/uploader/docker-compose.yml new file mode 100644 index 000000000..cb8981d64 --- /dev/null +++ b/services/pic-sure-services/uploader/docker-compose.yml @@ -0,0 +1,64 @@ +--- +version: '3' +services: + uploader: + image: lukesikinabch/gic-uploader:1.2.3 + container_name: uploader + ports: + - "5005:5005" + env_file: + - .env + depends_on: + - uploader-db + restart: always + volumes: + - $DOCKER_CONFIG_DIR/aws_uploads/:/gic_query_results/ + networks: + - picsure + - uploader + profiles: + - "production" + uploader-db: + image: mysql:8.0 + container_name: uploader-db + # This is super confusing. There are actually two .env files: one for the docker-compose environment itself + # and one for each container. This specifies the LATTER of those two envs + # The variables on the right side of the environment section are from the FORMER of these two envs + env_file: + - .env + environment: + MYSQL_ROOT_PASSWORD: $DATA_UPLOAD_DB_PASS + MYSQL_PASSWORD: $DATA_UPLOAD_DB_PASS + MYSQL_DATABASE: $DATA_UPLOAD_DB_DATABASE + MYSQL_USER: $DATA_UPLOAD_DB_USER + healthcheck: + test: [ "CMD", "mysqladmin" ,"ping", "-u", "root", "-p$DATA_UPLOAD_DB_PASS" ] + timeout: 20s + retries: 10 + networks: + - uploader + restart: always + volumes: + - /usr/local/pic-sure-services/uploader/data/seed.sql:/docker-entrypoint-initdb.d/seed.sql:ro + - uploader-db-data:/var/lib/mysql + migrations: + image: flyway/flyway:11-alpine + container_name: flyway + command: -url=jdbc:mysql://uploader-db:3306/${DATA_UPLOAD_DB_DATABASE}?allowPublicKeyRetrieval=true -schemas=${DATA_UPLOAD_DB_DATABASE} -user=${DATA_UPLOAD_DB_USER} -password=${DATA_UPLOAD_DB_PASS} -connectRetries=60 -validateMigrationNaming=true migrate + env_file: + - .env + volumes: + - ./flyway:/flyway/sql + networks: + - uploader + profiles: + - "migrate" + depends_on: + - "uploader-db" +volumes: + uploader-db-data: + +networks: + uploader: + picsure: + external: true diff --git a/services/pic-sure-services/uploader/env-proto b/services/pic-sure-services/uploader/env-proto new file mode 100644 index 000000000..c230b23fd --- /dev/null +++ b/services/pic-sure-services/uploader/env-proto @@ -0,0 +1,26 @@ +AWS_ACCESS_KEY_ID= +AWS_SECRET_ACCESS_KEY= +AWS_SESSION_TOKEN= +AWS_DATA_UPLOAD_ROLE=arn:aws:iam::111111111111:role/PicSureDataUploadRole +AWS_SHARED_SECRET= +AWS_S3_BUCKET_NAME= +AWS_REGION=us-east-1 +AWS_KEY_ID +AUTH_METHOD=user + +DATA_UPLOAD_DB_DATABASE=data-upload +DATA_UPLOAD_DB_HOST=uploader-db +DATA_UPLOAD_DB_PASS=mycoolpassword +DATA_UPLOAD_DB_USER=datauploaduser +DATA_UPLOAD_DB_ROOT_PASS=mycoolpassword + +FILE_SHARING_ROOT=/gic_query_results +DOCKER_CONFIG_DIR=/usr/local/picsure/config/ + +INSTITUTIONS=bch-dev +HOME_INSTITUTION_NAME=bch-dev +HOME_INSTITUTION_DISPLAY=BCH +HOME_INSTITUTION_LONG_DISPLAY=Boston Children's Hospital + +DEBUG_VARS= +PROXY_VARS= diff --git a/services/pic-sure-services/uploader/flyway/V1__initial.sql b/services/pic-sure-services/uploader/flyway/V1__initial.sql new file mode 100644 index 000000000..236fb2bf2 --- /dev/null +++ b/services/pic-sure-services/uploader/flyway/V1__initial.sql @@ -0,0 +1,8 @@ +CREATE TABLE IF NOT EXISTS `query_status` ( + QUERY BINARY(16) NOT NULL, + GENOMIC_STATUS VARCHAR(64) NOT NULL DEFAULT 'Unsent', + PHENOTYPIC_STATUS VARCHAR(64) NOT NULL DEFAULT 'Unsent', + APPROVED DATETIME, + SITE VARCHAR(64) NOT NULL DEFAULT '', + PRIMARY KEY (`QUERY`) +); diff --git a/services/pic-sure-services/uploader/flyway/V2__add_patient.sql b/services/pic-sure-services/uploader/flyway/V2__add_patient.sql new file mode 100644 index 000000000..7c767e1b5 --- /dev/null +++ b/services/pic-sure-services/uploader/flyway/V2__add_patient.sql @@ -0,0 +1,5 @@ +ALTER TABLE `query_status` + ADD PATIENT_STATUS VARCHAR(64) NOT NULL DEFAULT 'Unsent'; + +ALTER TABLE `query_status` + ADD QUERY_JSON_STATUS VARCHAR(64) NOT NULL DEFAULT 'Unsent'; \ No newline at end of file diff --git a/services/pic-sure-services/uploader/pom.xml b/services/pic-sure-services/uploader/pom.xml new file mode 100644 index 000000000..2089c83cf --- /dev/null +++ b/services/pic-sure-services/uploader/pom.xml @@ -0,0 +1,119 @@ + + + 4.0.0 + + edu.harvard.hms.dbmi.avillach + pic-sure-api + ${revision} + ../../../pom.xml + + edu.harvard.dbmi.avillach + uploader + dataupload + Data Upload Client + + 2.30.24 + + + + + + software.amazon.awssdk + bom + ${aws.version} + pom + import + + + + + + org.springframework.boot + spring-boot-starter-jdbc + + + org.springframework.boot + spring-boot-starter-web + + + + software.amazon.awssdk + s3 + ${aws.version} + + + + commons-logging + commons-logging + + + + + software.amazon.awssdk + lambda + ${aws.version} + + + software.amazon.awssdk + sts + ${aws.version} + + + software.amazon.awssdk + kms + ${aws.version} + + + software.amazon.awssdk + apache-client + ${aws.version} + + + software.amazon.encryption.s3 + amazon-s3-encryption-client-java + 3.1.0 + + + + edu.harvard.hms.dbmi.avillach + pic-sure-api-model + + + org.apache.httpcomponents.client5 + httpclient5 + + + + com.mysql + mysql-connector-j + runtime + + + org.springframework.boot + spring-boot-starter-test + test + + + org.testcontainers + junit-jupiter + test + + + org.testcontainers + mysql + test + + + + + + + org.springframework.boot + spring-boot-maven-plugin + + + + + diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/DatauploadApplication.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/DatauploadApplication.java new file mode 100644 index 000000000..40d8e061b --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/DatauploadApplication.java @@ -0,0 +1,13 @@ +package edu.harvard.dbmi.avillach.dataupload; + +import org.springframework.boot.SpringApplication; +import org.springframework.boot.autoconfigure.SpringBootApplication; + +@SpringBootApplication +public class DatauploadApplication { + + public static void main(String[] args) { + SpringApplication.run(DatauploadApplication.class, args); + } + +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/aws/AWSClientBuilder.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/aws/AWSClientBuilder.java new file mode 100644 index 000000000..ce74a0b1b --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/aws/AWSClientBuilder.java @@ -0,0 +1,92 @@ +package edu.harvard.dbmi.avillach.dataupload.aws; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.context.annotation.Profile; +import org.springframework.stereotype.Service; +import software.amazon.awssdk.auth.credentials.AwsSessionCredentials; +import software.amazon.awssdk.auth.credentials.InstanceProfileCredentialsProvider; +import software.amazon.awssdk.auth.credentials.StaticCredentialsProvider; +import software.amazon.awssdk.http.SdkHttpClient; +import software.amazon.awssdk.services.s3.S3Client; +import software.amazon.awssdk.services.s3.S3ClientBuilder; +import software.amazon.awssdk.services.sts.model.AssumeRoleRequest; +import software.amazon.awssdk.services.sts.model.AssumeRoleResponse; +import software.amazon.awssdk.services.sts.model.Credentials; + +import java.util.Map; +import java.util.Optional; + +@Profile("!dev") +@Service +public class AWSClientBuilder { + + private static final Logger log = LoggerFactory.getLogger(AWSClientBuilder.class); + + private final Map sites; + private final StsClientProvider stsClientProvider; + private final S3ClientBuilder s3ClientBuilder; + private final SdkHttpClient sdkHttpClient; + private final boolean retainRole; + + @Autowired + public AWSClientBuilder( + Map sites, StsClientProvider stsClientProvider, S3ClientBuilder s3ClientBuilder, + @Autowired(required = false) SdkHttpClient sdkHttpClient, @Value("${s3.retain_role:false}") boolean retainRole + ) { + this.sites = sites; + this.stsClientProvider = stsClientProvider; + this.s3ClientBuilder = s3ClientBuilder; + this.sdkHttpClient = sdkHttpClient; + this.retainRole = retainRole; + } + + public Optional buildClientForSite(String siteName) { + log.info("Building client for site {}", siteName); + if (!sites.containsKey(siteName)) { + log.warn("Could not find site {}", siteName); + return Optional.empty(); + } + + if (retainRole) { + log.info("s3.retain_role set to true. Will retain current role rather than assuming one for site"); + InstanceProfileCredentialsProvider credentialsProvider = InstanceProfileCredentialsProvider.create(); + S3Client client = s3ClientBuilder.credentialsProvider(credentialsProvider).build(); + return Optional.of(client); + } + + log.info("Found site, making assume role request"); + SiteAWSInfo site = sites.get(siteName); + AssumeRoleRequest roleRequest = AssumeRoleRequest.builder().roleArn(site.roleARN()) + .roleSessionName("test_session" + System.nanoTime()).externalId(site.externalId()).durationSeconds(60 * 60) // 1 hour + .build(); + Optional assumeRoleResponse = + stsClientProvider.createClient().map(c -> c.assumeRole(roleRequest)).map(AssumeRoleResponse::credentials); + if (assumeRoleResponse.isEmpty()) { + log.error("Error assuming role {} , no credentials returned", site.roleARN()); + return Optional.empty(); + } + log.info("Successfully assumed role {} for site {}", site.roleARN(), site.siteName()); + + log.info("Building S3 client for site {}", site.siteName()); + // Use the credentials from the role to create the S3 client + Credentials credentials = assumeRoleResponse.get(); + AwsSessionCredentials sessionCredentials = + AwsSessionCredentials.builder().accessKeyId(credentials.accessKeyId()).secretAccessKey(credentials.secretAccessKey()) + .sessionToken(credentials.sessionToken()).expirationTime(credentials.expiration()).build(); + StaticCredentialsProvider provider = StaticCredentialsProvider.create(sessionCredentials); + return Optional.of(buildFromProvider(provider)); + } + + private S3Client buildFromProvider(StaticCredentialsProvider provider) { + if (sdkHttpClient == null) { + return s3ClientBuilder.credentialsProvider(provider).build(); + } + log.info("Http proxy detected and added to S3 client"); + return s3ClientBuilder.credentialsProvider(provider).httpClient(sdkHttpClient).build(); + + } + +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/aws/AWSConfiguration.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/aws/AWSConfiguration.java new file mode 100644 index 000000000..143ee6d86 --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/aws/AWSConfiguration.java @@ -0,0 +1,94 @@ +package edu.harvard.dbmi.avillach.dataupload.aws; + +import org.apache.logging.log4j.util.Strings; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty; +import org.springframework.context.ConfigurableApplicationContext; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.scheduling.annotation.Scheduled; +import org.springframework.util.StringUtils; +import org.springframework.web.context.annotation.RequestScope; +import software.amazon.awssdk.auth.credentials.*; +import software.amazon.awssdk.http.SdkHttpClient; +import software.amazon.awssdk.regions.Region; +import software.amazon.awssdk.services.s3.S3Client; +import software.amazon.awssdk.services.s3.S3ClientBuilder; +import software.amazon.awssdk.services.sts.StsClient; +import software.amazon.awssdk.services.sts.StsClientBuilder; +import software.amazon.encryption.s3.S3EncryptionClient; + +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.stream.Stream; + +@ConditionalOnProperty(name = "production", havingValue = "true") +@Configuration +public class AWSConfiguration { + private static final Logger LOG = LoggerFactory.getLogger(AWSConfiguration.class); + + @Value("${aws.s3.institution:}") + private List institutions; + + @Value("${aws.s3.role_arns:}") + private List roleArns; + + @Value("${aws.s3.external_ids:}") + private List externalIDs; + + @Value("${aws.s3.buckets:}") + private List buckets; + + @Value("${aws.kms.key_ids:}") + private List kmsKeyIds; + + @Autowired + private ConfigurableApplicationContext context; + + @Autowired(required = false) + private SdkHttpClient sdkHttpClient; + + @Bean + @ConditionalOnProperty(name = "production", havingValue = "true") + Map roleARNs() { + boolean badConfig = Stream.of(roleArns, externalIDs, kmsKeyIds, buckets).filter(l -> l.size() != institutions.size()) + .peek(l -> LOG.error("Mismatched aws credentials {}", l)).findAny().isPresent(); + if (badConfig) { + context.close(); + return Map.of(); + } + HashMap roles = new HashMap<>(); + for (int i = 0; i < institutions.size(); i++) { + SiteAWSInfo info = new SiteAWSInfo(institutions.get(i), roleArns.get(i), externalIDs.get(i), buckets.get(i), kmsKeyIds.get(i)); + roles.put(info.siteName(), info); + } + return roles; + } + + @Bean + S3EncryptionClient.Builder encryptionClientBuilder() { + // This is a bean for mocking purposes + return S3EncryptionClient.builder(); + } + + @Bean + StsClientBuilder stsClientBuilder() { + // This is a bean for mocking purposes + return StsClient.builder(); + } + + @Bean + S3ClientBuilder s3ClientBuilder() { + return S3Client.builder(); + } + + @Bean + @RequestScope + StsClient getStsClient() { + return StsClient.builder().region(Region.US_EAST_1).build(); + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/aws/AWSCredentialsService.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/aws/AWSCredentialsService.java new file mode 100644 index 000000000..3163b301a --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/aws/AWSCredentialsService.java @@ -0,0 +1,73 @@ +package edu.harvard.dbmi.avillach.dataupload.aws; + +import org.apache.logging.log4j.util.Strings; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.context.ConfigurableApplicationContext; +import org.springframework.stereotype.Service; +import software.amazon.awssdk.auth.credentials.AwsBasicCredentials; +import software.amazon.awssdk.auth.credentials.AwsCredentials; +import software.amazon.awssdk.auth.credentials.AwsSessionCredentials; +import software.amazon.awssdk.auth.credentials.InstanceProfileCredentialsProvider; + +@Service +public class AWSCredentialsService { + + private static final Logger LOG = LoggerFactory.getLogger(AWSCredentialsService.class); + + private final String authMethod; + private final String secret; + private final String key; + private final String token; + private final ConfigurableApplicationContext context; + + + private AwsCredentials credentials; + + @Autowired + public AWSCredentialsService( + @Value("${aws.authentication.method:}") String authMethod, @Value("${aws.s3.access_key_secret:}") String secret, + @Value("${aws.s3.access_key_id:}") String key, @Value("${aws.s3.session_token:}") String token, + ConfigurableApplicationContext context + ) { + this.authMethod = authMethod; + this.secret = secret; + this.key = key; + this.token = token; + this.context = context; + } + + public AwsCredentials constructCredentials() { + // noinspection SwitchStatementWithTooFewBranches + return switch (authMethod) { + case "instance-profile" -> createInstanceProfileBasedCredentials(); + default -> createUserBasedCredentials(); + }; + } + + private AwsCredentials createUserBasedCredentials() { + LOG.info("Authentication method is user. Attempting to resolve user credentials."); + if (Strings.isBlank(key)) { + LOG.error("No AWS key. Can't create client. Exiting"); + context.close(); + return null; + } + if (Strings.isBlank(secret)) { + LOG.error("No AWS secret. Can't create client. Exiting"); + context.close(); + return null; + } + if (Strings.isBlank(token)) { + return AwsBasicCredentials.create(key, secret); + } else { + return AwsSessionCredentials.create(key, secret, token); + } + } + + private AwsCredentials createInstanceProfileBasedCredentials() { + LOG.info("Authentication method is instance-profile. Attempting to resolve instance profile credentials."); + return InstanceProfileCredentialsProvider.create().resolveCredentials(); + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/aws/S3StateVerifier.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/aws/S3StateVerifier.java new file mode 100644 index 000000000..a62574e97 --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/aws/S3StateVerifier.java @@ -0,0 +1,73 @@ +package edu.harvard.dbmi.avillach.dataupload.aws; + +import edu.harvard.dbmi.avillach.dataupload.hpds.HPDSConnectionVerifier; +import jakarta.annotation.PostConstruct; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty; +import org.springframework.stereotype.Component; +import software.amazon.awssdk.core.sync.RequestBody; +import software.amazon.awssdk.services.s3.model.*; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.time.Duration; +import java.time.temporal.ChronoUnit; +import java.util.Map; +import java.util.Optional; + +@ConditionalOnProperty(name = "production", havingValue = "true") +@Component +public class S3StateVerifier { + + private static final String testTempPrefix = "S3_DAEMON_INIT_TEST"; + private static final Logger LOG = LoggerFactory.getLogger(S3StateVerifier.class); + + private final Map sites; + private final AWSClientBuilder clientBuilder; + private final HPDSConnectionVerifier hpdsVerifier; + + @Autowired + public S3StateVerifier(Map sites, AWSClientBuilder clientBuilder, HPDSConnectionVerifier hpdsVerifier) { + this.sites = sites; + this.clientBuilder = clientBuilder; + this.hpdsVerifier = hpdsVerifier; + } + + @PostConstruct + private void verifyS3Status() { + sites.values().forEach(inst -> Thread.ofVirtual().start(() -> asyncVerify(inst))); + if (!hpdsVerifier.verifyConnection()) { + throw new RuntimeException("Not correctly connected to HPDS"); + } + } + + private void asyncVerify(SiteAWSInfo institution) { + LOG.info("Checking S3 connection to {} ...", institution.siteName()); + createTempFileWithText(institution).flatMap(p -> uploadFileFromPath(p, institution)).orElseThrow(); + LOG.info("S3 connection to {} verified.", institution.siteName()); + } + + private Optional uploadFileFromPath(Path p, SiteAWSInfo info) { + LOG.info("Verifying upload capabilities"); + RequestBody body = RequestBody.fromFile(p.toFile()); + PutObjectRequest request = PutObjectRequest.builder().bucket(info.bucket()).serverSideEncryption(ServerSideEncryption.AWS_KMS) + .ssekmsKeyId(info.kmsKeyID()).key(p.getFileName().toString()).build(); + return clientBuilder.buildClientForSite(info.siteName()).map(client -> client.putObject(request, body)) + .map(resp -> p.getFileName().toString()); + } + + private Optional createTempFileWithText(SiteAWSInfo info) { + try { + Path path = Files.createTempFile(testTempPrefix + "_" + info.siteName(), null); + LOG.info("Created a file with name {} to upload to {}", path.toString(), info.siteName()); + Files.writeString(path, "Howdy!"); + return Optional.of(path); + } catch (IOException e) { + LOG.error("Failed to create temp file. Daemon will likely be unable to write to S3!"); + return Optional.empty(); + } + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/aws/SiteAWSInfo.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/aws/SiteAWSInfo.java new file mode 100644 index 000000000..11b5af4d6 --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/aws/SiteAWSInfo.java @@ -0,0 +1,4 @@ +package edu.harvard.dbmi.avillach.dataupload.aws; + +public record SiteAWSInfo(String siteName, String roleARN, String externalId, String bucket, String kmsKeyID) { +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/aws/StsClientProvider.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/aws/StsClientProvider.java new file mode 100644 index 000000000..6ea86524e --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/aws/StsClientProvider.java @@ -0,0 +1,20 @@ +package edu.harvard.dbmi.avillach.dataupload.aws; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.stereotype.Service; +import software.amazon.awssdk.regions.Region; +import software.amazon.awssdk.services.sts.StsClient; + +import java.util.Optional; + +@Service +public class StsClientProvider { + + private static final Logger log = LoggerFactory.getLogger(StsClientProvider.class); + + public Optional createClient() { + StsClient client = StsClient.builder().region(Region.US_EAST_1).build(); + return Optional.of(client); + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/FileSystemConfig.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/FileSystemConfig.java new file mode 100644 index 000000000..dd34c08c9 --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/FileSystemConfig.java @@ -0,0 +1,30 @@ +package edu.harvard.dbmi.avillach.dataupload.hpds; + +import org.springframework.beans.factory.annotation.Value; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; + +import java.nio.file.Path; + +@Configuration +public class FileSystemConfig { + @Value("${file_sharing_root:/gic_query_results/}") + private String fileSharingRootDir; + + @Value("${enable_file_sharing:false}") + private boolean enableFileSharing; + + @Bean() + Path sharingRoot() { + if (!enableFileSharing) { + return Path.of("/dev/null"); + } + + Path path = Path.of(fileSharingRootDir); + if (!path.toFile().exists()) { + throw new RuntimeException(fileSharingRootDir + " DNE."); + } + + return path; + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/HPDSClient.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/HPDSClient.java new file mode 100644 index 000000000..c5180fdad --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/HPDSClient.java @@ -0,0 +1,89 @@ +package edu.harvard.dbmi.avillach.dataupload.hpds; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange.Query; +import edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange.ResultType; +import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest; +import edu.harvard.dbmi.avillach.domain.QueryRequest; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Service; +import org.springframework.web.client.RestClient; +import org.springframework.web.client.RestClientException; + +@Service +public class HPDSClient { + + private static final Logger LOG = LoggerFactory.getLogger(HPDSClient.class); + private static final String HPDS_URI = "http://hpds:8080/PIC-SURE/"; + private static final ObjectMapper mapper = new ObjectMapper(); + + private final RestClient restClient; + + @Autowired + public HPDSClient(RestClient restClient) { + this.restClient = restClient; + } + + public boolean writeTestData(Query query) { + return writeData(query, "test_upload"); + } + + public boolean writePhenotypicData(Query query) { + return writeData(query, "phenotypic"); + } + + public boolean writeGenomicData(Query query) { + return writeData(query, "genomic"); + } + + public boolean writePatientData(Query query) { + query.setExpectedResultType(ResultType.PATIENTS); + return writeData(query, "patients"); + } + + public boolean initializeQuery(Query query) { + QueryRequest req = new GeneralQueryRequest(); + req.setQuery(query); + String body = createBody(req); + + if (body == null) { + return false; + } + + return sendAndVerifyRequest(HPDS_URI + "query/sync", body); + } + + private boolean writeData(Query query, String mode) { + String body = createBody(query); + if (body == null) { + return false; + } + + return sendAndVerifyRequest(HPDS_URI + "write/" + mode, body); + } + + private boolean sendAndVerifyRequest(String uri, String body) { + try { + ResponseEntity response = + restClient.post().uri(uri).contentType(MediaType.APPLICATION_JSON).body(body).retrieve().toBodilessEntity(); + return response.getStatusCode().value() == 200; + } catch (RestClientException e) { + LOG.error("Error making request", e); + return false; + } + } + + private String createBody(Object query) { + try { + return mapper.writeValueAsString(query); + } catch (JsonProcessingException e) { + LOG.error("Error creating request body", e); + return null; + } + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/HPDSConnectionVerifier.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/HPDSConnectionVerifier.java new file mode 100644 index 000000000..39d574e88 --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/HPDSConnectionVerifier.java @@ -0,0 +1,53 @@ +package edu.harvard.dbmi.avillach.dataupload.hpds; + +import edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange.Query; +import edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange.ResultType; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Service; + +import java.io.File; +import java.nio.file.Path; + +@Service +public class HPDSConnectionVerifier { + + private static final Logger log = LoggerFactory.getLogger(HPDSConnectionVerifier.class); + + private final HPDSClient client; + private final Path sharingRoot; + private final UUIDGenerator uuidGenerator; + + @Autowired + public HPDSConnectionVerifier(HPDSClient client, Path sharingRoot, UUIDGenerator uuidGenerator) { + this.client = client; + this.sharingRoot = sharingRoot; + this.uuidGenerator = uuidGenerator; + } + + public boolean verifyConnection() { + log.info("Verifying connection to hpds by asking it to create a file and then verifying that the file exists."); + Query testQuery = new Query(); + testQuery.setPicSureId(uuidGenerator.generate().toString()); + testQuery.setId(testQuery.getPicSureId()); + testQuery.setExpectedResultType(ResultType.COUNT); + log.info("Created test query with UUID {}", testQuery.getPicSureId()); + + log.info("Sending test query to HPDS"); + boolean hpdsResponse = client.writeTestData(testQuery); + if (!hpdsResponse) { + log.info("HPDS returned non 200 exit code. Assuming failure."); + return false; + } + log.info("HPDS reported successfully writing the data. Verifying that the file exists"); + File testData = Path.of(sharingRoot.toString(), testQuery.getPicSureId(), "test_data.txt").toFile(); + + if (testData.exists() && testData.isFile()) { + log.info("File found! Connection to HPDS verified!"); + return testData.delete(); + } + log.info("File {} not found. HPDS is running, but the shared directory is probably misconfigured", testData.getPath()); + return false; + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/HttpClientConfig.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/HttpClientConfig.java new file mode 100644 index 000000000..41ba8e6e4 --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/HttpClientConfig.java @@ -0,0 +1,52 @@ +package edu.harvard.dbmi.avillach.dataupload.hpds; + +import org.apache.hc.client5.http.impl.classic.CloseableHttpClient; +import org.apache.hc.client5.http.impl.classic.HttpClients; +import org.apache.hc.client5.http.impl.io.PoolingHttpClientConnectionManagerBuilder; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.http.client.HttpComponentsClientHttpRequestFactory; +import org.springframework.util.StringUtils; +import org.springframework.web.client.RestClient; +import software.amazon.awssdk.http.SdkHttpClient; +import software.amazon.awssdk.http.apache.ApacheHttpClient; +import software.amazon.awssdk.http.apache.ProxyConfiguration; + +@Configuration +public class HttpClientConfig { + private static final Logger LOG = LoggerFactory.getLogger(HttpClientConfig.class); + + @Value("${http.proxyUser:}") + private String proxyUser; + + @Value("${http.proxyPassword:}") + private String proxyPassword; + + @Bean + public RestClient restClient(RestClient.Builder builder) { + CloseableHttpClient httpClient; + if (!StringUtils.hasLength(proxyUser)) { + httpClient = HttpClients.createDefault(); + } else { + LOG.info("Found proxy user {}, will configure proxy from system properties", proxyUser); + httpClient = + HttpClients.custom().setConnectionManager(PoolingHttpClientConnectionManagerBuilder.create().setMaxConnTotal(100).build()) + .useSystemProperties().build(); + } + return builder.requestFactory(new HttpComponentsClientHttpRequestFactory(httpClient)).build(); + } + + @Bean + public SdkHttpClient getSdkClient() { + if (!StringUtils.hasLength(proxyUser)) { + return null; + } + LOG.info("Found proxy user {}, will configure sdk proxy", proxyUser); + ProxyConfiguration proxy = + ProxyConfiguration.builder().useSystemPropertyValues(true).username(proxyUser).password(proxyPassword).build(); + return ApacheHttpClient.builder().proxyConfiguration(proxy).build(); + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/UUIDGenerator.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/UUIDGenerator.java new file mode 100644 index 000000000..7a8fe0a62 --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/UUIDGenerator.java @@ -0,0 +1,13 @@ +package edu.harvard.dbmi.avillach.dataupload.hpds; + +import org.springframework.stereotype.Service; + +import java.util.UUID; + +@Service +public class UUIDGenerator { + + public UUID generate() { + return UUID.randomUUID(); + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/hpdsartifactsdonotchange/DONOTCHANGE.txt b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/hpdsartifactsdonotchange/DONOTCHANGE.txt new file mode 100644 index 000000000..1dff610ea --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/hpdsartifactsdonotchange/DONOTCHANGE.txt @@ -0,0 +1,8 @@ +These files are copied directly from HPDS manually. Please only change these as you change them in HPDS. +We're doing this rather than referencing the artifacts directly because: +- HPDS depends on artifacts in the pic-sure repo +- We can't make HPDS pull those artifacts from Jitpack because FISMA +- Because HPDS relies on your m2 cache, we can't build it in Jitpack +- So we have no way to reference the artifacts directly that doesn't lean on your m2 local + - Which I refuse to do. I think this is clearer. + - Also, that won't work well with Docker builds \ No newline at end of file diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/hpdsartifactsdonotchange/Filter.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/hpdsartifactsdonotchange/Filter.java new file mode 100644 index 000000000..9bee608ed --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/hpdsartifactsdonotchange/Filter.java @@ -0,0 +1,101 @@ +package edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange; + +public interface Filter { + public boolean apply(T value); + + public static class DoubleFilter implements Filter { + + Double min, max; + + public Double getMin() { + return min; + } + + public void setMin(Double min) { + this.min = min; + } + + public Double getMax() { + return max; + } + + public void setMax(Double max) { + this.max = max; + } + + public DoubleFilter() { + + } + + public DoubleFilter(Double min, Double max) { + this.min = min; + this.max = max; + } + + public boolean apply(Double value) { + return value >= min && value <= max; + } + + public String toString() { + String strVal = ""; + if (min != null) { + strVal = "Greater than " + min; + if (max != null) { + strVal += " and "; + } + } + if (max != null) { + strVal += "Less than " + max; + } + return strVal; + } + } + public static class FloatFilter implements Filter { + + Float min, max; + + public Float getMin() { + return min; + } + + public void setMin(Float min) { + this.min = min; + } + + public Float getMax() { + return max; + } + + public void setMax(Float max) { + this.max = max; + } + + public FloatFilter() { + + } + + public FloatFilter(Float min, Float max) { + this.min = min; + this.max = max; + } + + public boolean apply(Float value) { + return value >= min && value <= max; + } + + public String toString() { + String strVal = ""; + if (min != null) { + strVal = "Greater than " + min; + if (max != null) { + strVal += " and "; + } + } + if (max != null) { + strVal += "Less than " + max; + } + return strVal; + } + } + +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/hpdsartifactsdonotchange/Query.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/hpdsartifactsdonotchange/Query.java new file mode 100644 index 000000000..4d995f9d1 --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/hpdsartifactsdonotchange/Query.java @@ -0,0 +1,169 @@ +package edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.*; + +public class Query { + + private static final Logger log = LoggerFactory.getLogger(Query.class); + + public Query() { + + } + + public Query(Query query) { + this.expectedResultType = query.expectedResultType; + this.crossCountFields = new ArrayList(query.crossCountFields); + this.fields = new ArrayList(query.fields); + this.requiredFields = new ArrayList(query.requiredFields); + this.anyRecordOf = new ArrayList(query.anyRecordOf); + this.numericFilters = new TreeMap(query.numericFilters); + this.categoryFilters = new TreeMap(query.categoryFilters); + this.variantInfoFilters = new ArrayList(); + if (query.variantInfoFilters != null) { + query.variantInfoFilters.forEach((filter) -> { + this.variantInfoFilters.add(new VariantInfoFilter(filter)); + }); + } + this.id = query.id; + this.picSureId = query.picSureId; + } + + private ResultType expectedResultType = ResultType.COUNT; + private List crossCountFields = new ArrayList<>(); + private List fields = new ArrayList<>(); + private List requiredFields = new ArrayList<>(); + private List anyRecordOf = new ArrayList<>(); + private List> anyRecordOfMulti = new ArrayList<>(); + private Map numericFilters = new HashMap<>(); + private Map categoryFilters = new HashMap<>(); + private List variantInfoFilters = new ArrayList<>(); + private String id; + + private String picSureId; + + + public ResultType getExpectedResultType() { + return expectedResultType; + } + + public List getCrossCountFields() { + return crossCountFields; + } + + public List getFields() { + return fields; + } + + public List getRequiredFields() { + return requiredFields; + } + + public List getAnyRecordOf() { + return anyRecordOf; + } + + public List> getAnyRecordOfMulti() { + return anyRecordOfMulti; + } + + public List> getAllAnyRecordOf() { + List> anyRecordOfMultiCopy = new ArrayList<>(anyRecordOfMulti); + anyRecordOfMultiCopy.add(anyRecordOf); + return anyRecordOfMultiCopy; + } + + public Map getNumericFilters() { + return numericFilters; + } + + public Map getCategoryFilters() { + return categoryFilters; + } + + public List getVariantInfoFilters() { + return variantInfoFilters; + } + + public String getId() { + return id; + } + + public void setExpectedResultType(ResultType expectedResultType) { + this.expectedResultType = expectedResultType; + } + + public void setCrossCountFields(Collection crossCountFields) { + this.crossCountFields = crossCountFields != null ? new ArrayList<>(crossCountFields) : new ArrayList<>(); + } + + public void setFields(Collection fields) { + this.fields = fields != null ? new ArrayList<>(fields) : new ArrayList<>(); + } + + public void setRequiredFields(Collection requiredFields) { + this.requiredFields = requiredFields != null ? new ArrayList<>(requiredFields) : new ArrayList<>(); + } + + public void setAnyRecordOf(Collection anyRecordOf) { + this.anyRecordOf = anyRecordOf != null ? new ArrayList<>(anyRecordOf) : new ArrayList<>(); + } + + public void setAnyRecordOfMulti(Collection> anyRecordOfMulti) { + this.anyRecordOfMulti = anyRecordOfMulti != null ? new ArrayList<>(anyRecordOfMulti) : new ArrayList<>(); + } + + public void setNumericFilters(Map numericFilters) { + this.numericFilters = numericFilters != null ? new HashMap<>(numericFilters) : new HashMap<>(); + } + + public void setCategoryFilters(Map categoryFilters) { + this.categoryFilters = categoryFilters != null ? new HashMap<>(categoryFilters) : new HashMap<>(); + } + + public void setVariantInfoFilters(Collection variantInfoFilters) { + this.variantInfoFilters = variantInfoFilters != null ? new ArrayList<>(variantInfoFilters) : new ArrayList<>(); + } + + public void setId(String id) { + this.id = id; + } + + public String getPicSureId() { + return picSureId; + } + + public void setPicSureId(String picSureId) { + this.picSureId = picSureId; + } + + public static class VariantInfoFilter { + public VariantInfoFilter() { + + } + + public VariantInfoFilter(VariantInfoFilter filter) { + this.numericVariantInfoFilters = new TreeMap<>(filter.numericVariantInfoFilters); + this.categoryVariantInfoFilters = new TreeMap<>(filter.categoryVariantInfoFilters); + } + + public Map numericVariantInfoFilters; + public Map categoryVariantInfoFilters; + } + + @Override + public boolean equals(Object object) { + if (this == object) return true; + if (object == null || getClass() != object.getClass()) return false; + Query query = (Query) object; + return getExpectedResultType() == query.getExpectedResultType() && Objects.equals(getId(), query.getId()) + && Objects.equals(getPicSureId(), query.getPicSureId()); + } + + @Override + public int hashCode() { + return Objects.hash(getExpectedResultType(), getId(), getPicSureId()); + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/hpdsartifactsdonotchange/ResultType.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/hpdsartifactsdonotchange/ResultType.java new file mode 100644 index 000000000..964e8095c --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/hpds/hpdsartifactsdonotchange/ResultType.java @@ -0,0 +1,85 @@ +package edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange; + +public enum ResultType { + /** + * Just a patient count + */ + COUNT, + /** + * Return a CSV with an observation for each concept for each patient included in the query. If there are multiple facts for a specific + * patient, you will get the one that happens to resolve from a binary search of the facts for the patient id. + */ + DATAFRAME, + + /** + * Create a dataframe, but do not allow conventional access to it. Instead, the dataframe will be accessed in the backend only, where it + * is sent to a S3 bucket by a GIC admin. + * + */ + SECRET_ADMIN_DATAFRAME, + /** + * Return one patient count for each concept path included in the crossCountFields + */ + CROSS_COUNT, + /** + * Return multiple patient count for each concept and its given variables included in the categoryFilters field + */ + CATEGORICAL_CROSS_COUNT, + /** + * Return one patient count for each concept path included in the numericFilters field + */ + CONTINUOUS_CROSS_COUNT, + /** + * Return all variant info column metadata + */ + INFO_COLUMN_LISTING, + /** + * Return the number of total observations for included patients and included fields. + */ + OBSERVATION_COUNT, + /** + * Return the number of observations for included patients and included fields, broken up across the included cross count fields. + */ + OBSERVATION_CROSS_COUNT, + /** + * This was developed for UDN, but is completely useless and should be deleted. + */ + DATAFRAME_MERGED, + /** + * Not completely implemented and currently dead code. Someone with statistics experience needs to develop a p-value based filter for + * the subset of patients. + */ + VARIANTS_OF_INTEREST, + /** + * The count is the size of the intersection of VariantSpecs that is the result of applying all INFO filters in the query. + * + * This is used by clients to limit queries to reasonable numbers of variants. + */ + VARIANT_COUNT_FOR_QUERY, + /** + * This returns the list of string representations of VariantSpecs involved in a query. + */ + VARIANT_LIST_FOR_QUERY, + /** + * This returns quasi-VCF lines for the variants expressed in the query. + */ + VCF_EXCERPT, + /** + * This returns quasi-VCF lines for the variants expressed in the query without patient data. + */ + AGGREGATE_VCF_EXCERPT, + /** + * This returns data to feed a timeline, TODO: add more details later. + */ + TIMELINE_DATA, + /** + * This exports data in the same format as the HPDS csv loader, which is suitable to time series analysis and/or loading into another + * instance of HPDS. + */ + DATAFRAME_TIMESERIES, + + /** + * Patients associated with this query + */ + PATIENTS +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/site/SiteConfiguration.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/site/SiteConfiguration.java new file mode 100644 index 000000000..61333decf --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/site/SiteConfiguration.java @@ -0,0 +1,57 @@ +package edu.harvard.dbmi.avillach.dataupload.site; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.context.ConfigurableApplicationContext; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.util.StringUtils; + +import java.util.ArrayList; +import java.util.List; +import java.util.function.Predicate; +import java.util.stream.Stream; + +@Configuration +public class SiteConfiguration { + + private static final Logger LOG = LoggerFactory.getLogger(SiteConfiguration.class); + + @Value("${aws.s3.institution:}") + private List allSites; + + @Value("${institution.name}") + private String home; + + @Value("${institution.short-display}") + private String display; + + @Value("${cumulus.bucket:}") + private String cumulus; + + @Autowired + private ConfigurableApplicationContext context; + + @Bean + public SiteListing getSiteInfo() { + List otherSites = allSites.stream().filter(Predicate.not(home::equals)).toList(); + if (otherSites.size() == allSites.size()) { + LOG.error("Home site {} not present in listing of institutions: {}", home, allSites); + context.close(); + return new SiteListing(List.of(), "", ""); + } + + // we want the home inst first. Makes frontend display a bit nicer + List sites = Stream.concat(Stream.of(home), otherSites.stream()).toList(); + + if (StringUtils.hasLength(cumulus)) { + LOG.info("Adding cumulus to sites"); + sites = new ArrayList<>(sites); + sites.addLast("cumulus"); + } + + return new SiteListing(sites, home, display); + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/site/SiteInfoController.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/site/SiteInfoController.java new file mode 100644 index 000000000..3442c5e54 --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/site/SiteInfoController.java @@ -0,0 +1,18 @@ +package edu.harvard.dbmi.avillach.dataupload.site; + +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.GetMapping; + +@Controller +public class SiteInfoController { + + @Autowired + private SiteListing institutions; + + @GetMapping("/sites") + public ResponseEntity listSites() { + return ResponseEntity.ok(institutions); + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/site/SiteListing.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/site/SiteListing.java new file mode 100644 index 000000000..3719617e4 --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/site/SiteListing.java @@ -0,0 +1,13 @@ +package edu.harvard.dbmi.avillach.dataupload.site; + +import java.util.List; + +/** + * A Site is an organization participating in GIC. Don't say institute! These names should be all lower case abbreviations for the site: + * bch, cchmc, pitt, washu, chop, uthsc, etc + * @param sites A list of all sites participating in data uploading + * @param homeSite The site where this application is installed + * @param homeSite The short display for the home site + */ +public record SiteListing(List sites, String homeSite, String homeDisplay) { +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/status/DataUploadStatuses.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/status/DataUploadStatuses.java new file mode 100644 index 000000000..0e7ca2d6c --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/status/DataUploadStatuses.java @@ -0,0 +1,11 @@ +package edu.harvard.dbmi.avillach.dataupload.status; + +import jakarta.annotation.Nullable; + +import java.time.LocalDate; + +public record DataUploadStatuses( + UploadStatus genomic, UploadStatus phenotypic, UploadStatus patient, UploadStatus query, String queryId, @Nullable LocalDate approved, + String site +) { +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/status/DataUploadStatusesMapper.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/status/DataUploadStatusesMapper.java new file mode 100644 index 000000000..c42709fb0 --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/status/DataUploadStatusesMapper.java @@ -0,0 +1,30 @@ +package edu.harvard.dbmi.avillach.dataupload.status; + +import org.springframework.jdbc.core.RowMapper; +import org.springframework.stereotype.Component; + +import java.sql.Date; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.UUID; + +@Component +public class DataUploadStatusesMapper implements RowMapper { + @Override + public DataUploadStatuses mapRow(ResultSet rs, int rowNum) throws SQLException { + UploadStatus genomic = UploadStatus.fromString(rs.getString("GENOMIC_STATUS")); + UploadStatus pheno = UploadStatus.fromString(rs.getString("PHENOTYPIC_STATUS")); + UploadStatus patient = UploadStatus.fromString(rs.getString("PATIENT_STATUS")); + UploadStatus queryStatus = UploadStatus.fromString(rs.getString("QUERY_JSON_STATUS")); + String query = fromDashlessString(rs.getString("QUERY")).toString(); + Date approved = rs.getDate("APPROVED"); + String site = rs.getString("SITE"); + return new DataUploadStatuses(genomic, pheno, patient, queryStatus, query, approved == null ? null : approved.toLocalDate(), site); + } + + private UUID fromDashlessString(String uuid) { + String dashed = + uuid.replaceFirst("(\\p{XDigit}{8})(\\p{XDigit}{4})(\\p{XDigit}{4})(\\p{XDigit}{4})(\\p{XDigit}+)", "$1-$2-$3-$4-$5"); + return UUID.fromString(dashed); + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/status/StatusController.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/status/StatusController.java new file mode 100644 index 000000000..e8fa924ec --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/status/StatusController.java @@ -0,0 +1,47 @@ +package edu.harvard.dbmi.avillach.dataupload.status; + +import jakarta.annotation.Nullable; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.format.annotation.DateTimeFormat; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.GetMapping; +import org.springframework.web.bind.annotation.PathVariable; +import org.springframework.web.bind.annotation.RequestParam; + +import java.time.LocalDate; +import java.time.format.DateTimeParseException; +import java.util.Objects; + +@Controller +public class StatusController { + + @Autowired + StatusService statusService; + + @GetMapping("/status/server") + public ResponseEntity getServerStatus() { + return ResponseEntity.ok(statusService.getClientStatus()); + } + + @GetMapping("/status/{queryId}") + public ResponseEntity getUploadStatus(@PathVariable("queryId") String queryId) { + return statusService.getStatus(queryId).map(ResponseEntity::ok).orElse(ResponseEntity.notFound().build()); + } + + @GetMapping("/status/{queryId}/approve") + public ResponseEntity getUploadStatus( + @PathVariable("queryId") String queryId, @RequestParam("date") String approvalDate + ) { + return statusService.approve(queryId, parseDate(approvalDate)).map(ResponseEntity::ok) + .orElse(ResponseEntity.internalServerError().build()); + } + + private LocalDate parseDate(@Nullable String date) { + try { + return LocalDate.parse(Objects.requireNonNull(date)); + } catch (DateTimeParseException | NullPointerException e) { + return LocalDate.now(); + } + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/status/StatusRepository.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/status/StatusRepository.java new file mode 100644 index 000000000..a689594ee --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/status/StatusRepository.java @@ -0,0 +1,91 @@ +package edu.harvard.dbmi.avillach.dataupload.status; + +import edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange.Query; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.jdbc.core.JdbcTemplate; +import org.springframework.stereotype.Repository; + +import java.time.LocalDate; +import java.util.Optional; + +@Repository +public class StatusRepository { + @Autowired + private JdbcTemplate template; + + @Autowired + private DataUploadStatusesMapper statusesMapper; + + public Optional getQueryStatus(String queryId) { + String sql = """ + SELECT + GENOMIC_STATUS, PHENOTYPIC_STATUS, PATIENT_STATUS, QUERY_JSON_STATUS, + hex(QUERY) as QUERY, APPROVED, SITE + FROM + query_status + WHERE + QUERY = unhex(?) + """; + return template.query(sql, statusesMapper, queryId.replace("-", "")).stream().findFirst(); + } + + public void setGenomicStatus(String queryId, UploadStatus status) { + String sql = """ + INSERT INTO query_status + (query, genomic_status) + VALUES (unhex(?), ?) + ON DUPLICATE KEY UPDATE genomic_status=? + """; + template.update(sql, queryId.replace("-", ""), status.toString(), status.toString()); + } + + public void setPhenotypicStatus(String queryId, UploadStatus status) { + String sql = """ + INSERT INTO query_status + (query, phenotypic_status) + VALUES (unhex(?), ?) + ON DUPLICATE KEY UPDATE phenotypic_status=? + """; + template.update(sql, queryId.replace("-", ""), status.toString(), status.toString()); + } + + public void setApproved(String queryId, LocalDate approvalDate) { + String sql = """ + INSERT INTO query_status + (QUERY, APPROVED) + VALUES (unhex(?), ?) + ON DUPLICATE KEY UPDATE APPROVED=? + """; + template.update(sql, queryId.replace("-", ""), approvalDate, approvalDate); + } + + public void setSite(String picSureId, String site) { + String sql = """ + INSERT INTO query_status + (QUERY, SITE) + VALUES (unhex(?), ?) + ON DUPLICATE KEY UPDATE SITE=? + """; + template.update(sql, picSureId.replace("-", ""), site, site); + } + + public void setPatientStatus(String queryId, UploadStatus status) { + String sql = """ + INSERT INTO query_status + (query, patient_status) + VALUES (unhex(?), ?) + ON DUPLICATE KEY UPDATE patient_status=? + """; + template.update(sql, queryId.replace("-", ""), status.toString(), status.toString()); + } + + public void setQueryUploadStatus(String queryId, UploadStatus status) { + String sql = """ + INSERT INTO query_status + (query, query_json_status) + VALUES (unhex(?), ?) + ON DUPLICATE KEY UPDATE query_json_status=? + """; + template.update(sql, queryId.replace("-", ""), status.toString(), status.toString()); + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/status/StatusService.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/status/StatusService.java new file mode 100644 index 000000000..dbabf2d62 --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/status/StatusService.java @@ -0,0 +1,55 @@ +package edu.harvard.dbmi.avillach.dataupload.status; + +import edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange.Query; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Service; + +import java.time.LocalDate; +import java.util.Optional; +import java.util.concurrent.atomic.AtomicReference; + +@Service +public class StatusService { + private final AtomicReference clientStatus = new AtomicReference<>("uninitialized"); + + @Autowired + private StatusRepository repository; + + + public String getClientStatus() { + return clientStatus.get(); + } + + public void setClientStatus(String clientStatus) { + this.clientStatus.set(clientStatus); + } + + public void setGenomicStatus(Query query, UploadStatus status) { + repository.setGenomicStatus(query.getPicSureId(), status); + } + + public void setPhenotypicStatus(Query query, UploadStatus status) { + repository.setPhenotypicStatus(query.getPicSureId(), status); + } + + public Optional getStatus(String queryId) { + return repository.getQueryStatus(queryId); + } + + public Optional approve(String queryId, LocalDate approvalDate) { + repository.setApproved(queryId, approvalDate); + return repository.getQueryStatus(queryId); + } + + public void setSite(Query query, String site) { + repository.setSite(query.getPicSureId(), site); + } + + public void setPatientStatus(Query query, UploadStatus uploadStatus) { + repository.setPatientStatus(query.getPicSureId(), uploadStatus); + } + + public void setQueryUploadStatus(Query query, UploadStatus uploadStatus) { + repository.setQueryUploadStatus(query.getPicSureId(), uploadStatus); + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/status/UploadStatus.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/status/UploadStatus.java new file mode 100644 index 000000000..abed3e14d --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/status/UploadStatus.java @@ -0,0 +1,11 @@ +package edu.harvard.dbmi.avillach.dataupload.status; + +import java.util.Arrays; + +public enum UploadStatus { + Uploading, Querying, Uploaded, Error, Unsent, Unknown, Queued; + + public static UploadStatus fromString(String status) { + return Arrays.stream(UploadStatus.values()).filter(v -> v.name().equalsIgnoreCase(status.trim())).findAny().orElse(Unknown); + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/upload/DataType.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/upload/DataType.java new file mode 100644 index 000000000..3f10b6d3d --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/upload/DataType.java @@ -0,0 +1,35 @@ +package edu.harvard.dbmi.avillach.dataupload.upload; + +import edu.harvard.dbmi.avillach.dataupload.hpds.HPDSClient; +import edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange.Query; +import edu.harvard.dbmi.avillach.dataupload.status.StatusService; +import edu.harvard.dbmi.avillach.dataupload.status.UploadStatus; + +import java.util.function.BiConsumer; +import java.util.function.Function; + +public enum DataType { + Genomic("genomic_data.tsv"), Phenotypic("phenotypic_data.csv"), Patient("patients.txt"); + + public final String fileName; + + DataType(String fileName) { + this.fileName = fileName; + } + + public BiConsumer getStatusSetter(StatusService statusService) { + return switch (this) { + case Genomic -> statusService::setGenomicStatus; + case Phenotypic -> statusService::setPhenotypicStatus; + case Patient -> statusService::setPatientStatus; + }; + } + + public Function getHPDSUpload(HPDSClient client) { + return switch (this) { + case Genomic -> client::writeGenomicData; + case Phenotypic -> client::writePhenotypicData; + case Patient -> client::writePatientData; + }; + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/upload/DataUploadController.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/upload/DataUploadController.java new file mode 100644 index 000000000..994e8f66e --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/upload/DataUploadController.java @@ -0,0 +1,75 @@ +package edu.harvard.dbmi.avillach.dataupload.upload; + +import edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange.Query; +import edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange.ResultType; +import edu.harvard.dbmi.avillach.dataupload.status.DataUploadStatuses; +import edu.harvard.dbmi.avillach.dataupload.status.UploadStatus; +import edu.harvard.dbmi.avillach.dataupload.status.StatusService; +import edu.harvard.dbmi.avillach.dataupload.upload.lambda.CumulusUploadService; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.PathVariable; +import org.springframework.web.bind.annotation.PostMapping; +import org.springframework.web.bind.annotation.RequestBody; +import org.springframework.web.bind.annotation.RequestParam; + +import java.time.LocalDate; +import java.util.List; +import java.util.Optional; + +@Controller +@ConditionalOnProperty(name = "production", havingValue = "true") +public class DataUploadController { + + private static final Logger LOG = LoggerFactory.getLogger(DataUploadController.class); + + @Autowired + private DataUploadService uploadService; + + @Autowired + private StatusService statusService; + + @Autowired + private CumulusUploadService cumulusUploadService; + + @Value("${aws.s3.institution:}") + private List institutions; + + @PostMapping("/upload/{site}") + public ResponseEntity startUpload( + @RequestBody Query query, @PathVariable String site, @RequestParam(value = "dataType") DataType dataType + ) { + if ("cumulus".equals(site)) { + LOG.info("Detected cumulus upload. Switching to cumulus upload service."); + boolean success = cumulusUploadService.asyncUpload(query); + return success ? ResponseEntity.ok(null) : ResponseEntity.internalServerError().body(null); + } + site = site.toLowerCase(); + query.setExpectedResultType(ResultType.DATAFRAME_TIMESERIES); + if (!institutions.contains(site)) { + LOG.info("Could not find site {} in list of sites: {}", site, institutions); + return ResponseEntity.notFound().build(); + } + Optional maybeStatus = statusService.getStatus(query.getPicSureId()); + // 404 if query not in DB yet. + if (maybeStatus.isEmpty()) { + return ResponseEntity.notFound().build(); + } + DataUploadStatuses statuses = maybeStatus.get(); + // 403 if query not approved, or was approved on a future date (please don't do that) + if (statuses.approved() == null || statuses.approved().isAfter(LocalDate.now())) { + return ResponseEntity.status(HttpStatus.UNAUTHORIZED).body(statuses); + } + // no-op if already uploading + if (statuses.phenotypic() == UploadStatus.Uploading || statuses.genomic() == UploadStatus.Uploading) { + LOG.warn("Attempting to reupload query {} which is stuck in Uploading status.", query.getPicSureId()); + } + return ResponseEntity.ok(uploadService.asyncUpload(query, site, dataType)); + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/upload/DataUploadService.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/upload/DataUploadService.java new file mode 100644 index 000000000..8f022a4f1 --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/upload/DataUploadService.java @@ -0,0 +1,239 @@ +package edu.harvard.dbmi.avillach.dataupload.upload; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.dbmi.avillach.dataupload.aws.AWSClientBuilder; +import edu.harvard.dbmi.avillach.dataupload.aws.SiteAWSInfo; +import edu.harvard.dbmi.avillach.dataupload.hpds.HPDSClient; +import edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange.Query; +import edu.harvard.dbmi.avillach.dataupload.status.DataUploadStatuses; +import edu.harvard.dbmi.avillach.dataupload.status.UploadStatus; +import edu.harvard.dbmi.avillach.dataupload.status.StatusService; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty; +import org.springframework.stereotype.Service; +import software.amazon.awssdk.awscore.exception.AwsServiceException; +import software.amazon.awssdk.core.exception.SdkClientException; +import software.amazon.awssdk.core.sync.RequestBody; +import software.amazon.awssdk.services.s3.S3Client; +import software.amazon.awssdk.services.s3.model.*; + +import java.io.IOException; +import java.io.RandomAccessFile; +import java.nio.ByteBuffer; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; +import java.util.Optional; +import java.util.concurrent.Semaphore; +import java.util.function.BiConsumer; + +@ConditionalOnProperty(name = "production", havingValue = "true") +@Service +public class DataUploadService { + + private static final Logger LOG = LoggerFactory.getLogger(DataUploadService.class); + private static final int SIXTEEN_MB = 16 * 1024 * 1024; + + @Autowired + private Semaphore uploadLock; + + @Value("${aws.s3.access_key_id}") + private String keyId; + + @Value("${institution.name}") + private String home; + + @Autowired + private AWSClientBuilder s3ClientBuilder; + + @Autowired + private HPDSClient hpds; + + @Autowired + private StatusService statusService; + + @Autowired + private Path sharingRoot; + + @Autowired + private Map roleARNs; + + private static final ObjectMapper mapper = new ObjectMapper(); + + public DataUploadStatuses asyncUpload(Query query, String site, DataType dataType) { + dataType.getStatusSetter(statusService).accept(query, UploadStatus.Queued); + Thread.ofVirtual().start(() -> uploadData(query, dataType, site)); + statusService.setSite(query, site); + return statusService.getStatus(query.getPicSureId()).orElse(null); // this should never happen. the status object is created during + // the set calls above + } + + protected void uploadData(Query query, DataType dataType, String site) { + LOG.info("Requesting lock for {} / {}", dataType, query.getPicSureId()); + try { + uploadLock.acquire(); + } catch (InterruptedException e) { + LOG.error("Failed to acquire. Abandoning upload"); + return; + } + + LOG.info("Starting upload {} process for uuid: {}", dataType, query.getPicSureId()); + BiConsumer statusSetter = dataType.getStatusSetter(statusService); + statusSetter.accept(query, UploadStatus.Querying); + boolean success = dataType.getHPDSUpload(hpds).apply(query); + if (!success) { + statusSetter.accept(query, UploadStatus.Error); + LOG.info("HPDS failed to write {} data. Status for {} set to error.", dataType, query.getPicSureId()); + uploadLock.release(); + return; + } else { + statusSetter.accept(query, UploadStatus.Uploading); + } + LOG.info("HPDS reported successfully writing {} data for {} to file.", dataType, query.getPicSureId()); + + Path data = Path.of(sharingRoot.toString(), query.getPicSureId(), dataType.fileName); + if (!Files.exists(data)) { + statusSetter.accept(query, UploadStatus.Error); + LOG.info("HPDS lied; file {} DNE. Status set to error", data); + uploadLock.release(); + return; + } + + LOG.info("File location verified. Uploading for {} to AWS", query.getPicSureId()); + success = uploadFileFromPath(data, roleARNs.get(site), query.getPicSureId()); + deleteFile(data); + if (success) { + statusSetter.accept(query, UploadStatus.Uploaded); + LOG.info("{} data for {} uploaded!", dataType, query.getPicSureId()); + } else { + statusSetter.accept(query, UploadStatus.Error); + } + uploadQueryJson(query, roleARNs.get(site)); + LOG.info("Releasing lock for {} / {}", dataType, query.getPicSureId()); + uploadLock.release(); + } + + private void uploadQueryJson(Query query, SiteAWSInfo site) { + UploadStatus queryUploadStatus = + statusService.getStatus(query.getPicSureId()).map(DataUploadStatuses::query).orElse(UploadStatus.Unsent); + if (queryUploadStatus == UploadStatus.Uploaded || queryUploadStatus == UploadStatus.Uploading) { + return; + } + statusService.setQueryUploadStatus(query, UploadStatus.Uploading); + LOG.info("Uploading query json for {}", query.getPicSureId()); + try { + String queryJson = mapper.writeValueAsString(query); + LOG.info("Created query JSON. Writing to file."); + Path jsonPath = Path.of(sharingRoot.toString(), query.getPicSureId(), "query.json"); + Files.writeString(jsonPath, queryJson); + if (!uploadFileFromPath(jsonPath, site, query.getPicSureId())) { + LOG.info("Failed to write query.json"); + statusService.setQueryUploadStatus(query, UploadStatus.Error); + } + Files.delete(jsonPath); + } catch (JsonProcessingException e) { + statusService.setQueryUploadStatus(query, UploadStatus.Error); + LOG.info("Failed to get query json: ", e); + } catch (IOException e) { + statusService.setQueryUploadStatus(query, UploadStatus.Error); + LOG.info("Failed to write query json: ", e); + } + LOG.info("Successfully uploaded query.json for {} to {}", query.getPicSureId(), site.siteName()); + statusService.setQueryUploadStatus(query, UploadStatus.Uploaded); + } + + private void deleteFile(Path data) { + try { + Files.delete(data); + } catch (IOException e) { + LOG.error("Could not data {}", data, e); + } + } + + private boolean uploadFileFromPath(Path p, SiteAWSInfo site, String dir) { + Optional maybeClient = s3ClientBuilder.buildClientForSite(site.siteName()); + if (maybeClient.isEmpty()) { + LOG.info("There is no client for site {}", site); + return false; + } + S3Client s3 = maybeClient.get(); + LOG.info("Starting multipart upload for file {} to site {} in dir {}", p, site, dir); + + CreateMultipartUploadRequest createRequest = + CreateMultipartUploadRequest.builder().bucket(site.bucket()).serverSideEncryption(ServerSideEncryption.AWS_KMS) + .ssekmsKeyId(site.kmsKeyID()).key(Path.of(dir, home + "_" + p.getFileName().toString()).toString()).build(); + String uploadId; + try { + uploadId = s3.createMultipartUpload(createRequest).uploadId(); + } catch (AwsServiceException e) { + LOG.error("Error creating multipart: ", e); + return false; + } + LOG.info("Created initial multipart request and notified S3"); + + LOG.info("Starting upload process..."); + List completedParts = uploadAllParts(p, site, dir, uploadId, s3); + if (completedParts.isEmpty()) { + return false; + } + LOG.info("Upload complete! Uploaded {} parts", completedParts.size()); + + LOG.info("Notifying S3 of completed upload..."); + CompletedMultipartUpload completedUpload = CompletedMultipartUpload.builder().parts(completedParts).build(); + + CompleteMultipartUploadRequest completeRequest = CompleteMultipartUploadRequest.builder().bucket(site.bucket()) + .key(Path.of(dir, home + "_" + p.getFileName().toString()).toString()).uploadId(uploadId).multipartUpload(completedUpload) + .build(); + + try { + s3.completeMultipartUpload(completeRequest); + } catch (AwsServiceException | SdkClientException e) { + LOG.error("Error finishing multipart: ", e); + return false; + } + LOG.info("Done uploading {} to {}", p.getFileName(), site.siteName()); + return true; + } + + private List uploadAllParts(Path p, SiteAWSInfo site, String dir, String uploadId, S3Client s3) { + List completedParts = new ArrayList<>(); + int part = 1; + ByteBuffer buffer = ByteBuffer.allocate(SIXTEEN_MB); + + try (RandomAccessFile file = new RandomAccessFile(p.toString(), "r")) { + long fileSize = file.length(); + long position = 0; + + while (position < fileSize) { + file.seek(position); + int bytesRead = file.getChannel().read(buffer); + + LOG.info("Uploading file {} part {}", p.getFileName(), part); + buffer.flip(); + UploadPartRequest uploadPartRequest = + UploadPartRequest.builder().bucket(site.bucket()).key(Path.of(dir, home + "_" + p.getFileName().toString()).toString()) + .uploadId(uploadId).partNumber(part).contentLength((long) bytesRead).build(); + + + UploadPartResponse response = s3.uploadPart(uploadPartRequest, RequestBody.fromByteBuffer(buffer)); + + completedParts.add(CompletedPart.builder().partNumber(part).eTag(response.eTag()).build()); + + buffer.clear(); + position += bytesRead; + part++; + } + } catch (IOException | AwsServiceException | SdkClientException e) { + LOG.error("Failed to upload file {}, part {}: ", p.getFileName(), part, e); + return List.of(); + } + LOG.info("Uploaded all parts, finishing"); + return completedParts; + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/upload/UploadConfig.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/upload/UploadConfig.java new file mode 100644 index 000000000..5daead1be --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/upload/UploadConfig.java @@ -0,0 +1,15 @@ +package edu.harvard.dbmi.avillach.dataupload.upload; + +import org.springframework.beans.factory.annotation.Value; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; + +import java.util.concurrent.Semaphore; + +@Configuration +public class UploadConfig { + @Bean + public Semaphore getUploadLock(@Value("${max_concurrent_uploads:1}") Integer maxConcurrent) { + return new Semaphore(maxConcurrent); + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/upload/lambda/CumulusUploadService.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/upload/lambda/CumulusUploadService.java new file mode 100644 index 000000000..02469efdf --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/upload/lambda/CumulusUploadService.java @@ -0,0 +1,107 @@ +package edu.harvard.dbmi.avillach.dataupload.upload.lambda; + +import edu.harvard.dbmi.avillach.dataupload.hpds.HPDSClient; +import edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange.Query; +import edu.harvard.dbmi.avillach.dataupload.status.StatusService; +import edu.harvard.dbmi.avillach.dataupload.status.UploadStatus; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Service; + +import java.io.IOException; +import java.io.OutputStream; +import java.io.RandomAccessFile; +import java.net.HttpURLConnection; +import java.net.URL; +import java.nio.ByteBuffer; +import java.nio.channels.FileChannel; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.Optional; + +@Service +public class CumulusUploadService { + private static final Logger log = LoggerFactory.getLogger(CumulusUploadService.class); + private final StatusService statusService; + private final POSTUrlFetcher urlFetcher; + private final HPDSClient hpdsClient; + private final Path sharingRoot; + + + @Autowired + public CumulusUploadService(StatusService statusService, POSTUrlFetcher urlFetcher, HPDSClient hpdsClient, Path sharingRoot) { + this.statusService = statusService; + this.urlFetcher = urlFetcher; + this.hpdsClient = hpdsClient; + this.sharingRoot = sharingRoot; + } + + public boolean asyncUpload(Query query) { + log.info("Async upload called"); + Thread.ofVirtual().start(() -> upload(query)); + return true; + } + + private void upload(Query query) { + log.info("Fetching upload URL"); + Optional uploadURL = urlFetcher.getPreSignedUploadURL(query.getPicSureId(), "patients.txt"); + if (uploadURL.isEmpty()) { + log.error("Could not get upload URL. Exiting"); + return; + } + + boolean written = hpdsClient.writePatientData(query); + if (!written) { + log.warn("HPDS did not write data. Exiting"); + return; + } + log.info("HPDS reported successfully writing {} data for {} to file.", "patients.txt", query.getPicSureId()); + + Path data = Path.of(sharingRoot.toString(), query.getPicSureId(), "patients.txt"); + if (!Files.exists(data)) { + log.info("HPDS lied; file {} DNE. Status set to error", data); + return; + } + + log.info("File location verified. Uploading for {} to AWS", query.getPicSureId()); + try { + boolean uploaded = uploadFileToPresignedUrl(uploadURL.get(), data); + if (uploaded) { + statusService.setPatientStatus(query, UploadStatus.Uploaded); + } + } catch (IOException e) { + log.error("Error uploading data: ", e); + } + log.info("Done uploading patients for query {}", query.getPicSureId()); + + } + + private boolean uploadFileToPresignedUrl(String presignedUrlString, Path filePath) throws IOException { + + URL presignedUrl = new URL(presignedUrlString); + HttpURLConnection connection = (HttpURLConnection) presignedUrl.openConnection(); + connection.setDoOutput(true); + connection.setRequestMethod("PUT"); + OutputStream out = connection.getOutputStream(); + + try (RandomAccessFile file = new RandomAccessFile(filePath.toString(), "r"); FileChannel inChannel = file.getChannel()) { + ByteBuffer buffer = ByteBuffer.allocate(8192); // Buffer size is 8k + + while (inChannel.read(buffer) > 0) { + buffer.flip(); + for (int i = 0; i < buffer.limit(); i++) { + out.write(buffer.get()); + } + buffer.clear(); + } + } catch (IOException e) { + log.error(e.getMessage(), e); + } + + out.close(); + connection.getResponseCode(); + log.info("HTTP response code is " + connection.getResponseCode()); + return HttpURLConnection.HTTP_OK == connection.getResponseCode(); + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/upload/lambda/POSTUrlFetcher.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/upload/lambda/POSTUrlFetcher.java new file mode 100644 index 000000000..d0bbb4985 --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/upload/lambda/POSTUrlFetcher.java @@ -0,0 +1,87 @@ +package edu.harvard.dbmi.avillach.dataupload.upload.lambda; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.dbmi.avillach.dataupload.aws.AWSCredentialsService; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Component; +import software.amazon.awssdk.auth.credentials.AwsCredentials; +import software.amazon.awssdk.auth.credentials.StaticCredentialsProvider; +import software.amazon.awssdk.regions.Region; +import software.amazon.awssdk.services.lambda.LambdaClient; +import software.amazon.awssdk.services.lambda.model.InvokeRequest; +import software.amazon.awssdk.services.lambda.model.InvokeResponse; +import software.amazon.awssdk.core.SdkBytes; + +import java.util.Optional; +import java.util.UUID; + +@Component +public class POSTUrlFetcher { + private static final Logger log = LoggerFactory.getLogger(POSTUrlFetcher.class); + + private final AWSCredentialsService credentialsService; + private final Region region; + private final String labdaARN; + private final String bucketName; + + @Autowired + public POSTUrlFetcher( + AWSCredentialsService credentialsService, @Value("${aws.region}") String region, @Value("${cumulus.lambda:}") String labdaARN, + @Value("${cumulus.bucket:}") String bucketName + ) { + this.credentialsService = credentialsService; + this.region = Region.of(region); + this.labdaARN = labdaARN; + this.bucketName = bucketName; + } + + public Optional getPreSignedUploadURL(String uploadUUID, String fileName) { + AwsCredentials awsCredentials = credentialsService.constructCredentials(); + StaticCredentialsProvider credentialsProvider = StaticCredentialsProvider.create(awsCredentials); + + + try (LambdaClient lambdaClient = LambdaClient.builder().region(region).credentialsProvider(credentialsProvider).build()) { + + String payload = new Payload(uploadUUID, fileName, bucketName).asJson(); + log.info("Created upload request payload of {}", payload); + + InvokeRequest invokeRequest = InvokeRequest.builder().functionName(labdaARN).payload(SdkBytes.fromUtf8String(payload)).build(); + + log.info("Invoking lambda"); + InvokeResponse invokeResponse = lambdaClient.invoke(invokeRequest); + log.info("Returning lambda response"); + return parseResponse(invokeResponse.payload().asUtf8String()); + } + } + + private Optional parseResponse(String raw) { + ObjectMapper objectMapper = new ObjectMapper(); + try { + JsonNode jsonNode = objectMapper.readTree(raw); + return Optional.ofNullable(jsonNode.get("presigned_url").asText()); + } catch (JsonProcessingException e) { + log.error("Error parsing json: ", e); + return Optional.empty(); + } + } + + private record Payload(String object_key, String bucket_name) { + Payload(String directory, String fileName, String bucketName) { + this(directory + "/" + fileName, bucketName); + } + + public String asJson() { + try { + return new ObjectMapper().writeValueAsString(this); + } catch (JsonProcessingException e) { + log.error("Could not make payload: ", e); + return ""; + } + } + } +} diff --git a/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/util/Pair.java b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/util/Pair.java new file mode 100644 index 000000000..28c4f7db7 --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/java/edu/harvard/dbmi/avillach/dataupload/util/Pair.java @@ -0,0 +1,4 @@ +package edu.harvard.dbmi.avillach.dataupload.util; + +public record Pair(F first, S second) { +} diff --git a/services/pic-sure-services/uploader/src/main/resources/application.properties b/services/pic-sure-services/uploader/src/main/resources/application.properties new file mode 100644 index 000000000..810a45b13 --- /dev/null +++ b/services/pic-sure-services/uploader/src/main/resources/application.properties @@ -0,0 +1,32 @@ +spring.datasource.url=jdbc:mysql://${DATA_UPLOAD_DB_HOST:data-upload}:3306/${DATA_UPLOAD_DB_DATABASE:dataupload} +spring.datasource.username=${DATA_UPLOAD_DB_USER:datauploaduser} +spring.datasource.password=${DATA_UPLOAD_DB_PASS:mycoolpassword} +spring.datasource.driver-class-name=com.mysql.cj.jdbc.Driver + +aws.s3.role_arns=${AWS_DATA_UPLOAD_ROLE} +aws.s3.external_ids=${AWS_SHARED_SECRET} +aws.s3.buckets=${AWS_S3_BUCKET_NAME} +aws.s3.access_key_id=${AWS_ACCESS_KEY_ID} +aws.s3.access_key_secret=${AWS_SECRET_ACCESS_KEY} +aws.s3.session_token=${AWS_SESSION_TOKEN:} +aws.s3.institution=${INSTITUTIONS} +aws.region=${AWS_REGION} +aws.kms.key_ids=${AWS_KEY_ID} +aws.authentication.method=${AUTH_METHOD:noauth} + +production=true +enable_file_sharing=true +file_sharing_root=${FILE_SHARING_ROOT} +institution.name=${HOME_INSTITUTION_NAME} +institution.short-display=${HOME_INSTITUTION_DISPLAY} +institution.long-display=${HOME_INSTITUTION_LONG_DISPLAY} +server.port=${PORT:80} + +spring.profiles.active=prod + +upload.lambda.cumulus.lambda=arn:aws:lambda:us-east-1:991175998352:function:cumulus_s3URLGen +upload.lambda.cumulus.bucket=991175998352-cumulus-dev + +# Logging File Output https://docs.spring.io/spring-boot/reference/features/logging.html#features.logging.file-output +# If you are adding additional log files please add them to /var/log/ directory. +logging.file.name=/var/log/uploader.log \ No newline at end of file diff --git a/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/DatauploadApplicationTests.java b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/DatauploadApplicationTests.java new file mode 100644 index 000000000..af8c49f1a --- /dev/null +++ b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/DatauploadApplicationTests.java @@ -0,0 +1,12 @@ +package edu.harvard.dbmi.avillach.dataupload; + +import org.junit.jupiter.api.Test; +import org.springframework.boot.test.context.SpringBootTest; + +@SpringBootTest +class DatauploadApplicationTests { + + @Test + void contextLoads() {} + +} diff --git a/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/aws/AWSClientBuilderTest.java b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/aws/AWSClientBuilderTest.java new file mode 100644 index 000000000..015d72971 --- /dev/null +++ b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/aws/AWSClientBuilderTest.java @@ -0,0 +1,119 @@ +package edu.harvard.dbmi.avillach.dataupload.aws; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.mockito.ArgumentMatcher; +import org.mockito.Mockito; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.test.context.ActiveProfiles; +import org.springframework.test.util.ReflectionTestUtils; +import software.amazon.awssdk.auth.credentials.AwsCredentialsProvider; +import software.amazon.awssdk.auth.credentials.AwsSessionCredentials; +import software.amazon.awssdk.auth.credentials.InstanceProfileCredentialsProvider; +import software.amazon.awssdk.auth.credentials.StaticCredentialsProvider; +import software.amazon.awssdk.services.s3.S3Client; +import software.amazon.awssdk.services.s3.S3ClientBuilder; +import software.amazon.awssdk.services.sts.StsClient; +import software.amazon.awssdk.services.sts.model.AssumeRoleRequest; +import software.amazon.awssdk.services.sts.model.AssumeRoleResponse; +import software.amazon.awssdk.services.sts.model.Credentials; + +import java.time.Instant; +import java.util.Map; +import java.util.Optional; + +@ActiveProfiles("aws_mock") +@SpringBootTest +class AWSClientBuilderTest { + + @MockBean + Map sites; + + @MockBean + StsClient stsClient; + + @MockBean + StsClientProvider stsClientProvider; + + @MockBean + S3ClientBuilder s3ClientBuilder; + + @Autowired + AWSClientBuilder subject; + + @Test + void shouldCreateCredentialsWithoutAssumingRole() { + S3Client s3Client = Mockito.mock(S3Client.class); + Mockito.when(sites.containsKey("bch")).thenReturn(true); + Mockito.when(s3ClientBuilder.credentialsProvider(Mockito.any(InstanceProfileCredentialsProvider.class))) + .thenReturn(s3ClientBuilder); + Mockito.when(s3ClientBuilder.build()).thenReturn(s3Client); + ReflectionTestUtils.setField(subject, "retainRole", true); + Optional actual = subject.buildClientForSite("bch"); + Assertions.assertEquals(Optional.of(s3Client), actual); + } + + @Test + void shouldNotBuildClientIfSiteDNE() { + Mockito.when(sites.get("Narnia")).thenReturn(null); + + Optional actual = subject.buildClientForSite("Narnia"); + Optional expected = Optional.empty(); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldNotBuildClientIfRoleRequestFails() { + SiteAWSInfo siteAWSInfo = new SiteAWSInfo("bch", "aws:arn:420", "external", "bucket", "aws:kms:420"); + Mockito.when(sites.get("bch")).thenReturn(siteAWSInfo); + Mockito.when(sites.containsKey("bch")).thenReturn(true); + + ArgumentMatcher requestMatcher = (r) -> r.roleArn().equals("aws:arn:420") + && r.roleSessionName().startsWith("test_session") && r.externalId().equals("external") && r.durationSeconds().equals(3600); + AssumeRoleResponse response = Mockito.mock(AssumeRoleResponse.class); + Mockito.when(stsClient.assumeRole(Mockito.argThat(requestMatcher))).thenReturn(response); + Mockito.when(stsClientProvider.createClient()).thenReturn(Optional.of(stsClient)); + + Optional actual = subject.buildClientForSite("bch"); + Optional expected = Optional.empty(); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldBuildClient() { + ReflectionTestUtils.setField(subject, "retainRole", false); + SiteAWSInfo siteAWSInfo = new SiteAWSInfo("bch", "aws:arn:420", "external", "bucket", "aws:kms:420"); + Mockito.when(sites.get("bch")).thenReturn(siteAWSInfo); + Mockito.when(sites.containsKey("bch")).thenReturn(true); + + Credentials credentials = Mockito.mock(Credentials.class); + Mockito.when(credentials.accessKeyId()).thenReturn("access_key_id"); + Mockito.when(credentials.secretAccessKey()).thenReturn("secret"); + Mockito.when(credentials.sessionToken()).thenReturn("session"); + Mockito.when(credentials.expiration()).thenReturn(Instant.MAX); + AssumeRoleResponse assumeRoleResponse = Mockito.mock(AssumeRoleResponse.class); + Mockito.when(assumeRoleResponse.credentials()).thenReturn(credentials); + AwsSessionCredentials sessionCredentials = + AwsSessionCredentials.builder().accessKeyId(credentials.accessKeyId()).secretAccessKey(credentials.secretAccessKey()) + .sessionToken(credentials.sessionToken()).expirationTime(credentials.expiration()).build(); + ArgumentMatcher requestMatcher = (r) -> r.roleArn().equals("aws:arn:420") + && r.roleSessionName().startsWith("test_session") && r.externalId().equals("external") && r.durationSeconds().equals(3600); + Mockito.when(stsClient.assumeRole(Mockito.argThat(requestMatcher))).thenReturn(assumeRoleResponse); + Mockito.when(stsClientProvider.createClient()).thenReturn(Optional.of(stsClient)); + + StaticCredentialsProvider provider = StaticCredentialsProvider.create(sessionCredentials); + ArgumentMatcher credsMatcher = (AwsCredentialsProvider p) -> p.toString().equals(provider.toString()); + S3Client s3Client = Mockito.mock(S3Client.class); + Mockito.when(s3ClientBuilder.credentialsProvider(Mockito.argThat(credsMatcher))).thenReturn(s3ClientBuilder); + Mockito.when(s3ClientBuilder.build()).thenReturn(s3Client); + + Optional actual = subject.buildClientForSite("bch"); + Optional expected = Optional.of(s3Client); + + Assertions.assertEquals(expected, actual); + } +} diff --git a/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/aws/AWSConfigurationTest.java b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/aws/AWSConfigurationTest.java new file mode 100644 index 000000000..40b1e9c3f --- /dev/null +++ b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/aws/AWSConfigurationTest.java @@ -0,0 +1,63 @@ +package edu.harvard.dbmi.avillach.dataupload.aws; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.mockito.InjectMocks; +import org.mockito.Mock; +import org.mockito.Mockito; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.context.ConfigurableApplicationContext; +import org.springframework.test.util.ReflectionTestUtils; +import software.amazon.awssdk.auth.credentials.AwsCredentials; +import software.amazon.awssdk.auth.credentials.AwsSessionCredentials; +import software.amazon.awssdk.regions.Region; +import software.amazon.awssdk.services.sts.StsClient; +import software.amazon.awssdk.services.sts.StsClientBuilder; + +import java.util.List; +import java.util.Map; + +import static org.junit.jupiter.api.Assertions.*; + +@SpringBootTest +class AWSConfigurationTest { + @Mock + ConfigurableApplicationContext context; + + @Mock + StsClientBuilder stsClientBuilder; + + @Mock + StsClient stsClient; + + @InjectMocks + AWSConfiguration subject; + + @Test + void shouldCreateRoles() { + ReflectionTestUtils.setField(subject, "institutions", List.of("i1", "i2")); + ReflectionTestUtils.setField(subject, "roleArns", List.of(":)", ">:|")); + ReflectionTestUtils.setField(subject, "externalIDs", List.of("frodo", "gimli")); + ReflectionTestUtils.setField(subject, "buckets", List.of("b1", "b2")); + ReflectionTestUtils.setField(subject, "kmsKeyIds", List.of("k1", "k2")); + + Map actual = subject.roleARNs(); + Map expected = + Map.of("i1", new SiteAWSInfo("i1", ":)", "frodo", "b1", "k1"), "i2", new SiteAWSInfo("i2", ">:|", "gimli", "b2", "k2")); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldNotCreateRoles() { + ReflectionTestUtils.setField(subject, "institutions", List.of("i1", "i2")); + ReflectionTestUtils.setField(subject, "roleArns", List.of(":)", ">:|", ":o")); + ReflectionTestUtils.setField(subject, "externalIDs", List.of("frodo", "gimli")); + ReflectionTestUtils.setField(subject, "buckets", List.of("b1", "b2")); + ReflectionTestUtils.setField(subject, "kmsKeyIds", List.of("k1", "k2")); + + subject.roleARNs(); + + Mockito.verify(context, Mockito.times(1)).close(); + } +} diff --git a/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/aws/AWSCredentialsServiceTest.java b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/aws/AWSCredentialsServiceTest.java new file mode 100644 index 000000000..81d799aac --- /dev/null +++ b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/aws/AWSCredentialsServiceTest.java @@ -0,0 +1,47 @@ +package edu.harvard.dbmi.avillach.dataupload.aws; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.mockito.InjectMocks; +import org.mockito.Mock; +import org.mockito.Mockito; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.context.ConfigurableApplicationContext; +import org.springframework.test.util.ReflectionTestUtils; +import software.amazon.awssdk.auth.credentials.AwsCredentials; +import software.amazon.awssdk.auth.credentials.AwsSessionCredentials; + +@SpringBootTest +class AWSCredentialsServiceTest { + + @Mock + ConfigurableApplicationContext context; + + @InjectMocks + AWSCredentialsService subject; + + @Test + void shouldCreateCredentials() { + ReflectionTestUtils.setField(subject, "authMethod", "user"); + ReflectionTestUtils.setField(subject, "secret", "s1"); + ReflectionTestUtils.setField(subject, "key", "k1"); + ReflectionTestUtils.setField(subject, "token", "t1"); + + AwsCredentials actual = subject.constructCredentials(); + AwsSessionCredentials expected = AwsSessionCredentials.create("k1", "s1", "t1"); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldNotCreateCredentials() { + ReflectionTestUtils.setField(subject, "authMethod", "user"); + ReflectionTestUtils.setField(subject, "secret", ""); + ReflectionTestUtils.setField(subject, "key", "k1"); + ReflectionTestUtils.setField(subject, "token", "t1"); + + subject.constructCredentials(); + + Mockito.verify(context, Mockito.times(1)).close(); + } +} diff --git a/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/hpds/HPDSClientTest.java b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/hpds/HPDSClientTest.java new file mode 100644 index 000000000..4b0ae6c4b --- /dev/null +++ b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/hpds/HPDSClientTest.java @@ -0,0 +1,86 @@ +package edu.harvard.dbmi.avillach.dataupload.hpds; + +import edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange.Query; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.http.HttpMethod; +import org.springframework.http.HttpStatus; +import org.springframework.test.web.client.MockRestServiceServer; +import org.springframework.web.client.RestClient; + +import static org.springframework.test.web.client.match.MockRestRequestMatchers.method; +import static org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo; +import static org.springframework.test.web.client.response.MockRestResponseCreators.withStatus; +import static org.springframework.test.web.client.response.MockRestResponseCreators.withSuccess; + +class HPDSClientTest { + + private static final String HPDS_URI = "http://hpds:8080/PIC-SURE/"; + + private MockRestServiceServer server; + private HPDSClient subject; + + @BeforeEach + void setUp() { + RestClient.Builder builder = RestClient.builder(); + server = MockRestServiceServer.bindTo(builder).build(); + subject = new HPDSClient(builder.build()); + } + + @Test + void shouldInitializeQuery() { + Query query = new Query(); + query.setPicSureId("my id"); + server.expect(requestTo(HPDS_URI + "query/sync")).andExpect(method(HttpMethod.POST)).andRespond(withSuccess()); + + boolean actual = subject.initializeQuery(query); + + Assertions.assertTrue(actual); + } + + @Test + void shouldNotInitializeQuery() { + Query query = new Query(); + query.setPicSureId("my id"); + server.expect(requestTo(HPDS_URI + "query/sync")).andExpect(method(HttpMethod.POST)).andRespond(withStatus(HttpStatus.NOT_FOUND)); + + boolean actual = subject.initializeQuery(query); + + Assertions.assertFalse(actual); + } + + @Test + void shouldWritePhenotypicData() { + Query query = new Query(); + query.setPicSureId("my id"); + server.expect(requestTo(HPDS_URI + "write/phenotypic")).andExpect(method(HttpMethod.POST)).andRespond(withSuccess()); + + boolean actual = subject.writePhenotypicData(query); + + Assertions.assertTrue(actual); + } + + @Test + void shouldNotWriteGenomicData() { + Query query = new Query(); + query.setPicSureId("my id"); + server.expect(requestTo(HPDS_URI + "write/genomic")).andExpect(method(HttpMethod.POST)) + .andRespond(withStatus(HttpStatus.INTERNAL_SERVER_ERROR)); + + boolean actual = subject.writeGenomicData(query); + + Assertions.assertFalse(actual); + } + + @Test + void shouldWriteTestData() { + Query query = new Query(); + query.setPicSureId("my id"); + server.expect(requestTo(HPDS_URI + "write/test_upload")).andExpect(method(HttpMethod.POST)).andRespond(withSuccess()); + + boolean actual = subject.writeTestData(query); + + Assertions.assertTrue(actual); + } +} diff --git a/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/hpds/HPDSConnectionVerifierTest.java b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/hpds/HPDSConnectionVerifierTest.java new file mode 100644 index 000000000..45aca06a5 --- /dev/null +++ b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/hpds/HPDSConnectionVerifierTest.java @@ -0,0 +1,82 @@ +package edu.harvard.dbmi.avillach.dataupload.hpds; + +import edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange.Query; +import edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange.ResultType; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.io.TempDir; +import org.mockito.Mockito; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.bean.override.mockito.MockitoBean; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.UUID; + +@SpringBootTest +class HPDSConnectionVerifierTest { + + @MockitoBean + private HPDSClient client; + + @MockitoBean + private UUIDGenerator generator; + + private final Query query = new Query(); + { + query.setPicSureId("9f1fc383-611b-4c6a-af37-a33c07feea5e"); + query.setId("9f1fc383-611b-4c6a-af37-a33c07feea5e"); + query.setExpectedResultType(ResultType.COUNT); + } + + @Test + void shouldFailWhenHPDS400s(@TempDir Path sharingRoot) { + Mockito.when(client.writeTestData(query)).thenReturn(false); + Mockito.when(generator.generate()).thenReturn(UUID.fromString("9f1fc383-611b-4c6a-af37-a33c07feea5e")); + HPDSConnectionVerifier subject = new HPDSConnectionVerifier(client, sharingRoot, generator); + + boolean result = subject.verifyConnection(); + + Assertions.assertFalse(result); + Mockito.verify(client, Mockito.times(1)).writeTestData(query); + } + + @Test + void shouldFailWhenHPDSDoesNotWrite(@TempDir Path sharingRoot) { + Mockito.when(client.writeTestData(query)).thenReturn(true); + Mockito.when(generator.generate()).thenReturn(UUID.fromString("9f1fc383-611b-4c6a-af37-a33c07feea5e")); + HPDSConnectionVerifier subject = new HPDSConnectionVerifier(client, sharingRoot, generator); + + boolean result = subject.verifyConnection(); + + Assertions.assertFalse(result); + Mockito.verify(client, Mockito.times(1)).writeTestData(query); + } + + @Test + void shouldFailWhenHPDSMakesADirectory(@TempDir Path sharingRoot) throws IOException { + Files.createDirectory(Path.of(sharingRoot.toString(), "9f1fc383-611b-4c6a-af37-a33c07feea5e")); + Files.createDirectory(Path.of(sharingRoot.toString(), "9f1fc383-611b-4c6a-af37-a33c07feea5e", "test_data.txt")); + + Mockito.when(client.writeTestData(query)).thenReturn(true); + Mockito.when(generator.generate()).thenReturn(UUID.fromString("9f1fc383-611b-4c6a-af37-a33c07feea5e")); + HPDSConnectionVerifier subject = new HPDSConnectionVerifier(client, sharingRoot, generator); + + Assertions.assertFalse(subject.verifyConnection()); + Mockito.verify(client, Mockito.times(1)).writeTestData(query); + } + + @Test + void shouldPass(@TempDir Path sharingRoot) throws IOException { + Files.createDirectory(Path.of(sharingRoot.toString(), "9f1fc383-611b-4c6a-af37-a33c07feea5e")); + Files.writeString(Path.of(sharingRoot.toString(), "9f1fc383-611b-4c6a-af37-a33c07feea5e", "test_data.txt"), "Howdy :)"); + + Mockito.when(client.writeTestData(query)).thenReturn(true); + Mockito.when(generator.generate()).thenReturn(UUID.fromString("9f1fc383-611b-4c6a-af37-a33c07feea5e")); + HPDSConnectionVerifier subject = new HPDSConnectionVerifier(client, sharingRoot, generator); + + Assertions.assertTrue(subject.verifyConnection()); + Mockito.verify(client, Mockito.times(1)).writeTestData(query); + } +} diff --git a/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/site/SiteConfigurationTest.java b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/site/SiteConfigurationTest.java new file mode 100644 index 000000000..997f1ee9a --- /dev/null +++ b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/site/SiteConfigurationTest.java @@ -0,0 +1,45 @@ +package edu.harvard.dbmi.avillach.dataupload.site; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.mockito.InjectMocks; +import org.mockito.Mock; +import org.mockito.Mockito; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.context.ConfigurableApplicationContext; +import org.springframework.test.util.ReflectionTestUtils; + +import java.util.List; + +@SpringBootTest +class SiteConfigurationTest { + + @Mock + ConfigurableApplicationContext context; + + @InjectMocks + SiteConfiguration subject; + + @Test + void shouldGetSiteInfo() { + ReflectionTestUtils.setField(subject, "allSites", List.of("cchmc", "bch")); + ReflectionTestUtils.setField(subject, "home", "bch"); + ReflectionTestUtils.setField(subject, "display", "BCH"); + + SiteListing actual = subject.getSiteInfo(); + SiteListing expected = new SiteListing(List.of("bch", "cchmc"), "bch", "BCH"); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldNotGetSiteInfo() { + ReflectionTestUtils.setField(subject, "allSites", List.of("cchmc", "narnia")); + ReflectionTestUtils.setField(subject, "home", "bch"); + ReflectionTestUtils.setField(subject, "display", "BCH"); + + subject.getSiteInfo(); + + Mockito.verify(context, Mockito.times(1)).close(); + } +} diff --git a/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/site/SiteInfoControllerTest.java b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/site/SiteInfoControllerTest.java new file mode 100644 index 000000000..fc47d4f22 --- /dev/null +++ b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/site/SiteInfoControllerTest.java @@ -0,0 +1,26 @@ +package edu.harvard.dbmi.avillach.dataupload.site; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.mockito.InjectMocks; +import org.mockito.Mock; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.ResponseEntity; + +@SpringBootTest +class SiteInfoControllerTest { + + @Mock + SiteListing listing; + + @InjectMocks + SiteInfoController subject; + + @Test + void shouldListSites() { + ResponseEntity actual = subject.listSites(); + + Assertions.assertEquals(listing, actual.getBody()); + Assertions.assertTrue(actual.getStatusCode().is2xxSuccessful()); + } +} diff --git a/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/status/StatusRepositoryTest.java b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/status/StatusRepositoryTest.java new file mode 100644 index 000000000..bbd787773 --- /dev/null +++ b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/status/StatusRepositoryTest.java @@ -0,0 +1,168 @@ +package edu.harvard.dbmi.avillach.dataupload.status; + +import edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange.Query; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.springframework.test.context.jdbc.Sql; +import org.testcontainers.containers.MySQLContainer; +import org.testcontainers.junit.jupiter.Container; +import org.testcontainers.junit.jupiter.Testcontainers; + +import java.time.LocalDate; +import java.util.Optional; +import java.util.UUID; + +@Testcontainers +@SpringBootTest +@Sql(scripts = {"/seed.sql"}) +class StatusRepositoryTest { + + @Container + static final MySQLContainer databaseContainer = new MySQLContainer<>("mysql:8.0").withReuse(true); + + @DynamicPropertySource + static void mySQLProperties(DynamicPropertyRegistry registry) { + registry.add("spring.datasource.url", databaseContainer::getJdbcUrl); + registry.add("spring.datasource.username", databaseContainer::getUsername); + registry.add("spring.datasource.password", databaseContainer::getPassword); + registry.add("spring.datasource.db", databaseContainer::getDatabaseName); + } + + @Autowired + StatusRepository subject; + + @Test + void shouldGetGenomicStatus() { + Query query = new Query(); + query.setPicSureId(UUID.fromString("33613336-3934-3761-2d38-3233312d3131").toString()); + + Optional actual = subject.getQueryStatus(query.getPicSureId()).map(DataUploadStatuses::genomic); + Optional expected = Optional.of(UploadStatus.Uploaded); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldGetPhenotypicStatus() { + Query query = new Query(); + query.setPicSureId(UUID.fromString("33613336-3934-3761-2d38-3233312d3131").toString()); + + Optional actual = subject.getQueryStatus(query.getPicSureId()).map(DataUploadStatuses::phenotypic); + Optional expected = Optional.of(UploadStatus.Error); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldSetGenomicStatus() { + Query query = new Query(); + query.setPicSureId(UUID.fromString("33613336-3934-3761-2d38-3233312d3131").toString()); + + subject.setGenomicStatus(query.getPicSureId(), UploadStatus.Uploading); + Optional actual = subject.getQueryStatus(query.getPicSureId()).map(DataUploadStatuses::genomic); + Optional expected = Optional.of(UploadStatus.Uploading); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldSetPhenotypicStatus() { + Query query = new Query(); + query.setPicSureId(UUID.fromString("33613336-3934-3761-2d38-3233312d3131").toString()); + + subject.setPhenotypicStatus(query.getPicSureId(), UploadStatus.Unsent); + Optional actual = subject.getQueryStatus(query.getPicSureId()).map(DataUploadStatuses::phenotypic); + Optional expected = Optional.of(UploadStatus.Unsent); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldSetStatusesOfNewQuery() { + Query query = new Query(); + query.setPicSureId(UUID.randomUUID().toString()); + + subject.setGenomicStatus(query.getPicSureId(), UploadStatus.Uploading); + + Optional actual = subject.getQueryStatus(query.getPicSureId()).map(DataUploadStatuses::phenotypic); + Optional expected = Optional.of(UploadStatus.Unsent); + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldGetApproved() { + Query query = new Query(); + query.setPicSureId(UUID.fromString("33613336-3934-3761-2d38-3233312d3131").toString()); + + Optional actual = subject.getQueryStatus(query.getPicSureId()).map(DataUploadStatuses::approved); + Optional expected = Optional.of(LocalDate.of(2022, 2, 22)); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldSetApprovedOfNewQuery() { + Query query = new Query(); + query.setPicSureId(UUID.randomUUID().toString()); + + subject.setApproved(query.getPicSureId(), LocalDate.of(2023, 1, 2)); + Optional actual = subject.getQueryStatus(query.getPicSureId()).map(DataUploadStatuses::approved); + Optional expected = Optional.of(LocalDate.of(2023, 1, 2)); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldGetQueryId() { + Query query = new Query(); + query.setPicSureId(UUID.fromString("33613336-3934-3761-2d38-3233312d3131").toString()); + + DataUploadStatuses actual = subject.getQueryStatus(query.getPicSureId()).orElseThrow(); + DataUploadStatuses expected = new DataUploadStatuses( + UploadStatus.Uploaded, UploadStatus.Error, UploadStatus.Unsent, UploadStatus.Uploading, "33613336-3934-3761-2d38-3233312d3131", + LocalDate.of(2022, 2, 22), "bch" + ); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldSetSite() { + Query query = new Query(); + query.setPicSureId(UUID.fromString("33613336-3934-3761-2d38-3233312d3131").toString()); + + subject.setSite(query.getPicSureId(), "Narnia"); + Optional actual = subject.getQueryStatus(query.getPicSureId()).map(DataUploadStatuses::site); + Optional expected = Optional.of("Narnia"); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldSetPatient() { + Query query = new Query(); + query.setPicSureId(UUID.fromString("33613336-3934-3761-2d38-3233312d3131").toString()); + + subject.setPatientStatus(query.getPicSureId(), UploadStatus.Uploaded); + Optional actual = subject.getQueryStatus(query.getPicSureId()).map(DataUploadStatuses::patient); + Optional expected = Optional.of(UploadStatus.Uploaded); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldSetQueryStatus() { + Query query = new Query(); + query.setPicSureId(UUID.fromString("33613336-3934-3761-2d38-3233312d3131").toString()); + + subject.setQueryUploadStatus(query.getPicSureId(), UploadStatus.Error); + Optional actual = subject.getQueryStatus(query.getPicSureId()).map(DataUploadStatuses::query); + Optional expected = Optional.of(UploadStatus.Error); + + Assertions.assertEquals(expected, actual); + } +} diff --git a/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/status/StatusServiceTest.java b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/status/StatusServiceTest.java new file mode 100644 index 000000000..bff8a7172 --- /dev/null +++ b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/status/StatusServiceTest.java @@ -0,0 +1,108 @@ +package edu.harvard.dbmi.avillach.dataupload.status; + +import edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange.Query; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.mockito.InjectMocks; +import org.mockito.Mock; +import org.mockito.Mockito; +import org.springframework.boot.test.context.SpringBootTest; + +import java.time.LocalDate; +import java.util.Optional; + +@SpringBootTest +class StatusServiceTest { + + @Mock + StatusRepository repository; + + @InjectMocks + StatusService subject; + + @Test + void shouldGetAndSet() { + String initial = subject.getClientStatus(); + Assertions.assertEquals("uninitialized", initial); + + subject.setClientStatus("spooky"); + String actual = subject.getClientStatus(); + Assertions.assertEquals("spooky", actual); + } + + @Test + void shouldSetGenomicStatus() { + Query q = new Query(); + q.setPicSureId(":)"); + + subject.setGenomicStatus(q, UploadStatus.Uploading); + + Mockito.verify(repository, Mockito.times(1)).setGenomicStatus(":)", UploadStatus.Uploading); + } + + @Test + void shouldSetPhenotypicStatus() { + Query q = new Query(); + q.setPicSureId(":)"); + + subject.setPhenotypicStatus(q, UploadStatus.Uploading); + + Mockito.verify(repository, Mockito.times(1)).setPhenotypicStatus(":)", UploadStatus.Uploading); + } + + @Test + void shouldSetSite() { + Query q = new Query(); + q.setPicSureId(":)"); + + subject.setSite(q, "narnia"); + + Mockito.verify(repository, Mockito.times(1)).setSite(":)", "narnia"); + } + + @Test + void shouldApprove() { + Query q = new Query(); + q.setPicSureId(":)"); + LocalDate now = LocalDate.now(); + + subject.approve(q.getPicSureId(), now); + + Mockito.verify(repository, Mockito.times(1)).setApproved(":)", now); + } + + @Test + void shouldGetQueryStatus() { + Query q = new Query(); + q.setPicSureId(":)"); + DataUploadStatuses statuses = new DataUploadStatuses( + UploadStatus.Error, UploadStatus.Error, UploadStatus.Unsent, UploadStatus.Unsent, ":)", LocalDate.now(), "bch" + ); + Mockito.when(repository.getQueryStatus(":)")).thenReturn(Optional.of(statuses)); + + Optional actual = subject.getStatus(q.getPicSureId()); + Optional expected = Optional.of(statuses); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldSetPatientStatus() { + Query q = new Query(); + q.setPicSureId(":)"); + + subject.setPatientStatus(q, UploadStatus.Uploading); + + Mockito.verify(repository, Mockito.times(1)).setPatientStatus(":)", UploadStatus.Uploading); + } + + @Test + void shouldSetQueryStatus() { + Query q = new Query(); + q.setPicSureId(":)"); + + subject.setQueryUploadStatus(q, UploadStatus.Uploading); + + Mockito.verify(repository, Mockito.times(1)).setQueryUploadStatus(":)", UploadStatus.Uploading); + } +} diff --git a/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/upload/DataUploadControllerTest.java b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/upload/DataUploadControllerTest.java new file mode 100644 index 000000000..3b91aeb84 --- /dev/null +++ b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/upload/DataUploadControllerTest.java @@ -0,0 +1,110 @@ +package edu.harvard.dbmi.avillach.dataupload.upload; + +import edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange.Query; +import edu.harvard.dbmi.avillach.dataupload.status.DataUploadStatuses; +import edu.harvard.dbmi.avillach.dataupload.status.UploadStatus; +import edu.harvard.dbmi.avillach.dataupload.status.StatusService; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.InjectMocks; +import org.mockito.Mock; +import org.mockito.Mockito; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.test.util.ReflectionTestUtils; + +import java.time.LocalDate; +import java.util.List; +import java.util.Optional; + +@SpringBootTest +class DataUploadControllerTest { + + @Mock + DataUploadService uploadService; + + @Mock + StatusService statusService; + + @InjectMocks + DataUploadController subject; + + @BeforeEach + public void init() { + ReflectionTestUtils.setField(subject, "institutions", List.of("bch", DataType.Genomic)); + } + + @Test + void shouldUpload() { + Query query = new Query(); + query.setPicSureId("my id"); + DataUploadStatuses before = new DataUploadStatuses( + UploadStatus.Unsent, UploadStatus.Unsent, UploadStatus.Unsent, UploadStatus.Unsent, query.getPicSureId(), LocalDate.EPOCH, "bch" + ); + DataUploadStatuses after = new DataUploadStatuses( + UploadStatus.Uploading, UploadStatus.Uploading, UploadStatus.Unsent, UploadStatus.Unsent, query.getPicSureId(), LocalDate.EPOCH, + "bch" + ); + Mockito.when(statusService.getStatus(query.getPicSureId())).thenReturn(Optional.of(before)); + Mockito.when(uploadService.asyncUpload(query, "bch", DataType.Genomic)).thenReturn(after); + + ResponseEntity actual = subject.startUpload(query, "bch", DataType.Genomic); + ResponseEntity expected = ResponseEntity.ok(after); + + Mockito.verify(uploadService, Mockito.times(1)).asyncUpload(query, "bch", DataType.Genomic); + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldSayNotFound() { + Query query = new Query(); + query.setPicSureId("my id"); + + Mockito.when(statusService.getStatus(query.getPicSureId())).thenReturn(Optional.empty()); + + ResponseEntity actual = subject.startUpload(query, "bch", DataType.Genomic); + + Assertions.assertEquals(HttpStatus.NOT_FOUND, actual.getStatusCode()); + } + + @Test + void shouldSayNotFoundForSite() { + Query query = new Query(); + query.setPicSureId("my id"); + + ResponseEntity actual = subject.startUpload(query, "foo", DataType.Genomic); + + Assertions.assertEquals(HttpStatus.NOT_FOUND, actual.getStatusCode()); + } + + @Test + void shouldBlockUnapproved() { + Query query = new Query(); + query.setPicSureId("my id"); + DataUploadStatuses nullApprovalDate = new DataUploadStatuses( + UploadStatus.Unsent, UploadStatus.Unsent, UploadStatus.Unsent, UploadStatus.Unsent, query.getPicSureId(), null, "bch" + ); + Mockito.when(statusService.getStatus(query.getPicSureId())).thenReturn(Optional.of(nullApprovalDate)); + + ResponseEntity actual = subject.startUpload(query, "bch", DataType.Genomic); + + Assertions.assertEquals(HttpStatus.UNAUTHORIZED, actual.getStatusCode()); + } + + @Test + void shouldBlockApprovedInFuture() { + Query query = new Query(); + query.setPicSureId("my id"); + DataUploadStatuses nullApprovalDate = new DataUploadStatuses( + UploadStatus.Unsent, UploadStatus.Unsent, UploadStatus.Unsent, UploadStatus.Unsent, query.getPicSureId(), LocalDate.MAX, "bch" + ); + Mockito.when(statusService.getStatus(query.getPicSureId())).thenReturn(Optional.of(nullApprovalDate)); + + ResponseEntity actual = subject.startUpload(query, "bch", DataType.Genomic); + + Assertions.assertEquals(HttpStatus.UNAUTHORIZED, actual.getStatusCode()); + } + +} diff --git a/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/upload/DataUploadServiceTest.java b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/upload/DataUploadServiceTest.java new file mode 100644 index 000000000..a34df7c8d --- /dev/null +++ b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/upload/DataUploadServiceTest.java @@ -0,0 +1,243 @@ +package edu.harvard.dbmi.avillach.dataupload.upload; + +import edu.harvard.dbmi.avillach.dataupload.aws.AWSClientBuilder; +import edu.harvard.dbmi.avillach.dataupload.aws.SiteAWSInfo; +import edu.harvard.dbmi.avillach.dataupload.hpds.HPDSClient; +import edu.harvard.dbmi.avillach.dataupload.hpds.hpdsartifactsdonotchange.Query; +import edu.harvard.dbmi.avillach.dataupload.status.DataUploadStatuses; +import edu.harvard.dbmi.avillach.dataupload.status.StatusService; +import edu.harvard.dbmi.avillach.dataupload.status.UploadStatus; +import edu.harvard.dbmi.avillach.domain.QueryStatus; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.io.TempDir; +import org.mockito.InjectMocks; +import org.mockito.Mock; +import org.mockito.Mockito; +import org.mockito.Spy; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.util.ReflectionTestUtils; +import software.amazon.awssdk.awscore.exception.AwsServiceException; +import software.amazon.awssdk.core.sync.RequestBody; +import software.amazon.awssdk.services.s3.S3Client; +import software.amazon.awssdk.services.s3.model.*; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.time.LocalDate; +import java.util.Date; +import java.util.Map; +import java.util.Optional; +import java.util.concurrent.Semaphore; + +@SpringBootTest +class DataUploadServiceTest { + + @Spy + Semaphore uploadLock = new Semaphore(1); + + @Mock + HPDSClient hpds; + + @Mock + StatusService statusService; + + @Mock + private Path sharingRoot; + + @Mock + S3Client s3Client; + + @Mock + AWSClientBuilder s3; + + @InjectMocks + DataUploadService subject; + + Map roleARNs = Map.of("bch", new SiteAWSInfo("bch", "", "myid", "", "")); + + @Test + void shouldNotUploadDataForHPDSError(@TempDir Path tempDir) throws InterruptedException { + Query q = new Query(); + q.setPicSureId("my-id"); + q.setId("my-id"); + + Mockito.when(sharingRoot.toString()).thenReturn(tempDir.toString()); + Mockito.when(hpds.writeGenomicData(q)).thenReturn(false); + + subject.uploadData(q, DataType.Genomic, "bch"); + + Mockito.verify(statusService, Mockito.times(1)).setGenomicStatus(q, UploadStatus.Querying); + Mockito.verify(statusService, Mockito.times(1)).setGenomicStatus(q, UploadStatus.Error); + Mockito.verify(uploadLock, Mockito.times(1)).acquire(); + Mockito.verify(uploadLock, Mockito.times(1)).release(); + } + + @Test + void shouldNotUploadDataIfFileDNE(@TempDir Path tempDir) throws InterruptedException { + Query q = new Query(); + q.setPicSureId("my-id"); + q.setId("my-id"); + + Mockito.when(sharingRoot.toString()).thenReturn(tempDir.toString()); + Mockito.when(hpds.writePhenotypicData(q)).thenReturn(true); + + subject.uploadData(q, DataType.Phenotypic, "bch"); + + Mockito.verify(statusService, Mockito.times(1)).setPhenotypicStatus(q, UploadStatus.Querying); + Mockito.verify(statusService, Mockito.times(1)).setPhenotypicStatus(q, UploadStatus.Uploading); + Mockito.verify(statusService, Mockito.times(1)).setPhenotypicStatus(q, UploadStatus.Error); + Mockito.verify(uploadLock, Mockito.times(1)).acquire(); + Mockito.verify(uploadLock, Mockito.times(1)).release(); + } + + @Test + void shouldNotUploadDataIfAWSUpset(@TempDir Path tempDir) throws IOException, InterruptedException { + Query q = new Query(); + q.setPicSureId("my-id"); + q.setId("my-id"); + + Files.createDirectory(Path.of(tempDir.toString(), q.getPicSureId())); + Files.writeString(Path.of(tempDir.toString(), q.getPicSureId(), DataType.Phenotypic.fileName), ":)"); + ReflectionTestUtils.setField(subject, "roleARNs", roleARNs); + DataUploadStatuses statuses = new DataUploadStatuses( + UploadStatus.Unsent, UploadStatus.Unsent, UploadStatus.Unsent, UploadStatus.Uploaded, q.getPicSureId(), LocalDate.MIN, "bch" + ); + + Mockito.when(statusService.getStatus(q.getPicSureId())).thenReturn(Optional.of(statuses)); + Mockito.when(sharingRoot.toString()).thenReturn(tempDir.toString()); + Mockito.when(hpds.writePhenotypicData(q)).thenReturn(true); + Mockito.when(s3.buildClientForSite("bch")).thenReturn(Optional.of(s3Client)); + Mockito.when(s3Client.createMultipartUpload(Mockito.any(CreateMultipartUploadRequest.class))) + .thenThrow(AwsServiceException.builder().build()); + + subject.uploadData(q, DataType.Phenotypic, "bch"); + + Mockito.verify(statusService, Mockito.times(1)).setPhenotypicStatus(q, UploadStatus.Querying); + Mockito.verify(statusService, Mockito.times(1)).setPhenotypicStatus(q, UploadStatus.Uploading); + Mockito.verify(s3Client, Mockito.times(1)).createMultipartUpload(Mockito.any(CreateMultipartUploadRequest.class)); + Mockito.verify(statusService, Mockito.times(1)).setPhenotypicStatus(q, UploadStatus.Error); + Mockito.verify(uploadLock, Mockito.times(1)).acquire(); + Mockito.verify(uploadLock, Mockito.times(1)).release(); + } + + @Test + void shouldNotUploadDataIfAWSUploadFails(@TempDir Path tempDir) throws IOException, InterruptedException { + Query q = new Query(); + q.setPicSureId("my-id"); + q.setId("my-id"); + + Files.createDirectory(Path.of(tempDir.toString(), q.getPicSureId())); + Files.writeString(Path.of(tempDir.toString(), q.getPicSureId(), DataType.Phenotypic.fileName), ":)"); + ReflectionTestUtils.setField(subject, "roleARNs", roleARNs); + CreateMultipartUploadResponse createResp = Mockito.mock(CreateMultipartUploadResponse.class); + Mockito.when(createResp.uploadId()).thenReturn("frank"); + DataUploadStatuses statuses = new DataUploadStatuses( + UploadStatus.Unsent, UploadStatus.Unsent, UploadStatus.Unsent, UploadStatus.Uploaded, q.getPicSureId(), LocalDate.MIN, "bch" + ); + + Mockito.when(statusService.getStatus(q.getPicSureId())).thenReturn(Optional.of(statuses)); + Mockito.when(sharingRoot.toString()).thenReturn(tempDir.toString()); + Mockito.when(hpds.writePhenotypicData(q)).thenReturn(true); + Mockito.when(s3.buildClientForSite("bch")).thenReturn(Optional.of(s3Client)); + Mockito.when(s3Client.createMultipartUpload(Mockito.any(CreateMultipartUploadRequest.class))).thenReturn(createResp); + Mockito.when(s3Client.uploadPart(Mockito.any(UploadPartRequest.class), Mockito.any(RequestBody.class))) + .thenThrow(AwsServiceException.builder().build()); + + subject.uploadData(q, DataType.Phenotypic, "bch"); + + Mockito.verify(statusService, Mockito.times(1)).setPhenotypicStatus(q, UploadStatus.Querying); + Mockito.verify(statusService, Mockito.times(1)).setPhenotypicStatus(q, UploadStatus.Uploading); + Mockito.verify(s3Client, Mockito.times(1)).createMultipartUpload(Mockito.any(CreateMultipartUploadRequest.class)); + Mockito.verify(s3Client, Mockito.times(1)).uploadPart(Mockito.any(UploadPartRequest.class), Mockito.any(RequestBody.class)); + Mockito.verify(statusService, Mockito.times(1)).setPhenotypicStatus(q, UploadStatus.Error); + Mockito.verify(uploadLock, Mockito.times(1)).acquire(); + Mockito.verify(uploadLock, Mockito.times(1)).release(); + } + + @Test + void shouldNotUploadDataWhenCompleteFails(@TempDir Path tempDir) throws IOException, InterruptedException { + Query q = new Query(); + q.setPicSureId("my-id"); + q.setId("my-id"); + + Path fileToUpload = Path.of(tempDir.toString(), q.getPicSureId(), DataType.Phenotypic.fileName); + Files.createDirectory(Path.of(tempDir.toString(), q.getPicSureId())); + Files.writeString(fileToUpload, ":)"); + ReflectionTestUtils.setField(subject, "roleARNs", roleARNs); + + CreateMultipartUploadResponse createResp = Mockito.mock(CreateMultipartUploadResponse.class); + Mockito.when(createResp.uploadId()).thenReturn("frank"); + UploadPartResponse uploadResp = Mockito.mock(UploadPartResponse.class); + Mockito.when(uploadResp.eTag()).thenReturn("gus"); + DataUploadStatuses statuses = new DataUploadStatuses( + UploadStatus.Unsent, UploadStatus.Unsent, UploadStatus.Unsent, UploadStatus.Uploaded, q.getPicSureId(), LocalDate.MIN, "bch" + ); + + Mockito.when(statusService.getStatus(q.getPicSureId())).thenReturn(Optional.of(statuses)); + Mockito.when(sharingRoot.toString()).thenReturn(tempDir.toString()); + Mockito.when(hpds.writePhenotypicData(q)).thenReturn(true); + Mockito.when(s3.buildClientForSite("bch")).thenReturn(Optional.of(s3Client)); + Mockito.when(s3Client.uploadPart(Mockito.any(UploadPartRequest.class), Mockito.any(RequestBody.class))).thenReturn(uploadResp); + Mockito.when(s3Client.createMultipartUpload(Mockito.any(CreateMultipartUploadRequest.class))).thenReturn(createResp); + Mockito.when(s3Client.completeMultipartUpload(Mockito.any(CompleteMultipartUploadRequest.class))) + .thenThrow(AwsServiceException.builder().build()); + + + subject.uploadData(q, DataType.Phenotypic, "bch"); + + Mockito.verify(statusService, Mockito.times(1)).setPhenotypicStatus(q, UploadStatus.Querying); + Mockito.verify(statusService, Mockito.times(1)).setPhenotypicStatus(q, UploadStatus.Uploading); + Mockito.verify(s3Client, Mockito.times(1)).createMultipartUpload(Mockito.any(CreateMultipartUploadRequest.class)); + Mockito.verify(s3Client, Mockito.times(1)).completeMultipartUpload(Mockito.any(CompleteMultipartUploadRequest.class)); + Mockito.verify(s3Client, Mockito.times(1)).uploadPart(Mockito.any(UploadPartRequest.class), Mockito.any(RequestBody.class)); + Mockito.verify(statusService, Mockito.times(1)).setPhenotypicStatus(q, UploadStatus.Error); + Assertions.assertFalse(Files.exists(fileToUpload)); + Mockito.verify(uploadLock, Mockito.times(1)).acquire(); + Mockito.verify(uploadLock, Mockito.times(1)).release(); + } + + @Test + void shouldUploadData(@TempDir Path tempDir) throws IOException, InterruptedException { + Query q = new Query(); + q.setPicSureId("my-id"); + q.setId("my-id"); + + Path fileToUpload = Path.of(tempDir.toString(), q.getPicSureId(), DataType.Phenotypic.fileName); + Files.createDirectory(Path.of(tempDir.toString(), q.getPicSureId())); + Files.writeString(fileToUpload, ":)"); + ReflectionTestUtils.setField(subject, "roleARNs", roleARNs); + + CreateMultipartUploadResponse createResp = Mockito.mock(CreateMultipartUploadResponse.class); + Mockito.when(createResp.uploadId()).thenReturn("frank"); + UploadPartResponse uploadResp = Mockito.mock(UploadPartResponse.class); + Mockito.when(uploadResp.eTag()).thenReturn("gus"); + + DataUploadStatuses statuses = new DataUploadStatuses( + UploadStatus.Unsent, UploadStatus.Unsent, UploadStatus.Unsent, UploadStatus.Unsent, q.getPicSureId(), LocalDate.MIN, "bch" + ); + Mockito.when(statusService.getStatus(q.getPicSureId())).thenReturn(Optional.of(statuses)); + Mockito.when(sharingRoot.toString()).thenReturn(tempDir.toString()); + Mockito.when(hpds.writePhenotypicData(q)).thenReturn(true); + Mockito.when(s3.buildClientForSite("bch")).thenReturn(Optional.of(s3Client)); + Mockito.when(s3Client.uploadPart(Mockito.any(UploadPartRequest.class), Mockito.any(RequestBody.class))).thenReturn(uploadResp); + Mockito.when(s3Client.createMultipartUpload(Mockito.any(CreateMultipartUploadRequest.class))).thenReturn(createResp); + + + subject.uploadData(q, DataType.Phenotypic, "bch"); + + Mockito.verify(statusService, Mockito.times(1)).setPhenotypicStatus(q, UploadStatus.Querying); + Mockito.verify(statusService, Mockito.times(1)).setPhenotypicStatus(q, UploadStatus.Uploading); + Mockito.verify(statusService, Mockito.times(1)).setQueryUploadStatus(q, UploadStatus.Uploading); + Mockito.verify(s3Client, Mockito.times(2)) // query json and pheno data + .createMultipartUpload(Mockito.any(CreateMultipartUploadRequest.class)); + Mockito.verify(s3Client, Mockito.times(2)).completeMultipartUpload(Mockito.any(CompleteMultipartUploadRequest.class)); + Mockito.verify(s3Client, Mockito.times(2)).uploadPart(Mockito.any(UploadPartRequest.class), Mockito.any(RequestBody.class)); + Mockito.verify(statusService, Mockito.times(1)).setPhenotypicStatus(q, UploadStatus.Uploaded); + Mockito.verify(statusService, Mockito.times(1)).setQueryUploadStatus(q, UploadStatus.Uploaded); + Assertions.assertFalse(Files.exists(fileToUpload)); + Mockito.verify(uploadLock, Mockito.times(1)).acquire(); + Mockito.verify(uploadLock, Mockito.times(1)).release(); + } +} diff --git a/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/upload/UploadConfigTest.java b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/upload/UploadConfigTest.java new file mode 100644 index 000000000..f1fb3ad28 --- /dev/null +++ b/services/pic-sure-services/uploader/src/test/java/edu/harvard/dbmi/avillach/dataupload/upload/UploadConfigTest.java @@ -0,0 +1,18 @@ +package edu.harvard.dbmi.avillach.dataupload.upload; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.boot.test.context.SpringBootTest; + +import java.util.concurrent.Semaphore; + +@SpringBootTest +class UploadConfigTest { + + @Test + void shouldGetLock() { + Semaphore lock = new UploadConfig().getUploadLock(1); + + Assertions.assertEquals(1, lock.availablePermits()); + } +} diff --git a/services/pic-sure-services/uploader/src/test/resources/application.properties b/services/pic-sure-services/uploader/src/test/resources/application.properties new file mode 100644 index 000000000..11683acda --- /dev/null +++ b/services/pic-sure-services/uploader/src/test/resources/application.properties @@ -0,0 +1,24 @@ +aws.s3.role_arns=${AWS_DATA_UPLOAD_ROLE:} +aws.s3.external_ids=${AWS_SHARED_SECRET:} +aws.s3.buckets=${AWS_S3_BUCKET_NAME:} +aws.s3.access_key_id=${AWS_ACCESS_KEY_ID:} +aws.s3.access_key_secret=${AWS_SECRET_ACCESS_KEY:} +aws.s3.session_token=${AWS_SESSION_TOKEN:} +aws.s3.institution=bch +aws.s3.lambda_name=arn:aws:lambda:us-east-1:991175998352:function:cumulus_s3URLGen +aws.region=us-east-1 +aws.kms.key_ids=${AWS_KEY_ID} +aws.authentication.method=${AUTH_METHOD:noauth} + +spring.datasource.url=jdbc:mysql://${DATA_UPLOAD_DB_HOST:data-upload}:3306/${DATA_UPLOAD_DB_DATABASE:} +spring.datasource.username=${DATA_UPLOAD_DB_USER:} +spring.datasource.password=${DATA_UPLOAD_DB_PASS:} +spring.datasource.driver-class-name=com.mysql.cj.jdbc.Driver + +production=false + +institution.name=bch +institution.short-display=BCH +institution.long-display=Boston Children's Hospital + +spring.profiles.active=dev \ No newline at end of file diff --git a/services/pic-sure-services/uploader/src/test/resources/seed.sql b/services/pic-sure-services/uploader/src/test/resources/seed.sql new file mode 100644 index 000000000..389854993 --- /dev/null +++ b/services/pic-sure-services/uploader/src/test/resources/seed.sql @@ -0,0 +1,15 @@ +DROP TABLE IF EXISTS `query_status`; + +CREATE TABLE `query_status` ( + QUERY BINARY(16) NOT NULL, + GENOMIC_STATUS VARCHAR(64) NOT NULL DEFAULT 'Unsent', + PHENOTYPIC_STATUS VARCHAR(64) NOT NULL DEFAULT 'Unsent', + PATIENT_STATUS VARCHAR(64) NOT NULL DEFAULT 'Unsent', + QUERY_JSON_STATUS VARCHAR(64) NOT NULL DEFAULT 'Unsent', + APPROVED DATETIME, + SITE VARCHAR(64) NOT NULL DEFAULT '', + PRIMARY KEY (`QUERY`) +); + +INSERT INTO `query_status` (QUERY, GENOMIC_STATUS, PHENOTYPIC_STATUS, PATIENT_STATUS, QUERY_JSON_STATUS, APPROVED, SITE) + VALUES (unhex('33613336393437612D383233312D3131'), 'Uploaded', 'Error', 'Unsent', 'Uploading', '2022-02-22', 'bch'); diff --git a/services/pic-sure-visualization-service/.dockerignore b/services/pic-sure-visualization-service/.dockerignore new file mode 100644 index 000000000..5c656c233 --- /dev/null +++ b/services/pic-sure-visualization-service/.dockerignore @@ -0,0 +1,11 @@ +.git +target/* +!target/pic-sure-visualization-service-*.jar +*.md +docker-compose.yml +.idea/ +*.iml +.DS_Store +.claude/ +.env +.env.* diff --git a/services/pic-sure-visualization-service/.gitignore b/services/pic-sure-visualization-service/.gitignore new file mode 100644 index 000000000..d25ca2a48 --- /dev/null +++ b/services/pic-sure-visualization-service/.gitignore @@ -0,0 +1,6 @@ +.idea +target +.DS_Store +.classpath +.project +.settings/ \ No newline at end of file diff --git a/services/pic-sure-visualization-service/.sdkmanrc b/services/pic-sure-visualization-service/.sdkmanrc new file mode 100644 index 000000000..d2344323e --- /dev/null +++ b/services/pic-sure-visualization-service/.sdkmanrc @@ -0,0 +1 @@ +java=25.0.3-tem diff --git a/services/pic-sure-visualization-service/Dockerfile b/services/pic-sure-visualization-service/Dockerfile new file mode 100644 index 000000000..85cdb7b2a --- /dev/null +++ b/services/pic-sure-visualization-service/Dockerfile @@ -0,0 +1,5 @@ +FROM amazoncorretto:25-alpine +EXPOSE 80 +COPY target/pic-sure-visualization-service-*.jar /pic-sure-visualization-service.jar + +ENTRYPOINT ["sh", "-c", "java ${JAVA_OPTS} -jar /pic-sure-visualization-service.jar"] diff --git a/services/pic-sure-visualization-service/code-formatting/eclipse-formatter.xml b/services/pic-sure-visualization-service/code-formatting/eclipse-formatter.xml new file mode 100644 index 000000000..e7cfababf --- /dev/null +++ b/services/pic-sure-visualization-service/code-formatting/eclipse-formatter.xml @@ -0,0 +1,402 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/services/pic-sure-visualization-service/dev.Dockerfile b/services/pic-sure-visualization-service/dev.Dockerfile new file mode 100644 index 000000000..18266db84 --- /dev/null +++ b/services/pic-sure-visualization-service/dev.Dockerfile @@ -0,0 +1,13 @@ +FROM maven:3.9-amazoncorretto-25 AS build + +COPY --from=m2_cache / /root/.m2/repository/ +COPY ./ /app + +WORKDIR /app +RUN mvn clean install -DskipTests -nsu -Dmaven.test.skip=true + +FROM amazoncorretto:25-alpine + +COPY --from=build /app/target/pic-sure-visualization-service-*.jar /pic-sure-visualization-service.jar + +ENTRYPOINT ["sh", "-c", "java ${JAVA_OPTS} -jar /pic-sure-visualization-service.jar"] diff --git a/services/pic-sure-visualization-service/jenkinsfile b/services/pic-sure-visualization-service/jenkinsfile new file mode 100644 index 000000000..7bf25f0dd --- /dev/null +++ b/services/pic-sure-visualization-service/jenkinsfile @@ -0,0 +1,122 @@ +pipeline { + agent any + + parameters { + string(name: 'git_hash', description: 'The Git hash to checkout', defaultValue: 'main') + string(name: 'DOCKER_REGISTRY', description: 'Docker registry URL (e.g., ECR URL)', defaultValue: 'hms-dbmi') + string(name: 'REPOSITORY_NAME', description: 'Docker repository name', defaultValue: 'pic-sure-visualization') + choice(name: 'DEPLOY_METHOD', description: 'Deployment method', choices: ['docker', 's3', 'none']) + string(name: 'TARGET_STACK', description: 'Target stack for deployment (required for s3 deploy)', defaultValue: '') + string(name: 'STACK_S3_BUCKET', description: 'S3 bucket for image upload (required for s3 deploy)', defaultValue: '') + } + + environment { + LATEST_TAG = 'LATEST' + VISUALIZATION_ENV_FILE = '/usr/local/docker-config/visualization/visualization.env' + } + + stages { + stage('init') { + steps { + script { + env.GIT_BRANCH_SHORT = sh(script: 'echo "${GIT_BRANCH}" | awk -F/ \'{print $NF}\'', returnStdout: true).trim() + env.GIT_COMMIT_SHORT = sh(script: 'echo "${GIT_COMMIT}" | cut -c1-7', returnStdout: true).trim() + env.IMAGE_TAG = "${env.GIT_BRANCH_SHORT}_${env.GIT_COMMIT_SHORT}" + env.IMAGE_NAME = "${params.DOCKER_REGISTRY}/${params.REPOSITORY_NAME}" + } + } + } + + stage('build jar (docker run)') { + steps { + sh ''' + set -euo pipefail + + # DOCKER_CONFIG_DIR is set in all-in-one but not BDC. + # In all-in-one the host path differs from the container path. + # In BDC the workspace mount is an identity map (host == container). + if [ -n "${DOCKER_CONFIG_DIR:-}" ]; then + MOUNT_PATH="$DOCKER_CONFIG_DIR/jenkins_home/workspace/$JOB_NAME" + else + MOUNT_PATH="/var/jenkins_home/workspace/${JOB_NAME}" + fi + + docker run --rm \ + -v "$MOUNT_PATH/:/app:Z" \ + -v maven_m2_cache:/root/.m2 \ + -w /app/services/pic-sure-visualization-service \ + maven:3.9-amazoncorretto-25 \ + sh -lc "mvn clean install -B -T 1C -DskipTests -Dmaven.test.skip=true" + + ls -lah services/pic-sure-visualization-service/target || true + ''' + } + } + + stage('build image') { + steps { + sh ''' + set -euo pipefail + + PROXY_ARGS="" + if [ -n "${http_proxy:-}" ]; then + PROXY_ARGS="--build-arg http_proxy=$http_proxy --build-arg https_proxy=$http_proxy --build-arg HTTP_PROXY=$http_proxy --build-arg HTTPS_PROXY=$http_proxy" + fi + if [ -n "${no_proxy:-}" ]; then + PROXY_ARGS="$PROXY_ARGS --build-arg no_proxy=$no_proxy --build-arg NO_PROXY=$no_proxy" + fi + + docker build --load $PROXY_ARGS -t "${IMAGE_NAME}:${IMAGE_TAG}" services/pic-sure-visualization-service + docker tag "${IMAGE_NAME}:${IMAGE_TAG}" "${IMAGE_NAME}:${LATEST_TAG}" + ''' + } + } + + stage('deploy') { + steps { + script { + if (params.DEPLOY_METHOD == 'docker') { + sh ''' + set -euo pipefail + + if [ ! -f "${VISUALIZATION_ENV_FILE}" ]; then + echo "Visualization env file not found: ${VISUALIZATION_ENV_FILE}" >&2 + exit 1 + fi + + set +e + docker stop visualization + docker rm visualization + set -e + + docker run --name=visualization --restart always \ + --network=picsure \ + --env-file "${VISUALIZATION_ENV_FILE}" \ + -d "${IMAGE_NAME}:${IMAGE_TAG}" + ''' + } else if (params.DEPLOY_METHOD == 's3') { + sh ''' + set -euo pipefail + + if [ -z "${TARGET_STACK:-}" ]; then + echo "TARGET_STACK is required for s3 deploy." >&2 + exit 1 + fi + S3_BUCKET="${STACK_S3_BUCKET:-${stack_s3_bucket:-}}" + + if [ -z "$S3_BUCKET" ]; then + echo "STACK_S3_BUCKET is required for s3 deploy." >&2 + exit 1 + fi + + docker save "${IMAGE_NAME}:${LATEST_TAG}" | gzip > pic-sure-visualization.tar.gz + aws s3 --sse=AES256 cp pic-sure-visualization.tar.gz "s3://${S3_BUCKET}/${TARGET_STACK}/containers/pic-sure-visualization.tar.gz" + ''' + } else { + echo "Deployment skipped." + } + } + } + } + } +} diff --git a/services/pic-sure-visualization-service/pom.xml b/services/pic-sure-visualization-service/pom.xml new file mode 100644 index 000000000..4c9f9f2b8 --- /dev/null +++ b/services/pic-sure-visualization-service/pom.xml @@ -0,0 +1,80 @@ + + + 4.0.0 + + + edu.harvard.hms.dbmi.avillach + pic-sure-api + ${revision} + ../../pom.xml + + + edu.harvard.dbmi.avillach + pic-sure-visualization-service + PIC-SURE Visualization Service + + + + + org.springframework.boot + spring-boot-starter-web + + + org.springframework.boot + spring-boot-starter-actuator + + + org.springframework.boot + spring-boot-starter-validation + + + + + edu.harvard.hms.dbmi.avillach.hpds + pic-sure-hpds-model + + + + + edu.harvard.hms.dbmi.avillach + pic-sure-api-model + + + + + edu.harvard.dbmi.avillach + pic-sure-logging-client + + + + + org.apache.httpcomponents.client5 + httpclient5 + + + + + org.apache.commons + commons-math3 + 3.6.1 + + + + + org.springframework.boot + spring-boot-starter-test + test + + + + + + + org.springframework.boot + spring-boot-maven-plugin + + + + diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/VisualizationApplication.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/VisualizationApplication.java new file mode 100644 index 000000000..46b8304a5 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/VisualizationApplication.java @@ -0,0 +1,12 @@ +package edu.harvard.dbmi.avillach.visualization; + +import org.springframework.boot.SpringApplication; +import org.springframework.boot.autoconfigure.SpringBootApplication; + +@SpringBootApplication +public class VisualizationApplication { + + public static void main(String[] args) { + SpringApplication.run(VisualizationApplication.class, args); + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/config/LoggingClientBean.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/config/LoggingClientBean.java new file mode 100644 index 000000000..9956da353 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/config/LoggingClientBean.java @@ -0,0 +1,29 @@ +package edu.harvard.dbmi.avillach.visualization.config; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingClientConfig; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; + +@Configuration +public class LoggingClientBean { + + private static final Logger logger = LoggerFactory.getLogger(LoggingClientBean.class); + + @Bean + public LoggingClient loggingClient( + @Value("${logging.audit.url:}") String loggingUrl, @Value("${logging.audit.api-key:}") String apiKey + ) { + if (loggingUrl.isBlank() || apiKey.isBlank()) { + logger.info("logging.audit.url or logging.audit.api-key not set; audit logging disabled"); + return LoggingClient.noOp(); + } + + LoggingClientConfig config = LoggingClientConfig.builder(loggingUrl, apiKey).clientType("visualization").build(); + logger.info("Audit logging enabled, sending to {}", loggingUrl); + return new LoggingClient(config); + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/config/RestClientConfig.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/config/RestClientConfig.java new file mode 100644 index 000000000..f386615c6 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/config/RestClientConfig.java @@ -0,0 +1,28 @@ +package edu.harvard.dbmi.avillach.visualization.config; + +import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.http.client.ClientHttpRequestFactoryBuilder; +import org.springframework.boot.http.client.ClientHttpRequestFactorySettings; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.web.client.RestClient; + +import java.time.Duration; + +@Configuration +public class RestClientConfig { + + @Value("${rest-template.connect-timeout}") + private int connectTimeout; + + @Value("${rest-template.read-timeout}") + private int readTimeout; + + @Bean + public RestClient restClient(RestClient.Builder builder) { + // detect() resolves Apache HttpClient 5 from the classpath (the platform HTTP-client winner). + ClientHttpRequestFactorySettings settings = ClientHttpRequestFactorySettings.defaults() + .withConnectTimeout(Duration.ofMillis(connectTimeout)).withReadTimeout(Duration.ofMillis(readTimeout)); + return builder.requestFactory(ClientHttpRequestFactoryBuilder.detect().build(settings)).build(); + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/controller/BinningController.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/controller/BinningController.java new file mode 100644 index 000000000..37ae6b535 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/controller/BinningController.java @@ -0,0 +1,33 @@ +package edu.harvard.dbmi.avillach.visualization.controller; + +import edu.harvard.dbmi.avillach.visualization.logging.AuditLoggingContext; +import edu.harvard.dbmi.avillach.visualization.model.ContinuousBinningRequest; +import edu.harvard.dbmi.avillach.visualization.service.VisualizationService; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.validation.Valid; +import org.springframework.http.ResponseEntity; +import org.springframework.web.bind.annotation.PostMapping; +import org.springframework.web.bind.annotation.RequestBody; +import org.springframework.web.bind.annotation.RestController; + +import java.util.Map; + +@RestController +public class BinningController { + + private final VisualizationService visualizationService; + + public BinningController(VisualizationService visualizationService) { + this.visualizationService = visualizationService; + } + + @PostMapping({"/bin/continuous", "/v3/bin/continuous"}) + public ResponseEntity>> binContinuous( + @Valid @RequestBody ContinuousBinningRequest request, HttpServletRequest servletRequest + ) { + AuditLoggingContext.addBinningRequestMetadata(servletRequest, request.query()); + Map> response = visualizationService.binContinuousData(request.query()); + AuditLoggingContext.addBinningResponseMetadata(servletRequest, response); + return ResponseEntity.ok(response); + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/controller/DistributionController.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/controller/DistributionController.java new file mode 100644 index 000000000..23b540a4a --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/controller/DistributionController.java @@ -0,0 +1,43 @@ +package edu.harvard.dbmi.avillach.visualization.controller; + +import edu.harvard.dbmi.avillach.visualization.logging.AuditLoggingContext; +import edu.harvard.dbmi.avillach.visualization.model.DistributionRequest; +import edu.harvard.dbmi.avillach.visualization.model.HpdsAccessContext; +import edu.harvard.dbmi.avillach.visualization.model.VisualizationResponse; +import edu.harvard.dbmi.avillach.visualization.service.HpdsAccessResolver; +import edu.harvard.dbmi.avillach.visualization.service.VisualizationService; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.validation.Valid; +import org.springframework.http.ResponseEntity; +import org.springframework.web.bind.annotation.PostMapping; +import org.springframework.web.bind.annotation.RequestBody; +import org.springframework.web.bind.annotation.RequestHeader; +import org.springframework.web.bind.annotation.RestController; + +@RestController +public class DistributionController { + + private final VisualizationService visualizationService; + private final HpdsAccessResolver hpdsAccessResolver; + + public DistributionController(VisualizationService visualizationService, HpdsAccessResolver hpdsAccessResolver) { + this.visualizationService = visualizationService; + this.hpdsAccessResolver = hpdsAccessResolver; + } + + @PostMapping("/distributions") + public ResponseEntity distributions( + @Valid @RequestBody DistributionRequest request, @RequestHeader(value = "Authorization", required = false) String authorization, + @RequestHeader(value = "X-User-Id", required = false) String gatewayUserId, HttpServletRequest servletRequest + ) { + HpdsAccessContext accessContext = hpdsAccessResolver.resolve(gatewayUserId, request.hpdsResourceUUID()); + AuditLoggingContext.addDistributionRequestMetadata( + servletRequest, accessContext.resourceUUID(), accessContext.accessType().getValue(), request.query(), + visualizationService.subQueryCount(request.query()) + ); + VisualizationResponse response = visualizationService + .generateDistributions(request.query(), accessContext, authorization, AuditLoggingContext.requestId(servletRequest)); + AuditLoggingContext.addDistributionResponseMetadata(servletRequest, response); + return ResponseEntity.ok(response); + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/controller/PicsureMetadataController.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/controller/PicsureMetadataController.java new file mode 100644 index 000000000..200c1a88e --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/controller/PicsureMetadataController.java @@ -0,0 +1,35 @@ +package edu.harvard.dbmi.avillach.visualization.controller; + +import edu.harvard.dbmi.avillach.domain.QueryFormat; +import edu.harvard.dbmi.avillach.domain.ResourceInfo; +import org.springframework.http.ResponseEntity; +import org.springframework.web.bind.annotation.PostMapping; +import org.springframework.web.bind.annotation.RestController; + +import java.util.List; +import java.util.Map; + +@RestController +public class PicsureMetadataController { + + @PostMapping("/info") + public ResponseEntity info() { + return ResponseEntity + .ok(new ResourceInfo().setName("PIC-SURE Visualization Service").setQueryFormats(List.of(distributionQueryFormat()))); + } + + @PostMapping("/query/format") + public ResponseEntity queryFormat() { + return ResponseEntity.ok(distributionQueryFormat()); + } + + private QueryFormat distributionQueryFormat() { + return new QueryFormat().setName("PIC-SURE Visualization Distributions").setDescription("Request format for POST /distributions") + .setSpecification( + Map.of( + "hpdsResourceUUID", "Configured authorized or open HPDS resource UUID", "query", + "PIC-SURE HPDS v3 query used to generate distribution charts" + ) + ); + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/error/BadVisualizationRequestException.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/error/BadVisualizationRequestException.java new file mode 100644 index 000000000..210851f72 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/error/BadVisualizationRequestException.java @@ -0,0 +1,12 @@ +package edu.harvard.dbmi.avillach.visualization.error; + +public class BadVisualizationRequestException extends VisualizationException { + + public BadVisualizationRequestException(String message) { + super(message); + } + + public BadVisualizationRequestException(String message, Throwable cause) { + super(message, cause); + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/error/GlobalExceptionHandler.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/error/GlobalExceptionHandler.java new file mode 100644 index 000000000..052fae539 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/error/GlobalExceptionHandler.java @@ -0,0 +1,90 @@ +package edu.harvard.dbmi.avillach.visualization.error; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.http.converter.HttpMessageNotReadableException; +import org.springframework.web.bind.MethodArgumentNotValidException; +import org.springframework.web.bind.annotation.ExceptionHandler; +import org.springframework.web.bind.annotation.RestControllerAdvice; +import org.springframework.web.client.HttpStatusCodeException; +import org.springframework.web.client.ResourceAccessException; +import org.springframework.web.servlet.resource.NoResourceFoundException; + +import java.util.Map; +import java.util.stream.Collectors; + +@RestControllerAdvice +public class GlobalExceptionHandler { + + private static final Logger logger = LoggerFactory.getLogger(GlobalExceptionHandler.class); + + @ExceptionHandler(BadVisualizationRequestException.class) + public ResponseEntity> handleBadVisualizationRequest(BadVisualizationRequestException e) { + logger.warn("Visualization request error: {}", e.getMessage()); + return ResponseEntity.badRequest().body(Map.of("error", e.getMessage())); + } + + @ExceptionHandler(HpdsUpstreamException.class) + public ResponseEntity> handleHpdsUpstreamException(HpdsUpstreamException e) { + logger.error("Upstream HPDS error: {}", e.getMessage()); + return ResponseEntity.status(HttpStatus.BAD_GATEWAY).body(Map.of("error", e.getMessage())); + } + + @ExceptionHandler(VisualizationConfigurationException.class) + public ResponseEntity> handleVisualizationConfigurationException(VisualizationConfigurationException e) { + logger.error("Service misconfiguration: {}", e.getMessage()); + return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR).body(Map.of("error", e.getMessage())); + } + + @ExceptionHandler(VisualizationException.class) + public ResponseEntity> handleVisualizationException(VisualizationException e) { + Throwable cause = e.getCause(); + + if (cause instanceof HttpStatusCodeException) { + logger.error("Upstream HPDS HTTP error: {}", e.getMessage()); + return ResponseEntity.status(HttpStatus.BAD_GATEWAY).body(Map.of("error", e.getMessage())); + } + + if (cause instanceof ResourceAccessException) { + logger.error("Upstream HPDS unreachable: {}", e.getMessage()); + return ResponseEntity.status(HttpStatus.BAD_GATEWAY).body(Map.of("error", e.getMessage())); + } + + logger.warn("Visualization error: {}", e.getMessage()); + return ResponseEntity.badRequest().body(Map.of("error", e.getMessage())); + } + + @ExceptionHandler(MethodArgumentNotValidException.class) + public ResponseEntity> handleValidationException(MethodArgumentNotValidException e) { + String errors = e.getBindingResult().getFieldErrors().stream().map(f -> f.getField() + ": " + f.getDefaultMessage()) + .collect(Collectors.joining(", ")); + logger.warn("Validation error: {}", errors); + return ResponseEntity.badRequest().body(Map.of("error", errors)); + } + + @ExceptionHandler(HttpMessageNotReadableException.class) + public ResponseEntity> handleUnreadableMessage(HttpMessageNotReadableException e) { + logger.warn("Malformed request body: {}", e.getMessage()); + return ResponseEntity.badRequest().body(Map.of("error", "Malformed request body")); + } + + @ExceptionHandler(IllegalArgumentException.class) + public ResponseEntity> handleIllegalArgument(IllegalArgumentException e) { + logger.warn("Bad request: {}", e.getMessage()); + return ResponseEntity.badRequest().body(Map.of("error", e.getMessage())); + } + + @ExceptionHandler(NoResourceFoundException.class) + public ResponseEntity> handleNoResourceFound(NoResourceFoundException e) { + logger.warn("Resource not found: {}", e.getResourcePath()); + return ResponseEntity.status(HttpStatus.NOT_FOUND).body(Map.of("error", "Not found")); + } + + @ExceptionHandler(Exception.class) + public ResponseEntity> handleGenericException(Exception e) { + logger.error("Unexpected error", e); + return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR).body(Map.of("error", "Internal server error")); + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/error/HpdsUpstreamException.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/error/HpdsUpstreamException.java new file mode 100644 index 000000000..49a20360d --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/error/HpdsUpstreamException.java @@ -0,0 +1,8 @@ +package edu.harvard.dbmi.avillach.visualization.error; + +public class HpdsUpstreamException extends VisualizationException { + + public HpdsUpstreamException(String message, Throwable cause) { + super(message, cause); + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/error/VisualizationConfigurationException.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/error/VisualizationConfigurationException.java new file mode 100644 index 000000000..0d11c49d1 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/error/VisualizationConfigurationException.java @@ -0,0 +1,8 @@ +package edu.harvard.dbmi.avillach.visualization.error; + +public class VisualizationConfigurationException extends VisualizationException { + + public VisualizationConfigurationException(String message) { + super(message); + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/error/VisualizationException.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/error/VisualizationException.java new file mode 100644 index 000000000..0e87cc3b7 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/error/VisualizationException.java @@ -0,0 +1,12 @@ +package edu.harvard.dbmi.avillach.visualization.error; + +public class VisualizationException extends RuntimeException { + + public VisualizationException(String message) { + super(message); + } + + public VisualizationException(String message, Throwable cause) { + super(message, cause); + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/logging/AuditLoggingContext.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/logging/AuditLoggingContext.java new file mode 100644 index 000000000..0fd03d8a7 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/logging/AuditLoggingContext.java @@ -0,0 +1,107 @@ +package edu.harvard.dbmi.avillach.visualization.logging; + +import edu.harvard.dbmi.avillach.visualization.model.CategoricalDistributionData; +import edu.harvard.dbmi.avillach.visualization.model.ContinuousDistributionData; +import edu.harvard.dbmi.avillach.visualization.model.VisualizationResponse; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import jakarta.servlet.http.HttpServletRequest; + +import java.util.ArrayList; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.UUID; + +public final class AuditLoggingContext { + + public static final String START_TIME_ATTR = "vizStartTime"; + public static final String REQUEST_ID_ATTR = "vizRequestId"; + public static final String METADATA_ATTR = "vizAuditMetadata"; + public static final String ACCESS_TYPE_ATTR = "vizAccessType"; + public static final String AUTHORIZATION_ATTR = "vizAuthorization"; + public static final String SESSION_ID_ATTR = "vizSessionId"; + + private AuditLoggingContext() {} + + public static String requestId(HttpServletRequest request) { + Object value = request.getAttribute(REQUEST_ID_ATTR); + return value != null ? value.toString() : null; + } + + public static void addMetadata(HttpServletRequest request, String key, Object value) { + if (value != null) { + metadata(request).put(key, value); + } + } + + public static void addDistributionRequestMetadata( + HttpServletRequest request, UUID resourceUUID, String accessType, Query query, int subQueryCount + ) { + addMetadata(request, "route", "distributions"); + addMetadata(request, "resource_uuid", resourceUUID == null ? null : resourceUUID.toString()); + addMetadata(request, "access_type", accessType); + List selectedConceptPaths = selectedConceptPaths(query); + addMetadata(request, "selected_concept_paths", selectedConceptPaths); + addMetadata(request, "selected_concept_count", selectedConceptPaths.size()); + addMetadata(request, "subquery_count", subQueryCount); + request.setAttribute(ACCESS_TYPE_ATTR, accessType); + } + + public static void addDistributionResponseMetadata(HttpServletRequest request, VisualizationResponse response) { + addMetadata(request, "categorical_series_count", response.categoricalData().size()); + addMetadata(request, "continuous_series_count", response.continuousData().size()); + addMetadata( + request, "categorical_series_titles", response.categoricalData().stream().map(CategoricalDistributionData::title).toList() + ); + addMetadata( + request, "continuous_series_titles", response.continuousData().stream().map(ContinuousDistributionData::title).toList() + ); + addMetadata( + request, "categorical_point_count", response.categoricalData().stream().mapToInt(data -> data.categoricalMap().size()).sum() + ); + addMetadata( + request, "continuous_point_count", response.continuousData().stream().mapToInt(data -> data.continuousMap().size()).sum() + ); + addMetadata( + request, "categorical_obfuscated", response.categoricalData().stream().anyMatch(CategoricalDistributionData::obfuscated) + ); + addMetadata(request, "continuous_obfuscated", response.continuousData().stream().anyMatch(ContinuousDistributionData::obfuscated)); + } + + public static void addBinningRequestMetadata(HttpServletRequest request, Map> input) { + addMetadata(request, "route", "bin_continuous"); + addMetadata(request, "input_variable_count", input.size()); + addMetadata(request, "input_point_count", pointCount(input)); + addMetadata(request, "selected_concept_paths", new ArrayList<>(input.keySet())); + } + + public static void addBinningResponseMetadata(HttpServletRequest request, Map> output) { + addMetadata(request, "output_variable_count", output.size()); + addMetadata(request, "output_point_count", pointCount(output)); + } + + @SuppressWarnings("unchecked") + static Map metadata(HttpServletRequest request) { + Object value = request.getAttribute(METADATA_ATTR); + if (value instanceof Map map) { + return (Map) map; + } + Map metadata = new LinkedHashMap<>(); + request.setAttribute(METADATA_ATTR, metadata); + return metadata; + } + + static List selectedConceptPaths(Query query) { + if (query == null) { + return List.of(); + } + if (query.select() != null && !query.select().isEmpty()) { + return new ArrayList<>(query.select()); + } + return query.allFilters().stream().map(filter -> filter.conceptPath()).distinct().toList(); + } + + private static int pointCount(Map> data) { + return data.values().stream().mapToInt(Map::size).sum(); + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/logging/AuditLoggingFilter.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/logging/AuditLoggingFilter.java new file mode 100644 index 000000000..3cbe82ca6 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/logging/AuditLoggingFilter.java @@ -0,0 +1,133 @@ +package edu.harvard.dbmi.avillach.visualization.logging; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.dbmi.avillach.logging.RequestInfo; +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.slf4j.MDC; +import org.springframework.stereotype.Component; +import org.springframework.web.filter.OncePerRequestFilter; + +import java.io.IOException; +import java.util.LinkedHashMap; +import java.util.Map; +import java.util.UUID; + +@Component +public class AuditLoggingFilter extends OncePerRequestFilter { + + private static final Logger logger = LoggerFactory.getLogger(AuditLoggingFilter.class); + private static final String REQUEST_ID_HEADER = "X-Request-Id"; + private static final String SESSION_ID_HEADER = "X-Session-Id"; + + private final LoggingClient loggingClient; + + public AuditLoggingFilter(LoggingClient loggingClient) { + this.loggingClient = loggingClient; + } + + @Override + protected boolean shouldNotFilter(HttpServletRequest request) { + return switch (request.getRequestURI()) { + case "/distributions", "/bin/continuous" -> false; + default -> true; + }; + } + + @Override + protected void doFilterInternal(HttpServletRequest request, HttpServletResponse response, FilterChain filterChain) + throws ServletException, IOException { + String requestId = resolveRequestId(request); + String sessionId = request.getHeader(SESSION_ID_HEADER); + long startTime = System.currentTimeMillis(); + Exception failure = null; + + request.setAttribute(AuditLoggingContext.START_TIME_ATTR, startTime); + request.setAttribute(AuditLoggingContext.REQUEST_ID_ATTR, requestId); + request.setAttribute(AuditLoggingContext.AUTHORIZATION_ATTR, request.getHeader("Authorization")); + request.setAttribute(AuditLoggingContext.SESSION_ID_ATTR, sessionId); + response.setHeader(REQUEST_ID_HEADER, requestId); + MDC.put("requestId", requestId); + + try { + filterChain.doFilter(request, response); + } catch (ServletException | IOException | RuntimeException e) { + failure = e; + throw e; + } finally { + long duration = System.currentTimeMillis() - startTime; + try { + sendEvent(request, response, requestId, sessionId, duration, failure); + } finally { + MDC.remove("requestId"); + } + } + } + + private void sendEvent( + HttpServletRequest request, HttpServletResponse response, String requestId, String sessionId, long duration, Exception failure + ) { + try { + String action = switch (request.getRequestURI()) { + case "/distributions" -> "visualization.distributions"; + case "/bin/continuous" -> "visualization.bin_continuous"; + default -> "visualization.request"; + }; + + LoggingEvent.Builder builder = LoggingEvent.builder("QUERY").action(action).sessionId(sessionId) + .request(requestInfo(request, response, requestId, duration)).metadata(AuditLoggingContext.metadata(request)); + + Map error = errorMap(response.getStatus(), failure); + if (!error.isEmpty()) { + builder.error(error); + } + + loggingClient.send(builder.build(), request.getHeader("Authorization"), requestId); + } catch (Exception e) { + logger.debug("Failed to send audit log event: {}", e.getMessage()); + } + } + + private static RequestInfo requestInfo(HttpServletRequest request, HttpServletResponse response, String requestId, long duration) { + return RequestInfo.builder().requestId(requestId).method(request.getMethod()).url(request.getRequestURI()) + .queryString(request.getQueryString()).srcIp(sourceIp(request)).httpUserAgent(request.getHeader("User-Agent")) + .httpContentType(request.getContentType()).status(response.getStatus()).duration(duration) + .referrer(request.getHeader("Referer")).build(); + } + + private static Map errorMap(int status, Exception failure) { + Map error = new LinkedHashMap<>(); + if (status >= 400) { + error.put("status", status); + error.put("error_type", status >= 500 ? "server_error" : "client_error"); + } + if (failure != null) { + error.put("exception", failure.getClass().getSimpleName()); + if (failure.getMessage() != null) { + error.put("message", failure.getMessage()); + } + } + return error; + } + + private static String resolveRequestId(HttpServletRequest request) { + String headerValue = request.getHeader(REQUEST_ID_HEADER); + if (headerValue != null && !headerValue.isBlank()) { + return headerValue; + } + return UUID.randomUUID().toString(); + } + + private static String sourceIp(HttpServletRequest request) { + String xff = request.getHeader("X-Forwarded-For"); + if (xff != null && !xff.isBlank()) { + return xff.split(",")[0].trim(); + } + return request.getRemoteAddr(); + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/AccessType.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/AccessType.java new file mode 100644 index 000000000..cd0405517 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/AccessType.java @@ -0,0 +1,17 @@ +package edu.harvard.dbmi.avillach.visualization.model; + +public enum AccessType { + + AUTHORIZED("authorized"), OPEN("open"); + + private final String value; + + AccessType(String value) { + this.value = value; + } + + public String getValue() { + return value; + } + +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/CategoricalDistributionData.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/CategoricalDistributionData.java new file mode 100644 index 000000000..2ce925a6c --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/CategoricalDistributionData.java @@ -0,0 +1,9 @@ +package edu.harvard.dbmi.avillach.visualization.model; + +import java.util.Map; + +public record CategoricalDistributionData( + String conceptPath, String title, boolean continuous, Map categoricalMap, boolean obfuscated, String xaxisName, + String yaxisName, Integer chartWidth, Integer chartHeight +) { +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/ContinuousBinningRequest.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/ContinuousBinningRequest.java new file mode 100644 index 000000000..3992c4fe0 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/ContinuousBinningRequest.java @@ -0,0 +1,8 @@ +package edu.harvard.dbmi.avillach.visualization.model; + +import jakarta.validation.constraints.NotNull; + +import java.util.Map; + +public record ContinuousBinningRequest(@NotNull(message = "Request must contain a 'query' field") Map> query) { +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/ContinuousDistributionData.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/ContinuousDistributionData.java new file mode 100644 index 000000000..16b7f4079 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/ContinuousDistributionData.java @@ -0,0 +1,9 @@ +package edu.harvard.dbmi.avillach.visualization.model; + +import java.util.Map; + +public record ContinuousDistributionData( + String conceptPath, String title, boolean continuous, Map continuousMap, boolean obfuscated, String xaxisName, + String yaxisName, Integer chartWidth, Integer chartHeight +) { +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/DistributionRequest.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/DistributionRequest.java new file mode 100644 index 000000000..d7d1b4760 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/DistributionRequest.java @@ -0,0 +1,13 @@ +package edu.harvard.dbmi.avillach.visualization.model; + +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import jakarta.validation.constraints.NotNull; + +import java.util.UUID; + +public record DistributionRequest( + // Optional legacy field: the removed resource registry's backend selector. Passed through to HPDS bodies; access + // type now comes from the gateway's X-User-Id header (see HpdsAccessResolver). + UUID hpdsResourceUUID, @NotNull(message = "Request must contain a 'query' field") Query query +) { +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/DistributionType.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/DistributionType.java new file mode 100644 index 000000000..0159c26b2 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/DistributionType.java @@ -0,0 +1,5 @@ +package edu.harvard.dbmi.avillach.visualization.model; + +public enum DistributionType { + CATEGORICAL, CONTINUOUS, +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/HpdsAccessContext.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/HpdsAccessContext.java new file mode 100644 index 000000000..99a25d0f5 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/HpdsAccessContext.java @@ -0,0 +1,6 @@ +package edu.harvard.dbmi.avillach.visualization.model; + +import java.util.UUID; + +public record HpdsAccessContext(UUID resourceUUID, AccessType accessType) { +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/ObfuscatedCount.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/ObfuscatedCount.java new file mode 100644 index 000000000..c915baa66 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/ObfuscatedCount.java @@ -0,0 +1,27 @@ +package edu.harvard.dbmi.avillach.visualization.model; + +/** + * One chart value as exchanged with aggregate-data-sharing and the frontend. + * + * @param count the numeric value the bar renders at + * @param display the human-readable label (e.g. "45000", "222 ±3", "< 10") + * @param variance half-width of the uncertainty band around count, or null when the value is exact (authorized path). Consumers render the + * band as [max(0, count - variance), count + variance]; below-threshold values are encoded as count 0 with variance threshold-1. + */ +public record ObfuscatedCount(int count, String display, Integer variance) { + + /** + * Convenience constructor for exact values carrying no uncertainty band. + */ + public ObfuscatedCount(int count, String display) { + this(count, display, null); + } + + /** + * Wraps a plain (non-obfuscated) integer count. The display is just the stringified number; this is the right factory for the + * authorized path where no threshold floor or variance applies. + */ + public static ObfuscatedCount ofInt(int count) { + return new ObfuscatedCount(count, Integer.toString(count), null); + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/VisualizationResponse.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/VisualizationResponse.java new file mode 100644 index 000000000..e0197e15d --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/model/VisualizationResponse.java @@ -0,0 +1,6 @@ +package edu.harvard.dbmi.avillach.visualization.model; + +import java.util.List; + +public record VisualizationResponse(List categoricalData, List continuousData) { +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/processing/BinningService.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/processing/BinningService.java new file mode 100644 index 000000000..4ca5441b8 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/processing/BinningService.java @@ -0,0 +1,123 @@ +package edu.harvard.dbmi.avillach.visualization.processing; + +import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; +import org.springframework.stereotype.Component; + +import java.util.*; + +@Component +public class BinningService { + + private static final double THIRD = 1.0 / 3.0; + + public Map> binContinuousData(Map> continuousDataMap) { + Map> result = new LinkedHashMap<>(); + for (Map.Entry> entry : continuousDataMap.entrySet()) { + result.put(entry.getKey(), bucketData(entry.getValue())); + } + return result; + } + + public Map bucketData(Map originalMap) { + if (originalMap == null || originalMap.isEmpty()) { + return new LinkedHashMap<>(); + } + + Map data = new LinkedHashMap<>(); + for (Map.Entry entry : originalMap.entrySet()) { + try { + data.put(Double.parseDouble(entry.getKey()), entry.getValue()); + } catch (NumberFormatException e) { + // skip non-numeric keys + } + } + + if (data.isEmpty()) { + return new LinkedHashMap<>(); + } + + boolean isSameMinMax = data.size() == 1; + + int numBins = calcNumBins(data); + double min = data.keySet().stream().min(Double::compareTo).orElse(0.0); + double max = data.keySet().stream().max(Double::compareTo).orElse(0.0); + + if (numBins <= 0) { + numBins = 1; + } + + double binSize = (max - min) / numBins; + if (binSize <= 0.0) { + binSize = 1.0; + } + + Map counts = createBinsAndMergeCounts(data, numBins, min, binSize); + + int bucketMax = counts.keySet().stream().max(Integer::compareTo).orElse(0); + Map results = new LinkedHashMap<>(); + Map> ranges = new HashMap<>(); + for (int key = 0; key <= bucketMax; key++) { + double rangeStart = min + (key * binSize); + double rangeEnd = min + ((key + 1) * binSize); + ranges.put(key, new ArrayList<>(List.of(rangeStart, rangeEnd))); + results.put(key, counts.getOrDefault(key, 0)); + } + + return createLabelsForBins(results, ranges, isSameMinMax); + } + + private static int calcNumBins(Map countMap) { + double[] keys = countMap.keySet().stream().mapToDouble(Double::doubleValue).toArray(); + DescriptiveStatistics da = new DescriptiveStatistics(keys); + double smallestKey = da.getMin(); + double largestKey = da.getMax(); + if (smallestKey == largestKey) return 1; + double binWidth = (3.5 * da.getStandardDeviation()) / Math.pow(countMap.size(), THIRD); + return (int) Math.round((largestKey - smallestKey) / binWidth); + } + + private static Map createBinsAndMergeCounts(Map data, int numBins, double min, double binSize) { + Map results = new LinkedHashMap<>(); + for (Map.Entry entry : data.entrySet()) { + int bin = (int) Math.floor((entry.getKey() - min) / binSize); + if (bin < numBins) { + results.merge(bin, entry.getValue(), Integer::sum); + } else { + // Value at the exact max — merge into last bin + results.merge(numBins - 1, entry.getValue(), Integer::sum); + } + } + return results; + } + + private static Map createLabelsForBins( + Map results, Map> ranges, boolean isSameMinMax + ) { + Map finalMap = new LinkedHashMap<>(); + String label = ""; + for (Map.Entry bucket : results.entrySet()) { + double minForLabel = ranges.get(bucket.getKey()).stream().min(Double::compareTo).orElse(0.0); + double maxForLabel = ranges.get(bucket.getKey()).stream().max(Double::compareTo).orElse(0.0); + if (minForLabel == maxForLabel || isSameMinMax) { + label = String.format("%.1f", minForLabel); + } else { + label = String.format("%.1f", minForLabel) + " - " + String.format("%.1f", maxForLabel); + } + // Adjacent bins can round to the same %.1f label; merge so counts aren't dropped + finalMap.merge(label, bucket.getValue(), Integer::sum); + } + + Integer lastCount = finalMap.get(label); + if (lastCount != null && finalMap.size() > 1) { + String newLabel = label; + int hasDash = label.indexOf(" -"); + if (hasDash > 0) { + newLabel = label.substring(0, hasDash); + } + finalMap.remove(label); + finalMap.merge(newLabel + " +", lastCount, Integer::sum); + } + + return finalMap; + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/processing/CategoricalAggregationService.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/processing/CategoricalAggregationService.java new file mode 100644 index 000000000..075fe1df6 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/processing/CategoricalAggregationService.java @@ -0,0 +1,77 @@ +package edu.harvard.dbmi.avillach.visualization.processing; + +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Component; + +import java.util.Collections; +import java.util.HashSet; +import java.util.LinkedHashMap; +import java.util.Map; +import java.util.Set; +import java.util.function.Supplier; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +@Component +public class CategoricalAggregationService { + + private static final int MAX_LABEL_LENGTH = 45; + + private final int maxCategories; + + public CategoricalAggregationService(@Value("${chart.categorical.max-categories:7}") int maxCategories) { + this.maxCategories = maxCategories; + } + + public Map aggregateTopN(Map axisMap) { + if (axisMap == null || axisMap.isEmpty()) { + return new LinkedHashMap<>(); + } + Map finalAxisMap = axisMap; + if (axisMap.size() > maxCategories) { + Supplier>> stream = + () -> finalAxisMap.entrySet().stream().sorted(Collections.reverseOrder(Map.Entry.comparingByValue())); + int otherSum = stream.get().skip(maxCategories).mapToInt(Map.Entry::getValue).sum(); + axisMap = stream.get().limit(maxCategories) + .collect(Collectors.toMap(Map.Entry::getKey, Map.Entry::getValue, Integer::sum, LinkedHashMap::new)); + axisMap = limitKeySize(axisMap).entrySet().stream().sorted(Collections.reverseOrder(Map.Entry.comparingByValue())) + .collect(Collectors.toMap(Map.Entry::getKey, Map.Entry::getValue, Integer::sum, LinkedHashMap::new)); + axisMap.merge("Other", otherSum, Integer::sum); + } else { + axisMap = limitKeySize(finalAxisMap).entrySet().stream().sorted(Collections.reverseOrder(Map.Entry.comparingByValue())) + .collect(Collectors.toMap(Map.Entry::getKey, Map.Entry::getValue, Integer::sum, LinkedHashMap::new)); + } + return axisMap; + } + + private static Map limitKeySize(Map axisMap) { + Map newAxisMap = new LinkedHashMap<>(); + Set keys = new HashSet<>(); + axisMap.forEach((key, value) -> { + String adjustedKey = key.length() < MAX_LABEL_LENGTH ? key : createAdjustedKey(axisMap, keys, key); + newAxisMap.merge(adjustedKey, value, Integer::sum); + keys.add(adjustedKey); + }); + return newAxisMap; + } + + private static String createAdjustedKey(Map axisMap, Set keys, String key) { + String keyPrefix = key.substring(0, MAX_LABEL_LENGTH); + boolean prefixExists = axisMap.keySet().stream().anyMatch(k -> !k.equals(key) && k.startsWith(keyPrefix)); + if (prefixExists) { + int countFromEnd = 6; + String proposedKey; + do { + int prefixLen = MAX_LABEL_LENGTH - 3 - countFromEnd; + int suffixStart = key.length() - countFromEnd; + if (prefixLen < 1 || suffixStart < 0) { + return key.substring(0, MAX_LABEL_LENGTH - 11) + "..." + String.format("%08x", key.hashCode()); + } + proposedKey = String.format("%s...%s", key.substring(0, prefixLen), key.substring(suffixStart)); + countFromEnd++; + } while (keys.contains(proposedKey)); + return proposedKey; + } + return keyPrefix + "..."; + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/processing/CategoricalDistributionProcessor.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/processing/CategoricalDistributionProcessor.java new file mode 100644 index 000000000..75e7a8f6a --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/processing/CategoricalDistributionProcessor.java @@ -0,0 +1,31 @@ +package edu.harvard.dbmi.avillach.visualization.processing; + +import edu.harvard.dbmi.avillach.visualization.model.CategoricalDistributionData; +import edu.harvard.dbmi.avillach.visualization.model.ObfuscatedCount; +import org.springframework.stereotype.Component; + +import java.util.ArrayList; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; + +@Component +public class CategoricalDistributionProcessor { + + public List process(Map> crossCounts, boolean obfuscated) { + List distributions = new ArrayList<>(); + for (Map.Entry> entry : crossCounts.entrySet()) { + if (DistributionMetadata.SKIP_KEYS.contains(entry.getKey()) || entry.getValue() == null || entry.getValue().isEmpty()) { + continue; + } + String title = DistributionMetadata.titleFor(entry.getKey()); + distributions.add( + new CategoricalDistributionData( + entry.getKey(), title, false, new LinkedHashMap<>(entry.getValue()), obfuscated, + DistributionMetadata.xAxisLabelFor(entry.getKey()), "Number of Participants", null, null + ) + ); + } + return distributions; + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/processing/ContinuousDistributionProcessor.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/processing/ContinuousDistributionProcessor.java new file mode 100644 index 000000000..65fd0c7b6 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/processing/ContinuousDistributionProcessor.java @@ -0,0 +1,31 @@ +package edu.harvard.dbmi.avillach.visualization.processing; + +import edu.harvard.dbmi.avillach.visualization.model.ContinuousDistributionData; +import edu.harvard.dbmi.avillach.visualization.model.ObfuscatedCount; +import org.springframework.stereotype.Component; + +import java.util.ArrayList; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; + +@Component +public class ContinuousDistributionProcessor { + + public List process(Map> crossCounts, boolean obfuscated) { + List distributions = new ArrayList<>(); + for (Map.Entry> entry : crossCounts.entrySet()) { + if (DistributionMetadata.SKIP_KEYS.contains(entry.getKey()) || entry.getValue() == null || entry.getValue().isEmpty()) { + continue; + } + String title = DistributionMetadata.titleFor(entry.getKey()); + distributions.add( + new ContinuousDistributionData( + entry.getKey(), title, true, new LinkedHashMap<>(entry.getValue()), obfuscated, + DistributionMetadata.xAxisLabelFor(entry.getKey()), "Number of Participants", null, null + ) + ); + } + return distributions; + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/processing/DistributionMetadata.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/processing/DistributionMetadata.java new file mode 100644 index 000000000..981455c99 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/processing/DistributionMetadata.java @@ -0,0 +1,28 @@ +package edu.harvard.dbmi.avillach.visualization.processing; + +import java.util.Set; + +final class DistributionMetadata { + + static final Set SKIP_KEYS = Set.of("\\_consents\\", "\\_harmonized_consent\\", "\\_topmed_consents\\", "\\_parent_consents\\"); + + private DistributionMetadata() {} + + static String titleFor(String conceptPath) { + String[] titleParts = conceptPath.split("\\\\"); + if (titleParts.length == 0) { + return conceptPath; + } + String leaf = titleParts[titleParts.length - 1]; + String parent = titleParts.length >= 2 ? titleParts[titleParts.length - 2] : ""; + return parent.isEmpty() ? leaf : parent + ": " + leaf; + } + + static String xAxisLabelFor(String conceptPath) { + String[] titleParts = conceptPath.split("\\\\"); + if (titleParts.length == 0) { + return conceptPath; + } + return titleParts[titleParts.length - 1]; + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/service/HpdsAccessResolver.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/service/HpdsAccessResolver.java new file mode 100644 index 000000000..c770ae5fa --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/service/HpdsAccessResolver.java @@ -0,0 +1,42 @@ +package edu.harvard.dbmi.avillach.visualization.service; + +import edu.harvard.dbmi.avillach.visualization.model.AccessType; +import edu.harvard.dbmi.avillach.visualization.model.HpdsAccessContext; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Component; + +import java.util.UUID; + +/** + * Decides AUTHORIZED vs OPEN treatment for a distributions request. The access type comes from the gateway's identity propagation, NOT from + * the request body: the {@code X-User-Id} header is gateway-owned (the gateway strips any client-supplied value and only injects it after + * successful PSAMA introspection), so its presence proves an authenticated caller and its absence means the request passed open-access + * validation instead. Clients cannot spoof it, unlike the legacy {@code hpdsResourceUUID} body field, which was the removed resource + * registry's backend selector. + * + *

    {@code hpdsResourceUUID} is still accepted for compatibility and passed through into HPDS request bodies (HPDS ignores the field); + * when the body omits it, the optionally-configured per-access-type UUID is used, and {@code null} is fine too. + */ +@Component +public class HpdsAccessResolver { + + private final UUID authorizedResourceUUID; + private final UUID openResourceUUID; + + public HpdsAccessResolver( + @Value("${hpds.resource.authorized.uuid:}") String authorizedUUID, @Value("${hpds.resource.open.uuid:}") String openUUID + ) { + this.authorizedResourceUUID = parseConfiguredUUID(authorizedUUID); + this.openResourceUUID = parseConfiguredUUID(openUUID); + } + + public HpdsAccessContext resolve(String gatewayUserId, UUID hpdsResourceUUID) { + boolean authorized = gatewayUserId != null && !gatewayUserId.isBlank(); + UUID resourceUUID = hpdsResourceUUID != null ? hpdsResourceUUID : (authorized ? authorizedResourceUUID : openResourceUUID); + return new HpdsAccessContext(resourceUUID, authorized ? AccessType.AUTHORIZED : AccessType.OPEN); + } + + private static UUID parseConfiguredUUID(String value) { + return value == null || value.isBlank() ? null : UUID.fromString(value); + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/service/HpdsClient.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/service/HpdsClient.java new file mode 100644 index 000000000..3b9d27596 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/service/HpdsClient.java @@ -0,0 +1,252 @@ +package edu.harvard.dbmi.avillach.visualization.service; + +import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest; +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.dbmi.avillach.logging.RequestInfo; +import edu.harvard.dbmi.avillach.visualization.model.AccessType; +import edu.harvard.dbmi.avillach.visualization.model.DistributionType; +import edu.harvard.dbmi.avillach.visualization.model.ObfuscatedCount; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import java.net.URI; +import java.util.ArrayList; +import java.util.Collections; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.UUID; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.core.ParameterizedTypeReference; +import org.springframework.http.*; +import org.springframework.stereotype.Component; +import org.springframework.web.client.HttpStatusCodeException; +import org.springframework.web.client.RestClient; + +@Component +public class HpdsClient { + + private static final Logger logger = LoggerFactory.getLogger(HpdsClient.class); + + private final RestClient restClient; + private final LoggingClient loggingClient; + private final String hpdsBaseUrl; + + public HpdsClient(RestClient restClient, LoggingClient loggingClient, @Value("${hpds.base-url}") String hpdsBaseUrl) { + this.restClient = restClient; + this.loggingClient = loggingClient; + this.hpdsBaseUrl = hpdsBaseUrl; + } + + public Map> getAuthCrossCounts(Query query, ResultType resultType, UUID resourceUUID, String bearerToken) { + return getAuthCrossCounts(query, resultType, resourceUUID, bearerToken, null, AccessType.AUTHORIZED, null); + } + + public Map> getAuthCrossCounts( + Query query, ResultType resultType, UUID resourceUUID, String bearerToken, String requestId, AccessType accessType, + DistributionType distributionKind + ) { + return queryCrossCounts( + query, resultType, resourceUUID, bearerToken, requestId, accessType, distributionKind, new ParameterizedTypeReference<>() {} + ); + } + + public Map> getOpenCrossCounts( + Query query, ResultType resultType, UUID resourceUUID, String bearerToken + ) { + return getOpenCrossCounts(query, resultType, resourceUUID, bearerToken, null, AccessType.OPEN, null); + } + + public Map> getOpenCrossCounts( + Query query, ResultType resultType, UUID resourceUUID, String bearerToken, String requestId, AccessType accessType, + DistributionType distributionKind + ) { + return queryCrossCounts( + query, resultType, resourceUUID, bearerToken, requestId, accessType, distributionKind, new ParameterizedTypeReference<>() {} + ); + } + + private Map queryCrossCounts( + Query query, ResultType resultType, UUID resourceUUID, String bearerToken, String requestId, AccessType accessType, + DistributionType distributionKind, ParameterizedTypeReference> typeRef + ) { + long startTime = System.currentTimeMillis(); + + Query subQuery = new Query( + query.select(), query.authorizationFilters(), query.phenotypicClause(), query.genomicFilters(), resultType, query.picsureId(), + query.id() + ); + + HttpHeaders headers = new HttpHeaders(); + headers.setContentType(MediaType.APPLICATION_JSON); + headers.setAccept(Collections.singletonList(MediaType.ALL)); + if (bearerToken != null && !bearerToken.isBlank()) { + headers.set("Authorization", bearerToken); + } + if (requestId != null && !requestId.isBlank()) { + headers.set("X-Request-Id", requestId); + } + + String url = hpdsBaseUrl + querySyncPath(accessType); + Object body = requestBody(subQuery, resourceUUID); + logger.info( + "Calling HPDS requestId={} accessType={} distributionKind={} resultType={} resourceUUID={} selectedConceptCount={} selectedConceptPaths={} url={}", + requestId, accessTypeValue(accessType), distributionKindValue(distributionKind), resultType, resourceUUID, + selectedConceptCount(subQuery), selectedConceptPaths(subQuery), url + ); + + try { + ResponseEntity> response = + restClient.post().uri(url).headers(h -> h.addAll(headers)).body(body).retrieve().toEntity(typeRef); + logger.info( + "HPDS call completed requestId={} accessType={} distributionKind={} resultType={} status={} durationMs={} responseSeriesCount={} responsePointCount={} responseSeriesKeys={}", + requestId, accessTypeValue(accessType), distributionKindValue(distributionKind), resultType, + response.getStatusCode().value(), System.currentTimeMillis() - startTime, seriesCount(response.getBody()), + responsePointCount(response.getBody()), responseSeriesKeys(response.getBody()) + ); + sendHpdsEvent( + subQuery, resultType, resourceUUID, requestId, bearerToken, accessType, distributionKind, url, + response.getStatusCode().value(), System.currentTimeMillis() - startTime, response.getBody(), null + ); + return response.getBody() != null ? response.getBody() : new LinkedHashMap<>(); + } catch (RuntimeException e) { + Integer status = e instanceof HttpStatusCodeException httpError ? httpError.getStatusCode().value() : null; + logger.warn( + "HPDS call failed requestId={} accessType={} distributionKind={} resultType={} status={} durationMs={} error={}", requestId, + accessTypeValue(accessType), distributionKindValue(distributionKind), resultType, status, + System.currentTimeMillis() - startTime, e.getMessage() + ); + sendHpdsEvent( + subQuery, resultType, resourceUUID, requestId, bearerToken, accessType, distributionKind, url, null, + System.currentTimeMillis() - startTime, null, e + ); + throw e; + } + } + + private static String accessTypeValue(AccessType accessType) { + return accessType != null ? accessType.getValue() : "unknown"; + } + + private static String distributionKindValue(DistributionType distributionKind) { + return distributionKind != null ? distributionKind.name().toLowerCase() : "unknown"; + } + + private static int selectedConceptCount(Query query) { + return query.select() != null ? query.select().size() : 0; + } + + private static List selectedConceptPaths(Query query) { + return query.select() != null ? query.select() : List.of(); + } + + private static int seriesCount(Map responseBody) { + return responseBody != null ? responseBody.size() : 0; + } + + private static List responseSeriesKeys(Map responseBody) { + return responseBody != null ? new ArrayList<>(responseBody.keySet()) : List.of(); + } + + private Object requestBody(Query subQuery, UUID resourceUUID) { + GeneralQueryRequest request = new GeneralQueryRequest(); + request.setResourceUUID(resourceUUID); + request.setQuery(subQuery); + request.setResourceCredentials(Map.of()); + return request; + } + + private String querySyncPath(AccessType accessType) { + return accessType == AccessType.OPEN ? "/query/sync" : "/v3/query/sync"; + } + + private void sendHpdsEvent( + Query query, ResultType resultType, UUID resourceUUID, String requestId, String bearerToken, AccessType accessType, + DistributionType distributionKind, String url, Integer status, long duration, Map responseBody, RuntimeException error + ) { + try { + Integer resolvedStatus = status; + if (resolvedStatus == null && error instanceof HttpStatusCodeException httpError) { + resolvedStatus = httpError.getStatusCode().value(); + } + LoggingEvent.Builder builder = LoggingEvent.builder("QUERY").action("visualization.hpds.query") + .request( + RequestInfo.builder().requestId(requestId).method("POST").url("/v3/query/sync").destIp(destinationHost(url)) + .destPort(destinationPort(url)).status(resolvedStatus).duration(duration).build() + ).metadata(hpdsMetadata(query, resultType, resourceUUID, accessType, distributionKind, responseBody)); + if (error != null) { + builder.error(errorMetadata(error, resolvedStatus)); + } + loggingClient.send(builder.build(), bearerToken, requestId); + } catch (Exception e) { + logger.debug("Failed to send HPDS audit log event: {}", e.getMessage()); + } + } + + private static Map hpdsMetadata( + Query query, ResultType resultType, UUID resourceUUID, AccessType accessType, DistributionType distributionKind, + Map responseBody + ) { + Map metadata = new LinkedHashMap<>(); + metadata.put("resource_uuid", resourceUUID.toString()); + metadata.put("result_type", resultType.toString()); + List selectedConceptPaths = query.select() != null ? query.select() : List.of(); + metadata.put("selected_concept_paths", selectedConceptPaths); + metadata.put("selected_concept_count", selectedConceptPaths.size()); + if (accessType != null) { + metadata.put("access_type", accessType.getValue()); + } + if (distributionKind != null) { + metadata.put("distribution_kind", distributionKind.name().toLowerCase()); + } + if (responseBody != null) { + metadata.put("response_series_count", responseBody.size()); + metadata.put("response_series_keys", new ArrayList<>(responseBody.keySet())); + metadata.put("response_point_count", responsePointCount(responseBody)); + } + return metadata; + } + + private static int responsePointCount(Map responseBody) { + if (responseBody == null) { + return 0; + } + int count = 0; + for (Object value : responseBody.values()) { + if (value instanceof Map series) { + count += series.size(); + } + } + return count; + } + + private static Map errorMetadata(RuntimeException error, Integer status) { + Map metadata = new LinkedHashMap<>(); + if (status == null && error instanceof HttpStatusCodeException httpError) { + status = httpError.getStatusCode().value(); + } + if (status != null) { + metadata.put("status", status); + } + metadata.put("exception", error.getClass().getSimpleName()); + if (error.getMessage() != null) { + metadata.put("message", error.getMessage()); + } + return metadata; + } + + private static String destinationHost(String url) { + return URI.create(url).getHost(); + } + + private static Integer destinationPort(String url) { + URI uri = URI.create(url); + int port = uri.getPort(); + if (port > 0) { + return port; + } + return "https".equalsIgnoreCase(uri.getScheme()) ? 443 : 80; + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/service/QueryDecomposer.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/service/QueryDecomposer.java new file mode 100644 index 000000000..8a3d9e1ca --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/service/QueryDecomposer.java @@ -0,0 +1,66 @@ +package edu.harvard.dbmi.avillach.visualization.service; + +import edu.harvard.dbmi.avillach.visualization.model.DistributionType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicFilter; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.PhenotypicFilterType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import java.util.ArrayList; +import java.util.LinkedHashSet; +import java.util.List; +import java.util.Set; +import org.springframework.stereotype.Component; + +@Component +public class QueryDecomposer { + + public record SubQueryDescriptor(Query query, ResultType resultType, DistributionType distributionKind) { + } + + public List decompose(Query query) { + List subQueries = new ArrayList<>(); + List allFilters = query.allFilters(); + + Set categoricalPaths = new LinkedHashSet<>(); + Set numericPaths = new LinkedHashSet<>(); + + for (PhenotypicFilter filter : allFilters) { + if (filter.isCategoricalFilter()) { + categoricalPaths.add(filter.conceptPath()); + } else if (filter.isNumericFilter()) { + numericPaths.add(filter.conceptPath()); + } else if ( + PhenotypicFilterType.REQUIRED.equals(filter.phenotypicFilterType()) + || PhenotypicFilterType.ANY_RECORD_OF.equals(filter.phenotypicFilterType()) + ) { + categoricalPaths.add(filter.conceptPath()); + numericPaths.add(filter.conceptPath()); + } + } + + // If no filters produced paths, fall back to the query's select field. + // This handles cases where the frontend sends explicit select paths without + // matching filter types (e.g. a query with select but only REQUIRED filters). + if (categoricalPaths.isEmpty() && numericPaths.isEmpty() && !query.select().isEmpty()) { + categoricalPaths.addAll(query.select()); + } + + if (!categoricalPaths.isEmpty()) { + Query categoricalQuery = new Query( + new ArrayList<>(categoricalPaths), query.authorizationFilters(), query.phenotypicClause(), query.genomicFilters(), + ResultType.CATEGORICAL_CROSS_COUNT, query.picsureId(), null + ); + subQueries.add(new SubQueryDescriptor(categoricalQuery, ResultType.CATEGORICAL_CROSS_COUNT, DistributionType.CATEGORICAL)); + } + + if (!numericPaths.isEmpty()) { + Query numericQuery = new Query( + new ArrayList<>(numericPaths), query.authorizationFilters(), query.phenotypicClause(), query.genomicFilters(), + ResultType.CONTINUOUS_CROSS_COUNT, query.picsureId(), null + ); + subQueries.add(new SubQueryDescriptor(numericQuery, ResultType.CONTINUOUS_CROSS_COUNT, DistributionType.CONTINUOUS)); + } + + return subQueries; + } +} diff --git a/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/service/VisualizationService.java b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/service/VisualizationService.java new file mode 100644 index 000000000..84b258b49 --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/java/edu/harvard/dbmi/avillach/visualization/service/VisualizationService.java @@ -0,0 +1,211 @@ +package edu.harvard.dbmi.avillach.visualization.service; + +import edu.harvard.dbmi.avillach.visualization.error.HpdsUpstreamException; +import edu.harvard.dbmi.avillach.visualization.error.VisualizationException; +import edu.harvard.dbmi.avillach.visualization.model.*; +import edu.harvard.dbmi.avillach.visualization.processing.BinningService; +import edu.harvard.dbmi.avillach.visualization.processing.CategoricalAggregationService; +import edu.harvard.dbmi.avillach.visualization.processing.CategoricalDistributionProcessor; +import edu.harvard.dbmi.avillach.visualization.processing.ContinuousDistributionProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import java.util.ArrayList; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.stereotype.Service; +import org.springframework.web.client.HttpStatusCodeException; +import org.springframework.web.client.ResourceAccessException; + +@Service +public class VisualizationService { + + private static final Logger logger = LoggerFactory.getLogger(VisualizationService.class); + + private final QueryDecomposer queryDecomposer; + private final HpdsClient hpdsClient; + private final CategoricalDistributionProcessor categoricalDistributionProcessor; + private final ContinuousDistributionProcessor continuousDistributionProcessor; + private final BinningService binningService; + private final CategoricalAggregationService categoricalAggregationService; + + public VisualizationService( + QueryDecomposer queryDecomposer, HpdsClient hpdsClient, CategoricalDistributionProcessor categoricalDistributionProcessor, + ContinuousDistributionProcessor continuousDistributionProcessor, BinningService binningService, + CategoricalAggregationService categoricalAggregationService + ) { + this.queryDecomposer = queryDecomposer; + this.hpdsClient = hpdsClient; + this.categoricalDistributionProcessor = categoricalDistributionProcessor; + this.continuousDistributionProcessor = continuousDistributionProcessor; + this.binningService = binningService; + this.categoricalAggregationService = categoricalAggregationService; + } + + public VisualizationResponse generateDistributions(Query query, HpdsAccessContext accessContext, String bearerToken) { + return generateDistributions(query, accessContext, bearerToken, null); + } + + public VisualizationResponse generateDistributions(Query query, HpdsAccessContext accessContext, String bearerToken, String requestId) { + List subQueries = queryDecomposer.decompose(query); + List categoricalData = new ArrayList<>(); + List continuousData = new ArrayList<>(); + logger.info( + "Generating visualization distributions requestId={} accessType={} resourceUUID={} subQueryCount={}", requestId, + accessContext.accessType().getValue(), accessContext.resourceUUID(), subQueries.size() + ); + + for (QueryDecomposer.SubQueryDescriptor descriptor : subQueries) { + try { + if (accessContext.accessType() == AccessType.AUTHORIZED) { + Map> crossCounts = requestId == null + ? hpdsClient + .getAuthCrossCounts(descriptor.query(), descriptor.resultType(), accessContext.resourceUUID(), bearerToken) + : hpdsClient.getAuthCrossCounts( + descriptor.query(), descriptor.resultType(), accessContext.resourceUUID(), bearerToken, requestId, + accessContext.accessType(), descriptor.distributionKind() + ); + logRawHpdsShape(descriptor, crossCounts); + + Map> processed = new LinkedHashMap<>(); + switch (descriptor.distributionKind()) { + case CONTINUOUS -> crossCounts + .forEach((concept, values) -> processed.put(concept, binningService.bucketData(nonNullValues(values)))); + case CATEGORICAL -> crossCounts.forEach( + (concept, values) -> processed.put(concept, categoricalAggregationService.aggregateTopN(nonNullValues(values))) + ); + } + addDistributions(descriptor, wrap(processed), false, categoricalData, continuousData); + } else { + Map> rawCrossCounts = requestId == null + ? hpdsClient + .getOpenCrossCounts(descriptor.query(), descriptor.resultType(), accessContext.resourceUUID(), bearerToken) + : hpdsClient.getOpenCrossCounts( + descriptor.query(), descriptor.resultType(), accessContext.resourceUUID(), bearerToken, requestId, + accessContext.accessType(), descriptor.distributionKind() + ); + logRawHpdsShape(descriptor, rawCrossCounts); + if (hasSeriesData(rawCrossCounts)) { + addDistributions(descriptor, rawCrossCounts, true, categoricalData, continuousData); + } + } + } catch (HttpStatusCodeException e) { + logger.error( + "HPDS returned HTTP {} for {} {} query", e.getStatusCode().value(), accessContext.accessType().getValue(), + descriptor.resultType(), e + ); + throw new HpdsUpstreamException("HPDS query failed with status " + e.getStatusCode().value() + ": " + e.getStatusText(), e); + } catch (ResourceAccessException e) { + logger.error("Could not reach HPDS for {} {} query", accessContext.accessType().getValue(), descriptor.resultType(), e); + throw new HpdsUpstreamException("HPDS query failed: " + e.getMessage(), e); + } catch (VisualizationException e) { + throw e; + } catch (Exception e) { + logger.error("Failed to execute {} {} query", accessContext.accessType().getValue(), descriptor.resultType(), e); + throw new HpdsUpstreamException("HPDS query failed: " + e.getMessage(), e); + } + } + + VisualizationResponse response = new VisualizationResponse(categoricalData, continuousData); + logger.info( + "Generated visualization distributions requestId={} accessType={} categoricalChartCount={} continuousChartCount={}", requestId, + accessContext.accessType().getValue(), categoricalData.size(), continuousData.size() + ); + return response; + } + + public int subQueryCount(Query query) { + return queryDecomposer.decompose(query).size(); + } + + private static Map nonNullValues(Map values) { + Map out = new LinkedHashMap<>(); + if (values == null) { + return out; + } + values.forEach((k, v) -> { + if (v != null) { + out.put(k, v); + } + }); + return out; + } + + private static Map> wrap(Map> input) { + Map> out = new LinkedHashMap<>(); + input.forEach((concept, values) -> { + Map wrappedValues = new LinkedHashMap<>(); + if (values != null) { + values.forEach((k, v) -> { + if (v != null) { + wrappedValues.put(k, ObfuscatedCount.ofInt(v)); + } + }); + } + out.put(concept, wrappedValues); + }); + return out; + } + + private void addDistributions( + QueryDecomposer.SubQueryDescriptor descriptor, Map> crossCounts, boolean isObfuscated, + List categoricalData, List continuousData + ) { + if (!hasSeriesData(crossCounts)) { + return; + } + switch (descriptor.distributionKind()) { + case CATEGORICAL -> { + List charts = categoricalDistributionProcessor.process(crossCounts, isObfuscated); + categoricalData.addAll(charts); + logCreatedCharts(descriptor, charts.size(), crossCounts, isObfuscated); + } + case CONTINUOUS -> { + List charts = continuousDistributionProcessor.process(crossCounts, isObfuscated); + continuousData.addAll(charts); + logCreatedCharts(descriptor, charts.size(), crossCounts, isObfuscated); + } + } + } + + private static void logRawHpdsShape(QueryDecomposer.SubQueryDescriptor descriptor, Map> rawCrossCounts) { + if (rawCrossCounts == null) { + return; + } + logger.info( + "HPDS cross-counts received distributionKind={} resultType={} rawSeriesCount={} rawPointCount={} rawSeriesKeys={}", + descriptor.distributionKind().name().toLowerCase(), descriptor.resultType(), rawCrossCounts.size(), + sourcePointCount(rawCrossCounts), new ArrayList<>(rawCrossCounts.keySet()) + ); + } + + private static void logCreatedCharts( + QueryDecomposer.SubQueryDescriptor descriptor, int chartCount, Map> crossCounts, + boolean isObfuscated + ) { + logger.info( + "Created visualization charts distributionKind={} resultType={} chartCount={} sourceSeriesCount={} sourcePointCount={} sourceSeriesKeys={} obfuscated={}", + descriptor.distributionKind().name().toLowerCase(), descriptor.resultType(), chartCount, crossCounts.size(), + sourcePointCount(crossCounts), new ArrayList<>(crossCounts.keySet()), isObfuscated + ); + } + + private static boolean hasSeriesData(Map> crossCounts) { + return (crossCounts != null && crossCounts.values().stream().anyMatch(values -> values != null && !values.isEmpty())); + } + + private static int sourcePointCount(Map> crossCounts) { + int count = 0; + for (Map values : crossCounts.values()) { + if (values != null) { + count += values.size(); + } + } + return count; + } + + public Map> binContinuousData(Map> continuousData) { + return binningService.binContinuousData(continuousData); + } +} diff --git a/services/pic-sure-visualization-service/src/main/resources/application.properties b/services/pic-sure-visualization-service/src/main/resources/application.properties new file mode 100644 index 000000000..f5eae7b5a --- /dev/null +++ b/services/pic-sure-visualization-service/src/main/resources/application.properties @@ -0,0 +1,27 @@ +server.port=8080 + +# HPDS-compatible query endpoint base URL. In all-in-one this is the sibling HPDS. +hpds.base-url=${HPDS_BASE_URL:http://hpds:8080/PIC-SURE} + +# HPDS resource UUIDs (used for open/auth routing) +hpds.resource.authorized.uuid=${AUTH_HPDS_RESOURCE_UUID:} +hpds.resource.open.uuid=${OPEN_HPDS_RESOURCE_UUID:} + +# Categorical chart limits +chart.categorical.max-categories=${CHART_MAX_CATEGORIES:7} + +# RestTemplate timeouts (ms) +rest-template.connect-timeout=${REST_TEMPLATE_CONNECT_TIMEOUT:5000} +rest-template.read-timeout=${REST_TEMPLATE_READ_TIMEOUT:30000} + +# Actuator: OFF BY DEFAULT. AIO's visualization.env sets PICSURE_ACTUATOR_EXPOSURE=health to enable a +# shallow health probe for the gateway /system/status aggregation; details stay hidden (never). +management.endpoints.web.exposure.include=${PICSURE_ACTUATOR_EXPOSURE:none} +management.endpoint.health.show-details=${PICSURE_ACTUATOR_DETAILS:never} + +# Audit logging (no-op if unset) +logging.audit.url=${LOGGING_SERVICE_URL:} +logging.audit.api-key=${LOGGING_API_KEY:} + +# Logging +logging.level.edu.harvard.dbmi.avillach.visualization=INFO diff --git a/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/HpdsCallIntegrationTest.java b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/HpdsCallIntegrationTest.java new file mode 100644 index 000000000..bc50fcd60 --- /dev/null +++ b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/HpdsCallIntegrationTest.java @@ -0,0 +1,260 @@ +package edu.harvard.dbmi.avillach.visualization; + +import static org.junit.jupiter.api.Assertions.*; +import static org.springframework.test.web.client.match.MockRestRequestMatchers.*; +import static org.springframework.test.web.client.response.MockRestResponseCreators.*; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status; + +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.dbmi.avillach.visualization.model.ObfuscatedCount; +import edu.harvard.dbmi.avillach.visualization.model.VisualizationResponse; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.Set; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.HttpMethod; +import org.springframework.http.MediaType; +import org.springframework.test.context.ActiveProfiles; +import org.springframework.test.web.client.MockRestServiceServer; +import org.springframework.test.web.servlet.MockMvc; +import org.springframework.test.web.servlet.MvcResult; +import org.springframework.boot.test.context.TestConfiguration; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Primary; +import org.springframework.context.annotation.Import; +import org.springframework.web.client.RestClient; + +@SpringBootTest +@AutoConfigureMockMvc +@ActiveProfiles("test") +@Import(HpdsCallIntegrationTest.MockHpdsRestClient.class) +class HpdsCallIntegrationTest { + + @TestConfiguration + static class MockHpdsRestClient { + static final RestClient.Builder BUILDER = RestClient.builder(); + static final MockRestServiceServer SERVER = MockRestServiceServer.bindTo(BUILDER).build(); + + @Bean + @Primary + RestClient mockBoundRestClient() { + return BUILDER.build(); + } + } + + private static final String AUTHORIZED_UUID = "550e8400-e29b-41d4-a716-446655440000"; + private static final String OPEN_UUID = "550e8400-e29b-41d4-a716-446655440001"; + + @Autowired + private MockMvc mockMvc; + + @Autowired + private ObjectMapper objectMapper; + + private MockRestServiceServer mockServer; + + @BeforeEach + void setUp() { + mockServer = MockHpdsRestClient.SERVER; + mockServer.reset(); + } + + @Test + void distributions_authorized_categoricalFilter_callsHpdsAndReturnsBarChart() throws Exception { + // Simulate HPDS response for categorical cross-counts + Map> hpdsResponse = new LinkedHashMap<>(); + hpdsResponse.put("\\demographics\\race\\", new LinkedHashMap<>(Map.of("White", 45000, "Black", 12000, "Asian", 8000))); + + mockServer.expect(requestTo("http://localhost:9999/mock-hpds/v3/query/sync")).andExpect(method(HttpMethod.POST)) + .andExpect(header("Authorization", "Bearer test-token")) + .andExpect(content().json("{\"query\":{\"expectedResultType\":\"CATEGORICAL_CROSS_COUNT\"}}")) + .andRespond(withSuccess(objectMapper.writeValueAsString(hpdsResponse), MediaType.APPLICATION_JSON)); + + // Build a v3 query with a categorical filter + Map query = Map.of( + "phenotypicClause", + Map.of("phenotypicFilterType", "FILTER", "conceptPath", "\\demographics\\race\\", "values", List.of("White", "Black")), + "select", List.of(), "authorizationFilters", List.of(), "genomicFilters", List.of() + ); + String body = objectMapper.writeValueAsString(Map.of("hpdsResourceUUID", AUTHORIZED_UUID, "query", query)); + + MvcResult result = mockMvc.perform( + post("/distributions").contentType(MediaType.APPLICATION_JSON).header("Authorization", "Bearer test-token") + .header("X-User-Id", "test-user").content(body) + ).andExpect(status().isOk()).andReturn(); + + mockServer.verify(); + + VisualizationResponse response = objectMapper.readValue(result.getResponse().getContentAsString(), VisualizationResponse.class); + assertNotNull(response); + assertFalse(response.categoricalData().isEmpty()); + assertEquals("demographics: race", response.categoricalData().get(0).title()); + assertFalse(response.categoricalData().get(0).obfuscated()); + + // Verify the frontend distribution DTO structure + assertNotNull(response.categoricalData().get(0).categoricalMap()); + assertFalse(response.categoricalData().get(0).categoricalMap().isEmpty()); + } + + @Test + void distributions_authorized_continuousFilter_callsHpdsAndReturnsHistogram() throws Exception { + // Simulate HPDS response for continuous cross-counts (raw values, not yet binned) + Map> hpdsResponse = new LinkedHashMap<>(); + Map bmiValues = new LinkedHashMap<>(); + bmiValues.put("18.0", 100); + bmiValues.put("22.0", 200); + bmiValues.put("26.0", 150); + bmiValues.put("30.0", 100); + bmiValues.put("35.0", 50); + hpdsResponse.put("\\measurements\\bmi\\", bmiValues); + + mockServer.expect(requestTo("http://localhost:9999/mock-hpds/v3/query/sync")).andExpect(method(HttpMethod.POST)) + .andExpect(content().json("{\"query\":{\"expectedResultType\":\"CONTINUOUS_CROSS_COUNT\"}}")) + .andRespond(withSuccess(objectMapper.writeValueAsString(hpdsResponse), MediaType.APPLICATION_JSON)); + + Map query = Map.of( + "phenotypicClause", Map.of("phenotypicFilterType", "FILTER", "conceptPath", "\\measurements\\bmi\\", "min", 18.0, "max", 40.0), + "select", List.of(), "authorizationFilters", List.of(), "genomicFilters", List.of() + ); + String body = objectMapper.writeValueAsString(Map.of("hpdsResourceUUID", AUTHORIZED_UUID, "query", query)); + + MvcResult result = mockMvc.perform( + post("/distributions").contentType(MediaType.APPLICATION_JSON).header("Authorization", "Bearer test-token") + .header("X-User-Id", "test-user").content(body) + ).andExpect(status().isOk()).andReturn(); + + mockServer.verify(); + + VisualizationResponse response = objectMapper.readValue(result.getResponse().getContentAsString(), VisualizationResponse.class); + assertFalse(response.continuousData().isEmpty()); + + // Verify binning happened — x labels should be ranges, not raw values + assertFalse(response.continuousData().get(0).continuousMap().containsKey("18.0"), "Raw value should have been binned into a range"); + + // Total counts preserved + int total = response.continuousData().get(0).continuousMap().values().stream().mapToInt(ObfuscatedCount::count).sum(); + assertEquals(600, total); + } + + @Test + void distributions_open_callsHpdsAndReturnsObfuscatedChart() throws Exception { + Map> hpdsResponse = new LinkedHashMap<>(); + hpdsResponse.put( + "\\demographics\\race\\", + new LinkedHashMap<>( + Map.of( + "White", new ObfuscatedCount(45000, "45000 ±3", 3), "Black", new ObfuscatedCount(12000, "12000"), "Other", + new ObfuscatedCount(0, "< 10", 9) + ) + ) + ); + + mockServer.expect(requestTo("http://localhost:9999/mock-hpds/query/sync")).andExpect(method(HttpMethod.POST)) + .andRespond(withSuccess(objectMapper.writeValueAsString(hpdsResponse), MediaType.APPLICATION_JSON)); + + Map query = Map.of( + "phenotypicClause", + Map.of("phenotypicFilterType", "FILTER", "conceptPath", "\\demographics\\race\\", "values", List.of("White")), "select", + List.of(), "authorizationFilters", List.of(), "genomicFilters", List.of() + ); + String body = objectMapper.writeValueAsString(Map.of("hpdsResourceUUID", OPEN_UUID, "query", query)); + + MvcResult result = mockMvc.perform(post("/distributions").contentType(MediaType.APPLICATION_JSON).content(body)) + .andExpect(status().isOk()).andReturn(); + + mockServer.verify(); + + VisualizationResponse response = objectMapper.readValue(result.getResponse().getContentAsString(), VisualizationResponse.class); + assertFalse(response.categoricalData().isEmpty()); + assertTrue(response.categoricalData().get(0).obfuscated()); + Map race = response.categoricalData().get(0).categoricalMap(); + assertEquals(new ObfuscatedCount(45000, "45000 ±3", 3), race.get("White")); + assertEquals(new ObfuscatedCount(12000, "12000"), race.get("Black")); + assertEquals(new ObfuscatedCount(0, "< 10", 9), race.get("Other")); + } + + @Test + void distributions_hpdsReturns500_returns502BadGateway() throws Exception { + mockServer.expect(requestTo("http://localhost:9999/mock-hpds/v3/query/sync")).andExpect(method(HttpMethod.POST)) + .andRespond(withServerError().body("{\"error\":\"internal error\"}")); + + Map query = Map.of( + "phenotypicClause", + Map.of("phenotypicFilterType", "FILTER", "conceptPath", "\\demographics\\race\\", "values", List.of("White")), "select", + List.of(), "authorizationFilters", List.of(), "genomicFilters", List.of() + ); + String body = objectMapper.writeValueAsString(Map.of("hpdsResourceUUID", AUTHORIZED_UUID, "query", query)); + + MvcResult result = mockMvc.perform( + post("/distributions").contentType(MediaType.APPLICATION_JSON).header("Authorization", "Bearer test-token") + .header("X-User-Id", "test-user").content(body) + ).andExpect(status().isBadGateway()).andReturn(); + + mockServer.verify(); + + String responseBody = result.getResponse().getContentAsString(); + assertTrue(responseBody.contains("HPDS query failed")); + } + + @Test + void distributions_hpdsTimeout_returns502BadGateway() throws Exception { + mockServer.expect(requestTo("http://localhost:9999/mock-hpds/v3/query/sync")).andExpect(method(HttpMethod.POST)) + .andRespond(withServiceUnavailable()); + + Map query = Map.of( + "phenotypicClause", + Map.of("phenotypicFilterType", "FILTER", "conceptPath", "\\demographics\\race\\", "values", List.of("White")), "select", + List.of(), "authorizationFilters", List.of(), "genomicFilters", List.of() + ); + String body = objectMapper.writeValueAsString(Map.of("hpdsResourceUUID", AUTHORIZED_UUID, "query", query)); + + mockMvc.perform( + post("/distributions").contentType(MediaType.APPLICATION_JSON).header("Authorization", "Bearer test-token") + .header("X-User-Id", "test-user").content(body) + ).andExpect(status().isBadGateway()); + + mockServer.verify(); + } + + @Test + void distributions_open_continuous_callsHpdsAndForwardsBinnedObfuscatedValues() throws Exception { + Map> hpdsResponse = new LinkedHashMap<>(); + hpdsResponse.put( + "\\measurements\\bmi\\", + new LinkedHashMap<>( + Map.of( + "18.0 - 24.0", new ObfuscatedCount(600, "600 ±3", 3), "24.0 - 30.0", new ObfuscatedCount(0, "< 10", 9), "30.0 +", + new ObfuscatedCount(150, "150 ±3", 3) + ) + ) + ); + + mockServer.expect(requestTo("http://localhost:9999/mock-hpds/query/sync")).andExpect(method(HttpMethod.POST)) + .andRespond(withSuccess(objectMapper.writeValueAsString(hpdsResponse), MediaType.APPLICATION_JSON)); + + Map query = Map.of( + "phenotypicClause", Map.of("phenotypicFilterType", "FILTER", "conceptPath", "\\measurements\\bmi\\", "min", 18.0, "max", 40.0), + "select", List.of(), "authorizationFilters", List.of(), "genomicFilters", List.of() + ); + String body = objectMapper.writeValueAsString(Map.of("hpdsResourceUUID", OPEN_UUID, "query", query)); + + MvcResult result = mockMvc.perform(post("/distributions").contentType(MediaType.APPLICATION_JSON).content(body)) + .andExpect(status().isOk()).andReturn(); + + mockServer.verify(); + + VisualizationResponse response = objectMapper.readValue(result.getResponse().getContentAsString(), VisualizationResponse.class); + assertFalse(response.continuousData().isEmpty()); + assertTrue(response.continuousData().get(0).obfuscated()); + Map bmi = response.continuousData().get(0).continuousMap(); + assertEquals(new ObfuscatedCount(600, "600 ±3", 3), bmi.get("18.0 - 24.0")); + assertEquals(new ObfuscatedCount(0, "< 10", 9), bmi.get("24.0 - 30.0")); + assertEquals(new ObfuscatedCount(150, "150 ±3", 3), bmi.get("30.0 +")); + } +} diff --git a/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/VisualizationIntegrationTest.java b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/VisualizationIntegrationTest.java new file mode 100644 index 000000000..94836a7b9 --- /dev/null +++ b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/VisualizationIntegrationTest.java @@ -0,0 +1,202 @@ +package edu.harvard.dbmi.avillach.visualization; + +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.dbmi.avillach.visualization.model.VisualizationResponse; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.MediaType; +import org.springframework.test.context.ActiveProfiles; +import org.springframework.test.context.TestPropertySource; +import org.springframework.test.web.servlet.MockMvc; +import org.springframework.test.web.servlet.MvcResult; + +import java.util.Map; + +import static org.junit.jupiter.api.Assertions.*; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get; +import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post; +import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status; + +@SpringBootTest +@AutoConfigureMockMvc +@ActiveProfiles("test") +// Production shape: no configured fallback UUIDs -- resourceUUID flows as null end-to-end (HpdsCallIntegrationTest +// covers the configured-fallback shape via the test profile's properties). +// Actuator is OFF BY DEFAULT (exposure defaults to 'none'); expose health so healthEndpoint_isPublic exercises the +// endpoint the AIO deployment enables via PICSURE_ACTUATOR_EXPOSURE=health. +@TestPropertySource( + properties = {"hpds.resource.authorized.uuid=", "hpds.resource.open.uuid=", "management.endpoints.web.exposure.include=health"} +) +class VisualizationIntegrationTest { + + private static final String AUTHORIZED_UUID = "550e8400-e29b-41d4-a716-446655440000"; + private static final String OPEN_UUID = "550e8400-e29b-41d4-a716-446655440001"; + + @Autowired + private MockMvc mockMvc; + + @Autowired + private ObjectMapper objectMapper; + + @Test + void healthEndpoint_isPublic() throws Exception { + mockMvc.perform(get("/actuator/health")).andExpect(status().isOk()); + } + + @Test + void distributions_withGatewayIdentity_returnsOk() throws Exception { + // Access type comes from the gateway-owned X-User-Id header; no hpdsResourceUUID needed (path-routed frontend omits it). + String body = objectMapper.writeValueAsString(Map.of("query", Map.of())); + + MvcResult result = mockMvc.perform( + post("/distributions").contentType(MediaType.APPLICATION_JSON).header("Authorization", "Bearer test-token") + .header("X-User-Id", "test-user").content(body) + ).andExpect(status().isOk()).andReturn(); + + VisualizationResponse response = objectMapper.readValue(result.getResponse().getContentAsString(), VisualizationResponse.class); + assertNotNull(response); + assertTrue(response.categoricalData().isEmpty()); + assertTrue(response.continuousData().isEmpty()); + } + + @Test + void distributions_withoutGatewayIdentity_isOpenAndReturnsOk() throws Exception { + String body = objectMapper.writeValueAsString(Map.of("query", Map.of())); + + MvcResult result = mockMvc.perform(post("/distributions").contentType(MediaType.APPLICATION_JSON).content(body)) + .andExpect(status().isOk()).andReturn(); + + VisualizationResponse response = objectMapper.readValue(result.getResponse().getContentAsString(), VisualizationResponse.class); + assertNotNull(response); + assertTrue(response.categoricalData().isEmpty()); + assertTrue(response.continuousData().isEmpty()); + } + + @Test + void distributions_withNoConfiguredUUIDsAndNoBodyUUID_returnsOk() throws Exception { + // Production-shape config: AUTH/OPEN_HPDS_RESOURCE_UUID unset and the path-routed frontend sends no body UUID. + // resourceUUID is null end-to-end (HPDS ignores the field; audit metadata must tolerate it). + String body = objectMapper.writeValueAsString(Map.of("query", Map.of())); + + mockMvc.perform(post("/distributions").contentType(MediaType.APPLICATION_JSON).header("X-User-Id", "test-user").content(body)) + .andExpect(status().isOk()); + } + + @Test + void distributions_legacyHpdsResourceUUID_isAcceptedAndIgnoredForAccessSelection() throws Exception { + // Legacy clients still send a body UUID; it no longer drives AUTHORIZED-vs-OPEN and unknown values are not rejected. + String body = + objectMapper.writeValueAsString(Map.of("hpdsResourceUUID", "550e8400-e29b-41d4-a716-446655440099", "query", Map.of())); + + mockMvc.perform(post("/distributions").contentType(MediaType.APPLICATION_JSON).header("X-User-Id", "test-user").content(body)) + .andExpect(status().isOk()); + } + + @Test + void distributions_nullQuery_returns400() throws Exception { + String body = "{\"hpdsResourceUUID\":\"" + AUTHORIZED_UUID + "\",\"query\":null}"; + + MvcResult result = mockMvc.perform(post("/distributions").contentType(MediaType.APPLICATION_JSON).content(body)) + .andExpect(status().isBadRequest()).andReturn(); + + assertTrue(result.getResponse().getContentAsString().contains("query")); + } + + @Test + void distributions_malformedJson_returns400() throws Exception { + MvcResult result = mockMvc.perform(post("/distributions").contentType(MediaType.APPLICATION_JSON).content("not valid json")) + .andExpect(status().isBadRequest()).andReturn(); + + assertTrue(result.getResponse().getContentAsString().contains("Malformed request body")); + } + + @Test + void oldVisualizationV3Routes_areRemoved() throws Exception { + mockMvc.perform(post("/visualization/v3/query/sync").contentType(MediaType.APPLICATION_JSON).content("{}")) + .andExpect(status().isNotFound()); + mockMvc.perform(post("/visualization/v3/bin/continuous").contentType(MediaType.APPLICATION_JSON).content("{}")) + .andExpect(status().isNotFound()); + mockMvc.perform(post("/visualization/v3/info").contentType(MediaType.APPLICATION_JSON).content("{}")) + .andExpect(status().isNotFound()); + } + + @Test + void binContinuous_nullQueryField_returns400() throws Exception { + MvcResult result = mockMvc.perform(post("/bin/continuous").contentType(MediaType.APPLICATION_JSON).content("{\"query\": null}")) + .andExpect(status().isBadRequest()).andReturn(); + + assertTrue(result.getResponse().getContentAsString().contains("error")); + } + + @Test + void binContinuous_invalidDataFormat_returns400() throws Exception { + MvcResult result = + mockMvc.perform(post("/bin/continuous").contentType(MediaType.APPLICATION_JSON).content("{\"query\": \"not a map\"}")) + .andExpect(status().isBadRequest()).andReturn(); + + assertTrue(result.getResponse().getContentAsString().contains("Malformed request body")); + } + + @Test + void binContinuous_rejectsRawDataFormat() throws Exception { + String body = objectMapper.writeValueAsString(Map.of("\\measurements\\bmi\\", Map.of("18.0", 100))); + + mockMvc.perform(post("/bin/continuous").contentType(MediaType.APPLICATION_JSON).content(body)).andExpect(status().isBadRequest()); + } + + @Test + void binContinuous_acceptsQueryRequestFormat() throws Exception { + Map requestBody = Map.of( + "query", Map.of("\\measurements\\bmi\\", Map.of("18.0", 100, "25.0", 200, "30.0", 150)), "resourceUUID", + "550e8400-e29b-41d4-a716-446655440000", "resourceCredentials", Map.of() + ); + + MvcResult result = mockMvc + .perform(post("/bin/continuous").contentType(MediaType.APPLICATION_JSON).content(objectMapper.writeValueAsString(requestBody))) + .andExpect(status().isOk()).andReturn(); + + @SuppressWarnings("unchecked") + Map> response = objectMapper.readValue(result.getResponse().getContentAsString(), Map.class); + assertTrue(response.containsKey("\\measurements\\bmi\\")); + assertFalse(response.get("\\measurements\\bmi\\").isEmpty()); + } + + @Test + void binContinuous_v3RouteAcceptsQueryRequestFormat() throws Exception { + Map requestBody = Map.of( + "query", Map.of("\\measurements\\bmi\\", Map.of("18.0", 100, "25.0", 200, "30.0", 150)), "resourceUUID", + "550e8400-e29b-41d4-a716-446655440000", "resourceCredentials", Map.of() + ); + + MvcResult result = mockMvc.perform( + post("/v3/bin/continuous").contentType(MediaType.APPLICATION_JSON).content(objectMapper.writeValueAsString(requestBody)) + ).andExpect(status().isOk()).andReturn(); + + @SuppressWarnings("unchecked") + Map> response = objectMapper.readValue(result.getResponse().getContentAsString(), Map.class); + assertTrue(response.containsKey("\\measurements\\bmi\\")); + assertFalse(response.get("\\measurements\\bmi\\").isEmpty()); + } + + @Test + void info_returnsResourceInfo() throws Exception { + MvcResult result = + mockMvc.perform(post("/info").contentType(MediaType.APPLICATION_JSON).content("{}")).andExpect(status().isOk()).andReturn(); + + String content = result.getResponse().getContentAsString(); + assertTrue(content.contains("PIC-SURE Visualization Service")); + assertTrue(content.contains("queryFormats")); + } + + @Test + void queryFormat_returnsDistributionFormat() throws Exception { + MvcResult result = mockMvc.perform(post("/query/format").contentType(MediaType.APPLICATION_JSON).content("{}")) + .andExpect(status().isOk()).andReturn(); + + String content = result.getResponse().getContentAsString(); + assertTrue(content.contains("POST /distributions")); + assertTrue(content.contains("hpdsResourceUUID")); + } +} diff --git a/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/error/GlobalExceptionHandlerTest.java b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/error/GlobalExceptionHandlerTest.java new file mode 100644 index 000000000..ea331c4cb --- /dev/null +++ b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/error/GlobalExceptionHandlerTest.java @@ -0,0 +1,125 @@ +package edu.harvard.dbmi.avillach.visualization.error; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.http.converter.HttpMessageNotReadableException; +import org.springframework.validation.BeanPropertyBindingResult; +import org.springframework.validation.FieldError; +import org.springframework.web.bind.MethodArgumentNotValidException; +import org.springframework.web.client.HttpClientErrorException; +import org.springframework.web.client.HttpServerErrorException; +import org.springframework.web.client.ResourceAccessException; + +import java.io.IOException; +import java.util.Map; + +import static org.junit.jupiter.api.Assertions.*; + +class GlobalExceptionHandlerTest { + + private GlobalExceptionHandler handler; + + @BeforeEach + void setUp() { + handler = new GlobalExceptionHandler(); + } + + @Test + void handleVisualizationException_clientError_returns400() { + BadVisualizationRequestException e = new BadVisualizationRequestException("Could not parse query: bad format"); + + ResponseEntity> response = handler.handleBadVisualizationRequest(e); + + assertEquals(HttpStatus.BAD_REQUEST, response.getStatusCode()); + assertEquals("Could not parse query: bad format", response.getBody().get("error")); + } + + @Test + void handleVisualizationException_hpdsHttpError_returns502() { + HttpServerErrorException cause = + HttpServerErrorException.create(HttpStatus.INTERNAL_SERVER_ERROR, "Internal Server Error", null, null, null); + HpdsUpstreamException e = new HpdsUpstreamException("HPDS query failed with status 500: Internal Server Error", cause); + + ResponseEntity> response = handler.handleHpdsUpstreamException(e); + + assertEquals(HttpStatus.BAD_GATEWAY, response.getStatusCode()); + assertTrue(response.getBody().get("error").contains("HPDS query failed")); + } + + @Test + void handleVisualizationException_hpds4xxError_returns502() { + HttpClientErrorException cause = HttpClientErrorException.create(HttpStatus.NOT_FOUND, "Not Found", null, null, null); + HpdsUpstreamException e = new HpdsUpstreamException("HPDS query failed with status 404: Not Found", cause); + + ResponseEntity> response = handler.handleHpdsUpstreamException(e); + + assertEquals(HttpStatus.BAD_GATEWAY, response.getStatusCode()); + } + + @Test + void handleVisualizationException_networkError_returns502() { + ResourceAccessException cause = new ResourceAccessException("Connection refused", new IOException("Connection refused")); + HpdsUpstreamException e = new HpdsUpstreamException("HPDS query failed: Connection refused", cause); + + ResponseEntity> response = handler.handleHpdsUpstreamException(e); + + assertEquals(HttpStatus.BAD_GATEWAY, response.getStatusCode()); + assertTrue(response.getBody().get("error").contains("Connection refused")); + } + + @Test + void handleVisualizationException_configError_returns500() { + VisualizationConfigurationException e = + new VisualizationConfigurationException("Authorized HPDS resource UUID (hpds.resource.authorized.uuid) is not configured"); + + ResponseEntity> response = handler.handleVisualizationConfigurationException(e); + + assertEquals(HttpStatus.INTERNAL_SERVER_ERROR, response.getStatusCode()); + assertTrue(response.getBody().get("error").contains("not configured")); + } + + @Test + void handleValidationException_returns400WithFieldErrors() { + BeanPropertyBindingResult bindingResult = new BeanPropertyBindingResult(null, "request"); + bindingResult.addError(new FieldError("request", "query", "must not be null")); + MethodArgumentNotValidException e = new MethodArgumentNotValidException(null, bindingResult); + + ResponseEntity> response = handler.handleValidationException(e); + + assertEquals(HttpStatus.BAD_REQUEST, response.getStatusCode()); + assertTrue(response.getBody().get("error").contains("query")); + assertTrue(response.getBody().get("error").contains("must not be null")); + } + + @Test + void handleUnreadableMessage_returns400() { + HttpMessageNotReadableException e = new HttpMessageNotReadableException("Could not read JSON", (Throwable) null, null); + + ResponseEntity> response = handler.handleUnreadableMessage(e); + + assertEquals(HttpStatus.BAD_REQUEST, response.getStatusCode()); + assertEquals("Malformed request body", response.getBody().get("error")); + } + + @Test + void handleIllegalArgument_returns400() { + IllegalArgumentException e = new IllegalArgumentException("invalid parameter"); + + ResponseEntity> response = handler.handleIllegalArgument(e); + + assertEquals(HttpStatus.BAD_REQUEST, response.getStatusCode()); + assertEquals("invalid parameter", response.getBody().get("error")); + } + + @Test + void handleGenericException_returns500() { + Exception e = new RuntimeException("something unexpected"); + + ResponseEntity> response = handler.handleGenericException(e); + + assertEquals(HttpStatus.INTERNAL_SERVER_ERROR, response.getStatusCode()); + assertEquals("Internal server error", response.getBody().get("error")); + } +} diff --git a/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/logging/AuditLoggingFilterTest.java b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/logging/AuditLoggingFilterTest.java new file mode 100644 index 000000000..0eb541b59 --- /dev/null +++ b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/logging/AuditLoggingFilterTest.java @@ -0,0 +1,126 @@ +package edu.harvard.dbmi.avillach.visualization.logging; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.ArgumentCaptor; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; +import org.slf4j.MDC; +import org.springframework.mock.web.MockFilterChain; +import org.springframework.mock.web.MockHttpServletRequest; +import org.springframework.mock.web.MockHttpServletResponse; + +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import java.io.IOException; +import java.util.Map; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.ArgumentMatchers.*; +import static org.mockito.Mockito.*; + +@ExtendWith(MockitoExtension.class) +class AuditLoggingFilterTest { + + @Mock + private LoggingClient loggingClient; + + private AuditLoggingFilter filter; + + @BeforeEach + void setUp() { + filter = new AuditLoggingFilter(loggingClient); + } + + @Test + void doFilter_generatesRequestIdAndLogsDistributions() throws ServletException, IOException { + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/distributions"); + request.setContentType("application/json"); + request.addHeader("Authorization", "Bearer token"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, new MockFilterChain()); + + assertNotNull(response.getHeader("X-Request-Id")); + assertNull(MDC.get("requestId")); + + ArgumentCaptor eventCaptor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(eventCaptor.capture(), eq("Bearer token"), eq(response.getHeader("X-Request-Id"))); + + LoggingEvent event = eventCaptor.getValue(); + assertEquals("QUERY", event.getEventType()); + assertEquals("visualization.distributions", event.getAction()); + assertEquals(response.getHeader("X-Request-Id"), event.getRequest().getRequestId()); + assertEquals("POST", event.getRequest().getMethod()); + assertEquals("/distributions", event.getRequest().getUrl()); + } + + @Test + void doFilter_preservesIncomingRequestIdAndSessionId() throws ServletException, IOException { + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/bin/continuous"); + request.addHeader("X-Request-Id", "incoming-request"); + request.addHeader("X-Session-Id", "session-1"); + MockHttpServletResponse response = new MockHttpServletResponse(); + + filter.doFilter(request, response, new MockFilterChain()); + + assertEquals("incoming-request", response.getHeader("X-Request-Id")); + ArgumentCaptor eventCaptor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(eventCaptor.capture(), isNull(), eq("incoming-request")); + assertEquals("visualization.bin_continuous", eventCaptor.getValue().getAction()); + assertEquals("session-1", eventCaptor.getValue().getSessionId()); + } + + @Test + void doFilter_includesContextMetadata() throws ServletException, IOException { + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/bin/continuous"); + MockHttpServletResponse response = new MockHttpServletResponse(); + FilterChain chain = (req, resp) -> { + AuditLoggingContext.addMetadata((MockHttpServletRequest) req, "route", "bin_continuous"); + AuditLoggingContext.addMetadata((MockHttpServletRequest) req, "output_point_count", 2); + }; + + filter.doFilter(request, response, chain); + + ArgumentCaptor eventCaptor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(eventCaptor.capture(), isNull(), anyString()); + assertEquals("bin_continuous", eventCaptor.getValue().getMetadata().get("route")); + assertEquals(2, eventCaptor.getValue().getMetadata().get("output_point_count")); + } + + @Test + void doFilter_skipsHealthAndCompatibilityRoutes() throws ServletException, IOException { + filter.doFilter(new MockHttpServletRequest("POST", "/info"), new MockHttpServletResponse(), new MockFilterChain()); + filter.doFilter(new MockHttpServletRequest("POST", "/query/format"), new MockHttpServletResponse(), new MockFilterChain()); + filter.doFilter(new MockHttpServletRequest("GET", "/actuator/health"), new MockHttpServletResponse(), new MockFilterChain()); + + verifyNoInteractions(loggingClient); + } + + @Test + void doFilter_statusFailureAddsErrorMetadata() throws ServletException, IOException { + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/distributions"); + MockHttpServletResponse response = new MockHttpServletResponse(); + FilterChain chain = (req, resp) -> ((MockHttpServletResponse) resp).setStatus(400); + + filter.doFilter(request, response, chain); + + ArgumentCaptor eventCaptor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(eventCaptor.capture(), isNull(), anyString()); + Map error = eventCaptor.getValue().getError(); + assertEquals(400, error.get("status")); + assertEquals("client_error", error.get("error_type")); + } + + @Test + void doFilter_loggingClientThrowsDoesNotPropagate() { + MockHttpServletRequest request = new MockHttpServletRequest("POST", "/distributions"); + MockHttpServletResponse response = new MockHttpServletResponse(); + doThrow(new RuntimeException("logging down")).when(loggingClient).send(any(), any(), any()); + + assertDoesNotThrow(() -> filter.doFilter(request, response, new MockFilterChain())); + } +} diff --git a/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/model/ObfuscatedCountShapeTest.java b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/model/ObfuscatedCountShapeTest.java new file mode 100644 index 000000000..909cecd2e --- /dev/null +++ b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/model/ObfuscatedCountShapeTest.java @@ -0,0 +1,66 @@ +package edu.harvard.dbmi.avillach.visualization.model; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNull; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import org.junit.jupiter.api.Test; + +/** + * Pins the JSON wire shape that the visualization resource exchanges with aggregate-data-sharing. If either side renames a field, this test + * fails BEFORE the cross-repo contract silently breaks in production. + */ +class ObfuscatedCountShapeTest { + + private final ObjectMapper mapper = new ObjectMapper(); + + @Test + void serializesAsCountDisplayAndVarianceFields() throws JsonProcessingException { + ObfuscatedCount value = new ObfuscatedCount(222, "222 ±3", 3); + + String json = mapper.writeValueAsString(value); + + assertEquals("{\"count\":222,\"display\":\"222 ±3\",\"variance\":3}", json); + } + + @Test + void serializesExactValuesWithNullVariance() throws JsonProcessingException { + ObfuscatedCount value = ObfuscatedCount.ofInt(45000); + + String json = mapper.writeValueAsString(value); + + assertEquals("{\"count\":45000,\"display\":\"45000\",\"variance\":null}", json); + } + + @Test + void deserializesFromAggSideShape() throws JsonProcessingException { + String aggSideJson = "{\"count\":0,\"display\":\"< 10\",\"variance\":9}"; + + ObfuscatedCount value = mapper.readValue(aggSideJson, ObfuscatedCount.class); + + assertEquals(0, value.count()); + assertEquals("< 10", value.display()); + assertEquals(Integer.valueOf(9), value.variance()); + } + + @Test + void deserializesWhenVarianceIsAbsent() throws JsonProcessingException { + String aggSideJson = "{\"count\":12000,\"display\":\"12000\"}"; + + ObfuscatedCount value = mapper.readValue(aggSideJson, ObfuscatedCount.class); + + assertEquals(12000, value.count()); + assertEquals("12000", value.display()); + assertNull(value.variance()); + } + + @Test + void ofInt_factory_producesStringifiedDisplayAndNullVariance() { + ObfuscatedCount value = ObfuscatedCount.ofInt(45000); + + assertEquals(45000, value.count()); + assertEquals("45000", value.display()); + assertNull(value.variance()); + } +} diff --git a/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/processing/BinningServiceTest.java b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/processing/BinningServiceTest.java new file mode 100644 index 000000000..45d5291c2 --- /dev/null +++ b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/processing/BinningServiceTest.java @@ -0,0 +1,233 @@ +package edu.harvard.dbmi.avillach.visualization.processing; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +import java.util.LinkedHashMap; +import java.util.Map; + +import static org.junit.jupiter.api.Assertions.*; + +class BinningServiceTest { + + private BinningService binningService; + + @BeforeEach + void setUp() { + binningService = new BinningService(); + } + + @Test + void bucketData_emptyMap_returnsEmpty() { + Map result = binningService.bucketData(Map.of()); + assertTrue(result.isEmpty()); + } + + @Test + void bucketData_singleValue_returnsSingleBin() { + Map input = new LinkedHashMap<>(); + input.put("25.0", 100); + + Map result = binningService.bucketData(input); + + assertEquals(1, result.size()); + assertEquals(100, result.values().iterator().next()); + } + + @Test + void bucketData_multipleValues_createsBins() { + Map input = new LinkedHashMap<>(); + input.put("10.0", 5); + input.put("20.0", 10); + input.put("30.0", 15); + input.put("40.0", 20); + input.put("50.0", 25); + input.put("60.0", 30); + input.put("70.0", 35); + input.put("80.0", 40); + input.put("90.0", 45); + input.put("100.0", 50); + + Map result = binningService.bucketData(input); + + assertFalse(result.isEmpty()); + // Last bin should end with "+" + String lastKey = result.keySet().stream().reduce((first, second) -> second).orElse(""); + assertTrue(lastKey.endsWith("+")); + // Total counts should be preserved + int totalInput = input.values().stream().mapToInt(Integer::intValue).sum(); + int totalOutput = result.values().stream().mapToInt(Integer::intValue).sum(); + assertEquals(totalInput, totalOutput); + } + + @Test + void bucketData_nullMap_returnsEmpty() { + Map result = binningService.bucketData(null); + assertTrue(result.isEmpty()); + } + + @Test + void binContinuousData_processeseMultipleEntries() { + Map> input = new LinkedHashMap<>(); + Map bmiData = new LinkedHashMap<>(); + bmiData.put("18.0", 100); + bmiData.put("25.0", 200); + bmiData.put("30.0", 150); + input.put("\\measurements\\bmi\\", bmiData); + + Map> result = binningService.binContinuousData(input); + + assertTrue(result.containsKey("\\measurements\\bmi\\")); + assertFalse(result.get("\\measurements\\bmi\\").isEmpty()); + } + + @Test + void bucketData_stringKeysThatParseToSameDouble_mergesIntoSingleEntry() { + // "5.0" and "5.0000" both parse to Double 5.0, so the LinkedHashMap + // will have only one entry (second overwrites first). This tests that single-value + // behavior works correctly after dedup. + Map input = new LinkedHashMap<>(); + input.put("5.0", 10); + input.put("5.0000", 20); + + Map result = binningService.bucketData(input); + + assertNotNull(result); + assertEquals(1, result.size()); + // Second value (20) overwrites first (10) in the Double-keyed map + assertEquals(20, result.values().iterator().next()); + } + + @Test + void bucketData_singleUniqueValue_returnsSingleBin() { + Map input = new LinkedHashMap<>(); + input.put("10.0", 50); + + Map result = binningService.bucketData(input); + + assertNotNull(result); + assertEquals(1, result.size()); + assertEquals(50, result.values().iterator().next()); + } + + @Test + void bucketData_fractionalRange_producesCorrectBins() { + // Range 0.0 to 2.0 with many data points at fractional values. + // With the old integer binSize, ceil(2.0/3) = 1, which would produce + // bins [0,1), [1,2), [2,3) — oversized and wrong boundaries. + // With double binSize = 0.667, bins are properly fractional. + Map input = new LinkedHashMap<>(); + for (int i = 0; i <= 20; i++) { + input.put(String.valueOf(i * 0.1), 10); + } + + Map result = binningService.bucketData(input); + + assertFalse(result.isEmpty()); + // Total counts preserved + int totalInput = input.values().stream().mapToInt(Integer::intValue).sum(); + int totalOutput = result.values().stream().mapToInt(Integer::intValue).sum(); + assertEquals(totalInput, totalOutput); + // Bin boundaries should be fractional, not integer-rounded + for (String label : result.keySet()) { + if (label.contains(" - ")) { + String[] parts = label.split(" - "); + double lower = Double.parseDouble(parts[0]); + double upper = Double.parseDouble(parts[1]); + assertTrue(upper > lower, "Bin range should have upper > lower: " + label); + } + } + } + + @Test + void bucketData_allValuesAtZero_returnsSingleBin() { + Map input = new LinkedHashMap<>(); + input.put("0.0", 500); + + Map result = binningService.bucketData(input); + + assertFalse(result.isEmpty(), "A dataset with values at 0.0 should produce a bin, not empty"); + assertEquals(1, result.size()); + assertEquals(500, result.values().iterator().next()); + } + + @Test + void bucketData_unsortedInput_returnsBinsInAscendingOrder() { + // HPDS does not guarantee value order; bins must come back sorted regardless, + // and the "+" relabel must land on the highest bin, not the last-encountered one. + Map input = new LinkedHashMap<>(); + input.put("90.0", 45); + input.put("10.0", 5); + input.put("50.0", 25); + input.put("100.0", 50); + input.put("30.0", 15); + input.put("70.0", 35); + input.put("20.0", 10); + input.put("80.0", 40); + input.put("40.0", 20); + input.put("60.0", 30); + + Map result = binningService.bucketData(input); + + double previousLower = Double.NEGATIVE_INFINITY; + for (String label : result.keySet()) { + double lower = Double.parseDouble(label.split(" ")[0]); + assertTrue(lower > previousLower, "Bins must be in ascending order, got: " + result.keySet()); + previousLower = lower; + } + String lastKey = result.keySet().stream().reduce((first, second) -> second).orElse(""); + assertTrue(lastKey.endsWith("+"), "Highest bin should carry the + label, got: " + lastKey); + int totalInput = input.values().stream().mapToInt(Integer::intValue).sum(); + int totalOutput = result.values().stream().mapToInt(Integer::intValue).sum(); + assertEquals(totalInput, totalOutput); + } + + @Test + void bucketData_multiBinGap_fillsEveryEmptyBinWithZero() { + // A dense cluster plus one far outlier leaves a run of several empty bins between them; + // each must render as a zero bar rather than being silently omitted. + Map input = new LinkedHashMap<>(); + for (int i = 0; i <= 100; i++) { + input.put(String.valueOf(i * 0.1), 10); + } + input.put("100.0", 10); + + Map result = binningService.bucketData(input); + + long zeroBins = result.values().stream().filter(v -> v == 0).count(); + assertTrue(zeroBins >= 2, "Runs of empty bins should be zero-filled, got: " + result); + int totalInput = input.values().stream().mapToInt(Integer::intValue).sum(); + int totalOutput = result.values().stream().mapToInt(Integer::intValue).sum(); + assertEquals(totalInput, totalOutput); + } + + @Test + void bucketData_collidingRoundedLabels_mergesCountsInsteadOfDropping() { + // Many distinct values in a tiny range produce bins whose %.1f-rounded labels collide; + // counts must merge rather than the earlier bin being overwritten. + Map input = new LinkedHashMap<>(); + for (int i = 0; i <= 40; i++) { + input.put(String.valueOf(1.0 + i * 0.001), 10); + } + + Map result = binningService.bucketData(input); + + int totalInput = input.values().stream().mapToInt(Integer::intValue).sum(); + int totalOutput = result.values().stream().mapToInt(Integer::intValue).sum(); + assertEquals(totalInput, totalOutput, "Counts must never be lost to label collisions: " + result); + } + + @Test + void bucketData_singleNumericValueAmongNonNumericKeys_labelsAsSingleValue() { + // isSameMinMax must be computed after non-numeric keys are dropped + Map input = new LinkedHashMap<>(); + input.put("not-a-number", 5); + input.put("25.0", 100); + + Map result = binningService.bucketData(input); + + assertEquals(1, result.size()); + assertEquals("25.0", result.keySet().iterator().next(), "Single data point should not be labeled as a range"); + assertEquals(100, result.values().iterator().next()); + } +} diff --git a/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/processing/CategoricalAggregationServiceTest.java b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/processing/CategoricalAggregationServiceTest.java new file mode 100644 index 000000000..a331630c3 --- /dev/null +++ b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/processing/CategoricalAggregationServiceTest.java @@ -0,0 +1,158 @@ +package edu.harvard.dbmi.avillach.visualization.processing; + +import static org.junit.jupiter.api.Assertions.*; + +import java.util.LinkedHashMap; +import java.util.Map; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +class CategoricalAggregationServiceTest { + + private CategoricalAggregationService service; + + @BeforeEach + void setUp() { + service = new CategoricalAggregationService(7); + } + + @Test + void aggregateTopN_moreThanMaxCategories_createsOtherBucket() { + Map categories = new LinkedHashMap<>(); + categories.put("Cat1", 100); + categories.put("Cat2", 90); + categories.put("Cat3", 80); + categories.put("Cat4", 70); + categories.put("Cat5", 60); + categories.put("Cat6", 50); + categories.put("Cat7", 40); + categories.put("Cat8", 30); + categories.put("Cat9", 20); + + Map result = service.aggregateTopN(categories); + + assertTrue(result.containsKey("Other")); + assertEquals(50, result.get("Other")); + } + + @Test + void aggregateTopN_exactlyOneOverMax_createsOtherBucket() { + Map categories = new LinkedHashMap<>(); + categories.put("Cat1", 100); + categories.put("Cat2", 90); + categories.put("Cat3", 80); + categories.put("Cat4", 70); + categories.put("Cat5", 60); + categories.put("Cat6", 50); + categories.put("Cat7", 40); + categories.put("Cat8", 30); + + Map result = service.aggregateTopN(categories); + + assertTrue(result.containsKey("Other")); + assertEquals(30, result.get("Other")); + assertEquals(8, result.size()); + } + + @Test + void aggregateTopN_exactlyAtMax_noOtherBucket() { + Map categories = new LinkedHashMap<>(); + categories.put("Cat1", 100); + categories.put("Cat2", 90); + categories.put("Cat3", 80); + categories.put("Cat4", 70); + categories.put("Cat5", 60); + categories.put("Cat6", 50); + categories.put("Cat7", 40); + + Map result = service.aggregateTopN(categories); + + assertFalse(result.containsKey("Other")); + assertEquals(7, result.size()); + } + + @Test + void aggregateTopN_truncatesLongKeys() { + String longKey = "a".repeat(60); + Map categories = new LinkedHashMap<>(); + categories.put(longKey, 100); + + Map result = service.aggregateTopN(categories); + + assertFalse(result.containsKey(longKey)); + assertTrue(result.keySet().iterator().next().length() <= 48, "Long keys should be truncated"); + } + + @Test + void aggregateTopN_nullInput_returnsEmptyMap() { + Map result = service.aggregateTopN(null); + assertNotNull(result); + assertTrue(result.isEmpty()); + } + + @Test + void aggregateTopN_emptyInput_returnsEmptyMap() { + Map result = service.aggregateTopN(new java.util.LinkedHashMap<>()); + assertNotNull(result); + assertTrue(result.isEmpty()); + } + + @Test + void aggregateTopN_singleLongKeyNoCollision_usesSimpleTruncation() { + String longKey = "a".repeat(60); + Map categories = new LinkedHashMap<>(); + categories.put(longKey, 100); + + Map result = service.aggregateTopN(categories); + + String adjusted = result.keySet().iterator().next(); + assertEquals("a".repeat(45) + "...", adjusted); + assertEquals(100, result.get(adjusted)); + } + + @Test + void aggregateTopN_realCategoryNamedOther_sumsWithTailBucket() { + Map categories = new LinkedHashMap<>(); + categories.put("Cat1", 100); + categories.put("Cat2", 90); + categories.put("Cat3", 80); + categories.put("Cat4", 70); + categories.put("Cat5", 60); + categories.put("Cat6", 50); + categories.put("Other", 40); + categories.put("Cat8", 30); + categories.put("Cat9", 20); + + Map result = service.aggregateTopN(categories); + + assertEquals(90, result.get("Other"), "Real 'Other' category must sum with tail bucket, not be overwritten"); + assertEquals( + categories.values().stream().mapToInt(Integer::intValue).sum(), result.values().stream().mapToInt(Integer::intValue).sum(), + "Total count must be preserved" + ); + } + + @Test + void aggregateTopN_manyKeysSharingFullPrefix_doesNotCrashLoop() { + // Pre-fix: createAdjustedKey's disambiguation loop crashes with + // StringIndexOutOfBoundsException around the 38th key because the + // character budget (MAX_LABEL_LENGTH - 3 - countFromEnd) goes negative + // once enough variants are already in the seen-keys set. + CategoricalAggregationService largeService = new CategoricalAggregationService(50); + Map categories = new LinkedHashMap<>(); + String prefix = "a".repeat(45); + String suffix = "a".repeat(42); + for (int i = 0; i < 50; i++) { + String key = prefix + (char) ('A' + i) + suffix; + categories.put(key, 1000 - i); + } + + Map result = largeService.aggregateTopN(categories); + + assertEquals(50, result.size(), "All 50 keys should produce distinct adjusted labels"); + assertEquals( + categories.values().stream().mapToInt(Integer::intValue).sum(), result.values().stream().mapToInt(Integer::intValue).sum(), + "Total counts must not be lost during disambiguation" + ); + } +} diff --git a/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/processing/CategoricalDistributionProcessorTest.java b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/processing/CategoricalDistributionProcessorTest.java new file mode 100644 index 000000000..aa77a2e50 --- /dev/null +++ b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/processing/CategoricalDistributionProcessorTest.java @@ -0,0 +1,116 @@ +package edu.harvard.dbmi.avillach.visualization.processing; + +import static org.junit.jupiter.api.Assertions.*; + +import edu.harvard.dbmi.avillach.visualization.model.CategoricalDistributionData; +import edu.harvard.dbmi.avillach.visualization.model.ObfuscatedCount; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +class CategoricalDistributionProcessorTest { + + private CategoricalDistributionProcessor processor; + + @BeforeEach + void setUp() { + processor = new CategoricalDistributionProcessor(); + } + + @Test + void process_simpleCategoricalData_returnsDistributionData() { + Map> data = new LinkedHashMap<>(); + data.put( + "\\demographics\\race\\", + new LinkedHashMap<>( + Map.of( + "White", new ObfuscatedCount(45000, "45000"), "Black", new ObfuscatedCount(12000, "12000"), "Asian", + new ObfuscatedCount(8000, "8000") + ) + ) + ); + + List result = processor.process(data, false); + + assertEquals(1, result.size()); + CategoricalDistributionData distribution = result.get(0); + assertEquals("\\demographics\\race\\", distribution.conceptPath()); + assertEquals("demographics: race", distribution.title()); + assertFalse(distribution.continuous()); + assertFalse(distribution.obfuscated()); + ObfuscatedCount white = distribution.categoricalMap().get("White"); + assertEquals(45000, white.count()); + assertEquals("45000", white.display()); + assertEquals("race", distribution.xaxisName()); + assertEquals("Number of Participants", distribution.yaxisName()); + } + + @Test + void process_obfuscatedValues_passedThroughUnchanged() { + Map> data = new LinkedHashMap<>(); + data.put( + "\\demographics\\race\\", + new LinkedHashMap<>(Map.of("White", new ObfuscatedCount(45000, "45000 ±3", 3), "Black", new ObfuscatedCount(0, "< 10", 9))) + ); + + List result = processor.process(data, true); + + assertEquals(1, result.size()); + assertTrue(result.get(0).obfuscated()); + ObfuscatedCount white = result.get(0).categoricalMap().get("White"); + assertEquals(45000, white.count()); + assertEquals("45000 ±3", white.display()); + assertEquals(Integer.valueOf(3), white.variance()); + ObfuscatedCount black = result.get(0).categoricalMap().get("Black"); + assertEquals(0, black.count()); + assertEquals("< 10", black.display()); + assertEquals(Integer.valueOf(9), black.variance()); + } + + @Test + void process_skipsConsentKeysAndEmptySeries() { + Map> data = new LinkedHashMap<>(); + data.put("\\_consents\\", Map.of("consent1", new ObfuscatedCount(100, "100"))); + data.put("\\_harmonized_consent\\", Map.of("consent2", new ObfuscatedCount(200, "200"))); + data.put("\\empty\\", Map.of()); + data.put("\\demographics\\race\\", new LinkedHashMap<>(Map.of("White", new ObfuscatedCount(45000, "45000")))); + + List result = processor.process(data, false); + + assertEquals(1, result.size()); + } + + @Test + void process_nullInnerMap_skippedWithoutCrash() { + Map> data = new LinkedHashMap<>(); + data.put("\\demographics\\race\\", null); + data.put("\\demographics\\sex\\", new LinkedHashMap<>(Map.of("Female", new ObfuscatedCount(100, "100")))); + + List result = processor.process(data, false); + + assertEquals(1, result.size()); + assertEquals("\\demographics\\sex\\", result.get(0).conceptPath()); + } + + @Test + void metadata_extractsTitleAndXAxisLabel() { + assertEquals("demographics: race", DistributionMetadata.titleFor("\\demographics\\race\\")); + assertEquals("race", DistributionMetadata.xAxisLabelFor("\\demographics\\race\\")); + assertEquals("race", DistributionMetadata.titleFor("race")); + } + + @Test + void metadata_depthOnePath_hasNoLeadingColon() { + assertEquals("age", DistributionMetadata.titleFor("\\age\\")); + assertEquals("age", DistributionMetadata.xAxisLabelFor("\\age\\")); + } + + @Test + void metadata_multiWordVariableName_keepsFullNameForXAxis() { + assertEquals( + "family history of heart attack", DistributionMetadata.xAxisLabelFor("\\demographics\\family history of heart attack\\") + ); + } +} diff --git a/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/processing/ContinuousDistributionProcessorTest.java b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/processing/ContinuousDistributionProcessorTest.java new file mode 100644 index 000000000..e5029d979 --- /dev/null +++ b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/processing/ContinuousDistributionProcessorTest.java @@ -0,0 +1,95 @@ +package edu.harvard.dbmi.avillach.visualization.processing; + +import static org.junit.jupiter.api.Assertions.*; + +import edu.harvard.dbmi.avillach.visualization.model.ContinuousDistributionData; +import edu.harvard.dbmi.avillach.visualization.model.ObfuscatedCount; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +class ContinuousDistributionProcessorTest { + + private ContinuousDistributionProcessor processor; + + @BeforeEach + void setUp() { + processor = new ContinuousDistributionProcessor(); + } + + @Test + void process_preBinnedValues_returnsContinuousDistribution() { + Map> data = new LinkedHashMap<>(); + data.put( + "\\measurements\\bmi\\", + new LinkedHashMap<>( + Map.of( + "18.0 - 24.0", new ObfuscatedCount(600, "600"), "24.0 - 30.0", new ObfuscatedCount(700, "700"), "30.0 +", + new ObfuscatedCount(150, "150") + ) + ) + ); + + List result = processor.process(data, false); + + assertEquals(1, result.size()); + ContinuousDistributionData distribution = result.get(0); + assertEquals("\\measurements\\bmi\\", distribution.conceptPath()); + assertEquals("measurements: bmi", distribution.title()); + assertTrue(distribution.continuous()); + assertFalse(distribution.obfuscated()); + ObfuscatedCount firstBin = distribution.continuousMap().get("18.0 - 24.0"); + assertEquals(600, firstBin.count()); + assertEquals("600", firstBin.display()); + } + + @Test + void process_obfuscatedValues_passedThroughUnchanged() { + Map> data = new LinkedHashMap<>(); + data.put( + "\\measurements\\bmi\\", + new LinkedHashMap<>( + Map.of("18.0 - 22.0", new ObfuscatedCount(500, "500 ±3", 3), "22.0 - 26.0", new ObfuscatedCount(0, "< 10", 9)) + ) + ); + + List result = processor.process(data, true); + + assertEquals(1, result.size()); + assertTrue(result.get(0).obfuscated()); + ObfuscatedCount lo = result.get(0).continuousMap().get("18.0 - 22.0"); + assertEquals(500, lo.count()); + assertEquals("500 ±3", lo.display()); + assertEquals(Integer.valueOf(3), lo.variance()); + ObfuscatedCount hi = result.get(0).continuousMap().get("22.0 - 26.0"); + assertEquals(0, hi.count()); + assertEquals("< 10", hi.display()); + assertEquals(Integer.valueOf(9), hi.variance()); + } + + @Test + void process_skipsConsentKeysAndEmptySeries() { + Map> data = new LinkedHashMap<>(); + data.put("\\_consents\\", Map.of("1.0", new ObfuscatedCount(100, "100"))); + data.put("\\empty\\", Map.of()); + data.put("\\measurements\\bmi\\", new LinkedHashMap<>(Map.of("25.0", new ObfuscatedCount(100, "100")))); + + List result = processor.process(data, false); + + assertEquals(1, result.size()); + } + + @Test + void process_nullInnerMap_skippedWithoutCrash() { + Map> data = new LinkedHashMap<>(); + data.put("\\measurements\\bmi\\", null); + data.put("\\measurements\\age\\", new LinkedHashMap<>(Map.of("25.0", new ObfuscatedCount(100, "100")))); + + List result = processor.process(data, false); + + assertEquals(1, result.size()); + assertEquals("\\measurements\\age\\", result.get(0).conceptPath()); + } +} diff --git a/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/service/HpdsClientTest.java b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/service/HpdsClientTest.java new file mode 100644 index 000000000..aae8bdade --- /dev/null +++ b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/service/HpdsClientTest.java @@ -0,0 +1,157 @@ +package edu.harvard.dbmi.avillach.visualization.service; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.ArgumentMatchers.eq; +import static org.mockito.Mockito.verify; +import static org.springframework.test.web.client.match.MockRestRequestMatchers.*; +import static org.springframework.test.web.client.response.MockRestResponseCreators.withSuccess; + +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.dbmi.avillach.visualization.error.VisualizationException; +import edu.harvard.dbmi.avillach.visualization.model.AccessType; +import edu.harvard.dbmi.avillach.visualization.model.DistributionType; +import edu.harvard.dbmi.avillach.visualization.model.ObfuscatedCount; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.Query; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.UUID; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.ArgumentCaptor; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; +import org.springframework.http.HttpMethod; +import org.springframework.http.MediaType; +import org.springframework.test.web.client.MockRestServiceServer; +import org.springframework.web.client.RestClient; + +@ExtendWith(MockitoExtension.class) +class HpdsClientTest { + + private static final UUID RESOURCE_UUID = UUID.fromString("550e8400-e29b-41d4-a716-446655440000"); + + private final ObjectMapper objectMapper = new ObjectMapper(); + + @Mock + private LoggingClient loggingClient; + + private MockRestServiceServer mockServer; + private HpdsClient client; + + @BeforeEach + void setUp() { + RestClient.Builder builder = RestClient.builder(); + mockServer = MockRestServiceServer.bindTo(builder).build(); + client = new HpdsClient(builder.build(), loggingClient, "http://localhost:9999/mock-hpds"); + } + + @Test + void getAuthCrossCounts_withNullResourceUUID_stillQueriesHpds() throws Exception { + // Registry removal: the path-routed frontend sends no resource UUID and none may be configured; HPDS + // ignores the body field, so a null UUID must not be rejected client-side. + Map> expected = new LinkedHashMap<>(); + expected.put("\\test\\", Map.of("a", 1)); + + mockServer.expect(requestTo("http://localhost:9999/mock-hpds/v3/query/sync")).andExpect(method(HttpMethod.POST)) + .andExpect(content().json("{\"resourceUUID\":null}")) + .andRespond(withSuccess(objectMapper.writeValueAsString(expected), MediaType.APPLICATION_JSON)); + + Query query = new Query(List.of(), List.of(), null, List.of(), null, null, null); + Map> result = client.getAuthCrossCounts( + query, ResultType.CATEGORICAL_CROSS_COUNT, null, "Bearer token", "request-1", AccessType.AUTHORIZED, + DistributionType.CATEGORICAL + ); + + assertEquals(expected, result); + mockServer.verify(); + } + + @Test + void getAuthCrossCounts_postsHpdsQueryRequest() throws Exception { + Map> expected = new LinkedHashMap<>(); + expected.put("\\test\\", Map.of("a", 1)); + + mockServer.expect(requestTo("http://localhost:9999/mock-hpds/v3/query/sync")).andExpect(method(HttpMethod.POST)) + .andExpect(header("Authorization", "Bearer token")).andExpect(header("X-Request-Id", "request-1")) + .andExpect(header("Accept", MediaType.ALL_VALUE)).andExpect(content().contentType(MediaType.APPLICATION_JSON)) + .andExpect(content().json("{\"resourceUUID\":\"" + RESOURCE_UUID + "\"}")) + .andExpect(content().json("{\"query\":{\"expectedResultType\":\"CATEGORICAL_CROSS_COUNT\"}}")) + .andExpect(content().json("{\"resourceCredentials\":{}}")) + .andRespond(withSuccess(objectMapper.writeValueAsString(expected), MediaType.APPLICATION_JSON)); + + Query query = new Query(List.of(), List.of(), null, List.of(), null, null, null); + Map> result = client.getAuthCrossCounts( + query, ResultType.CATEGORICAL_CROSS_COUNT, RESOURCE_UUID, "Bearer token", "request-1", AccessType.AUTHORIZED, + DistributionType.CATEGORICAL + ); + + assertEquals(expected, result); + mockServer.verify(); + + ArgumentCaptor eventCaptor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(eventCaptor.capture(), eq("Bearer token"), eq("request-1")); + LoggingEvent event = eventCaptor.getValue(); + assertEquals("QUERY", event.getEventType()); + assertEquals("visualization.hpds.query", event.getAction()); + assertEquals("request-1", event.getRequest().getRequestId()); + assertEquals(200, event.getRequest().getStatus()); + assertEquals("authorized", event.getMetadata().get("access_type")); + assertEquals("categorical", event.getMetadata().get("distribution_kind")); + } + + @Test + void getAuthCrossCounts_logsHpdsResponseShape() throws Exception { + Map ageValues = new LinkedHashMap<>(); + ageValues.put("18.0", 2); + ageValues.put("19.0", 3); + + Map> expected = new LinkedHashMap<>(); + expected.put("\\Nhanes\\demographics\\AGE\\", ageValues); + + mockServer.expect(requestTo("http://localhost:9999/mock-hpds/v3/query/sync")).andExpect(method(HttpMethod.POST)) + .andExpect(header("Authorization", "Bearer token")).andExpect(header("X-Request-Id", "request-2")) + .andExpect(content().json("{\"query\":{\"expectedResultType\":\"CONTINUOUS_CROSS_COUNT\"}}")) + .andRespond(withSuccess(objectMapper.writeValueAsString(expected), MediaType.APPLICATION_JSON)); + + Query query = new Query(List.of("\\Nhanes\\demographics\\AGE\\"), List.of(), null, List.of(), null, null, null); + Map> result = client.getAuthCrossCounts( + query, ResultType.CONTINUOUS_CROSS_COUNT, RESOURCE_UUID, "Bearer token", "request-2", AccessType.AUTHORIZED, + DistributionType.CONTINUOUS + ); + + assertEquals(expected, result); + mockServer.verify(); + + ArgumentCaptor eventCaptor = ArgumentCaptor.forClass(LoggingEvent.class); + verify(loggingClient).send(eventCaptor.capture(), eq("Bearer token"), eq("request-2")); + LoggingEvent event = eventCaptor.getValue(); + assertEquals(1, event.getMetadata().get("response_series_count")); + assertEquals(2, event.getMetadata().get("response_point_count")); + assertEquals(List.of("\\Nhanes\\demographics\\AGE\\"), event.getMetadata().get("response_series_keys")); + } + + @Test + void getOpenCrossCounts_postsHpdsQueryRequestWithoutAuthorizationHeader() throws Exception { + Map> expected = new LinkedHashMap<>(); + expected.put("\\test\\", Map.of("a", new ObfuscatedCount(1, "1"))); + + mockServer.expect(requestTo("http://localhost:9999/mock-hpds/query/sync")).andExpect(method(HttpMethod.POST)) + .andExpect(headerDoesNotExist("Authorization")).andExpect(header("Accept", MediaType.ALL_VALUE)) + .andExpect(content().json("{\"resourceUUID\":\"" + RESOURCE_UUID + "\"}")) + .andExpect(content().json("{\"query\":{\"expectedResultType\":\"CATEGORICAL_CROSS_COUNT\"}}")) + .andExpect(content().json("{\"resourceCredentials\":{}}")) + .andRespond(withSuccess(objectMapper.writeValueAsString(expected), MediaType.APPLICATION_JSON)); + + Query query = new Query(List.of(), List.of(), null, List.of(), null, null, null); + Map> result = + client.getOpenCrossCounts(query, ResultType.CATEGORICAL_CROSS_COUNT, RESOURCE_UUID, null); + + assertEquals(expected, result); + mockServer.verify(); + } +} diff --git a/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/service/QueryDecomposerTest.java b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/service/QueryDecomposerTest.java new file mode 100644 index 000000000..e9730141f --- /dev/null +++ b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/service/QueryDecomposerTest.java @@ -0,0 +1,105 @@ +package edu.harvard.dbmi.avillach.visualization.service; + +import static org.junit.jupiter.api.Assertions.*; + +import edu.harvard.dbmi.avillach.visualization.model.DistributionType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.*; +import java.util.List; +import java.util.Set; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +class QueryDecomposerTest { + + private QueryDecomposer decomposer; + + @BeforeEach + void setUp() { + decomposer = new QueryDecomposer(); + } + + @Test + void decompose_withCategoricalFilter_returnsCategoricalSubQuery() { + PhenotypicFilter catFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\demographics\\race\\", Set.of("White", "Black"), null, null, null); + Query query = new Query(List.of(), List.of(), catFilter, List.of(), null, null, null); + + List result = decomposer.decompose(query); + + assertEquals(1, result.size()); + assertEquals(ResultType.CATEGORICAL_CROSS_COUNT, result.get(0).resultType()); + assertEquals(DistributionType.CATEGORICAL, result.get(0).distributionKind()); + assertEquals(List.of("\\demographics\\race\\"), result.get(0).query().select()); + } + + @Test + void decompose_withNumericFilter_returnsContinuousSubQuery() { + PhenotypicFilter numFilter = new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\measurements\\bmi\\", null, 18.0, 40.0, null); + Query query = new Query(List.of(), List.of(), numFilter, List.of(), null, null, null); + + List result = decomposer.decompose(query); + + assertEquals(1, result.size()); + assertEquals(ResultType.CONTINUOUS_CROSS_COUNT, result.get(0).resultType()); + assertEquals(DistributionType.CONTINUOUS, result.get(0).distributionKind()); + } + + @Test + void decompose_withBothFilterTypes_returnsTwoSubQueries() { + PhenotypicFilter catFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\demographics\\race\\", Set.of("White"), null, null, null); + PhenotypicFilter numFilter = new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\measurements\\bmi\\", null, 18.0, 40.0, null); + PhenotypicSubquery subquery = new PhenotypicSubquery(null, List.of(catFilter, numFilter), Operator.AND); + Query query = new Query(List.of(), List.of(), subquery, List.of(), null, null, null); + + List result = decomposer.decompose(query); + + assertEquals(2, result.size()); + } + + @Test + void decompose_withNoFilters_returnsEmpty() { + Query query = new Query(List.of(), List.of(), null, List.of(), null, null, null); + + List result = decomposer.decompose(query); + + assertTrue(result.isEmpty()); + } + + @Test + void decompose_withRequiredFilter_treatsTypeAsUnknown() { + PhenotypicFilter required = new PhenotypicFilter(PhenotypicFilterType.REQUIRED, "\\demographics\\AGE\\", null, null, null, null); + Query query = new Query(List.of(), List.of(), required, List.of(), null, null, null); + + List result = decomposer.decompose(query); + + assertEquals(2, result.size()); + assertEquals(ResultType.CATEGORICAL_CROSS_COUNT, result.get(0).resultType()); + assertEquals(ResultType.CONTINUOUS_CROSS_COUNT, result.get(1).resultType()); + } + + @Test + void decompose_withSelectButNoFilters_fallsBackToSelectAsCategorical() { + Query query = new Query(List.of("\\demographics\\race\\", "\\demographics\\sex\\"), List.of(), null, List.of(), null, null, null); + + List result = decomposer.decompose(query); + + assertEquals(1, result.size()); + assertEquals(ResultType.CATEGORICAL_CROSS_COUNT, result.get(0).resultType()); + assertEquals(List.of("\\demographics\\race\\", "\\demographics\\sex\\"), result.get(0).query().select()); + } + + @Test + void decompose_withFiltersAndSelect_ignoresSelectFallback() { + PhenotypicFilter catFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\demographics\\race\\", Set.of("White"), null, null, null); + Query query = new Query(List.of("\\some\\other\\path\\"), List.of(), catFilter, List.of(), null, null, null); + + List result = decomposer.decompose(query); + + assertEquals(1, result.size()); + // Should use the filter path, not the select path + assertEquals(List.of("\\demographics\\race\\"), result.get(0).query().select()); + } +} diff --git a/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/service/VisualizationServiceTest.java b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/service/VisualizationServiceTest.java new file mode 100644 index 000000000..8b03aca89 --- /dev/null +++ b/services/pic-sure-visualization-service/src/test/java/edu/harvard/dbmi/avillach/visualization/service/VisualizationServiceTest.java @@ -0,0 +1,227 @@ +package edu.harvard.dbmi.avillach.visualization.service; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.ArgumentMatchers.*; +import static org.mockito.Mockito.*; + +import edu.harvard.dbmi.avillach.visualization.model.AccessType; +import edu.harvard.dbmi.avillach.visualization.model.HpdsAccessContext; +import edu.harvard.dbmi.avillach.visualization.model.ObfuscatedCount; +import edu.harvard.dbmi.avillach.visualization.model.VisualizationResponse; +import edu.harvard.dbmi.avillach.visualization.processing.BinningService; +import edu.harvard.dbmi.avillach.visualization.processing.CategoricalAggregationService; +import edu.harvard.dbmi.avillach.visualization.processing.CategoricalDistributionProcessor; +import edu.harvard.dbmi.avillach.visualization.processing.ContinuousDistributionProcessor; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType; +import edu.harvard.hms.dbmi.avillach.hpds.data.query.v3.*; +import java.util.*; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; + +@ExtendWith(MockitoExtension.class) +class VisualizationServiceTest { + + private static final UUID AUTHORIZED_UUID = UUID.fromString("550e8400-e29b-41d4-a716-446655440000"); + private static final UUID OPEN_UUID = UUID.fromString("550e8400-e29b-41d4-a716-446655440001"); + + @Mock + private HpdsClient hpdsClient; + + private VisualizationService service; + + @BeforeEach + void setUp() { + QueryDecomposer decomposer = new QueryDecomposer(); + BinningService binningService = new BinningService(); + CategoricalAggregationService aggregationService = new CategoricalAggregationService(7); + CategoricalDistributionProcessor categoricalProcessor = new CategoricalDistributionProcessor(); + ContinuousDistributionProcessor continuousProcessor = new ContinuousDistributionProcessor(); + service = + new VisualizationService(decomposer, hpdsClient, categoricalProcessor, continuousProcessor, binningService, aggregationService); + } + + @Test + void generateDistributions_authorized_categoricalFilter() { + PhenotypicFilter catFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\demographics\\race\\", Set.of("White", "Black"), null, null, null); + Query query = new Query(List.of(), List.of(), catFilter, List.of(), null, null, null); + + Map> crossCounts = new LinkedHashMap<>(); + crossCounts.put("\\demographics\\race\\", new LinkedHashMap<>(Map.of("White", 45000, "Black", 12000))); + when(hpdsClient.getAuthCrossCounts(any(), eq(ResultType.CATEGORICAL_CROSS_COUNT), eq(AUTHORIZED_UUID), any())) + .thenReturn(crossCounts); + + VisualizationResponse response = + service.generateDistributions(query, new HpdsAccessContext(AUTHORIZED_UUID, AccessType.AUTHORIZED), "Bearer token"); + + assertFalse(response.categoricalData().isEmpty()); + assertEquals("demographics: race", response.categoricalData().get(0).title()); + assertFalse(response.categoricalData().get(0).obfuscated()); + } + + @Test + void generateDistributions_open_withObfuscation() { + PhenotypicFilter catFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\demographics\\race\\", Set.of("White"), null, null, null); + Query query = new Query(List.of(), List.of(), catFilter, List.of(), null, null, null); + + Map> openCrossCounts = new LinkedHashMap<>(); + openCrossCounts.put( + "\\demographics\\race\\", + new LinkedHashMap<>(Map.of("White", new ObfuscatedCount(45000, "45000±3", 3), "Other", new ObfuscatedCount(0, "< 10", 9))) + ); + when(hpdsClient.getOpenCrossCounts(any(), eq(ResultType.CATEGORICAL_CROSS_COUNT), eq(OPEN_UUID), any())) + .thenReturn(openCrossCounts); + + VisualizationResponse response = service.generateDistributions(query, new HpdsAccessContext(OPEN_UUID, AccessType.OPEN), null); + + assertFalse(response.categoricalData().isEmpty()); + assertTrue(response.categoricalData().get(0).obfuscated()); + } + + @Test + void generateDistributions_open_setsObfuscatedFromAccessTypeRegardlessOfValues() { + PhenotypicFilter catFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\demographics\\race\\", Set.of("White"), null, null, null); + Query query = new Query(List.of(), List.of(), catFilter, List.of(), null, null, null); + + // All values look like plain integers — no markers at all. + Map> openCrossCounts = new LinkedHashMap<>(); + openCrossCounts.put( + "\\demographics\\race\\", + new LinkedHashMap<>(Map.of("White", new ObfuscatedCount(45000, "45000"), "Black", new ObfuscatedCount(12000, "12000"))) + ); + when(hpdsClient.getOpenCrossCounts(any(), eq(ResultType.CATEGORICAL_CROSS_COUNT), eq(OPEN_UUID), any())) + .thenReturn(openCrossCounts); + + VisualizationResponse response = service.generateDistributions(query, new HpdsAccessContext(OPEN_UUID, AccessType.OPEN), null); + + assertTrue( + response.categoricalData().get(0).obfuscated(), "OPEN access must set obfuscated=true even if values contain no markers" + ); + } + + @Test + void generateDistributions_noFilters_returnsEmptyCharts() { + Query query = new Query(List.of(), List.of(), null, List.of(), null, null, null); + + VisualizationResponse response = + service.generateDistributions(query, new HpdsAccessContext(AUTHORIZED_UUID, AccessType.AUTHORIZED), "Bearer token"); + + assertTrue(response.categoricalData().isEmpty()); + assertTrue(response.continuousData().isEmpty()); + } + + @Test + void generateDistributions_authorized_continuousFilter_binsData() { + PhenotypicFilter numFilter = new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\measurements\\bmi\\", null, 18.0, 40.0, null); + Query query = new Query(List.of(), List.of(), numFilter, List.of(), null, null, null); + + Map rawValues = new LinkedHashMap<>(); + rawValues.put("18.0", 100); + rawValues.put("22.0", 200); + rawValues.put("26.0", 150); + rawValues.put("30.0", 100); + rawValues.put("35.0", 50); + Map> crossCounts = new LinkedHashMap<>(); + crossCounts.put("\\measurements\\bmi\\", rawValues); + when(hpdsClient.getAuthCrossCounts(any(), eq(ResultType.CONTINUOUS_CROSS_COUNT), eq(AUTHORIZED_UUID), any())) + .thenReturn(crossCounts); + + VisualizationResponse response = + service.generateDistributions(query, new HpdsAccessContext(AUTHORIZED_UUID, AccessType.AUTHORIZED), "Bearer token"); + + assertFalse(response.continuousData().isEmpty()); + int totalOutput = response.continuousData().get(0).continuousMap().values().stream().mapToInt(ObfuscatedCount::count).sum(); + assertEquals(600, totalOutput); + } + + @Test + void generateDistributions_selectFallback_whenNoFilters() { + Query query = new Query(List.of("\\demographics\\race\\"), List.of(), null, List.of(), null, null, null); + + Map> crossCounts = new LinkedHashMap<>(); + crossCounts.put("\\demographics\\race\\", new LinkedHashMap<>(Map.of("White", 100))); + when(hpdsClient.getAuthCrossCounts(any(), eq(ResultType.CATEGORICAL_CROSS_COUNT), eq(AUTHORIZED_UUID), any())) + .thenReturn(crossCounts); + + VisualizationResponse response = + service.generateDistributions(query, new HpdsAccessContext(AUTHORIZED_UUID, AccessType.AUTHORIZED), "Bearer token"); + + assertFalse(response.categoricalData().isEmpty()); + assertEquals("demographics: race", response.categoricalData().get(0).title()); + } + + @Test + void generateDistributions_requiredNumericFilter_skipsEmptyCategoricalAndReturnsHistogram() { + PhenotypicFilter required = new PhenotypicFilter(PhenotypicFilterType.REQUIRED, "\\demographics\\AGE\\", null, null, null, null); + Query query = new Query(List.of(), List.of(), required, List.of(), null, null, null); + + Map> emptyCategoricalCounts = new LinkedHashMap<>(); + emptyCategoricalCounts.put("\\demographics\\AGE\\", new LinkedHashMap<>()); + when(hpdsClient.getAuthCrossCounts(any(), eq(ResultType.CATEGORICAL_CROSS_COUNT), eq(AUTHORIZED_UUID), any())) + .thenReturn(emptyCategoricalCounts); + + Map> continuousCounts = new LinkedHashMap<>(); + continuousCounts.put("\\demographics\\AGE\\", new LinkedHashMap<>(Map.of("18.0", 2, "19.0", 3))); + when(hpdsClient.getAuthCrossCounts(any(), eq(ResultType.CONTINUOUS_CROSS_COUNT), eq(AUTHORIZED_UUID), any())) + .thenReturn(continuousCounts); + + VisualizationResponse response = + service.generateDistributions(query, new HpdsAccessContext(AUTHORIZED_UUID, AccessType.AUTHORIZED), "Bearer token"); + + assertEquals(1, response.continuousData().size()); + assertTrue(response.categoricalData().isEmpty()); + } + + @Test + void generateDistributions_authorized_categoricalWithManyCategories_aggregatesToOther() { + PhenotypicFilter catFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\demographics\\race\\", Set.of("A", "B"), null, null, null); + Query query = new Query(List.of(), List.of(), catFilter, List.of(), null, null, null); + + Map manyCategories = new LinkedHashMap<>(); + for (int i = 1; i <= 9; i++) { + manyCategories.put("Cat" + i, 100 - i * 5); + } + Map> crossCounts = new LinkedHashMap<>(); + crossCounts.put("\\demographics\\race\\", manyCategories); + when(hpdsClient.getAuthCrossCounts(any(), eq(ResultType.CATEGORICAL_CROSS_COUNT), eq(AUTHORIZED_UUID), any())) + .thenReturn(crossCounts); + + VisualizationResponse response = + service.generateDistributions(query, new HpdsAccessContext(AUTHORIZED_UUID, AccessType.AUTHORIZED), "Bearer token"); + + assertFalse(response.categoricalData().isEmpty()); + assertTrue( + response.categoricalData().get(0).categoricalMap().containsKey("Other"), + "VisualizationService should run CategoricalAggregationService on AUTH categorical data" + ); + } + + @Test + void generateDistributions_authorized_nullCountInResponse_skipsNullEntries() { + PhenotypicFilter catFilter = + new PhenotypicFilter(PhenotypicFilterType.FILTER, "\\demographics\\race\\", Set.of("White"), null, null, null); + Query query = new Query(List.of(), List.of(), catFilter, List.of(), null, null, null); + + Map values = new LinkedHashMap<>(); + values.put("White", 45000); + values.put("Black", null); + Map> crossCounts = new LinkedHashMap<>(); + crossCounts.put("\\demographics\\race\\", values); + when(hpdsClient.getAuthCrossCounts(any(), eq(ResultType.CATEGORICAL_CROSS_COUNT), eq(AUTHORIZED_UUID), any())) + .thenReturn(crossCounts); + + VisualizationResponse response = + service.generateDistributions(query, new HpdsAccessContext(AUTHORIZED_UUID, AccessType.AUTHORIZED), "Bearer token"); + + assertFalse(response.categoricalData().isEmpty()); + Map race = response.categoricalData().get(0).categoricalMap(); + assertEquals(new ObfuscatedCount(45000, "45000"), race.get("White")); + assertFalse(race.containsKey("Black"), "Null counts must be skipped, not crash"); + } +} diff --git a/services/pic-sure-visualization-service/src/test/resources/application-test.properties b/services/pic-sure-visualization-service/src/test/resources/application-test.properties new file mode 100644 index 000000000..fe8864e3e --- /dev/null +++ b/services/pic-sure-visualization-service/src/test/resources/application-test.properties @@ -0,0 +1,6 @@ +hpds.base-url=http://localhost:9999/mock-hpds +hpds.resource.authorized.uuid=550e8400-e29b-41d4-a716-446655440000 +hpds.resource.open.uuid=550e8400-e29b-41d4-a716-446655440001 +chart.categorical.max-categories=7 +rest-template.connect-timeout=5000 +rest-template.read-timeout=30000 diff --git a/services/picsure-dictionary/.dockerignore b/services/picsure-dictionary/.dockerignore new file mode 100644 index 000000000..175f028ab --- /dev/null +++ b/services/picsure-dictionary/.dockerignore @@ -0,0 +1,4 @@ +.gitignore +.git +.idea +.env diff --git a/services/picsure-dictionary/.github/workflows/linting.yml b/services/picsure-dictionary/.github/workflows/linting.yml new file mode 100644 index 000000000..00393f22a --- /dev/null +++ b/services/picsure-dictionary/.github/workflows/linting.yml @@ -0,0 +1,31 @@ +# This workflow will build a Java project with Maven, and cache/restore any dependencies to improve the workflow execution time +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-maven + +# This workflow uses actions that are not certified by GitHub. +# They are provided by a third-party and are governed by +# separate terms of service, privacy policy, and support +# documentation. + +name: Lint Project + +on: + push: + branches: [ "main", "release" ] + pull_request: + branches: [ "main", "release" ] + +jobs: + build: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + - name: Set up JDK + uses: actions/setup-java@v4 + with: + java-version: '21' + distribution: 'temurin' + cache: maven + - name: Lint Project + run: mvn spotless:check && cd aggregate && mvn spotless:check diff --git a/services/picsure-dictionary/.github/workflows/maven.yml b/services/picsure-dictionary/.github/workflows/maven.yml new file mode 100644 index 000000000..e1eb69527 --- /dev/null +++ b/services/picsure-dictionary/.github/workflows/maven.yml @@ -0,0 +1,47 @@ +# This workflow will build a Java project with Maven, and cache/restore any dependencies to improve the workflow execution time +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-maven + +# This workflow uses actions that are not certified by GitHub. +# They are provided by a third-party and are governed by +# separate terms of service, privacy policy, and support +# documentation. + +name: Build and Run Tests + +on: + push: + branches: [ "main", "release" ] + pull_request: + branches: [ "main", "release" ] + +jobs: + build: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + - name: Set up JDK + uses: actions/setup-java@v4 + with: + java-version: '25' + distribution: 'temurin' + cache: maven + - name: Build with Maven + run: mvn -B package --file pom.xml + env: + GITHUB_TOKEN: ${{ github.token }} + build-aggregate: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Set up JDK + uses: actions/setup-java@v4 + with: + java-version: '25' + distribution: 'temurin' + cache: maven + - name: Build with Maven + run: cd aggregate && mvn -B package --file pom.xml + env: + GITHUB_TOKEN: ${{ github.token }} diff --git a/services/picsure-dictionary/.gitignore b/services/picsure-dictionary/.gitignore new file mode 100644 index 000000000..c6ee66478 --- /dev/null +++ b/services/picsure-dictionary/.gitignore @@ -0,0 +1,60 @@ +# Compiled class file +*.class + +# Log file +*.log + +# BlueJ files +*.ctxt + +# Mobile Tools for Java (J2ME) +.mtj.tmp/ + +# Package Files # +*.jar +*.war +*.nar +*.ear +*.zip +*.tar.gz +*.rar + +# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml +hs_err_pid* +replay_pid* + +target/ +!.mvn/wrapper/maven-wrapper.jar +!**/src/main/**/target/ +!**/src/test/**/target/ + +### STS ### +.apt_generated +.classpath +.factorypath +.project +.settings +.springBeans +.sts4-cache + +### IntelliJ IDEA ### +.idea +*.iws +*.iml +*.ipr + +### NetBeans ### +/nbproject/private/ +/nbbuild/ +/dist/ +/nbdist/ +/.nb-gradle/ +build/ +!**/src/main/**/build/ +!**/src/test/**/build/ + +### VS Code ### +.vscode/ + +.env +db/flyway/flyway.conf \ No newline at end of file diff --git a/services/picsure-dictionary/.sdkmanrc b/services/picsure-dictionary/.sdkmanrc new file mode 100644 index 000000000..d2344323e --- /dev/null +++ b/services/picsure-dictionary/.sdkmanrc @@ -0,0 +1 @@ +java=25.0.3-tem diff --git a/services/picsure-dictionary/Dockerfile b/services/picsure-dictionary/Dockerfile new file mode 100644 index 000000000..5eb3a6a3c --- /dev/null +++ b/services/picsure-dictionary/Dockerfile @@ -0,0 +1,18 @@ +FROM amazoncorretto:25-alpine + +COPY target/dictionary-*.jar /dictionary.jar + +# Time zone +ENV TZ="UTC" + +ARG DATASOURCE_URL +ARG DATASOURCE_USERNAME +ARG SPRING_PROFILE + +# If a --env-file is passed in, you can override these values +ENV DATASOURCE_URL=${DATASOURCE_URL} +ENV DATASOURCE_USERNAME=${DATASOURCE_USERNAME} +ENV SPRING_PROFILE=${SPRING_PROFILE} + +# Default to no profile +ENTRYPOINT java $DEBUG_VARS $PROXY_VARS -Xmx8192m ${JAVA_OPTS} -jar /dictionary.jar --spring.profiles.active=${SPRING_PROFILE:-} \ No newline at end of file diff --git a/services/picsure-dictionary/JSONS.md b/services/picsure-dictionary/JSONS.md new file mode 100644 index 000000000..d71dff182 --- /dev/null +++ b/services/picsure-dictionary/JSONS.md @@ -0,0 +1,705 @@ +# JSON for Dictionary API + +## Concepts + +**List, no filter, page 0, page size 10** + +Request: +```bash +curl --location 'https://nhanes-dev.hms.harvard.edu/picsure/proxy/dictionary-api/concepts/?page_number=0&page_size=5' \ +--header 'Content-Type: application/json' \ +--header 'Authorization: Token ADD_TOKEN_HERE' \ +--data '{"facets": [], "search": ""}' +``` + +Response: +```json +{ + "totalPages": 9, + "totalElements": 90, + "pageable": { + "pageNumber": 0, + "pageSize": 10, + "sort": { + "unsorted": true, + "sorted": false, + "empty": true + }, + "offset": 0, + "unpaged": false, + "paged": true + }, + "numberOfElements": 10, + "first": true, + "last": false, + "size": 10, + "content": [ + { + "conceptPath": "\\ACT Diagnosis ICD-10\\", + "name": "", + "display": "", + "dataset": "1", + "values": [], + "children": null, + "meta": null + }, + { + "conceptPath": "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\", + "name": "", + "display": "", + "dataset": "1", + "values": [], + "children": null, + "meta": null + }, + { + "conceptPath": "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\", + "name": "", + "display": "", + "dataset": "1", + "values": [], + "children": null, + "meta": null + }, + { + "conceptPath": "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\", + "name": "", + "display": "", + "dataset": "1", + "values": [], + "children": null, + "meta": null + }, + { + "conceptPath": "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.5 Severe persistent asthma\\", + "name": "", + "display": "", + "dataset": "1", + "values": [], + "children": null, + "meta": null + }, + { + "conceptPath": "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.5 Severe persistent asthma\\J45.51 Severe persistent asthma with (acute) exacerbation\\", + "name": "J45.51 Severe persistent asthma with (acute) exacerbation", + "display": "J45.51 Severe persistent asthma with (acute) exacerbation", + "dataset": "1", + "values": [], + "children": null, + "meta": null + }, + { + "conceptPath": "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.5 Severe persistent asthma\\J45.52 Severe persistent asthma with status asthmaticus\\", + "name": "J45.52 Severe persistent asthma with status asthmaticus", + "display": "J45.52 Severe persistent asthma with status asthmaticus", + "dataset": "1", + "values": [], + "children": null, + "meta": null + }, + { + "conceptPath": "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.9 Other and unspecified asthma\\", + "name": "", + "display": "", + "dataset": "1", + "values": [], + "children": null, + "meta": null + }, + { + "conceptPath": "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.9 Other and unspecified asthma\\J45.90 Unspecified asthma\\", + "name": "", + "display": "", + "dataset": "1", + "values": [], + "children": null, + "meta": null + }, + { + "conceptPath": "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.9 Other and unspecified asthma\\J45.90 Unspecified asthma\\J45.901 Unspecified asthma with (acute) exacerbation\\", + "name": "J45.901 Unspecified asthma with (acute) exacerbation", + "display": "J45.901 Unspecified asthma with (acute) exacerbation", + "dataset": "1", + "values": [], + "children": null, + "meta": null + } + ], + "number": 0, + "sort": { + "unsorted": true, + "sorted": false, + "empty": true + }, + "empty": false +} +``` + +**List, no filter, page 10, page size 5** + +Request: +```bash +curl --location 'https://nhanes-dev.hms.harvard.edu/picsure/proxy/dictionary-api/concepts/?page_number=5&page_size=10' \ +--header 'Content-Type: application/json' \ +--header 'Authorization: Token ADD_TOKEN_HERE' \ +--data '{"facets": [], "search": ""}' +``` + +Response: +```json +{ + "totalPages": 18, + "totalElements": 90, + "pageable": { + "pageNumber": 10, + "pageSize": 5, + "sort": { + "unsorted": true, + "sorted": false, + "empty": true + }, + "offset": 50, + "unpaged": false, + "paged": true + }, + "numberOfElements": 5, + "first": false, + "last": false, + "size": 5, + "content": [ + { + "conceptPath": "\\phs000007\\pht000022\\", + "name": "pht000022", + "display": "ex0_20s", + "dataset": "phs000007", + "values": [], + "children": null, + "meta": null + }, + { + "conceptPath": "\\phs000007\\pht000022\\phv00004260\\", + "name": "", + "display": "", + "dataset": "phs000007", + "values": [], + "children": null, + "meta": null + }, + { + "conceptPath": "\\phs000007\\pht000022\\phv00004260\\FM219\\", + "name": "phv00004260", + "display": "FM219", + "dataset": "phs000007", + "min": 0, + "max": 0, + "meta": null + }, + { + "conceptPath": "\\phs000007\\pht000033\\", + "name": "pht000033", + "display": "ex1_4s", + "dataset": "phs000007", + "values": [], + "children": null, + "meta": null + }, + { + "conceptPath": "\\phs000007\\pht000033\\phv00008849\\", + "name": "", + "display": "", + "dataset": "phs000007", + "values": [], + "children": null, + "meta": null + } + ], + "number": 10, + "sort": { + "unsorted": true, + "sorted": false, + "empty": true + }, + "empty": false +} +``` + +**List, filter by study ID facet = phs002715** + +Request: +```bash +curl --location 'https://nhanes-dev.hms.harvard.edu/picsure/proxy/dictionary-api/concepts' \ +--header 'Content-Type: application/json' \ +--header 'Authorization: Token ADD_TOKEN_HERE' \ +--data '{"facets": [{ + "name": "phs002715", + "count": 44, + "category": "study_ids_dataset_ids" + }], "search": ""}' +``` + +Response: +```json +{ + "totalPages": 1, + "totalElements": 3, + "pageable": { + "pageNumber": 0, + "pageSize": 10, + "sort": { + "unsorted": true, + "sorted": false, + "empty": true + }, + "offset": 0, + "paged": true, + "unpaged": false + }, + "numberOfElements": 3, + "first": true, + "last": true, + "size": 10, + "content": [ + { + "conceptPath": "\\phs002715\\", + "name": "", + "display": "", + "dataset": "phs002715", + "values": [], + "children": null, + "meta": null + }, + { + "conceptPath": "\\phs002715\\age\\", + "name": "AGE_CATEGORY", + "display": "age", + "dataset": "phs002715", + "values": [], + "children": null, + "meta": null + }, + { + "conceptPath": "\\phs002715\\nsrr_ever_smoker\\", + "name": "nsrr_ever_smoker", + "display": "nsrr_ever_smoker", + "dataset": "phs002715", + "values": [], + "children": null, + "meta": null + } + ], + "number": 0, + "sort": { + "unsorted": true, + "sorted": false, + "empty": true + }, + "empty": false +} +``` + +**Detail, GIC concept** + +Request: +```bash +curl --location 'https://nhanes-dev.hms.harvard.edu/picsure/proxy/dictionary-api/concepts/detail/1' \ +--header 'Content-Type: application/json' \ +--header 'Authorization: Token ADD_TOKEN_HERE' \ +--data '\ACT Diagnosis ICD-10\J00-J99 Diseases of the respiratory system (J00-J99)\J40-J47 Chronic lower respiratory diseases (J40-J47)\J45 Asthma\J45.5 Severe persistent asthma\J45.52 Severe persistent asthma with status asthmaticus\' +``` + +Response: +```json +{ + "type": "Categorical", + "conceptPath": "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.5 Severe persistent asthma\\J45.52 Severe persistent asthma with status asthmaticus\\", + "name": "J45.52 Severe persistent asthma with status asthmaticus", + "display": "J45.52 Severe persistent asthma with status asthmaticus", + "dataset": "1", + "values": [], + "children": null, + "meta": { + "values": "J45.52 Severe persistent asthma with status asthmaticus", + "description": "Approximate Synonyms:\nSevere persistent allergic asthma in status asthmaticus\nSevere persistent allergic asthma with status asthmaticus\nSevere persistent asthma in status asthmaticus\nSevere persistent asthma with allergic rhinitis in status asthmaticus\nSevere persistent asthma with allergic rhinitis with status asthmaticus" + } +} +``` + +**Detail, BDC concept** + +Request: +```bash +curl --location 'https://nhanes-dev.hms.harvard.edu/picsure/proxy/dictionary-api/concepts/detail/phs000007' \ +--header 'Content-Type: application/json' \ +--header 'Authorization: Token ADD_TOKEN_HERE' \ +--data '\phs000007\pht000033\phv00008849\D080\' +``` + +Response: +```json +{ + "type": "Continuous", + "conceptPath": "\\phs000007\\pht000033\\phv00008849\\D080\\", + "name": "phv00008849", + "display": "D080", + "dataset": "phs000007", + "min": 0, + "max": 0, + "meta": { + "unique_identifier": "no", + "stigmatizing": "no", + "bdc_open_access": "yes", + "values": "5", + "description": "# 12 OZ CUPS OF CAFFEINATED COLA/DAY", + "free_text": "no" + } +} +``` + +## Facets + +**List, no filter** + +Request: +```bash +curl --location 'https://nhanes-dev.hms.harvard.edu/picsure/proxy/dictionary-api/facets/?page_number=0&page_size=10' \ +--header 'Content-Type: application/json' \ +--header 'Authorization: Token ADD_TOKEN_HERE' \ +--data '{"facets": [], "search": ""}' +``` + +Response: +```json +[ + { + "name": "study_ids_dataset_ids", + "display": "Study IDs/Dataset IDs", + "description": "", + "facets": [ + { + "name": "1", + "display": "GIC", + "description": null, + "count": 44, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "2", + "display": "National Health and Nutrition Examination Survey", + "description": null, + "count": 7, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "3", + "display": "1000 Genomes Project", + "description": null, + "count": 0, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "phs002715", + "display": "NSRR CFS", + "description": null, + "count": 3, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "phs000284", + "display": "CFS", + "description": null, + "count": 7, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "phs000007", + "display": "FHS", + "description": null, + "count": 10, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "phs002385", + "display": "HCT_for_SCD", + "description": null, + "count": 4, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "phs003463", + "display": "RECOVER_Adult", + "description": null, + "count": 3, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "phs003543", + "display": "NSRR_HSHC", + "description": null, + "count": 0, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "phs002808", + "display": "nuMoM2b", + "description": null, + "count": 9, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "phs003566", + "display": "SPRINT", + "description": null, + "count": 3, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "phs001963", + "display": "DEMENTIA-SEQ", + "description": null, + "count": 0, + "children": null, + "category": "study_ids_dataset_ids" + } + ] + }, + { + "name": "nsrr_harmonized", + "display": "Common Data Element Collection", + "description": "", + "facets": [ + { + "name": "LOINC", + "display": "LOINC", + "description": null, + "count": 1, + "children": null, + "category": "nsrr_harmonized" + }, + { + "name": "PhenX", + "display": "PhenX", + "description": null, + "count": 1, + "children": null, + "category": "nsrr_harmonized" + }, + { + "name": "gad_7", + "display": "Generalized Anxiety Disorder Assessment (GAD-7)", + "description": null, + "count": 0, + "children": null, + "category": "nsrr_harmonized" + }, + { + "name": "taps_tool", + "display": "NIDA CTN Common Data Elements = TAPS Tool", + "description": null, + "count": 1, + "children": null, + "category": "nsrr_harmonized" + } + ] + } +] +``` + +**List, filter by study ID facet = phs002715** + +Request: +```bash +curl --location 'https://nhanes-dev.hms.harvard.edu/picsure/proxy/dictionary-api/facets/' \ +--header 'Content-Type: application/json' \ +--header 'Authorization: Token ADD_TOKEN_HERE' \ +--data '{"facets": [{ + "name": "phs002715", + "count": 44, + "category": "study_ids_dataset_ids" + }], "search": ""}' +``` + +Response: +```json +[ + { + "name": "study_ids_dataset_ids", + "display": "Study IDs/Dataset IDs", + "description": "", + "facets": [ + { + "name": "1", + "display": "GIC", + "description": null, + "count": 0, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "2", + "display": "National Health and Nutrition Examination Survey", + "description": null, + "count": 0, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "3", + "display": "1000 Genomes Project", + "description": null, + "count": 0, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "phs002715", + "display": "NSRR CFS", + "description": null, + "count": 3, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "phs000284", + "display": "CFS", + "description": null, + "count": 0, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "phs000007", + "display": "FHS", + "description": null, + "count": 0, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "phs002385", + "display": "HCT_for_SCD", + "description": null, + "count": 0, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "phs003463", + "display": "RECOVER_Adult", + "description": null, + "count": 0, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "phs003543", + "display": "NSRR_HSHC", + "description": null, + "count": 0, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "phs002808", + "display": "nuMoM2b", + "description": null, + "count": 0, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "phs003566", + "display": "SPRINT", + "description": null, + "count": 0, + "children": null, + "category": "study_ids_dataset_ids" + }, + { + "name": "phs001963", + "display": "DEMENTIA-SEQ", + "description": null, + "count": 0, + "children": null, + "category": "study_ids_dataset_ids" + } + ] + }, + { + "name": "nsrr_harmonized", + "display": "Common Data Element Collection", + "description": "", + "facets": [ + { + "name": "LOINC", + "display": "LOINC", + "description": null, + "count": 0, + "children": null, + "category": "nsrr_harmonized" + }, + { + "name": "PhenX", + "display": "PhenX", + "description": null, + "count": 0, + "children": null, + "category": "nsrr_harmonized" + }, + { + "name": "gad_7", + "display": "Generalized Anxiety Disorder Assessment (GAD-7)", + "description": null, + "count": 0, + "children": null, + "category": "nsrr_harmonized" + }, + { + "name": "taps_tool", + "display": "NIDA CTN Common Data Elements = TAPS Tool", + "description": null, + "count": 0, + "children": null, + "category": "nsrr_harmonized" + } + ] + } +] +``` + +**Detail** + +Request: +```bash +curl --location --request GET 'https://nhanes-dev.hms.harvard.edu/picsure/proxy/dictionary-api/facets/study_ids_dataset_ids/1' \ +--header 'Content-Type: application/json' \ +--header 'Authorization: Token ADD_TOKEN_HERE' \ +--data '{"facets": [{ + "name": "phs002715", + "count": 44, + "category": "study_ids_dataset_ids" + }], "search": ""}' +``` + +Response: +```json +{ + "name": "1", + "display": "GIC", + "description": null, + "count": null, + "children": null, + "category": "study_ids_dataset_ids" +} + +``` \ No newline at end of file diff --git a/services/picsure-dictionary/LICENSE b/services/picsure-dictionary/LICENSE new file mode 100644 index 000000000..261eeb9e9 --- /dev/null +++ b/services/picsure-dictionary/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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Building that +dataset involves building a query that sets a series of constraints on variables present in that PIC-SURE. Large +PIC-SURE servers can have tens of thousands of variables, making the query building process complex. +Users need a mechanism to find the variables they want to query on. Currently, different implementations of PIC-SURE +have developed competing solutions to this problem. None of these solutions fully meet PIC-SURE's variable refinement +needs, and all the current solutions are fraught with architectural shortcomings, necessitating the need for a full +replacement. +The Dictionary Project's goal is to create a unified process for enabling the filtration of variables and the creation +of a query. It needs to work across our current projects, and, in anticipation of our push to productize PIC-SURE, it +needs to be workable for new PIC-SURE installations. + +## Contribution + +### Requirements + +- Java 21 +- Maven + +### Setup + +1. Copy the linting commit hook: +`cp code-formatting/pre-commit.sh .git/hooks/pre-commit` +2. Do a clean build of the project: +`mvn clean install` + +## Usage + +### Create Env File + +```shell +cp env.example .env +vi .env +``` + +### Start DB + +```shell +docker compose up -d --build dictionary-db +``` + +Once up, do some sanity checks in the database: + +```shell +docker exec -ti dictionary-db psql -U picsure dictionary +``` + +### Start API + +```shell +docker compose up -d --build +``` + +### Run DB Migrations + +Set up your flyway conf: +```shell +source .env +rm -f db/flyway/flyway.conf +echo "flyway.url=jdbc:postgresql://$POSTGRES_HOST:5432/$POSTGRES_DB" >> db/flyway/flyway.conf +echo "flyway.user=$POSTGRES_USER" >> db/flyway/flyway.conf +echo "flyway.password=$POSTGRES_PASSWORD" >> db/flyway/flyway.conf +``` +```shell +docker run --rm -ti --name dictionary-flyway \ + --env-file $DOCKER_CONFIG_DIR/dictionary/dictionary.env \ + -v ./db/flyway:/flyway/sql \ + -v ./db/flyway/flyway.conf:/flyway/conf/flyway.conf \ + --network dictionary \ + flyway/flyway:11-alpine -connectRetries=60 -validateMigrationNaming=true migrate +``` diff --git a/services/picsure-dictionary/aggregate/.sdkmanrc b/services/picsure-dictionary/aggregate/.sdkmanrc new file mode 100644 index 000000000..d2344323e --- /dev/null +++ b/services/picsure-dictionary/aggregate/.sdkmanrc @@ -0,0 +1 @@ +java=25.0.3-tem diff --git a/services/picsure-dictionary/aggregate/Dockerfile b/services/picsure-dictionary/aggregate/Dockerfile new file mode 100644 index 000000000..560819912 --- /dev/null +++ b/services/picsure-dictionary/aggregate/Dockerfile @@ -0,0 +1,18 @@ +FROM amazoncorretto:25-alpine + +COPY target/dump-*.jar /dump.jar + +# Time zone +ENV TZ="UTC" + +ARG DATASOURCE_URL +ARG DATASOURCE_USERNAME +ARG SPRING_PROFILE + +# If a --env-file is passed in, you can override these values +ENV DATASOURCE_URL=${DATASOURCE_URL} +ENV DATASOURCE_USERNAME=${DATASOURCE_USERNAME} +ENV SPRING_PROFILE=${SPRING_PROFILE} + +# Default to no profile +ENTRYPOINT java $DEBUG_VARS $PROXY_VARS -Xmx4192m ${JAVA_OPTS} -jar /dump.jar --spring.profiles.active=${SPRING_PROFILE:-production} \ No newline at end of file diff --git a/services/picsure-dictionary/aggregate/pom.xml b/services/picsure-dictionary/aggregate/pom.xml new file mode 100644 index 000000000..3a1f98465 --- /dev/null +++ b/services/picsure-dictionary/aggregate/pom.xml @@ -0,0 +1,92 @@ + + + 4.0.0 + + edu.harvard.hms.dbmi.avillach + pic-sure-api + ${revision} + ../../../pom.xml + + edu.harvard.dbmi.avillach + dump + dump + Data Dictionary Dump API + + + com.fasterxml.jackson.datatype + jackson-datatype-jsr310 + + + com.fasterxml.jackson.core + jackson-core + + + com.fasterxml.jackson.core + jackson-databind + + + org.springframework.boot + spring-boot-starter-jdbc + + + org.springframework.boot + spring-boot-starter-web + + + org.springframework.data + spring-data-commons + + + + org.postgresql + postgresql + runtime + + + org.springframework.boot + spring-boot-starter-test + test + + + org.springframework.boot + spring-boot-testcontainers + test + + + org.testcontainers + junit-jupiter + test + + + org.testcontainers + postgresql + test + + + org.apache.httpcomponents.client5 + httpclient5 + + + edu.harvard.dbmi.avillach + pic-sure-logging-client + + + + + + + org.springframework.boot + spring-boot-maven-plugin + + + org.apache.maven.plugins + maven-surefire-plugin + + -Dnet.bytebuddy.experimental=true + + + + + + diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/AuditAttributes.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/AuditAttributes.java new file mode 100644 index 000000000..395886de6 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/AuditAttributes.java @@ -0,0 +1,29 @@ +package edu.harvard.dbmi.avillach.dump; + +import jakarta.servlet.http.HttpServletRequest; +import java.util.HashMap; +import java.util.Map; + +public final class AuditAttributes { + public static final String EVENT_TYPE = "audit.event_type"; + public static final String ACTION = "audit.action"; + private static final String METADATA = "audit.metadata"; + + private AuditAttributes() {} + + public static void putMetadata(HttpServletRequest request, String key, Object value) { + if (request != null && key != null && value != null) { + getMetadata(request).put(key, value); + } + } + + @SuppressWarnings("unchecked") + public static Map getMetadata(HttpServletRequest request) { + Map metadata = (Map) request.getAttribute(METADATA); + if (metadata == null) { + metadata = new HashMap<>(); + request.setAttribute(METADATA, metadata); + } + return metadata; + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/AuditInterceptor.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/AuditInterceptor.java new file mode 100644 index 000000000..a9a8eac28 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/AuditInterceptor.java @@ -0,0 +1,21 @@ +package edu.harvard.dbmi.avillach.dump; + +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import org.springframework.web.method.HandlerMethod; +import org.springframework.web.servlet.HandlerInterceptor; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +public class AuditInterceptor implements HandlerInterceptor { + @Override + public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) { + if (handler instanceof HandlerMethod handlerMethod) { + AuditEvent auditEvent = handlerMethod.getMethodAnnotation(AuditEvent.class); + if (auditEvent != null) { + request.setAttribute(AuditAttributes.EVENT_TYPE, auditEvent.type()); + request.setAttribute(AuditAttributes.ACTION, auditEvent.action()); + } + } + return true; + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/AuditLoggingFilter.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/AuditLoggingFilter.java new file mode 100644 index 000000000..0eb59ad4b --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/AuditLoggingFilter.java @@ -0,0 +1,115 @@ +package edu.harvard.dbmi.avillach.dump; + +import java.io.IOException; +import java.util.HashMap; +import java.util.Map; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.web.filter.OncePerRequestFilter; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.dbmi.avillach.logging.RequestInfo; +import edu.harvard.dbmi.avillach.logging.SessionIdResolver; +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +public class AuditLoggingFilter extends OncePerRequestFilter { + + private static final Logger log = LoggerFactory.getLogger(AuditLoggingFilter.class); + + private final String destIpConfig; + private final Integer destPortConfig; + private final LoggingClient loggingClient; + + public AuditLoggingFilter(LoggingClient loggingClient, String destIp, Integer destPort) { + this.loggingClient = loggingClient; + this.destIpConfig = destIp; + this.destPortConfig = destPort; + } + + @Override + protected boolean shouldNotFilter(HttpServletRequest request) { + return request.getRequestURI().startsWith("/actuator"); + } + + @Override + protected void doFilterInternal(HttpServletRequest request, HttpServletResponse response, FilterChain filterChain) + throws ServletException, IOException { + + long startTime = System.currentTimeMillis(); + try { + filterChain.doFilter(request, response); + } finally { + try { + if (loggingClient == null || !loggingClient.isEnabled()) return; + + String fullPath = request.getRequestURI(); + String method = request.getMethod(); + long duration = System.currentTimeMillis() - startTime; + + String eventType = (String) request.getAttribute(AuditAttributes.EVENT_TYPE); + String action = (String) request.getAttribute(AuditAttributes.ACTION); + if (eventType == null) eventType = "OTHER"; + if (action == null) action = method.toLowerCase(); + + String srcIp = extractSourceIp(request); + String destIp = destIpConfig != null ? destIpConfig : request.getLocalAddr(); + int destPort = destPortConfig != null ? destPortConfig : request.getLocalPort(); + + int responseStatus = response.getStatus(); + String contentType = response.getContentType(); + Long bytes = parseContentLength(response.getHeader("Content-Length")); + + RequestInfo requestInfo = RequestInfo.builder().method(method).url(fullPath).srcIp(srcIp).destIp(destIp).destPort(destPort) + .httpUserAgent(request.getHeader("User-Agent")).status(responseStatus).duration(duration).httpContentType(contentType) + .bytes(bytes).build(); + + Map metadata = new HashMap<>(); + String sessionId = SessionIdResolver.resolve(request.getHeader("X-Session-Id"), srcIp, request.getHeader("User-Agent")); + + AuditAttributes.getMetadata(request).forEach(metadata::putIfAbsent); + + Map errorMap = null; + if (responseStatus >= 400) { + errorMap = new HashMap<>(); + errorMap.put("status", responseStatus); + errorMap.put("error_type", responseStatus >= 500 ? "server_error" : "client_error"); + } + + LoggingEvent.Builder eventBuilder = + LoggingEvent.builder(eventType).action(action).sessionId(sessionId).request(requestInfo).metadata(metadata); + if (errorMap != null) eventBuilder.error(errorMap); + LoggingEvent event = eventBuilder.build(); + + String authHeader = request.getHeader("Authorization"); + String requestId = request.getHeader("X-Request-Id"); + if (authHeader != null || requestId != null) { + loggingClient.send(event, authHeader, requestId); + } else { + loggingClient.send(event); + } + } catch (Exception e) { + log.warn("AuditLoggingFilter failed to log request", e); + } + } + } + + static String extractSourceIp(HttpServletRequest request) { + String xff = request.getHeader("X-Forwarded-For"); + if (xff != null && !xff.isEmpty()) return xff.split(",")[0].trim(); + return request.getRemoteAddr(); + } + + static Long parseContentLength(String header) { + if (header == null) return null; + try { + return Long.parseLong(header); + } catch (NumberFormatException e) { + return null; + } + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/DumpApplication.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/DumpApplication.java new file mode 100644 index 000000000..68b5a6ad9 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/DumpApplication.java @@ -0,0 +1,13 @@ +package edu.harvard.dbmi.avillach.dump; + +import org.springframework.boot.SpringApplication; +import org.springframework.boot.autoconfigure.SpringBootApplication; + +@SpringBootApplication +public class DumpApplication { + + public static void main(String[] args) { + SpringApplication.run(DumpApplication.class, args); + } + +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/LoggingConfig.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/LoggingConfig.java new file mode 100644 index 000000000..0a08bb6c0 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/LoggingConfig.java @@ -0,0 +1,48 @@ +package edu.harvard.dbmi.avillach.dump; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingClientFactory; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.web.servlet.FilterRegistrationBean; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.web.servlet.config.annotation.InterceptorRegistry; +import org.springframework.web.servlet.config.annotation.WebMvcConfigurer; + +@Configuration +public class LoggingConfig implements WebMvcConfigurer { + + @Value("${DEST_IP:#{null}}") + private String destIp; + + @Value("${DEST_PORT:#{null}}") + private Integer destPort; + + @Bean + public LoggingClient loggingClient() { + return LoggingClientFactory.create("dump"); + } + + @Bean + public AuditLoggingFilter auditLoggingFilter(LoggingClient loggingClient) { + return new AuditLoggingFilter(loggingClient, destIp, destPort); + } + + @Bean + public FilterRegistrationBean auditLoggingFilterRegistration(AuditLoggingFilter auditLoggingFilter) { + FilterRegistrationBean registration = new FilterRegistrationBean<>(auditLoggingFilter); + registration.addUrlPatterns("/*"); + registration.setOrder(1); + return registration; + } + + @Bean + public AuditInterceptor auditInterceptor() { + return new AuditInterceptor(); + } + + @Override + public void addInterceptors(InterceptorRegistry registry) { + registry.addInterceptor(auditInterceptor()); + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/ConceptNodeDump.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/ConceptNodeDump.java new file mode 100644 index 000000000..6bc5c9886 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/ConceptNodeDump.java @@ -0,0 +1,129 @@ +package edu.harvard.dbmi.avillach.dump.entities; + +import com.fasterxml.jackson.annotation.JsonIgnore; +import com.fasterxml.jackson.annotation.JsonProperty; + +import java.util.ArrayList; +import java.util.List; +import java.util.Objects; + +public final class ConceptNodeDump implements DumpRow { + + private String datasetRef; + private String name; + private String display; + private String conceptType; + private String conceptPath; + private List children = new ArrayList<>(); + private Integer conceptNodeId; + private Integer parentId; + private String parentPath; + + public ConceptNodeDump() {} + + public void setParentId(Integer parentId) { + this.parentId = parentId; + } + + public void setConceptNodeId(Integer conceptNodeId) { + this.conceptNodeId = conceptNodeId; + } + + public void setDatasetRef(String datasetRef) { + this.datasetRef = datasetRef; + } + + public void setName(String name) { + this.name = name; + } + + public void setDisplay(String display) { + this.display = display; + } + + public void setConceptType(String conceptType) { + this.conceptType = conceptType; + } + + public void setConceptPath(String conceptPath) { + this.conceptPath = conceptPath; + } + + public void setChildren(List children) { + this.children = children; + } + + public ConceptNodeDump( + String datasetRef, String name, String display, String conceptType, String conceptPath, Integer conceptNodeId, Integer parentId + ) { + this.datasetRef = datasetRef; + this.name = name; + this.display = display; + this.conceptType = conceptType; + this.conceptPath = conceptPath; + this.conceptNodeId = conceptNodeId; + this.parentId = parentId; + } + + public String datasetRef() { + return datasetRef; + } + + public String name() { + return name; + } + + public String display() { + return display; + } + + public String conceptType() { + return conceptType; + } + + public String conceptPath() { + return conceptPath; + } + + public List children() { + return children; + } + + public void addChild(ConceptNodeDump child) { + children.add(child); + } + + @Override + public boolean equals(Object obj) { + if (obj == this) return true; + if (obj == null || obj.getClass() != this.getClass()) return false; + var that = (ConceptNodeDump) obj; + return Objects.equals(this.datasetRef, that.datasetRef) && Objects.equals(this.name, that.name) + && Objects.equals(this.display, that.display) && Objects.equals(this.conceptType, that.conceptType) + && Objects.equals(this.conceptPath, that.conceptPath) && Objects.equals(this.children, that.children); + } + + @Override + public int hashCode() { + return Objects.hash(datasetRef, name, display, conceptType, conceptPath, children); + } + + @JsonIgnore + public Integer conceptNodeId() { + return conceptNodeId; + } + + @JsonIgnore + public Integer parentId() { + return parentId; + } + + @JsonIgnore + public String parentPath() { + return parentPath; + } + + public void setParentPath(String parentPath) { + this.parentPath = parentPath; + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/ConceptNodeMetaDump.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/ConceptNodeMetaDump.java new file mode 100644 index 000000000..2414d1c05 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/ConceptNodeMetaDump.java @@ -0,0 +1,4 @@ +package edu.harvard.dbmi.avillach.dump.entities; + +public record ConceptNodeMetaDump(String conceptPath, String key, String value) implements DumpRow { +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/DumpRow.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/DumpRow.java new file mode 100644 index 000000000..99e599746 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/DumpRow.java @@ -0,0 +1,4 @@ +package edu.harvard.dbmi.avillach.dump.entities; + +public sealed interface DumpRow permits ConceptNodeDump, FacetDump, FacetCategoryDump, ConceptNodeMetaDump, FacetCategoryMetaDump, FacetMetaDump, FacetConceptPair { +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/FacetCategoryDump.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/FacetCategoryDump.java new file mode 100644 index 000000000..2659be57c --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/FacetCategoryDump.java @@ -0,0 +1,4 @@ +package edu.harvard.dbmi.avillach.dump.entities; + +public record FacetCategoryDump(String name, String display, String description) implements DumpRow { +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/FacetCategoryMetaDump.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/FacetCategoryMetaDump.java new file mode 100644 index 000000000..d5ed771ce --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/FacetCategoryMetaDump.java @@ -0,0 +1,4 @@ +package edu.harvard.dbmi.avillach.dump.entities; + +public record FacetCategoryMetaDump(String categoryName, String key, String value) implements DumpRow { +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/FacetConceptPair.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/FacetConceptPair.java new file mode 100644 index 000000000..1815548a3 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/FacetConceptPair.java @@ -0,0 +1,4 @@ +package edu.harvard.dbmi.avillach.dump.entities; + +public record FacetConceptPair(String facetName, String facetCategory, String conceptPath) implements DumpRow { +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/FacetDump.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/FacetDump.java new file mode 100644 index 000000000..01fbdaf1e --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/FacetDump.java @@ -0,0 +1,127 @@ +package edu.harvard.dbmi.avillach.dump.entities; + +import com.fasterxml.jackson.annotation.JsonIgnore; + +import java.util.ArrayList; +import java.util.List; +import java.util.Objects; + +public final class FacetDump implements DumpRow { + private String name; + private String display; + private String description; + private String facetCategoryName; + private List children = new ArrayList<>(); + private int facetID; + private Integer parentID; + private String parentName; + + public FacetDump() {} + + public FacetDump( + String name, String display, String description, String facetCategoryName, List children, int facetID, Integer parentID + ) { + this.name = name; + this.display = display; + this.description = description; + this.facetCategoryName = facetCategoryName; + this.children = children; + this.facetID = facetID; + this.parentID = parentID; + } + + public FacetDump(String name, String display, String description, String facetCategoryName, int facetID, Integer parentID) { + this(name, display, description, facetCategoryName, new ArrayList<>(), facetID, parentID); + } + + public void addChild(FacetDump child) { + children.add(child); + } + + public String name() { + return name; + } + + public String display() { + return display; + } + + public String description() { + return description; + } + + public String facetCategoryName() { + return facetCategoryName; + } + + public List children() { + return children; + } + + @Override + public boolean equals(Object obj) { + if (obj == this) return true; + if (obj == null || obj.getClass() != this.getClass()) return false; + var that = (FacetDump) obj; + return Objects.equals(this.name, that.name) && Objects.equals(this.display, that.display) + && Objects.equals(this.description, that.description) && Objects.equals(this.facetCategoryName, that.facetCategoryName) + && Objects.equals(this.children, that.children); + } + + @Override + public int hashCode() { + return Objects.hash(name, display, description, facetCategoryName, children); + } + + @Override + public String toString() { + return "FacetDump[" + "name=" + name + ", " + "display=" + display + ", " + "description=" + description + ", " + + "facetCategoryName=" + facetCategoryName + ", " + "children=" + children + ']'; + } + + @JsonIgnore + public int facetID() { + return facetID; + } + + @JsonIgnore + public Integer parentID() { + return parentID; + } + + public void setName(String name) { + this.name = name; + } + + public void setDisplay(String display) { + this.display = display; + } + + public void setDescription(String description) { + this.description = description; + } + + public void setFacetCategoryName(String facetCategoryName) { + this.facetCategoryName = facetCategoryName; + } + + public void setChildren(List children) { + this.children = children; + } + + public void setFacetID(int facetID) { + this.facetID = facetID; + } + + public void setParentID(Integer parentID) { + this.parentID = parentID; + } + + public String parentName() { + return parentName; + } + + public void setParentName(String parentName) { + this.parentName = parentName; + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/FacetMetaDump.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/FacetMetaDump.java new file mode 100644 index 000000000..b7ef2cdd5 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/entities/FacetMetaDump.java @@ -0,0 +1,4 @@ +package edu.harvard.dbmi.avillach.dump.entities; + +public record FacetMetaDump(String facetName, String categoryName, String key, String value) implements DumpRow { +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/DumpController.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/DumpController.java new file mode 100644 index 000000000..e1a840f9e --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/DumpController.java @@ -0,0 +1,39 @@ +package edu.harvard.dbmi.avillach.dump.local; + +import edu.harvard.dbmi.avillach.dump.entities.DumpRow; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.*; + +import java.time.format.DateTimeFormatter; +import java.util.List; + +@Controller +public class DumpController { + private final DumpService dumpService; + private final DateTimeFormatter isoFormat = DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss.SSS"); + + public DumpController(DumpService dumpService) { + this.dumpService = dumpService; + } + + @AuditEvent(type = "DATA_ACCESS", action = "dump.table") + @GetMapping("/dump/{table}") + public ResponseEntity> dumpTable(@PathVariable DumpTable table) { + List rows = dumpService.dumpTable(table); + return ResponseEntity.ok(rows); + } + + @AuditEvent(type = "OTHER", action = "dump.last_updated") + @GetMapping("/last-updated") + public ResponseEntity getLastUpdated() { + return ResponseEntity.ok(dumpService.getLastUpdate().format(isoFormat)); + } + + @AuditEvent(type = "OTHER", action = "dump.db_version") + @GetMapping("/database-version") + public ResponseEntity getDBVersion() { + return ResponseEntity.ok(dumpService.getDatabaseVersion()); + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/DumpRepository.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/DumpRepository.java new file mode 100644 index 000000000..ccaeedffa --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/DumpRepository.java @@ -0,0 +1,170 @@ +package edu.harvard.dbmi.avillach.dump.local; + +import edu.harvard.dbmi.avillach.dump.entities.ConceptNodeDump; +import edu.harvard.dbmi.avillach.dump.entities.DumpRow; +import edu.harvard.dbmi.avillach.dump.entities.FacetDump; +import edu.harvard.dbmi.avillach.dump.local.extractor.*; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.jdbc.core.namedparam.MapSqlParameterSource; +import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate; +import org.springframework.stereotype.Repository; + +import java.time.LocalDateTime; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.function.Function; +import java.util.stream.Collectors; +import java.util.stream.Gatherer; +import java.util.stream.Gatherers; + +@Repository +public class DumpRepository { + private final NamedParameterJdbcTemplate template; + private final ConceptNodeMetaDumpMapper conceptMetaMapper; + private final ConceptNodeDumpExtractor conceptNodeDumpExtractor; + private final FacetCategoryDumpMapper facetCategoryMapper; + private final FacetCategoryMetaDumpMapper facetCategoryMetaMapper; + private final FacetMetaDumpMapper facetMetaMapper; + private final FacetDumpMapper facetMapper; + private final FacetConceptPairMapper facetConceptPairMapper; + private final MapSqlParameterSource NO_PARAMS = new MapSqlParameterSource(); + + @Autowired + public DumpRepository( + NamedParameterJdbcTemplate template, ConceptNodeMetaDumpMapper conceptMetaMapper, ConceptNodeDumpExtractor conceptNodeDumpExtractor, + FacetCategoryDumpMapper facetCategoryMapper, FacetCategoryMetaDumpMapper facetCategoryMetaMapper, + FacetMetaDumpMapper facetMetaMapper, FacetDumpMapper facetMapper, FacetConceptPairMapper facetConceptPairMapper + ) { + this.template = template; + this.conceptMetaMapper = conceptMetaMapper; + this.conceptNodeDumpExtractor = conceptNodeDumpExtractor; + this.facetCategoryMapper = facetCategoryMapper; + this.facetCategoryMetaMapper = facetCategoryMetaMapper; + this.facetMetaMapper = facetMetaMapper; + this.facetMapper = facetMapper; + this.facetConceptPairMapper = facetConceptPairMapper; + } + + public LocalDateTime getLastUpdated() { + String sql = "SELECT LAST_UPDATED FROM update_info ORDER BY LAST_UPDATED DESC LIMIT 1"; + return template.queryForList(sql, NO_PARAMS, LocalDateTime.class).stream().findFirst().orElse(LocalDateTime.now()); + } + + public List getAllConcepts() { + List roots = new ArrayList<>(); + Map parents = new HashMap<>(); + String sql = """ + SELECT + dataset.REF, concept_node.CONCEPT_NODE_ID, + concept_node.NAME, concept_node.DISPLAY, + concept_node.CONCEPT_TYPE, concept_node.CONCEPT_PATH, + parent.CONCEPT_NODE_ID AS PARENT_ID + FROM + concept_node + LEFT JOIN concept_node parent ON concept_node.parent_id = parent.concept_node_id + JOIN dataset ON concept_node.dataset_id = dataset.dataset_id + ORDER BY length(concept_node.CONCEPT_PATH) ASC + """; + List nodes = template.query(sql, NO_PARAMS, conceptNodeDumpExtractor); + for (ConceptNodeDump node : nodes) { + parents.put(node.conceptNodeId(), node); + if (node.parentId() == 0) { + roots.add(node); + } else { + parents.get(node.parentId()).addChild(node); + } + } + return roots; + } + + public List getAllConceptNodeMetas() { + String sql = """ + SELECT CONCEPT_PATH, KEY, VALUE + FROM concept_node_meta + INNER JOIN concept_node ON concept_node_meta.CONCEPT_NODE_ID = concept_node.CONCEPT_NODE_ID + """; + return template.query(sql, NO_PARAMS, conceptMetaMapper); + } + + public List getAllFacets() { + String sql = """ + SELECT + facet.NAME, facet.DISPLAY, facet.DESCRIPTION, + facet_category.NAME AS FACET_CATEGORY_NAME, FACET_ID, PARENT_ID + FROM facet + JOIN facet_category ON facet.facet_category_id = facet_category.facet_category_id + WHERE PARENT_ID IS NULL + """; + List roots = template.query(sql, NO_PARAMS, facetMapper); + sql = """ + SELECT + facet.NAME, facet.DISPLAY, facet.DESCRIPTION, + facet_category.NAME AS FACET_CATEGORY_NAME, FACET_ID, PARENT_ID + FROM facet + JOIN facet_category ON facet.facet_category_id = facet_category.facet_category_id + WHERE PARENT_ID IN (:parentIDs) + """; + HashMap allFacets = + new HashMap<>(roots.stream().collect(Collectors.toMap(FacetDump::facetID, Function.identity()))); + List currentTier = roots; + while (!currentTier.isEmpty()) { + List parentIds = currentTier.stream().map(FacetDump::facetID).toList(); + List children = template.query(sql, new MapSqlParameterSource("parentIDs", parentIds), facetMapper); + for (FacetDump child : children) { + allFacets.get(child.parentID()).addChild(child); + allFacets.put(child.facetID(), child); + } + currentTier = children; + } + return roots; + } + + public List getAllFacetCategories() { + String sql = """ + SELECT NAME, DISPLAY, DESCRIPTION + FROM facet_category + """; + return template.query(sql, NO_PARAMS, facetCategoryMapper); + } + + public List getAllFacetMetas() { + String sql = """ + SELECT facet.NAME AS FACET, facet_category.NAME AS FACET_CATEGORY, KEY, VALUE + FROM facet_meta + JOIN facet ON facet.facet_id = facet_meta.facet_id + JOIN facet_category ON facet.facet_category_id = facet_category.facet_category_id + """; + return template.query(sql, NO_PARAMS, facetMetaMapper); + } + + public List getAllFacetCategoryMetas() { + String sql = """ + SELECT NAME, KEY, VALUE + FROM facet_category_meta + JOIN facet_category ON facet_category.facet_category_id = facet_category_meta.facet_category_id + """; + return template.query(sql, NO_PARAMS, facetCategoryMetaMapper); + } + + public List getAllFacetConceptPairs() { + String sql = """ + SELECT + facet.name AS FACET, + facet_category.name AS FACET_CATEGORY, + concept_node.CONCEPT_PATH AS CONCEPT_PATH + FROM + facet__concept_node fcn + JOIN facet ON fcn.facet_id = facet.facet_id + JOIN facet_category ON facet.facet_category_id = facet_category.facet_category_id + JOIN concept_node ON fcn.concept_node_id = concept_node.concept_node_id + """; + return template.query(sql, NO_PARAMS, facetConceptPairMapper); + } + + public Integer getDatabaseVersion() { + String sql = "SELECT DATABASE_VERSION FROM update_info"; + return template.queryForObject(sql, NO_PARAMS, Integer.class); + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/DumpService.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/DumpService.java new file mode 100644 index 000000000..e9f1ee5bb --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/DumpService.java @@ -0,0 +1,37 @@ +package edu.harvard.dbmi.avillach.dump.local; + +import edu.harvard.dbmi.avillach.dump.entities.DumpRow; +import org.springframework.data.domain.Pageable; +import org.springframework.stereotype.Service; + +import java.time.LocalDateTime; +import java.util.List; + +@Service +public class DumpService { + private final DumpRepository repository; + + public DumpService(DumpRepository repository) { + this.repository = repository; + } + + public List dumpTable(DumpTable table) { + return switch (table) { + case ConceptNode -> repository.getAllConcepts(); + case FacetCategory -> repository.getAllFacetCategories(); + case Facet -> repository.getAllFacets(); + case FacetConceptNode -> repository.getAllFacetConceptPairs(); + case ConceptNodeMeta -> repository.getAllConceptNodeMetas(); + case FacetCategoryMeta -> repository.getAllFacetCategoryMetas(); + case FacetMeta -> repository.getAllFacetMetas(); + }; + } + + public LocalDateTime getLastUpdate() { + return repository.getLastUpdated(); + } + + public Integer getDatabaseVersion() { + return repository.getDatabaseVersion(); + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/DumpTable.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/DumpTable.java new file mode 100644 index 000000000..c40d3b0b7 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/DumpTable.java @@ -0,0 +1,27 @@ +package edu.harvard.dbmi.avillach.dump.local; + +public enum DumpTable { + // The ordering of the enums in this list matters. + // Each table should come before its dependant tables so that rows + // can be dropped cleanly + // spotless:off + FacetConceptNode("facet__concept_node"), + ConceptNodeMeta("concept_node_meta"), + ConceptNode("concept_node"), + FacetMeta("facet_meta"), + Facet("facet"), + FacetCategoryMeta("facet_category_meta"), + FacetCategory("facet_category"), + ; + // spotless:on + + private final String sqlName; + + DumpTable(String sqlName) { + this.sqlName = sqlName; + } + + public String getSqlName() { + return sqlName; + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/UpdateInfo.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/UpdateInfo.java new file mode 100644 index 000000000..6e3519be4 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/UpdateInfo.java @@ -0,0 +1,12 @@ +package edu.harvard.dbmi.avillach.dump.local; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.databind.annotation.JsonSerialize; +import com.fasterxml.jackson.datatype.jsr310.ser.LocalDateSerializer; + +import java.time.LocalDateTime; + +@JsonAutoDetect(fieldVisibility = JsonAutoDetect.Visibility.ANY) +@JsonSerialize +public record UpdateInfo(@JsonSerialize(using = LocalDateSerializer.class) LocalDateTime lastUpdate) { +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/ConceptNodeDumpExtractor.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/ConceptNodeDumpExtractor.java new file mode 100644 index 000000000..19a54e5f0 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/ConceptNodeDumpExtractor.java @@ -0,0 +1,19 @@ +package edu.harvard.dbmi.avillach.dump.local.extractor; + +import edu.harvard.dbmi.avillach.dump.entities.ConceptNodeDump; +import org.springframework.jdbc.core.RowMapper; +import org.springframework.stereotype.Component; + +import java.sql.ResultSet; +import java.sql.SQLException; + +@Component +public class ConceptNodeDumpExtractor implements RowMapper { + @Override + public ConceptNodeDump mapRow(ResultSet rs, int rowNum) throws SQLException { + return new ConceptNodeDump( + rs.getString("REF"), rs.getString("NAME"), rs.getString("DISPLAY"), rs.getString("CONCEPT_TYPE"), rs.getString("CONCEPT_PATH"), + rs.getInt("CONCEPT_NODE_ID"), rs.getInt("PARENT_ID") + ); + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/ConceptNodeMetaDumpMapper.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/ConceptNodeMetaDumpMapper.java new file mode 100644 index 000000000..df991feb3 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/ConceptNodeMetaDumpMapper.java @@ -0,0 +1,16 @@ +package edu.harvard.dbmi.avillach.dump.local.extractor; + +import edu.harvard.dbmi.avillach.dump.entities.ConceptNodeMetaDump; +import org.springframework.jdbc.core.RowMapper; +import org.springframework.stereotype.Component; + +import java.sql.ResultSet; +import java.sql.SQLException; + +@Component +public class ConceptNodeMetaDumpMapper implements RowMapper { + @Override + public ConceptNodeMetaDump mapRow(ResultSet rs, int rowNum) throws SQLException { + return new ConceptNodeMetaDump(rs.getString("CONCEPT_PATH"), rs.getString("KEY"), rs.getString("VALUE")); + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/FacetCategoryDumpMapper.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/FacetCategoryDumpMapper.java new file mode 100644 index 000000000..ec7aef719 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/FacetCategoryDumpMapper.java @@ -0,0 +1,16 @@ +package edu.harvard.dbmi.avillach.dump.local.extractor; + +import edu.harvard.dbmi.avillach.dump.entities.FacetCategoryDump; +import org.springframework.jdbc.core.RowMapper; +import org.springframework.stereotype.Component; + +import java.sql.ResultSet; +import java.sql.SQLException; + +@Component +public class FacetCategoryDumpMapper implements RowMapper { + @Override + public FacetCategoryDump mapRow(ResultSet rs, int rowNum) throws SQLException { + return new FacetCategoryDump(rs.getString("NAME"), rs.getString("DISPLAY"), rs.getString("DESCRIPTION")); + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/FacetCategoryMetaDumpMapper.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/FacetCategoryMetaDumpMapper.java new file mode 100644 index 000000000..e2e613279 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/FacetCategoryMetaDumpMapper.java @@ -0,0 +1,16 @@ +package edu.harvard.dbmi.avillach.dump.local.extractor; + +import edu.harvard.dbmi.avillach.dump.entities.FacetCategoryMetaDump; +import org.springframework.jdbc.core.RowMapper; +import org.springframework.stereotype.Component; + +import java.sql.ResultSet; +import java.sql.SQLException; + +@Component +public class FacetCategoryMetaDumpMapper implements RowMapper { + @Override + public FacetCategoryMetaDump mapRow(ResultSet rs, int rowNum) throws SQLException { + return new FacetCategoryMetaDump(rs.getString("NAME"), rs.getString("KEY"), rs.getString("VALUE")); + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/FacetConceptPairMapper.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/FacetConceptPairMapper.java new file mode 100644 index 000000000..c0e4979ea --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/FacetConceptPairMapper.java @@ -0,0 +1,17 @@ +package edu.harvard.dbmi.avillach.dump.local.extractor; + +import edu.harvard.dbmi.avillach.dump.entities.ConceptNodeMetaDump; +import edu.harvard.dbmi.avillach.dump.entities.FacetConceptPair; +import org.springframework.jdbc.core.RowMapper; +import org.springframework.stereotype.Component; + +import java.sql.ResultSet; +import java.sql.SQLException; + +@Component +public class FacetConceptPairMapper implements RowMapper { + @Override + public FacetConceptPair mapRow(ResultSet rs, int rowNum) throws SQLException { + return new FacetConceptPair(rs.getString("FACET"), rs.getString("FACET_CATEGORY"), rs.getString("CONCEPT_PATH")); + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/FacetDumpMapper.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/FacetDumpMapper.java new file mode 100644 index 000000000..8141f1588 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/FacetDumpMapper.java @@ -0,0 +1,20 @@ +package edu.harvard.dbmi.avillach.dump.local.extractor; + +import edu.harvard.dbmi.avillach.dump.entities.FacetDump; +import edu.harvard.dbmi.avillach.dump.entities.FacetMetaDump; +import org.springframework.jdbc.core.RowMapper; +import org.springframework.stereotype.Component; + +import java.sql.ResultSet; +import java.sql.SQLException; + +@Component +public class FacetDumpMapper implements RowMapper { + @Override + public FacetDump mapRow(ResultSet rs, int rowNum) throws SQLException { + return new FacetDump( + rs.getString("NAME"), rs.getString("DISPLAY"), rs.getString("DESCRIPTION"), rs.getString("FACET_CATEGORY_NAME"), + rs.getInt("FACET_ID"), rs.getInt("PARENT_ID") + ); + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/FacetMetaDumpMapper.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/FacetMetaDumpMapper.java new file mode 100644 index 000000000..929baf32a --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/local/extractor/FacetMetaDumpMapper.java @@ -0,0 +1,16 @@ +package edu.harvard.dbmi.avillach.dump.local.extractor; + +import edu.harvard.dbmi.avillach.dump.entities.FacetMetaDump; +import org.springframework.jdbc.core.RowMapper; +import org.springframework.stereotype.Component; + +import java.sql.ResultSet; +import java.sql.SQLException; + +@Component +public class FacetMetaDumpMapper implements RowMapper { + @Override + public FacetMetaDump mapRow(ResultSet rs, int rowNum) throws SQLException { + return new FacetMetaDump(rs.getString("FACET"), rs.getString("FACET_CATEGORY"), rs.getString("KEY"), rs.getString("VALUE")); + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/DataRefreshService.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/DataRefreshService.java new file mode 100644 index 000000000..778ac1592 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/DataRefreshService.java @@ -0,0 +1,79 @@ +package edu.harvard.dbmi.avillach.dump.remote; + +import edu.harvard.dbmi.avillach.dump.remote.api.RemoteDictionaryAPI; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.stereotype.Service; + +import java.time.LocalDateTime; +import java.util.List; +import java.util.Optional; +import java.util.function.Predicate; + +@Service +public class DataRefreshService { + + private static final Logger log = LoggerFactory.getLogger(DataRefreshService.class); + + private final RemoteDictionaryRepository repository; + private final RemoteDictionaryAPI api; + + private final List> updateSequence; + + public DataRefreshService(RemoteDictionaryRepository repository, RemoteDictionaryAPI api) { + this.repository = repository; + this.api = api; + updateSequence = List.of( + (d) -> updateObject(repository::addConceptsForSite, api::fetchConcepts, "concepts", d), + (d) -> updateObject(repository::addFacetCategoriesForSite, api::fetchFacetCategories, "facet categories", d), + (d) -> updateObject(repository::addFacetsForSite, api::fetchFacets, "facets", d), + (d) -> updateObject(repository::addFacetConceptPairsForSite, api::fetchFacetConceptPairs, "facet concept pairs", d), + (d) -> updateObject(repository::addConceptMetasForSite, api::fetchConceptMetas, "concept metas", d), + (d) -> updateObject(repository::addFacetCategoryMetasForSite, api::fetchFacetCategoryMetas, "facet category metas", d), + (d) -> updateObject(repository::addFacetMetasForSite, api::fetchFacetMetas, "facet metas", d) + ); + } + + public void refreshDictionary(RemoteDictionary dictionary) { + log.info("Updating {}", dictionary.fullName()); + repository.dropValuesForSite(dictionary.name()); + log.info("All values for site {} have been dropped", dictionary.fullName()); + boolean success = true; + for (int i = 0; i < updateSequence.size() && success; i++) { + success = updateSequence.get(i).test(dictionary); + } + if (success) { + LocalDateTime updated = LocalDateTime.now(); + log.info("Done refreshing values for site {}, setting local update time to {}", dictionary.fullName(), updated); + repository.setUpdateTimestamp(dictionary.name(), updated); + } else { + log.warn("Failed to refresh values for site {}", dictionary.fullName()); + } + repository.pruneHangingEntries(); + } + + @FunctionalInterface + private interface RepoAddFn { + void addObjects(String name, List rows); + } + + @FunctionalInterface + private interface PullObjectsFn { + Optional> fetchFromRemote(String name); + } + + private boolean updateObject(RepoAddFn adder, PullObjectsFn puller, String objectName, RemoteDictionary site) { + log.info("Refreshing {} for {}", objectName, site.fullName()); + Optional> maybeRows = puller.fetchFromRemote(site.name()); + if (maybeRows.isEmpty()) { + log.error("Error updating {}. Wiping {} and giving up", objectName, site.fullName()); + repository.dropValuesForSite(site.name()); + repository.pruneHangingEntries(); + return false; + } + log.info("Successfully fetched {} rows of {} for {}", maybeRows.get().size(), objectName, site.fullName()); + adder.addObjects(site.name(), maybeRows.get()); + log.info("Added {} for {}", objectName, site.fullName()); + return true; + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDictionary.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDictionary.java new file mode 100644 index 000000000..3288e0d12 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDictionary.java @@ -0,0 +1,5 @@ +package edu.harvard.dbmi.avillach.dump.remote; + + +public record RemoteDictionary(String name, String fullName) { +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDictionaryPullConfig.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDictionaryPullConfig.java new file mode 100644 index 000000000..1622fdffa --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDictionaryPullConfig.java @@ -0,0 +1,25 @@ +package edu.harvard.dbmi.avillach.dump.remote; + +import org.springframework.boot.context.properties.ConfigurationProperties; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.scheduling.annotation.EnableScheduling; + +import java.util.List; + +@Configuration +@EnableScheduling +@ConfigurationProperties(prefix = "remote") +public class RemoteDictionaryPullConfig { + + private List dictionaries; + + @Bean + public List getDictionaries() { + return dictionaries; + } + + public void setDictionaries(List dictionaries) { + this.dictionaries = dictionaries; + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDictionaryRepository.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDictionaryRepository.java new file mode 100644 index 000000000..f5ec126ed --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDictionaryRepository.java @@ -0,0 +1,373 @@ +package edu.harvard.dbmi.avillach.dump.remote; + +import edu.harvard.dbmi.avillach.dump.entities.*; +import edu.harvard.dbmi.avillach.dump.util.MapExtractor; +import org.apache.catalina.util.ExactRateLimiter; +import org.apache.catalina.util.RateLimiter; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.jdbc.core.JdbcTemplate; +import org.springframework.jdbc.core.namedparam.MapSqlParameterSource; +import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate; +import org.springframework.jdbc.core.namedparam.SqlParameterSourceUtils; +import org.springframework.stereotype.Repository; + +import javax.sql.DataSource; +import java.sql.Connection; +import java.sql.SQLException; +import java.sql.Statement; +import java.time.LocalDateTime; +import java.util.*; +import java.util.concurrent.Semaphore; +import java.util.stream.Collectors; +import java.util.stream.Gatherers; + +@Repository +public class RemoteDictionaryRepository { + + private static final Logger log = LoggerFactory.getLogger(RemoteDictionaryRepository.class); + private final NamedParameterJdbcTemplate template; + + @Autowired + public RemoteDictionaryRepository(NamedParameterJdbcTemplate template) { + this.template = template; + } + + public LocalDateTime getUpdateTimestamp(String name) { + String sql = "SELECT LAST_UPDATED FROM remote_dictionary WHERE NAME = :dictName"; + MapSqlParameterSource params = new MapSqlParameterSource().addValue("dictName", name); + return template.queryForList(sql, params, LocalDateTime.class).stream().findFirst().orElse(LocalDateTime.MIN); + } + + public void dropValuesForSite(String name) { + String sql = """ + DELETE FROM concept_node__remote_dictionary + WHERE REMOTE_DICTIONARY_ID = ( + SELECT REMOTE_DICTIONARY_ID + FROM remote_dictionary + WHERE NAME = :dictName + ) + """; + MapSqlParameterSource params = new MapSqlParameterSource().addValue("dictName", name); + int unpairedConcepts = template.update(sql, params); + log.info("Unpaired {} concepts while dropping values for site {}", unpairedConcepts, name); + } + + public void setUpdateTimestamp(String name, LocalDateTime updateTime) { + String sql = """ + UPDATE remote_dictionary + SET LAST_UPDATED = :updated + WHERE NAME = :dictName + """; + MapSqlParameterSource params = new MapSqlParameterSource().addValue("dictName", name).addValue("updated", updateTime); + template.update(sql, params); + } + + /** + * WARNING: If you invoke this method in a non-aggregate dictionary environment, it will wipe your database This function prunes all + * facets, concepts, categories and their metas that are not associated with a remote dictionary. + */ + public void pruneHangingEntries() { + // delete all facet concepts that aren't associated with a concept from a remote dict + String facetConceptSQL = """ + DELETE FROM facet__concept_node + WHERE NOT EXISTS ( + SELECT 1 + FROM concept_node__remote_dictionary + WHERE facet__concept_node.concept_node_id = concept_node__remote_dictionary.concept_node_id + ) + """; + // delete all concept metas that aren't associated with a concept from a remote dict + String conceptMetaSQL = """ + DELETE FROM concept_node_meta + WHERE NOT EXISTS ( + SELECT 1 + FROM concept_node__remote_dictionary + WHERE concept_node_meta.concept_node_id = concept_node__remote_dictionary.concept_node_id + ) + """; + // delete all facet metas that aren't associated with a concept from a remote dict + String facetMetaSQL = """ + DELETE FROM facet_meta + WHERE NOT EXISTS ( + SELECT 1 + FROM facet__concept_node + INNER JOIN concept_node__remote_dictionary remote ON remote.concept_node_id = facet__concept_node.concept_node_id + WHERE facet__concept_node.facet_id = facet_meta.facet_id + ) + """; + // delete all facets that aren't associated with a concept from a remote dict + String facetSQL = """ + DELETE FROM facet + WHERE NOT EXISTS ( + SELECT 1 + FROM facet__concept_node + INNER JOIN concept_node__remote_dictionary remote ON remote.concept_node_id = facet__concept_node.concept_node_id + WHERE facet__concept_node.facet_id = facet.facet_id + ) + """; + // delete all concepts that aren't associated with a concept from a remote dict + // this needs to be done recursively so that non leaf nodes are released as well + String conceptSQL = """ + WITH RECURSIVE delete_concepts_until_empty AS ( + DELETE FROM concept_node + WHERE + NOT EXISTS ( + SELECT 1 + FROM concept_node child + WHERE child.parent_id = concept_node.concept_node_id + ) + AND + NOT EXISTS ( + SELECT 1 + FROM concept_node__remote_dictionary + WHERE concept_node.concept_node_id = concept_node__remote_dictionary.concept_node_id + ) + RETURNING concept_node_id + ) + -- Recursive part continues until no more rows are deleted + SELECT COUNT(*) FROM delete_concepts_until_empty; + """; + // delete facet metas that belong to categories with no facets + String facetCategoryMetaSQL = """ + DELETE FROM facet_category_meta + WHERE NOT EXISTS ( + SELECT 1 + FROM facet + WHERE facet.facet_category_id = facet_category_meta.facet_category_id + ) + """; + // delete facet categories with no facets + String facetCategorySQL = """ + DELETE FROM facet_category + WHERE NOT EXISTS ( + SELECT 1 + FROM facet + WHERE facet.facet_category_id = facet_category.facet_category_id + ) + """; + log.info("Pruning facet concepts"); + int pruned = template.update(facetConceptSQL, new MapSqlParameterSource()); + log.info("Pruned {} facet concepts", pruned); + log.info("Pruning concept metas"); + pruned = template.update(conceptMetaSQL, new MapSqlParameterSource()); + log.info("Pruned {} facet metas", pruned); + log.info("Pruning facet metas"); + pruned = template.update(facetMetaSQL, new MapSqlParameterSource()); + log.info("Pruned {} facet metas", pruned); + log.info("Pruning facets"); + pruned = template.update(facetSQL, new MapSqlParameterSource()); + log.info("Pruned {} facets", pruned); + log.info("Pruning concepts"); + template.queryForObject(conceptSQL, new MapSqlParameterSource(), Integer.class); + log.info("Pruned {} concepts", pruned); + log.info("Pruning facet category metas"); + pruned = template.update(facetCategoryMetaSQL, new MapSqlParameterSource()); + log.info("Pruned {} facet category metas", pruned); + log.info("Pruning facet categories"); + pruned = template.update(facetCategorySQL, new MapSqlParameterSource()); + log.info("Pruned {} facet categories", pruned); + } + + public void addConceptsForSite(String name, List concepts) { + log.info("Starting concept ingest for {}", name); + // initialize datasets if DNE + createEmptyDatasets(concepts.stream().map(ConceptNodeDump::datasetRef).distinct().toList()); + Map datasets = getDatasetRefs(); + log.info("Initialized datasets"); + // add the concepts one tier at a time + Set allConcepts = addConcepts(concepts, datasets); + + // get the ID of the remote data set being updated + String remoteIDQuery = "SELECT REMOTE_DICTIONARY_ID FROM remote_dictionary WHERE NAME = :name"; + Integer siteId = template.queryForObject(remoteIDQuery, new MapSqlParameterSource("name", name), Integer.class); + + log.info("Pairing added concepts to site {}", name); + String pairSQL = "INSERT INTO concept_node__remote_dictionary (CONCEPT_NODE_ID, REMOTE_DICTIONARY_ID) VALUES (:nodeID, :dictID)"; + MapSqlParameterSource[] params = allConcepts.stream().map(id -> new MapSqlParameterSource("nodeID", id).addValue("dictID", siteId)) + .toArray(MapSqlParameterSource[]::new); + template.batchUpdate(pairSQL, params); + log.info("Done ingesting concepts for {}", name); + } + + private Set addConcepts(List concepts, Map datasets) { + concepts.forEach(c -> c.setParentId(null)); + String childSQL = """ + INSERT INTO concept_node (DATASET_ID, NAME, DISPLAY, CONCEPT_TYPE, CONCEPT_PATH, PARENT_ID) + SELECT :datasetRef, :name, :display, :conceptType, :conceptPath, CONCEPT_NODE_ID + FROM concept_node AS parent + WHERE parent.CONCEPT_PATH_MD5 = md5(:parentPath::text) + ON CONFLICT (concept_path_md5) DO NOTHING + """; + String rootSQL = """ + INSERT INTO concept_node (DATASET_ID, NAME, DISPLAY, CONCEPT_TYPE, CONCEPT_PATH) + VALUES (:datasetRef, :name, :display, :conceptType, :conceptPath) + ON CONFLICT (concept_path_md5) DO NOTHING + """; + String idSQL = """ + WITH paths AS (SELECT unnest(:paths) AS CONCEPT) + SELECT CONCEPT_NODE_ID + FROM concept_node + INNER JOIN paths ON concept_node.concept_path = paths.CONCEPT + """; + Set allConcepts = new HashSet<>(); + + int tier = 0; + int count = 0; + while (!concepts.isEmpty()) { + log.info("Ingesting tier {}, starting concept count {}", tier++, count += concepts.size()); + concepts.forEach(concept -> concept.children().forEach(c -> c.setParentPath(concept.conceptPath()))); + String sql = concepts.getFirst().parentId() == null ? rootSQL : childSQL; + for (List conceptBucket : concepts.stream().gather(Gatherers.windowFixed(1000)).toList()) { + template + .batchUpdate(sql, conceptBucket.stream().map(c -> createParamMap(c, datasets)).toArray(MapSqlParameterSource[]::new)); + MapSqlParameterSource params = + new MapSqlParameterSource("paths", conceptBucket.stream().map(ConceptNodeDump::conceptPath).toArray(String[]::new)); + List conceptIds = template.queryForList(idSQL, params, Integer.class); + allConcepts.addAll(conceptIds); + } + concepts = concepts.stream().map(ConceptNodeDump::children).flatMap(List::stream).toList(); + count += concepts.size(); + } + return allConcepts; + } + + private MapSqlParameterSource createParamMap(ConceptNodeDump concept, Map datasets) { + return new MapSqlParameterSource().addValue("datasetRef", datasets.get(concept.datasetRef())).addValue("name", concept.name()) + .addValue("display", concept.display()).addValue("conceptType", concept.conceptType()) + .addValue("conceptPath", concept.conceptPath()).addValue("parentPath", concept.parentPath()); + } + + private Map getDatasetRefs() { + String sql = "SELECT REF, DATASET_ID FROM dataset"; + return template.query(sql, new MapSqlParameterSource(), new MapExtractor("REF", "DATASET_ID")).entrySet().stream() + .collect(Collectors.toMap(Map.Entry::getKey, e -> Integer.parseInt(e.getValue()))); + } + + private void createEmptyDatasets(List datasets) { + String sql = """ + INSERT INTO dataset (REF, FULL_NAME, ABBREVIATION) + VALUES (:ref, :ref, :ref) + ON CONFLICT (REF) DO NOTHING + """; + MapSqlParameterSource[] params = + datasets.stream().map(ds -> new MapSqlParameterSource("ref", ds)).toArray(MapSqlParameterSource[]::new); + template.batchUpdate(sql, params); + } + + public void addFacetCategoriesForSite(String name, List categories) { + log.info("Starting facet category ingest for {}", name); + String sql = """ + INSERT INTO facet_category (NAME, DISPLAY, DESCRIPTION) + VALUES (:name, :display, :description) + ON CONFLICT (NAME) DO NOTHING + """; + categories.stream() + .map( + c -> new MapSqlParameterSource().addValue("name", c.name()).addValue("display", c.display()) + .addValue("description", c.description()) + ).forEach(params -> template.update(sql, params)); + log.info("Done ingesting facet categories for {}", name); + } + + public void addFacetsForSite(String name, List facets) { + log.info("Starting facet ingest for {}", name); + // set all parent names + String sql = """ + INSERT INTO facet (NAME, DISPLAY, DESCRIPTION, FACET_CATEGORY_ID, PARENT_ID) + SELECT :name, :display, :description, facet_category.FACET_CATEGORY_ID, parent.FACET_ID + FROM facet_category + LEFT JOIN facet AS parent ON parent.FACET_CATEGORY_ID = facet_category.FACET_CATEGORY_ID AND parent.name = :parentName + WHERE facet_category.NAME = :facetCategoryName + ON CONFLICT DO NOTHING + """; + List currentTier = facets; + while (!currentTier.isEmpty()) { + for (FacetDump facet : currentTier) { + MapSqlParameterSource params = new MapSqlParameterSource().addValue("name", facet.name()) + .addValue("display", facet.display()).addValue("description", facet.description()) + .addValue("parentName", facet.parentName()).addValue("facetCategoryName", facet.facetCategoryName()); + template.update(sql, params); + facet.children().forEach(c -> c.setParentName(facet.name())); + } + currentTier = currentTier.stream().map(FacetDump::children).flatMap(List::stream).toList(); + } + log.info("Done ingesting facets for {}", name); + } + + public void addFacetCategoryMetasForSite(String name, List categoryMetas) { + log.info("Starting facet category meta ingest for {}", name); + String sql = """ + INSERT INTO facet_category_meta (FACET_CATEGORY_ID, KEY, VALUE) + SELECT FACET_CATEGORY_ID, :key, :value + FROM facet_category + WHERE NAME = :facetCategoryName + ON CONFLICT DO NOTHING + """; + for (FacetCategoryMetaDump meta : categoryMetas) { + MapSqlParameterSource params = new MapSqlParameterSource().addValue("key", meta.key()).addValue("value", meta.value()) + .addValue("facetCategoryName", meta.categoryName()); + template.update(sql, params); + } + log.info("Done ingesting facet category metas for {}", name); + } + + public void addFacetMetasForSite(String name, List facetMetas) { + log.info("Starting facet meta ingest for {}", name); + String sql = """ + INSERT INTO facet_meta (FACET_ID, KEY, VALUE) + SELECT FACET_ID, :key, :value + FROM facet + JOIN facet_category ON facet.FACET_CATEGORY_ID = facet_category.FACET_CATEGORY_ID + WHERE facet.name = :facetName AND facet_category.name = :categoryName + ON CONFLICT DO NOTHING + """; + for (FacetMetaDump meta : facetMetas) { + MapSqlParameterSource params = new MapSqlParameterSource().addValue("key", meta.key()).addValue("value", meta.value()) + .addValue("facetName", meta.facetName()).addValue("categoryName", meta.categoryName()); + template.update(sql, params); + } + log.info("Done ingesting facet metas for {}", name); + } + + public void addConceptMetasForSite(String name, List conceptMetas) { + log.info("Starting concept meta ingest for {}", name); + String sql = """ + INSERT INTO concept_node_meta (CONCEPT_NODE_ID, KEY, VALUE) + SELECT CONCEPT_NODE_ID, :key, :value + FROM concept_node + WHERE CONCEPT_PATH_MD5 = md5(:conceptPath::text) + ON CONFLICT DO NOTHING + """; + MapSqlParameterSource[] params = conceptMetas.stream() + .map( + meta -> new MapSqlParameterSource().addValue("conceptPath", meta.conceptPath()).addValue("key", meta.key()) + .addValue("value", meta.value()) + ).toArray(MapSqlParameterSource[]::new); + template.batchUpdate(sql, params); + log.info("Done ingesting concept metas for {}", name); + } + + public void addFacetConceptPairsForSite(String name, List pairs) { + log.info("Starting facet concept pair ingest for {}", name); + String sql = """ + INSERT INTO facet__concept_node (FACET_ID, CONCEPT_NODE_ID) + SELECT FACET_ID, CONCEPT_NODE_ID + FROM facet + JOIN facet_category ON facet.FACET_CATEGORY_ID = facet_category.FACET_CATEGORY_ID + INNER JOIN concept_node ON concept_node.CONCEPT_PATH_MD5 = md5(:conceptPath::text) + WHERE + facet.NAME = :facetName + AND facet_category.NAME = :categoryName + ON CONFLICT DO NOTHING + """; + MapSqlParameterSource[] params = pairs.stream() + .map( + pair -> new MapSqlParameterSource().addValue("conceptPath", pair.conceptPath()).addValue("facetName", pair.facetName()) + .addValue("categoryName", pair.facetCategory()) + ).toArray(MapSqlParameterSource[]::new); + template.batchUpdate(sql, params); + log.info("Done ingesting facet concept pairs for {}", name); + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDumpSchedulingService.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDumpSchedulingService.java new file mode 100644 index 000000000..2ac83bad0 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDumpSchedulingService.java @@ -0,0 +1,70 @@ +package edu.harvard.dbmi.avillach.dump.remote; + +import edu.harvard.dbmi.avillach.dump.local.DumpRepository; +import edu.harvard.dbmi.avillach.dump.remote.api.RemoteDictionaryAPI; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty; +import org.springframework.context.annotation.Profile; +import org.springframework.scheduling.annotation.Scheduled; +import org.springframework.stereotype.Service; + +import java.time.LocalDateTime; +import java.util.List; +import java.util.Optional; + +@Service +@Profile({"aggregate"}) +public class RemoteDumpSchedulingService { + + private static final Logger log = LoggerFactory.getLogger(RemoteDumpSchedulingService.class); + private final List dictionaries; + private final RemoteDictionaryRepository repository; + private final DumpRepository localRepository; + private final RemoteDictionaryAPI api; + private final DataRefreshService refreshService; + + @Autowired + public RemoteDumpSchedulingService( + List dictionaries, RemoteDictionaryRepository repository, DumpRepository localRepository, RemoteDictionaryAPI api, + DataRefreshService refreshService + ) { + this.dictionaries = dictionaries; + this.repository = repository; + this.localRepository = localRepository; + this.api = api; + this.refreshService = refreshService; + } + + @Scheduled(fixedRateString = "PT1H", initialDelayString = "PT10S") + public void pollForUpdates() { + log.info("Polling {} remote dictionaries for updates...", dictionaries.size()); + dictionaries.stream().filter(this::shouldUpdate).forEach(refreshService::refreshDictionary); + + } + + private boolean shouldUpdate(RemoteDictionary dictionary) { + log.info("Polling {} for last update time", dictionary.fullName()); + Optional maybeRemoteUpdate = api.fetchUpdateTimestamp(dictionary.name()); + Optional maybeDatabaseVersion = api.fetchDatabaseVersion(dictionary.name()); + if (maybeRemoteUpdate.isEmpty() || maybeDatabaseVersion.isEmpty()) { + log.warn("Error reaching server {}. Will not update.", dictionary.fullName()); + return false; + } + + Integer remoteVersion = maybeDatabaseVersion.get(); + Integer localVersion = localRepository.getDatabaseVersion(); + if (!localVersion.equals(remoteVersion)) { + log.warn("Database version mismatch. Remote: {} != Local: {}", remoteVersion, localVersion); + return false; + } + + LocalDateTime remoteUpdate = maybeRemoteUpdate.get(); + log.info("The remote dictionary for {} was last updated at {}", dictionary.fullName(), remoteUpdate); + LocalDateTime localUpdate = repository.getUpdateTimestamp(dictionary.name()); + log.info("The last local update for {} was {}", dictionary.fullName(), localUpdate); + return localUpdate.isBefore(remoteUpdate); + } + +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/api/HttpClientConfig.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/api/HttpClientConfig.java new file mode 100644 index 000000000..eaa461d2e --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/api/HttpClientConfig.java @@ -0,0 +1,35 @@ +package edu.harvard.dbmi.avillach.dump.remote.api; + +import org.apache.hc.client5.http.impl.classic.CloseableHttpClient; +import org.apache.hc.client5.http.impl.classic.HttpClients; +import org.apache.hc.client5.http.impl.io.PoolingHttpClientConnectionManagerBuilder; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.http.client.HttpComponentsClientHttpRequestFactory; +import org.springframework.util.StringUtils; +import org.springframework.web.client.RestClient; + +@Configuration +public class HttpClientConfig { + private static final Logger LOG = LoggerFactory.getLogger(HttpClientConfig.class); + + @Value("${http.proxyUser:}") + private String proxyUser; + + @Bean + public RestClient restClient(RestClient.Builder builder) { + CloseableHttpClient httpClient; + if (!StringUtils.hasLength(proxyUser)) { + LOG.info("No proxy user found, making default client."); + httpClient = HttpClients.custom() + .setConnectionManager(PoolingHttpClientConnectionManagerBuilder.create().setMaxConnTotal(100).build()).build(); + } else { + LOG.info("Found proxy user {}, will configure proxy from system properties", proxyUser); + httpClient = HttpClients.custom().useSystemProperties().build(); + } + return builder.requestFactory(new HttpComponentsClientHttpRequestFactory(httpClient)).build(); + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/api/RemoteDictionaryAPI.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/api/RemoteDictionaryAPI.java new file mode 100644 index 000000000..f1de36112 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/remote/api/RemoteDictionaryAPI.java @@ -0,0 +1,96 @@ +package edu.harvard.dbmi.avillach.dump.remote.api; + +import com.fasterxml.jackson.core.type.TypeReference; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule; +import edu.harvard.dbmi.avillach.dump.entities.*; +import edu.harvard.dbmi.avillach.dump.local.DumpTable; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Service; +import org.springframework.util.StringUtils; +import org.springframework.web.client.RestClient; + +import java.time.LocalDateTime; +import java.time.format.DateTimeFormatter; +import java.util.List; +import java.util.Optional; + +@Service +public class RemoteDictionaryAPI { + + private final DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss.SSS"); + private static final Logger log = LoggerFactory.getLogger(RemoteDictionaryAPI.class); + private final RestClient restClient; + private final ObjectMapper mapper; + private static final String rootURL = "http://passthru:80/dictionary-dump/"; + + @Autowired + public RemoteDictionaryAPI(RestClient restClient, ObjectMapper mapper) { + this.restClient = restClient; + this.mapper = mapper; + mapper.registerModule(new JavaTimeModule()); + } + + public Optional fetchUpdateTimestamp(String name) { + return runRequest(new TypeReference() {}, rootURL + name + "/last-updated").filter(StringUtils::hasLength) + .map(iso -> LocalDateTime.parse(iso, formatter)); + } + + public Optional fetchDatabaseVersion(String siteName) { + return runRequest(new TypeReference() {}, rootURL + siteName + "/database-version"); + } + + public Optional> fetchConcepts(String siteName) { + return runRequest(new TypeReference>() {}, rootURL + siteName + "/dump/" + DumpTable.ConceptNode.name()); + } + + public Optional> fetchFacetCategories(String siteName) { + return runRequest(new TypeReference>() {}, rootURL + siteName + "/dump/" + DumpTable.FacetCategory.name()); + } + + public Optional> fetchFacets(String siteName) { + return runRequest(new TypeReference>() {}, rootURL + siteName + "/dump/" + DumpTable.Facet.name()); + } + + public Optional> fetchConceptMetas(String siteName) { + return runRequest( + new TypeReference>() {}, rootURL + siteName + "/dump/" + DumpTable.ConceptNodeMeta.name() + ); + } + + public Optional> fetchFacetCategoryMetas(String siteName) { + return runRequest( + new TypeReference>() {}, rootURL + siteName + "/dump/" + DumpTable.FacetCategoryMeta.name() + ); + } + + public Optional> fetchFacetMetas(String siteName) { + return runRequest(new TypeReference>() {}, rootURL + siteName + "/dump/" + DumpTable.FacetMeta.name()); + } + + public Optional> fetchFacetConceptPairs(String siteName) { + return runRequest( + new TypeReference>() {}, rootURL + siteName + "/dump/" + DumpTable.FacetConceptNode.name() + ); + } + + @SuppressWarnings("unchecked") + private Optional runRequest(TypeReference returnType, String url) { + try { + String entityStr = restClient.get().uri(url).retrieve().body(String.class); + if (entityStr == null) { + return Optional.empty(); + } + if (returnType.getType().equals(entityStr.getClass())) { + return Optional.of((T) entityStr); + } else { + return Optional.of(mapper.readValue(entityStr, returnType)); + } + } catch (Exception e) { + log.info("Exception running request:: ", e); + return Optional.empty(); + } + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/util/JacksonConfig.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/util/JacksonConfig.java new file mode 100644 index 000000000..a9622bce6 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/util/JacksonConfig.java @@ -0,0 +1,20 @@ +package edu.harvard.dbmi.avillach.dump.util; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.databind.ObjectMapper; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.context.annotation.Primary; + +@Configuration +public class JacksonConfig { + @Bean + @Primary + public ObjectMapper objectMapper() { + ObjectMapper mapper = new ObjectMapper(); + mapper.setVisibility( + mapper.getSerializationConfig().getDefaultVisibilityChecker().withFieldVisibility(JsonAutoDetect.Visibility.ANY) + ); + return mapper; + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/util/MapExtractor.java b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/util/MapExtractor.java new file mode 100644 index 000000000..17335d1b8 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/java/edu/harvard/dbmi/avillach/dump/util/MapExtractor.java @@ -0,0 +1,27 @@ +package edu.harvard.dbmi.avillach.dump.util; + +import org.springframework.dao.DataAccessException; +import org.springframework.jdbc.core.ResultSetExtractor; + +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.HashMap; +import java.util.Map; + +public class MapExtractor implements ResultSetExtractor> { + private final String keyName, valueName; + + public MapExtractor(String keyName, String valueName) { + this.keyName = keyName; + this.valueName = valueName; + } + + @Override + public Map extractData(ResultSet rs) throws SQLException, DataAccessException { + Map map = new HashMap<>(); + while (rs.next() && rs.getString(keyName) != null) { + map.put(rs.getString(keyName), rs.getString(valueName)); + } + return map; + } +} diff --git a/services/picsure-dictionary/aggregate/src/main/resources/application-bdc-dev.properties b/services/picsure-dictionary/aggregate/src/main/resources/application-bdc-dev.properties new file mode 100644 index 000000000..b2d7de1ea --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/resources/application-bdc-dev.properties @@ -0,0 +1,18 @@ +spring.application.name=dictionary +spring.datasource.url=jdbc:postgresql://localhost:5432/dictionary_db?currentSchema=dict +spring.datasource.username=username +spring.datasource.password=password +spring.datasource.driver-class-name=org.postgresql.Driver +server.port=80 + +dashboard.columns={abbreviation:'Abbreviation',name:'Name',clinvars:'Clinical Variables'} +dashboard.column-order=abbreviation,name,clinvars +dashboard.nonmeta-columns=abbreviation,name +dashboard.enable.extra_details=true +dashboard.enable.bdc_hack=true + +filtering.unfilterable_concepts=stigmatized + +# Logging File Output https://docs.spring.io/spring-boot/reference/features/logging.html#features.logging.file-output +# If you are adding additional log files please add them to /var/log/ directory. +logging.file.name=/var/log/dictionary.log \ No newline at end of file diff --git a/services/picsure-dictionary/aggregate/src/main/resources/application-bdc.properties b/services/picsure-dictionary/aggregate/src/main/resources/application-bdc.properties new file mode 100644 index 000000000..89496f3af --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/resources/application-bdc.properties @@ -0,0 +1,15 @@ +spring.application.name=dictionary +spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.PostgreSQLDialect +spring.datasource.driver-class-name=com.amazonaws.secretsmanager.sql.AWSSecretsManagerPostgreSQLDriver +spring.datasource.url=jdbc-secretsmanager:postgresql://${DATASOURCE_URL}/picsure?useUnicode=true&characterEncoding=UTF-8&autoReconnect=true&autoReconnectForPools=true¤tSchema=dict +spring.datasource.username=${DATASOURCE_USERNAME} +server.port=80 + +dashboard.enable.extra_details=true +dashboard.enable.bdc_hack=true + +filtering.unfilterable_concepts=stigmatized + +# Logging File Output https://docs.spring.io/spring-boot/reference/features/logging.html#features.logging.file-output +# If you are adding additional log files please add them to /var/log/ directory. +logging.file.name=/var/log/dictionary.log diff --git a/services/picsure-dictionary/aggregate/src/main/resources/application.properties b/services/picsure-dictionary/aggregate/src/main/resources/application.properties new file mode 100644 index 000000000..000ea382b --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/main/resources/application.properties @@ -0,0 +1,21 @@ +spring.profiles.active=production +spring.application.name=dictionary +spring.datasource.url=jdbc:postgresql://${POSTGRES_HOST}:5432/${POSTGRES_DB}?currentSchema=dict +spring.datasource.username=${POSTGRES_USER} +spring.datasource.password=${POSTGRES_PASSWORD} +spring.datasource.driver-class-name=org.postgresql.Driver + +server.port=80 + +dashboard.columns={abbreviation:'Abbreviation',name:'Name',clinvars:'Clinical Variables'} +dashboard.column-order=abbreviation,name,clinvars +dashboard.nonmeta-columns=abbreviation,name +dashboard.enable.extra_details=true +dashboard.enable.bdc_hack=false +dashboard.layout.type=default + +filtering.unfilterable_concepts=stigmatized + +# Logging File Output https://docs.spring.io/spring-boot/reference/features/logging.html#features.logging.file-output +# If you are adding additional log files please add them to /var/log/ directory. +logging.file.name=/var/log/aggdict.log \ No newline at end of file diff --git a/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/local/DumpControllerAuditEventTest.java b/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/local/DumpControllerAuditEventTest.java new file mode 100644 index 000000000..0e506006f --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/local/DumpControllerAuditEventTest.java @@ -0,0 +1,31 @@ +package edu.harvard.dbmi.avillach.dump.local; + +import static org.junit.jupiter.api.Assertions.*; + +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import org.junit.jupiter.api.Test; + +import java.lang.reflect.Method; + +class DumpControllerAuditEventTest { + + private void assertAuditEvent(Class controller, String methodName, Class[] params, String expectedType, String expectedAction) + throws Exception { + Method method = controller.getMethod(methodName, params); + AuditEvent event = method.getAnnotation(AuditEvent.class); + assertNotNull(event, controller.getSimpleName() + "." + methodName + " missing @AuditEvent"); + assertEquals(expectedType, event.type(), controller.getSimpleName() + "." + methodName + " wrong type"); + assertEquals(expectedAction, event.action(), controller.getSimpleName() + "." + methodName + " wrong action"); + } + + @Test + void dumpController() throws Exception { + Class c = DumpController.class; + // dumpTable(DumpTable table) + assertAuditEvent(c, "dumpTable", new Class[] {DumpTable.class}, "DATA_ACCESS", "dump.table"); + // getLastUpdated() + assertAuditEvent(c, "getLastUpdated", new Class[] {}, "OTHER", "dump.last_updated"); + // getDBVersion() + assertAuditEvent(c, "getDBVersion", new Class[] {}, "OTHER", "dump.db_version"); + } +} diff --git a/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/local/DumpControllerTest.java b/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/local/DumpControllerTest.java new file mode 100644 index 000000000..ae10d05f3 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/local/DumpControllerTest.java @@ -0,0 +1,53 @@ +package edu.harvard.dbmi.avillach.dump.local; + +import edu.harvard.dbmi.avillach.dump.entities.DumpRow; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.mockito.Mockito; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.bean.override.mockito.MockitoBean; +import org.springframework.http.ResponseEntity; + +import java.time.LocalDateTime; +import java.util.List; + +@SpringBootTest +class DumpControllerTest { + + @Autowired + DumpController subject; + + @MockitoBean + DumpService service; + + @Test + void shouldGetDump() { + Mockito.when(service.dumpTable(DumpTable.ConceptNode)).thenReturn(List.of()); + + ResponseEntity> actual = subject.dumpTable(DumpTable.ConceptNode); + + Assertions.assertTrue(actual.getStatusCode().is2xxSuccessful()); + Assertions.assertEquals(List.of(), actual.getBody()); + } + + @Test + void shouldGetLastUpdatedAsISOTimestamp() { + LocalDateTime time = LocalDateTime.of(2020, 1, 1, 0, 0, 0, 0); + Mockito.when(service.getLastUpdate()).thenReturn(time); + + ResponseEntity actual = subject.getLastUpdated(); + + Assertions.assertEquals(200, actual.getStatusCode().value()); + Assertions.assertEquals("2020-01-01T00:00:00.000", actual.getBody()); + } + + @Test + void shouldGetDatabaseVersion() { + Mockito.when(service.getDatabaseVersion()).thenReturn(3); + ResponseEntity actual = subject.getDBVersion(); + + Assertions.assertEquals(200, actual.getStatusCode().value()); + Assertions.assertEquals(3, actual.getBody()); + } +} diff --git a/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/local/DumpRepositoryTest.java b/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/local/DumpRepositoryTest.java new file mode 100644 index 000000000..6c0620564 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/local/DumpRepositoryTest.java @@ -0,0 +1,106 @@ +package edu.harvard.dbmi.avillach.dump.local; + +import edu.harvard.dbmi.avillach.dump.entities.ConceptNodeDump; +import edu.harvard.dbmi.avillach.dump.entities.DumpRow; +import edu.harvard.dbmi.avillach.dump.entities.FacetCategoryDump; +import edu.harvard.dbmi.avillach.dump.entities.FacetDump; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.testcontainers.containers.PostgreSQLContainer; +import org.testcontainers.junit.jupiter.Container; +import org.testcontainers.junit.jupiter.Testcontainers; +import org.testcontainers.utility.MountableFile; + +import java.time.LocalDateTime; +import java.util.List; + +@Testcontainers +@SpringBootTest +class DumpRepositoryTest { + + @Autowired + DumpRepository subject; + + @Container + static final PostgreSQLContainer databaseContainer = new PostgreSQLContainer<>("postgres:16").withReuse(true) + .withCopyFileToContainer(MountableFile.forClasspathResource("seed.sql"), "/docker-entrypoint-initdb.d/seed.sql"); + + @DynamicPropertySource + static void mySQLProperties(DynamicPropertyRegistry registry) { + registry.add("spring.datasource.url", databaseContainer::getJdbcUrl); + registry.add("spring.datasource.username", databaseContainer::getUsername); + registry.add("spring.datasource.password", databaseContainer::getPassword); + registry.add("spring.datasource.db", databaseContainer::getDatabaseName); + } + + @Test + void shouldDumpFacets() { + List concepts = subject.getAllConcepts(); + // very lazy test. The logic for recursing through the dump would have been way too much for a test + Assertions.assertNotNull(concepts); + } + + @Test + void shouldGetLastUpdatedTime() { + LocalDateTime actual = subject.getLastUpdated(); + LocalDateTime expected = LocalDateTime.of(2020, 2, 2, 0, 0, 0); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldGetAllConceptNodeMetas() { + List actual = subject.getAllConceptNodeMetas(); + + Assertions.assertEquals(117, actual.size()); + } + + @Test + void shouldGetAllFacets() { + List actual = (List) subject.getAllFacets(); + long actualChildCount = actual.stream().map(FacetDump::children).flatMap(List::stream).count(); + Assertions.assertEquals(16, actual.size()); + Assertions.assertEquals(2, actualChildCount); + } + + @Test + void shouldGetAllFacetMetas() { + List actual = subject.getAllFacetMetas(); + Assertions.assertEquals(3, actual.size()); + } + + @Test + void shouldGetAllFacetCategories() { + List actual = subject.getAllFacetCategories(); + + List expected = List.of( + new FacetCategoryDump("study_ids_dataset_ids", "Study IDs/Dataset IDs", ""), + new FacetCategoryDump("nsrr_harmonized", "Common Data Element Collection", ""), + new FacetCategoryDump("cde", "NSRR Harmonized", "") + ); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldGetAllFacetCategoryMetas() { + List actual = subject.getAllFacetCategoryMetas(); + Assertions.assertEquals(1, actual.size()); + } + + @Test + void shouldGetAllFacetConceptPairs() { + List actual = subject.getAllFacetConceptPairs(); + Assertions.assertEquals(94, actual.size()); + } + + @Test + void shouldGetDatabaseVersion() { + Integer actual = subject.getDatabaseVersion(); + Assertions.assertEquals(3, actual); + } +} diff --git a/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/local/DumpServiceTest.java b/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/local/DumpServiceTest.java new file mode 100644 index 000000000..a96b5b2e8 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/local/DumpServiceTest.java @@ -0,0 +1,52 @@ +package edu.harvard.dbmi.avillach.dump.local; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.mockito.Mockito; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.bean.override.mockito.MockitoBean; + +import java.time.LocalDateTime; + +@SpringBootTest +class DumpServiceTest { + + @Autowired + DumpService subject; + + @MockitoBean + DumpRepository repository; + + @Test + void shouldCallAllMethods() { + subject.dumpTable(DumpTable.ConceptNode); + Mockito.verify(repository, Mockito.times(1)).getAllConcepts(); + subject.dumpTable(DumpTable.FacetCategory); + Mockito.verify(repository, Mockito.times(1)).getAllFacetCategories(); + subject.dumpTable(DumpTable.Facet); + Mockito.verify(repository, Mockito.times(1)).getAllFacets(); + subject.dumpTable(DumpTable.FacetConceptNode); + Mockito.verify(repository, Mockito.times(1)).getAllFacetConceptPairs(); + subject.dumpTable(DumpTable.ConceptNodeMeta); + Mockito.verify(repository, Mockito.times(1)).getAllConceptNodeMetas(); + subject.dumpTable(DumpTable.FacetCategoryMeta); + Mockito.verify(repository, Mockito.times(1)).getAllFacetCategoryMetas(); + subject.dumpTable(DumpTable.FacetMeta); + Mockito.verify(repository, Mockito.times(1)).getAllFacetMetas(); + } + + @Test + void shouldGetLastUpdate() { + Mockito.when(repository.getLastUpdated()).thenReturn(LocalDateTime.MIN); + LocalDateTime actual = subject.getLastUpdate(); + Assertions.assertEquals(LocalDateTime.MIN, actual); + } + + @Test + void shouldGetDatabaseVersion() { + Mockito.when(repository.getDatabaseVersion()).thenReturn(3); + Integer actual = subject.getDatabaseVersion(); + Assertions.assertEquals(3, actual); + } +} diff --git a/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/remote/DataRefreshServiceTest.java b/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/remote/DataRefreshServiceTest.java new file mode 100644 index 000000000..e324d8b99 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/remote/DataRefreshServiceTest.java @@ -0,0 +1,62 @@ +package edu.harvard.dbmi.avillach.dump.remote; + +import edu.harvard.dbmi.avillach.dump.remote.api.RemoteDictionaryAPI; +import org.junit.jupiter.api.Test; +import org.mockito.Mockito; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.bean.override.mockito.MockitoBean; + +import java.util.List; +import java.util.Optional; + +@SpringBootTest +class DataRefreshServiceTest { + + @MockitoBean + RemoteDictionaryRepository repository; + + @MockitoBean + RemoteDictionaryAPI api; + + @Autowired + DataRefreshService subject; + + RemoteDictionary bch = new RemoteDictionary("bch", "Boston Children's"); + + @Test + void shouldNotRefreshIfConceptsFails() { + Mockito.when(api.fetchConcepts("bch")).thenReturn(Optional.empty()); + + subject.refreshDictionary(bch); + + Mockito.verify(repository, Mockito.times(2)).dropValuesForSite("bch"); + Mockito.verify(repository, Mockito.times(2)).pruneHangingEntries(); + Mockito.verifyNoMoreInteractions(repository); + } + + @Test + void shouldRefreshIfAllFetchesWork() { + Mockito.when(api.fetchConcepts("bch")).thenReturn(Optional.of(List.of())); + Mockito.when(api.fetchFacetCategories("bch")).thenReturn(Optional.of(List.of())); + Mockito.when(api.fetchFacets("bch")).thenReturn(Optional.of(List.of())); + Mockito.when(api.fetchFacetConceptPairs("bch")).thenReturn(Optional.of(List.of())); + Mockito.when(api.fetchConceptMetas("bch")).thenReturn(Optional.of(List.of())); + Mockito.when(api.fetchFacetMetas("bch")).thenReturn(Optional.of(List.of())); + Mockito.when(api.fetchFacetCategoryMetas("bch")).thenReturn(Optional.of(List.of())); + Mockito.when(api.fetchFacetMetas("bch")).thenReturn(Optional.of(List.of())); + + subject.refreshDictionary(bch); + + Mockito.verify(repository, Mockito.times(1)).dropValuesForSite("bch"); + Mockito.verify(repository, Mockito.times(1)).pruneHangingEntries(); + Mockito.verify(repository, Mockito.times(1)).addConceptsForSite("bch", List.of()); + Mockito.verify(repository, Mockito.times(1)).addFacetCategoriesForSite("bch", List.of()); + Mockito.verify(repository, Mockito.times(1)).addFacetsForSite("bch", List.of()); + Mockito.verify(repository, Mockito.times(1)).addConceptMetasForSite("bch", List.of()); + Mockito.verify(repository, Mockito.times(1)).addFacetConceptPairsForSite("bch", List.of()); + Mockito.verify(repository, Mockito.times(1)).addFacetMetasForSite("bch", List.of()); + Mockito.verify(repository, Mockito.times(1)).addFacetCategoryMetasForSite("bch", List.of()); + Mockito.verify(repository, Mockito.times(1)).addFacetMetasForSite("bch", List.of()); + } +} diff --git a/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDictionaryRepositoryInsertTest.java b/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDictionaryRepositoryInsertTest.java new file mode 100644 index 000000000..731e6f0cb --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDictionaryRepositoryInsertTest.java @@ -0,0 +1,152 @@ +package edu.harvard.dbmi.avillach.dump.remote; + +import edu.harvard.dbmi.avillach.dump.entities.*; +import org.junit.jupiter.api.*; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.jdbc.core.JdbcTemplate; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.testcontainers.containers.PostgreSQLContainer; +import org.testcontainers.junit.jupiter.Container; +import org.testcontainers.junit.jupiter.Testcontainers; +import org.testcontainers.utility.MountableFile; + +import java.time.LocalDateTime; +import java.time.Month; +import java.util.List; + + +@Testcontainers +@SpringBootTest +class RemoteDictionaryRepositoryInsertTest { + + @Autowired + JdbcTemplate template; + + @Container + static final PostgreSQLContainer databaseContainer = new PostgreSQLContainer<>("postgres:16").withReuse(true) + .withCopyFileToContainer(MountableFile.forClasspathResource("seed.sql"), "/docker-entrypoint-initdb.d/seed.sql"); + + @DynamicPropertySource + static void mySQLProperties(DynamicPropertyRegistry registry) { + registry.add("spring.datasource.url", databaseContainer::getJdbcUrl); + registry.add("spring.datasource.username", databaseContainer::getUsername); + registry.add("spring.datasource.password", databaseContainer::getPassword); + registry.add("spring.datasource.db", databaseContainer::getDatabaseName); + } + + @Autowired + RemoteDictionaryRepository subject; + + @Test + void shouldAddConceptHierarchy() { + fixWeirdSeedBug(); + ConceptNodeDump top = new ConceptNodeDump("GIC-2", "GIC", "GIC", "internal", "\\GIC", null, null); + ConceptNodeDump middle = new ConceptNodeDump("GIC-2", "concepts", "concepts", "internal", "\\GIC\\concepts", null, null); + ConceptNodeDump middleB = new ConceptNodeDump("GIC-2", "seq", "seq", "internal", "\\GIC\\seq", null, null); + ConceptNodeDump leafA1 = new ConceptNodeDump("GIC-2", "1", "1", "categorical", "\\GIC\\concepts\\1", null, null); + ConceptNodeDump leafA2 = new ConceptNodeDump("GIC-2", "2", "2", "categorical", "\\GIC\\concepts\\2", null, null); + ConceptNodeDump leafB1 = new ConceptNodeDump("GIC-2", "1", "1", "categorical", "\\GIC\\seq\\1", null, null); + ConceptNodeDump leafB2 = new ConceptNodeDump("GIC-2", "2", "2", "categorical", "\\GIC\\seq\\2", null, null); + top.addChild(middle); + top.addChild(middleB); + middle.addChild(leafA1); + middle.addChild(leafA2); + middleB.addChild(leafB1); + middleB.addChild(leafB2); + + String countQ = """ + SELECT count(*) + FROM concept_node + JOIN dataset ON concept_node.DATASET_ID = dataset.DATASET_ID + WHERE dataset.REF = 'GIC-2' + """; + Integer gicConcepts = template.queryForObject(countQ, Integer.class); + Assertions.assertEquals(0, gicConcepts); + + subject.addConceptsForSite("bch", List.of(top)); + + gicConcepts = template.queryForObject(countQ, Integer.class); + Assertions.assertEquals(7, gicConcepts); + } + + @Test + void shouldAddFacets() { + FacetDump child = new FacetDump("foo", "Foo", "fooer", "study_ids_dataset_ids", 1, null); + FacetDump parent = new FacetDump("fooz", "Fooz", "fooerz", "study_ids_dataset_ids", List.of(child), 1, null); + + Integer before = template.queryForObject("SELECT count(*) FROM facet", Integer.class); + subject.addFacetsForSite("bch", List.of(parent, parent)); + Integer after = template.queryForObject("SELECT count(*) FROM facet", Integer.class); + Assertions.assertEquals(before + 2, after); + } + + @Test + void shouldAddFacetCategory() { + FacetCategoryDump cat = new FacetCategoryDump("name", "display", "description"); + + Integer before = template.queryForObject("SELECT count(*) FROM facet_category", Integer.class); + subject.addFacetCategoriesForSite("bch", List.of(cat, cat)); + Integer after = template.queryForObject("SELECT count(*) FROM facet_category", Integer.class); + Assertions.assertEquals(before + 1, after); + } + + @Test + void shouldAddFacetCategoryMeta() { + FacetCategoryMetaDump meta = new FacetCategoryMetaDump("study_ids_dataset_ids", "key", "value"); + + Integer before = template.queryForObject("SELECT count(*) FROM facet_category_meta", Integer.class); + subject.addFacetCategoryMetasForSite("bch", List.of(meta, meta)); + Integer after = template.queryForObject("SELECT count(*) FROM facet_category_meta", Integer.class); + Assertions.assertEquals(before + 1, after); + } + + @Test + void shouldAddFacetMeta() { + FacetMetaDump meta = new FacetMetaDump("phs002715", "study_ids_dataset_ids", "key", "value"); + + Integer before = template.queryForObject("SELECT count(*) FROM facet_meta", Integer.class); + subject.addFacetMetasForSite("bch", List.of(meta, meta)); + Integer after = template.queryForObject("SELECT count(*) FROM facet_meta", Integer.class); + Assertions.assertEquals(before + 1, after); + } + + @Test + void shouldPair() { + FacetConceptPair pair = new FacetConceptPair("phs002715", "study_ids_dataset_ids", "\\Consent Type\\GIC Consent\\"); + + Integer before = template.queryForObject("SELECT count(*) FROM facet__concept_node", Integer.class); + subject.addFacetConceptPairsForSite("bch", List.of(pair, pair)); + Integer after = template.queryForObject("SELECT count(*) FROM facet__concept_node", Integer.class); + Assertions.assertEquals(before + 1, after); + } + + @Test + void shouldAddConceptMetas() { + fixWeirdSeedBug(); + ConceptNodeMetaDump pair = new ConceptNodeMetaDump("\\Consent Type\\GIC Consent\\", "key123123", "value"); + + Integer before = template.queryForObject("SELECT count(*) FROM concept_node_meta", Integer.class); + subject.addConceptMetasForSite("bch", List.of(pair, pair)); + Integer after = template.queryForObject("SELECT count(*) FROM concept_node_meta", Integer.class); + Assertions.assertEquals(before + 1, after); + } + + private void fixWeirdSeedBug() { + List queries = List.of( + "INSERT INTO dataset (REF, FULL_NAME, ABBREVIATION) VALUES ('test', 'test', 'test')", + "INSERT INTO concept_node (DATASET_ID, NAME, DISPLAY, CONCEPT_TYPE, CONCEPT_PATH) VALUES (23, 'test', 'test', 'continuous', '\\a')", + "INSERT INTO concept_node (DATASET_ID, NAME, DISPLAY, CONCEPT_TYPE, CONCEPT_PATH) VALUES (23, 'test', 'test', 'continuous', '\\a')", + "INSERT INTO concept_node_meta (CONCEPT_NODE_ID, KEY, VALUE) VALUES (216, 'K', 'V')", + "INSERT INTO concept_node_meta (CONCEPT_NODE_ID, KEY, VALUE) VALUES (216, 'K', 'V')" + ); + + for (String query : queries) { + try { + template.update(query); + } catch (Exception ignored) { + } + } + } +} diff --git a/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDictionaryRepositoryTest.java b/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDictionaryRepositoryTest.java new file mode 100644 index 000000000..6214e7549 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDictionaryRepositoryTest.java @@ -0,0 +1,197 @@ +package edu.harvard.dbmi.avillach.dump.remote; + +import edu.harvard.dbmi.avillach.dump.entities.ConceptNodeDump; +import org.junit.jupiter.api.*; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.jdbc.core.JdbcTemplate; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.testcontainers.containers.PostgreSQLContainer; +import org.testcontainers.junit.jupiter.Container; +import org.testcontainers.junit.jupiter.Testcontainers; +import org.testcontainers.utility.MountableFile; + +import java.time.LocalDateTime; +import java.time.Month; +import java.util.List; + + +@Testcontainers +@SpringBootTest +class RemoteDictionaryRepositoryTest { + + @Autowired + JdbcTemplate template; + + @Container + static final PostgreSQLContainer databaseContainer = new PostgreSQLContainer<>("postgres:16").withReuse(true) + .withCopyFileToContainer(MountableFile.forClasspathResource("seed.sql"), "/docker-entrypoint-initdb.d/seed.sql"); + + @DynamicPropertySource + static void mySQLProperties(DynamicPropertyRegistry registry) { + registry.add("spring.datasource.url", databaseContainer::getJdbcUrl); + registry.add("spring.datasource.username", databaseContainer::getUsername); + registry.add("spring.datasource.password", databaseContainer::getPassword); + registry.add("spring.datasource.db", databaseContainer::getDatabaseName); + } + + @Autowired + RemoteDictionaryRepository subject; + + @Test + void shouldDropValuesForSite() { + String sql = """ + SELECT count(*) + FROM concept_node__remote_dictionary + WHERE REMOTE_DICTIONARY_ID = ( + SELECT REMOTE_DICTIONARY_ID + FROM remote_dictionary + WHERE NAME = 'bch' + ) + """; + Integer count = template.queryForObject(sql, Integer.class); + Integer siteCount = template.queryForObject("SELECT count(*) FROM remote_dictionary WHERE NAME = 'bch'", Integer.class); + Assertions.assertEquals(7, count); + Assertions.assertEquals(1, siteCount); + + subject.dropValuesForSite("bch"); + + count = template.queryForObject(sql, Integer.class); + Assertions.assertEquals(0, count); + } + + @Test + void shouldGetTimestampForSite() { + LocalDateTime actual = subject.getUpdateTimestamp("foo"); + LocalDateTime expected = LocalDateTime.of(1800, Month.JANUARY, 1, 0, 0); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldGetDefaultTimestampForSiteThatDNE() { + LocalDateTime actual = subject.getUpdateTimestamp("brap"); + LocalDateTime expected = LocalDateTime.MIN; + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldUpdateTimestampForSite() { + LocalDateTime actual = subject.getUpdateTimestamp("bar"); + LocalDateTime expected = LocalDateTime.of(2000, Month.JANUARY, 1, 0, 0); + Assertions.assertEquals(expected, actual); + + subject.setUpdateTimestamp("bar", LocalDateTime.of(2025, Month.JANUARY, 1, 0, 0)); + + expected = LocalDateTime.of(2025, Month.JANUARY, 1, 0, 0); + actual = subject.getUpdateTimestamp("bar"); + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldPruneHangingEntries() { + String orphanSQL = """ + SELECT count(*) + FROM facet__concept_node + WHERE NOT EXISTS ( + SELECT 1 + FROM concept_node__remote_dictionary + WHERE facet__concept_node.concept_node_id = concept_node__remote_dictionary.concept_node_id + ) + UNION ALL + SELECT count(*) + FROM concept_node_meta + WHERE NOT EXISTS ( + SELECT 1 + FROM concept_node__remote_dictionary + WHERE concept_node_meta.concept_node_id = concept_node__remote_dictionary.concept_node_id + ) + UNION ALL + SELECT count(*) + FROM facet_meta + WHERE NOT EXISTS ( + SELECT 1 + FROM facet__concept_node + WHERE facet__concept_node.facet_id = facet_meta.facet_id + ) + UNION ALL + SELECT count(*) + FROM facet + WHERE NOT EXISTS ( + SELECT 1 + FROM facet__concept_node + WHERE facet__concept_node.facet_id = facet.facet_id + ) + UNION ALL + SELECT count(*) + FROM concept_node + WHERE + NOT EXISTS ( + SELECT 1 + FROM concept_node child + WHERE child.parent_id = concept_node.concept_node_id + ) + AND + NOT EXISTS ( + SELECT 1 + FROM concept_node__remote_dictionary + WHERE concept_node.concept_node_id = concept_node__remote_dictionary.concept_node_id + ) + UNION ALL + SELECT count(*) + FROM facet_category + WHERE NOT EXISTS ( + SELECT 1 + FROM facet + WHERE facet.facet_category_id = facet_category.facet_category_id + ) + UNION ALL + SELECT count(*) + FROM facet_category_meta + WHERE NOT EXISTS ( + SELECT 1 + FROM facet + WHERE facet.facet_category_id = facet_category_meta.facet_category_id + ) + """; + String allSQL = """ + SELECT count(*) + FROM facet__concept_node + UNION ALL + SELECT count(*) + FROM concept_node_meta + UNION ALL + SELECT count(*) + FROM facet_meta + UNION ALL + SELECT count(*) + FROM facet + UNION ALL + SELECT count(*) + FROM concept_node + UNION ALL + SELECT count(*) + FROM facet_category + UNION ALL + SELECT count(*) + FROM facet_category_meta + """; + List beforeActual = template.queryForList(orphanSQL, Integer.class); + List beforeAllActual = template.queryForList(allSQL, Integer.class); + List beforeExpected = List.of(2, 2, 0, 6, 1, 1, 0); + List beforeAllExpected = List.of(94, 117, 3, 18, 92, 3, 1); + Assertions.assertEquals(beforeExpected, beforeActual); + Assertions.assertEquals(beforeAllExpected, beforeAllActual); + + subject.pruneHangingEntries(); + + List afterActual = template.queryForList(orphanSQL, Integer.class); + List afterAllActual = template.queryForList(allSQL, Integer.class); + List afterExpected = List.of(0, 0, 0, 0, 0, 0, 0); + List afterAllExpected = List.of(92, 115, 3, 12, 91, 2, 1); + Assertions.assertEquals(afterExpected, afterActual); + Assertions.assertEquals(afterAllExpected, afterAllActual); + } +} diff --git a/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDumpSchedulingServiceTest.java b/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDumpSchedulingServiceTest.java new file mode 100644 index 000000000..10e962a2b --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/remote/RemoteDumpSchedulingServiceTest.java @@ -0,0 +1,79 @@ +package edu.harvard.dbmi.avillach.dump.remote; + +import edu.harvard.dbmi.avillach.dump.local.DumpRepository; +import edu.harvard.dbmi.avillach.dump.remote.api.RemoteDictionaryAPI; +import org.junit.jupiter.api.Test; +import org.mockito.Mockito; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.bean.override.mockito.MockitoBean; +import org.springframework.test.context.ActiveProfiles; + +import java.time.LocalDateTime; +import java.util.Optional; + +@SpringBootTest +@ActiveProfiles("aggregate") +class RemoteDumpSchedulingServiceTest { + + @MockitoBean + RemoteDictionaryRepository repository; + + @MockitoBean + RemoteDictionaryAPI api; + + @MockitoBean + DataRefreshService dataRefreshService; + + @MockitoBean + DumpRepository dumpRepository; + + @Autowired + RemoteDumpSchedulingService subject; + + @Test + void shouldUpdateNewDictionary() { + Mockito.when(api.fetchUpdateTimestamp("bch")).thenReturn(Optional.of(LocalDateTime.now())); + Mockito.when(api.fetchUpdateTimestamp("foo")).thenReturn(Optional.of(LocalDateTime.now())); + Mockito.when(repository.getUpdateTimestamp("bch")).thenReturn(LocalDateTime.MIN); + Mockito.when(repository.getUpdateTimestamp("foo")).thenReturn(LocalDateTime.MIN); + Mockito.when(api.fetchDatabaseVersion("bch")).thenReturn(Optional.of(3)); + Mockito.when(api.fetchDatabaseVersion("foo")).thenReturn(Optional.of(3)); + Mockito.when(dumpRepository.getDatabaseVersion()).thenReturn(3); + + subject.pollForUpdates(); + + Mockito.verify(dataRefreshService, Mockito.times(1)).refreshDictionary(new RemoteDictionary("bch", "Boston Children's")); + Mockito.verify(dataRefreshService, Mockito.times(1)).refreshDictionary(new RemoteDictionary("foo", "Foo Made Up Hospital")); + } + + @Test + void shouldNotUpdateCurrentDictionary() { + Mockito.when(api.fetchUpdateTimestamp("bch")).thenReturn(Optional.of(LocalDateTime.MIN)); + Mockito.when(api.fetchUpdateTimestamp("foo")).thenReturn(Optional.of(LocalDateTime.MIN)); + Mockito.when(repository.getUpdateTimestamp("bch")).thenReturn(LocalDateTime.MIN); + Mockito.when(repository.getUpdateTimestamp("foo")).thenReturn(LocalDateTime.MIN); + Mockito.when(api.fetchDatabaseVersion("bch")).thenReturn(Optional.of(3)); + Mockito.when(api.fetchDatabaseVersion("foo")).thenReturn(Optional.of(3)); + Mockito.when(dumpRepository.getDatabaseVersion()).thenReturn(3); + + subject.pollForUpdates(); + + Mockito.verifyNoInteractions(dataRefreshService); + } + + @Test + void shouldNotUpdateDictionaryWhenVersionsNotMatched() { + Mockito.when(api.fetchUpdateTimestamp("bch")).thenReturn(Optional.of(LocalDateTime.now())); + Mockito.when(api.fetchUpdateTimestamp("foo")).thenReturn(Optional.of(LocalDateTime.now())); + Mockito.when(repository.getUpdateTimestamp("bch")).thenReturn(LocalDateTime.MIN); + Mockito.when(repository.getUpdateTimestamp("foo")).thenReturn(LocalDateTime.MIN); + Mockito.when(api.fetchDatabaseVersion("bch")).thenReturn(Optional.of(3)); + Mockito.when(api.fetchDatabaseVersion("foo")).thenReturn(Optional.of(3)); + Mockito.when(dumpRepository.getDatabaseVersion()).thenReturn(4); + + subject.pollForUpdates(); + + Mockito.verifyNoInteractions(dataRefreshService); + } +} diff --git a/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/remote/api/RemoteDictionaryAPITest.java b/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/remote/api/RemoteDictionaryAPITest.java new file mode 100644 index 000000000..51b162a2c --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/test/java/edu/harvard/dbmi/avillach/dump/remote/api/RemoteDictionaryAPITest.java @@ -0,0 +1,146 @@ +package edu.harvard.dbmi.avillach.dump.remote.api; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.dbmi.avillach.dump.entities.*; +import edu.harvard.dbmi.avillach.dump.util.JacksonConfig; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.springframework.http.MediaType; +import org.springframework.test.web.client.MockRestServiceServer; +import org.springframework.web.client.RestClient; + +import java.time.LocalDateTime; +import java.time.format.DateTimeFormatter; +import java.util.List; +import java.util.Optional; + +import static org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo; +import static org.springframework.test.web.client.response.MockRestResponseCreators.withSuccess; + +class RemoteDictionaryAPITest { + + private static final String ROOT = "http://passthru:80/dictionary-dump/"; + private final DateTimeFormatter dateTimeFormatter = DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss.SSS"); + private final ObjectMapper mapper = new JacksonConfig().objectMapper(); + + private MockRestServiceServer server; + private RemoteDictionaryAPI subject; + + @BeforeEach + void setUp() { + RestClient.Builder builder = RestClient.builder(); + server = MockRestServiceServer.bindTo(builder).build(); + subject = new RemoteDictionaryAPI(builder.build(), mapper); + } + + @Test + void shouldFetchTimestamp() { + LocalDateTime now = LocalDateTime.parse(LocalDateTime.now().format(dateTimeFormatter), dateTimeFormatter); + server.expect(requestTo(ROOT + "bch/last-updated")).andRespond(withSuccess(now.format(dateTimeFormatter), MediaType.TEXT_PLAIN)); + + Optional actual = subject.fetchUpdateTimestamp("bch"); + Optional expected = Optional.of(now); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldFetchDatabaseVersion() { + Integer version = 3; + server.expect(requestTo(ROOT + "bch/database-version")).andRespond(withSuccess(version.toString(), MediaType.TEXT_PLAIN)); + + Optional actual = subject.fetchDatabaseVersion("bch"); + Optional expected = Optional.of(version); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldFetchConceptNodes() { + List concepts = List.of(new ConceptNodeDump("a", "b", "c", "d", "e", 1, 2)); + server.expect(requestTo(ROOT + "bch/dump/ConceptNode")).andRespond(json(concepts)); + + Optional> actual = subject.fetchConcepts("bch"); + + Assertions.assertTrue(actual.isPresent()); + Assertions.assertEquals(concepts, actual.get()); + } + + @Test + void shouldFetchFacetCategories() { + List facetCats = List.of(new FacetCategoryDump("foo", "bar", "desc")); + server.expect(requestTo(ROOT + "bch/dump/FacetCategory")).andRespond(json(facetCats)); + + Optional> actual = subject.fetchFacetCategories("bch"); + + Assertions.assertTrue(actual.isPresent()); + Assertions.assertEquals(facetCats, actual.get()); + } + + @Test + void shouldFetchFacets() { + FacetDump child = new FacetDump("1", "1", "1", "1", List.of(), 2, 1); + List facets = List.of(new FacetDump("foo", "bar", "baz", "qux", List.of(child), 1, null)); + server.expect(requestTo(ROOT + "bch/dump/Facet")).andRespond(json(facets)); + + Optional> actual = subject.fetchFacets("bch"); + + Assertions.assertTrue(actual.isPresent()); + Assertions.assertEquals(facets, actual.get()); + } + + @Test + void shouldFetchPairs() { + List pairs = List.of(new FacetConceptPair("name", "cat", "path")); + server.expect(requestTo(ROOT + "bch/dump/FacetConceptNode")).andRespond(json(pairs)); + + Optional> actual = subject.fetchFacetConceptPairs("bch"); + + Assertions.assertTrue(actual.isPresent()); + Assertions.assertEquals(pairs, actual.get()); + } + + @Test + void shouldFetchConceptMetas() { + List metas = List.of(new ConceptNodeMetaDump("path", "k", "v")); + server.expect(requestTo(ROOT + "bch/dump/ConceptNodeMeta")).andRespond(json(metas)); + + Optional> actual = subject.fetchConceptMetas("bch"); + + Assertions.assertTrue(actual.isPresent()); + Assertions.assertEquals(metas, actual.get()); + } + + @Test + void shouldFetchFacetCategoryMetas() { + List metas = List.of(new FacetCategoryMetaDump("facet cat", "k", "v")); + server.expect(requestTo(ROOT + "bch/dump/FacetCategoryMeta")).andRespond(json(metas)); + + Optional> actual = subject.fetchFacetCategoryMetas("bch"); + + Assertions.assertTrue(actual.isPresent()); + Assertions.assertEquals(metas, actual.get()); + } + + @Test + void shouldFetchFacetMetas() { + List metas = List.of(new FacetMetaDump("facet", "cat", "k", "v")); + server.expect(requestTo(ROOT + "bch/dump/FacetMeta")).andRespond(json(metas)); + + Optional> actual = subject.fetchFacetMetas("bch"); + + Assertions.assertTrue(actual.isPresent()); + Assertions.assertEquals(metas, actual.get()); + } + + private org.springframework.test.web.client.ResponseCreator json(Object jsonBody) { + try { + return withSuccess(mapper.writeValueAsString(jsonBody), MediaType.APPLICATION_JSON); + } catch (JsonProcessingException e) { + Assertions.fail(e); + throw new IllegalStateException(e); + } + } +} diff --git a/services/picsure-dictionary/aggregate/src/test/resources/application.properties b/services/picsure-dictionary/aggregate/src/test/resources/application.properties new file mode 100644 index 000000000..fa66299dc --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/test/resources/application.properties @@ -0,0 +1,20 @@ +spring.profiles.active=test +spring.application.name=dictionary +spring.datasource.url=jdbc:postgresql://localhost:5432/search +spring.datasource.username=picsure +spring.datasource.password=foo +spring.datasource.driver-class-name=org.postgresql.Driver + +dashboard.columns={abbreviation:'Abbreviation',melast:'This one goes last',name:'Name',clinvars:'Clinical Variables',participants:'Participants'} +dashboard.column-order=abbreviation,name,clinvars +dashboard.nonmeta-columns=abbreviation,name +dashboard.enable.extra_details=true +dashboard.enable.bdc_hack=false +dashboard.layout.type=default + +filtering.unfilterable_concepts=stigmatized + +remote.dictionaries[0].name=bch +remote.dictionaries[0].full_name=Boston Children's +remote.dictionaries[1].name=foo +remote.dictionaries[1].full_name=Foo Made Up Hospital diff --git a/services/picsure-dictionary/aggregate/src/test/resources/seed.sql b/services/picsure-dictionary/aggregate/src/test/resources/seed.sql new file mode 100644 index 000000000..9ac86c1b6 --- /dev/null +++ b/services/picsure-dictionary/aggregate/src/test/resources/seed.sql @@ -0,0 +1,1134 @@ +-- +-- PostgreSQL database dump +-- + +-- Dumped from database version 16.3 +-- Dumped by pg_dump version 16.3 + +SET statement_timeout = 0; +SET lock_timeout = 0; +SET idle_in_transaction_session_timeout = 0; +SET client_encoding = 'UTF8'; +SET standard_conforming_strings = on; +SELECT pg_catalog.set_config('search_path', '', false); +SET check_function_bodies = false; +SET xmloption = content; +SET client_min_messages = warning; +SET row_security = off; + +-- +-- Name: dict; Type: SCHEMA; Schema: -; Owner: picsure +-- + +CREATE SCHEMA dict; + +-- +-- Name: pg_trgm; Type: EXTENSION; Schema: -; Owner: - +-- + +CREATE EXTENSION IF NOT EXISTS pg_trgm WITH SCHEMA public; + + +-- +-- Name: EXTENSION pg_trgm; Type: COMMENT; Schema: -; Owner: +-- + +COMMENT ON EXTENSION pg_trgm IS 'text similarity measurement and index searching based on trigrams'; + + +SET default_tablespace = ''; + +SET default_table_access_method = heap; + +-- +-- Name: concept_node; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.concept_node ( + concept_node_id integer NOT NULL, + dataset_id integer NOT NULL, + name character varying(512) NOT NULL, + display character varying(512) NOT NULL, + concept_type character varying(32) DEFAULT 'Interior'::character varying NOT NULL, + concept_path character varying(10000) DEFAULT 'INVALID'::character varying NOT NULL, + parent_id integer, + searchable_fields tsvector +); + +-- +-- Name: concept_node_concept_node_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.concept_node ALTER COLUMN concept_node_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.concept_node_concept_node_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +-- +-- Name: concept_node_meta; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.concept_node_meta ( + concept_node_meta_id integer NOT NULL, + concept_node_id integer NOT NULL, + key character varying(256) NOT NULL, + value text NOT NULL +); + +-- +-- Name: concept_node_meta_concept_node_meta_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.concept_node_meta ALTER COLUMN concept_node_meta_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.concept_node_meta_concept_node_meta_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +-- +-- Name: consent; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.consent ( + consent_id integer NOT NULL, + dataset_id integer NOT NULL, + consent_code character varying(512) NOT NULL, + description character varying(512) NOT NULL, + authz character varying(512) NOT NULL, + PARTICIPANT_COUNT INT NOT NULL DEFAULT 12, + VARIABLE_COUNT INT NOT NULL DEFAULT 99, + SAMPLE_COUNT INT NOT NULL DEFAULT 14 +); + +-- +-- Name: consent_consent_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.consent ALTER COLUMN consent_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.consent_consent_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +-- +-- Name: dataset; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.dataset ( + dataset_id integer NOT NULL, + ref character varying(512) NOT NULL, + full_name character varying(512) NOT NULL, + abbreviation character varying(512) NOT NULL, + description text DEFAULT ''::text +); + +-- +-- Name: dataset_dataset_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.dataset ALTER COLUMN dataset_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.dataset_dataset_id_seq + START WITH 30 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +-- +-- Name: dataset_meta; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.dataset_meta ( + dataset_meta_id integer NOT NULL, + dataset_id integer NOT NULL, + key character varying(256) NOT NULL, + value text NOT NULL +); + +-- +-- Name: dataset_meta_dataset_meta_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.dataset_meta ALTER COLUMN dataset_meta_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.dataset_meta_dataset_meta_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +-- +-- Name: facet; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.facet ( + facet_id integer NOT NULL, + facet_category_id integer NOT NULL, + name character varying(512) NOT NULL, + display character varying(512) NOT NULL, + description text DEFAULT ''::text, + parent_id integer +); + +-- +-- Name: facet__concept_node; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.facet__concept_node ( + facet__concept_node_id integer NOT NULL, + facet_id integer NOT NULL, + concept_node_id integer NOT NULL +); + +-- +-- Name: facet__concept_node_facet__concept_node_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.facet__concept_node ALTER COLUMN facet__concept_node_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.facet__concept_node_facet__concept_node_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +-- +-- Name: facet_category; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.facet_category ( + facet_category_id integer NOT NULL, + name character varying(512) NOT NULL, + display character varying(512) NOT NULL, + description text DEFAULT ''::text +); + +-- +-- Name: facet_category_facet_category_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.facet_category ALTER COLUMN facet_category_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.facet_category_facet_category_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +-- +-- Name: facet_category_meta; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.facet_category_meta ( + facet_category_meta_id integer NOT NULL, + facet_category_id integer NOT NULL, + key character varying(256) NOT NULL, + value text NOT NULL +); + +-- +-- Name: facet_category_meta_facet_category_meta_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.facet_category_meta ALTER COLUMN facet_category_meta_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.facet_category_meta_facet_category_meta_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +-- +-- Name: facet_facet_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.facet ALTER COLUMN facet_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.facet_facet_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +-- +-- Name: facet_meta; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.facet_meta ( + facet_meta_id integer NOT NULL, + facet_id integer NOT NULL, + key character varying(256) NOT NULL, + value text NOT NULL +); + +-- +-- Name: facet_meta_facet_meta_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.facet_meta ALTER COLUMN facet_meta_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.facet_meta_facet_meta_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +CREATE TABLE IF NOT EXISTS public.update_info ( + LAST_UPDATED TIMESTAMP NOT NULL DEFAULT '2000-01-01 00:00:00', + DATABASE_VERSION INT NOT NULL DEFAULT 3 +); + +CREATE TABLE IF NOT EXISTS public.remote_dictionary ( + REMOTE_DICTIONARY_ID SERIAL PRIMARY KEY, + NAME CHARACTER VARYING(512) NOT NULL, + UUID UUID NOT NULL, + LAST_UPDATED TIMESTAMP +); + + +-- +-- Data for Name: concept_node; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.concept_node (concept_node_id, dataset_id, name, display, concept_type, concept_path, parent_id, searchable_fields) FROM stdin; +209 14 categorical \\Bio Specimens\\ \N 'bio':1 'specimen':2 +180 14 categorical \\ACT Diagnosis ICD-10\\ \N '-10':4 'act':1 'diagnosi':2 'icd':3 +191 14 categorical \\ACT Lab Test Results\\ \N 'act':1 'lab':2 'result':4 'test':3 +197 14 categorical \\ACT Medications\\ \N 'act':1 'medic':2 +202 14 categorical \\ACT Procedures CPT\\ \N 'act':1 'cpt':3 'procedur':2 +215 14 categorical \\Consent Type\\ \N 'consent':1 'type':2 +219 15 categorical \\NHANES\\ \N 'nhane':1 +226 19 categorical \\phs000007\\ \N 'phs000007':1 +236 18 categorical \\phs000284\\ \N 'phs000284':1 +243 20 categorical \\phs002385\\ \N 'phs002385':1 +247 17 \\phs002715\\ \N 'phs002715':1 +250 23 categorical \\phs002808\\ \N 'phs002808':1 +259 21 categorical \\phs003463\\ \N 'phs003463':1 +262 24 categorical \\phs003566\\ \N 'phs003566':1 +265 14 categorical \\Variant Data Type\\ \N 'data':2 'type':3 'variant':1 +181 14 categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\ 180 '-10':4 'act':1 'diagnosi':2 'diseas':8 'icd':3 'j00':6,14 'j00-j99':5,13 'j99':7,15 'respiratori':11 'system':12 +182 14 categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\ 181 '-10':4 'act':1 'chronic':19 'diagnosi':2 'diseas':8,22 'icd':3 'j00':6,14 'j00-j99':5,13 'j40':17,24 'j40-j47':16,23 'j47':18,25 'j99':7,15 'lower':20 'respiratori':11,21 'system':12 +183 14 categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\ 182 '-10':4 'act':1 'asthma':27 'chronic':19 'diagnosi':2 'diseas':8,22 'icd':3 'j00':6,14 'j00-j99':5,13 'j40':17,24 'j40-j47':16,23 'j45':26 'j47':18,25 'j99':7,15 'lower':20 'respiratori':11,21 'system':12 +184 14 categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.5 Severe persistent asthma\\ 183 '-10':4 'act':1 'asthma':27,31 'chronic':19 'diagnosi':2 'diseas':8,22 'icd':3 'j00':6,14 'j00-j99':5,13 'j40':17,24 'j40-j47':16,23 'j45':26 'j45.5':28 'j47':18,25 'j99':7,15 'lower':20 'persist':30 'respiratori':11,21 'sever':29 'system':12 +223 15 categorical \\NHANES\\questionnaire\\ 219 'nhane':1 'questionnair':2 +263 24 Visit01 Visit01 categorical \\phs003566\\Visit01\\ 262 'phs003566':1 'visit01':2,3 +185 14 J45.51 Severe persistent asthma with (acute) exacerbation J45.51 Severe persistent asthma with (acute) exacerbation categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.5 Severe persistent asthma\\J45.51 Severe persistent asthma with (acute) exacerbation\\ 184 '-10':4 'act':1 'acut':37,44 'asthma':27,31,35,42 'chronic':19 'diagnosi':2 'diseas':8,22 'exacerb':38,45 'icd':3 'j00':6,14 'j00-j99':5,13 'j40':17,24 'j40-j47':16,23 'j45':26 'j45.5':28 'j45.51':32,39 'j47':18,25 'j99':7,15 'lower':20 'persist':30,34,41 'respiratori':11,21 'sever':29,33,40 'system':12 +186 14 J45.52 Severe persistent asthma with status asthmaticus J45.52 Severe persistent asthma with status asthmaticus categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.5 Severe persistent asthma\\J45.52 Severe persistent asthma with status asthmaticus\\ 184 '-10':4 'act':1 'allerg':50,57,72,81 'approxim':46 'asthma':27,31,35,42,51,58,64,70,79,89 'asthmaticus':38,45,54,61,67,76,85,92 'chronic':19 'diagnosi':2 'diseas':8,22 'icd':3 'j00':6,14 'j00-j99':5,13 'j40':17,24 'j40-j47':16,23 'j45':26 'j45.5':28 'j45.52':32,39,86 'j47':18,25 'j99':7,15 'lower':20 'persist':30,34,41,49,56,63,69,78,88 'respiratori':11,21 'rhiniti':73,82 'sever':29,33,40,48,55,62,68,77,87 'status':37,44,53,60,66,75,84,91 'synonym':47 'system':12 +187 14 categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.9 Other and unspecified asthma\\ 183 '-10':4 'act':1 'asthma':27,32 'chronic':19 'diagnosi':2 'diseas':8,22 'icd':3 'j00':6,14 'j00-j99':5,13 'j40':17,24 'j40-j47':16,23 'j45':26 'j45.9':28 'j47':18,25 'j99':7,15 'lower':20 'respiratori':11,21 'system':12 'unspecifi':31 +188 14 categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.9 Other and unspecified asthma\\J45.90 Unspecified asthma\\ 187 '-10':4 'act':1 'asthma':27,32,35 'chronic':19 'diagnosi':2 'diseas':8,22 'icd':3 'j00':6,14 'j00-j99':5,13 'j40':17,24 'j40-j47':16,23 'j45':26 'j45.9':28 'j45.90':33 'j47':18,25 'j99':7,15 'lower':20 'respiratori':11,21 'system':12 'unspecifi':31,34 +189 14 J45.901 Unspecified asthma with (acute) exacerbation J45.901 Unspecified asthma with (acute) exacerbation categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.9 Other and unspecified asthma\\J45.90 Unspecified asthma\\J45.901 Unspecified asthma with (acute) exacerbation\\ 188 '-10':4 'act':1 'acut':40,46,50,60,64,74,83 'allerg':55,57,71 'approxim':48 'asthma':27,32,35,38,44,53,58,62,69,78,81 'chronic':19 'diagnosi':2 'diseas':8,22 'exacerb':41,47,51,61,65,75,76,84 'flare':67 'flare-up':66 'icd':3 'j00':6,14 'j00-j99':5,13 'j40':17,24 'j40-j47':16,23 'j45':26 'j45.9':28 'j45.90':33 'j45.901':36,42,79 'j47':18,25 'j99':7,15 'lower':20 'respiratori':11,21 'rhiniti':56,72 'synonym':49 'system':12 'unspecifi':31,34,37,43,80 +231 19 categorical \\phs000007\\pht000022\\phv00004260\\ 230 'phs000007':1 'pht000022':2 'phv00004260':3 +232 19 phv00004260 FM219 Continuous \\phs000007\\pht000022\\phv00004260\\FM219\\ 231 '0':17 '1':18 '12':6 'caffein':10 'cola':11 'cup':8 'day':12 'fm219':4,5 'oz':7 'phs000007':1 'pht000022':2 'phv00004260':3 'yes':16 +190 14 J45.902 Unspecified asthma with status asthmaticus J45.902 Unspecified asthma with status asthmaticus categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.9 Other and unspecified asthma\\J45.90 Unspecified asthma\\J45.902 Unspecified asthma with status asthmaticus\\ 188 '-10':4 'act':1 'allerg':52,59,72 'approxim':48 'asthma':27,32,35,38,44,50,57,64,67,71,77,83 'asthmaticus':41,47,56,63,70,75,80,86 'chronic':19 'diagnosi':2 'diseas':8,22 'extrins':76 'icd':3 'j00':6,14 'j00-j99':5,13 'j40':17,24 'j40-j47':16,23 'j45':26 'j45.9':28 'j45.90':33 'j45.902':36,42,81 'j47':18,25 'j99':7,15 'lower':20 'respiratori':11,21 'rhiniti':53,60 'status':40,46,55,62,66,69,74,79,85 'synonym':49 'system':12 'unspecifi':31,34,37,43,82 +192 14 categorical \\ACT Lab Test Results\\Virus\\ 191 'act':1 'lab':2 'result':4 'test':3 'virus':5 +193 14 categorical \\ACT Lab Test Results\\Virus\\Hepatitis B virus\\ 192 'act':1 'b':7 'hepat':6 'lab':2 'result':4 'test':3 'virus':5,8 +194 14 categorical \\ACT Lab Test Results\\Virus\\Hepatitis B virus\\Hepatitis B virus core Ab\\ 193 'ab':13 'act':1 'b':7,10 'core':12 'hepat':6,9 'lab':2 'result':4 'test':3 'virus':5,8,11 +195 14 Hepatitis B virus core Ab Hepatitis B virus core Ab categorical \\ACT Lab Test Results\\Virus\\Hepatitis B virus\\Hepatitis B virus core Ab\\Hepatitis B virus core Ab [Presence] in Serum by Immunoassay\\ 194 'ab':13,18,28 'act':1 'b':7,10,15,25 'core':12,17,27 'hepat':6,9,14,24 'immunoassay':23 'lab':2 'presenc':19 'result':4 'serum':21 'test':3 'virus':5,8,11,16,26 +196 14 Hepatitis B virus core Ab Hepatitis B virus core Ab categorical \\ACT Lab Test Results\\Virus\\Hepatitis B virus\\Hepatitis B virus core Ab\\Hepatitis B virus core Ab [Presence] in Serum\\ 194 'ab':13,18,26 'act':1 'b':7,10,15,23 'core':12,17,25 'hepat':6,9,14,22 'lab':2 'presenc':19 'result':4 'serum':21 'test':3 'virus':5,8,11,16,24 +198 14 categorical \\ACT Medications\\C [Preparations]\\ 197 'act':1 'c':3 'medic':2 'prepar':4 +199 14 categorical \\ACT Medications\\C [Preparations]\\Cefpodoxime\\ 198 'act':1 'c':3 'cefpodoxim':5 'medic':2 'prepar':4 +200 14 categorical \\ACT Medications\\C [Preparations]\\Cefpodoxime\\Cefpodoxime Oral Tablet\\ 199 'act':1 'c':3 'cefpodoxim':5,6 'medic':2 'oral':7 'prepar':4 'tablet':8 +201 14 Cefpodoxime Oral Tablet Cefpodoxime Oral Tablet categorical \\ACT Medications\\C [Preparations]\\Cefpodoxime\\Cefpodoxime Oral Tablet\\Cefpodoxime 100 Mg Oral Tablet\\ 200 '100':10 'act':1 'c':3 'cefpodoxim':5,6,9,14 'medic':2 'mg':11 'oral':7,12,15 'prepar':4 'tablet':8,13,16 +203 14 categorical \\ACT Procedures CPT\\Medicine Services and Procedures\\ 202 'act':1 'cpt':3 'medicin':4 'procedur':2,7 'servic':5 +204 14 categorical \\ACT Procedures CPT\\Medicine Services and Procedures\\Neurology and Neuromuscular Procedures\\ 203 'act':1 'cpt':3 'medicin':4 'neurolog':8 'neuromuscular':10 'procedur':2,7,11 'servic':5 +241 18 phv00122507 age Continuous \\phs000284\\pht001902\\phv00122507\\age\\ 240 '0':11 '21':12 'age':4,5,6 'phs000284':1 'pht001902':2 'phv00122507':3 'yes':10 +205 14 categorical \\ACT Procedures CPT\\Medicine Services and Procedures\\Neurology and Neuromuscular Procedures\\Special Eeg Testing Procedures\\ 204 'act':1 'cpt':3 'eeg':13 'medicin':4 'neurolog':8 'neuromuscular':10 'procedur':2,7,11,15 'servic':5 'special':12 'test':14 +206 14 Special Eeg Testing Procedures Special Eeg Testing Procedures categorical \\ACT Procedures CPT\\Medicine Services and Procedures\\Neurology and Neuromuscular Procedures\\Special Eeg Testing Procedures\\Pharmacological or physical activation requiring physician or other qualified health care professional attendance during EEG recording of activation phase (eg, thiopental activation test)\\ 205 'act':1 'activ':19,33,37 'attend':28 'care':26 'cpt':3 'eeg':13,30,40 'eg':35 'health':25 'medicin':4 'neurolog':8 'neuromuscular':10 'pharmacolog':16 'phase':34 'physic':18 'physician':21 'procedur':2,7,11,15,42 'profession':27 'qualifi':24 'record':31 'requir':20 'servic':5 'special':12,39 'test':14,38,41 'thiopent':36 +207 14 Special Eeg Testing Procedures Special Eeg Testing Procedures categorical \\ACT Procedures CPT\\Medicine Services and Procedures\\Neurology and Neuromuscular Procedures\\Special Eeg Testing Procedures\\Wada activation test for hemispheric function, including electroencephalographic (EEG) monitoring\\ 205 'act':1 'activ':17 'cpt':3 'eeg':13,24,27 'electroencephalograph':23 'function':21 'hemispher':20 'includ':22 'medicin':4 'monitor':25 'neurolog':8 'neuromuscular':10 'procedur':2,7,11,15,29 'servic':5 'special':12,26 'test':14,18,28 'wada':16 +208 14 Medicine Services and Procedures Medicine Services and Procedures categorical \\ACT Procedures CPT\\Medicine Services and Procedures\\Non-Face-To-Face Nonphysician Services\\ 203 'act':1 'cpt':3 'face':10,12 'medicin':4,15 'non':9 'non-face-to-fac':8 'nonphysician':13 'procedur':2,7,18 'servic':5,14,16 +210 14 categorical \\Bio Specimens\\HumanFluid\\ 209 'bio':1 'humanfluid':3 'specimen':2 +211 14 SPECIMENS:HF.BLD.000 Quantity SPECIMENS:HF.BLD.000 Quantity Continuous \\Bio Specimens\\HumanFluid\\Blood (Whole)\\SPECIMENS:HF.BLD.000 Quantity\\ 210 '000':8,12 '100':18 '500':19 'bio':1 'biosampl':15,17 'blood':4 'gic':14 'hf.bld':7,11 'humanfluid':3 'quantiti':9,13 'specimen':2,6,10 'whole':5 'wholeblood':16 +212 14 HumanTissue HumanTissue categorical \\Bio Specimens\\HumanTissue\\ 212 'bio':1 'humantissu':3,4 'specimen':2 'true':5 +213 14 categorical \\Bio Specimens\\NucleicAcid\\ 209 'bio':1 'nucleicacid':3 'specimen':2 +214 14 DNA DNA categorical \\Bio Specimens\\NucleicAcid\\DNA\\ 213 'bio':1 'dna':4,5 'nucleicacid':3 'specimen':2 'true':6 +216 14 Consent Type Consent Type categorical \\Consent Type\\GIC Consent\\ 215 '2':15 'align':10 'consent':1,4,5,18 'gic':3,17 'irb':13 'patient':8 'phase':14 'protocol':16 'type':2,6 +217 14 Consent Type Consent Type categorical \\Consent Type\\GIC Legacy Consent\\ 215 '2':18 'align':13 'consent':1,5,6,22 'gic':3,20 'irb':16 'legaci':4,21 'patient':9 'phase':17 'protocol':19 'type':2,7 +218 14 Consent Type Consent Type categorical \\Consent Type\\Waiver of Consent\\ 215 'consent':1,5,6,12,15 'patient':8 'type':2,7 'waiv':11 'waiver':3,13 +220 15 categorical \\NHANES\\examination\\ 219 'examin':2 'nhane':1 +221 15 physical fitness physical fitness categorical \\NHANES\\examination\\physical fitness\\ 220 'examin':2 'fit':4,6 'nhane':1 'physic':3,5 +222 15 CVDS1HR Stage 1 heart rate (per min) Continuous \\NHANES\\examination\\physical fitness\\Stage 1 heart rate (per min) 221 '0':63 '1':6,12,50 '150':64 'autom':23 'automat':44 'blood':24 'captur':29,43 'comput':33 'direct':30 'end':47 'enter':55 'event':37 'examin':2 'fit':4 'heart':7,13,17,39,60 'manual':54 'min':10,16 'monitor':27,62 'nhane':1 'per':9,15 'physic':3 'pressure/heart':25 'rate':8,14,18,26,40,61 'read':57 'stage':5,11,49 'system':34 'taken':20 'technician':52 'would':53 +224 15 disease disease categorical \\NHANES\\questionnaire\\disease\\ 223 'diseas':3,4 'nhane':1 'questionnair':2 +225 15 MCQ300a Any family with heart attack or angina? categorical \\NHANES\\questionnaire\\disease\\Any family with heart attack or angina?\\ 224 '50':61 'age':59 'an-gi-na':53 'angina':10,17,52 'attack':8,15,50 'biolog':28 'blood':31 'brother':38 'close':27 'deceas':21 'diseas':3 'ever':39 'famili':5,12 'father':34 'gi':55 'health':43 'heart':7,14,49 'includ':18,33 'live':19 'mother':35 'na':56 'nhane':1 'profession':44 'questionnair':2 'relat':32 's/your':26 'sister':36 'sp':25 'told':40 'yes':62 +227 19 pht000021 ex0_19s categorical \\phs000007\\pht000021\\ 226 '19':10 '19s':4 'clinic':5 'cohort':8 'ex0':3 'exam':6,9 'origin':7 'phs000007':1 'pht000021':2 +228 19 categorical \\phs000007\\pht000021\\phv00003844\\ 227 'phs000007':1 'pht000021':2 'phv00003844':3 +229 19 phv00003844 FL200 Continuous \\phs000007\\pht000021\\phv00003844\\FL200\\ 228 '0':17 '12':6 '3':18 'caffein':10 'cola':11 'cup':8 'day':12 'fl200':4,5 'oz':7 'phs000007':1 'pht000021':2 'phv00003844':3 'yes':16 +230 19 pht000022 ex0_20s categorical \\phs000007\\pht000022\\ 226 '20':10 '20s':4 'clinic':5 'cohort':8 'ex0':3 'exam':6,9 'origin':7 'phs000007':1 'pht000022':2 +233 19 pht000033 ex1_4s categorical \\phs000007\\pht000033\\ 226 '4':10 '4s':4 'clinic':5 'cohort':8 'ex1':3 'exam':6,9 'offspr':7 'phs000007':1 'pht000033':2 +234 19 categorical \\phs000007\\pht000033\\phv00008849\\ 233 'phs000007':1 'pht000033':2 'phv00008849':3 +235 19 phv00008849 D080 Continuous \\phs000007\\pht000033\\phv00008849\\D080\\ 234 '0':16 '12':6 '5':17 'caffein':10 'cola/day':11 'cup':8 'd080':4,5 'oz':7 'phs000007':1 'pht000033':2 'phv00008849':3 'yes':15 +237 18 pht001902 CFS_CARe_Subject_Phenotypes categorical \\phs000284\\pht001902\\ 236 'adults/children':16 'care':4,7 'cfs':3,8 'cleveland':9 'famili':10 'health':14 'phenotyp':6,15 'phs000284':1 'pht001902':2 'sleep':12 'studi':11 'subject':5 +238 18 categorical \\phs000284\\pht001902\\phv00122360\\ 237 'phs000284':1 'pht001902':2 'phv00122360':3 +239 18 phv00122360 RECOCC categorical \\phs000284\\pht001902\\phv00122360\\RECOCC\\ 238 'account':10 'occup':8 'phs000284':1 'pht001902':2 'phv00122360':3 'recent':7 'recocc':4,5 +240 18 categorical \\phs000284\\pht001902\\phv00122507\\ 237 'phs000284':1 'pht001902':2 'phv00122507':3 +242 18 phv00122622 PERART Continuous \\phs000284\\pht001902\\phv00122622\\PERART\\ 242 '0':14 '30':15 'artifact':9 'perart':4,5 'phs000284':1 'pht001902':2 'phv00122622':3 'time':7 'yes':13 +244 20 AGE AGE continuous \\phs002385\\AGE\\ 243 '42':9 'age':2,3,5 'hct':16 'patient':4 'phs002385':1 'pre':15 'pre-hct':14 'transplant':7 'year':8 'yes':13,17 +245 20 RACEG RACEG categorical \\phs002385\\RACEG\\ 243 'phs002385':1 'race':4 'raceg':2,3 'regroup':5 'report':7 'yes':11 +246 20 TXNUM TXNUM continuous \\phs002385\\TXNUM\\ 243 '1':6 'hct':13 'number':5 'phs002385':1 'pre':12 'pre-hct':11 'transplant':4 'txnum':2,3 'yes':7,14 +248 17 AGE_CATEGORY age categorical \\phs002715\\age\\ 247 '21':8 'age':2,3,6 'categori':7 'particip':4 'phs002715':1 'yes':12 +249 17 nsrr_ever_smoker nsrr_ever_smoker categorical \\phs002715\\nsrr_ever_smoker\\ 247 'ever':3,6 'nsrr':2,5 'phs002715':1 'smoker':4,7,8 'status':9 'yes':10,14 +251 23 categorical \\phs002808\\1 Administrative Data Forms\\ 250 '1':2 'administr':3 'data':4 'form':5 'phs002808':1 +252 23 \\phs002808\\1 Administrative Data Forms\\AFC No Future Contact\\ 1 Administrative Data Forms / AFC No Future Contact categorical \\phs002808\\1 Administrative Data Forms\\AFC No Future Contact\\ 251 '1':2,10 'administr':3,11 'afc':6,14 'contact':9,17 'data':4,12 'form':5,13 'futur':8,16 'phs002808':1 +253 23 AFCA03A AFCA03A categorical \\phs002808\\1 Administrative Data Forms\\AFC No Future Contact\\AFCA03A\\ 252 '1':2 'administr':3 'afc':6,12 'afca03a':10,11 'consent':19 'contact':9,17,23 'data':4 'end':15 'form':5 'futur':8,16,21 'numom2b':22 'phs002808':1 'reason':13 'withdrew':18 'yes':27 +254 23 \\phs002808\\1 Administrative Data Forms\\H01 Heart Health Study Contact Information\\ 1 Administrative Data Forms / H01 Heart Health Study Contact Information categorical \\phs002808\\1 Administrative Data Forms\\H01 Heart Health Study Contact Information\\ 251 '1':2,12 'administr':3,13 'contact':10,20 'data':4,14 'form':5,15 'h01':6,16 'health':8,18 'heart':7,17 'inform':11,21 'phs002808':1 'studi':9,19 +255 23 V5AD09A5_SP V5AD09A5_SP categorical \\phs002808\\1 Administrative Data Forms\\H01 Heart Health Study Contact Information\\V5AD09A5_SP\\ 254 '1':2 'administr':3 'care':27 'contact':10 'data':4 'doctor':24 'field':39 'follow':20 'form':5 'h01':6 'health':8,26 'heart':7 'infect':40 'inform':11 'kidney':36 'phs002808':1 'problem':21 'profession':28 'sp':13,15 'specifi':38 'studi':9 'told':29 'v5a':16 'v5ad09a5':12,14 'yes':42 +256 23 categorical \\phs002808\\3a Visit Forms\\ 250 '3a':2 'form':4 'phs002808':1 'visit':3 +257 23 \\phs002808\\3a Visit Forms\\V5A Maternal Interview 2-7 Years Postpartum\\T01H01B\\ 3a Visit Forms / V5A Maternal Interview 2-7 Years Postpartum categorical \\phs002808\\3a Visit Forms\\V5A Maternal Interview 2-7 Years Postpartum\\ 256 '-7':9,19 '2':8,18 '3a':2,12 'form':4,14 'interview':7,17 'matern':6,16 'phs002808':1 'postpartum':11,21 'v5a':5,15 'visit':3,13 'year':10,20 +258 23 T01H01B T01H01B categorical \\phs002808\\3a Visit Forms\\V5A Maternal Interview 2-7 Years Postpartum\\T01H01B\\ 257 '-7':9 '2':8 '3a':2 'blood':23 'current':17 'form':4 'high':22 'interview':7 'matern':6 'medic':19 'phs002808':1 'postpartum':11 'prescrib':18 'pressur':24 't01':14 't01h01b':12,13 'v5a':5 'visit':3 'year':10 'yes':25,28 +260 21 enrollment_alcohol_and_tobacco alcohol_and_tobacco categorical \\phs003463\\alcohol_and_tobacco_enrollment\\ 259 'adult':25 'alcohol':2,6,15 'answers.tsv':20 'associ':10 'enrol':5,14 'file':21 'pair':13 'phs003463':1 'recov':24 'studi':26 'tobacco':4,8,17 'variabl':9 'visit/form':12 +261 21 alco_tobaccopre_enrollment_alcohol_and_tobacco alco_tobaccopre_enrollment_alcohol_and_tobacco categorical \\phs003463\\alcohol_and_tobacco_enrollment\\alco_tobaccopre_enrollment_alcohol_and_tobacco\\ 260 'alco':6,12 'alcohol':2,9,15 'enrol':5,8,14 'phs003463':1 'tobacco':4,11,17 'tobaccopr':7,13 +264 24 visit01_original_ecgsamplebase VISIT01_ORIGINAL_ECGSAMPLEBASE continuous \\phs003566\\Visit01\\VISIT01_ORIGINAL_ECGSAMPLEBASE\\ 263 'ecgsamplebas':5,8 'origin':4,7 'phs003566':1 'visit01':2,3,6 +266 14 Genotype array Genotype array categorical \\Variant Data Type\\Genotype array\\ 265 'array':5,7,9 'data':2 'genotyp':4,6,8 'true':10 'type':3 'variant':1 +267 14 Low coverage WGS Low coverage WGS categorical \\Variant Data Type\\Low coverage WGS\\ 265 'coverag':5,8,11 'data':2 'low':4,7,10 'true':13 'type':3 'variant':1 'wgs':6,9,12 +268 14 WES WES categorical \\Variant Data Type\\WES\\ 265 'data':2 'exom':7 'sequenc':8 'true':9 'type':3 'variant':1 'wes':4,5 'whole':6 +269 14 WGS WGS categorical \\Variant Data Type\\WGS\\ 265 'data':2 'genom':7 'sequenc':8 'true':9 'type':3 'variant':1 'wgs':4,5 'whole':6 +270 26 harmonized_var harmonized_var continuous \\phs003566\\harmonized_var\\ 263 'ecgsamplebas':5,8 'origin':4,7 'phs003566':1 'visit01':2,3,6 +271 26 value_example value_example continuous \\phs003566\\value_example\\ 263 'ecgsamplebas':5,8 'origin':4,7 'phs003566':1 'visit01':2,3,6 +\. + + +-- +-- Data for Name: concept_node_meta; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.concept_node_meta (concept_node_meta_id, concept_node_id, key, value) FROM stdin; +19 186 description Approximate Synonyms:\nSevere persistent allergic asthma in status asthmaticus\nSevere persistent allergic asthma with status asthmaticus\nSevere persistent asthma in status asthmaticus\nSevere persistent asthma with allergic rhinitis in status asthmaticus\nSevere persistent asthma with allergic rhinitis with status asthmaticus +20 186 values ["J45.52 Severe persistent asthma with status asthmaticus"] +21 189 description Approximate Synonyms:\nAcute exacerbation of asthma with allergic rhinitis\nAllergic asthma with acute exacerbation\nAsthma, with acute exacerbation (flare-up)\nAsthma, with allergic rhinitis with acute exacerbation\nExacerbation of asthma +22 189 values ["J45.901 Unspecified asthma with (acute) exacerbation"] +23 190 description Approximate Synonyms:\nAsthma with allergic rhinitis in status asthmaticus\nAsthma with allergic rhinitis with status asthmaticus\nAsthma with status\nAsthma with status asthmaticus\nAsthma, allergic with status asthmaticus\nExtrinsic asthma with status asthmaticus +24 190 values ["J45.902 Unspecified asthma with status asthmaticus"] +25 211 description GIC biosample: wholeblood +26 211 data_source Biosample +27 212 values ["TRUE"] +28 214 values ["TRUE"] +29 216 description Those patients who align with the IRB Phase 2 protocols +30 216 values ["GIC Consent"] +31 217 description Those patients who DO NOT align with the IRB Phase 2 protocols +32 217 values ["GIC Legacy Consent"] +33 218 description Patients who have waived consent +34 218 values ["Waiver of Consent"] +35 222 description Heart rate is taken by the automated blood pressure/heart rate monitor and captured directly into the computer system. In the event the heart rate is not captured automatically at the end of stage 1, the technician would manually enter the readings from the heart rate monitor. +37 225 description Including living and deceased, were any of {SP's/your} close biological that is, blood relatives including father, mother, sisters or brothers, ever told by a health professional that they had a heart attack or angina (an-gi-na) before the age of 50? +38 225 values ["Yes"] +39 229 description # 12 OZ CUPS OF CAFFEINATED COLA / DAY +41 229 stigmatized false +42 229 unique_identifier false +43 229 free_text false +44 229 bdc_open_access true +45 232 description # 12 OZ CUPS OF CAFFEINATED COLA / DAY +47 232 stigmatized false +48 232 unique_identifier false +49 232 free_text false +50 232 bdc_open_access true +51 235 description # 12 OZ CUPS OF CAFFEINATED COLA/DAY +53 235 stigmatized false +54 235 unique_identifier false +55 235 free_text false +56 235 bdc_open_access true +57 239 description Most recent occupation (A) +58 239 values ["ACCOUNTANT"] +59 241 description Age +61 241 stigmatized false +62 241 unique_identifier false +63 241 free_text false +64 241 bdc_open_access true +65 242 description % of time in artifacts +67 242 stigmatized false +68 242 unique_identifier false +69 242 free_text false +70 242 bdc_open_access true +71 244 description Patient age at transplant, years +72 244 values [42] +73 244 stigmatized false +74 244 unique_identifier false +75 244 free_text false +76 244 bdc_open_access true +77 244 hct status pre-hct +78 244 computed variable yes +79 245 description Race (regrouped) +80 245 values ["Not Reported"] +81 245 stigmatized false +82 245 unique_identifier false +83 245 free_text false +84 245 bdc_open_access true +85 246 description Transplant Number +86 246 values [1] +87 246 stigmatized true +88 246 unique_identifier false +89 246 free_text false +90 246 bdc_open_access false +91 246 hct status pre-hct +92 246 computed variable yes +93 248 description Participant's age (category) +94 248 values [21] +95 248 stigmatized false +96 248 unique_identifier false +97 248 free_text false +98 248 bdc_open_access true +99 249 description Smoker status +100 249 values ["true"] +101 249 stigmatized false +102 249 unique_identifier false +103 249 free_text false +104 249 bdc_open_access true +105 253 description (AFC) Reason for ending future contact: Withdrew consent for future nuMoM2b contact +106 253 values ["No"] +107 253 unique_identifier false +108 253 free_text false +109 253 bdc_open_access true +110 255 description (V5A) Which of the following problems have a doctor or health care professional told you that you have with your kidney?: Other - Specify Field +111 255 values ["infection"] +112 255 unique_identifier false +113 255 free_text true +114 255 bdc_open_access false +115 258 description (T01) Are you currently prescribed medication for your high blood pressure? +116 258 values ["Yes"] +117 258 unique_identifier false +118 258 free_text false +119 258 bdc_open_access true +120 266 description Genotype array +121 266 values ["TRUE"] +122 267 description Low coverage WGS +123 267 values ["TRUE"] +124 268 description Whole exome sequencing +40 229 values [0, 3] +46 232 values [0, 1] +52 235 values [0.57,6.77] +60 241 values ["5E-21", "7E+33"] +125 268 values ["TRUE"] +126 269 description Whole genome sequencing +127 269 values ["TRUE"] +128 227 description Clinic Exam, Original Cohort Exam 19 +129 230 description Clinic Exam, Original Cohort Exam 20 +130 233 description Clinic Exam, Offspring Cohort Exam 4 +131 237 description CARe_CFS (Cleveland Family Study) - Sleep and Health Phenotype (Adults/Children) +132 260 description Variables associated with visit/form pair enrollment_alcohol_and_tobacco in the answers.tsv file in the RECOVER Adult study +133 211 values [100, 500] +36 222 values [0, 150] +66 242 values [0, 30] +134 270 values [0, 21] +135 271 values ['gremlin', 'origin'] +\. + + +-- +-- Data for Name: consent; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.consent (consent_id, dataset_id, consent_code, description, authz) FROM stdin; +4 17 c1 Disease-Specific (Heart, Lung, Blood, and Sleep Disorders, IRB, NPU) (DS-HLBS-IRB-NPU) /programs/NSRR/projects/NSRR-CFS_DS-HLBS-IRB-NPU +5 18 c1 Disease-Specific (Heart, Lung, Blood, and Sleep Disorders, IRB, NPU) (DS-HLBS-IRB-NPU) /programs/parent/projects/CFS_ +6 19 c1 Health/Medical/Biomedical (IRB, MDS) (HMB-IRB-MDS) /programs/parent/projects/FHS_ +7 19 c2 Health/Medical/Biomedical (IRB, NPU, MDS) (HMB-IRB-NPU-MDS) /programs/parent/projects/FHS_ +8 20 c1 General Research Use (GRU) /programs/BioLINCC/projects/CIBMTR_ +9 21 c1 General Research Use (GRU) /programs/RECOVER/projects/RC_Adult_ +10 22 c1 General Research Use (GRU) /programs/NSRR/projects/SR_HCHS_ +11 23 c1 General Research Use (IRB) (GRU-IRB) /programs/topmed/projects/nuMoM2b_ +12 24 c1 General Research Use (IRB) (GRU-IRB) /programs/Imaging/projects/SPRINT_ +13 25 c1 GRU +\. + + +-- +-- Data for Name: dataset; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.dataset (dataset_id, ref, full_name, abbreviation, description) FROM stdin; +14 1 Genomic Information Commons GIC The GIC utilizes the ACT ontology to ensure data alignment across the sites. This project also includes other variables of interest as defined by the Governance Committee, such as biosamples, consents, etc. +15 2 National Health and Nutrition Examination Survey NHANES The National Health and Nutrition Examination Survey (NHANES) is a program of studies designed to assess the health and nutritional status of adults and children in the United States. +16 3 1000 Genomes Project 1000 Genomes The 1000 Genomes Project created a catalogue of common human genetic variation, using openly consented samples from people who declared themselves to be healthy. The reference data resources generated by the project remain heavily used by the biomedical science community. +17 phs002715 National Sleep Research Resource (NSRR): Cleveland Family Study (CFS) NSRR CFS The Cleveland Family Study (CFS) is a family-based study of sleep apnea, consisting of 2,284 individuals (46% African American) from 361 families studied on up to 4 occasions over a period of 16 years. The study began in 1990 with the initial aims of quantifying the familial aggregation of sleep apnea. National Institutes of Health (NIH) renewals provided expansion of the original cohort, including increased minority recruitment, and longitudinal follow-up, with the last exam occurring in February 2006. The CFS was designed to provide fundamental epidemiological data on risk factors for sleep disordered breathing (SDB). The sample was selected by identifying affected probands who had laboratory diagnosed obstructive sleep apnea. All first-degree relatives, spouses and available second-degree relatives of affected probands were studied. In addition, during the first 5 study years, neighborhood control families were identified through a neighborhood proband, and his/her spouses and first-degree relatives. Each exam, occurring at approximately 4-year intervals, included new enrollment as well as follow up exams for previously enrolled subjects. For the first three visits, data, including an overnight sleep study, were collected in participants' homes while the last visit occurred in a general clinical research center (GCRC). Phenotypic characterization of the entire cohort included overnight sleep apnea studies, blood pressure, spirometry, anthropometry and questionnaires. Currently, data of 710 individuals are available for use through BioData Catalyst (with genotype data available through dbGaP).\n\nThe National Sleep Research Resource (NSRR) is a NIH-supported sleep data repository that offers free access to large collections of de-identified physiological signals and related clinical data from a large range of cohort studies, clinical trials and other data sources from children and adults, including healthy individuals from the community and individuals with known sleep or other health disorders. The goals of NSRR are to facilitate rigorous research that requires access to large or more diverse data sets, including raw physiological signals, to promote a better understanding of risk factors for sleep and circadian disorders and/or the impact of sleep disturbances on health-related outcomes. Data from over 15 data sources and more than 40,000 individual sleep studies, many linked to dozens if not hundreds of clinical data elements, are available (as of Feb. 2022). Query tools are available to identify variables of interest, and their meta-data and provenance. +18 phs000284 NHLBI Cleveland Family Study (CFS) Candidate Gene Association Resource (CARe) CFS The Cleveland Family Study is the largest family-based study of sleep apnea world-wide, consisting of 2284 individuals (46% African American) from 361 families studied on up to 4 occasions over a period of 16 years. The study was begun in 1990 with the initial aims of quantifying the familial aggregation of sleep apnea. NIH renewals provided expansion of the original cohort (including increased minority recruitment) and longitudinal follow-up, with the last exam occurring in February 2006. Index probands (n=275) were recruited from 3 area hospital sleep labs if they had a confirmed diagnosis of sleep apnea and at least 2 first-degree relatives available to be studied. In the first 5 years of the study, neighborhood control probands (n=87) with at least 2 living relatives available for study were selected at random from a list provided by the index family and also studied. All available first degree relatives and spouses of the case and control probands also were recruited. Second-degree relatives, including half-sibs, aunts, uncles and grandparents, were also included if they lived near the first degree relatives (cases or controls), or if the family had been found to have two or more relatives with sleep apnea. Blood was sampled and DNA isolated for participants seen in the last two exam cycles (n=1447). The sample, which is enriched with individuals with sleep apnea, also contains a high prevalence of individuals with sleep apnea-related traits, including: obesity, impaired glucose tolerance, and HTN.\n\nPhenotyping data have been collected over 4 exam cycles, each occurring ~every 4 years. The last three exams targeted all subjects who had been studied at earlier exams, as well as new minority families and family members of previously studied probands who had been unavailable at prior exams. Data from one, two, three and four visits are available for 412, 630, 329 and 67, participants, respectively. In the first 3 exams, participants underwent overnight in-home sleep studies, allowing determination of the number and duration of hypopneas and apneas, sleep period, heart rate, and oxygen saturation levels; anthropometry (weight, height, and waist, hip, and neck circumferences); resting blood pressure; spirometry; standardized questionnaire evaluation of symptoms, medications, sleep patterns, quality of life, daytime sleepiness measures and health history; venipuncture and measurement of total and HDL cholesterol. The 4th exam (2001-2006) was designed to collect more detailed measurements of sleep, metabolic and CVD phenotypes and included measurement of state-of-the-art polysomnography, with both collection of blood and measurement of blood pressure before and after sleep, and anthropometry, upper airway assessments, spirometry, exhaled nitric oxide, and ECG performed the morning after the sleep study.\n\nData have been collected by trained research assistants or GCRC nurses following written Manuals of Procedures who were certified following standard approaches for each study procedure. Ongoing data quality, with assessment of within or between individual drift, has been monitored on an ongoing basis, using statistical techniques as well as regular re-certification procedures. Between and within scorer reliabilities for key sleep apnea indices have been excellent, with intra-class correlation coefficients (ICCs) exceeding 0.92 for the apnea-hypopnea index (AHI). Sleep staging, assessed with epoch specific comparisons, also demonstrate excellent reliability for stage identification (kappas>0.82). There has been no evidence of significant time trends-between or within scorers- for the AHI variables. We also have evaluated the night-to-night variability of the AHI and other sleep variables in 91 subjects, with each measurement made 1-3 months apart. There is high night to night consistency for the AHI (ICC: 0.80), the arousal index (0.76), and the % sleep time in slow-wave sleep (0.73). We have demonstrated the comparability of the apnea estimates (AHI) determined from limited channel studies obtained at in-home settings with in full in-laboratory polysomnography. In addition to our published validation study, we more recently compared the AHI in 169 Cleveland Family Study participants undergoing both assessments (in-home and in-laboratory) within one week apart. These showed excellent levels of agreement (ICC=0.83), demonstrating the feasibility of examining data from either in-home or in-laboratory studies for apnea phenotyping. Data collected in the GCRC were obtained, when possible, with comparable, if not identical techniques, as were the same measures collected at prior exams performed in the participants' homes. To address the comparability of data collected over different exams, we calculated the crude age-adjusted correlations ~3 year within individual correlations between measures made in the most recent GCRC exam with measures made in a prior exam and demonstrated excellent levels of agreement for BMI (r=.91); waist circumference (0.91); FVC (0.88); and FEV1 (0.86). As expected due to higher biological and measurement variability, 149 somewhat lower 3-year correlations were demonstrated for SBP (0.56); Diastolic BP (0.48); AHI (0.62); and nocturnal oxygen desaturation (0.60). +19 phs000007 Framingham Cohort FHS Startup of Framingham Heart Study. Cardiovascular disease (CVD) is the leading cause of death and serious illness in the United States. In 1948, the Framingham Heart Study (FHS) -- under the direction of the National Heart Institute (now known as the National Heart, Lung, and Blood Institute, NHLBI) -- embarked on a novel and ambitious project in health research. At the time, little was known about the general causes of heart disease and stroke, but the death rates for CVD had been increasing steadily since the beginning of the century and had become an American epidemic.\n\nThe objective of the FHS was to identify the common factors or characteristics that contribute to CVD by following its development over a long period of time in a large group of participants who had not yet developed overt symptoms of CVD or suffered a heart attack or stroke.\n\nDesign of Framingham Heart Study. In 1948, the researchers recruited 5,209 men and women between the ages of 30 and 62 from the town of Framingham, Massachusetts, and began the first round of extensive physical examinations and lifestyle interviews that they would later analyze for common patterns related to CVD development. Since 1948, the subjects have returned to the study every two years for an examination consisting of a detailed medical history, physical examination, and laboratory tests, and in 1971, the study enrolled a second-generation cohort -- 5,124 of the original participants' adult children and their spouses -- to participate in similar examinations. The second examination of the Offspring cohort occurred eight years after the first examination, and subsequent examinations have occurred approximately every four years thereafter. In April 2002 the Study entered a new phase: the enrollment of a third generation of participants, the grandchildren of the original cohort. The first examination of the Third Generation Study was completed in July 2005 and involved 4,095 participants. Thus, the FHS has evolved into a prospective, community-based, three generation family study. The FHS is a joint project of the National Heart, Lung and Blood Institute and Boston University.\n\nResearch Areas in the Framingham Heart Study. Over the years, careful monitoring of the FHS population has led to the identification of the major CVD risk factors -- high blood pressure, high blood cholesterol, smoking, obesity, diabetes, and physical inactivity -- as well as a great deal of valuable information on the effects of related factors such as blood triglyceride and HDL cholesterol levels, age, gender, and psychosocial issues. Risk factors have been identified for the major components of CVD, including coronary heart disease, stroke, intermittent claudication, and heart failure. It is also clear from research in the FHS and other studies that substantial subclinical vascular disease occurs in the blood vessels, heart and brain that precedes clinical CVD. With recent advances in technology, the FHS has enhanced its research capabilities and capitalized on its inherent resources by the conduct of high resolution imaging to detect and quantify subclinical vascular disease in the major blood vessels, heart and brain. These studies have included ultrasound studies of the heart (echocardiography) and carotid arteries, computed tomography studies of the heart and aorta, and magnetic resonance imaging studies of the brain, heart, and aorta. Although the Framingham cohort is primarily white, the importance of the major CVD risk factors identified in this group have been shown in other studies to apply almost universally among racial and ethnic groups, even though the patterns of distribution may vary from group to group. In the past half century, the Study has produced approximately 1,200 articles in leading medical journals. The concept of CVD risk factors has become an integral part of the modern medical curriculum and has led to the development of effective treatment and preventive strategies in clinical practice.\n\nIn addition to research studies focused on risk factors, subclinical CVD and clinically apparent CVD, Framingham investigators have also collaborated with leading researchers from around the country and throughout the world on projects involving some of the major chronic illnesses in men and women, including dementia, osteoporosis and arthritis, nutritional deficiencies, eye diseases, hearing disorders, and chronic obstructive lung diseases.\n\nGenetic Research in the Framingham Heart Study. While pursuing the Study's established research goals, the NHLBI and the Framingham investigators has expanded its research mission into the study of genetic factors underlying CVD and other disorders. Over the past two decades, DNA has been collected from blood samples and from immortalized cell lines obtained from Original Cohort participants, members of the Offspring Cohort and the Third Generation Cohort. Several large-scale genotyping projects have been conducted in the past decade. Genome-wide linkage analysis has been conducted using genotypes of approximately 400 microsatellite markers that have been completed in over 9,300 subjects in all three generations. Analyses using microsatellite markers completed in the original cohort and offspring cohorts have resulted in over 100 publications, including many publications from the Genetics Analysis Workshop 13. Several other recent collaborative projects have completed thousands of SNP genotypes for candidate gene regions in subsets of FHS subjects with available DNA. These projects include the Cardiogenomics Program of the NHLBI's Programs for Genomics Applications, the genotyping of ~3000 SNPs in inflammation genes, and the completion of a genome-wide scan of 100,000 SNPs using the Affymetrix 100K Genechip.\n\nFramingham Cohort Phenotype Data. The phenotype database contains a vast array of phenotype information available in all three generations. These will include the quantitative measures of the major risk factors such as systolic blood pressure, total and HDL cholesterol, fasting glucose, and cigarette use, as well as anthropomorphic measures such as body mass index, biomarkers such as fibrinogen and CRP, and electrocardiography measures such as the QT interval. Many of these measures have been collected repeatedly in the original and offspring cohorts. Also included in the SHARe database will be an array of recently collected biomarkers, subclinical disease imaging measures, clinical CVD outcomes as well as an array of ancillary studies. The phenotype data is located here in the top-level study phs000007 Framingham Cohort. To view the phenotype variables collected from the Framingham Cohort, please click on the Variables tab above. +20 phs002385 Hematopoietic Cell Transplant for Sickle Cell Disease (HCT for SCD) HCT_for_SCD The Center for International Blood and Marrow Transplant Research (CIBMTR) is a hematopoietic cell transplant registry that was established in 1972 at the Medical College of Wisconsin. The overarching goal of the registry is to study trends in transplantations and to advance the understanding and application of allogeneic hematopoietic cell transplantation for malignant and non-malignant diseases. Included in this dataset are children, adolescents and young adults with severe sickle cell disease who received an allogeneic hematopoietic cell transplant in the United States and provided written informed consent for research.\n\nHematopoietic cell transplant for sickle cell disease is curative. Offering this treatment for patients with severe disease is challenging as only about 20-25% of patients expected to benefit have an HLA-matched sibling. Consequently, several transplantations have utilized an HLA-matched or mismatched unrelated adult donor and HLA-mismatched relative. Transplantation strategies have also evolved over time that has included transplant conditioning regimens of varying intensity, grafts other than bone marrow and novel approaches to overcome the donor-recipient histocompatibility barrier and limit graft-versus-host disease. The data that is available for sickle cell disease transplants have been utilized to report on outcomes after transplantation and compare outcomes after transplantation of grafts HLA-matched related, HLA-mismatched related, HLA-matched and HLA-mismatched unrelated donors. Collectively, these data have advanced our knowledge and understanding of hematopoietic cell transplant for this disease. These data can also serve as contemporaneous controls for comparison with other more recent curative treatments like gene therapy and gene editing. +21 phs003463 Researching COVID to Enhance Recovery (RECOVER): Adult Observational Cohort Study RECOVER_Adult +22 phs003543 National Sleep Research Resource (NSRR): (HSHC) NSRR_HSHC +23 phs002808 Nulliparous Pregnancy Outcomes Study: Monitoring Mothers-to-be Heart Health Study (nuMoM2b Heart Health Study) nuMoM2b +24 phs003566 Systolic Blood Pressure Intervention Trial (SPRINT-Imaging) SPRINT +25 phs001963 DEMENTIA-SEQ: WGS in Lewy Body Dementia and Frontotemporal Dementia DEMENTIA-SEQ +26 harmonized My Cool Harmonized Dataset abv harmony +\. + + +-- +-- Data for Name: dataset_meta; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.dataset_meta (dataset_meta_id, dataset_id, key, value) FROM stdin; +1 17 focus Sleep Apnea Syndromes +2 18 focus Sleep Apnea Syndromes +3 19 focus Cardiovascular Disease +4 20 focus Sickle Cell Disease +5 21 focus Covid-19 +6 22 focus Sleep Apnea Syndromes +7 23 focus Hypertension +8 24 focus Imaging +9 25 focus Lewy Body Disease +10 17 design Prospective Longitudinal Cohort +11 18 design Prospective Longitudinal Cohort +12 19 design Prospective Longitudinal Cohort +13 20 design Prospective Longitudinal Cohort +14 21 design Clinical Trial +15 22 design Prospective Longitudinal Cohort +16 23 design Prospective Longitudinal Cohort +17 25 design Case-Control +18 25 category code Case-Control +19 25 focus display Lewy Body Disease +20 25 condition coding system urn:oid:2.16.840.1.113883.6.177 +21 25 condition coding code D020961 +22 25 condition coding display Lewy Body Disease +23 25 description Lewy body dementia, amyotrophic lateral sclerosis/frontotemporal dementia, and multiple system atrophy are age-related, neurodegenerative syndromes that are poorly understood. Delineating the genetic risk that is driving the pathophysiology of these neurological diseases is fundamental for understanding disease mechanisms and for developing disease-modifying treatments.
    \\n\\n\\n\\n In version 1 of the study/dbGaP deposition, we performed a whole-genome sequencing study consisting of 7,403 total samples, including 2,633 genomes from patients with Lewy body dementia, 2,641 frontotemporal dementia patients, and 1,980 neurologically healthy controls. Of these, 6,907 were uploaded to dbGaP as the basis of the DementiaSeq, phs001963 dataset. The data relating to these samples are available on dbGaP.\\n\\n\\n\\n In version 2 of this study/dbGaP deposition, we made much of these data available on Anvil. More specifically, data for 6,254 of these samples were also uploaded to the ALS Compute platform on AnVIL. The data for the remaining 653 samples are only available on dbGaP. The dbGaP/AnVIL Table lists the availability of dbGaP and AnVIL for each individual sample: phd008475.\\n\\nIn version 3 of the study/dbGaP deposition, we added whole-genome sequence data generated using DNA samples obtained from 683 patients diagnosed with multiple system atrophy.\\n +24 25 sponsor display National Institute on Aging +25 20 additional information Cure SCi Metadata Catalog +26 17 clinvars 500 +27 18 clinvars 12321 +28 19 clinvars 12546 +29 20 clinvars 7567 +30 21 clinvars 654645 +31 22 clinvars 434 +32 23 clinvars 2 +33 24 clinvars 333 +34 25 clinvars 653 +36 17 participants 23432 +37 18 participants 867876 +38 19 participants 3435 +39 20 participants 33 +40 21 participants 6654 +41 22 participants 53435 +42 23 participants 111 +43 24 participants 2222 +44 25 participants 65 +\. + + +-- +-- Data for Name: facet; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.facet (facet_id, facet_category_id, name, display, description, parent_id) FROM stdin; +20 2 LOINC LOINC \N \N +21 2 PhenX PhenX \N \N +22 1 1 GIC \N \N +23 1 2 National Health and Nutrition Examination Survey \N \N +24 1 3 1000 Genomes Project \N \N +25 1 phs002715 NSRR CFS \N \N +26 1 phs000284 CFS \N \N +27 1 phs000007 FHS \N \N +28 1 phs002385 HCT_for_SCD \N \N +29 1 phs003463 RECOVER_Adult \N \N +30 1 phs003543 NSRR_HSHC \N \N +31 1 phs002808 nuMoM2b \N \N +32 1 phs003566 SPRINT \N \N +33 1 phs001963 DEMENTIA-SEQ \N \N +55 1 NEST_1 My Nested Facet 1 \N 33 +56 1 NEST_2 My Nested Facet 2 \N 33 +19 2 gad_7 Generalized Anxiety Disorder Assessment (GAD-7) \N \N +18 2 taps_tool NIDA CTN Common Data Elements = TAPS Tool \N \N +\. + + +-- +-- Data for Name: facet__concept_node; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.facet__concept_node (facet__concept_node_id, facet_id, concept_node_id) FROM stdin; +1 22 180 +2 22 181 +3 22 182 +4 22 183 +5 22 184 +6 22 185 +7 22 186 +8 22 187 +9 22 188 +10 22 189 +11 22 190 +12 22 191 +13 22 192 +14 22 193 +15 22 194 +16 22 195 +17 22 196 +18 22 197 +19 22 198 +20 22 199 +21 22 200 +22 22 201 +23 22 202 +24 22 203 +25 22 204 +26 22 205 +27 22 206 +28 22 207 +29 22 208 +30 22 209 +31 22 210 +32 22 211 +33 22 212 +34 22 213 +35 22 214 +36 22 215 +37 22 216 +38 22 217 +39 22 218 +40 23 219 +41 23 220 +42 23 221 +43 23 222 +44 23 223 +45 23 224 +46 23 225 +47 27 226 +48 27 227 +49 27 228 +50 27 229 +51 27 230 +52 27 231 +53 27 232 +54 27 233 +55 27 234 +56 27 235 +57 26 236 +58 26 237 +59 26 238 +60 26 239 +61 26 240 +62 26 241 +63 26 242 +64 28 243 +65 28 244 +66 28 245 +67 28 246 +68 25 247 +69 25 248 +70 25 249 +71 31 250 +72 31 251 +73 31 252 +74 31 253 +75 31 254 +76 31 255 +77 31 256 +78 31 257 +79 31 258 +80 29 259 +81 29 260 +82 29 261 +83 32 262 +84 32 263 +85 32 264 +86 22 265 +87 22 266 +88 22 267 +89 22 268 +90 22 269 +91 18 261 +92 20 229 +93 21 229 +94 21 271 +\. + + +-- +-- Data for Name: facet_category; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.facet_category (facet_category_id, name, display, description) FROM stdin; +1 study_ids_dataset_ids Study IDs/Dataset IDs +2 nsrr_harmonized Common Data Element Collection +3 cde NSRR Harmonized +\. + + +-- +-- Data for Name: facet_category_meta; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.facet_category_meta (facet_category_meta_id, facet_category_id, key, value) FROM stdin; +1 1 my_key my_value +\. + + +-- +-- Data for Name: facet_meta; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.facet_meta (facet_meta_id, facet_id, key, value) FROM stdin; +1 25 full_name National Sleep Research Resource +2 26 full_name Chronic Fatigue Syndrome +3 27 full_name Framingham Heart Study +\. + + +-- +-- Name: concept_node_concept_node_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.concept_node_concept_node_id_seq', 269, true); + + +-- +-- Name: concept_node_meta_concept_node_meta_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.concept_node_meta_concept_node_meta_id_seq', 133, true); + + +-- +-- Name: consent_consent_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.consent_consent_id_seq', 13, true); + + +-- +-- Name: dataset_dataset_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.dataset_dataset_id_seq', 25, true); + + +-- +-- Name: dataset_meta_dataset_meta_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.dataset_meta_dataset_meta_id_seq', 25, true); + + +-- +-- Name: facet__concept_node_facet__concept_node_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.facet__concept_node_facet__concept_node_id_seq', 93, true); + + +-- +-- Name: facet_category_facet_category_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.facet_category_facet_category_id_seq', 4, true); + + +-- +-- Name: facet_category_meta_facet_category_meta_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.facet_category_meta_facet_category_meta_id_seq', 1, false); + + +-- +-- Name: facet_facet_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.facet_facet_id_seq', 33, true); + + +-- +-- Name: facet_meta_facet_meta_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.facet_meta_facet_meta_id_seq', 1, false); + + +-- +-- Name: concept_node_meta concept_node_meta_key_concept_node_id_key; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.concept_node_meta + ADD CONSTRAINT concept_node_meta_key_concept_node_id_key UNIQUE (key, concept_node_id); + + +-- +-- Name: concept_node_meta concept_node_meta_pkey; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.concept_node_meta + ADD CONSTRAINT concept_node_meta_pkey PRIMARY KEY (concept_node_meta_id); + + +-- +-- Name: concept_node concept_node_pkey; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.concept_node + ADD CONSTRAINT concept_node_pkey PRIMARY KEY (concept_node_id); + + +-- +-- Name: consent consent_consent_code_dataset_id_key; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.consent + ADD CONSTRAINT consent_consent_code_dataset_id_key UNIQUE (consent_code, dataset_id); + + +-- +-- Name: consent consent_pkey; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.consent + ADD CONSTRAINT consent_pkey PRIMARY KEY (consent_id); + + +-- +-- Name: dataset_meta dataset_meta_key_dataset_id_key; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.dataset_meta + ADD CONSTRAINT dataset_meta_key_dataset_id_key UNIQUE (key, dataset_id); + + +-- +-- Name: dataset dataset_pkey; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.dataset + ADD CONSTRAINT dataset_pkey PRIMARY KEY (dataset_id); + + +-- +-- Name: dataset dataset_ref_key; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.dataset + ADD CONSTRAINT dataset_ref_key UNIQUE (ref); + + +-- +-- Name: facet__concept_node facet__concept_node_facet_id_concept_node_id_key; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet__concept_node + ADD CONSTRAINT facet__concept_node_facet_id_concept_node_id_key UNIQUE (facet_id, concept_node_id); + + +-- +-- Name: facet__concept_node facet__concept_node_pkey; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet__concept_node + ADD CONSTRAINT facet__concept_node_pkey PRIMARY KEY (facet__concept_node_id); + + +-- +-- Name: facet_category_meta facet_category_meta_key_facet_category_id_key; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet_category_meta + ADD CONSTRAINT facet_category_meta_key_facet_category_id_key UNIQUE (key, facet_category_id); + + +-- +-- Name: facet_category facet_category_name_key; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet_category + ADD CONSTRAINT facet_category_name_key UNIQUE (name); + + +-- +-- Name: facet_category facet_category_pkey; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet_category + ADD CONSTRAINT facet_category_pkey PRIMARY KEY (facet_category_id); + + +-- +-- Name: facet_meta facet_meta_key_facet_id_key; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet_meta + ADD CONSTRAINT facet_meta_key_facet_id_key UNIQUE (key, facet_id); + + +-- +-- Name: facet facet_name_facet_category_id_key; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet + ADD CONSTRAINT facet_name_facet_category_id_key UNIQUE (name, facet_category_id); + + +-- +-- Name: facet facet_pkey; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet + ADD CONSTRAINT facet_pkey PRIMARY KEY (facet_id); + + +-- +-- Name: concept_node_concept_path_idx; Type: INDEX; Schema: dict; Owner: picsure +-- + +CREATE UNIQUE INDEX concept_node_concept_path_idx ON public.concept_node USING btree (md5((concept_path)::text)); + + +-- +-- Name: facet fk_category; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet + ADD CONSTRAINT fk_category FOREIGN KEY (facet_category_id) REFERENCES public.facet_category(facet_category_id); + + +-- +-- Name: concept_node_meta fk_concept_node; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.concept_node_meta + ADD CONSTRAINT fk_concept_node FOREIGN KEY (concept_node_id) REFERENCES public.concept_node(concept_node_id); + + +-- +-- Name: facet__concept_node fk_concept_node; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet__concept_node + ADD CONSTRAINT fk_concept_node FOREIGN KEY (concept_node_id) REFERENCES public.concept_node(concept_node_id); + + +-- +-- Name: facet_meta fk_facet; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet_meta + ADD CONSTRAINT fk_facet FOREIGN KEY (facet_id) REFERENCES public.facet(facet_id); + + +-- +-- Name: facet__concept_node fk_facet; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet__concept_node + ADD CONSTRAINT fk_facet FOREIGN KEY (facet_id) REFERENCES public.facet(facet_id); + + +-- +-- Name: facet_category_meta fk_facet_category; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet_category_meta + ADD CONSTRAINT fk_facet_category FOREIGN KEY (facet_category_id) REFERENCES public.facet_category(facet_category_id); + + +-- +-- Name: concept_node fk_parent; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.concept_node + ADD CONSTRAINT fk_parent FOREIGN KEY (parent_id) REFERENCES public.concept_node(concept_node_id); + + +-- +-- Name: facet fk_parent; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet + ADD CONSTRAINT fk_parent FOREIGN KEY (parent_id) REFERENCES public.facet(facet_id); + + +-- +-- Name: dataset_meta fk_study; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.dataset_meta + ADD CONSTRAINT fk_study FOREIGN KEY (dataset_id) REFERENCES public.dataset(dataset_id); + + +-- +-- Name: concept_node fk_study; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.concept_node + ADD CONSTRAINT fk_study FOREIGN KEY (dataset_id) REFERENCES public.dataset(dataset_id); + + +CREATE TABLE IF NOT EXISTS public.dataset_harmonization +( + dataset_harmonization_id INT NOT NULL GENERATED BY DEFAULT AS IDENTITY, + harmonized_dataset_id INT NOT NULL, + source_dataset_id INT NOT NULL, + UNIQUE (harmonized_dataset_id, source_dataset_id), + CONSTRAINT fk_harmonized_dataset_id FOREIGN KEY (harmonized_dataset_id) REFERENCES public.dataset (dataset_id), + CONSTRAINT fk_source_dataset_id FOREIGN KEY (source_dataset_id) REFERENCES public.dataset (dataset_id) +); + +INSERT INTO public.dataset_harmonization (dataset_harmonization_id, harmonized_dataset_id, source_dataset_id) VALUES + (1, 26, 25), + (1, 26, 24), + (1, 26, 23), + (1, 26, 22); + + +INSERT INTO public.update_info (LAST_UPDATED, DATABASE_VERSION) VALUES + ('2020-02-02 00:00:00', 3); + + +CREATE TABLE IF NOT EXISTS public.concept_node__remote_dictionary ( + CONCEPT_NODE_ID integer NOT NULL, + REMOTE_DICTIONARY_ID integer NOT NULL, + CONSTRAINT fk_remote_dictionary FOREIGN KEY (REMOTE_DICTIONARY_ID) REFERENCES public.remote_dictionary(REMOTE_DICTIONARY_ID), + CONSTRAINT fk_concept_node FOREIGN KEY (CONCEPT_NODE_ID) REFERENCES public.concept_node(CONCEPT_NODE_ID) +); + +INSERT INTO public.remote_dictionary (REMOTE_DICTIONARY_ID, NAME, UUID, LAST_UPDATED) VALUES + (1, 'bch', '3c13f873-1ff1-42f7-8382-75ac82c49ffc', '2024-01-01'), + (2, 'foo', '498226bf-e18e-4f0f-81f5-dd242914df95', '1800-01-01'), + (3, 'bar', '498226bf-e18e-4f0f-81f5-dd242914df96', '2000-01-01'); + +INSERT INTO public.concept_node__remote_dictionary (CONCEPT_NODE_ID, REMOTE_DICTIONARY_ID) VALUES + (261, 1), + (264, 1), + (266, 1), + (267, 1), + (268, 1), + (269, 1), + (270, 1), + (267, 2), + (268, 2), + (269, 2), + (209, 3), (180, 3), (191, 3), (197, 3), (202, 3), (215, 3), (219, 3), (226, 3), (236, 3), (243, 3), + (247, 3), (250, 3), (259, 3), (262, 3), (265, 3), (181, 3), (182, 3), (183, 3), (184, 3), (223, 3), + (263, 3), (185, 3), (186, 3), (187, 3), (188, 3), (189, 3), (231, 3), (232, 3), (190, 3), (192, 3), + (193, 3), (194, 3), (195, 3), (196, 3), (198, 3), (199, 3), (200, 3), (201, 3), (203, 3), (204, 3), + (241, 3), (205, 3), (206, 3), (207, 3), (208, 3), (210, 3), (211, 3), (212, 3), (213, 3), (214, 3), + (216, 3), (217, 3), (218, 3), (220, 3), (221, 3), (222, 3), (224, 3), (225, 3), (227, 3), (228, 3), + (229, 3), (230, 3), (233, 3), (234, 3), (235, 3), (237, 3), (238, 3), (239, 3), (240, 3), (242, 3), + (244, 3), (245, 3), (246, 3), (248, 3), (249, 3), (251, 3), (252, 3), (253, 3), (254, 3), (255, 3), + (256, 3), (257, 3), (258, 3), (261, 3), (264, 3), (266, 3), (267, 3), (268, 3), (269, 3); + +-- +-- PostgreSQL database dump complete +-- + +ALTER TABLE public.concept_node ADD COLUMN concept_path_md5 text GENERATED ALWAYS AS (md5(concept_path::text)) STORED; +CREATE UNIQUE INDEX idx_concept_node_md5 ON public.concept_node(concept_path_md5); \ No newline at end of file diff --git a/services/picsure-dictionary/bdc.Dockerfile b/services/picsure-dictionary/bdc.Dockerfile new file mode 100644 index 000000000..0d550f8af --- /dev/null +++ b/services/picsure-dictionary/bdc.Dockerfile @@ -0,0 +1,19 @@ +FROM amazoncorretto:25-alpine + +# Copy jar and access token from maven build +COPY target/dictionary-*.jar /dictionary.jar + +# Time zone +ENV TZ="UTC" + +ARG DATASOURCE_URL +ARG DATASOURCE_USERNAME +ARG SPRING_PROFILE + +# If a --env-file is passed in, you can override these values +ENV DATASOURCE_URL=${DATASOURCE_URL} +ENV DATASOURCE_USERNAME=${DATASOURCE_USERNAME} +ENV SPRING_PROFILE=${SPRING_PROFILE} + +# Default to no profile +ENTRYPOINT java $DEBUG_VARS $PROXY_VARS -Xmx8192m ${JAVA_OPTS} -jar /dictionary.jar --spring.profiles.active=${SPRING_PROFILE:-} \ No newline at end of file diff --git a/services/picsure-dictionary/code-formatting/eclipse-formatter.xml b/services/picsure-dictionary/code-formatting/eclipse-formatter.xml new file mode 100644 index 000000000..e7cfababf --- /dev/null +++ b/services/picsure-dictionary/code-formatting/eclipse-formatter.xml @@ -0,0 +1,402 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/services/picsure-dictionary/code-formatting/pre-commit.sh b/services/picsure-dictionary/code-formatting/pre-commit.sh new file mode 100755 index 000000000..18f1a0a65 --- /dev/null +++ b/services/picsure-dictionary/code-formatting/pre-commit.sh @@ -0,0 +1,36 @@ +#!/bin/sh -e +CWD=$(pwd) +cd $(git rev-parse --show-toplevel) +format_cmd="" + +# skip if NO_VERIFY env var set +if [ "$NO_VERIFY" ]; then + echo 'code formatting skipped' 1>&2 + exit 0 +fi + +# I'm not great at bash, so this is a bit ugly, but I'll explain each pipe +# 1. Get all staged files +# 2. Reduce to just .java files +# 3. Replace newlines with commas (this was really hard to do in sed) +# 4. Replace commas with $,^.* +# 5. Crop off the last 4 chars +# This results in foo.java$,^.*bar.java$,^.*baz.java$ +# I then append ^.* to the beginning of that. +STAGED_JAVA_FILES_AS_REGEX=$(git diff --staged --name-only --diff-filter=ACMR | grep '.java$' | tr '\n' ',' | sed -e 's/,/$,^.*/g' | sed 's/.\{4\}$//') +FILES_TO_RESTAGE=$(git diff --staged --name-only --diff-filter=ACMR) +if [ -n "$STAGED_JAVA_FILES_AS_REGEX" ]; then + echo "Found the following staged java files to format: $STAGED_JAVA_FILES_AS_REGEX" + mvn spotless:apply -DspotlessFiles=^.*$STAGED_JAVA_FILES_AS_REGEX + git add $FILES_TO_RESTAGE +fi + +STAGED_JAVA_FILES_AS_REGEX=$(git diff --staged --name-only --diff-filter=ACMR | grep '.java$' | grep 'aggregate' | tr '\n' ',' | sed -e 's/,/$,^.*/g' | sed 's/.\{4\}$//') +FILES_TO_RESTAGE=$(git diff --staged --name-only --diff-filter=ACMR) +if [ -n "$STAGED_JAVA_FILES_AS_REGEX" ]; then + echo "Found the following staged java files to format: $STAGED_JAVA_FILES_AS_REGEX" + mvn -f aggregate/pom.xml spotless:apply -DspotlessFiles=^.*$STAGED_JAVA_FILES_AS_REGEX + git add $FILES_TO_RESTAGE +fi + +cd $CWD \ No newline at end of file diff --git a/services/picsure-dictionary/db/dml/backfill_fcn_is_queryable.sql b/services/picsure-dictionary/db/dml/backfill_fcn_is_queryable.sql new file mode 100644 index 000000000..177b010d9 --- /dev/null +++ b/services/picsure-dictionary/db/dml/backfill_fcn_is_queryable.sql @@ -0,0 +1,28 @@ +-- Backfill/resync is_queryable on facet__concept_node from concept_node. +-- +-- Run once after deploying V10__add_fcn_is_queryable.sql. +-- Triggers maintain the column going forward: +-- trg_set_fcn_is_queryable (BEFORE INSERT/UPDATE on fcn) +-- trg_cascade_is_queryable_to_fcn (AFTER UPDATE OF is_queryable on concept_node) +-- +-- Safe to re-run if facet__concept_node is truncated/reloaded. +-- WHERE guard skips rows already correct, avoiding unnecessary writes. + +UPDATE dict.facet__concept_node fcn +SET is_queryable = cn.is_queryable +FROM dict.concept_node cn +WHERE cn.concept_node_id = fcn.concept_node_id + AND fcn.is_queryable IS DISTINCT FROM cn.is_queryable; + +-- Verification: compare counts +SELECT + COUNT(*) AS total_fcn, + COUNT(*) FILTER (WHERE is_queryable = TRUE) AS queryable, + COUNT(*) FILTER (WHERE is_queryable = FALSE) AS non_queryable +FROM dict.facet__concept_node; + +-- Mismatch check: should return 0 +SELECT COUNT(*) AS mismatches +FROM dict.facet__concept_node fcn +JOIN dict.concept_node cn ON cn.concept_node_id = fcn.concept_node_id +WHERE fcn.is_queryable IS DISTINCT FROM cn.is_queryable; diff --git a/services/picsure-dictionary/db/dml/backfill_is_queryable.sql b/services/picsure-dictionary/db/dml/backfill_is_queryable.sql new file mode 100644 index 000000000..b4ef54e25 --- /dev/null +++ b/services/picsure-dictionary/db/dml/backfill_is_queryable.sql @@ -0,0 +1,45 @@ +-- Backfill/resync is_queryable for all existing concept_node rows. +-- +-- Run this once after deploying V7__add_queryable_column.sql and V8__add_is_queryable_trigger.sql. +-- The trigger (trg_sync_is_queryable) maintains the column for all future ETL operations, +-- but existing rows need a one-time update since the column was added with DEFAULT FALSE. +-- +-- Safe to re-run if concept_node is truncated/reloaded, or if is_queryable needs resyncing. +-- The WHERE guard skips rows already correct, avoiding unnecessary writes on large tables. +-- +-- NOTE: uses value <> '' to match the trigger condition exactly (V8__add_is_queryable_trigger.sql). +-- Expects the dict schema search_path to be set (or qualify as dict.concept_node below). + +UPDATE concept_node cn +SET is_queryable = EXISTS ( + SELECT 1 + FROM concept_node_meta cnm + WHERE cnm.concept_node_id = cn.concept_node_id + AND cnm.key = 'values' + AND cnm.value <> '' +) +WHERE cn.is_queryable IS DISTINCT FROM EXISTS ( + SELECT 1 + FROM concept_node_meta cnm + WHERE cnm.concept_node_id = cn.concept_node_id + AND cnm.key = 'values' + AND cnm.value <> '' +); + +-- Verification: compare counts +SELECT + COUNT(*) AS total_concepts, + COUNT(*) FILTER (WHERE is_queryable = TRUE) AS queryable_concepts, + COUNT(*) FILTER (WHERE is_queryable = FALSE) AS non_queryable_concepts +FROM concept_node; + +-- Mismatch check: should return 0 +SELECT COUNT(*) AS mismatches +FROM concept_node cn +WHERE cn.is_queryable IS DISTINCT FROM EXISTS ( + SELECT 1 + FROM concept_node_meta cnm + WHERE cnm.concept_node_id = cn.concept_node_id + AND cnm.key = 'values' + AND cnm.value <> '' +); diff --git a/services/picsure-dictionary/db/dml/rebuild_searchable_fields.sql b/services/picsure-dictionary/db/dml/rebuild_searchable_fields.sql new file mode 100644 index 000000000..94e27bcf7 --- /dev/null +++ b/services/picsure-dictionary/db/dml/rebuild_searchable_fields.sql @@ -0,0 +1,77 @@ +-- ============================================================ +-- rebuild_searchable_fields.sql +-- +-- Standalone DML script that rebuilds the searchable_fields +-- tsvector column on concept_node. This is the exact SQL that +-- the dictionaryweights micro app generates from weights.csv. +-- +-- Source of truth: dictionaryweights/weights.csv +-- If weights.csv changes, this script must be regenerated. +-- +-- Usage: +-- psql -d dictionary -f rebuild_searchable_fields.sql +-- (or run block-by-block in a SQL client) +-- +-- Weight tiers (A = highest priority, D = lowest): +-- A: concept_node.DISPLAY, concept_node.CONCEPT_PATH +-- B: dataset.FULL_NAME, dataset.DESCRIPTION +-- C: parent.DISPLAY, grandparent.DISPLAY +-- D: concept_node_meta_str.values (whitelisted keys, values capped at 60K) +-- +-- Uses 'english' language config to match query-layer +-- to_tsquery('english', ...) stemming behavior. +-- ============================================================ + +UPDATE concept_node +SET SEARCHABLE_FIELDS = data_table.search_vector +FROM +( + SELECT + setweight(to_tsvector('english', replace(coalesce(concept_node.DISPLAY, ''), '_', ' ')), 'A') || + setweight(to_tsvector('english', replace(coalesce(concept_node.CONCEPT_PATH, ''), '_', ' ')), 'A') || + setweight(to_tsvector('english', replace(coalesce(dataset.FULL_NAME, ''), '_', ' ')), 'B') || + setweight(to_tsvector('english', replace(coalesce(dataset.DESCRIPTION, ''), '_', ' ')), 'B') || + setweight(to_tsvector('english', replace(coalesce(parent.DISPLAY, ''), '_', ' ')), 'C') || + setweight(to_tsvector('english', replace(coalesce(grandparent.DISPLAY, ''), '_', ' ')), 'C') || + setweight(to_tsvector('english', replace(coalesce(concept_node_meta_str.values, ''), '_', ' ')), 'D') + AS search_vector, + concept_node.concept_node_id AS search_key + FROM + concept_node + LEFT JOIN + ( + SELECT + concept_node_id AS id, + string_agg(DISTINCT safe_value, ' ') AS values + FROM ( + SELECT concept_node_id, value AS safe_value + FROM concept_node_meta + WHERE value <> '' + AND key IN ('description','derived_values','variable_type','comment','domain','Question','question','unit') + UNION ALL + SELECT concept_node_id, left(value, 60000) AS safe_value + FROM concept_node_meta + WHERE value <> '' AND key = 'values' + ) AS filtered_meta + GROUP BY + concept_node_id + ) AS concept_node_meta_str ON concept_node_meta_str.id = concept_node.concept_node_id + LEFT JOIN dataset AS study ON concept_node.dataset_id = study.dataset_id + LEFT JOIN concept_node AS parent ON concept_node.parent_id = parent.concept_node_id + LEFT JOIN concept_node AS grandparent ON parent.parent_id = grandparent.concept_node_id + LEFT JOIN ( + SELECT + dataset_node.name AS NAME, + dataset_node.display AS FULL_NAME, + dataset_node.concept_path AS CONCEPT_PATH, + description_concept_node_meta.VALUE AS DESCRIPTION + FROM + concept_node AS dataset_node + JOIN concept_node_meta AS description_concept_node_meta ON description_concept_node_meta.KEY = 'description' AND description_concept_node_meta.concept_node_id = dataset_node.concept_node_id + ---------------------------------------------------------------------------------------------------- + -- This join is saying "find me the concept node that shares the first two nodes of this concept + -- and then stops". So for /a/b/c/d/e/f/, it finds concept /a/b/ + ---------------------------------------------------------------------------------------------------- + ) AS dataset ON dataset.concept_path = REGEXP_REPLACE(concept_node.concept_path, '(^\\[^\\]*\\[^\\]*\\)(.*$)', '\1') +) AS data_table +WHERE concept_node.concept_node_id = data_table.search_key; diff --git a/services/picsure-dictionary/db/flyway/V10__add_fcn_is_queryable.sql b/services/picsure-dictionary/db/flyway/V10__add_fcn_is_queryable.sql new file mode 100644 index 000000000..f3a5dd509 --- /dev/null +++ b/services/picsure-dictionary/db/flyway/V10__add_fcn_is_queryable.sql @@ -0,0 +1,58 @@ +-- Add is_queryable column to facet__concept_node +-- Eliminates the expensive concept_node JOIN from every facet query (~2100ms → ~800ms) +-- Maintained by two triggers: +-- 1. trg_set_fcn_is_queryable: sets value on INSERT/UPDATE from concept_node +-- 2. trg_cascade_is_queryable_to_fcn: cascades concept_node.is_queryable changes + + +ALTER TABLE dict.facet__concept_node + ADD COLUMN IF NOT EXISTS is_queryable BOOLEAN NOT NULL DEFAULT FALSE; + +-- Backfill from concept_node.is_queryable (populated by V7) +UPDATE dict.facet__concept_node fcn +SET is_queryable = cn.is_queryable +FROM dict.concept_node cn +WHERE cn.concept_node_id = fcn.concept_node_id; + +-- Trigger 1: set is_queryable on fcn INSERT/UPDATE (covers ETL reload) +CREATE OR REPLACE FUNCTION dict.set_fcn_is_queryable() RETURNS TRIGGER AS $$ +BEGIN + NEW.is_queryable := ( + SELECT cn.is_queryable + FROM dict.concept_node cn + WHERE cn.concept_node_id = NEW.concept_node_id + ); + RETURN NEW; +END; +$$ LANGUAGE plpgsql; + +DROP TRIGGER IF EXISTS trg_set_fcn_is_queryable ON dict.facet__concept_node; +CREATE TRIGGER trg_set_fcn_is_queryable + BEFORE INSERT OR UPDATE ON dict.facet__concept_node + FOR EACH ROW EXECUTE FUNCTION dict.set_fcn_is_queryable(); + +-- Trigger 2: cascade concept_node.is_queryable changes to fcn +CREATE OR REPLACE FUNCTION dict.cascade_is_queryable_to_fcn() RETURNS TRIGGER AS $$ +BEGIN + IF OLD.is_queryable IS DISTINCT FROM NEW.is_queryable THEN + UPDATE dict.facet__concept_node + SET is_queryable = NEW.is_queryable + WHERE concept_node_id = NEW.concept_node_id; + END IF; + RETURN NEW; +END; +$$ LANGUAGE plpgsql; + +DROP TRIGGER IF EXISTS trg_cascade_is_queryable_to_fcn ON dict.concept_node; +CREATE TRIGGER trg_cascade_is_queryable_to_fcn + AFTER UPDATE OF is_queryable ON dict.concept_node + FOR EACH ROW EXECUTE FUNCTION dict.cascade_is_queryable_to_fcn(); + +-- Partial indexes (equivalent to matview indexes from Step 17B) +CREATE INDEX IF NOT EXISTS idx_fcn_queryable_fid_cid + ON dict.facet__concept_node(facet_id, concept_node_id) + WHERE is_queryable = TRUE; + +CREATE INDEX IF NOT EXISTS idx_fcn_queryable_cid + ON dict.facet__concept_node(concept_node_id) + WHERE is_queryable = TRUE; diff --git a/services/picsure-dictionary/db/flyway/V1__add_update_info.sql b/services/picsure-dictionary/db/flyway/V1__add_update_info.sql new file mode 100644 index 000000000..06133cbd0 --- /dev/null +++ b/services/picsure-dictionary/db/flyway/V1__add_update_info.sql @@ -0,0 +1,5 @@ +CREATE TABLE IF NOT EXISTS dict.update_info ( + LAST_UPDATED TIMESTAMP NOT NULL DEFAULT '2000-01-01 00:00:00' +); + +INSERT INTO dict.update_info (LAST_UPDATED) VALUES ('2000-01-01 00:00:00'); \ No newline at end of file diff --git a/services/picsure-dictionary/db/flyway/V2__add_aggregate.sql b/services/picsure-dictionary/db/flyway/V2__add_aggregate.sql new file mode 100644 index 000000000..9959cf90b --- /dev/null +++ b/services/picsure-dictionary/db/flyway/V2__add_aggregate.sql @@ -0,0 +1,13 @@ +CREATE TABLE dict.remote_dictionary ( + REMOTE_DICTIONARY_ID SERIAL PRIMARY KEY, + NAME CHARACTER VARYING(512) NOT NULL, + UUID UUID NOT NULL, + LAST_UPDATED TIMESTAMP +); + +CREATE TABLE dict.concept_node__remote_dictionary ( + CONCEPT_NODE_ID integer NOT NULL, + REMOTE_DICTIONARY_ID integer NOT NULL, + CONSTRAINT fk_remote_dictionary FOREIGN KEY (REMOTE_DICTIONARY_ID) REFERENCES dict.remote_dictionary(REMOTE_DICTIONARY_ID), + CONSTRAINT fk_concept_node FOREIGN KEY (CONCEPT_NODE_ID) REFERENCES dict.concept_node(CONCEPT_NODE_ID) +); \ No newline at end of file diff --git a/services/picsure-dictionary/db/flyway/V3__add_version.sql b/services/picsure-dictionary/db/flyway/V3__add_version.sql new file mode 100644 index 000000000..33a32529e --- /dev/null +++ b/services/picsure-dictionary/db/flyway/V3__add_version.sql @@ -0,0 +1 @@ +ALTER TABLE dict.update_info ADD DATABASE_VERSION INT NOT NULL DEFAULT 3; \ No newline at end of file diff --git a/services/picsure-dictionary/db/flyway/V4__add_md5.sql b/services/picsure-dictionary/db/flyway/V4__add_md5.sql new file mode 100644 index 000000000..62c4db5af --- /dev/null +++ b/services/picsure-dictionary/db/flyway/V4__add_md5.sql @@ -0,0 +1,5 @@ +ALTER TABLE dict.concept_node ADD COLUMN concept_path_md5 text GENERATED ALWAYS AS (md5(concept_path::text)) STORED; +CREATE UNIQUE INDEX idx_concept_node_md5 ON dict.concept_node(concept_path_md5); + +-- backwards compatible change, keep db version at 3 +UPDATE dict.update_info SET DATABASE_VERSION = 3; \ No newline at end of file diff --git a/services/picsure-dictionary/db/flyway/V5__add_cascade.sql b/services/picsure-dictionary/db/flyway/V5__add_cascade.sql new file mode 100644 index 000000000..e0a9d9cff --- /dev/null +++ b/services/picsure-dictionary/db/flyway/V5__add_cascade.sql @@ -0,0 +1,121 @@ +alter table dict.concept_node + drop constraint fk_study; + +alter table dict.concept_node + add constraint fk_study + foreign key (dataset_id) references dict.dataset + on delete cascade; + +alter table dict.concept_node + drop constraint fk_parent; + +alter table dict.concept_node + add constraint fk_parent + foreign key (dataset_id) references dict.dataset + on delete cascade; + +alter table dict.concept_node__remote_dictionary + drop constraint fk_remote_dictionary; + +alter table dict.concept_node__remote_dictionary + add constraint fk_remote_dictionary + foreign key (remote_dictionary_id) references dict.remote_dictionary + on delete cascade; + +alter table dict.concept_node__remote_dictionary + drop constraint fk_concept_node; + +alter table dict.concept_node__remote_dictionary + add constraint fk_concept_node + foreign key (concept_node_id) references dict.concept_node + on delete cascade; + + +alter table dict.concept_node_meta + drop constraint fk_concept_node; + +alter table dict.concept_node_meta + add constraint fk_concept_node + foreign key (concept_node_id) references dict.concept_node + on delete cascade; + + +alter table dict.dataset_harmonization + drop constraint fk_harmonized_dataset_id; + +alter table dict.dataset_harmonization + add constraint fk_harmonized_dataset_id + foreign key (harmonized_dataset_id) references dict.dataset + on delete cascade; + +alter table dict.dataset_harmonization + drop constraint fk_source_dataset_id; + +alter table dict.dataset_harmonization + add constraint fk_source_dataset_id + foreign key (source_dataset_id) references dict.dataset + on delete cascade; + + +alter table dict.dataset_meta + drop constraint fk_study; + +alter table dict.dataset_meta + add constraint fk_study + foreign key (dataset_id) references dict.dataset + on delete cascade; + + +alter table dict.facet + drop constraint fk_category; + +alter table dict.facet + add constraint fk_category + foreign key (facet_category_id) references dict.facet_category + on delete cascade; + +alter table dict.facet + drop constraint fk_parent; + +alter table dict.facet + add constraint fk_parent + foreign key (parent_id) references dict.facet + on delete cascade; + + +alter table dict.facet__concept_node + drop constraint fk_concept_node; + +alter table dict.facet__concept_node + add constraint fk_concept_node + foreign key (concept_node_id) references dict.concept_node + on delete cascade; + +alter table dict.facet__concept_node + drop constraint fk_facet; + +alter table dict.facet__concept_node + add constraint fk_facet + foreign key (facet_id) references dict.facet + on delete cascade; + + +alter table dict.facet_category_meta + drop constraint fk_facet_category; + +alter table dict.facet_category_meta + add constraint fk_facet_category + foreign key (facet_category_id) references dict.facet_category + on delete cascade; + + +alter table dict.facet_meta + drop constraint fk_facet; + +alter table dict.facet_meta + add constraint fk_facet + foreign key (facet_id) references dict.facet + on delete cascade; + +-- backwards compatible change, keep db version at 3 +UPDATE dict.update_info SET DATABASE_VERSION = 3; diff --git a/services/picsure-dictionary/db/flyway/V6__add_search_indexes.sql b/services/picsure-dictionary/db/flyway/V6__add_search_indexes.sql new file mode 100644 index 000000000..1877c49b3 --- /dev/null +++ b/services/picsure-dictionary/db/flyway/V6__add_search_indexes.sql @@ -0,0 +1,13 @@ +-- ALS-11334: Add indexes for search query optimization +-- GIN index enables Bitmap Index Scan on tsvector (1,500x faster) +-- Meta covering index optimizes the 4-6 LEFT JOINs per query +-- Dataset FK index enables consent filtering without seq scan + +CREATE INDEX IF NOT EXISTS idx_concept_node_searchable_fields_gin + ON dict.concept_node USING GIN (searchable_fields); + +CREATE INDEX IF NOT EXISTS idx_concept_node_meta_covering + ON dict.concept_node_meta(concept_node_id, key); + +CREATE INDEX IF NOT EXISTS idx_concept_node_dataset_id + ON dict.concept_node(dataset_id); diff --git a/services/picsure-dictionary/db/flyway/V7__add_queryable_column.sql b/services/picsure-dictionary/db/flyway/V7__add_queryable_column.sql new file mode 100644 index 000000000..d840082df --- /dev/null +++ b/services/picsure-dictionary/db/flyway/V7__add_queryable_column.sql @@ -0,0 +1,16 @@ +-- Add is_queryable boolean to concept_node for fast displayability filtering. +-- Replaces the expensive JOIN concept_node_meta WHERE key='values' AND value<>'' +-- that was costing 932K index lookups per facet query. + +ALTER TABLE dict.concept_node ADD COLUMN IF NOT EXISTS is_queryable BOOLEAN NOT NULL DEFAULT FALSE; + +UPDATE dict.concept_node cn SET is_queryable = TRUE +WHERE EXISTS ( + SELECT 1 FROM dict.concept_node_meta cnm + WHERE cnm.concept_node_id = cn.concept_node_id + AND cnm.key = 'values' AND cnm.value <> '' +); + +CREATE INDEX IF NOT EXISTS idx_concept_node_queryable + ON dict.concept_node (concept_node_id) + WHERE is_queryable = TRUE; diff --git a/services/picsure-dictionary/db/flyway/V8__add_is_queryable_trigger.sql b/services/picsure-dictionary/db/flyway/V8__add_is_queryable_trigger.sql new file mode 100644 index 000000000..3afd6dfc9 --- /dev/null +++ b/services/picsure-dictionary/db/flyway/V8__add_is_queryable_trigger.sql @@ -0,0 +1,19 @@ +CREATE OR REPLACE FUNCTION dict.sync_is_queryable() RETURNS TRIGGER AS $$ +DECLARE + target_id INT := coalesce(NEW.concept_node_id, OLD.concept_node_id); +BEGIN + IF (NEW.key IS NOT NULL AND NEW.key = 'values') OR (OLD.key IS NOT NULL AND OLD.key = 'values') THEN + UPDATE dict.concept_node SET is_queryable = EXISTS ( + SELECT 1 FROM dict.concept_node_meta + WHERE concept_node_id = target_id + AND key = 'values' AND value <> '' + ) + WHERE concept_node_id = target_id; + END IF; + RETURN coalesce(NEW, OLD); +END; +$$ LANGUAGE plpgsql; + +CREATE TRIGGER trg_sync_is_queryable + AFTER INSERT OR UPDATE OR DELETE ON dict.concept_node_meta + FOR EACH ROW EXECUTE FUNCTION dict.sync_is_queryable(); diff --git a/services/picsure-dictionary/db/flyway/V9__add_fcn_concept_node_id_index.sql b/services/picsure-dictionary/db/flyway/V9__add_fcn_concept_node_id_index.sql new file mode 100644 index 000000000..f188368f8 --- /dev/null +++ b/services/picsure-dictionary/db/flyway/V9__add_fcn_concept_node_id_index.sql @@ -0,0 +1,2 @@ +CREATE INDEX IF NOT EXISTS idx_fcn_concept_node_id + ON dict.facet__concept_node(concept_node_id); diff --git a/services/picsure-dictionary/db/schema.sql b/services/picsure-dictionary/db/schema.sql new file mode 100644 index 000000000..3c209b931 --- /dev/null +++ b/services/picsure-dictionary/db/schema.sql @@ -0,0 +1,120 @@ +CREATE schema dict; + +CREATE TABLE dict.dataset ( + DATASET_ID INT GENERATED BY DEFAULT AS IDENTITY, + REF VARCHAR(512) NOT NULL, + FULL_NAME VARCHAR(512) NOT NULL, + ABBREVIATION VARCHAR(512) NOT NULL, + DESCRIPTION TEXT DEFAULT '', + PRIMARY KEY (DATASET_ID), + UNIQUE (REF) +); + +CREATE TABLE dict.dataset_meta ( + DATASET_META_ID INT GENERATED BY DEFAULT AS IDENTITY, + DATASET_ID INT NOT NULL, + KEY VARCHAR(256) NOT NULL, + VALUE TEXT NOT NULL, + UNIQUE (KEY, DATASET_ID), + CONSTRAINT fk_study FOREIGN KEY(DATASET_ID) REFERENCES dict.dataset(DATASET_ID) +); + +CREATE TABLE dict.consent ( + CONSENT_ID INT GENERATED BY DEFAULT AS IDENTITY, + DATASET_ID INT NOT NULL, + CONSENT_CODE VARCHAR(512) NOT NULL, + DESCRIPTION VARCHAR(512) NOT NULL, + PARTICIPANT_COUNT INT NOT NULL DEFAULT 12, + VARIABLE_COUNT INT NOT NULL DEFAULT 99, + SAMPLE_COUNT INT NOT NULL DEFAULT 14, + AUTHZ VARCHAR(512) NOT NULL, + PRIMARY KEY (CONSENT_ID), + UNIQUE (CONSENT_CODE, DATASET_ID) +); + +CREATE TABLE dict.concept_node ( + CONCEPT_NODE_ID INT GENERATED BY DEFAULT AS IDENTITY, + DATASET_ID INT NOT NULL, + NAME VARCHAR NOT NULL, + DISPLAY VARCHAR NOT NULL, + CONCEPT_TYPE VARCHAR(32) NOT NULL DEFAULT 'Interior', + CONCEPT_PATH VARCHAR(10000) NOT NULL DEFAULT 'INVALID', + PARENT_ID INT, + SEARCHABLE_FIELDS TSVECTOR, + PRIMARY KEY (CONCEPT_NODE_ID), + CONSTRAINT fk_parent FOREIGN KEY (PARENT_ID) REFERENCES dict.CONCEPT_NODE(CONCEPT_NODE_ID), + CONSTRAINT fk_study FOREIGN KEY (DATASET_ID) REFERENCES dict.dataset(DATASET_ID) +); +CREATE UNIQUE INDEX concept_node_concept_path_idx ON dict.CONCEPT_NODE (md5(CONCEPT_PATH)); + +CREATE TABLE dict.concept_node_meta ( + CONCEPT_NODE_META_ID INT GENERATED BY DEFAULT AS IDENTITY, + CONCEPT_NODE_ID INT NOT NULL, + KEY VARCHAR(256) NOT NULL, + VALUE TEXT NOT NULL, + PRIMARY KEY (CONCEPT_NODE_META_ID), + UNIQUE (KEY, CONCEPT_NODE_ID), + CONSTRAINT fk_CONCEPT_NODE FOREIGN KEY (CONCEPT_NODE_ID) REFERENCES dict.CONCEPT_NODE(CONCEPT_NODE_ID) +); +CREATE TABLE dict.facet_category ( + FACET_CATEGORY_ID INT GENERATED BY DEFAULT AS IDENTITY, + NAME VARCHAR(512) NOT NULL, + DISPLAY VARCHAR(512) NOT NULL, + DESCRIPTION TEXT DEFAULT '', + PRIMARY KEY (FACET_CATEGORY_ID), + UNIQUE (NAME) +); + +CREATE TABLE dict.facet ( + FACET_ID INT GENERATED BY DEFAULT AS IDENTITY, + FACET_CATEGORY_ID INT NOT NULL, + NAME VARCHAR(512) NOT NULL, + DISPLAY VARCHAR(512) NOT NULL, + DESCRIPTION TEXT DEFAULT '', + PARENT_ID INT, + PRIMARY KEY (FACET_ID), + UNIQUE (NAME, FACET_CATEGORY_ID), + CONSTRAINT fk_parent FOREIGN KEY (PARENT_ID) REFERENCES dict.facet(FACET_ID), + CONSTRAINT fk_category FOREIGN KEY (FACET_CATEGORY_ID) REFERENCES dict.facet_category(FACET_CATEGORY_ID) +); + +CREATE TABLE dict.facet_meta ( + FACET_META_ID INT GENERATED BY DEFAULT AS IDENTITY, + FACET_ID INT NOT NULL, + KEY VARCHAR(256) NOT NULL, + VALUE TEXT NOT NULL, + UNIQUE (KEY, FACET_ID), + CONSTRAINT fk_facet FOREIGN KEY(FACET_ID) REFERENCES dict.facet(FACET_ID) +); + +CREATE TABLE dict.facet_category_meta ( + FACET_CATEGORY_META_ID INT GENERATED BY DEFAULT AS IDENTITY, + FACET_CATEGORY_ID INT NOT NULL, + KEY VARCHAR(256) NOT NULL, + VALUE TEXT NOT NULL, + UNIQUE (KEY, FACET_CATEGORY_ID), + CONSTRAINT fk_facet_category FOREIGN KEY(FACET_CATEGORY_ID) REFERENCES dict.facet_category(FACET_CATEGORY_ID) +); + +CREATE TABLE dict.facet__concept_node ( + FACET__CONCEPT_NODE_ID INT GENERATED BY DEFAULT AS IDENTITY, + FACET_ID INT NOT NULL, + CONCEPT_NODE_ID INT NOT NULL, + PRIMARY KEY (FACET__CONCEPT_NODE_ID), + UNIQUE (FACET_ID, CONCEPT_NODE_ID), + CONSTRAINT fk_facet FOREIGN KEY (FACET_ID) REFERENCES dict.facet(FACET_ID), + CONSTRAINT fk_concept_node FOREIGN KEY (CONCEPT_NODE_ID) REFERENCES dict.concept_node(CONCEPT_NODE_ID) +); + +CREATE TABLE IF NOT EXISTS dict.dataset_harmonization +( + dataset_harmonization_id INT NOT NULL GENERATED BY DEFAULT AS IDENTITY, + harmonized_dataset_id INT NOT NULL, + source_dataset_id INT NOT NULL, + UNIQUE (harmonized_dataset_id, source_dataset_id), + CONSTRAINT fk_harmonized_dataset_id FOREIGN KEY (harmonized_dataset_id) + REFERENCES dict.dataset (dataset_id), + CONSTRAINT fk_source_dataset_id FOREIGN KEY (source_dataset_id) + REFERENCES dict.dataset (dataset_id) +); + diff --git a/services/picsure-dictionary/dictionaryweights/.gitignore b/services/picsure-dictionary/dictionaryweights/.gitignore new file mode 100644 index 000000000..549e00a2a --- /dev/null +++ b/services/picsure-dictionary/dictionaryweights/.gitignore @@ -0,0 +1,33 @@ +HELP.md +target/ +!.mvn/wrapper/maven-wrapper.jar +!**/src/main/**/target/ +!**/src/test/**/target/ + +### STS ### +.apt_generated +.classpath +.factorypath +.project +.settings +.springBeans +.sts4-cache + +### IntelliJ IDEA ### +.idea +*.iws +*.iml +*.ipr + +### NetBeans ### +/nbproject/private/ +/nbbuild/ +/dist/ +/nbdist/ +/.nb-gradle/ +build/ +!**/src/main/**/build/ +!**/src/test/**/build/ + +### VS Code ### +.vscode/ diff --git a/services/picsure-dictionary/dictionaryweights/.sdkmanrc b/services/picsure-dictionary/dictionaryweights/.sdkmanrc new file mode 100644 index 000000000..d2344323e --- /dev/null +++ b/services/picsure-dictionary/dictionaryweights/.sdkmanrc @@ -0,0 +1 @@ +java=25.0.3-tem diff --git a/services/picsure-dictionary/dictionaryweights/Dockerfile b/services/picsure-dictionary/dictionaryweights/Dockerfile new file mode 100644 index 000000000..cc8838382 --- /dev/null +++ b/services/picsure-dictionary/dictionaryweights/Dockerfile @@ -0,0 +1,25 @@ +FROM maven:3.9-eclipse-temurin-22-alpine AS build + +COPY pom.xml . + +RUN mvn -B dependency:go-offline + +COPY src src + +RUN mvn -B package -DskipTests + +FROM amazoncorretto:22-alpine + +# Copy jar and access token from maven build +COPY --from=build target/dictionaryweights-*.jar /dictionaryweights.jar + +ARG DATASOURCE_URL +ARG DATASOURCE_USERNAME +ARG SPRING_PROFILE + +# If a --env-file is passed in, you can override these values +ENV DATASOURCE_URL=${DATASOURCE_URL} +ENV DATASOURCE_USERNAME=${DATASOURCE_USERNAME} +ENV SPRING_PROFILE=${SPRING_PROFILE} + +ENTRYPOINT java -jar /dictionaryweights.jar --spring.profiles.active=${SPRING_PROFILE:-} \ No newline at end of file diff --git a/services/picsure-dictionary/dictionaryweights/README.md b/services/picsure-dictionary/dictionaryweights/README.md new file mode 100644 index 000000000..39e635296 --- /dev/null +++ b/services/picsure-dictionary/dictionaryweights/README.md @@ -0,0 +1,11 @@ +## Docker commands for local development +### Docker build +```bash +docker build --no-cache --build-arg SPRING_PROFILE=bdc-dev -t weights:latest . +``` + +### Docker run +You will need a local weights.csv file. +```bash + docker run --rm -t --name dictionary-weights --network=host -v ./weights.csv:/weights.csv weights:latest +``` \ No newline at end of file diff --git a/services/picsure-dictionary/dictionaryweights/pom.xml b/services/picsure-dictionary/dictionaryweights/pom.xml new file mode 100644 index 000000000..6c3804989 --- /dev/null +++ b/services/picsure-dictionary/dictionaryweights/pom.xml @@ -0,0 +1,63 @@ + + + 4.0.0 + + edu.harvard.hms.dbmi.avillach + pic-sure-api + ${revision} + ../../../pom.xml + + edu.harvard.dbmi.avillach + dictionaryweights + dictionaryweights + Creates weights + + + org.springframework.boot + spring-boot-starter-jdbc + + + + org.postgresql + postgresql + runtime + + + + org.springframework.boot + spring-boot-starter-test + test + + + org.springframework.boot + spring-boot-testcontainers + test + + + org.testcontainers + junit-jupiter + test + + + org.testcontainers + postgresql + test + + + com.amazonaws.secretsmanager + aws-secretsmanager-jdbc + 2.0.2 + + + + + + + org.springframework.boot + spring-boot-maven-plugin + + + + + diff --git a/services/picsure-dictionary/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/DataSourceVerifier.java b/services/picsure-dictionary/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/DataSourceVerifier.java new file mode 100644 index 000000000..9e3630847 --- /dev/null +++ b/services/picsure-dictionary/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/DataSourceVerifier.java @@ -0,0 +1,39 @@ +package edu.harvard.dbmi.avillach.dictionary.datasource; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.context.event.ContextRefreshedEvent; +import org.springframework.context.event.EventListener; +import org.springframework.stereotype.Service; + +import javax.sql.DataSource; +import java.sql.Connection; +import java.sql.SQLException; + +@Service +public class DataSourceVerifier { + + private static final Logger LOG = LoggerFactory.getLogger(DataSourceVerifier.class); + + private final DataSource dataSource; + + @Autowired + public DataSourceVerifier(DataSource dataSource) { + this.dataSource = dataSource; + } + + @EventListener(ContextRefreshedEvent.class) + public void verifyDataSourceConnection() { + try (Connection connection = dataSource.getConnection()) { + if (connection != null) { + LOG.info("Datasource connection verified successfully."); + } else { + LOG.info("Failed to obtain a connection from the datasource."); + } + } catch (SQLException e) { + LOG.info("Error verifying datasource connection: {}", e.getMessage()); + } + } + +} diff --git a/services/picsure-dictionary/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/DictionaryWeightsApplication.java b/services/picsure-dictionary/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/DictionaryWeightsApplication.java new file mode 100644 index 000000000..8f3e6ca91 --- /dev/null +++ b/services/picsure-dictionary/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/DictionaryWeightsApplication.java @@ -0,0 +1,65 @@ +package edu.harvard.dbmi.avillach.dictionaryweights; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.CommandLineRunner; +import org.springframework.boot.SpringApplication; +import org.springframework.boot.autoconfigure.SpringBootApplication; +import org.springframework.context.annotation.Bean; + +import java.io.File; +import java.io.IOException; +import java.nio.file.Files; +import java.util.List; + +@SpringBootApplication +public class DictionaryWeightsApplication { + + private static final Logger LOG = LoggerFactory.getLogger(DictionaryWeightsApplication.class); + + @Autowired + WeightingParser parser; + + @Autowired + WeightUpdateCreator updateCreator; + + @Autowired + WeightUpdateApplier updateApplier; + + @Value("${weights.filename}") + private String weightingFileName; + + + public static void main(String[] args) throws IOException { + SpringApplication.run(DictionaryWeightsApplication.class, args); + } + + @Bean + public CommandLineRunner commandLineRunner() { + return ignored -> { + LOG.info("Starting weighting..."); + File file = new File(weightingFileName); + if (!file.exists() || file.isDirectory()) { + LOG.error("File not found {}", weightingFileName); + System.exit(1); + } + + LOG.info("Found weighting file. Parsing weights..."); + List rawWeights = Files.readAllLines(file.toPath()); + List weightings = parser.parseWeights(rawWeights); + LOG.info("Found {} weights", weightings.size()); + if (weightings.isEmpty()) { + LOG.warn("Since no weightings were parsed, exiting."); + System.exit(1); + } + + String update = updateCreator.createUpdate(weightings); + updateApplier.applyUpdate(update); + LOG.info("Done. Exiting"); + System.exit(0); + }; + } + +} diff --git a/services/picsure-dictionary/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/Weight.java b/services/picsure-dictionary/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/Weight.java new file mode 100644 index 000000000..57dad5c56 --- /dev/null +++ b/services/picsure-dictionary/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/Weight.java @@ -0,0 +1,14 @@ +package edu.harvard.dbmi.avillach.dictionaryweights; + +import java.util.Set; + +public record Weight(String key, String tier) { + + private static final Set VALID_TIERS = Set.of("A", "B", "C", "D"); + + public Weight { + if (tier == null || !VALID_TIERS.contains(tier)) { + throw new IllegalArgumentException("Tier must be one of: A, B, C, D"); + } + } +} diff --git a/services/picsure-dictionary/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightUpdateApplier.java b/services/picsure-dictionary/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightUpdateApplier.java new file mode 100644 index 000000000..652249831 --- /dev/null +++ b/services/picsure-dictionary/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightUpdateApplier.java @@ -0,0 +1,21 @@ +package edu.harvard.dbmi.avillach.dictionaryweights; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.jdbc.core.JdbcTemplate; +import org.springframework.stereotype.Service; + +@Service +public class WeightUpdateApplier { + + private static final Logger LOG = LoggerFactory.getLogger(WeightUpdateApplier.class); + + @Autowired + JdbcTemplate template; + + public void applyUpdate(String query) { + LOG.info("Applying query to DB"); + template.update(query); + } +} diff --git a/services/picsure-dictionary/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightUpdateCreator.java b/services/picsure-dictionary/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightUpdateCreator.java new file mode 100644 index 000000000..7b4bf7737 --- /dev/null +++ b/services/picsure-dictionary/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightUpdateCreator.java @@ -0,0 +1,99 @@ +package edu.harvard.dbmi.avillach.dictionaryweights; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.stereotype.Service; + +import java.util.List; +import java.util.regex.Pattern; +import java.util.stream.Collectors; + +/** + * Generates the SQL UPDATE statement that populates the searchable_fields tsvector column on concept_node. Each field is wrapped in + * {@code setweight(to_tsvector(...), tier)} and concatenated with {@code ||} to produce a single weighted tsvector per concept. + * + *

    Weight tiers (A/B/C/D) control ranking via {@code ts_rank}/{@code ts_rank_cd}: A = highest priority (display name, path), D = lowest + * (meta values).

    + * + *

    Underscores in field values are replaced with spaces before tsvector conversion so that terms like {@code pasc_pg2023} are tokenized + * as two independent terms ({@code pasc}, {@code pg2023}) rather than a single file-path token.

    + * + *

    Meta values are filtered to a whitelist of searchable keys (description, values, derived_values, variable_type, comment, domain, + * question, unit) to avoid indexing non-searchable content like DRS URIs or numeric identifiers. The 'values' key is capped at 60k + * characters to handle imaging datasets with very large categorical value sets.

    + * + *

    The tsvector is built with the 'english' language configuration to match the query layer's use of {@code to_tsquery('english', ...)}. + * Without this, the server default ({@code pg_catalog.simple}) applies no stemming, causing mismatches for words like "Coding" (stored as + * 'coding' but queried as 'code:*').

    + */ +@Service +public class WeightUpdateCreator { + + private static final Logger LOG = LoggerFactory.getLogger(WeightUpdateCreator.class); + private static final Pattern SAFE_SQL_IDENTIFIER = Pattern.compile("^[a-zA-Z_][a-zA-Z0-9_.]*$"); + + /** + * Builds the UPDATE statement from the given weight configuration. Each weight entry specifies a field name and a tier (A/B/C/D). The + * field is wrapped in {@code setweight(to_tsvector('english', replace(coalesce(FIELD, ''), '_', ' ')), 'TIER')} and all entries are + * joined with {@code ||}. + */ + public String createUpdate(List weights) { + LOG.info("Turning {} weights into a setweight query", weights.size()); + String searchVector = weights.stream().map(w -> { + if (!SAFE_SQL_IDENTIFIER.matcher(w.key()).matches()) { + throw new IllegalArgumentException("Unsafe SQL identifier in weight key: " + w.key()); + } + return "setweight(to_tsvector('english', replace(coalesce(%s, ''), '_', ' ')), '%s')".formatted(w.key(), w.tier()); + }).collect(Collectors.joining(" ||\n ")); + return """ + UPDATE concept_node + SET SEARCHABLE_FIELDS = data_table.search_vector + FROM + ( + SELECT + %s + AS search_vector, + concept_node.concept_node_id AS search_key + FROM + concept_node + LEFT JOIN + ( + SELECT + concept_node_id AS id, + string_agg(DISTINCT safe_value, ' ') AS values + FROM ( + SELECT concept_node_id, value AS safe_value + FROM concept_node_meta + WHERE value <> '' + AND key IN ('description','derived_values','variable_type','comment','domain','Question','question','unit') + UNION ALL + SELECT concept_node_id, left(value, 60000) AS safe_value + FROM concept_node_meta + WHERE value <> '' AND key = 'values' + ) AS filtered_meta + GROUP BY + concept_node_id + ) AS concept_node_meta_str ON concept_node_meta_str.id = concept_node.concept_node_id + LEFT JOIN dataset AS study ON concept_node.dataset_id = study.dataset_id + LEFT JOIN concept_node AS parent ON concept_node.parent_id = parent.concept_node_id + LEFT JOIN concept_node AS grandparent ON parent.parent_id = grandparent.concept_node_id + LEFT JOIN ( + SELECT + dataset_node.name AS NAME, + dataset_node.display AS FULL_NAME, + dataset_node.concept_path AS CONCEPT_PATH, + description_concept_node_meta.VALUE AS DESCRIPTION + FROM + concept_node AS dataset_node + JOIN concept_node_meta AS description_concept_node_meta ON description_concept_node_meta.KEY = 'description' AND description_concept_node_meta.concept_node_id = dataset_node.concept_node_id + ---------------------------------------------------------------------------------------------------- + -- This join is saying "find me the concept node that shares the first two nodes of this concept + -- and then stops". So for /a/b/c/d/e/f/, it finds concept /a/b/ + ---------------------------------------------------------------------------------------------------- + ) AS dataset ON dataset.concept_path = REGEXP_REPLACE(concept_node.concept_path, '(^\\\\[^\\\\]*\\\\[^\\\\]*\\\\)(.*$)', '\\1') + ) AS data_table + WHERE concept_node.concept_node_id = data_table.search_key; + """ + .formatted(searchVector); + } +} diff --git a/services/picsure-dictionary/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightingParser.java b/services/picsure-dictionary/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightingParser.java new file mode 100644 index 000000000..bca393fe0 --- /dev/null +++ b/services/picsure-dictionary/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightingParser.java @@ -0,0 +1,39 @@ +package edu.harvard.dbmi.avillach.dictionaryweights; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.stereotype.Service; + +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.stream.Stream; + +@Service +public class WeightingParser { + private static final Logger LOG = LoggerFactory.getLogger(WeightingParser.class); + private static final Set VALID_TIERS = Set.of("A", "B", "C", "D"); + private static final Map NUMERIC_TIER_MAP = Map.of("1", "A", "2", "B", "3", "C", "4", "D"); + + public List parseWeights(List weights) { + return weights.stream().flatMap(this::parseWeight).toList(); + } + + private Stream parseWeight(String line) { + String[] split = line.split(","); + if (split.length != 2) { + LOG.warn("Failed to parse line {}, expected two column CSV", line); + return Stream.empty(); + } + + String raw = split[1].trim().toUpperCase(); + String tier = NUMERIC_TIER_MAP.getOrDefault(raw, raw); + if (!VALID_TIERS.contains(tier)) { + LOG.warn("Failed to parse line {} because {} is not a valid tier (A/B/C/D)", line, raw); + return Stream.empty(); + } + + return Stream.of(new Weight(split[0].trim(), tier)); + } + +} diff --git a/services/picsure-dictionary/dictionaryweights/src/main/resources/application-bdc-dev.properties b/services/picsure-dictionary/dictionaryweights/src/main/resources/application-bdc-dev.properties new file mode 100644 index 000000000..5b79313e4 --- /dev/null +++ b/services/picsure-dictionary/dictionaryweights/src/main/resources/application-bdc-dev.properties @@ -0,0 +1,9 @@ +spring.application.name=dictionaryweights +spring.main.web-application-type=none + +spring.datasource.url=jdbc:postgresql://localhost:5432/dictionary_db?currentSchema=dict +spring.datasource.username=username +spring.datasource.password=password +spring.datasource.driver-class-name=org.postgresql.Driver + +weights.filename=/weights.csv \ No newline at end of file diff --git a/services/picsure-dictionary/dictionaryweights/src/main/resources/application-bdc.properties b/services/picsure-dictionary/dictionaryweights/src/main/resources/application-bdc.properties new file mode 100644 index 000000000..1c97a8133 --- /dev/null +++ b/services/picsure-dictionary/dictionaryweights/src/main/resources/application-bdc.properties @@ -0,0 +1,9 @@ +spring.application.name=dictionaryweights +spring.main.web-application-type=none + +spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.PostgreSQLDialect +spring.datasource.driver-class-name=com.amazonaws.secretsmanager.sql.AWSSecretsManagerPostgreSQLDriver +spring.datasource.url=jdbc-secretsmanager:postgresql://${DATASOURCE_URL}/picsure?useUnicode=true&characterEncoding=UTF-8&autoReconnect=true&autoReconnectForPools=true¤tSchema=dict +spring.datasource.username=${DATASOURCE_USERNAME} + +weights.filename=/weights.csv \ No newline at end of file diff --git a/services/picsure-dictionary/dictionaryweights/src/main/resources/application.properties b/services/picsure-dictionary/dictionaryweights/src/main/resources/application.properties new file mode 100644 index 000000000..f58d101a5 --- /dev/null +++ b/services/picsure-dictionary/dictionaryweights/src/main/resources/application.properties @@ -0,0 +1,9 @@ +spring.application.name=dictionaryweights +spring.main.web-application-type=none + +spring.datasource.url=jdbc:postgresql://${POSTGRES_HOST}:5432/${POSTGRES_DB}?currentSchema=dict +spring.datasource.username=${POSTGRES_USER} +spring.datasource.password=${POSTGRES_PASSWORD} +spring.datasource.driver-class-name=org.postgresql.Driver + +weights.filename=/weights.csv \ No newline at end of file diff --git a/services/picsure-dictionary/dictionaryweights/src/test/java/edu/harvard/dbmi/avillach/dictionaryweights/DictionaryWeightsApplicationTests.java b/services/picsure-dictionary/dictionaryweights/src/test/java/edu/harvard/dbmi/avillach/dictionaryweights/DictionaryWeightsApplicationTests.java new file mode 100644 index 000000000..275e6babb --- /dev/null +++ b/services/picsure-dictionary/dictionaryweights/src/test/java/edu/harvard/dbmi/avillach/dictionaryweights/DictionaryWeightsApplicationTests.java @@ -0,0 +1,18 @@ +package edu.harvard.dbmi.avillach.dictionaryweights; + +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; +import org.springframework.boot.test.context.SpringBootTest; + +@Disabled( + "Pre-existing (predates monorepo adoption): the app's CommandLineRunner calls System.exit on startup, " + + "which kills the surefire fork for any @SpringBootTest. This test never ran in the old repo's CI either. " + + "Re-enable once the runner's exit handling moves out of the bean (tracked as Phase 4 follow-up)." +) +@SpringBootTest +class DictionaryWeightsApplicationTests { + + @Test + void contextLoads() {} + +} diff --git a/services/picsure-dictionary/dictionaryweights/src/test/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightUpdateCreatorTest.java b/services/picsure-dictionary/dictionaryweights/src/test/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightUpdateCreatorTest.java new file mode 100644 index 000000000..27e38f86a --- /dev/null +++ b/services/picsure-dictionary/dictionaryweights/src/test/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightUpdateCreatorTest.java @@ -0,0 +1,35 @@ +package edu.harvard.dbmi.avillach.dictionaryweights; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +import java.util.List; + +class WeightUpdateCreatorTest { + WeightUpdateCreator subject = new WeightUpdateCreator(); + + @Test + void shouldCreateQueryForWeights() { + List weights = List.of(new Weight("TABLE_A.COLUMN", "A"), new Weight("TABLE_B.COLUMN", "B")); + + String actual = subject.createUpdate(weights); + + // Verify setweight structure with tier labels + Assertions.assertTrue( + actual.contains("setweight(to_tsvector('english', replace(coalesce(TABLE_A.COLUMN, ''), '_', ' ')), 'A')"), + "Should contain setweight for TABLE_A.COLUMN with tier A" + ); + Assertions.assertTrue( + actual.contains("setweight(to_tsvector('english', replace(coalesce(TABLE_B.COLUMN, ''), '_', ' ')), 'B')"), + "Should contain setweight for TABLE_B.COLUMN with tier B" + ); + // Verify fields are concatenated with || + Assertions.assertTrue(actual.contains("||"), "Should concatenate tsvectors with ||"); + // Verify underscore replacement uses space (not slash) + Assertions.assertTrue(actual.contains("'_', ' '"), "Should replace underscores with spaces"); + Assertions.assertFalse(actual.contains("'_', '/'"), "Should not replace underscores with slashes"); + // Verify output is a search_vector, not search_str + Assertions.assertTrue(actual.contains("AS search_vector"), "Should output as search_vector"); + Assertions.assertFalse(actual.contains("concat("), "Should not use concat (old pattern)"); + } +} diff --git a/services/picsure-dictionary/dictionaryweights/weights.csv b/services/picsure-dictionary/dictionaryweights/weights.csv new file mode 100644 index 000000000..f2fbc99fb --- /dev/null +++ b/services/picsure-dictionary/dictionaryweights/weights.csv @@ -0,0 +1,7 @@ +concept_node.DISPLAY,A +concept_node.CONCEPT_PATH,A +dataset.FULL_NAME,B +dataset.DESCRIPTION,B +parent.DISPLAY,C +grandparent.DISPLAY,C +concept_node_meta_str.values,D diff --git a/services/picsure-dictionary/dictonaryReqeust.http b/services/picsure-dictionary/dictonaryReqeust.http new file mode 100644 index 000000000..55e8c21d6 --- /dev/null +++ b/services/picsure-dictionary/dictonaryReqeust.http @@ -0,0 +1,45 @@ +# curl 'https://dev.picsure.biodatacatalyst.nhlbi.nih.gov/picsure/proxy/dictionary-api/concepts?page_number=1&page_size=1' +# -H 'origin: https://dev.picsure.biodatacatalyst.nhlbi.nih.gov' +# -H 'referer: https://dev.picsure.biodatacatalyst.nhlbi.nih.gov/' +# --data-raw '{"facets":[],"search":"","consents":[]}' +POST http://localhost:80/concepts?page_number=0&page_size=100 +Content-Type: application/json + +{"facets":[],"search":"lipid triglyceride"} + +### + +POST http://localhost:80/search +Content-Type: application/json + +{"@type":"GeneralQueryRequest","resourceCredentials":{},"query":{"searchTerm":"throat sore acute #8","includedTags":[], + "excludedTags":[],"returnTags":"true","offset":0,"limit":100000},"resourceUUID":null} + +### + +POST http://localhost:80/concepts/detail +Content-Type: application/json + +["\\phs000993\\pht005015\\phv00253191\\BODY_SITE\\", "\\phs002913\\W2Q_COV_REINFEC_2_OTH\\"] + +### + +POST https://predev.picsure.biodatacatalyst.nhlbi.nih.gov/picsure/proxy/dictionary-api/concepts/detail +Content-Type: application/json + +["\\phs000993\\pht005015\\phv00253191\\BODY_SITE\\", "\\phs002913\\W2Q_COV_REINFEC_2_OTH\\"] + +### +# This request is used by our grafana dashboard to check if search is available. +POST https://predev.picsure.biodatacatalyst.nhlbi.nih.gov/picsure/search/02e23f52-f354-4e8b-992c-d37c8b9ba140 +Content-Type: application/json +Authorization: Bearer + +{ + "query": { + "@type": "GeneralQueryRequest", + "resourceCredentials": {}, + "query": "Genetic Epidemiology of COPD (COPDGene)", + "resourceUUID": null + } +} \ No newline at end of file diff --git a/services/picsure-dictionary/docker-compose.dev.yml b/services/picsure-dictionary/docker-compose.dev.yml new file mode 100644 index 000000000..9432c52a3 --- /dev/null +++ b/services/picsure-dictionary/docker-compose.dev.yml @@ -0,0 +1,30 @@ +# Use for local development. This file will create the "dictionary" network. +# The Production file expects the network to already exist. +version: '3.3' + +services: + dictionary-db: + container_name: dictionary-db + image: postgres:16-alpine + volumes: + - picsure-search:/var/lib/postgresql/data + - ./db/schema.sql:/docker-entrypoint-initdb.d/schema.sql:ro + env_file: .env + networks: + - dictionary + dictionary-api: + container_name: dictionary-api + image: avillach/dictionary-api:latest + build: . + depends_on: + - dictionary-db + restart: always + env_file: .env + networks: + - dictionary + +volumes: + picsure-search: + +networks: + dictionary: \ No newline at end of file diff --git a/services/picsure-dictionary/docker-compose.yml b/services/picsure-dictionary/docker-compose.yml new file mode 100644 index 000000000..7eb5e8231 --- /dev/null +++ b/services/picsure-dictionary/docker-compose.yml @@ -0,0 +1,46 @@ +version: '3.3' + +services: + dictionary-db: + container_name: dictionary-db + image: postgres:16-alpine + volumes: + - $DOCKER_CONFIG_DIR/dictionary/db/data:/var/lib/postgresql/data + - $DOCKER_CONFIG_DIR/dictionary/db/schema.sql:/docker-entrypoint-initdb.d/schema.sql:ro + env_file: .env + restart: always + networks: + - dictionary + dictionary-api: + container_name: dictionary-api + image: avillach/dictionary-api:latest + build: . + depends_on: + - dictionary-db + restart: always + env_file: .env + networks: + - dictionary + - picsure + dictionary-dump: + container_name: dictionary-dump + image: avillach/dictionary-dump:latest + build: ./aggregate + depends_on: + - dictionary-db + restart: always + env_file: .env + volumes: + - $DOCKER_CONFIG_DIR/dictionary/dump/application.properties:/application.properties + networks: + - dictionary + - picsure + +volumes: + picsure-search: + +networks: + dictionary: + external: true + picsure: + external: true diff --git a/services/picsure-dictionary/env.example b/services/picsure-dictionary/env.example new file mode 100644 index 000000000..23cc90145 --- /dev/null +++ b/services/picsure-dictionary/env.example @@ -0,0 +1,4 @@ +POSTGRES_HOST=dictionary-db +POSTGRES_DB=dictionary +POSTGRES_USER=picsure +POSTGRES_PASSWORD=changeme diff --git a/services/picsure-dictionary/pom.xml b/services/picsure-dictionary/pom.xml new file mode 100644 index 000000000..9a8ad23e1 --- /dev/null +++ b/services/picsure-dictionary/pom.xml @@ -0,0 +1,94 @@ + + + 4.0.0 + + edu.harvard.hms.dbmi.avillach + pic-sure-api + ${revision} + ../../pom.xml + + edu.harvard.dbmi.avillach + dictionary + dictionary + Data Dictionary API + + + org.springframework.boot + spring-boot-starter-jdbc + + + org.springframework.boot + spring-boot-starter-actuator + + + org.springframework.boot + spring-boot-starter-web + + + org.springframework.data + spring-data-commons + + + org.springframework.boot + spring-boot-starter-cache + + + + com.github.ben-manes.caffeine + caffeine + + + + org.postgresql + postgresql + runtime + + + org.springframework.boot + spring-boot-starter-test + test + + + org.springframework.boot + spring-boot-testcontainers + test + + + org.testcontainers + junit-jupiter + test + + + org.testcontainers + postgresql + test + + + com.amazonaws.secretsmanager + aws-secretsmanager-jdbc + 2.0.2 + + + edu.harvard.dbmi.avillach + pic-sure-logging-client + + + + + + + org.springframework.boot + spring-boot-maven-plugin + + + org.apache.maven.plugins + maven-surefire-plugin + + -Dnet.bytebuddy.experimental=true + + + + + + diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/AuditAttributes.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/AuditAttributes.java new file mode 100644 index 000000000..1fec10a50 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/AuditAttributes.java @@ -0,0 +1,29 @@ +package edu.harvard.dbmi.avillach.dictionary; + +import jakarta.servlet.http.HttpServletRequest; +import java.util.HashMap; +import java.util.Map; + +public final class AuditAttributes { + public static final String EVENT_TYPE = "audit.event_type"; + public static final String ACTION = "audit.action"; + private static final String METADATA = "audit.metadata"; + + private AuditAttributes() {} + + public static void putMetadata(HttpServletRequest request, String key, Object value) { + if (request != null && key != null && value != null) { + getMetadata(request).put(key, value); + } + } + + @SuppressWarnings("unchecked") + public static Map getMetadata(HttpServletRequest request) { + Map metadata = (Map) request.getAttribute(METADATA); + if (metadata == null) { + metadata = new HashMap<>(); + request.setAttribute(METADATA, metadata); + } + return metadata; + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/AuditInterceptor.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/AuditInterceptor.java new file mode 100644 index 000000000..1fb713f2d --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/AuditInterceptor.java @@ -0,0 +1,21 @@ +package edu.harvard.dbmi.avillach.dictionary; + +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import org.springframework.web.method.HandlerMethod; +import org.springframework.web.servlet.HandlerInterceptor; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +public class AuditInterceptor implements HandlerInterceptor { + @Override + public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) { + if (handler instanceof HandlerMethod handlerMethod) { + AuditEvent auditEvent = handlerMethod.getMethodAnnotation(AuditEvent.class); + if (auditEvent != null) { + request.setAttribute(AuditAttributes.EVENT_TYPE, auditEvent.type()); + request.setAttribute(AuditAttributes.ACTION, auditEvent.action()); + } + } + return true; + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/AuditLoggingFilter.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/AuditLoggingFilter.java new file mode 100644 index 000000000..b7a36a87f --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/AuditLoggingFilter.java @@ -0,0 +1,116 @@ +package edu.harvard.dbmi.avillach.dictionary; + +import java.io.IOException; +import java.util.HashMap; +import java.util.Map; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.web.filter.OncePerRequestFilter; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingEvent; +import edu.harvard.dbmi.avillach.logging.RequestInfo; +import edu.harvard.dbmi.avillach.logging.SessionIdResolver; +import jakarta.servlet.FilterChain; +import jakarta.servlet.ServletException; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; + +public class AuditLoggingFilter extends OncePerRequestFilter { + + private static final Logger log = LoggerFactory.getLogger(AuditLoggingFilter.class); + + private final String destIpConfig; + private final Integer destPortConfig; + private final LoggingClient loggingClient; + + public AuditLoggingFilter(LoggingClient loggingClient, String destIp, Integer destPort) { + this.loggingClient = loggingClient; + this.destIpConfig = destIp; + this.destPortConfig = destPort; + } + + @Override + protected boolean shouldNotFilter(HttpServletRequest request) { + return request.getRequestURI().startsWith("/actuator"); + } + + @Override + protected void doFilterInternal(HttpServletRequest request, HttpServletResponse response, FilterChain filterChain) + throws ServletException, IOException { + + long startTime = System.currentTimeMillis(); + try { + filterChain.doFilter(request, response); + } finally { + try { + if (loggingClient == null || !loggingClient.isEnabled()) return; + + String fullPath = request.getRequestURI(); + String method = request.getMethod(); + long duration = System.currentTimeMillis() - startTime; + + String eventType = (String) request.getAttribute(AuditAttributes.EVENT_TYPE); + String action = (String) request.getAttribute(AuditAttributes.ACTION); + if (eventType == null) eventType = "OTHER"; + if (action == null) action = method.toLowerCase(); + + String srcIp = extractSourceIp(request); + String destIp = destIpConfig != null ? destIpConfig : request.getLocalAddr(); + int destPort = destPortConfig != null ? destPortConfig : request.getLocalPort(); + + int responseStatus = response.getStatus(); + String contentType = response.getContentType(); + Long bytes = parseContentLength(response.getHeader("Content-Length")); + + String queryString = request.getQueryString(); + RequestInfo requestInfo = RequestInfo.builder().method(method).url(fullPath).queryString(queryString).srcIp(srcIp) + .destIp(destIp).destPort(destPort).httpUserAgent(request.getHeader("User-Agent")).status(responseStatus) + .duration(duration).httpContentType(contentType).bytes(bytes).build(); + + Map metadata = new HashMap<>(); + String sessionId = SessionIdResolver.resolve(request.getHeader("X-Session-Id"), srcIp, request.getHeader("User-Agent")); + + AuditAttributes.getMetadata(request).forEach(metadata::putIfAbsent); + + Map errorMap = null; + if (responseStatus >= 400) { + errorMap = new HashMap<>(); + errorMap.put("status", responseStatus); + errorMap.put("error_type", responseStatus >= 500 ? "server_error" : "client_error"); + } + + LoggingEvent.Builder eventBuilder = + LoggingEvent.builder(eventType).action(action).sessionId(sessionId).request(requestInfo).metadata(metadata); + if (errorMap != null) eventBuilder.error(errorMap); + LoggingEvent event = eventBuilder.build(); + + String authHeader = request.getHeader("Authorization"); + String requestId = request.getHeader("X-Request-Id"); + if (authHeader != null || requestId != null) { + loggingClient.send(event, authHeader, requestId); + } else { + loggingClient.send(event); + } + } catch (Exception e) { + log.warn("AuditLoggingFilter failed to log request", e); + } + } + } + + static String extractSourceIp(HttpServletRequest request) { + String xff = request.getHeader("X-Forwarded-For"); + if (xff != null && !xff.isEmpty()) return xff.split(",")[0].trim(); + return request.getRemoteAddr(); + } + + static Long parseContentLength(String header) { + if (header == null) return null; + try { + return Long.parseLong(header); + } catch (NumberFormatException e) { + return null; + } + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/DictionaryApplication.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/DictionaryApplication.java new file mode 100644 index 000000000..40fee5600 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/DictionaryApplication.java @@ -0,0 +1,15 @@ +package edu.harvard.dbmi.avillach.dictionary; + +import org.springframework.boot.SpringApplication; +import org.springframework.boot.autoconfigure.SpringBootApplication; +import org.springframework.cache.annotation.EnableCaching; + +@SpringBootApplication +@EnableCaching +public class DictionaryApplication { + + public static void main(String[] args) { + SpringApplication.run(DictionaryApplication.class, args); + } + +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/LoggingConfig.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/LoggingConfig.java new file mode 100644 index 000000000..b13c6a405 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/LoggingConfig.java @@ -0,0 +1,48 @@ +package edu.harvard.dbmi.avillach.dictionary; + +import edu.harvard.dbmi.avillach.logging.LoggingClient; +import edu.harvard.dbmi.avillach.logging.LoggingClientFactory; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.web.servlet.FilterRegistrationBean; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.web.servlet.config.annotation.InterceptorRegistry; +import org.springframework.web.servlet.config.annotation.WebMvcConfigurer; + +@Configuration +public class LoggingConfig implements WebMvcConfigurer { + + @Value("${DEST_IP:#{null}}") + private String destIp; + + @Value("${DEST_PORT:#{null}}") + private Integer destPort; + + @Bean + public LoggingClient loggingClient() { + return LoggingClientFactory.create("dictionary"); + } + + @Bean + public AuditLoggingFilter auditLoggingFilter(LoggingClient loggingClient) { + return new AuditLoggingFilter(loggingClient, destIp, destPort); + } + + @Bean + public FilterRegistrationBean auditLoggingFilterRegistration(AuditLoggingFilter auditLoggingFilter) { + FilterRegistrationBean registration = new FilterRegistrationBean<>(auditLoggingFilter); + registration.addUrlPatterns("/*"); + registration.setOrder(1); + return registration; + } + + @Bean + public AuditInterceptor auditInterceptor() { + return new AuditInterceptor(); + } + + @Override + public void addInterceptors(InterceptorRegistry registry) { + registry.addInterceptor(auditInterceptor()); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptController.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptController.java new file mode 100644 index 000000000..4706227cc --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptController.java @@ -0,0 +1,132 @@ +package edu.harvard.dbmi.avillach.dictionary.concept; + +import edu.harvard.dbmi.avillach.dictionary.AuditAttributes; +import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept; +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import jakarta.servlet.http.HttpServletRequest; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.data.domain.Page; +import org.springframework.data.domain.PageImpl; +import org.springframework.data.domain.PageRequest; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.*; + +import java.util.List; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.Executors; +import java.util.concurrent.Future; + +@Controller +public class ConceptController { + + private final ConceptService conceptService; + + @Autowired + private HttpServletRequest httpRequest; + + @Value("${concept.tree.max_depth:5}") + private Integer MAX_DEPTH; + + + public ConceptController(@Autowired ConceptService conceptService) { + this.conceptService = conceptService; + } + + + @AuditEvent(type = "SEARCH", action = "concept.search") + @PostMapping(path = "/concepts") + public ResponseEntity> listConcepts( + @RequestBody Filter filter, @RequestParam(name = "page_number", defaultValue = "0", required = false) int page, + @RequestParam(name = "page_size", defaultValue = "10", required = false) int size + ) { + PageRequest pagination = PageRequest.of(page, size); + + // Run count and list in parallel — both are independent and cached separately + long count; + List concepts; + try (ExecutorService executor = Executors.newVirtualThreadPerTaskExecutor()) { + Future countFuture = executor.submit(() -> conceptService.countConcepts(filter)); + Future> conceptsFuture = executor.submit(() -> conceptService.listConcepts(filter, pagination)); + count = countFuture.get(); + concepts = conceptsFuture.get(); + } catch (InterruptedException e) { + Thread.currentThread().interrupt(); + throw new RuntimeException("Parallel concept query interrupted", e); + } catch (Exception e) { + throw new RuntimeException("Parallel concept query failed", e); + } + + PageImpl pageResp = new PageImpl<>(concepts, pagination, count); + + AuditAttributes.putMetadata(httpRequest, "search_term", filter.search() != null ? filter.search() : ""); + AuditAttributes.putMetadata(httpRequest, "result_count", String.valueOf(count)); + + return ResponseEntity.ok(pageResp); + } + + @AuditEvent(type = "DATA_ACCESS", action = "concept.dump") + @GetMapping(path = "/concepts/dump") + public ResponseEntity> dumpConcepts( + @RequestParam(name = "page_number", defaultValue = "0", required = false) int page, + @RequestParam(name = "page_size", defaultValue = "10", required = false) int size + ) { + PageRequest pagination = PageRequest.of(page, size); + PageImpl pageResp = new PageImpl<>( + conceptService.listDetailedConcepts(new Filter(List.of(), "", List.of()), pagination), pagination, + conceptService.countConcepts(new Filter(List.of(), "", List.of())) + ); + + return ResponseEntity.ok(pageResp); + } + + @AuditEvent(type = "SEARCH", action = "concept.detail") + @PostMapping(path = "/concepts/detail/{dataset}") + public ResponseEntity conceptDetail(@PathVariable(name = "dataset") String dataset, @RequestBody() String conceptPath) { + return conceptService.conceptDetail(dataset, conceptPath).map(ResponseEntity::ok).orElse(ResponseEntity.notFound().build()); + } + + @AuditEvent(type = "SEARCH", action = "concept.detail") + @PostMapping(path = "/concepts/detail") + public ResponseEntity> conceptsDetail(@RequestBody() List conceptPaths) { + return ResponseEntity.ok(conceptService.conceptsWithDetail(conceptPaths)); + } + + @AuditEvent(type = "SEARCH", action = "concept.tree") + @PostMapping(path = "/concepts/tree/{dataset}") + public ResponseEntity conceptTree( + @PathVariable(name = "dataset") String dataset, @RequestBody() String conceptPath, + @RequestParam(name = "depth", required = false, defaultValue = "2") Integer depth + ) { + if (depth < 0 || depth > MAX_DEPTH) { + return ResponseEntity.badRequest().build(); + } + return conceptService.conceptTree(dataset, conceptPath, depth).map(ResponseEntity::ok).orElse(ResponseEntity.notFound().build()); + } + + @AuditEvent(type = "SEARCH", action = "concept.hierarchy") + @PostMapping(path = "/concepts/hierarchy/{dataset}") + public ResponseEntity> conceptHierarchy( + @PathVariable(name = "dataset") String dataset, @RequestBody() String conceptPath + ) { + List body = conceptService.conceptHierarchy(dataset, conceptPath); + if (body.isEmpty()) { + return ResponseEntity.notFound().build(); + } + return ResponseEntity.ok(body); + } + + @AuditEvent(type = "SEARCH", action = "concept.tree") + @GetMapping(path = "/concepts/tree") + public ResponseEntity> allConceptTrees( + @RequestParam(name = "depth", required = false, defaultValue = "2") Integer depth + ) { + if (depth < 0 || depth > MAX_DEPTH) { + return ResponseEntity.badRequest().build(); + } + + return ResponseEntity.ok(conceptService.allConceptTrees(depth)); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptDecoratorService.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptDecoratorService.java new file mode 100644 index 000000000..788551faf --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptDecoratorService.java @@ -0,0 +1,69 @@ +package edu.harvard.dbmi.avillach.dictionary.concept; + +import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept; +import edu.harvard.dbmi.avillach.dictionary.dataset.Dataset; +import edu.harvard.dbmi.avillach.dictionary.dataset.DatasetService; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.context.annotation.Lazy; +import org.springframework.stereotype.Service; + +import java.util.List; +import java.util.Optional; +import java.util.function.Predicate; +import java.util.stream.Stream; + +@Service +public class ConceptDecoratorService { + + private static final Logger LOG = LoggerFactory.getLogger(ConceptDecoratorService.class); + private final boolean enabled; + private final ConceptService conceptService; + private final DatasetService datasetService; + + private static final int COMPLIANT = 4, NON_COMPLIANT_TABLED = 3, NON_COMPLIANT_UNTABLED = 2, WEIRD_1 = 1, WEIRD_0 = 0; + + @Autowired + public ConceptDecoratorService( + @Value("${dashboard.enable.extra_details}") boolean enabled, @Lazy ConceptService conceptService, DatasetService datasetService // circular + // dep + ) { + this.enabled = enabled; + this.conceptService = conceptService; + this.datasetService = datasetService; + } + + + public Concept populateParentConcepts(Concept concept) { + if (!enabled) { + return concept; + } + + // In some environments, certain parent concepts have critical details that we need to add to the detailed response + List conceptNodes = Stream.of(concept.conceptPath().split("\\\\")).filter(Predicate.not(String::isBlank)).toList(); + // you have to double escape the slash. Once for strings, and once for regex + + return switch (conceptNodes.size()) { + case NON_COMPLIANT_UNTABLED -> populateNonCompliantTabledConcept(concept, conceptNodes); + case WEIRD_0, WEIRD_1 -> { + LOG.warn("Ignoring decoration request for weird concept path {}", concept.conceptPath()); + yield concept; + } + default -> populateTabledConcept(concept, conceptNodes); + }; + } + + private Concept populateTabledConcept(Concept concept, List conceptNodes) { + String tablePath = "\\" + String.join("\\", conceptNodes.subList(0, 2)) + "\\"; + Dataset study = datasetService.getDataset(concept.dataset()).orElse(null); + Concept table = conceptService.conceptDetailWithoutAncestors(concept.dataset(), tablePath).orElse(null); + return concept.withStudy(study).withTable(table); + } + + private Concept populateNonCompliantTabledConcept(Concept concept, List conceptNodes) { + Dataset study = datasetService.getDataset(concept.dataset()).orElse(null); + return concept.withStudy(study); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptFilterQueryGenerator.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptFilterQueryGenerator.java new file mode 100644 index 000000000..aac9e89f2 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptFilterQueryGenerator.java @@ -0,0 +1,326 @@ +package edu.harvard.dbmi.avillach.dictionary.concept; + +import edu.harvard.dbmi.avillach.dictionary.facet.Facet; +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import edu.harvard.dbmi.avillach.dictionary.filter.QueryParamPair; +import edu.harvard.dbmi.avillach.dictionary.util.QueryUtility; +import edu.harvard.dbmi.avillach.dictionary.util.SchemaDetector; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.data.domain.Pageable; +import org.springframework.jdbc.core.namedparam.MapSqlParameterSource; +import org.springframework.stereotype.Component; +import org.springframework.util.CollectionUtils; +import org.springframework.util.StringUtils; + +import java.util.List; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +/** + * Builds dynamic SQL for concept search queries. Handles facet filtering, consent-based dataset scoping, full-text search ranking, and + * pagination. The generated queries use INTERSECT to AND facet categories together and a ranking CTE to order results. + */ +@Component +public class ConceptFilterQueryGenerator { + private final List disallowedMetaFields; + private final SchemaDetector schemaDetector; + + /** + * CTE fragment that computes a rank adjustment multiplier per concept. Concepts flagged with disallowed meta keys (e.g. + * stigmatized=true) get a multiplier of 0, pushing them to the bottom of search results without excluding them entirely. + */ + private static final String RANK_ADJUSTMENTS = """ + , allow_filtering AS ( + SELECT + concept_node_meta.concept_node_id AS concept_node_id, + (concept_node_meta.value <> 'true')::int AS rank_adjustment + FROM + concept_node_meta + WHERE + concept_node_meta.KEY IN (:disallowed_meta_keys) + ) + """; + + /** + * WHERE clause fragment that restricts results to datasets the user has consent for. Resolves both direct consent codes (phs000123.c1) + * and harmonized dataset mappings. Expects a :consents named parameter containing the user's consent list. + */ + private static final String CONSENT_QUERY = """ + dataset.dataset_id IN ( + SELECT + consent.dataset_id + FROM consent + LEFT JOIN dataset ON dataset.dataset_id = consent.dataset_id + WHERE + concat(dataset.ref, '.', consent.consent_code) IN (:consents) OR + (dataset.ref IN (:consents) AND consent.consent_code = '') + UNION + SELECT + dataset_harmonization.harmonized_dataset_id + FROM consent + JOIN dataset_harmonization ON dataset_harmonization.source_dataset_id = consent.dataset_id + LEFT JOIN dataset ON dataset.dataset_id = dataset_harmonization.source_dataset_id + WHERE + concat(dataset.ref, '.', consent.consent_code) IN (:consents) OR + (dataset.ref IN (:consents) AND consent.consent_code = '') + ) AND + """; + + @Autowired + public ConceptFilterQueryGenerator( + @Value("${filtering.unfilterable_concepts}") List disallowedMetaFields, SchemaDetector schemaDetector + ) { + this.disallowedMetaFields = disallowedMetaFields; + this.schemaDetector = schemaDetector; + } + + /** + * This generates a query that will return a list of concept_node IDs for the given filter.

    A filter object has a list of facets, + * each belonging to a category. Within a category, facets are ORed together. Between categories, facets are ANDed together. In SQL, + * this is represented as N clauses for N facets, all INTERSECTed together. Search also acts as its own special facet here. + * + * @param filter universal filter object for the page + * @param pageable pagination, if applicable + * @return the query and parameters needed to get a list of concepts for the filter + */ + public QueryParamPair generateFilterQuery(Filter filter, Pageable pageable) { + MapSqlParameterSource params = new MapSqlParameterSource(); + params.addValue("disallowed_meta_keys", disallowedMetaFields); + List clauses = new java.util.ArrayList<>(List.of()); + if (!CollectionUtils.isEmpty(filter.facets())) { + clauses.addAll(createFacetFilter(filter, params)); + } + if (StringUtils.hasLength(filter.search())) { + params.addValue("search", filter.search().trim()); + } + if (!CollectionUtils.isEmpty(filter.consents())) { + params.addValue("consents", filter.consents()); + } + // Only add the base filter when it contributes conditions beyond is_queryable. + // For facet-only with no search and no consents, createFacetFilter already checks + // is_queryable = TRUE, so the INTERSECT with createValuelessNodeFilter (which just adds + // "WHERE is_queryable = TRUE AND TRUE") is redundant and prevents parallel execution. + if ( + StringUtils.hasLength(filter.search()) || !CollectionUtils.isEmpty(filter.consents()) + || CollectionUtils.isEmpty(filter.facets()) + ) { + clauses.add(createValuelessNodeFilter(filter.search(), filter.consents())); + } + String superQuery = getSuperQuery(pageable, clauses, params); + + return new QueryParamPair(superQuery, params); + } + + /** + * Creates the base concept search clause. Filters to displayable concepts (those with a non-empty 'values' meta key), applies full-text + * search if present, and scopes by consent if authenticated. + */ + private String createValuelessNodeFilter(String search, List consents) { + String rankQuery = "0"; + String searchCondition = ""; + if (StringUtils.hasLength(search)) { + rankQuery = QueryUtility.SEARCH_QUERY; + searchCondition = QueryUtility.SEARCH_WHERE; + } + // CONSENT_QUERY ends with "AND" so it can be chained with other conditions. Strip the trailing AND here + // because this string is assembled separately and joined via Stream.of() below — it must stand alone. + String consentCondition = CollectionUtils.isEmpty(consents) ? "" : CONSENT_QUERY.strip().replaceAll("\\s+AND\\s*$", ""); + String whereClause = Stream.of(searchCondition, consentCondition).filter(StringUtils::hasLength) + .collect(Collectors.joining("\n AND ")); + if (!StringUtils.hasLength(whereClause)) { + whereClause = "TRUE"; + } + return """ + SELECT + concept_node.concept_node_id, + (%s) as rank + FROM + concept_node + LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_id + WHERE + %s + AND %s + """.formatted(rankQuery, schemaDetector.conceptNodeQueryableClause("concept_node"), whereClause); + } + + /** + * Creates one INTERSECT clause per facet category. Within a category, selected facets are ORed; across categories, clauses are ANDed + * via INTERSECT. Each clause returns concept_node_ids with their search rank. + */ + private List createFacetFilter(Filter filter, MapSqlParameterSource params) { + String consentWhere = CollectionUtils.isEmpty(filter.consents()) ? "" : CONSENT_QUERY; + return filter.facets().stream().collect(Collectors.groupingBy(Facet::category)).entrySet().stream().map(facetsForCategory -> { + params + // The templating here is to namespace the params for each facet category in the query + .addValue( + "facets_for_category_%s".formatted(facetsForCategory.getKey()), + facetsForCategory.getValue().stream().map(Facet::name).toList() + ).addValue("category_%s".formatted(facetsForCategory.getKey()), facetsForCategory.getKey()); + String rankQuery = "0"; + String rankWhere = ""; + if (StringUtils.hasLength(filter.search())) { + rankQuery = QueryUtility.SEARCH_QUERY; + rankWhere = QueryUtility.SEARCH_WHERE + " AND "; + } + return """ + ( + SELECT + facet__concept_node.concept_node_id AS concept_node_id, + max(%s) as rank + FROM facet + LEFT JOIN facet__concept_node ON facet__concept_node.facet_id = facet.facet_id + JOIN facet_category ON facet_category.facet_category_id = facet.facet_category_id + JOIN concept_node ON concept_node.concept_node_id = facet__concept_node.concept_node_id + LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_id + WHERE + %s + AND %s + %s + facet.name IN (:facets_for_category_%s ) AND facet_category.name = :category_%s + GROUP BY + facet__concept_node.concept_node_id + ) + """.formatted( + rankQuery, schemaDetector.conceptNodeQueryableClause("concept_node"), rankWhere, consentWhere, facetsForCategory.getKey(), + facetsForCategory.getKey() + ); + }).toList(); + } + + /** + * Generates an optimized count query that avoids the CTE/ranking/allow_filtering overhead of {@link #generateFilterQuery}. Uses EXISTS + * with concept_node as the driving table, which enables parallel execution and leverages idx_fcn_concept_node_id. + */ + public QueryParamPair generateCountQuery(Filter filter) { + MapSqlParameterSource params = new MapSqlParameterSource(); + String searchCondition = ""; + if (StringUtils.hasLength(filter.search())) { + params.addValue("search", filter.search().trim()); + searchCondition = " AND " + QueryUtility.SEARCH_WHERE; + } + String consentCondition = ""; + if (!CollectionUtils.isEmpty(filter.consents())) { + params.addValue("consents", filter.consents()); + consentCondition = " AND " + CONSENT_QUERY.strip().replaceAll("\\s+AND\\s*$", ""); + } + + if (CollectionUtils.isEmpty(filter.facets())) { + // No facets: count all queryable concepts matching search/consents + String sql = """ + SELECT count(*) + FROM concept_node + LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_id + WHERE %s + %s + %s + """.formatted(schemaDetector.conceptNodeQueryableClause("concept_node"), searchCondition, consentCondition); + return new QueryParamPair(sql, params); + } + + // Group facets by category — each category produces an EXISTS clause + var grouped = filter.facets().stream().collect(Collectors.groupingBy(Facet::category)); + + List existsClauses = grouped.entrySet().stream().map(entry -> { + String categoryKey = entry.getKey(); + params.addValue("facets_for_category_%s".formatted(categoryKey), entry.getValue().stream().map(Facet::name).toList()); + params.addValue("category_%s".formatted(categoryKey), categoryKey); + return """ + EXISTS ( + SELECT 1 FROM facet__concept_node fcn_%1$s + WHERE fcn_%1$s.concept_node_id = cn.concept_node_id + AND fcn_%1$s.facet_id IN ( + SELECT f.facet_id FROM facet f + JOIN facet_category fc ON fc.facet_category_id = f.facet_category_id + WHERE f.name IN (:facets_for_category_%1$s) AND fc.name = :category_%1$s + ) + ) + """.formatted(categoryKey); + }).toList(); + + String existsWhere = String.join(" AND ", existsClauses); + + String sql = """ + SELECT count(*) + FROM concept_node cn + LEFT JOIN dataset ON cn.dataset_id = dataset.dataset_id + WHERE %s + AND %s + %s + %s + """.formatted( + schemaDetector.conceptNodeQueryableClause("cn"), existsWhere, searchCondition.replace("concept_node.", "cn."), consentCondition + ); + return new QueryParamPair(sql, params); + } + + public QueryParamPair generateLegacyFilterQuery(Filter filter, Pageable pageable) { + MapSqlParameterSource params = new MapSqlParameterSource(); + params.addValue("disallowed_meta_keys", disallowedMetaFields); + List clauses = new java.util.ArrayList<>(List.of()); + if (StringUtils.hasLength(filter.search())) { + params.addValue("dynamic_tsquery", filter.search().trim()); + } + clauses.add(createDynamicValuelessNodeFilter(filter.search())); + String superQuery = getSuperQuery(pageable, clauses, params); + + return new QueryParamPair(superQuery, params); + } + + private String createDynamicValuelessNodeFilter(String search) { + String rankQuery = "0 as rank"; + String whereClause = "TRUE"; + if (StringUtils.hasLength(search)) { + rankQuery = "ts_rank_cd(searchable_fields, to_tsquery(:dynamic_tsquery)) AS rank"; + whereClause = "concept_node.searchable_fields @@ to_tsquery(:dynamic_tsquery)"; + } + return """ + SELECT + concept_node.concept_node_id, + %s + FROM + concept_node + LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_id + WHERE + %s + AND %s + """.formatted(rankQuery, schemaDetector.conceptNodeQueryableClause("concept_node"), whereClause); + } + + /** + * Wraps all filter clauses into a single ranked CTE (concepts_filtered_sorted). Clauses are INTERSECTed, then joined with the rank + * adjustment CTE to produce a final ordering where unfilterable concepts are demoted. Adds LIMIT/OFFSET if paged. + */ + private static String getSuperQuery(Pageable pageable, List clauses, MapSqlParameterSource params) { + String query = "(\n" + String.join("\n\tINTERSECT\n", clauses) + "\n)"; + String superQuery = """ + WITH q AS ( + %s + ) + %s + SELECT q.concept_node_id AS concept_node_id, max((1 + rank) * coalesce(rank_adjustment, 1)) AS rank + FROM q + LEFT JOIN allow_filtering ON allow_filtering.concept_node_id = q.concept_node_id + GROUP BY q.concept_node_id + ORDER BY max((1 + rank) * coalesce(rank_adjustment, 1)) DESC, q.concept_node_id ASC + """.formatted(query, RANK_ADJUSTMENTS); + // explanation of ORDER BY max((1 + rank) * coalesce(rank_adjustment, 1)) DESC + // you want to sort the best matches first, BUT anything that is marked as unfilterable should be put last + // coalesce will return the first non null value; this solves rows that aren't marked as filterable or not + // I then multiply that by 1 + rank instead of just rank so that a rank value of 0 for an unfilterable var + // is placed below a rank value of 0 for a filterable var + // Finally, I add the concept node id to the sort to keep it stable for ties, otherwise pagination gets weird + + if (pageable.isPaged()) { + superQuery = superQuery + """ + LIMIT :limit + OFFSET :offset + """; + params.addValue("limit", pageable.getPageSize()).addValue("offset", pageable.getOffset()); + } + + superQuery = " concepts_filtered_sorted AS (\n" + superQuery + "\n)"; + return superQuery; + } + +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptMetaExtractor.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptMetaExtractor.java new file mode 100644 index 000000000..5d01e13d9 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptMetaExtractor.java @@ -0,0 +1,41 @@ +package edu.harvard.dbmi.avillach.dictionary.concept; + +import edu.harvard.dbmi.avillach.dictionary.concept.model.CategoricalConcept; +import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept; +import edu.harvard.dbmi.avillach.dictionary.concept.model.ConceptShell; +import org.springframework.dao.DataAccessException; +import org.springframework.jdbc.core.ResultSetExtractor; +import org.springframework.stereotype.Component; + +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.Arrays; +import java.util.HashMap; +import java.util.Map; +import java.util.stream.Collectors; + +@Component +public class ConceptMetaExtractor implements ResultSetExtractor>> { + + @Override + public Map> extractData(ResultSet rs) throws SQLException, DataAccessException { + Map> sets = new HashMap<>(); + while (rs.next()) { + Concept key = new ConceptShell(rs.getString("concept_path"), rs.getString("dataset_name")); + Map meta = sets.getOrDefault(key, new HashMap<>()); + String rawKey = rs.getString("KEY"); + if (rawKey == null || rawKey.isBlank()) { + throw new IllegalStateException( + "parseMetaData() Missing metadata key. Entry: " + rs.getString("concept_path") + " " + rs.getString("dataset_name") + ); + } + meta.put( + Arrays.stream(rawKey.split("_")).filter(word -> !word.isBlank()) + .map(word -> word.substring(0, 1).toUpperCase() + word.substring(1).toLowerCase()).collect(Collectors.joining(" ")), + rs.getString("VALUE") + ); + sets.put(key, meta); + } + return sets; + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepository.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepository.java new file mode 100644 index 000000000..018c06ede --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepository.java @@ -0,0 +1,344 @@ +package edu.harvard.dbmi.avillach.dictionary.concept; + +import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept; +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import edu.harvard.dbmi.avillach.dictionary.filter.QueryParamPair; +import edu.harvard.dbmi.avillach.dictionary.util.MapExtractor; +import edu.harvard.dbmi.avillach.dictionary.util.MapExtractorWithPrettyKeys; +import edu.harvard.dbmi.avillach.dictionary.util.QueryUtility; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.data.domain.Pageable; +import org.springframework.jdbc.core.namedparam.MapSqlParameterSource; +import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate; +import org.springframework.stereotype.Repository; +import org.springframework.transaction.annotation.Transactional; +import org.springframework.util.StringUtils; + +import java.util.List; +import java.util.Map; +import java.util.Optional; +import java.util.Set; + + +@Repository +public class ConceptRepository { + + private final NamedParameterJdbcTemplate template; + private final ConceptRowMapper mapper; + private final ConceptFilterQueryGenerator filterGen; + private final ConceptMetaExtractor conceptMetaExtractor; + private final ConceptResultSetExtractor conceptResultSetExtractor; + private final ConceptRowWithMetaMapper conceptRowWithMetaMapper; + private final List disallowedMetaFields; + private final Set noShowList; + + + @Autowired + public ConceptRepository( + NamedParameterJdbcTemplate template, ConceptRowMapper mapper, ConceptFilterQueryGenerator filterGen, + ConceptMetaExtractor conceptMetaExtractor, ConceptResultSetExtractor conceptResultSetExtractor, + ConceptRowWithMetaMapper conceptRowWithMetaMapper, @Value("${filtering.unfilterable_concepts}") List disallowedMetaFields, + @Value("#{'${metadata.no_show_list}'}") Set noShowList + ) { + this.template = template; + this.mapper = mapper; + this.filterGen = filterGen; + this.conceptMetaExtractor = conceptMetaExtractor; + this.conceptResultSetExtractor = conceptResultSetExtractor; + this.conceptRowWithMetaMapper = conceptRowWithMetaMapper; + this.disallowedMetaFields = disallowedMetaFields; + this.noShowList = noShowList; + } + + + @Transactional(readOnly = true) + public List getConcepts(Filter filter, Pageable pageable) { + template.getJdbcTemplate().execute("SET LOCAL work_mem = '64MB'"); + QueryParamPair filterQ = filterGen.generateFilterQuery(filter, pageable); + String sql = QueryUtility.ALLOW_FILTERING_Q + ", " + filterQ.query() + + """ + SELECT + concept_node.*, + ds.REF as dataset, + ds.abbreviation AS studyAcronym, + continuous_min.VALUE as min, continuous_max.VALUE as max, + categorical_values.VALUE as values, + coalesce(allow_filtering.allowFiltering, TRUE) AS allowFiltering, + meta_description.VALUE AS description + FROM + concept_node + INNER JOIN concepts_filtered_sorted ON concepts_filtered_sorted.concept_node_id = concept_node.concept_node_id + LEFT JOIN dataset AS ds ON concept_node.dataset_id = ds.dataset_id + LEFT JOIN concept_node_meta AS meta_description ON concept_node.concept_node_id = meta_description.concept_node_id AND meta_description.KEY = 'description' + LEFT JOIN concept_node_meta AS continuous_min ON concept_node.concept_node_id = continuous_min.concept_node_id AND continuous_min.KEY = 'min' + LEFT JOIN concept_node_meta AS continuous_max ON concept_node.concept_node_id = continuous_max.concept_node_id AND continuous_max.KEY = 'max' + LEFT JOIN concept_node_meta AS categorical_values ON concept_node.concept_node_id = categorical_values.concept_node_id AND categorical_values.KEY = 'values' + LEFT JOIN allow_filtering ON concept_node.concept_node_id = allow_filtering.concept_node_id + ORDER BY + concepts_filtered_sorted.rank DESC, concept_node.concept_node_id ASC + """; + MapSqlParameterSource params = filterQ.params().addValue("disallowed_meta_keys", disallowedMetaFields); + + return template.query(sql, params, mapper); + } + + @Transactional(readOnly = true) + public long countConcepts(Filter filter) { + template.getJdbcTemplate().execute("SET LOCAL work_mem = '64MB'"); + QueryParamPair pair = filterGen.generateCountQuery(filter); + Long count = template.queryForObject(pair.query(), pair.params(), Long.class); + return count == null ? 0 : count; + } + + public Optional getConcept(String dataset, String conceptPath) { + String sql = QueryUtility.ALLOW_FILTERING_Q + + """ + SELECT + concept_node.*, + ds.REF as dataset, + ds.abbreviation AS studyAcronym, + continuous_min.VALUE as min, continuous_max.VALUE as max, + categorical_values.VALUE as values, + coalesce(allow_filtering.allowFiltering, TRUE) AS allowFiltering, + meta_description.VALUE AS description + FROM + concept_node + LEFT JOIN dataset AS ds ON concept_node.dataset_id = ds.dataset_id + LEFT JOIN concept_node_meta AS meta_description ON concept_node.concept_node_id = meta_description.concept_node_id AND meta_description.KEY = 'description' + LEFT JOIN concept_node_meta AS continuous_min ON concept_node.concept_node_id = continuous_min.concept_node_id AND continuous_min.KEY = 'min' + LEFT JOIN concept_node_meta AS continuous_max ON concept_node.concept_node_id = continuous_max.concept_node_id AND continuous_max.KEY = 'max' + LEFT JOIN concept_node_meta AS categorical_values ON concept_node.concept_node_id = categorical_values.concept_node_id AND categorical_values.KEY = 'values' + LEFT JOIN allow_filtering ON concept_node.concept_node_id = allow_filtering.concept_node_id + WHERE + concept_node.concept_path = :conceptPath + AND ds.REF = :dataset + """; + MapSqlParameterSource params = new MapSqlParameterSource().addValue("conceptPath", conceptPath).addValue("dataset", dataset) + .addValue("disallowed_meta_keys", disallowedMetaFields); + return template.query(sql, params, mapper).stream().findFirst(); + } + + public Map getConceptMeta(String dataset, String conceptPath) { + String sql = """ + SELECT + concept_node_meta.KEY, concept_node_meta.VALUE + FROM + concept_node + LEFT JOIN concept_node_meta ON concept_node.concept_node_id = concept_node_meta.concept_node_id + LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_id + WHERE + concept_node.concept_path = :conceptPath + AND concept_node_meta.key NOT IN (:noShowList) + AND dataset.REF = :dataset + """; + MapSqlParameterSource params = new MapSqlParameterSource().addValue("conceptPath", conceptPath).addValue("dataset", dataset) + .addValue("noShowList", noShowList); + return template.query(sql, params, new MapExtractorWithPrettyKeys("KEY", "VALUE")); + } + + public Map> getConceptMetaForConcepts(List concepts) { + String sql = """ + SELECT + concept_node_meta.KEY, concept_node_meta.VALUE, + concept_node.CONCEPT_PATH AS concept_path, dataset.REF AS dataset_name + FROM + concept_node + LEFT JOIN concept_node_meta ON concept_node.concept_node_id = concept_node_meta.concept_node_id + LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_id + WHERE + (concept_node.CONCEPT_PATH, dataset.REF) IN (:pairs) + AND + concept_node_meta.key NOT IN (:noShowList) + ORDER BY concept_node.CONCEPT_PATH, dataset.REF + """; + List pairs = concepts.stream().map(c -> new String[] {c.conceptPath(), c.dataset()}).toList(); + MapSqlParameterSource params = new MapSqlParameterSource().addValue("pairs", pairs).addValue("noShowList", noShowList); + + return template.query(sql, params, conceptMetaExtractor); + + } + + public Optional getConceptTree(String dataset, String conceptPath, int depth) { + // if this is for the absolute root of this dataset's ontology, conceptPath + // will be empty, and we should just find the parentless concept instead. + String rootConceptMatch = + StringUtils.hasLength(conceptPath) ? "concept_node.CONCEPT_PATH = :path" : "concept_node.PARENT_ID IS NULL"; + String sql = QueryUtility.ALLOW_FILTERING_Q + + """ + , core_query AS ( + WITH RECURSIVE nodes AS ( + SELECT + concept_node_id, parent_id, 0 AS depth + FROM + concept_node + LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_id + WHERE + %s + AND dataset.REF = :dataset + UNION + SELECT + child_nodes.concept_node_id, child_nodes.parent_id, parent_node.depth+ 1 + FROM + concept_node child_nodes + INNER JOIN nodes parent_node ON child_nodes.parent_id = parent_node.concept_node_id + LEFT JOIN dataset ON child_nodes.dataset_id = dataset.dataset_id + ) + SELECT + depth, child_nodes.concept_node_id + FROM + nodes parent_node + INNER JOIN concept_node child_nodes ON child_nodes.parent_id = parent_node.concept_node_id + WHERE + depth <= :depth + UNION + SELECT + 0 as depth, concept_node.concept_node_id + FROM + concept_node + LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_id + WHERE + %s + AND dataset.REF = :dataset + UNION + SELECT + -1 as depth, concept_node.concept_node_id + FROM + concept_node + WHERE + concept_node.concept_node_id = ( + SELECT + parent_id + FROM + concept_node + LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_id + WHERE + %s + AND dataset.REF = :dataset + ) + ORDER BY depth ASC + ) + SELECT + concept_node.*, + ds.REF AS dataset, + ds.abbreviation AS studyAcronym, + continuous_min.VALUE AS min, continuous_max.VALUE AS max, + categorical_values.VALUE AS values, + meta_description.VALUE AS description, + coalesce(allow_filtering.allowFiltering, TRUE) AS allowFiltering, + core_query.depth AS depth, + EXISTS ( + SELECT 1 + FROM concept_node child_check + WHERE child_check.parent_id = concept_node.concept_node_id + ) AS hasChildren + FROM + concept_node + INNER JOIN core_query ON concept_node.concept_node_id = core_query.concept_node_id + LEFT JOIN dataset AS ds ON concept_node.dataset_id = ds.dataset_id + LEFT JOIN concept_node_meta AS meta_description ON concept_node.concept_node_id = meta_description.concept_node_id AND meta_description.KEY = 'description' + LEFT JOIN concept_node_meta AS continuous_min ON concept_node.concept_node_id = continuous_min.concept_node_id AND continuous_min.KEY = 'min' + LEFT JOIN concept_node_meta AS continuous_max ON concept_node.concept_node_id = continuous_max.concept_node_id AND continuous_max.KEY = 'max' + LEFT JOIN concept_node_meta AS categorical_values ON concept_node.concept_node_id = categorical_values.concept_node_id AND categorical_values.KEY = 'values' + LEFT JOIN allow_filtering ON concept_node.concept_node_id = allow_filtering.concept_node_id + WHERE + core_query.depth < :depth + ORDER BY LENGTH(concept_node.concept_path) + """ + .formatted(rootConceptMatch, rootConceptMatch, rootConceptMatch); + MapSqlParameterSource params = new MapSqlParameterSource().addValue("path", conceptPath).addValue("dataset", dataset) + .addValue("depth", depth).addValue("disallowed_meta_keys", disallowedMetaFields); + + if (depth < 0) { + return Optional.empty(); + } + + return Optional.ofNullable(template.query(sql, params, conceptResultSetExtractor)); + } + + public List getConceptHierarchy(String dataset, String conceptPath) { + String sql = + """ + WITH RECURSIVE nodes AS ( + SELECT c.concept_node_id, c.parent_id + FROM concept_node c + LEFT JOIN dataset ON c.dataset_id = dataset.dataset_id + WHERE c.concept_path = :path AND dataset.REF = :dataset + UNION ALL + SELECT c.concept_node_id, c.parent_id + FROM concept_node c + INNER JOIN nodes n ON n.parent_id = c.concept_node_id + ) + SELECT + concept_node.*, + ds.REF as dataset, + ds.abbreviation AS studyAcronym, + continuous_min.VALUE as min, continuous_max.VALUE as max, + categorical_values.VALUE as values, + FALSE AS allowFiltering, + meta_description.VALUE AS description + FROM + concept_node + INNER JOIN nodes n on n.concept_node_id = concept_node.concept_node_id + LEFT JOIN dataset AS ds ON concept_node.dataset_id = ds.dataset_id + LEFT JOIN concept_node_meta AS meta_description ON concept_node.concept_node_id = meta_description.concept_node_id AND meta_description.KEY = 'description' + LEFT JOIN concept_node_meta AS continuous_min ON concept_node.concept_node_id = continuous_min.concept_node_id AND continuous_min.KEY = 'min' + LEFT JOIN concept_node_meta AS continuous_max ON concept_node.concept_node_id = continuous_max.concept_node_id AND continuous_max.KEY = 'max' + LEFT JOIN concept_node_meta AS categorical_values ON concept_node.concept_node_id = categorical_values.concept_node_id AND categorical_values.KEY = 'values' + """; + MapSqlParameterSource params = new MapSqlParameterSource().addValue("path", conceptPath).addValue("dataset", dataset); + return template.query(sql, params, mapper); + } + + + public List getConceptsByPathWithMetadata(List conceptPaths) { + String sql = QueryUtility.ALLOW_FILTERING_Q + ", " + + """ + filtered_concepts AS ( + SELECT + concept_node.* + FROM + concept_node + WHERE + concept_path IN (:conceptPaths) + ), + aggregated_meta AS ( + SELECT + concept_node_meta.concept_node_id, + json_agg(json_build_object('key', concept_node_meta.key, 'value', concept_node_meta.value)) AS metadata + FROM + concept_node_meta + WHERE + concept_node_meta.concept_node_id IN ( + SELECT concept_node_id FROM filtered_concepts + ) + AND + concept_node_meta.key NOT IN (:noShowList) + GROUP BY + concept_node_meta.concept_node_id + ) + SELECT + concept_node.*, + ds.REF as dataset, + ds.abbreviation AS studyAcronym, + continuous_min.VALUE as min, continuous_max.VALUE as max, + categorical_values.VALUE as values, + coalesce(allow_filtering.allowFiltering, TRUE) AS allowFiltering, + meta_description.VALUE AS description, + coalesce(aggregated_meta.metadata, '[]'::json) AS metadata + FROM + filtered_concepts as concept_node + LEFT JOIN dataset AS ds ON concept_node.dataset_id = ds.dataset_id + LEFT JOIN concept_node_meta AS meta_description ON concept_node.concept_node_id = meta_description.concept_node_id AND meta_description.KEY = 'description' + LEFT JOIN concept_node_meta AS continuous_min ON concept_node.concept_node_id = continuous_min.concept_node_id AND continuous_min.KEY = 'min' + LEFT JOIN concept_node_meta AS continuous_max ON concept_node.concept_node_id = continuous_max.concept_node_id AND continuous_max.KEY = 'max' + LEFT JOIN concept_node_meta AS categorical_values ON concept_node.concept_node_id = categorical_values.concept_node_id AND categorical_values.KEY = 'values' + LEFT JOIN allow_filtering ON concept_node.concept_node_id = allow_filtering.concept_node_id + LEFT JOIN aggregated_meta ON concept_node.concept_node_id = aggregated_meta.concept_node_id + """; + + MapSqlParameterSource params = new MapSqlParameterSource().addValue("conceptPaths", conceptPaths) + .addValue("disallowed_meta_keys", disallowedMetaFields).addValue("noShowList", noShowList); + return template.query(sql, params, conceptRowWithMetaMapper); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptResultSetExtractor.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptResultSetExtractor.java new file mode 100644 index 000000000..1d1a9ea4e --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptResultSetExtractor.java @@ -0,0 +1,58 @@ +package edu.harvard.dbmi.avillach.dictionary.concept; + +import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept; +import edu.harvard.dbmi.avillach.dictionary.concept.model.ConceptType; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.dao.DataAccessException; +import org.springframework.jdbc.core.ResultSetExtractor; +import org.springframework.stereotype.Component; + +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.*; + +@Component +public class ConceptResultSetExtractor implements ResultSetExtractor { + @Autowired + private ConceptResultSetUtil conceptResultSetUtil; + + private record ConceptWithId(Concept c, int id, boolean hasChildren) { + } + + @Override + public Concept extractData(ResultSet rs) throws SQLException, DataAccessException { + Map> conceptsByParentId = new HashMap<>(); + ConceptWithId root = null; + while (rs.next()) { + Concept c = switch (ConceptType.toConcept(rs.getString("concept_type"))) { + case Categorical -> conceptResultSetUtil.mapCategorical(rs); + case Continuous -> conceptResultSetUtil.mapContinuous(rs); + }; + ConceptWithId conceptWithId = new ConceptWithId(c, rs.getInt("concept_node_id"), rs.getBoolean("hasChildren")); + if (root == null) { + root = conceptWithId; + } + + int parentId = rs.getInt("parent_id"); + // weirdness: null value for int is 0, so to check for missing parent value, you need the wasNull check + if (!rs.wasNull()) { + List concepts = conceptsByParentId.getOrDefault(parentId, new ArrayList<>()); + concepts.add(conceptWithId); + conceptsByParentId.put(parentId, concepts); + } + } + + + return root == null ? null : seedChildren(root, conceptsByParentId); + } + + private Concept seedChildren(ConceptWithId root, Map> conceptsByParentId) { + if (root.hasChildren) { + List children = conceptsByParentId.getOrDefault(root.id, List.of()).stream() + .map(conceptWithId -> seedChildren(conceptWithId, conceptsByParentId)).toList(); + return root.c.withChildren(children); + } else { + return root.c; + } + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptResultSetUtil.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptResultSetUtil.java new file mode 100644 index 000000000..0307999fe --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptResultSetUtil.java @@ -0,0 +1,65 @@ +package edu.harvard.dbmi.avillach.dictionary.concept; + +import edu.harvard.dbmi.avillach.dictionary.concept.model.CategoricalConcept; +import edu.harvard.dbmi.avillach.dictionary.concept.model.ContinuousConcept; +import edu.harvard.dbmi.avillach.dictionary.util.JsonBlobParser; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Component; + +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.List; +import java.util.Map; + +@Component +public class ConceptResultSetUtil { + + private final JsonBlobParser jsonBlobParser; + + @Autowired + public ConceptResultSetUtil(JsonBlobParser jsonBlobParser) { + this.jsonBlobParser = jsonBlobParser; + } + + public CategoricalConcept mapCategoricalWithMetadata(ResultSet rs) throws SQLException { + Map metadata = jsonBlobParser.parseMetaData(rs.getString("metadata")); + return new CategoricalConcept( + rs.getString("concept_path"), rs.getString("name"), rs.getString("display"), rs.getString("dataset"), + rs.getString("description"), null, rs.getBoolean("allowFiltering"), rs.getString("studyAcronym"), null, metadata + ); + + } + + private CategoricalConcept getCategoricalConcept(ResultSet rs) throws SQLException { + return new CategoricalConcept( + rs.getString("concept_path"), rs.getString("name"), rs.getString("display"), rs.getString("dataset"), + rs.getString("description"), rs.getString("values") == null ? List.of() : jsonBlobParser.parseValues(rs.getString("values")), + rs.getBoolean("allowFiltering"), rs.getString("studyAcronym"), null, null + ); + } + + public ContinuousConcept mapContinuousWithMetadata(ResultSet rs) throws SQLException { + Map metadata = jsonBlobParser.parseMetaData(rs.getString("metadata")); + return new ContinuousConcept( + rs.getString("concept_path"), rs.getString("name"), rs.getString("display"), rs.getString("dataset"), + rs.getString("description"), rs.getBoolean("allowFiltering"), null, null, rs.getString("studyAcronym"), metadata + ); + } + + private ContinuousConcept getContinuousConcept(ResultSet rs) throws SQLException { + return new ContinuousConcept( + rs.getString("concept_path"), rs.getString("name"), rs.getString("display"), rs.getString("dataset"), + rs.getString("description"), rs.getBoolean("allowFiltering"), jsonBlobParser.parseMin(rs.getString("values")), + jsonBlobParser.parseMax(rs.getString("values")), rs.getString("studyAcronym"), null + ); + } + + public ContinuousConcept mapContinuous(ResultSet rs) throws SQLException { + return getContinuousConcept(rs); + } + + public CategoricalConcept mapCategorical(ResultSet rs) throws SQLException { + return getCategoricalConcept(rs); + } + +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRowMapper.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRowMapper.java new file mode 100644 index 000000000..2e59b3e1b --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRowMapper.java @@ -0,0 +1,27 @@ +package edu.harvard.dbmi.avillach.dictionary.concept; + +import edu.harvard.dbmi.avillach.dictionary.concept.model.*; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.jdbc.core.RowMapper; +import org.springframework.stereotype.Component; +import org.springframework.util.StringUtils; + +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.List; +import java.util.Map; + +@Component +public class ConceptRowMapper implements RowMapper { + + @Autowired + ConceptResultSetUtil conceptResultSetUtil; + + @Override + public Concept mapRow(ResultSet rs, int rowNum) throws SQLException { + return switch (ConceptType.toConcept(rs.getString("concept_type"))) { + case Categorical -> conceptResultSetUtil.mapCategorical(rs); + case Continuous -> conceptResultSetUtil.mapContinuous(rs); + }; + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRowWithMetaMapper.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRowWithMetaMapper.java new file mode 100644 index 000000000..c12a02da0 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRowWithMetaMapper.java @@ -0,0 +1,30 @@ +package edu.harvard.dbmi.avillach.dictionary.concept; + +import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept; +import edu.harvard.dbmi.avillach.dictionary.concept.model.ConceptType; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.jdbc.core.RowMapper; +import org.springframework.stereotype.Component; + +import java.sql.ResultSet; +import java.sql.SQLException; + +@Component +public class ConceptRowWithMetaMapper implements RowMapper { + + private final ConceptResultSetUtil conceptResultSetUtil; + + @Autowired + public ConceptRowWithMetaMapper(ConceptResultSetUtil conceptResultSetUtil) { + this.conceptResultSetUtil = conceptResultSetUtil; + } + + @Override + public Concept mapRow(ResultSet rs, int rowNum) throws SQLException { + return switch (ConceptType.toConcept(rs.getString("concept_type"))) { + case Categorical -> conceptResultSetUtil.mapCategoricalWithMetadata(rs); + case Continuous -> conceptResultSetUtil.mapContinuousWithMetadata(rs); + }; + } + +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptService.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptService.java new file mode 100644 index 000000000..4a6727660 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptService.java @@ -0,0 +1,92 @@ +package edu.harvard.dbmi.avillach.dictionary.concept; + +import edu.harvard.dbmi.avillach.dictionary.concept.model.CategoricalConcept; +import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept; +import edu.harvard.dbmi.avillach.dictionary.concept.model.ConceptShell; +import edu.harvard.dbmi.avillach.dictionary.concept.model.ContinuousConcept; +import edu.harvard.dbmi.avillach.dictionary.dataset.Dataset; +import edu.harvard.dbmi.avillach.dictionary.dataset.DatasetService; +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.cache.annotation.Cacheable; +import org.springframework.data.domain.Pageable; +import org.springframework.stereotype.Service; + +import java.util.List; +import java.util.Map; +import java.util.Optional; + +@Service +public class ConceptService { + + private final ConceptRepository conceptRepository; + private final DatasetService datasetService; + private final ConceptDecoratorService conceptDecoratorService; + + @Autowired + public ConceptService( + ConceptRepository conceptRepository, DatasetService datasetService, ConceptDecoratorService conceptDecoratorService + ) { + this.conceptRepository = conceptRepository; + this.datasetService = datasetService; + this.conceptDecoratorService = conceptDecoratorService; + } + + @Cacheable("concepts") + public List listConcepts(Filter filter, Pageable page) { + return conceptRepository.getConcepts(filter, page); + } + + public List listDetailedConcepts(Filter filter, Pageable page) { + List concepts = conceptRepository.getConcepts(filter, page); + Map> metas = conceptRepository.getConceptMetaForConcepts(concepts); + return concepts.stream().map(concept -> (Concept) switch (concept) { + case ContinuousConcept cont -> new ContinuousConcept(cont, metas.getOrDefault(cont, Map.of())); + case CategoricalConcept cat -> new CategoricalConcept(cat, metas.getOrDefault(cat, Map.of())); + case ConceptShell ignored -> throw new RuntimeException("Concept shell escaped to API"); + }).toList(); + } + + @Cacheable("concepts_count") + public long countConcepts(Filter filter) { + return conceptRepository.countConcepts(filter); + } + + public Optional conceptDetail(String dataset, String conceptPath) { + return getConcept(dataset, conceptPath, true); + } + + private Optional getConcept(String dataset, String conceptPath, boolean addAncestors) { + Optional concept = conceptRepository.getConcept(dataset, conceptPath).map(core -> { + var meta = conceptRepository.getConceptMeta(dataset, conceptPath); + return switch (core) { + case ContinuousConcept cont -> new ContinuousConcept(cont, meta); + case CategoricalConcept cat -> new CategoricalConcept(cat, meta); + case ConceptShell ignored -> throw new RuntimeException("Concept shell escaped to API"); + }; + }); + return addAncestors ? concept.map(conceptDecoratorService::populateParentConcepts) : concept; + } + + public Optional conceptTree(String dataset, String conceptPath, int depth) { + return conceptRepository.getConceptTree(dataset, conceptPath, depth); + } + + public List conceptHierarchy(String dataset, String conceptPath) { + return conceptRepository.getConceptHierarchy(dataset, conceptPath); + } + + + public List allConceptTrees(int depth) { + return datasetService.getAllDatasets().stream().map(Dataset::ref).map(ref -> conceptTree(ref, null, depth)) + .filter(Optional::isPresent).map(Optional::get).toList(); + } + + public Optional conceptDetailWithoutAncestors(String dataset, String conceptPath) { + return getConcept(dataset, conceptPath, false); + } + + public List conceptsWithDetail(List conceptPaths) { + return this.conceptRepository.getConceptsByPathWithMetadata(conceptPaths); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/CategoricalConcept.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/CategoricalConcept.java new file mode 100644 index 000000000..135a43aca --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/CategoricalConcept.java @@ -0,0 +1,82 @@ +package edu.harvard.dbmi.avillach.dictionary.concept.model; + +import com.fasterxml.jackson.annotation.JsonProperty; +import edu.harvard.dbmi.avillach.dictionary.dataset.Dataset; +import jakarta.annotation.Nullable; + +import java.util.List; +import java.util.Map; +import java.util.Objects; + +public record CategoricalConcept( + String conceptPath, String name, String display, String dataset, String description, + + List values, boolean allowFiltering, String studyAcronym, + + @Nullable List children, + + @Nullable Map meta, + + @Nullable Concept table, + + @Nullable Dataset study + +) implements Concept { + + public CategoricalConcept( + String conceptPath, String name, String display, String dataset, String description, List values, boolean allowFiltering, + String studyAcronym, @Nullable List children, @Nullable Map meta + ) { + this(conceptPath, name, display, dataset, description, values, allowFiltering, studyAcronym, children, meta, null, null); + } + + public CategoricalConcept(CategoricalConcept core, Map meta) { + this( + core.conceptPath, core.name, core.display, core.dataset, core.description, core.values, core.allowFiltering, core.studyAcronym, + core.children, meta + ); + } + + public CategoricalConcept(String conceptPath, String dataset) { + this(conceptPath, "", "", dataset, "", List.of(), false, "", List.of(), null); + } + + + @JsonProperty("type") + @Override + public ConceptType type() { + return ConceptType.Categorical; + } + + @Override + public CategoricalConcept withChildren(List children) { + return new CategoricalConcept( + conceptPath, name, display, dataset, description, values, allowFiltering, studyAcronym, children, meta + ); + } + + @Override + public Concept withTable(Concept table) { + return new CategoricalConcept( + conceptPath, name, display, dataset, description, values, allowFiltering, studyAcronym, children, meta, table, study + ); + } + + @Override + public Concept withStudy(Dataset study) { + return new CategoricalConcept( + conceptPath, name, display, dataset, description, values, allowFiltering, studyAcronym, children, meta, table, study + ); + } + + @Override + public boolean equals(Object object) { + return conceptEquals(object); + } + + @Override + public int hashCode() { + return Objects.hash(conceptPath, dataset); + } + +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/Concept.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/Concept.java new file mode 100644 index 000000000..17443bc3d --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/Concept.java @@ -0,0 +1,79 @@ +package edu.harvard.dbmi.avillach.dictionary.concept.model; + +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; +import com.fasterxml.jackson.annotation.JsonSubTypes; +import com.fasterxml.jackson.annotation.JsonTypeInfo; +import edu.harvard.dbmi.avillach.dictionary.dataset.Dataset; +import jakarta.annotation.Nullable; + +import java.util.List; +import java.util.Map; +import java.util.Objects; + + +@JsonIgnoreProperties(ignoreUnknown = true) +// All this Json annotation stuff is doing is telling Jackson how to handle this polymorphic type. Essentially: +// - The types are defined by their name. +// - The name is set in the 'type' property +// - For each possible Concept type, here is what the 'type' property will be +@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, property = "type") +@JsonSubTypes( + {@JsonSubTypes.Type(value = ContinuousConcept.class, name = "Continuous"), + @JsonSubTypes.Type(value = CategoricalConcept.class, name = "Categorical"),} +) +public sealed interface Concept permits CategoricalConcept, ConceptShell, ContinuousConcept { + + /** + * @return The complete concept path for this concept (// delimited) + */ + String conceptPath(); + + /** + * @return The name, i.e. the right most concept in the concept path + */ + String name(); + + /** + * @return The display name for end users + */ + String display(); + + + /** + * @return The unique name for the study / dataset that this concept belongs to + */ + String dataset(); + + String studyAcronym(); + + /** + * @return The type of this concept + */ + ConceptType type(); + + Concept table(); + + Dataset study(); + + Map meta(); + + @Nullable + List children(); + + default boolean allowFiltering() { + return false; + } + + Concept withChildren(List children); + + Concept withTable(Concept table); + + Concept withStudy(Dataset study); + + default boolean conceptEquals(Object object) { + if (this == object) return true; + if (!(object instanceof Concept)) return false; + Concept that = (Concept) object; + return Objects.equals(dataset(), that.dataset()) && Objects.equals(conceptPath(), that.conceptPath()); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ConceptShell.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ConceptShell.java new file mode 100644 index 000000000..871c34f8d --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ConceptShell.java @@ -0,0 +1,74 @@ +package edu.harvard.dbmi.avillach.dictionary.concept.model; + +import edu.harvard.dbmi.avillach.dictionary.dataset.Dataset; + +import java.util.List; +import java.util.Map; +import java.util.Objects; + +public record ConceptShell(String conceptPath, String dataset) implements Concept { + @Override + public String name() { + return "Shell. Not for external use."; + } + + @Override + public String display() { + return "Shell. Not for external use."; + } + + @Override + public String studyAcronym() { + return "Shell. Not for external use."; + } + + @Override + public ConceptType type() { + return ConceptType.Continuous; + } + + @Override + public Concept table() { + return null; + } + + @Override + public Dataset study() { + return null; + } + + @Override + public Map meta() { + return Map.of(); + } + + @Override + public List children() { + return List.of(); + } + + @Override + public ConceptShell withChildren(List children) { + return this; + } + + @Override + public Concept withTable(Concept table) { + return this; + } + + @Override + public Concept withStudy(Dataset study) { + return this; + } + + @Override + public boolean equals(Object object) { + return conceptEquals(object); + } + + @Override + public int hashCode() { + return Objects.hash(conceptPath, dataset); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ConceptType.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ConceptType.java new file mode 100644 index 000000000..33f9f3939 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ConceptType.java @@ -0,0 +1,23 @@ +package edu.harvard.dbmi.avillach.dictionary.concept.model; + +import org.springframework.util.StringUtils; + +public enum ConceptType { + /** + * i.e. Eye color: brown, blue, hazel, etc. + */ + Categorical, + + /** + * i.e. Age: 0 - 150 Also known as numeric (to me) + */ + Continuous; + + public static ConceptType toConcept(String in) { + return switch (StringUtils.capitalize(in)) { + case "Continuous" -> Continuous; + default -> Categorical; + }; + } + +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ContinuousConcept.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ContinuousConcept.java new file mode 100644 index 000000000..f0b5cdb61 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ContinuousConcept.java @@ -0,0 +1,82 @@ +package edu.harvard.dbmi.avillach.dictionary.concept.model; + +import com.fasterxml.jackson.annotation.JsonProperty; +import edu.harvard.dbmi.avillach.dictionary.dataset.Dataset; +import jakarta.annotation.Nullable; + +import java.util.List; +import java.util.Map; +import java.util.Objects; + +public record ContinuousConcept( + String conceptPath, String name, String display, String dataset, String description, boolean allowFiltering, + + @Nullable Double min, @Nullable Double max, String studyAcronym, Map meta, @Nullable List children, + + @Nullable Concept table, + + @Nullable Dataset study +) implements Concept { + + public ContinuousConcept( + String conceptPath, String name, String display, String dataset, String description, boolean allowFiltering, @Nullable Double min, + @Nullable Double max, String studyAcronym, Map meta, @Nullable List children + ) { + this(conceptPath, name, display, dataset, description, allowFiltering, min, max, studyAcronym, meta, children, null, null); + } + + public ContinuousConcept(ContinuousConcept core, Map meta) { + this( + core.conceptPath, core.name, core.display, core.dataset, core.description, core.allowFiltering, core.min, core.max, + core.studyAcronym, meta, core.children + ); + } + + public ContinuousConcept(String conceptPath, String dataset) { + this(conceptPath, "", "", dataset, "", true, null, null, "", null, List.of()); + } + + public ContinuousConcept( + String conceptPath, String name, String display, String dataset, String description, boolean allowFiltering, @Nullable Double min, + @Nullable Double max, String studyAcronym, Map meta + ) { + this(conceptPath, name, display, dataset, description, allowFiltering, min, max, studyAcronym, meta, null); + } + + @JsonProperty("type") + @Override + public ConceptType type() { + return ConceptType.Continuous; + } + + @Override + public ContinuousConcept withChildren(List children) { + return new ContinuousConcept( + conceptPath, name, display, dataset, description, allowFiltering, min, max, studyAcronym, meta, children + ); + } + + @Override + public Concept withTable(Concept table) { + return new ContinuousConcept( + conceptPath, name, display, dataset, description, allowFiltering, min, max, studyAcronym, meta, children, table, study + ); + } + + @Override + public Concept withStudy(Dataset study) { + return new ContinuousConcept( + conceptPath, name, display, dataset, description, allowFiltering, min, max, studyAcronym, meta, children, table, study + ); + } + + @Override + public boolean equals(Object object) { + return conceptEquals(object); + } + + @Override + public int hashCode() { + return Objects.hash(conceptPath, dataset); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/Dashboard.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/Dashboard.java new file mode 100644 index 000000000..3595270b2 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/Dashboard.java @@ -0,0 +1,7 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboard; + +import java.util.List; +import java.util.Map; + +public record Dashboard(List columns, List> rows) { +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardColumn.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardColumn.java new file mode 100644 index 000000000..f8a59fbb2 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardColumn.java @@ -0,0 +1,4 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboard; + +public record DashboardColumn(String dataElement, String label) { +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardConfig.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardConfig.java new file mode 100644 index 000000000..0dfb5b8a5 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardConfig.java @@ -0,0 +1,41 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboard; + +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; + +import java.util.List; +import java.util.Map; + +@Configuration +public class DashboardConfig { + private final Map labelDisplayElementPairs; + private final List columnOrder; + + @Autowired + public DashboardConfig( + @Value("#{${dashboard.columns}}") Map labelDisplayElementPairs, + @Value("${dashboard.column-order}") List columnOrder + ) { + this.labelDisplayElementPairs = labelDisplayElementPairs; + this.columnOrder = columnOrder; + } + + @Bean + public List getColumns() { + return labelDisplayElementPairs.entrySet().stream().map(e -> new DashboardColumn(e.getKey(), e.getValue())) + .sorted((a, b) -> Integer.compare(calculateOrder(a), calculateOrder(b))).toList(); + } + + private int calculateOrder(DashboardColumn column) { + if (columnOrder.contains(column.dataElement())) { + return columnOrder.indexOf(column.dataElement()); + } else { + return Integer.MAX_VALUE; + } + } + + + +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardController.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardController.java new file mode 100644 index 000000000..1f8b56a9a --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardController.java @@ -0,0 +1,23 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboard; + +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.GetMapping; + +@Controller +public class DashboardController { + private final DashboardService dashboardService; + + @Autowired + public DashboardController(DashboardService dashboardService) { + this.dashboardService = dashboardService; + } + + @AuditEvent(type = "OTHER", action = "dashboard.read") + @GetMapping("/dashboard") + public ResponseEntity getDashboard() { + return ResponseEntity.ok(dashboardService.getDashboard()); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardRepository.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardRepository.java new file mode 100644 index 000000000..93e10d632 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardRepository.java @@ -0,0 +1,111 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboard; + +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.dao.DataAccessException; +import org.springframework.jdbc.core.ResultSetExtractor; +import org.springframework.jdbc.core.namedparam.MapSqlParameterSource; +import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate; +import org.springframework.stereotype.Repository; + +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.*; +import java.util.function.Predicate; + +@Repository +public class DashboardRepository { + private final NamedParameterJdbcTemplate template; + private final List columns; + private final Set nonMetaColumns; + private final DashboardRowResultSetExtractor extractor; + + @Autowired + public DashboardRepository( + NamedParameterJdbcTemplate template, List columns, + @Value("${dashboard.nonmeta-columns}") Set nonMetaColumns, DashboardRowResultSetExtractor extractor + ) { + this.template = template; + this.columns = columns; + this.nonMetaColumns = nonMetaColumns; + this.extractor = extractor; + } + + private static final class ListMapExtractor implements ResultSetExtractor>> { + + @Override + public List> extractData(ResultSet rs) throws SQLException, DataAccessException { + List> rows = new ArrayList<>(); + while (rs.next()) { + Map row = new HashMap<>(); + for (int i = 0; i < rs.getMetaData().getColumnCount(); i++) { + String key = rs.getMetaData().getColumnName(i + 1); + row.put(key, rs.getString(key)); + } + rows.add(row); + } + return rows; + } + } + + public List> getHackyBDCRows() { + String sql = + """ + SELECT + dataset.dataset_id as dataset_id, + dataset.abbreviation AS abbreviation, + dataset.full_name AS name, + CASE + WHEN consent.variable_count > -1 THEN consent.variable_count::text + ELSE 'N/A' + END + AS clinvars, + CASE + WHEN consent.participant_count > -1 THEN consent.participant_count::text + ELSE 'N/A' + END + AS participants, + CASE + WHEN consent.sample_count > -1 THEN consent.sample_count::text + ELSE 'N/A' + END + AS samples, + CASE + WHEN (consent.consent_code IS NOT NULL AND consent.consent_code != '') THEN concat(study_accession_meta.value, '.', consent.consent_code) + ELSE study_accession_meta.value + END + AS accession, + program_name.value as program_name, + study_focus_meta.value AS study_focus, + additional_info_meta.value AS additional_info_link + FROM + dataset + LEFT JOIN consent ON consent.dataset_id = dataset.dataset_id + LEFT JOIN dataset_meta AS study_focus_meta ON study_focus_meta.dataset_id = dataset.dataset_id AND study_focus_meta.KEY = 'study_focus' + LEFT JOIN dataset_meta AS study_accession_meta ON study_accession_meta.dataset_id = dataset.dataset_id AND study_accession_meta.KEY = 'study_accession' + LEFT JOIN dataset_meta AS additional_info_meta ON additional_info_meta.dataset_id = dataset.dataset_id AND additional_info_meta.KEY = 'study_link' + LEFT JOIN dataset_meta AS program_name ON program_name.dataset_id = dataset.dataset_id AND program_name.KEY = 'program_name' + WHERE dataset.dataset_id NOT IN (select dataset_id from dataset_meta where KEY = 'show_dashboad' and VALUE = 'false') + ORDER BY name ASC, abbreviation ASC + """; + return template.query(sql, new ListMapExtractor()); + } + + public List> getRows() { + String sql = """ + SELECT + abbreviation, full_name AS name, + dataset_meta.KEY AS key, + dataset_meta.VALUE AS value + FROM + dataset + JOIN dataset_meta ON dataset.dataset_id = dataset_meta.dataset_id + WHERE + dataset_meta.KEY IN (:keys) + ORDER BY name ASC, abbreviation ASC + """; + List keys = columns.stream().map(DashboardColumn::dataElement).filter(Predicate.not(nonMetaColumns::contains)).toList(); + MapSqlParameterSource params = new MapSqlParameterSource().addValue("keys", keys); + return template.query(sql, params, extractor); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardRowResultSetExtractor.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardRowResultSetExtractor.java new file mode 100644 index 000000000..be374f0c5 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardRowResultSetExtractor.java @@ -0,0 +1,64 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboard; + +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.dao.DataAccessException; +import org.springframework.jdbc.core.ResultSetExtractor; +import org.springframework.stereotype.Component; + +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.stream.Collectors; + +@Component +public class DashboardRowResultSetExtractor implements ResultSetExtractor>> { + // This is a template of all the configured columns. + // It's used to ensure that empty values exist for all cells, + // even if there is no matching val in the database. + private final Map template; + + @Autowired + public DashboardRowResultSetExtractor(List columns) { + template = columns.stream().collect(Collectors.toMap(DashboardColumn::dataElement, (ignored) -> "")); + } + + @Override + public List> extractData(ResultSet rs) throws SQLException, DataAccessException { + String currentName = ""; + String currentAbbreviation = ""; + boolean beforeStart = true; + Map row = new HashMap<>(template); + List> rows = new ArrayList<>(); + while (rs.next()) { + String abbreviation = rs.getString("abbreviation"); + String name = rs.getString("name"); + if (beforeStart) { + currentName = name; + currentAbbreviation = abbreviation; + beforeStart = false; + } + // start of new row + if (!currentAbbreviation.equals(abbreviation) || !currentName.equals(name)) { + // finish up the old row by adding non-meta fields + row.put("abbreviation", currentAbbreviation); + row.put("name", currentName); + rows.add(row); + // start new row + currentName = name; + currentAbbreviation = abbreviation; + row = new HashMap<>(template); + } + row.put(rs.getString("key"), rs.getString("value")); + } + // add the last row to the response only if there has been at least one set in the result set + if (!beforeStart) { + row.put("abbreviation", currentAbbreviation); + row.put("name", currentName); + rows.add(row); + } + return rows; + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardService.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardService.java new file mode 100644 index 000000000..0d9315bee --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardService.java @@ -0,0 +1,42 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboard; + +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Service; + +import java.util.List; +import java.util.Map; + +@Service +public class DashboardService { + + private final DashboardRepository repository; + private final List columns; + private final boolean bdcHack; + + @Autowired + public DashboardService( + DashboardRepository repository, List columns, @Value("${dashboard.enable.bdc_hack}") boolean bdcHack + ) { + this.repository = repository; + this.columns = columns; + this.bdcHack = bdcHack; + } + + public Dashboard getDashboard() { + if (bdcHack) { + List> rows = repository.getHackyBDCRows(); + return new Dashboard(hackyBDCColumns, rows); + } + List> rows = repository.getRows(); + return new Dashboard(columns, rows); + } + + private static final List hackyBDCColumns = List.of( + new DashboardColumn("abbreviation", "Abbreviation"), new DashboardColumn("name", "Name"), + new DashboardColumn("study_focus", "Study Focus"), new DashboardColumn("program_name", "Program"), + new DashboardColumn("participants", "Participants"), new DashboardColumn("clinvars", "Clinical Variables"), + new DashboardColumn("samples", "Samples Sequenced"), new DashboardColumn("accession", "Accession"), + new DashboardColumn("additional_info_link", "Study Link") + ); +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawer.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawer.java new file mode 100644 index 000000000..b8a107eed --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawer.java @@ -0,0 +1,9 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer; + +import java.util.List; + +public record DashboardDrawer( + int datasetId, String studyFullname, String studyAbbreviation, List consentGroups, String studySummary, List studyFocus, + String studyDesign, String sponsor +) { +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerController.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerController.java new file mode 100644 index 000000000..964488bcc --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerController.java @@ -0,0 +1,29 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer; + +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.*; + +import java.util.List; + +@Controller +@RequestMapping("/dashboard-drawer") +public class DashboardDrawerController { + + @Autowired + private DashboardDrawerService dashboardDrawerService; + + @AuditEvent(type = "OTHER", action = "dashboard_drawer.list") + @GetMapping + public ResponseEntity> findAll() { + return dashboardDrawerService.findAll().map(ResponseEntity::ok).orElseGet(() -> ResponseEntity.notFound().build()); + } + + @AuditEvent(type = "OTHER", action = "dashboard_drawer.read") + @GetMapping("/{id}") + public ResponseEntity findByDatasetId(@PathVariable Integer id) { + return dashboardDrawerService.findByDatasetId(id).map(ResponseEntity::ok).orElseGet(() -> ResponseEntity.notFound().build()); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerRepository.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerRepository.java new file mode 100644 index 000000000..1f9897fce --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerRepository.java @@ -0,0 +1,62 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer; + +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.jdbc.core.namedparam.MapSqlParameterSource; +import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate; +import org.springframework.stereotype.Repository; + +import java.util.*; + +@Repository +public class DashboardDrawerRepository { + + private final NamedParameterJdbcTemplate template; + + @Autowired + public DashboardDrawerRepository(NamedParameterJdbcTemplate template) { + this.template = template; + } + + public Optional> getDashboardDrawerRows() { + + String sql = """ + SELECT d.dataset_id, + MAX(d.full_name) study_fullname, + MAX(d.abbreviation) study_abbreviation, + ARRAY_AGG(DISTINCT c.description) consent_groups, + MAX(d.description) study_summary, + ARRAY_AGG(DISTINCT dm.value) FILTER (where dm.key IN ('study_focus')) study_focus, + MAX(DISTINCT dm.value) FILTER (where dm.key IN ('study_design')) study_design, + MAX(DISTINCT dm.value) FILTER (where dm.key IN ('sponsor')) sponsor + FROM dataset d + JOIN dataset_meta dm ON d.dataset_id = dm.dataset_id + LEFT JOIN consent c ON d.dataset_id = c.dataset_id + GROUP BY d.dataset_id + """; + + return Optional.of(template.query(sql, new DashboardDrawerRowMapper())); + + } + + public Optional getDashboardDrawerRowsByDatasetId(Integer datasetId) { + String sql = """ + SELECT d.dataset_id dataset_id, + MAX(d.full_name) study_fullname, + MAX(d.abbreviation) study_abbreviation, + ARRAY_AGG(DISTINCT c.description) consent_groups, + MAX(d.description) study_summary, + ARRAY_AGG(DISTINCT dm.value) FILTER (where dm.key IN ('study_focus')) study_focus, + MAX(DISTINCT dm.value) FILTER (where dm.key IN ('study_design')) study_design, + MAX(DISTINCT dm.value) FILTER (where dm.key IN ('sponsor')) sponsor + FROM dataset d + JOIN dataset_meta dm ON d.dataset_id = dm.dataset_id + JOIN consent c ON d.dataset_id = c.dataset_id + where d.dataset_id = :datasetId + GROUP BY d.dataset_id + """; + MapSqlParameterSource params = new MapSqlParameterSource(); + params.addValue("datasetId", datasetId); + + return template.query(sql, params, new DashboardDrawerRowMapper()).stream().findFirst(); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerRowMapper.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerRowMapper.java new file mode 100644 index 000000000..eb555acb8 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerRowMapper.java @@ -0,0 +1,35 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer; + +import org.springframework.jdbc.core.RowMapper; + +import java.sql.ResultSet; +import java.sql.SQLException; +import java.sql.Array; // For handling SQL Array +import java.util.Arrays; +import java.util.List; + +public class DashboardDrawerRowMapper implements RowMapper { + + @Override + public DashboardDrawer mapRow(ResultSet rs, int rowNum) throws SQLException { + return new DashboardDrawer( + rs.getInt("dataset_id"), rs.getString("study_fullname"), rs.getString("study_abbreviation"), + convertSqlArrayToList(rs.getArray("consent_groups")), rs.getString("study_summary"), + convertSqlArrayToList(rs.getArray("study_focus")), rs.getString("study_design"), rs.getString("sponsor") + ); + } + + private List convertSqlArrayToList(Array sqlArray) throws SQLException { + if (sqlArray == null) { + return List.of(); + } else { + Object[] arrayContents = (Object[]) sqlArray.getArray(); + // Check if the array contains a single empty value + if (arrayContents.length == 1 && "".equals(arrayContents[0])) { + return List.of(); + } else { + return Arrays.asList((String[]) sqlArray.getArray()); + } + } + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerService.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerService.java new file mode 100644 index 000000000..32eee0505 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerService.java @@ -0,0 +1,48 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer; + +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.stereotype.Service; + +import java.util.ArrayList; +import java.util.List; +import java.util.Optional; + +@Service +public class DashboardDrawerService { + + private final DashboardDrawerRepository repository; + private final String dashboardLayout; + + @Autowired + public DashboardDrawerService(DashboardDrawerRepository repository, @Value("${dashboard.layout.type:default}") String dashboardLayout) { + this.repository = repository; + this.dashboardLayout = dashboardLayout; + } + + /** + * Retrieves the Dashboard Drawer for all datasets. + * + * @return All Dashboard Instances and their metadata. + */ + public Optional> findAll() { + if (dashboardLayout.equalsIgnoreCase("default")) { + return repository.getDashboardDrawerRows(); + } + return Optional.of(new ArrayList<>()); + } + + /** + * Retrieves the Dashboard Drawer for a specific dataset. + * + * + * @param datasetId the ID of the dataset to fetch. + * @return a single Dashboard instance with drawer-specific metadata. + */ + public Optional findByDatasetId(Integer datasetId) { + if (dashboardLayout.equalsIgnoreCase("default")) { + return repository.getDashboardDrawerRowsByDatasetId(datasetId); + } + return Optional.empty(); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dataset/Dataset.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dataset/Dataset.java new file mode 100644 index 000000000..b6f1b64fb --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dataset/Dataset.java @@ -0,0 +1,16 @@ +package edu.harvard.dbmi.avillach.dictionary.dataset; + +import jakarta.annotation.Nullable; + +import java.util.Map; + +public record Dataset(String ref, String fullName, String abbreviation, String description, @Nullable Map meta) { + + public Dataset(String ref, String fullName, String abbreviation, String description) { + this(ref, fullName, abbreviation, description, null); + } + + public Dataset withMeta(Map meta) { + return new Dataset(ref, fullName, abbreviation, description, meta); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetMapper.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetMapper.java new file mode 100644 index 000000000..a6488c7bf --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetMapper.java @@ -0,0 +1,15 @@ +package edu.harvard.dbmi.avillach.dictionary.dataset; + +import org.springframework.jdbc.core.RowMapper; +import org.springframework.stereotype.Component; + +import java.sql.ResultSet; +import java.sql.SQLException; + +@Component +public class DatasetMapper implements RowMapper { + @Override + public Dataset mapRow(ResultSet rs, int rowNum) throws SQLException { + return new Dataset(rs.getString("ref"), rs.getString("full_name"), rs.getString("abbreviation"), rs.getString("description")); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetRepository.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetRepository.java new file mode 100644 index 000000000..11e3b2e92 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetRepository.java @@ -0,0 +1,63 @@ +package edu.harvard.dbmi.avillach.dictionary.dataset; + +import edu.harvard.dbmi.avillach.dictionary.util.MapExtractorWithPrettyKeys; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.jdbc.core.namedparam.MapSqlParameterSource; +import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate; +import org.springframework.stereotype.Repository; + +import java.util.List; +import java.util.Map; +import java.util.Optional; + +@Repository +public class DatasetRepository { + private final NamedParameterJdbcTemplate template; + private final DatasetMapper mapper; + private final MapExtractorWithPrettyKeys metaExtractor = new MapExtractorWithPrettyKeys("key", "value"); + + @Autowired + public DatasetRepository(NamedParameterJdbcTemplate template, DatasetMapper mapper) { + this.template = template; + this.mapper = mapper; + } + + public Optional getDataset(String ref) { + String sql = """ + SELECT + ref, full_name, abbreviation, description + FROM + dataset + WHERE + dataset.REF = :ref + """; + + MapSqlParameterSource params = new MapSqlParameterSource().addValue("ref", ref); + + return template.query(sql, params, mapper).stream().findAny(); + } + + public Map getDatasetMeta(String ref) { + String sql = """ + SELECT + key, value + FROM + dataset_meta + LEFT JOIN dataset ON dataset_meta.dataset_id = dataset.dataset_id + WHERE + dataset.REF = :ref + """; + MapSqlParameterSource params = new MapSqlParameterSource().addValue("ref", ref); + return template.query(sql, params, metaExtractor); + } + + public List getAllDatasets() { + String sql = """ + SELECT + ref, full_name, abbreviation, description + FROM + dataset + """; + return template.query(sql, new MapSqlParameterSource(), mapper); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetService.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetService.java new file mode 100644 index 000000000..c16e15cab --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetService.java @@ -0,0 +1,29 @@ +package edu.harvard.dbmi.avillach.dictionary.dataset; + +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Service; + +import java.util.List; +import java.util.Map; +import java.util.Optional; + +@Service +public class DatasetService { + + private final DatasetRepository repository; + + + @Autowired + public DatasetService(DatasetRepository repository) { + this.repository = repository; + } + + public Optional getDataset(String ref) { + Map meta = repository.getDatasetMeta(ref); + return repository.getDataset(ref).map(ds -> ds.withMeta(meta)); + } + + public List getAllDatasets() { + return repository.getAllDatasets(); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/datasource/DataSourceVerifier.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/datasource/DataSourceVerifier.java new file mode 100644 index 000000000..e3fc2a5b9 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/datasource/DataSourceVerifier.java @@ -0,0 +1,40 @@ +package edu.harvard.dbmi.avillach.dictionary.datasource; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.context.annotation.Configuration; +import org.springframework.context.annotation.Profile; +import org.springframework.context.event.ContextRefreshedEvent; +import org.springframework.context.event.EventListener; + +import javax.sql.DataSource; +import java.sql.Connection; +import java.sql.SQLException; + +@Profile("!test") +@Configuration +public class DataSourceVerifier { + + private static final Logger LOG = LoggerFactory.getLogger(DataSourceVerifier.class); + + private final DataSource dataSource; + + @Autowired + public DataSourceVerifier(DataSource dataSource) { + this.dataSource = dataSource; + } + + @EventListener(ContextRefreshedEvent.class) + public void verifyDataSourceConnection() { + try (Connection connection = dataSource.getConnection()) { + if (connection != null) { + LOG.info("Datasource connection verified successfully."); + } + } catch (SQLException e) { + LOG.info("Failed to obtain a connection from the datasource."); + LOG.debug("Error verifying datasource connection: {}", e.getMessage()); + } + } + +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/Facet.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/Facet.java new file mode 100644 index 000000000..6c93a58e4 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/Facet.java @@ -0,0 +1,23 @@ +package edu.harvard.dbmi.avillach.dictionary.facet; + +import jakarta.annotation.Nullable; + +import java.util.List; +import java.util.Map; + +public record Facet( + String name, String display, String description, String fullName, @Nullable Integer count, @Nullable List children, + String category, @Nullable Map meta +) { + public Facet(Facet core, Map meta) { + this(core.name(), core.display(), core.description(), core.fullName(), core.count(), core.children(), core.category(), meta); + } + + public Facet(String name, String category) { + this(name, "", "", "", null, null, category, null); + } + + public Facet withChildren(List children) { + return new Facet(this.name, this.display, this.description, this.fullName, this.count, children, this.category, this.meta); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetCategory.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetCategory.java new file mode 100644 index 000000000..d775ee696 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetCategory.java @@ -0,0 +1,9 @@ +package edu.harvard.dbmi.avillach.dictionary.facet; + +import java.util.List; + +public record FacetCategory(String name, String display, String description, List facets) { + public FacetCategory(FacetCategory core, List facets) { + this(core.name(), core.display(), core.description(), facets); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetCategoryExtractor.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetCategoryExtractor.java new file mode 100644 index 000000000..5c1325182 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetCategoryExtractor.java @@ -0,0 +1,57 @@ +package edu.harvard.dbmi.avillach.dictionary.facet; + +import org.springframework.dao.DataAccessException; +import org.springframework.jdbc.core.ResultSetExtractor; +import org.springframework.util.StringUtils; + +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.*; +import java.util.stream.Collectors; + +public class FacetCategoryExtractor implements ResultSetExtractor> { + + private record Pair(String parent, String category) { + Pair(Facet facet) { + this(facet.name(), facet.category()); + } + }; + + @Override + public List extractData(ResultSet rs) throws SQLException, DataAccessException { + List facets = new ArrayList<>(); + Map categories = new HashMap<>(); + Map> childrenForParent = new HashMap<>(); + + while (rs.next()) { + // build out all the facets and make shells of the facet categories + String category = rs.getString("category_name"); + Facet facet = new Facet( + rs.getString("name"), rs.getString("display"), rs.getString("description"), rs.getString("full_name"), + rs.getInt("facet_count"), List.of(), category, null + ); + FacetCategory facetCategory = + new FacetCategory(category, rs.getString("category_display"), rs.getString("category_description"), List.of()); + String parentName = rs.getString("parent_name"); + if (StringUtils.hasLength(parentName)) { + Pair key = new Pair(parentName, category); + List facetsForParent = childrenForParent.getOrDefault(key, new ArrayList<>()); + facetsForParent.add(facet); + childrenForParent.put(key, facetsForParent); + } else { + facets.add(facet); + } + categories.put(category, facetCategory); + } + facets = facets.stream().map(f -> f.withChildren(childrenForParent.getOrDefault(new Pair(f), List.of()))).toList(); + // group facets by category, then add them to their respective category + Map> grouped = facets.stream().collect(Collectors.groupingBy(Facet::category)); + return categories.entrySet().stream() + .map( + e -> new FacetCategory( + e.getValue(), + grouped.getOrDefault(e.getKey(), List.of()).stream().sorted(Comparator.comparingInt(Facet::count).reversed()).toList() + ) + ).toList(); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetController.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetController.java new file mode 100644 index 000000000..2a9b2d42a --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetController.java @@ -0,0 +1,34 @@ +package edu.harvard.dbmi.avillach.dictionary.facet; + +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.*; + +import java.util.List; + +@Controller +public class FacetController { + + private final FacetService facetService; + + + @Autowired + public FacetController(FacetService facetService) { + this.facetService = facetService; + } + + @AuditEvent(type = "SEARCH", action = "facet.search") + @PostMapping(path = "/facets") + public ResponseEntity> getFacets(@RequestBody Filter filter) { + return ResponseEntity.ok(facetService.getFacets(filter)); + } + + @AuditEvent(type = "SEARCH", action = "facet.detail") + @GetMapping(path = "/facets/{facetCategory}/{facet}") + public ResponseEntity facetDetails(@PathVariable String facetCategory, @PathVariable String facet) { + return facetService.facetDetails(facetCategory, facet).map(ResponseEntity::ok).orElse(ResponseEntity.notFound().build()); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetMapper.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetMapper.java new file mode 100644 index 000000000..299e12199 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetMapper.java @@ -0,0 +1,19 @@ +package edu.harvard.dbmi.avillach.dictionary.facet; + +import org.springframework.jdbc.core.RowMapper; +import org.springframework.stereotype.Component; + +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.List; + +@Component +public class FacetMapper implements RowMapper { + @Override + public Facet mapRow(ResultSet rs, int rowNum) throws SQLException { + return new Facet( + rs.getString("name"), rs.getString("display"), rs.getString("description"), rs.getString("full_name"), null, List.of(), + rs.getString("category"), null + ); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetQueryGenerator.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetQueryGenerator.java new file mode 100644 index 000000000..50ad183b6 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetQueryGenerator.java @@ -0,0 +1,523 @@ +package edu.harvard.dbmi.avillach.dictionary.facet; + +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import edu.harvard.dbmi.avillach.dictionary.filter.QueryParamPair; +import edu.harvard.dbmi.avillach.dictionary.util.QueryUtility; +import edu.harvard.dbmi.avillach.dictionary.util.SchemaDetector; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.jdbc.core.namedparam.MapSqlParameterSource; +import org.springframework.stereotype.Component; +import org.springframework.util.CollectionUtils; +import org.springframework.util.StringUtils; + +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +/** + * Builds dynamic SQL for facet count queries. Supports three modes: no facets selected, single category selected, and multi-category + * selected. Each mode has search and no-search variants. Facet counts reflect how many displayable concepts match each facet, scoped by the + * current search term and consent restrictions. + */ +@Component +public class FacetQueryGenerator { + + private final String fcnQueryable; + private final String fcnQueryable2; + + private static final String CONSENT_QUERY = """ + dataset.dataset_id IN ( + SELECT + consent.dataset_id + FROM consent + LEFT JOIN dataset ON dataset.dataset_id = consent.dataset_id + WHERE + concat(dataset.ref, '.', consent.consent_code) IN (:consents) OR + (dataset.ref IN (:consents) AND consent.consent_code = '') + UNION + SELECT + dataset_harmonization.harmonized_dataset_id + FROM consent + JOIN dataset_harmonization ON dataset_harmonization.source_dataset_id = consent.dataset_id + LEFT JOIN dataset ON dataset.dataset_id = dataset_harmonization.source_dataset_id + WHERE + concat(dataset.ref, '.', consent.consent_code) IN (:consents) OR + (dataset.ref IN (:consents) AND consent.consent_code = '') + ) AND + """; + + @Autowired + public FacetQueryGenerator(SchemaDetector schemaDetector) { + this.fcnQueryable = schemaDetector.fcnQueryableClause("fcn"); + this.fcnQueryable2 = schemaDetector.fcnQueryableClause("fcn2"); + } + + public String createFacetSQLAndPopulateParams(Filter filter, MapSqlParameterSource params) { + Map> groupedFacets = + (filter.facets() == null ? Stream.of() : filter.facets().stream()).collect(Collectors.groupingBy(Facet::category)); + String consentWhere = ""; + if (!CollectionUtils.isEmpty(filter.consents())) { + params.addValue("consents", filter.consents()); + consentWhere = CONSENT_QUERY; + } + if (CollectionUtils.isEmpty(filter.facets())) { + if (StringUtils.hasLength(filter.search())) { + return createNoFacetSQLWithSearch(filter.search(), consentWhere, params); + } else { + return createNoFacetSQLNoSearch(params, consentWhere); + } + } else if (groupedFacets.size() == 1) { + if (StringUtils.hasLength(filter.search())) { + return createSingleCategorySQLWithSearch(filter.facets(), filter.search(), consentWhere, params); + } else { + return createSingleCategorySQLNoSearch(filter.facets(), consentWhere, params); + } + } else { + if (StringUtils.hasLength(filter.search())) { + return createMultiCategorySQLWithSearch(groupedFacets, filter.search(), consentWhere, params); + } else { + return createMultiCategorySQLNoSearch(groupedFacets, consentWhere, params); + } + } + } + + /** + * Returns independent count queries for multi-category facet requests, one per category block plus one for unselected categories. Each + * query uses inline subqueries against base tables (no CTEs) for optimal planner cardinality estimation. Returns (facet_name, + * category_name, facet_count) rows for merging in Java. + */ + public List createMultiCategoryCountBlocks(Filter filter) { + Map> groupedFacets = + (filter.facets() == null ? Stream.of() : filter.facets().stream()).collect(Collectors.groupingBy(Facet::category)); + MapSqlParameterSource params = new MapSqlParameterSource(); + String consentWhere = ""; + String consentJoins = ""; + if (!CollectionUtils.isEmpty(filter.consents())) { + params.addValue("consents", filter.consents()); + consentWhere = CONSENT_QUERY; + consentJoins = """ + LEFT JOIN concept_node ON concept_node.concept_node_id = fcn.concept_node_id + LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_id"""; + } + + Map categoryKeys = createSQLSafeCategoryKeys(groupedFacets.keySet().stream().toList()); + boolean hasSearch = StringUtils.hasLength(filter.search()); + if (hasSearch) { + params.addValue("search", filter.search()); + } + + List allSelectedFacets = + groupedFacets.values().stream().flatMap(List::stream).map(f -> new String[] {f.category(), f.name()}).toList(); + params.addValue("all_selected_facets", allSelectedFacets); + params.addValue("num_categories", groupedFacets.size()); + params.addValue("num_other_categories", groupedFacets.size() - 1); + params.addValue("all_selected_facet_categories", groupedFacets.keySet()); + groupedFacets.keySet().forEach(category -> params.addValue("facet_category_" + categoryKeys.get(category), category)); + + String searchJoin = hasSearch ? "JOIN concept_node ON concept_node.concept_node_id = fcn2.concept_node_id" : ""; + String searchWhere = hasSearch ? "AND " + QueryUtility.SEARCH_WHERE : ""; + + List blocks = new ArrayList<>(); + + // One block per selected category: inline IN subquery excludes this category + for (String category : groupedFacets.keySet()) { + String block = """ + SELECT facet.name AS facet_name, fc.name AS category_name, count(*) AS facet_count + FROM facet + JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id + JOIN facet_category fc ON fc.facet_category_id = facet.facet_category_id + %s + WHERE %s + AND %s + fc.name = :facet_category_%s + AND fcn.concept_node_id IN ( + SELECT fcn2.concept_node_id + FROM facet__concept_node fcn2 + JOIN facet f2 ON f2.facet_id = fcn2.facet_id + JOIN facet_category fc2 ON fc2.facet_category_id = f2.facet_category_id + %s + WHERE %s + AND fc2.name != :facet_category_%s + AND (fc2.name, f2.name) IN (:all_selected_facets) + %s + GROUP BY fcn2.concept_node_id + HAVING count(DISTINCT fc2.name) = :num_other_categories + ) + GROUP BY facet.name, fc.name + """.formatted( + consentJoins, fcnQueryable, consentWhere, categoryKeys.get(category), searchJoin, fcnQueryable2, categoryKeys.get(category), + searchWhere + ); + blocks.add(new QueryParamPair(block, params)); + } + + // One block for unselected categories: inline IN subquery requires ALL categories + String unselectedBlock = """ + SELECT facet.name AS facet_name, fc.name AS category_name, count(*) AS facet_count + FROM facet + JOIN facet_category fc ON fc.facet_category_id = facet.facet_category_id + JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id + %s + WHERE %s + AND %s + fc.name NOT IN (:all_selected_facet_categories) + AND fcn.concept_node_id IN ( + SELECT fcn2.concept_node_id + FROM facet__concept_node fcn2 + JOIN facet f2 ON f2.facet_id = fcn2.facet_id + JOIN facet_category fc2 ON fc2.facet_category_id = f2.facet_category_id + %s + WHERE %s + AND (fc2.name, f2.name) IN (:all_selected_facets) + %s + GROUP BY fcn2.concept_node_id + HAVING count(DISTINCT fc2.name) = :num_categories + ) + GROUP BY facet.name, fc.name + """.formatted(consentJoins, fcnQueryable, consentWhere, searchJoin, fcnQueryable2, searchWhere); + blocks.add(new QueryParamPair(unselectedBlock, params)); + + return blocks; + } + + private Map createSQLSafeCategoryKeys(List categories) { + HashMap keys = new HashMap<>(); + for (int i = 0; i < categories.size(); i++) { + keys.put(categories.get(i), "cat_" + i); + } + return keys; + } + + private String createMultiCategorySQLWithSearch( + Map> facets, String search, String consentWhere, MapSqlParameterSource params + ) { + Map categoryKeys = createSQLSafeCategoryKeys(facets.keySet().stream().toList()); + params.addValue("search", search); + String consentJoins = StringUtils.hasLength(consentWhere) ? """ + LEFT JOIN concept_node ON concept_node.concept_node_id = fcn.concept_node_id + LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_id""" : ""; + + List allSelectedFacets = + facets.values().stream().flatMap(List::stream).map(f -> new String[] {f.category(), f.name()}).toList(); + params.addValue("all_selected_facets", allSelectedFacets); + params.addValue("num_categories", facets.size()); + params.addValue("num_other_categories", facets.size() - 1); + params.addValue("all_selected_facet_categories", facets.keySet()); + facets.keySet().forEach(category -> params.addValue("facet_category_" + categoryKeys.get(category), category)); + + // Each UNION block has an inline IN subquery with concept_node JOIN for search + String selectedFacetsQuery = facets.keySet().stream() + .map( + category -> """ + ( + SELECT facet.facet_id, count(*) AS facet_count + FROM facet + JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id + JOIN facet_category fc ON fc.facet_category_id = facet.facet_category_id + %s + WHERE %s + AND %s + fc.name = :facet_category_%s + AND fcn.concept_node_id IN ( + SELECT fcn2.concept_node_id + FROM facet__concept_node fcn2 + JOIN facet f2 ON f2.facet_id = fcn2.facet_id + JOIN facet_category fc2 ON fc2.facet_category_id = f2.facet_category_id + JOIN concept_node ON concept_node.concept_node_id = fcn2.concept_node_id + WHERE %s + AND fc2.name != :facet_category_%s + AND (fc2.name, f2.name) IN (:all_selected_facets) + AND %s + GROUP BY fcn2.concept_node_id + HAVING count(DISTINCT fc2.name) = :num_other_categories + ) + GROUP BY facet.facet_id + ORDER BY facet_count DESC + )""".formatted( + consentJoins, fcnQueryable, consentWhere, categoryKeys.get(category), fcnQueryable2, categoryKeys.get(category), + QueryUtility.SEARCH_WHERE + ) + ).collect(Collectors.joining("\n\tUNION\n")); + + String unselectedFacetsQuery = """ + UNION + ( + SELECT facet.facet_id, count(*) AS facet_count + FROM facet + JOIN facet_category fc ON fc.facet_category_id = facet.facet_category_id + JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id + %s + WHERE %s + AND %s + fc.name NOT IN (:all_selected_facet_categories) + AND fcn.concept_node_id IN ( + SELECT fcn2.concept_node_id + FROM facet__concept_node fcn2 + JOIN facet f2 ON f2.facet_id = fcn2.facet_id + JOIN facet_category fc2 ON fc2.facet_category_id = f2.facet_category_id + JOIN concept_node ON concept_node.concept_node_id = fcn2.concept_node_id + WHERE %s + AND (fc2.name, f2.name) IN (:all_selected_facets) + AND %s + GROUP BY fcn2.concept_node_id + HAVING count(DISTINCT fc2.name) = :num_categories + ) + GROUP BY facet.facet_id + ORDER BY facet_count DESC + )""".formatted(consentJoins, fcnQueryable, consentWhere, fcnQueryable2, QueryUtility.SEARCH_WHERE); + + return selectedFacetsQuery + "\n" + unselectedFacetsQuery; + } + + private String createMultiCategorySQLNoSearch(Map> facets, String consentWhere, MapSqlParameterSource params) { + Map categoryKeys = createSQLSafeCategoryKeys(facets.keySet().stream().toList()); + String consentJoins = StringUtils.hasLength(consentWhere) ? """ + LEFT JOIN concept_node ON concept_node.concept_node_id = fcn.concept_node_id + LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_id""" : ""; + + List allSelectedFacets = + facets.values().stream().flatMap(List::stream).map(f -> new String[] {f.category(), f.name()}).toList(); + params.addValue("all_selected_facets", allSelectedFacets); + params.addValue("num_categories", facets.size()); + params.addValue("num_other_categories", facets.size() - 1); + params.addValue("all_selected_facet_categories", facets.keySet()); + facets.keySet().forEach(category -> params.addValue("facet_category_" + categoryKeys.get(category), category)); + + // Each UNION block has an inline IN subquery against base tables (no CTE). + // This lets the planner see real pg_statistics and choose Hash Semi Join. + String selectedFacetsQuery = facets.keySet().stream().map(category -> """ + ( + SELECT facet.facet_id, count(*) AS facet_count + FROM facet + JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id + JOIN facet_category fc ON fc.facet_category_id = facet.facet_category_id + %s + WHERE %s + AND %s + fc.name = :facet_category_%s + AND fcn.concept_node_id IN ( + SELECT fcn2.concept_node_id + FROM facet__concept_node fcn2 + JOIN facet f2 ON f2.facet_id = fcn2.facet_id + JOIN facet_category fc2 ON fc2.facet_category_id = f2.facet_category_id + WHERE %s + AND fc2.name != :facet_category_%s + AND (fc2.name, f2.name) IN (:all_selected_facets) + GROUP BY fcn2.concept_node_id + HAVING count(DISTINCT fc2.name) = :num_other_categories + ) + GROUP BY facet.facet_id + ORDER BY facet_count DESC + )""".formatted(consentJoins, fcnQueryable, consentWhere, categoryKeys.get(category), fcnQueryable2, categoryKeys.get(category))) + .collect(Collectors.joining("\n\tUNION\n")); + + String unselectedFacetsQuery = """ + UNION + ( + SELECT facet.facet_id, count(*) AS facet_count + FROM facet + JOIN facet_category fc ON fc.facet_category_id = facet.facet_category_id + JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id + %s + WHERE %s + AND %s + fc.name NOT IN (:all_selected_facet_categories) + AND fcn.concept_node_id IN ( + SELECT fcn2.concept_node_id + FROM facet__concept_node fcn2 + JOIN facet f2 ON f2.facet_id = fcn2.facet_id + JOIN facet_category fc2 ON fc2.facet_category_id = f2.facet_category_id + WHERE %s + AND (fc2.name, f2.name) IN (:all_selected_facets) + GROUP BY fcn2.concept_node_id + HAVING count(DISTINCT fc2.name) = :num_categories + ) + GROUP BY facet.facet_id + ORDER BY facet_count DESC + )""".formatted(consentJoins, fcnQueryable, consentWhere, fcnQueryable2); + + return selectedFacetsQuery + "\n" + unselectedFacetsQuery; + } + + private String createSingleCategorySQLWithSearch(List facets, String search, String consentWhere, MapSqlParameterSource params) { + params.addValue("facet_category_name", facets.getFirst().category()); + params.addValue("facets", facets.stream().map(Facet::name).toList()); + params.addValue("search", search); + String consentJoins = StringUtils.hasLength(consentWhere) ? """ + LEFT JOIN concept_node ON concept_node.concept_node_id = fcn.concept_node_id + LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_id""" : ""; + // Part 1: facets in the matched category that are displayable + match search + // Part 2: facets from other categories for concepts matching selected facets + search + return """ + ( + SELECT + facet.facet_id, count(*) as facet_count + FROM + facet + JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id + JOIN facet_category fc on fc.facet_category_id = facet.facet_category_id + JOIN concept_node ON concept_node.concept_node_id = fcn.concept_node_id + LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_id + WHERE + %s + AND %s + fc.name = :facet_category_name + AND %s + GROUP BY + facet.facet_id + ORDER BY + facet_count DESC + ) + UNION + ( + WITH matching_concepts AS ( + SELECT + DISTINCT(fcn.concept_node_id) AS concept_node_id + FROM + facet + JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id + JOIN facet_category fc on fc.facet_category_id = facet.facet_category_id + JOIN concept_node ON concept_node.concept_node_id = fcn.concept_node_id + WHERE + %s + AND fc.name = :facet_category_name + AND facet.name IN (:facets) + AND %s + ) + SELECT + facet.facet_id, count(*) as facet_count + FROM + facet + JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id + JOIN facet_category fc on fc.facet_category_id = facet.facet_category_id + %s + JOIN matching_concepts ON fcn.concept_node_id = matching_concepts.concept_node_id + WHERE + %s + AND %s + fc.name <> :facet_category_name + GROUP BY + facet.facet_id + ORDER BY + facet_count DESC + ) + """.formatted( + fcnQueryable, consentWhere, QueryUtility.SEARCH_WHERE, fcnQueryable, QueryUtility.SEARCH_WHERE, consentJoins, fcnQueryable, + consentWhere + ); + } + + private String createSingleCategorySQLNoSearch(List facets, String consentWhere, MapSqlParameterSource params) { + params.addValue("facet_category_name", facets.getFirst().category()); + params.addValue("facets", facets.stream().map(Facet::name).toList()); + String consentJoins = StringUtils.hasLength(consentWhere) ? """ + LEFT JOIN concept_node ON concept_node.concept_node_id = fcn.concept_node_id + LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_id""" : ""; + // return all the facets in the matched category that are displayable + // UNION + // all the facets from other categories that match concepts that match selected facets from this category + return """ + ( + SELECT + facet.facet_id, count(*) as facet_count + FROM + facet + JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id + JOIN facet_category fc on fc.facet_category_id = facet.facet_category_id + %s + WHERE + %s + AND %s + fc.name = :facet_category_name + GROUP BY + facet.facet_id + ORDER BY + facet_count DESC + ) + UNION + ( + WITH matching_concepts AS ( + SELECT + DISTINCT(fcn.concept_node_id) AS concept_node_id + FROM + facet + JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id + JOIN facet_category fc on fc.facet_category_id = facet.facet_category_id + WHERE + %s + AND fc.name = :facet_category_name + AND facet.name IN (:facets) + ) + SELECT + facet.facet_id, count(*) as facet_count + FROM + facet + JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id + JOIN facet_category fc on fc.facet_category_id = facet.facet_category_id + %s + JOIN matching_concepts ON fcn.concept_node_id = matching_concepts.concept_node_id + WHERE + %s + AND %s + fc.name <> :facet_category_name + GROUP BY + facet.facet_id + ORDER BY + facet_count DESC + ) + """.formatted(consentJoins, fcnQueryable, consentWhere, fcnQueryable, consentJoins, fcnQueryable, consentWhere); + } + + private String createNoFacetSQLWithSearch(String search, String consentWhere, MapSqlParameterSource params) { + // return all the facets that match concepts that + // match search + // are displayable + params.addValue("search", search); + String datasetJoin = StringUtils.hasLength(consentWhere) ? "LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_id" : ""; + return """ + SELECT + facet.facet_id, count(*) as facet_count + FROM + facet + JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id + JOIN facet_category fc on fc.facet_category_id = facet.facet_category_id + JOIN concept_node ON concept_node.concept_node_id = fcn.concept_node_id + %s + WHERE + %s + AND %s + %s + GROUP BY + facet.facet_id + ORDER BY + facet_count DESC + """.formatted(datasetJoin, fcnQueryable, consentWhere, QueryUtility.SEARCH_WHERE); + + } + + private String createNoFacetSQLNoSearch(MapSqlParameterSource params, String consents) { + String consentJoins = StringUtils.hasLength(consents) ? """ + LEFT JOIN concept_node ON concept_node.concept_node_id = fcn.concept_node_id + LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_id""" : ""; + String whereClause = StringUtils.hasLength(consents) ? consents.strip().replaceAll("\\s+AND\\s*$", "") : "TRUE"; + return """ + SELECT + facet.facet_id, count(*) as facet_count + FROM + facet + JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id + JOIN facet_category fc on fc.facet_category_id = facet.facet_category_id + %s + WHERE + %s + AND %s + GROUP BY + facet.facet_id + ORDER BY + facet_count DESC + """.formatted(consentJoins, fcnQueryable, whereClause); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetRepository.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetRepository.java new file mode 100644 index 000000000..43ad60984 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetRepository.java @@ -0,0 +1,193 @@ +package edu.harvard.dbmi.avillach.dictionary.facet; + +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import edu.harvard.dbmi.avillach.dictionary.filter.QueryParamPair; +import edu.harvard.dbmi.avillach.dictionary.util.MapExtractor; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.jdbc.core.namedparam.MapSqlParameterSource; +import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate; +import org.springframework.jdbc.datasource.SingleConnectionDataSource; +import org.springframework.stereotype.Repository; +import org.springframework.transaction.annotation.Transactional; + +import javax.sql.DataSource; +import java.sql.Connection; +import java.sql.SQLException; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Optional; + +@Repository +public class FacetRepository { + + private final NamedParameterJdbcTemplate template; + + private final FacetMapper mapper; + + private final FacetQueryGenerator generator; + + @Autowired + public FacetRepository(NamedParameterJdbcTemplate template, FacetQueryGenerator generator, FacetMapper mapper) { + this.template = template; + this.generator = generator; + this.mapper = mapper; + } + + @Transactional(readOnly = true) + public List getFacets(Filter filter) { + template.getJdbcTemplate().execute("SET LOCAL work_mem = '64MB'"); + MapSqlParameterSource params = new MapSqlParameterSource(); + String innerSQL = generator.createFacetSQLAndPopulateParams(filter, params); + // return a list of facets and the number of concepts associated with them + String sql = + """ + WITH facet_counts_q AS ( + %s + ) + SELECT + facet_category.name AS category_name, + parent_facet.name AS parent_name, + facet_counts_q.facet_count AS facet_count, + facet_category.display as category_display, + facet_category.description as category_description, + facet.name, facet.display, facet.description, + facet_meta_full_name.value AS full_name + FROM + facet + LEFT JOIN facet_counts_q ON facet.facet_id = facet_counts_q.facet_id + LEFT JOIN facet_category ON facet_category.facet_category_id = facet.facet_category_id + LEFT JOIN facet as parent_facet ON facet.parent_id = parent_facet.facet_id + LEFT JOIN facet_meta AS facet_meta_full_name ON facet.facet_id = facet_meta_full_name.facet_id AND facet_meta_full_name.KEY = 'full_name' + + """ + .formatted(innerSQL); + + return template.query(sql, params, new FacetCategoryExtractor()); + } + + /** + * Returns all facets with metadata (category, display, parent, full_name) but no counts. Used as the base for merging parallel count + * results. + */ + public List getFacetMetadata() { + String sql = + """ + SELECT + facet_category.name AS category_name, + parent_facet.name AS parent_name, + 0 AS facet_count, + facet_category.display AS category_display, + facet_category.description AS category_description, + facet.name, facet.display, facet.description, + facet_meta_full_name.value AS full_name + FROM + facet + LEFT JOIN facet_category ON facet_category.facet_category_id = facet.facet_category_id + LEFT JOIN facet AS parent_facet ON facet.parent_id = parent_facet.facet_id + LEFT JOIN facet_meta AS facet_meta_full_name ON facet.facet_id = facet_meta_full_name.facet_id AND facet_meta_full_name.KEY = 'full_name' + """; + return template.query(sql, new FacetCategoryExtractor()); + } + + /** + * Executes a single count block on its own connection with work_mem set. Designed to be called from virtual threads for parallel + * execution. Returns a map of (category_name + "|" + facet_name) → count. + */ + public Map executeCountBlock(QueryParamPair block) throws SQLException { + DataSource ds = template.getJdbcTemplate().getDataSource(); + try (Connection conn = ds.getConnection()) { + conn.setAutoCommit(false); + conn.setReadOnly(true); + conn.createStatement().execute("SET LOCAL work_mem = '64MB'"); + + NamedParameterJdbcTemplate localTemplate = new NamedParameterJdbcTemplate(new SingleConnectionDataSource(conn, true)); + Map counts = localTemplate.query(block.query(), block.params(), rs -> { + Map map = new HashMap<>(); + while (rs.next()) { + String key = rs.getString("category_name") + "|" + rs.getString("facet_name"); + map.put(key, rs.getInt("facet_count")); + } + return map; + }); + conn.commit(); + return counts; + } + } + + public Map getFacetCategoryOrder(List categoryNames) { + if (categoryNames.isEmpty()) { + return Map.of(); + } + + String sql = """ + SELECT + facet_category.name as name, + facet_category_meta.value as order + FROM + facet_category_meta + LEFT JOIN facet_category ON facet_category.facet_category_id = facet_category_meta.facet_category_id + WHERE + facet_category_meta.key = 'order' + AND facet_category.name IN (:category_names) + """; + MapSqlParameterSource params = new MapSqlParameterSource().addValue("category_names", categoryNames); + return template.query(sql, params, new MapExtractor("name", "order")); + } + + public Optional getFacet(String facetCategory, String facet) { + String sql = + """ + SELECT + facet_category.name AS category, + facet.name, facet.display, facet.description, + facet_meta_full_name.value AS full_name + FROM + facet + LEFT JOIN facet_category ON facet_category.facet_category_id = facet.facet_category_id + LEFT JOIN facet_meta AS facet_meta_full_name ON facet.facet_id = facet_meta_full_name.facet_id AND facet_meta_full_name.KEY = 'full_name' + WHERE + facet.name = :facetName + AND facet_category.name = :facetCategory + """; + MapSqlParameterSource params = new MapSqlParameterSource().addValue("facetCategory", facetCategory).addValue("facetName", facet); + return template.query(sql, params, mapper).stream().findFirst().map(f -> f.withChildren(getFacetChildren(f.category(), f.name()))); + } + + private List getFacetChildren(String facetCategory, String parentFacetName) { + String sql = + """ + SELECT + facet_category.name AS category, + facet.name, facet.display, facet.description, + facet_meta_full_name.value AS full_name + FROM + facet + LEFT JOIN facet as parent_facet ON facet.parent_id = parent_facet.facet_id + LEFT JOIN facet_category ON facet_category.facet_category_id = facet.facet_category_id + LEFT JOIN facet_meta AS facet_meta_full_name ON facet.facet_id = facet_meta_full_name.facet_id AND facet_meta_full_name.KEY = 'full_name' + WHERE + parent_facet.name = :facetName + AND facet_category.name = :facetCategory + """; + MapSqlParameterSource params = + new MapSqlParameterSource().addValue("facetCategory", facetCategory).addValue("facetName", parentFacetName); + return template.query(sql, params, mapper); + } + + public Map getFacetMeta(String facetCategory, String facet) { + String sql = """ + SELECT + facet_meta.KEY, facet_meta.VALUE + FROM + facet_meta + LEFT JOIN facet ON facet.facet_id = facet_meta.facet_id + LEFT JOIN facet_category ON facet_category.facet_category_id = facet.facet_category_id + WHERE + facet.name = :facetName + AND facet_category.name = :facetCategory + """; + MapSqlParameterSource params = new MapSqlParameterSource().addValue("facetCategory", facetCategory).addValue("facetName", facet); + return template.query(sql, params, new MapExtractor("KEY", "VALUE")); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetService.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetService.java new file mode 100644 index 000000000..fbb9809ab --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetService.java @@ -0,0 +1,108 @@ +package edu.harvard.dbmi.avillach.dictionary.facet; + +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import edu.harvard.dbmi.avillach.dictionary.filter.QueryParamPair; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.cache.annotation.Cacheable; +import org.springframework.stereotype.Service; + +import java.util.*; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.Executors; +import java.util.concurrent.Future; +import java.util.stream.Collectors; + +@Service +public class FacetService { + + private static final Logger LOG = LoggerFactory.getLogger(FacetService.class); + + private final FacetRepository repository; + private final FacetQueryGenerator generator; + + @Autowired + public FacetService(FacetRepository repository, FacetQueryGenerator generator) { + this.repository = repository; + this.generator = generator; + } + + @Cacheable("facets") + public List getFacets(Filter filter) { + List facetCategories = + isMultiCategory(filter) ? getMultiCategoryFacetsParallel(filter) : repository.getFacets(filter); + + if (facetCategories.isEmpty()) { + return facetCategories; + } + + return applyOrdering(facetCategories); + } + + private boolean isMultiCategory(Filter filter) { + if (filter.facets() == null || filter.facets().isEmpty()) { + return false; + } + long categoryCount = filter.facets().stream().map(Facet::category).distinct().count(); + return categoryCount > 1; + } + + private List getMultiCategoryFacetsParallel(Filter filter) { + List blocks = generator.createMultiCategoryCountBlocks(filter); + + // Execute count blocks in parallel using virtual threads + Map mergedCounts = new HashMap<>(); + try (ExecutorService executor = Executors.newVirtualThreadPerTaskExecutor()) { + List>> futures = + blocks.stream().map(block -> executor.submit(() -> repository.executeCountBlock(block))).toList(); + + for (Future> future : futures) { + mergedCounts.putAll(future.get()); + } + } catch (InterruptedException e) { + Thread.currentThread().interrupt(); + throw new RuntimeException("Parallel facet count execution interrupted", e); + } catch (Exception e) { + throw new RuntimeException("Parallel facet count execution failed", e); + } + + // Get metadata (fast — just facet table data, no counts) + List metadata = repository.getFacetMetadata(); + + // Inject counts into metadata + return metadata.stream().map(cat -> new FacetCategory(cat, cat.facets().stream().map(f -> { + String key = f.category() + "|" + f.name(); + int count = mergedCounts.getOrDefault(key, 0); + // Rebuild facet with count, preserving children with their own counts + List children = f.children() == null ? List.of() : f.children().stream().map(child -> { + String childKey = child.category() + "|" + child.name(); + int childCount = mergedCounts.getOrDefault(childKey, 0); + return new Facet( + child.name(), child.display(), child.description(), child.fullName(), childCount, child.children(), child.category(), + child.meta() + ); + }).toList(); + return new Facet(f.name(), f.display(), f.description(), f.fullName(), count, children, f.category(), f.meta()); + }).sorted(Comparator.comparingInt(Facet::count).reversed()).toList())).toList(); + } + + private List applyOrdering(List facetCategories) { + List categoryNames = facetCategories.stream().map(FacetCategory::name).toList(); + Map order = repository.getFacetCategoryOrder(categoryNames); + + if (order.isEmpty()) { + return facetCategories.stream().sorted(Comparator.comparing(FacetCategory::display)).toList(); + } + + int unordered = order.values().stream().map(Integer::parseInt).reduce(Integer.MIN_VALUE, Math::max) + 1; + return facetCategories.stream().sorted(Comparator.comparing((FacetCategory fc) -> { + String orderValue = order.get(fc.name()); + return orderValue != null ? Integer.parseInt(orderValue) : unordered; + }).thenComparing(FacetCategory::display)).toList(); + } + + public Optional facetDetails(String facetCategory, String facet) { + return repository.getFacet(facetCategory, facet).map(f -> new Facet(f, repository.getFacetMeta(facetCategory, facet))); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FilterPreProcessor.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FilterPreProcessor.java new file mode 100644 index 000000000..3c6eda127 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FilterPreProcessor.java @@ -0,0 +1,58 @@ +package edu.harvard.dbmi.avillach.dictionary.facet; + +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import edu.harvard.dbmi.avillach.dictionary.filter.FilterProcessor; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.core.MethodParameter; +import org.springframework.http.HttpInputMessage; +import org.springframework.http.converter.HttpMessageConverter; +import org.springframework.web.bind.annotation.ControllerAdvice; +import org.springframework.web.servlet.mvc.method.annotation.RequestBodyAdvice; + +import java.io.IOException; +import java.lang.reflect.Type; + +@ControllerAdvice +public class FilterPreProcessor implements RequestBodyAdvice { + + private final FilterProcessor filterProcessor; + + @Autowired + public FilterPreProcessor(FilterProcessor filterProcessor) { + this.filterProcessor = filterProcessor; + } + + + @Override + public boolean supports(MethodParameter methodParameter, Type targetType, Class> converterType) { + return true; + } + + @Override + public HttpInputMessage beforeBodyRead( + HttpInputMessage inputMessage, MethodParameter parameter, Type targetType, Class> converterType + ) throws IOException { + return inputMessage; + } + + @Override + public Object afterBodyRead( + Object body, HttpInputMessage inputMessage, MethodParameter parameter, Type targetType, + Class> converterType + ) { + if (body instanceof Filter filter) { + return filterProcessor.processsFilter(filter); + } + return body; + } + + + + @Override + public Object handleEmptyBody( + Object body, HttpInputMessage inputMessage, MethodParameter parameter, Type targetType, + Class> converterType + ) { + return body; + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/filter/Filter.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/filter/Filter.java new file mode 100644 index 000000000..c6f7fa3db --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/filter/Filter.java @@ -0,0 +1,11 @@ +package edu.harvard.dbmi.avillach.dictionary.filter; + +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; +import edu.harvard.dbmi.avillach.dictionary.facet.Facet; +import jakarta.annotation.Nullable; + +import java.util.List; + +@JsonIgnoreProperties(ignoreUnknown = true) +public record Filter(@Nullable List facets, @Nullable String search, @Nullable List consents) { +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/filter/FilterProcessor.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/filter/FilterProcessor.java new file mode 100644 index 000000000..eb7d93d28 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/filter/FilterProcessor.java @@ -0,0 +1,49 @@ +package edu.harvard.dbmi.avillach.dictionary.filter; + +import edu.harvard.dbmi.avillach.dictionary.facet.Facet; +import org.springframework.stereotype.Component; + +import java.util.ArrayList; +import java.util.Comparator; +import java.util.List; +import java.util.function.Function; + +/** + * Preprocesses filter input before query generation. Sorts facets and consents for stable cache keys, and sanitizes the search string to + * prevent tsquery syntax errors from special characters. + */ +@Component +public class FilterProcessor { + + private static final int MAX_SEARCH_LENGTH = 200; + + public Filter processsFilter(Filter filter) { + List newFacets = filter.facets(); + List newConsents = filter.consents(); + if (filter.facets() != null) { + newFacets = new ArrayList<>(filter.facets()); + newFacets.sort(Comparator.comparing(Facet::name)); + } + if (filter.consents() != null) { + newConsents = new ArrayList<>(newConsents); + newConsents.sort(Comparator.comparing(Function.identity())); + } + filter = new Filter(newFacets, sanitizeSearch(filter.search()), newConsents); + return filter; + } + + /** + * Sanitizes a raw search string for safe use in PostgreSQL to_tsquery(). Strips all characters that are not Unicode letters, digits, or + * whitespace — this prevents tsquery operator injection (&, |, !, :, *, etc.). Collapses runs of whitespace and trims. Returns + * empty string for input that contains only special characters (e.g. "&"), which downstream code treats as no search. + */ + static String sanitizeSearch(String search) { + if (search == null) { + return null; + } + if (search.length() > MAX_SEARCH_LENGTH) { + search = search.substring(0, MAX_SEARCH_LENGTH); + } + return search.replaceAll("[^\\p{L}\\p{N}\\s]", " ").replaceAll("\\s+", " ").trim(); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/filter/QueryParamPair.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/filter/QueryParamPair.java new file mode 100644 index 000000000..ae26e4845 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/filter/QueryParamPair.java @@ -0,0 +1,6 @@ +package edu.harvard.dbmi.avillach.dictionary.filter; + +import org.springframework.jdbc.core.namedparam.MapSqlParameterSource; + +public record QueryParamPair(String query, MapSqlParameterSource params) { +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/info/InfoController.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/info/InfoController.java new file mode 100644 index 000000000..fd8642e9f --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/info/InfoController.java @@ -0,0 +1,20 @@ +package edu.harvard.dbmi.avillach.dictionary.info; + +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.PostMapping; +import org.springframework.web.bind.annotation.RequestBody; + +import java.util.List; +import java.util.UUID; + +@Controller +public class InfoController { + + @AuditEvent(type = "OTHER", action = "info") + @PostMapping("/info") + public ResponseEntity getInfo(@RequestBody Object ignored) { + return ResponseEntity.ok(new InfoResponse(UUID.nameUUIDFromBytes(":)".getBytes()), ":)", List.of())); + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/info/InfoResponse.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/info/InfoResponse.java new file mode 100644 index 000000000..5717fbffb --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/info/InfoResponse.java @@ -0,0 +1,7 @@ +package edu.harvard.dbmi.avillach.dictionary.info; + +import java.util.List; +import java.util.UUID; + +public record InfoResponse(UUID id, String name, List queryFormats) { +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchController.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchController.java new file mode 100644 index 000000000..8fa99dbce --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchController.java @@ -0,0 +1,42 @@ +package edu.harvard.dbmi.avillach.dictionary.legacysearch; + +import edu.harvard.dbmi.avillach.dictionary.AuditAttributes; +import edu.harvard.dbmi.avillach.dictionary.legacysearch.model.LegacyResponse; +import edu.harvard.dbmi.avillach.dictionary.legacysearch.model.LegacySearchQuery; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import jakarta.servlet.http.HttpServletRequest; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.ResponseEntity; +import org.springframework.stereotype.Controller; +import org.springframework.web.bind.annotation.RequestBody; +import org.springframework.web.bind.annotation.RequestMapping; + +import java.io.IOException; + +@Controller +public class LegacySearchController { + + private final LegacySearchService legacySearchService; + private final LegacySearchQueryMapper legacySearchQueryMapper; + + @Autowired + private HttpServletRequest httpRequest; + + @Autowired + public LegacySearchController(LegacySearchService legacySearchService, LegacySearchQueryMapper legacySearchQueryMapper) { + this.legacySearchService = legacySearchService; + this.legacySearchQueryMapper = legacySearchQueryMapper; + } + + @AuditEvent(type = "SEARCH", action = "search.legacy") + @RequestMapping(path = "/search") + public ResponseEntity legacySearch(@RequestBody String jsonString) throws IOException { + LegacySearchQuery legacySearchQuery = legacySearchQueryMapper.mapFromJson(jsonString); + AuditAttributes.putMetadata( + httpRequest, "search_term", legacySearchQuery.filter().search() != null ? legacySearchQuery.filter().search() : "" + ); + return ResponseEntity + .ok(new LegacyResponse(legacySearchService.getSearchResults(legacySearchQuery.filter(), legacySearchQuery.pageable()))); + } + +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchQueryMapper.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchQueryMapper.java new file mode 100644 index 000000000..8a23d3cd2 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchQueryMapper.java @@ -0,0 +1,61 @@ +package edu.harvard.dbmi.avillach.dictionary.legacysearch; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import edu.harvard.dbmi.avillach.dictionary.legacysearch.model.LegacySearchQuery; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.data.domain.PageRequest; +import org.springframework.stereotype.Component; + +import java.io.IOException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.stream.Collectors; + +@Component +public class LegacySearchQueryMapper { + + private static final ObjectMapper objectMapper = new ObjectMapper(); + private static final Logger log = LoggerFactory.getLogger(LegacySearchQueryMapper.class); + + public LegacySearchQueryMapper() {} + + public LegacySearchQuery mapFromJson(String jsonString) throws IOException { + JsonNode rootNode = objectMapper.readTree(jsonString); + JsonNode queryNode = rootNode.get("query"); + + String searchTerm = queryNode.get("searchTerm").asText(); + int limit = queryNode.get("limit").asInt(); + searchTerm = constructTsQuery(searchTerm); + log.debug("Constructed Search Term: {}", searchTerm); + return new LegacySearchQuery(new Filter(List.of(), searchTerm, List.of()), PageRequest.of(0, limit)); + } + + // An attempt to provide OR search that will produce similar results to legacy search-prototype + private String constructTsQuery(String searchTerm) { + // Split on the | to enable or queries + String[] orGroups = searchTerm.split("\\|"); + List orClauses = new ArrayList<>(); + + for (String group : orGroups) { + // To replicate legacy search we will split using its regex [\\s\\p{Punct}]+ + String[] tokens = group.trim().split("[\\s\\p{Punct}]+"); + + // Now we will combine the tokens in this group and '&' them together. + String andClause = Arrays.stream(tokens).filter(token -> !token.isBlank()) // remove empty tokens. + .map(token -> token + ":*") // add the wild card for search + .collect(Collectors.joining(" & ")); + + if (!andClause.isBlank()) { + orClauses.add(andClause); + } + } + + + return String.join(" | ", orClauses); + } + +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchRepository.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchRepository.java new file mode 100644 index 000000000..4ecdea3db --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchRepository.java @@ -0,0 +1,79 @@ +package edu.harvard.dbmi.avillach.dictionary.legacysearch; + +import edu.harvard.dbmi.avillach.dictionary.concept.ConceptFilterQueryGenerator; +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import edu.harvard.dbmi.avillach.dictionary.filter.QueryParamPair; +import edu.harvard.dbmi.avillach.dictionary.legacysearch.model.SearchResult; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.data.domain.Pageable; +import org.springframework.jdbc.core.namedparam.MapSqlParameterSource; +import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate; +import org.springframework.stereotype.Repository; + +import java.util.List; + +import static edu.harvard.dbmi.avillach.dictionary.util.QueryUtility.ALLOW_FILTERING_Q; + +@Repository +public class LegacySearchRepository { + + private final ConceptFilterQueryGenerator filterGen; + private final NamedParameterJdbcTemplate template; + private final List disallowedMetaFields; + private final SearchResultRowMapper searchResultRowMapper; + + @Autowired + public LegacySearchRepository( + ConceptFilterQueryGenerator filterGen, NamedParameterJdbcTemplate template, + @Value("${filtering.unfilterable_concepts}") List disallowedMetaFields, SearchResultRowMapper searchResultRowMapper + ) { + this.filterGen = filterGen; + this.template = template; + this.disallowedMetaFields = disallowedMetaFields; + this.searchResultRowMapper = searchResultRowMapper; + } + + public List getLegacySearchResults(Filter filter, Pageable pageable) { + QueryParamPair filterQ = filterGen.generateLegacyFilterQuery(filter, pageable); + String sql = ALLOW_FILTERING_Q + ", " + filterQ.query() + """ + SELECT concept_node.concept_path AS conceptPath, + concept_node.display AS display, + concept_node.name AS name, + concept_node.concept_type AS conceptType, + ds.REF as dataset, + ds.abbreviation AS studyAcronym, + ds.full_name as dsFullName, + continuous_min.VALUE as min, + continuous_max.VALUE as max, + categorical_values.VALUE as values, + allow_filtering.allowFiltering AS allowFiltering, + meta_description.VALUE AS description, + stigmatized.value AS stigmatized, + parent.name AS parentName, + parent.display AS parentDisplay + FROM concept_node + INNER JOIN concepts_filtered_sorted ON concepts_filtered_sorted.concept_node_id = concept_node.concept_node_id + LEFT JOIN dataset AS ds ON concept_node.dataset_id = ds.dataset_id + LEFT JOIN concept_node_meta AS meta_description + ON concept_node.concept_node_id = meta_description.concept_node_id AND + meta_description.KEY = 'description' + LEFT JOIN concept_node_meta AS continuous_min + ON concept_node.concept_node_id = continuous_min.concept_node_id AND continuous_min.KEY = 'min' + LEFT JOIN concept_node_meta AS continuous_max + ON concept_node.concept_node_id = continuous_max.concept_node_id AND continuous_max.KEY = 'max' + LEFT JOIN concept_node_meta AS categorical_values + ON concept_node.concept_node_id = categorical_values.concept_node_id AND + categorical_values.KEY = 'values' + LEFT JOIN concept_node_meta AS stigmatized ON concept_node.concept_node_id = stigmatized.concept_node_id AND + stigmatized.KEY = 'stigmatized' + LEFT JOIN concept_node AS parent ON parent.concept_node_id = concept_node.parent_id + LEFT JOIN allow_filtering ON concept_node.concept_node_id = allow_filtering.concept_node_id + ORDER BY concepts_filtered_sorted.rank DESC, concept_node.concept_node_id ASC + """; + MapSqlParameterSource params = filterQ.params().addValue("disallowed_meta_keys", disallowedMetaFields); + + return template.query(sql, params, searchResultRowMapper); + } + +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchService.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchService.java new file mode 100644 index 000000000..e7462c2f2 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchService.java @@ -0,0 +1,23 @@ +package edu.harvard.dbmi.avillach.dictionary.legacysearch; + +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import edu.harvard.dbmi.avillach.dictionary.legacysearch.model.Results; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.data.domain.Pageable; +import org.springframework.stereotype.Service; + +@Service +public class LegacySearchService { + + private final LegacySearchRepository legacySearchRepository; + + @Autowired + public LegacySearchService(LegacySearchRepository legacySearchRepository) { + this.legacySearchRepository = legacySearchRepository; + } + + public Results getSearchResults(Filter filter, Pageable pageable) { + return new Results(legacySearchRepository.getLegacySearchResults(filter, pageable)); + } + +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/MetadataResultSetUtil.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/MetadataResultSetUtil.java new file mode 100644 index 000000000..635853400 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/MetadataResultSetUtil.java @@ -0,0 +1,118 @@ +package edu.harvard.dbmi.avillach.dictionary.legacysearch; + +import edu.harvard.dbmi.avillach.dictionary.legacysearch.model.CategoricalMetadata; +import edu.harvard.dbmi.avillach.dictionary.legacysearch.model.ContinuousMetadata; +import edu.harvard.dbmi.avillach.dictionary.legacysearch.model.Result; +import edu.harvard.dbmi.avillach.dictionary.util.JsonBlobParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Component; +import org.springframework.util.StringUtils; + +import java.nio.charset.StandardCharsets; +import java.security.MessageDigest; +import java.security.NoSuchAlgorithmException; +import java.sql.ResultSet; +import java.sql.SQLException; + + +@Component +public class MetadataResultSetUtil { + + private final static Logger log = LoggerFactory.getLogger(MetadataResultSetUtil.class); + private final JsonBlobParser jsonBlobParser; + + @Autowired + public MetadataResultSetUtil(JsonBlobParser jsonBlobParser) { + this.jsonBlobParser = jsonBlobParser; + } + + public Result mapContinuousMetadata(ResultSet rs) throws SQLException { + String hashedVarId = hashVarId(rs.getString("conceptPath")); + String description = getDescription(rs); + String parentName = getParentName(rs); + String parentDisplay = getParentDisplay(rs); + String dsFullName = getDatasetFullName(rs); + + String max = String.valueOf(jsonBlobParser.parseMax(rs.getString("values"))); + String min = String.valueOf(jsonBlobParser.parseMin(rs.getString("values"))); + + ContinuousMetadata metadata = new ContinuousMetadata( + rs.getString("stigmatized"), rs.getString("display"), description, min, rs.getString("conceptPath"), parentName, + rs.getString("conceptPath"), rs.getString("name"), parentDisplay, description, // changed + "{}", "", parentName, max, description, rs.getString("dataset"), hashedVarId, rs.getString("conceptType"), rs.getString("name"), + rs.getString("dataset"), rs.getString("stigmatized"), rs.getString("display"), rs.getString("studyAcronym"), dsFullName, + parentName, parentDisplay, rs.getString("conceptPath"), min, max + ); + return new Result( + metadata, jsonBlobParser.parseValues(rs.getString("values")), rs.getString("dataset"), parentName, rs.getString("name"), false, + true + ); + } + + public Result mapCategoricalMetadata(ResultSet rs) throws SQLException { + String hashedVarId = hashVarId(rs.getString("conceptPath")); + String description = getDescription(rs); + String parentName = getParentName(rs); + String parentDisplay = getParentDisplay(rs); + String dsFullName = getDatasetFullName(rs); + + CategoricalMetadata metadata = new CategoricalMetadata( + rs.getString("stigmatized"), rs.getString("display"), description, "", rs.getString("conceptPath"), parentName, + rs.getString("conceptPath"), rs.getString("name"), parentDisplay, description, "{}", "", parentName, "", description, + rs.getString("dataset"), hashedVarId, rs.getString("conceptType"), rs.getString("name"), rs.getString("dataset"), + rs.getString("stigmatized"), rs.getString("display"), rs.getString("studyAcronym"), dsFullName, parentName, parentDisplay, + rs.getString("conceptPath") + ); + + return new Result( + metadata, jsonBlobParser.parseValues(rs.getString("values")), rs.getString("dataset"), parentName, rs.getString("name"), true, + false + ); + } + + + + private static String hashVarId(String hpdsPath) { + String hashedVarId = ""; + try { + MessageDigest digest = MessageDigest.getInstance("SHA-256"); + byte[] encodedHash = digest.digest(hpdsPath.getBytes(StandardCharsets.UTF_8)); + hashedVarId = bytesToHex(encodedHash); + } catch (NoSuchAlgorithmException e) { + log.error(e.getMessage()); + } + + return hashedVarId; + } + + private static String bytesToHex(byte[] hash) { + StringBuilder hexString = new StringBuilder(2 * hash.length); + for (byte b : hash) { + String hex = Integer.toHexString(0xff & b); + if (hex.length() == 1) { + hexString.append('0'); + } + hexString.append(hex); + } + return hexString.toString(); + } + + private String getParentDisplay(ResultSet rs) throws SQLException { + return StringUtils.hasLength("parentDisplay") ? rs.getString("parentDisplay") : ""; + } + + private String getParentName(ResultSet rs) throws SQLException { + return StringUtils.hasLength(rs.getString("parentName")) ? rs.getString("parentName") : "All Variables"; + } + + private String getDescription(ResultSet rs) throws SQLException { + return StringUtils.hasLength(rs.getString("description")) ? rs.getString("description") : ""; + } + + private String getDatasetFullName(ResultSet rs) throws SQLException { + return StringUtils.hasLength(rs.getString("dsFullName")) ? rs.getString("dsFullName") : ""; + } + +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/SearchResultRowMapper.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/SearchResultRowMapper.java new file mode 100644 index 000000000..cb5130925 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/SearchResultRowMapper.java @@ -0,0 +1,38 @@ +package edu.harvard.dbmi.avillach.dictionary.legacysearch; + +import edu.harvard.dbmi.avillach.dictionary.concept.model.ConceptType; +import edu.harvard.dbmi.avillach.dictionary.legacysearch.model.Result; +import edu.harvard.dbmi.avillach.dictionary.legacysearch.model.SearchResult; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.jdbc.core.RowMapper; +import org.springframework.stereotype.Component; + +import java.sql.ResultSet; +import java.sql.SQLException; + +@Component +public class SearchResultRowMapper implements RowMapper { + + private final MetadataResultSetUtil metadataResultSetUtil; + + @Autowired + public SearchResultRowMapper(MetadataResultSetUtil metadataResultSetUtil) { + this.metadataResultSetUtil = metadataResultSetUtil; + } + + @Override + public SearchResult mapRow(ResultSet rs, int rowNum) throws SQLException { + return mapSearchResults(rs); + } + + private SearchResult mapSearchResults(ResultSet rs) throws SQLException { + Result result = switch (ConceptType.toConcept(rs.getString("conceptType"))) { + case Categorical -> this.metadataResultSetUtil.mapCategoricalMetadata(rs); + case Continuous -> this.metadataResultSetUtil.mapContinuousMetadata(rs); + }; + + return new SearchResult(result); + } + + +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/CategoricalMetadata.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/CategoricalMetadata.java new file mode 100644 index 000000000..79de4606b --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/CategoricalMetadata.java @@ -0,0 +1,23 @@ +package edu.harvard.dbmi.avillach.dictionary.legacysearch.model; + +import com.fasterxml.jackson.annotation.JsonProperty; + +public record CategoricalMetadata( + @JsonProperty("columnmeta_is_stigmatized") String columnmetaIsStigmatized, @JsonProperty("columnmeta_name") String columnmetaName, + @JsonProperty("description") String description, @JsonProperty("columnmeta_min") String columnmetaMin, + @JsonProperty("HPDS_PATH") String hpdsPath, @JsonProperty("derived_group_id") String derivedGroupId, + @JsonProperty("columnmeta_hpds_path") String columnmetaHpdsPath, @JsonProperty("columnmeta_var_id") String columnmetaVarId, + @JsonProperty("columnmeta_var_group_description") String columnmetaVarGroupDescription, + @JsonProperty("derived_var_description") String derivedVarDescription, + @JsonProperty("derived_variable_level_data") String derivedVariableLevelData, @JsonProperty("data_hierarchy") String dataHierarchy, + @JsonProperty("derived_group_description") String derivedGroupDescription, @JsonProperty("columnmeta_max") String columnmetaMax, + @JsonProperty("columnmeta_description") String columnmetaDescription, @JsonProperty("derived_study_id") String derivedStudyId, + @JsonProperty("hashed_var_id") String hashedVarId, @JsonProperty("columnmeta_data_type") String columnmetaDataType, + @JsonProperty("derived_var_id") String derivedVarId, @JsonProperty("columnmeta_study_id") String columnmetaStudyId, + @JsonProperty("is_stigmatized") String isStigmatized, @JsonProperty("derived_var_name") String derivedVarName, + @JsonProperty("derived_study_abv_name") String derivedStudyAbvName, + @JsonProperty("derived_study_description") String derivedStudyDescription, + @JsonProperty("columnmeta_var_group_id") String columnmetaVarGroupId, @JsonProperty("derived_group_name") String derivedGroupName, + @JsonProperty("columnmeta_HPDS_PATH") String columnmetaHpdsPathAlternate +) implements Metadata { +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/ContinuousMetadata.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/ContinuousMetadata.java new file mode 100644 index 000000000..a0671946f --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/ContinuousMetadata.java @@ -0,0 +1,24 @@ +package edu.harvard.dbmi.avillach.dictionary.legacysearch.model; + +import com.fasterxml.jackson.annotation.JsonProperty; + +public record ContinuousMetadata( + @JsonProperty("columnmeta_is_stigmatized") String columnmetaIsStigmatized, @JsonProperty("columnmeta_name") String columnmetaName, + @JsonProperty("description") String description, @JsonProperty("columnmeta_min") String columnmetaMin, + @JsonProperty("HPDS_PATH") String hpdsPath, @JsonProperty("derived_group_id") String derivedGroupId, + @JsonProperty("columnmeta_hpds_path") String columnmetaHpdsPath, @JsonProperty("columnmeta_var_id") String columnmetaVarId, + @JsonProperty("columnmeta_var_group_description") String columnmetaVarGroupDescription, + @JsonProperty("derived_var_description") String derivedVarDescription, + @JsonProperty("derived_variable_level_data") String derivedVariableLevelData, @JsonProperty("data_hierarchy") String dataHierarchy, + @JsonProperty("derived_group_description") String derivedGroupDescription, @JsonProperty("columnmeta_max") String columnmetaMax, + @JsonProperty("columnmeta_description") String columnmetaDescription, @JsonProperty("derived_study_id") String derivedStudyId, + @JsonProperty("hashed_var_id") String hashedVarId, @JsonProperty("columnmeta_data_type") String columnmetaDataType, + @JsonProperty("derived_var_id") String derivedVarId, @JsonProperty("columnmeta_study_id") String columnmetaStudyId, + @JsonProperty("is_stigmatized") String isStigmatized, @JsonProperty("derived_var_name") String derivedVarName, + @JsonProperty("derived_study_abv_name") String derivedStudyAbvName, + @JsonProperty("derived_study_description") String derivedStudyDescription, + @JsonProperty("columnmeta_var_group_id") String columnmetaVarGroupId, @JsonProperty("derived_group_name") String derivedGroupName, + @JsonProperty("columnmeta_HPDS_PATH") String columnmetaHpdsPathAlternate, @JsonProperty("min") String min, + @JsonProperty("max") String max +) implements Metadata { +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/LegacyResponse.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/LegacyResponse.java new file mode 100644 index 000000000..7655c6c4f --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/LegacyResponse.java @@ -0,0 +1,6 @@ +package edu.harvard.dbmi.avillach.dictionary.legacysearch.model; + +import com.fasterxml.jackson.annotation.JsonProperty; + +public record LegacyResponse(@JsonProperty("results") Results results) { +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/LegacySearchQuery.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/LegacySearchQuery.java new file mode 100644 index 000000000..1147a8581 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/LegacySearchQuery.java @@ -0,0 +1,7 @@ +package edu.harvard.dbmi.avillach.dictionary.legacysearch.model; + +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import org.springframework.data.domain.Pageable; + +public record LegacySearchQuery(Filter filter, Pageable pageable) { +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/Metadata.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/Metadata.java new file mode 100644 index 000000000..d3d40d479 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/Metadata.java @@ -0,0 +1,4 @@ +package edu.harvard.dbmi.avillach.dictionary.legacysearch.model; + +public sealed interface Metadata permits ContinuousMetadata, CategoricalMetadata { +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/Result.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/Result.java new file mode 100644 index 000000000..ba3a51d94 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/Result.java @@ -0,0 +1,12 @@ +package edu.harvard.dbmi.avillach.dictionary.legacysearch.model; + +import com.fasterxml.jackson.annotation.JsonProperty; + +import java.util.List; + +public record Result( + Metadata metadata, List values, @JsonProperty("studyId") String studyId, @JsonProperty("dtId") String dtId, + @JsonProperty("varId") String varId, @JsonProperty("is_categorical") boolean isCategorical, + @JsonProperty("is_continuous") boolean isContinuous +) { +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/Results.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/Results.java new file mode 100644 index 000000000..fa37331b8 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/Results.java @@ -0,0 +1,8 @@ +package edu.harvard.dbmi.avillach.dictionary.legacysearch.model; + +import com.fasterxml.jackson.annotation.JsonProperty; + +import java.util.List; + +public record Results(@JsonProperty("searchResults") List searchResults) { +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/SearchResult.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/SearchResult.java new file mode 100644 index 000000000..d6a7f5380 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/model/SearchResult.java @@ -0,0 +1,6 @@ +package edu.harvard.dbmi.avillach.dictionary.legacysearch.model; + +import com.fasterxml.jackson.annotation.JsonProperty; + +public record SearchResult(@JsonProperty("result") Result result) { +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/memory/MemoryCheck.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/memory/MemoryCheck.java new file mode 100644 index 000000000..dd40e7f93 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/memory/MemoryCheck.java @@ -0,0 +1,19 @@ +package edu.harvard.dbmi.avillach.dictionary.memory; + +import jakarta.annotation.PostConstruct; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.context.annotation.Configuration; + +@Configuration +public class MemoryCheck { + + private static final Logger LOG = LoggerFactory.getLogger(MemoryCheck.class); + + @PostConstruct + public void checkMemory() { + long maxMemory = Runtime.getRuntime().maxMemory() / (1024 * 1024); + LOG.info("Max Heap Memory (Xmx): {} MB", maxMemory); + } + +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/util/CacheConfig.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/util/CacheConfig.java new file mode 100644 index 000000000..c5cda0ffc --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/util/CacheConfig.java @@ -0,0 +1,32 @@ +package edu.harvard.dbmi.avillach.dictionary.util; + +import com.github.benmanes.caffeine.cache.Caffeine; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.cache.CacheManager; +import org.springframework.cache.caffeine.CaffeineCacheManager; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; + +import java.util.concurrent.TimeUnit; + +@Configuration +public class CacheConfig { + + @Value("${cache.duration-minutes:60}") + private int cacheDurationMinutes; + + @Value("${cache.maximum-size:5000}") + private int cacheMaximumSize; + + @Bean + public Caffeine caffeineConfig() { + return Caffeine.newBuilder().expireAfterAccess(cacheDurationMinutes, TimeUnit.MINUTES).maximumSize(cacheMaximumSize); + } + + @Bean + public CacheManager cacheManager(Caffeine caffeine) { + CaffeineCacheManager caffeineCacheManager = new CaffeineCacheManager(); + caffeineCacheManager.setCaffeine(caffeine); + return caffeineCacheManager; + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/util/JsonBlobParser.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/util/JsonBlobParser.java new file mode 100644 index 000000000..865525b17 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/util/JsonBlobParser.java @@ -0,0 +1,104 @@ +package edu.harvard.dbmi.avillach.dictionary.util; + + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.core.type.TypeReference; +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.stereotype.Component; + + +import java.math.BigDecimal; +import java.math.BigInteger; +import java.util.*; +import java.util.stream.Collectors; + +@Component +public class JsonBlobParser { + + private final static Logger log = LoggerFactory.getLogger(JsonBlobParser.class); + private final ObjectMapper objectMapper = new ObjectMapper(); + + public JsonBlobParser() {} + + public List parseValues(String valuesArr) { + try { + JsonNode arr = objectMapper.readTree(valuesArr); + if (!arr.isArray()) { + return List.of(); + } + ArrayList vals = new ArrayList<>(); + for (JsonNode node : arr) { + if (!node.isTextual()) { + return List.of(); + } + vals.add(node.asText()); + } + return vals; + } catch (JsonProcessingException ex) { + return List.of(); + } + } + + public Double parseMin(String valuesArr) { + return parseFromIndex(valuesArr, 0); + } + + protected Double parseFromIndex(String valuesArr, int index) { + try { + JsonNode arr = objectMapper.readTree(valuesArr); + if (!arr.isArray() || arr.size() != 2) { + return 0D; + } + JsonNode raw = arr.get(index); + if (raw.isNumber()) { + return raw.doubleValue(); + } + if (raw.isTextual()) { + return Double.parseDouble(raw.asText()); + } + return 0D; + } catch (JsonProcessingException ex) { + log.warn("Invalid json array for values: ", ex); + return 0D; + } catch (NumberFormatException ex) { + log.warn("Valid json array but invalid val within: ", ex); + return 0D; + } + } + + public Double parseMax(String valuesArr) { + return parseFromIndex(valuesArr, 1); + } + + public Map parseMetaData(String jsonMetaData) { + Map metadata; + + try { + List> maps = objectMapper.readValue(jsonMetaData, new TypeReference>>() {}); + // convert the list to a flat map + Map map = new HashMap<>(); + for (Map entry : maps) { + String rawKey = entry.get("key"); + if (rawKey == null || rawKey.isBlank()) { + throw new IllegalStateException("parseMetaData() Missing metadata key. Entry: " + entry); + } + String prettyKey = Arrays.stream(rawKey.split("_")).filter(word -> !word.isBlank()) + .map(word -> word.substring(0, 1).toUpperCase() + word.substring(1).toLowerCase()).collect(Collectors.joining(" ")); + if (map.put(prettyKey, entry.get("value")) != null) { + throw new IllegalStateException( + "parseMetaData() Duplicate key found in metadata. Key: " + prettyKey + "(" + entry.get("key") + ") Value: " + + entry.get("value") + ); + } + } + metadata = map; + } catch (JsonProcessingException e) { + throw new RuntimeException(e); + } + + return metadata; + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/util/MapExtractor.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/util/MapExtractor.java new file mode 100644 index 000000000..0f1b1fadf --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/util/MapExtractor.java @@ -0,0 +1,27 @@ +package edu.harvard.dbmi.avillach.dictionary.util; + +import org.springframework.dao.DataAccessException; +import org.springframework.jdbc.core.ResultSetExtractor; + +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.HashMap; +import java.util.Map; + +public class MapExtractor implements ResultSetExtractor> { + private final String keyName, valueName; + + public MapExtractor(String keyName, String valueName) { + this.keyName = keyName; + this.valueName = valueName; + } + + @Override + public Map extractData(ResultSet rs) throws SQLException, DataAccessException { + Map map = new HashMap<>(); + while (rs.next() && rs.getString(keyName) != null) { + map.put(rs.getString(keyName), rs.getString(valueName)); + } + return map; + } +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/util/MapExtractorWithPrettyKeys.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/util/MapExtractorWithPrettyKeys.java new file mode 100644 index 000000000..e0d2a9459 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/util/MapExtractorWithPrettyKeys.java @@ -0,0 +1,40 @@ +package edu.harvard.dbmi.avillach.dictionary.util; + +import org.springframework.dao.DataAccessException; +import org.springframework.jdbc.core.ResultSetExtractor; + +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.Arrays; +import java.util.HashMap; +import java.util.Map; +import java.util.stream.Collectors; + +public class MapExtractorWithPrettyKeys implements ResultSetExtractor> { + private final String keyName, valueName; + + public MapExtractorWithPrettyKeys(String keyName, String valueName) { + this.keyName = keyName; + this.valueName = valueName; + } + + + @Override + public Map extractData(ResultSet rs) throws SQLException, DataAccessException { + Map map = new HashMap<>(); + while (rs.next()) { + String rawKey = rs.getString(keyName); + if (rawKey == null || rawKey.isBlank()) { + continue; + } + String prettyKey = Arrays.stream(rawKey.split("_")).filter(token -> !token.isBlank()) + .map(token -> token.substring(0, 1).toUpperCase() + token.substring(1).toLowerCase()).collect(Collectors.joining(" ")); + String previous = map.putIfAbsent(prettyKey, rs.getString(valueName)); + if (previous != null) { + throw new IllegalStateException("Duplicate pretty metadata key: " + prettyKey); + } + } + return map; + } + +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/util/QueryUtility.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/util/QueryUtility.java new file mode 100644 index 000000000..f01556d00 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/util/QueryUtility.java @@ -0,0 +1,38 @@ +package edu.harvard.dbmi.avillach.dictionary.util; + +/** + * Shared SQL fragments used by concept and facet query generators. + */ +public class QueryUtility { + + /** + * CTE that determines whether each concept should be filterable in the UI. Concepts with disallowed meta keys set to 'true' (e.g. + * stigmatized) are marked as non-filterable, which demotes them in search ranking. Expects a :disallowed_meta_keys named parameter. + */ + public static final String ALLOW_FILTERING_Q = """ + WITH allow_filtering AS ( + SELECT + concept_node_meta.concept_node_id AS concept_node_id, + (concept_node_meta.value <> 'true') AS allowFiltering + FROM + concept_node_meta + WHERE + concept_node_meta.KEY IN (:disallowed_meta_keys) + ) + """; + + /** + * Converts a pre-sanitized search string into a prefix-matching tsquery. Input is sanitized by FilterProcessor.sanitizeSearch() before + * reaching SQL — only contains Unicode letters, digits, and single spaces. Splits on whitespace, appends :* to each word, and ANDs them + * together. e.g. "ear infection" becomes to_tsquery('english', 'ear:* & infection:*') + */ + private static final String TSQUERY_EXPR = "to_tsquery('english', regexp_replace(trim(:search), '\\s+', ':* & ', 'g') || ':*')"; + + public static final String SEARCH_QUERY = "ts_rank_cd(searchable_fields, " + TSQUERY_EXPR + ")"; + + /** + * WHERE clause filter for full-text search. Uses the GIN-indexed searchable_fields tsvector column with prefix matching via to_tsquery. + * Expects a :search named parameter that has been pre-sanitized by FilterProcessor. + */ + public static final String SEARCH_WHERE = "concept_node.searchable_fields @@ " + TSQUERY_EXPR; +} diff --git a/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/util/SchemaDetector.java b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/util/SchemaDetector.java new file mode 100644 index 000000000..89df4a1c7 --- /dev/null +++ b/services/picsure-dictionary/src/main/java/edu/harvard/dbmi/avillach/dictionary/util/SchemaDetector.java @@ -0,0 +1,72 @@ +package edu.harvard.dbmi.avillach.dictionary.util; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.sql.init.dependency.DependsOnDatabaseInitialization; +import org.springframework.jdbc.core.JdbcTemplate; +import org.springframework.stereotype.Component; + +import java.util.Objects; + +@Component +@DependsOnDatabaseInitialization +public class SchemaDetector { + + private static final Logger LOG = LoggerFactory.getLogger(SchemaDetector.class); + + private static final String CHECK_COLUMN_SQL = """ + SELECT EXISTS ( + SELECT 1 + FROM information_schema.columns + WHERE table_schema = current_schema() + AND table_name = ? + AND column_name = 'is_queryable' + ) + """; + + private final boolean conceptNodeQueryable; + private final boolean fcnQueryable; + + @Autowired + public SchemaDetector(JdbcTemplate jdbcTemplate) { + boolean cnQueryable = false; + boolean fcnQ = false; + try { + cnQueryable = Objects.requireNonNullElse(jdbcTemplate.queryForObject(CHECK_COLUMN_SQL, Boolean.class, "concept_node"), false); + fcnQ = Objects.requireNonNullElse(jdbcTemplate.queryForObject(CHECK_COLUMN_SQL, Boolean.class, "facet__concept_node"), false); + } catch (Exception e) { + LOG.warn("Schema detection failed ({}), defaulting to legacy query paths", e.getMessage()); + } + this.conceptNodeQueryable = cnQueryable; + this.fcnQueryable = fcnQ; + LOG.info( + "Schema detection: concept_node.is_queryable {} | facet__concept_node.is_queryable {}", + conceptNodeQueryable ? "found" : "NOT FOUND — legacy fallback", fcnQueryable ? "found" : "NOT FOUND — legacy fallback" + ); + } + + /** + * Returns a SQL WHERE clause fragment for concept_node queryability. Fast path: {@code alias.is_queryable = TRUE} Legacy fallback: + * EXISTS subquery against concept_node_meta. + */ + public String conceptNodeQueryableClause(String alias) { + if (conceptNodeQueryable) { + return alias + ".is_queryable = TRUE"; + } + return "EXISTS (SELECT 1 FROM concept_node_meta cnm_q WHERE cnm_q.concept_node_id = " + alias + + ".concept_node_id AND cnm_q.key = 'values' AND cnm_q.value <> '')"; + } + + /** + * Returns a SQL WHERE clause fragment for facet__concept_node queryability. Fast path: {@code alias.is_queryable = TRUE} Legacy + * fallback: EXISTS subquery joining concept_node_meta via concept_node. + */ + public String fcnQueryableClause(String alias) { + if (fcnQueryable) { + return alias + ".is_queryable = TRUE"; + } + return "EXISTS (SELECT 1 FROM concept_node_meta cnm_q WHERE cnm_q.concept_node_id = " + alias + + ".concept_node_id AND cnm_q.key = 'values' AND cnm_q.value <> '')"; + } +} diff --git a/services/picsure-dictionary/src/main/resources/README.md b/services/picsure-dictionary/src/main/resources/README.md new file mode 100644 index 000000000..ceda736da --- /dev/null +++ b/services/picsure-dictionary/src/main/resources/README.md @@ -0,0 +1,3 @@ +# Application Properties +filtering.unfilterable_concepts - comma delimited list of metadata keys which, when 'true', should not be filterable in open access/public access (stigmatizing, identifying, open text, etc) +metadata.no_show_list - comma delimited list of metadata keys which should not be shown in the more information modal of each concept. By default, values are not shown here. diff --git a/services/picsure-dictionary/src/main/resources/application-bdc-dev.properties b/services/picsure-dictionary/src/main/resources/application-bdc-dev.properties new file mode 100644 index 000000000..b753beb6d --- /dev/null +++ b/services/picsure-dictionary/src/main/resources/application-bdc-dev.properties @@ -0,0 +1,24 @@ +spring.application.name=dictionary +spring.datasource.url=jdbc:postgresql://localhost:5432/dictionary_db?currentSchema=dict +spring.datasource.username=username +spring.datasource.password=password +spring.datasource.driver-class-name=org.postgresql.Driver +server.port=80 +spring.datasource.hikari.maximum-pool-size=25 + +dashboard.columns={abbreviation:'Abbreviation',name:'Name',clinvars:'Clinical Variables'} +dashboard.column-order=abbreviation,name,clinvars +dashboard.nonmeta-columns=abbreviation,name +dashboard.enable.extra_details=true +dashboard.enable.bdc_hack=true + +filtering.unfilterable_concepts=stigmatized + +metadata.no_show_list=values,stigmatized,derived_values,drs_uri,,# + +cache.duration-minutes=120 +cache.maximum-size=10000 + +# Logging File Output https://docs.spring.io/spring-boot/reference/features/logging.html#features.logging.file-output +# If you are adding additional log files please add them to /var/log/ directory. +logging.file.name=/var/log/dictionary.log diff --git a/services/picsure-dictionary/src/main/resources/application-bdc.properties b/services/picsure-dictionary/src/main/resources/application-bdc.properties new file mode 100644 index 000000000..a0ff723a4 --- /dev/null +++ b/services/picsure-dictionary/src/main/resources/application-bdc.properties @@ -0,0 +1,19 @@ +spring.application.name=dictionary +spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.PostgreSQLDialect +spring.datasource.driver-class-name=com.amazonaws.secretsmanager.sql.AWSSecretsManagerPostgreSQLDriver +spring.datasource.url=jdbc-secretsmanager:postgresql://${DATASOURCE_URL}/picsure?useUnicode=true&characterEncoding=UTF-8&autoReconnect=true&autoReconnectForPools=true¤tSchema=dict +spring.datasource.username=${DATASOURCE_USERNAME} +server.port=80 +dashboard.enable.extra_details=true +dashboard.enable.bdc_hack=true +filtering.unfilterable_concepts=stigmatized +metadata.no_show_list=values,stigmatized,derived_values,drs_uri,,#,logical_min,logical_max,description +# Logging File Output https://docs.spring.io/spring-boot/reference/features/logging.html#features.logging.file-output +# If you are adding additional log files please add them to /var/log/ directory. +logging.file.name=/var/log/dictionary.log +# performance tuning +server.tomcat.threads.max=300 +cache.duration-minutes=120 +cache.maximum-size=100000 + +spring.datasource.hikari.maximum-pool-size=25 \ No newline at end of file diff --git a/services/picsure-dictionary/src/main/resources/application.properties b/services/picsure-dictionary/src/main/resources/application.properties new file mode 100644 index 000000000..0f1b2d4ca --- /dev/null +++ b/services/picsure-dictionary/src/main/resources/application.properties @@ -0,0 +1,34 @@ +spring.application.name=dictionary +spring.datasource.url=jdbc:postgresql://${POSTGRES_HOST}:5432/${POSTGRES_DB}?currentSchema=dict +spring.datasource.username=${POSTGRES_USER} +spring.datasource.password=${POSTGRES_PASSWORD} +spring.datasource.driver-class-name=org.postgresql.Driver + +server.port=80 + +# Actuator: OFF BY DEFAULT (no Spring Security in front of this service). AIO's dictionary.env sets +# PICSURE_ACTUATOR_EXPOSURE=health to enable a shallow health probe; details stay hidden by default +# (PICSURE_ACTUATOR_DETAILS=never) so no datasource/component internals leak. +management.endpoints.web.exposure.include=${PICSURE_ACTUATOR_EXPOSURE:none} +management.endpoint.health.show-details=${PICSURE_ACTUATOR_DETAILS:never} +management.endpoint.health.probes.enabled=true + +dashboard.columns={abbreviation:'Abbreviation',name:'Name',clinvars:'Clinical Variables'} +dashboard.column-order=abbreviation,name,clinvars +dashboard.nonmeta-columns=abbreviation,name +dashboard.enable.extra_details=true +dashboard.enable.bdc_hack=false +dashboard.layout.type=default + +filtering.unfilterable_concepts=stigmatized + +metadata.no_show_list=values + +concept.tree.max_depth=100 + +cache.duration-minutes=60 +cache.maximum-size=5000 + +# Logging File Output https://docs.spring.io/spring-boot/reference/features/logging.html#features.logging.file-output +# If you are adding additional log files please add them to /var/log/ directory. +logging.file.name=/var/log/dictionary.log diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/ControllerAuditEventTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/ControllerAuditEventTest.java new file mode 100644 index 000000000..ffd38ee34 --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/ControllerAuditEventTest.java @@ -0,0 +1,72 @@ +package edu.harvard.dbmi.avillach.dictionary; + +import static org.junit.jupiter.api.Assertions.*; + +import edu.harvard.dbmi.avillach.dictionary.concept.ConceptController; +import edu.harvard.dbmi.avillach.dictionary.dashboard.DashboardController; +import edu.harvard.dbmi.avillach.dictionary.dashboarddrawer.DashboardDrawerController; +import edu.harvard.dbmi.avillach.dictionary.facet.FacetController; +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import edu.harvard.dbmi.avillach.dictionary.info.InfoController; +import edu.harvard.dbmi.avillach.dictionary.legacysearch.LegacySearchController; +import edu.harvard.dbmi.avillach.logging.AuditEvent; +import org.junit.jupiter.api.Test; + +import java.lang.reflect.Method; +import java.util.List; + +class ControllerAuditEventTest { + + private void assertAuditEvent(Class controller, String methodName, Class[] params, String expectedType, String expectedAction) + throws Exception { + Method method = controller.getMethod(methodName, params); + AuditEvent event = method.getAnnotation(AuditEvent.class); + assertNotNull(event, controller.getSimpleName() + "." + methodName + " missing @AuditEvent"); + assertEquals(expectedType, event.type(), controller.getSimpleName() + "." + methodName + " wrong type"); + assertEquals(expectedAction, event.action(), controller.getSimpleName() + "." + methodName + " wrong action"); + } + + @Test + void conceptController() throws Exception { + Class c = ConceptController.class; + assertAuditEvent(c, "listConcepts", new Class[] {Filter.class, int.class, int.class}, "SEARCH", "concept.search"); + assertAuditEvent(c, "dumpConcepts", new Class[] {int.class, int.class}, "DATA_ACCESS", "concept.dump"); + assertAuditEvent(c, "conceptDetail", new Class[] {String.class, String.class}, "SEARCH", "concept.detail"); + assertAuditEvent(c, "conceptsDetail", new Class[] {List.class}, "SEARCH", "concept.detail"); + assertAuditEvent(c, "conceptTree", new Class[] {String.class, String.class, Integer.class}, "SEARCH", "concept.tree"); + assertAuditEvent(c, "conceptHierarchy", new Class[] {String.class, String.class}, "SEARCH", "concept.hierarchy"); + assertAuditEvent(c, "allConceptTrees", new Class[] {Integer.class}, "SEARCH", "concept.tree"); + } + + @Test + void facetController() throws Exception { + Class c = FacetController.class; + assertAuditEvent(c, "getFacets", new Class[] {Filter.class}, "SEARCH", "facet.search"); + assertAuditEvent(c, "facetDetails", new Class[] {String.class, String.class}, "SEARCH", "facet.detail"); + } + + @Test + void dashboardController() throws Exception { + Class c = DashboardController.class; + assertAuditEvent(c, "getDashboard", new Class[] {}, "OTHER", "dashboard.read"); + } + + @Test + void dashboardDrawerController() throws Exception { + Class c = DashboardDrawerController.class; + assertAuditEvent(c, "findAll", new Class[] {}, "OTHER", "dashboard_drawer.list"); + assertAuditEvent(c, "findByDatasetId", new Class[] {Integer.class}, "OTHER", "dashboard_drawer.read"); + } + + @Test + void infoController() throws Exception { + Class c = InfoController.class; + assertAuditEvent(c, "getInfo", new Class[] {Object.class}, "OTHER", "info"); + } + + @Test + void legacySearchController() throws Exception { + Class c = LegacySearchController.class; + assertAuditEvent(c, "legacySearch", new Class[] {String.class}, "SEARCH", "search.legacy"); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/DictionaryApplicationTests.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/DictionaryApplicationTests.java new file mode 100644 index 000000000..58c4c1f77 --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/DictionaryApplicationTests.java @@ -0,0 +1,12 @@ +package edu.harvard.dbmi.avillach.dictionary; + +import org.junit.jupiter.api.Test; +import org.springframework.boot.test.context.SpringBootTest; + +@SpringBootTest +class DictionaryApplicationTests { + + @Test + void contextLoads() {} + +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/TestDictionaryApplication.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/TestDictionaryApplication.java new file mode 100644 index 000000000..6cc5fe4c5 --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/TestDictionaryApplication.java @@ -0,0 +1,23 @@ +package edu.harvard.dbmi.avillach.dictionary; + +import org.springframework.boot.SpringApplication; +import org.springframework.boot.test.context.TestConfiguration; +import org.springframework.boot.testcontainers.service.connection.ServiceConnection; +import org.springframework.context.annotation.Bean; +import org.testcontainers.containers.PostgreSQLContainer; +import org.testcontainers.utility.DockerImageName; + +@TestConfiguration(proxyBeanMethods = false) +public class TestDictionaryApplication { + + @Bean + @ServiceConnection + PostgreSQLContainer postgresContainer() { + return new PostgreSQLContainer<>(DockerImageName.parse("postgres:latest")); + } + + public static void main(String[] args) { + SpringApplication.from(DictionaryApplication::main).with(TestDictionaryApplication.class).run(args); + } + +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptControllerTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptControllerTest.java new file mode 100644 index 000000000..bece327a0 --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptControllerTest.java @@ -0,0 +1,186 @@ +package edu.harvard.dbmi.avillach.dictionary.concept; + +import edu.harvard.dbmi.avillach.dictionary.concept.model.CategoricalConcept; +import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept; +import edu.harvard.dbmi.avillach.dictionary.concept.model.ContinuousConcept; +import edu.harvard.dbmi.avillach.dictionary.facet.Facet; +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.Mockito; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.data.domain.Page; +import org.springframework.data.domain.Pageable; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.mock.web.MockHttpServletRequest; +import org.springframework.test.context.ActiveProfiles; +import org.springframework.web.context.request.RequestContextHolder; +import org.springframework.web.context.request.ServletRequestAttributes; + +import java.util.List; +import java.util.Map; +import java.util.Optional; + +@SpringBootTest(properties = {"concept.tree.max_depth=1"}) +@ActiveProfiles("test") +class ConceptControllerTest { + + @MockBean + ConceptService conceptService; + + @Autowired + ConceptController subject; + + @BeforeEach + void setUp() { + MockHttpServletRequest mockRequest = new MockHttpServletRequest(); + RequestContextHolder.setRequestAttributes(new ServletRequestAttributes(mockRequest)); + } + + @Test + void shouldListConcepts() { + List expected = List.of( + new CategoricalConcept("/foo", "foo", "Foo", "my_dataset", "foo!", List.of(), true, "", null, Map.of()), + new CategoricalConcept("/foo//bar", "bar", "Bar", "my_dataset", "foo!", List.of("a", "b"), true, "", List.of(), Map.of()), + new ContinuousConcept("/foo//baz", "baz", "Baz", "my_dataset", "foo!", true, 0D, 100D, "", Map.of()) + ); + Filter filter = + new Filter(List.of(new Facet("questionare", "Questionare", "?", "Questionare", 1, null, "category", null)), "foo", List.of()); + Mockito.when(conceptService.listConcepts(filter, Pageable.ofSize(10).withPage(1))).thenReturn(expected); + Mockito.when(conceptService.countConcepts(filter)).thenReturn(100L); + + Page actual = subject.listConcepts(filter, 1, 10).getBody(); + + Assertions.assertEquals(expected, actual.get().toList()); + Assertions.assertEquals(100L, actual.getTotalElements()); + } + + @Test + void shouldGetConceptDetails() { + CategoricalConcept expected = + new CategoricalConcept("/foo//bar", "bar", "Bar", "my_dataset", "foo!", List.of("a", "b"), true, "", List.of(), Map.of()); + Mockito.when(conceptService.conceptDetail("my_dataset", "/foo//bar")).thenReturn(Optional.of(expected)); + + ResponseEntity actual = subject.conceptDetail("my_dataset", "/foo//bar"); + + Assertions.assertEquals(expected, actual.getBody()); + Assertions.assertEquals(HttpStatus.OK, actual.getStatusCode()); + } + + @Test + void shouldNotGetConceptDetails() { + Mockito.when(conceptService.conceptDetail("my_dataset", "/foo//asdsad")).thenReturn(Optional.empty()); + + ResponseEntity actual = subject.conceptDetail("my_dataset", "/foo//bar"); + + Assertions.assertEquals(HttpStatus.NOT_FOUND, actual.getStatusCode()); + } + + @Test + void shouldGetConceptTree() { + Concept fooBar = + new CategoricalConcept("/foo//bar", "bar", "Bar", "my_dataset", "foo!", List.of("a", "b"), true, "", List.of(), Map.of()); + Concept fooBaz = new ContinuousConcept("/foo//baz", "baz", "Baz", "my_dataset", "foo!", true, 0D, 100D, "", Map.of()); + CategoricalConcept foo = + new CategoricalConcept("/foo", "foo", "Foo", "my_dataset", "foo!", List.of(), true, "", List.of(fooBar, fooBaz), Map.of()); + + Mockito.when(conceptService.conceptTree("my_dataset", "/foo", 1)).thenReturn(Optional.of(foo)); + + ResponseEntity actual = subject.conceptTree("my_dataset", "/foo", 1); + + Assertions.assertEquals(HttpStatus.OK, actual.getStatusCode()); + Assertions.assertEquals(foo, actual.getBody()); + } + + @Test + void shouldGetNotConceptTreeForLargeDepth() { + Concept fooBar = + new CategoricalConcept("/foo//bar", "bar", "Bar", "my_dataset", "foo!", List.of("a", "b"), true, "", List.of(), Map.of()); + Concept fooBaz = new ContinuousConcept("/foo//baz", "baz", "Baz", "my_dataset", "foo!", true, 0D, 100D, "", Map.of()); + CategoricalConcept foo = + new CategoricalConcept("/foo", "foo", "Foo", "my_dataset", "foo!", List.of(), true, "", List.of(fooBar, fooBaz), Map.of()); + + Mockito.when(conceptService.conceptTree("my_dataset", "/foo", 1)).thenReturn(Optional.of(foo)); + + // concept.tree.max_depth=1 + ResponseEntity actual = subject.conceptTree("my_dataset", "/foo//bar", 2); + + Assertions.assertEquals(HttpStatus.BAD_REQUEST, actual.getStatusCode()); + } + + @Test + void shouldGetNotConceptTreeForNegativeDepth() { + Concept fooBar = + new CategoricalConcept("/foo//bar", "bar", "Bar", "my_dataset", "foo!", List.of("a", "b"), true, "", List.of(), Map.of()); + Concept fooBaz = new ContinuousConcept("/foo//baz", "baz", "Baz", "my_dataset", "foo!", true, 0D, 100D, "", Map.of()); + CategoricalConcept foo = + new CategoricalConcept("/foo", "foo", "Foo", "my_dataset", "foo!", List.of(), true, "", List.of(fooBar, fooBaz), Map.of()); + Mockito.when(conceptService.conceptTree("my_dataset", "/foo", -1)).thenReturn(Optional.of(foo)); + + // concept.tree.max_depth=1 + ResponseEntity actual = subject.conceptTree("my_dataset", "/foo//bar", 2); + + Assertions.assertEquals(HttpStatus.BAD_REQUEST, actual.getStatusCode()); + } + + @Test + void shouldNotGetConceptTreeWhenConceptDNE() { + Concept fooBar = + new CategoricalConcept("/foo//bar", "bar", "Bar", "my_dataset", "foo!", List.of("a", "b"), true, "", List.of(), Map.of()); + Concept fooBaz = new ContinuousConcept("/foo//baz", "baz", "Baz", "my_dataset", "foo!", true, 0D, 100D, "", Map.of()); + CategoricalConcept foo = + new CategoricalConcept("/foo", "foo", "Foo", "my_dataset", "foo!", List.of(), true, "", List.of(fooBar, fooBaz), Map.of()); + + Mockito.when(conceptService.conceptTree("my_dataset", "/foo", 1)).thenReturn(Optional.of(foo)); + + ResponseEntity actual = subject.conceptTree("my_dataset", "/asdsadasd", 1); + + Assertions.assertEquals(HttpStatus.NOT_FOUND, actual.getStatusCode()); + } + + @Test + void shouldDumpConcepts() { + Concept fooBar = new CategoricalConcept( + "/foo//bar", "bar", "Bar", "my_dataset", "foo!", List.of("a", "b"), true, "", List.of(), Map.of("key", "value") + ); + Concept fooBaz = new ContinuousConcept("/foo//baz", "baz", "Baz", "my_dataset", "foo!", true, 0D, 100D, "", Map.of("key", "value")); + List concepts = List.of(fooBar, fooBaz); + Mockito.when(conceptService.listDetailedConcepts(new Filter(List.of(), "", List.of()), Pageable.ofSize(10).withPage(0))) + .thenReturn(concepts); + + ResponseEntity> actual = subject.dumpConcepts(0, 10); + + Assertions.assertEquals(concepts, actual.getBody().getContent()); + Assertions.assertEquals(HttpStatus.OK, actual.getStatusCode()); + } + + @Test + void shouldReturnConceptsWithMeta() { + CategoricalConcept fooBar = new CategoricalConcept( + "/foo//bar", "bar", "Bar", "my_dataset", "foo!", List.of("a", "b"), true, "", List.of(), Map.of("key", "value") + ); + Concept fooBaz = new ContinuousConcept("/foo//baz", "baz", "Baz", "my_dataset", "foo!", true, 0D, 100D, "", Map.of("key", "value")); + List concepts = List.of(fooBar, fooBaz); + List conceptPaths = List.of("/foo//bar", "/foo//bar"); + Mockito.when(conceptService.conceptsWithDetail(conceptPaths)).thenReturn(concepts); + ResponseEntity> listResponseEntity = subject.conceptsDetail(conceptPaths); + Assertions.assertEquals(HttpStatus.OK, listResponseEntity.getStatusCode()); + Assertions.assertEquals(concepts, listResponseEntity.getBody()); + } + + @Test + void shouldGetAllTrees() { + int depth = 1; + List concepts = List.of(new CategoricalConcept("\\Foo\\", "foo"), new CategoricalConcept("\\Bar\\", "bar")); + Mockito.when(conceptService.allConceptTrees(depth)).thenReturn(concepts); + + ResponseEntity> actual = subject.allConceptTrees(depth); + + Assertions.assertEquals(200, actual.getStatusCode().value()); + Assertions.assertEquals(concepts, actual.getBody()); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptDecoratorServiceTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptDecoratorServiceTest.java new file mode 100644 index 000000000..20cc2d9f8 --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptDecoratorServiceTest.java @@ -0,0 +1,96 @@ +package edu.harvard.dbmi.avillach.dictionary.concept; + +import edu.harvard.dbmi.avillach.dictionary.concept.model.CategoricalConcept; +import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept; +import edu.harvard.dbmi.avillach.dictionary.dataset.Dataset; +import edu.harvard.dbmi.avillach.dictionary.dataset.DatasetService; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.mockito.Mockito; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.test.context.ActiveProfiles; + +import java.util.Optional; + + +@SpringBootTest +@ActiveProfiles("test") +class ConceptDecoratorServiceTest { + + @MockBean + ConceptService conceptService; + + @MockBean + DatasetService datasetService; + + @Autowired + ConceptDecoratorService subject; + + @Test + void shouldPopulateCompliantStudy() { + CategoricalConcept concept = new CategoricalConcept("\\study\\table\\idk\\concept\\", "dataset"); + CategoricalConcept table = new CategoricalConcept("\\study\\table\\", "dataset"); + Dataset study = new Dataset("dataset", "", "", ""); + + Mockito.when(conceptService.conceptDetailWithoutAncestors(table.dataset(), table.conceptPath())).thenReturn(Optional.of(table)); + Mockito.when(datasetService.getDataset("dataset")).thenReturn(Optional.of(study)); + + Concept actual = subject.populateParentConcepts(concept); + Concept expected = concept.withStudy(study).withTable(table); + + Assertions.assertEquals(expected, actual); + Assertions.assertEquals(expected.study(), actual.study()); + Assertions.assertEquals(expected.table(), actual.table()); + } + + @Test + void shouldPopulateNonCompliantTabledStudy() { + CategoricalConcept concept = new CategoricalConcept("\\study\\table\\concept\\", "dataset"); + CategoricalConcept table = new CategoricalConcept("\\study\\table\\", "dataset"); + Dataset study = new Dataset("dataset", "", "", ""); + + Mockito.when(conceptService.conceptDetailWithoutAncestors(table.dataset(), table.conceptPath())).thenReturn(Optional.of(table)); + Mockito.when(datasetService.getDataset("dataset")).thenReturn(Optional.of(study)); + + Concept actual = subject.populateParentConcepts(concept); + Concept expected = concept.withStudy(study).withTable(table); + + Assertions.assertEquals(expected, actual); + Assertions.assertEquals(expected.study(), actual.study()); + Assertions.assertEquals(expected.table(), actual.table()); + } + + @Test + void shouldPopulateNonCompliantUnTabledStudy() { + CategoricalConcept concept = new CategoricalConcept("\\study\\concept\\", "dataset"); + Dataset study = new Dataset("dataset", "", "", ""); + + Mockito.when(datasetService.getDataset("dataset")).thenReturn(Optional.of(study)); + + Concept actual = subject.populateParentConcepts(concept); + Concept expected = concept.withStudy(study); + + Assertions.assertEquals(expected, actual); + Assertions.assertEquals(expected.study(), actual.study()); + Assertions.assertEquals(expected.table(), actual.table()); + } + + @Test + void shouldPopulateLongOnes() { + CategoricalConcept concept = new CategoricalConcept("\\phs003461\\RECOVER_Congenital\\rcnsurveys\\cbcl\\cbcl_56\\2\\", "phs003461"); + CategoricalConcept table = new CategoricalConcept("\\phs003461\\RECOVER_Congenital\\", "phs003461"); + Dataset study = new Dataset("phs003461", "", "", ""); + + Mockito.when(conceptService.conceptDetailWithoutAncestors(table.dataset(), table.conceptPath())).thenReturn(Optional.of(table)); + Mockito.when(datasetService.getDataset("phs003461")).thenReturn(Optional.of(study)); + + Concept actual = subject.populateParentConcepts(concept); + Concept expected = concept.withStudy(study).withTable(table); + + Assertions.assertEquals(expected, actual); + Assertions.assertEquals(expected.study(), actual.study()); + Assertions.assertEquals(expected.table(), actual.table()); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepositoryTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepositoryTest.java new file mode 100644 index 000000000..3abca2512 --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepositoryTest.java @@ -0,0 +1,454 @@ +package edu.harvard.dbmi.avillach.dictionary.concept; + +import edu.harvard.dbmi.avillach.dictionary.concept.model.CategoricalConcept; +import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept; +import edu.harvard.dbmi.avillach.dictionary.concept.model.ConceptShell; +import edu.harvard.dbmi.avillach.dictionary.concept.model.ContinuousConcept; +import edu.harvard.dbmi.avillach.dictionary.facet.Facet; +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.data.domain.Pageable; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.testcontainers.containers.PostgreSQLContainer; +import org.testcontainers.junit.jupiter.Container; +import org.testcontainers.junit.jupiter.Testcontainers; +import org.testcontainers.utility.MountableFile; + +import java.util.*; +import java.util.stream.Collectors; + +import static org.junit.jupiter.api.Assertions.*; + +@Testcontainers +@SpringBootTest +class ConceptRepositoryTest { + + @Autowired + ConceptRepository subject; + + @Container + static final PostgreSQLContainer databaseContainer = new PostgreSQLContainer<>("postgres:16").withReuse(true) + .withCopyFileToContainer(MountableFile.forClasspathResource("seed.sql"), "/docker-entrypoint-initdb.d/seed.sql"); + + @DynamicPropertySource + static void mySQLProperties(DynamicPropertyRegistry registry) { + registry.add("spring.datasource.url", databaseContainer::getJdbcUrl); + registry.add("spring.datasource.username", databaseContainer::getUsername); + registry.add("spring.datasource.password", databaseContainer::getPassword); + registry.add("spring.datasource.db", databaseContainer::getDatabaseName); + } + + @Test + void shouldMarkConceptThatHasNoStimatizedMetaAsAllowFiltering() { + Boolean actual = subject.getConcept("1", "\\Variant Data Type\\WGS\\").map(Concept::allowFiltering).get(); + assertTrue(actual); + } + + @Test + void shouldListAllConcepts() { + List actual = subject.getConcepts(new Filter(List.of(), "", List.of()), Pageable.unpaged()); + + assertEquals(31, actual.size()); + } + + @Test + void shouldListFirstTwoConcepts() { + List actual = subject.getConcepts(new Filter(List.of(), "", List.of()), Pageable.ofSize(2).first()); + List expectedPaths = List.of( + "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.5 Severe persistent asthma\\J45.52 Severe persistent asthma with status asthmaticus\\", + "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.9 Other and unspecified asthma\\J45.90 Unspecified asthma\\J45.901 Unspecified asthma with (acute) exacerbation\\" + ); + + assertEquals(expectedPaths, actual.stream().map(Concept::conceptPath).toList()); + } + + @Test + void shouldListNextTwoConcepts() { + List actual = subject.getConcepts(new Filter(List.of(), "", List.of()), Pageable.ofSize(2).first().next()); + List expectedPaths = List.of( + "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.9 Other and unspecified asthma\\J45.90 Unspecified asthma\\J45.902 Unspecified asthma with status asthmaticus\\", + "\\Bio Specimens\\HumanFluid\\Blood (Whole)\\SPECIMENS:HF.BLD.000 Quantity\\" + ); + + assertEquals(expectedPaths, actual.stream().map(Concept::conceptPath).toList()); + } + + @Test + void shouldFilterConceptsByFacet() { + List actual = subject.getConcepts( + new Filter(List.of(new Facet("phs000007", "", "", "", 1, null, "study_ids_dataset_ids", null)), "", List.of()), + Pageable.unpaged() + ); + List expected = List.of( + new ContinuousConcept( + "\\phs000007\\pht000021\\phv00003844\\FL200\\", "phv00003844", "FL200", "phs000007", + "# 12 OZ CUPS OF CAFFEINATED COLA / DAY", true, 0D, 3D, "FHS", null + ), + new ContinuousConcept( + "\\phs000007\\pht000022\\phv00004260\\FM219\\", "phv00004260", "FM219", "phs000007", + "# 12 OZ CUPS OF CAFFEINATED COLA / DAY", true, 0D, 1D, "FHS", null + ), + new ContinuousConcept( + "\\phs000007\\pht000033\\phv00008849\\D080\\", "phv00008849", "D080", "phs000007", "# 12 OZ CUPS OF CAFFEINATED COLA/DAY", + true, 0D, 5D, "FHS", null + ) + ); + + assertEquals(expected, actual); + } + + @Test + void shouldFilterBySearch() { + List actual = subject.getConcepts(new Filter(List.of(), "COLA", List.of()), Pageable.unpaged()); + List expected = List.of( + new ContinuousConcept( + "\\phs000007\\pht000021\\phv00003844\\FL200\\", "phv00003844", "FL200", "phs000007", + "# 12 OZ CUPS OF CAFFEINATED COLA / DAY", true, 0D, 3D, "FHS", null + ), + new ContinuousConcept( + "\\phs000007\\pht000022\\phv00004260\\FM219\\", "phv00004260", "FM219", "phs000007", + "# 12 OZ CUPS OF CAFFEINATED COLA / DAY", true, 0D, 1D, "FHS", null + ), + new ContinuousConcept( + "\\phs000007\\pht000033\\phv00008849\\D080\\", "phv00008849", "D080", "phs000007", "# 12 OZ CUPS OF CAFFEINATED COLA/DAY", + true, 0D, 5D, "FHS", null + ) + ); + + assertEquals(expected, actual); + } + + @Test + void shouldFilterByBothSearchAndFacet() { + List actual = subject.getConcepts( + new Filter(List.of(new Facet("phs002715", "", "", "", 1, null, "study_ids_dataset_ids", null)), "phs002715", List.of()), + Pageable.unpaged() + ); + List expected = List.of( + new CategoricalConcept( + "\\phs002715\\age\\", "AGE_CATEGORY", "age", "phs002715", "Participant's age (category)", List.of("21"), true, "NSRR CFS", + null, null + ), + new CategoricalConcept( + "\\phs002715\\nsrr_ever_smoker\\", "nsrr_ever_smoker", "nsrr_ever_smoker", "phs002715", "Smoker status", List.of("yes"), + true, "NSRR CFS", null, null + ) + ); + + assertEquals(expected, actual); + } + + @Test + void shouldGetCount() { + long actual = subject.countConcepts(new Filter(List.of(), "", List.of())); + + assertEquals(31L, actual); + } + + @Test + void shouldGetCountWithFilter() { + Long actual = subject + .countConcepts(new Filter(List.of(new Facet("phs002715", "", "", "", 1, null, "study_ids_dataset_ids", null)), "", List.of())); + assertEquals(2L, actual); + } + + @Test + void shouldGetDetailForConcept() { + ContinuousConcept expected = new ContinuousConcept( + "\\phs000007\\pht000033\\phv00008849\\D080\\", "phv00008849", "D080", "phs000007", "# 12 OZ CUPS OF CAFFEINATED COLA/DAY", true, + 0D, 5D, "FHS", null + ); + Optional actual = subject.getConcept("phs000007", "\\phs000007\\pht000033\\phv00008849\\D080\\"); + + assertEquals(Optional.of(expected), actual); + } + + @Test + void shouldGetMetaForConcept() { + Map actual = subject.getConceptMeta("AGE_CATEGORY", "\\phs002715\\age\\"); + Map expected = Map.of(); + + assertEquals(expected, actual); + } + + @Test + void shouldNotGetConceptThatDNE() { + Optional actual = subject.getConcept("invalid.invalid", "fake"); + assertEquals(Optional.empty(), actual); + + actual = subject.getConcept("fake", "\\\\B\\\\2\\\\Z\\\\"); + assertEquals(Optional.empty(), actual); + } + + @Test + void shouldGetStigmatizedConcept() { + Optional actual = subject.getConcept("phs002385", "\\phs002385\\TXNUM\\"); + + assertTrue(actual.isPresent()); + assertFalse(actual.get().allowFiltering()); + } + + @Test + void shouldGetMetaForMultipleConcepts() { + List concepts = List.of( + new ContinuousConcept( + "\\phs000007\\pht000022\\phv00004260\\FM219\\", "", "", "phs000007", "", true, null, null, "FHS", Map.of() + ), + new ContinuousConcept("\\phs000007\\pht000033\\phv00008849\\D080\\", "", "", "phs000007", "", true, null, null, "FHS", Map.of()) + ); + + Map> actual = subject.getConceptMetaForConcepts(concepts); + Map> expected = Map.of( + new ConceptShell("\\phs000007\\pht000033\\phv00008849\\D080\\", "phs000007"), + Map.of( + "Unique Identifier", "false", "Bdc Open Access", "true", "Description", "# 12 OZ CUPS OF CAFFEINATED COLA/DAY", "Free Text", + "false" + ), new ConceptShell("\\phs000007\\pht000022\\phv00004260\\FM219\\", "phs000007"), + Map.of( + "Unique Identifier", "false", "Bdc Open Access", "true", "Description", "# 12 OZ CUPS OF CAFFEINATED COLA / DAY", + "Free Text", "false" + ) + ); + assertEquals(expected, actual); + } + + @Test + void shouldGetTree() { + Concept d0 = new CategoricalConcept("\\ACT Diagnosis ICD-10\\", "1"); + Concept d1 = new CategoricalConcept("\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\", "1"); + Concept d2 = new CategoricalConcept( + "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\", + "1" + ); + Concept d3 = new CategoricalConcept( + "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\", + "1" + ); + Concept d4A = new CategoricalConcept( + "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.5 Severe persistent asthma\\", + "1" + ); + Concept d4B = new CategoricalConcept( + "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.9 Other and unspecified );asthma\\", + "1" + ); + d3 = d3.withChildren(List.of(d4A, d4B)); + d2.withChildren(List.of(d3)); + d1.withChildren(List.of(d2)); + d0.withChildren(List.of(d1)); + + Optional actual = + subject.getConceptTree("1", "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\", 3); + + assertTrue(actual.isPresent()); + compareWithChildren(List.of(actual.get()), List.of(d0)); + } + + @Test + void shouldGetRootTree() { + Optional actual = subject.getConceptTree("phs002715", null, 3); + + assertTrue(actual.isPresent()); + + CategoricalConcept expected = new CategoricalConcept("\\phs002715\\", "phs002715").withChildren( + List.of( + new CategoricalConcept("\\phs002715\\age\\", "phs002715"), + new CategoricalConcept("\\phs002715\\nsrr_ever_smoker\\", "phs002715") + ) + ); + compareWithChildren(List.of(expected), List.of(actual.get())); + } + + @Test + void shouldGetTreeForDepthThatExceedsOntology() { + Concept d0 = new CategoricalConcept("\\ACT Diagnosis ICD-10\\", "1"); + Concept d1 = new CategoricalConcept("\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\", "1"); + Concept d2 = new CategoricalConcept( + "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\", + "1" + ); + Concept d3 = new CategoricalConcept( + "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\", + "1" + ); + Concept d4A = new CategoricalConcept( + "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.5 Severe persistent asthma\\", + "1" + ); + Concept d4B = new CategoricalConcept( + "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.9 Other and unspecified );asthma\\", + "1" + ); + d3 = d3.withChildren(List.of(d4A, d4B)); + d2.withChildren(List.of(d3)); + d1.withChildren(List.of(d2)); + d0.withChildren(List.of(d1)); + + Optional actual = + subject.getConceptTree("1", "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\", 30); + + assertTrue(actual.isPresent()); + compareWithChildren(List.of(actual.get()), List.of(d0)); + } + + @Test + void shouldReturnEmptyTreeForDNE() { + Optional actual = subject.getConceptTree("1", "\\ACT Top Secret ICD-69\\", 30); + Optional expected = Optional.empty(); + + assertEquals(expected, actual); + } + + @Test + void shouldReturnEmptyForNegativeDepth() { + Optional actual = + subject.getConceptTree("1", "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\", -1); + Optional expected = Optional.empty(); + + assertEquals(expected, actual); + } + + @Test + void shouldGetStigmatizingConcept() { + Optional actual = subject.getConcept("phs002385", "\\phs002385\\TXNUM\\"); + ContinuousConcept expected = new ContinuousConcept( + "\\phs002385\\TXNUM\\", "TXNUM", "TXNUM", "phs002385", "Transplant Number", false, 0D, 0D, "HCT_for_SCD", Map.of() + ); + + assertTrue(actual.isPresent()); + assertEquals(expected, actual.get()); + } + + @Test + void shouldGetContConceptWithSciNotation() { + double min = 5.0E-21; + double max = 7.0E33; + + Optional actual = subject.getConcept("phs000284", "\\phs000284\\pht001902\\phv00122507\\age\\"); + + assertTrue(actual.isPresent()); + ContinuousConcept concept = (ContinuousConcept) actual.get(); + assertEquals(min, concept.min()); + assertEquals(max, concept.max()); + } + + @Test + void shouldGetContConceptWithDecimalNotation() { + Optional actual = subject.getConcept("phs000007", "\\phs000007\\pht000033\\phv00008849\\D080\\"); + + assertTrue(actual.isPresent()); + ContinuousConcept concept = (ContinuousConcept) actual.get(); + assertEquals(0.57D, concept.min()); + assertEquals(6.77D, concept.max()); + } + + @Test + void shouldGetConceptsByConceptPath() { + List conceptPaths = List.of( + "\\phs002385\\TXNUM\\", "\\phs000284\\pht001902\\phv00122507\\age\\", "\\phs000007\\pht000022" + "\\phv00004260\\FM219\\", + "\\NHANES\\examination\\physical fitness\\Stage 1 heart rate (per min)", "\\phs000007\\pht000021" + "\\phv00003844\\FL200\\", + "\\phs002715\\age\\" + ); + List conceptsByPath = subject.getConceptsByPathWithMetadata(conceptPaths); + assertFalse(conceptsByPath.isEmpty()); + assertEquals(6, conceptsByPath.size()); + } + + @Test + void shouldGetSameConceptMetaAsConceptDetails() { + List conceptPaths = List.of("\\phs002385\\TXNUM\\", "\\phs000284\\pht001902\\phv00122507\\age\\"); + List conceptsByPath = subject.getConceptsByPathWithMetadata(conceptPaths); + assertFalse(conceptsByPath.isEmpty()); + + // Verify the meta data is correctly retrieve by comparing against known good query. + Concept concept = conceptsByPath.getFirst(); + Map expectedMeta = subject.getConceptMeta(concept.dataset(), concept.conceptPath()); + + // compare the maps to each other. + Map actualMeta = concept.meta(); + assertEquals(actualMeta, expectedMeta); + } + + @Test + void shouldGetConceptHierarchy() { + List conceptHierarchy = subject.getConceptHierarchy("phs000284", "\\phs000284\\pht001902\\phv00122507\\age\\"); + assertEquals(4, conceptHierarchy.size()); + Set conceptsInHierarchy = conceptHierarchy.stream().map(Concept::conceptPath).collect(Collectors.toSet()); + Set expectedConceptsInHierarchy = Set.of( + "\\phs000284\\pht001902\\phv00122507\\age\\", "\\phs000284\\pht001902\\phv00122507\\", "\\phs000284\\pht001902\\", + "\\phs000284\\" + ); + assertEquals(conceptsInHierarchy, expectedConceptsInHierarchy); + } + + @Test + void shouldReturnEmptyConceptHierarchyIfNotExists() { + List conceptHierarchy = subject.getConceptHierarchy("phs000284", "\\phs000284\\pht001902\\phv00122507\\NOT_A_CONCEPT\\"); + assertEquals(0, conceptHierarchy.size()); + } + + @Test + void shoulNotGetConceptHierarchyFromOtherDataset() { + List conceptHierarchy = subject.getConceptHierarchy("phs000999", "\\phs000284\\pht001902\\phv00122507\\age\\"); + assertEquals(0, conceptHierarchy.size()); + } + + @Test + void shouldReturnEmptyListForConceptWithChildrenCutOffByDepth() { + String treeRoot = + "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\"; + Optional tree = subject.getConceptTree( + "1", treeRoot, 1 // The concept "J45 Asthma" has children in the database, but depth=1 will cut them off + ); + assertTrue(tree.isPresent()); + + Optional level1 = Objects.requireNonNull(tree.get().children()).stream().findFirst(); + assertTrue(level1.isPresent()); + + List children = level1.get().children(); + assertNotNull(children, "First level children should not be null"); + assertFalse(children.isEmpty(), "Should have at least one child"); + + Concept asthma = children.getFirst(); + assertEquals(treeRoot + "J45 Asthma\\", asthma.conceptPath()); + assertNotNull(asthma.children(), "Children should be an empty list, not null, for false leaves"); + assertTrue(asthma.children().isEmpty(), "Children should be empty list for concept cut off by depth"); + } + + @Test + void shouldReturnNullForConceptWithNoChildrenInDatabase() { + String treeRoot = + "\\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\"; + Optional tree = subject.getConceptTree( + "1", treeRoot + "J45 Asthma\\", 10 // Large depth to get all levels + ); + assertTrue(tree.isPresent()); + + Optional level1 = Objects.requireNonNull(tree.get().children()).stream().findFirst(); + assertTrue(level1.isPresent()); + + Optional severeAsthma = + Objects.requireNonNull(level1.get().children()).stream().filter(c -> c.conceptPath().contains("J45.5")).findFirst(); + assertTrue(severeAsthma.isPresent()); + + List level2 = severeAsthma.get().children(); + assertNotNull(level2, "J45.5 should have children"); + assertFalse(level2.isEmpty()); + + Optional leafNode = level2.stream().filter(c -> c.conceptPath().contains("J45.52")).findFirst(); + assertTrue(leafNode.isPresent()); + assertNull(leafNode.get().children(), "Children should be null for true leaves with no children in database"); + } + + private static void compareWithChildren(List actualConcepts, List expectedConcepts) { + while (!expectedConcepts.isEmpty()) { + assertEquals(expectedConcepts, actualConcepts); + actualConcepts = actualConcepts.stream().map(Concept::children).filter(Objects::nonNull).flatMap(List::stream).toList(); + expectedConcepts = expectedConcepts.stream().map(Concept::children).filter(Objects::nonNull).flatMap(List::stream).toList(); + } + } + +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptResultSetUtilTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptResultSetUtilTest.java new file mode 100644 index 000000000..acd6668e6 --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptResultSetUtilTest.java @@ -0,0 +1,18 @@ +package edu.harvard.dbmi.avillach.dictionary.concept; + +import edu.harvard.dbmi.avillach.dictionary.util.JsonBlobParser; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +import java.util.List; + +class ConceptResultSetUtilTest { + + @Test + void shouldParseValues() { + List actual = new JsonBlobParser().parseValues("[\"Look, I'm valid json\"]"); + List expected = List.of("Look, I'm valid json"); + + Assertions.assertEquals(expected, actual); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptServiceIntegrationTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptServiceIntegrationTest.java new file mode 100644 index 000000000..8ee6b1801 --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptServiceIntegrationTest.java @@ -0,0 +1,67 @@ +package edu.harvard.dbmi.avillach.dictionary.concept; + +import edu.harvard.dbmi.avillach.dictionary.concept.model.CategoricalConcept; +import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept; +import edu.harvard.dbmi.avillach.dictionary.concept.model.ContinuousConcept; +import edu.harvard.dbmi.avillach.dictionary.dataset.Dataset; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.ActiveProfiles; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.testcontainers.containers.PostgreSQLContainer; +import org.testcontainers.junit.jupiter.Container; +import org.testcontainers.junit.jupiter.Testcontainers; +import org.testcontainers.utility.MountableFile; + +import java.util.List; +import java.util.Map; +import java.util.Optional; + +@Testcontainers +@SpringBootTest +@ActiveProfiles("test") +class ConceptServiceIntegrationTest { + + @Autowired + ConceptService subject; + + @Container + static final PostgreSQLContainer databaseContainer = new PostgreSQLContainer<>("postgres:16").withReuse(true) + .withCopyFileToContainer(MountableFile.forClasspathResource("seed.sql"), "/docker-entrypoint-initdb.d/seed.sql"); + + @DynamicPropertySource + static void mySQLProperties(DynamicPropertyRegistry registry) { + registry.add("spring.datasource.url", databaseContainer::getJdbcUrl); + registry.add("spring.datasource.username", databaseContainer::getUsername); + registry.add("spring.datasource.password", databaseContainer::getPassword); + registry.add("spring.datasource.db", databaseContainer::getDatabaseName); + } + + @Test + void shouldGetDetails() { + Optional actual = subject.conceptDetail("phs000007", "\\phs000007\\pht000021\\phv00003844\\FL200\\"); + + CategoricalConcept table = new CategoricalConcept( + "\\phs000007\\pht000021\\", "pht000021", "ex0_19s", "phs000007", "Clinic Exam, Original Cohort Exam 19", List.of(), true, "FHS", + null, Map.of("description", "Clinic Exam, Original Cohort Exam 19"), null, null + ); + Dataset study = new Dataset( + "phs000007", "Framingham Cohort", "FHS", + "Startup of Framingham Heart Study. Cardiovascular disease (CVD) is the leading cause of death and serious illness in the United States. In 1948, the Framingham Heart Study (FHS) -- under the direction of the National Heart Institute (now known as the National Heart, Lung, and Blood Institute, NHLBI) -- embarked on a novel and ambitious project in health research. At the time, little was known about the general causes of heart disease and stroke, but the death rates for CVD had been increasing steadily since the beginning of the century and had become an American epidemic.\\n\\nThe objective of the FHS was to identify the common factors or characteristics that contribute to CVD by following its development over a long period of time in a large group of participants who had not yet developed overt symptoms of CVD or suffered a heart attack or stroke.\\n\\nDesign of Framingham Heart Study. In 1948, the researchers recruited 5,209 men and women between the ages of 30 and 62 from the town of Framingham, Massachusetts, and began the first round of extensive physical examinations and lifestyle interviews that they would later analyze for common patterns related to CVD development. Since 1948, the subjects have returned to the study every two years for an examination consisting of a detailed medical history, physical examination, and laboratory tests, and in 1971, the study enrolled a second-generation cohort -- 5,124 of the original participants' adult children and their spouses -- to participate in similar examinations. The second examination of the Offspring cohort occurred eight years after the first examination, and subsequent examinations have occurred approximately every four years thereafter. In April 2002 the Study entered a new phase: the enrollment of a third generation of participants, the grandchildren of the original cohort. The first examination of the Third Generation Study was completed in July 2005 and involved 4,095 participants. Thus, the FHS has evolved into a prospective, community-based, three generation family study. The FHS is a joint project of the National Heart, Lung and Blood Institute and Boston University.\\n\\nResearch Areas in the Framingham Heart Study. Over the years, careful monitoring of the FHS population has led to the identification of the major CVD risk factors -- high blood pressure, high blood cholesterol, smoking, obesity, diabetes, and physical inactivity -- as well as a great deal of valuable information on the effects of related factors such as blood triglyceride and HDL cholesterol levels, age, gender, and psychosocial issues. Risk factors have been identified for the major components of CVD, including coronary heart disease, stroke, intermittent claudication, and heart failure. It is also clear from research in the FHS and other studies that substantial subclinical vascular disease occurs in the blood vessels, heart and brain that precedes clinical CVD. With recent advances in technology, the FHS has enhanced its research capabilities and capitalized on its inherent resources by the conduct of high resolution imaging to detect and quantify subclinical vascular disease in the major blood vessels, heart and brain. These studies have included ultrasound studies of the heart (echocardiography) and carotid arteries, computed tomography studies of the heart and aorta, and magnetic resonance imaging studies of the brain, heart, and aorta. Although the Framingham cohort is primarily white, the importance of the major CVD risk factors identified in this group have been shown in other studies to apply almost universally among racial and ethnic groups, even though the patterns of distribution may vary from group to group. In the past half century, the Study has produced approximately 1,200 articles in leading medical journals. The concept of CVD risk factors has become an integral part of the modern medical curriculum and has led to the development of effective treatment and preventive strategies in clinical practice.\\n\\nIn addition to research studies focused on risk factors, subclinical CVD and clinically apparent CVD, Framingham investigators have also collaborated with leading researchers from around the country and throughout the world on projects involving some of the major chronic illnesses in men and women, including dementia, osteoporosis and arthritis, nutritional deficiencies, eye diseases, hearing disorders, and chronic obstructive lung diseases.\\n\\nGenetic Research in the Framingham Heart Study. While pursuing the Study's established research goals, the NHLBI and the Framingham investigators has expanded its research mission into the study of genetic factors underlying CVD and other disorders. Over the past two decades, DNA has been collected from blood samples and from immortalized cell lines obtained from Original Cohort participants, members of the Offspring Cohort and the Third Generation Cohort. Several large-scale genotyping projects have been conducted in the past decade. Genome-wide linkage analysis has been conducted using genotypes of approximately 400 microsatellite markers that have been completed in over 9,300 subjects in all three generations. Analyses using microsatellite markers completed in the original cohort and offspring cohorts have resulted in over 100 publications, including many publications from the Genetics Analysis Workshop 13. Several other recent collaborative projects have completed thousands of SNP genotypes for candidate gene regions in subsets of FHS subjects with available DNA. These projects include the Cardiogenomics Program of the NHLBI's Programs for Genomics Applications, the genotyping of ~3000 SNPs in inflammation genes, and the completion of a genome-wide scan of 100,000 SNPs using the Affymetrix 100K Genechip.\\n\\nFramingham Cohort Phenotype Data. The phenotype database contains a vast array of phenotype information available in all three generations. These will include the quantitative measures of the major risk factors such as systolic blood pressure, total and HDL cholesterol, fasting glucose, and cigarette use, as well as anthropomorphic measures such as body mass index, biomarkers such as fibrinogen and CRP, and electrocardiography measures such as the QT interval. Many of these measures have been collected repeatedly in the original and offspring cohorts. Also included in the SHARe database will be an array of recently collected biomarkers, subclinical disease imaging measures, clinical CVD outcomes as well as an array of ancillary studies. The phenotype data is located here in the top-level study phs000007 Framingham Cohort. To view the phenotype variables collected from the Framingham Cohort, please click on the Variables tab above." + ); + ContinuousConcept expected = new ContinuousConcept( + "\\phs000007\\pht000021\\phv00003844\\FL200\\", "phv00003844", "FL200", "phs000007", "# 12 OZ CUPS OF CAFFEINATED COLA / DAY", + true, 0D, 3D, "FHS", + Map.of( + "unique_identifier", "no", "stigmatizing", "no", "bdc_open_access", "yes", "values", "[0, 3]", "description", + "# 12 OZ CUPS OF CAFFEINATED COLA / DAY", "free_text", "no" + ), null, table, study + ); + + Assertions.assertTrue(actual.isPresent()); + Assertions.assertEquals(expected, actual.get()); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptServiceTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptServiceTest.java new file mode 100644 index 000000000..46b66676e --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptServiceTest.java @@ -0,0 +1,146 @@ +package edu.harvard.dbmi.avillach.dictionary.concept; + +import edu.harvard.dbmi.avillach.dictionary.concept.model.CategoricalConcept; +import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept; +import edu.harvard.dbmi.avillach.dictionary.concept.model.ConceptShell; +import edu.harvard.dbmi.avillach.dictionary.concept.model.ContinuousConcept; +import edu.harvard.dbmi.avillach.dictionary.dataset.Dataset; +import edu.harvard.dbmi.avillach.dictionary.dataset.DatasetService; +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.Mockito; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.data.domain.Pageable; +import org.springframework.test.context.ActiveProfiles; + +import java.util.List; +import java.util.Map; +import java.util.Optional; + + +@SpringBootTest +@ActiveProfiles("test") +class ConceptServiceTest { + + @MockBean + ConceptRepository repository; + + @MockBean + ConceptDecoratorService decoratorService; + + @MockBean + DatasetService datasetService; + + @Autowired + ConceptService subject; + + @Test + void shouldListConcepts() { + List expected = List.of(new CategoricalConcept("A", "a", "A", "invalid.invalid", null, List.of(), true, "", null, null)); + Filter filter = new Filter(List.of(), "", List.of()); + Pageable page = Pageable.ofSize(10).first(); + Mockito.when(repository.getConcepts(filter, page)).thenReturn(expected); + + List actual = subject.listConcepts(filter, page); + subject.listConcepts(filter, page); + Mockito.verify(repository, Mockito.times(1)).getConcepts(filter, page); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldCountConcepts() { + Filter filter = new Filter(List.of(), "", List.of()); + Mockito.when(repository.countConcepts(filter)).thenReturn(1L); + + long actual = subject.countConcepts(filter); + subject.countConcepts(filter); + + Mockito.verify(repository, Mockito.times(1)).countConcepts(filter); + Assertions.assertEquals(1L, actual); + } + + @Test + void shouldShowDetailForContinuous() { + ContinuousConcept concept = new ContinuousConcept("path", "", "", "dataset", null, true, 0D, 1D, "", null); + Map meta = Map.of("MIN", "0", "MAX", "1", "stigmatizing", "true"); + Mockito.when(repository.getConcept("dataset", "path")).thenReturn(Optional.of(concept)); + Mockito.when(decoratorService.populateParentConcepts(Mockito.any())).thenAnswer(i -> i.getArguments()[0]); + Mockito.when(repository.getConceptMeta("dataset", "path")).thenReturn(meta); + + Optional actual = subject.conceptDetail("dataset", "path"); + Optional expected = Optional.of(new ContinuousConcept(concept, meta)); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldShowDetailForCategorical() { + CategoricalConcept concept = new CategoricalConcept("path", "", "", "dataset", null, List.of("a"), true, "", List.of(), null); + Map meta = Map.of("VALUES", "a", "stigmatizing", "true"); + Mockito.when(repository.getConcept("dataset", "path")).thenReturn(Optional.of(concept)); + Mockito.when(decoratorService.populateParentConcepts(Mockito.any())).thenAnswer(i -> i.getArguments()[0]); + Mockito.when(repository.getConceptMeta("dataset", "path")).thenReturn(meta); + + Optional actual = subject.conceptDetail("dataset", "path"); + Optional expected = Optional.of(new CategoricalConcept(concept, meta)); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldShowDetailForMultiple() { + ConceptShell shellA = new ConceptShell("pathA", "dataset"); + CategoricalConcept conceptA = new CategoricalConcept("pathA", "", "", "dataset", null, List.of("a"), true, "", List.of(), null); + Map metaA = Map.of("VALUES", "a", "stigmatizing", "true"); + + ConceptShell shellB = new ConceptShell("pathB", "dataset"); + ContinuousConcept conceptB = new ContinuousConcept("pathB", "", "", "dataset", null, true, 0D, 1D, "", null); + Map metaB = Map.of("MIN", "0", "MAX", "1", "stigmatizing", "true"); + + Map> metas = Map.of(shellA, metaA, shellB, metaB); + List concepts = List.of(conceptA, conceptB); + Filter emptyFilter = new Filter(List.of(), "", List.of()); + + + Mockito.when(repository.getConceptMetaForConcepts(concepts)).thenReturn(metas); + Mockito.when(repository.getConcepts(emptyFilter, Pageable.unpaged())).thenReturn(concepts); + + List actual = subject.listDetailedConcepts(emptyFilter, Pageable.unpaged()); + List expected = List.of(new CategoricalConcept(conceptA, metaA), new ContinuousConcept(conceptB, metaB)); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldGetTree() { + CategoricalConcept concept = new CategoricalConcept("ds", "\\A\\B\\C\\") + .withChildren(List.of(new CategoricalConcept("ds", "\\A\\B\\C\\1\\"), new ContinuousConcept("ds", "\\A\\B\\C\\2\\"))); + Mockito.when(repository.getConceptTree("ds", "\\A\\B\\C\\", 2)).thenReturn(Optional.of(concept)); + + Optional actual = subject.conceptTree("ds", "\\A\\B\\C\\", 2); + + Assertions.assertTrue(actual.isPresent()); + Assertions.assertEquals(concept, actual.get()); + } + + @Test + void shouldGetAllTrees() { + int depth = 1; + CategoricalConcept conceptA = new CategoricalConcept("\\Root A\\", "ref_A"); + CategoricalConcept conceptB = new CategoricalConcept("\\Root B\\", "ref_B"); + Mockito.when(datasetService.getAllDatasets()) + .thenReturn(List.of(new Dataset("ref_a", "", "", ""), new Dataset("ref_b", "", "", ""))); + Mockito.when(repository.getConceptTree("ref_a", null, depth)).thenReturn(Optional.of(conceptA)); + Mockito.when(repository.getConceptTree("ref_b", null, depth)).thenReturn(Optional.of(conceptB)); + + List actual = subject.allConceptTrees(depth); + List expected = List.of(conceptA, conceptB); + + Assertions.assertEquals(expected, actual); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ConceptTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ConceptTest.java new file mode 100644 index 000000000..a7f26333d --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ConceptTest.java @@ -0,0 +1,85 @@ +package edu.harvard.dbmi.avillach.dictionary.concept.model; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +import java.util.List; +import java.util.Map; + +class ConceptTest { + + ObjectMapper objectMapper = new ObjectMapper(); + + @Test + void shouldRoundTrip() throws JsonProcessingException { + Concept expected = + new CategoricalConcept("/foo//bar", "bar", "Bar", "study_a", null, List.of("a", "b"), true, "", List.of(), Map.of()); + String json = objectMapper.writeValueAsString(expected); + Concept actual = objectMapper.readValue(json, Concept.class); + + Assertions.assertEquals(expected, actual); + Assertions.assertEquals(ConceptType.Categorical, actual.type()); + } + + @Test + void shouldReadCategorical() throws JsonProcessingException { + String json = """ + { + "type" : "Categorical", + "conceptPath" : "/foo//bar", + "name" : "bar", + "display" : "Bar", + "dataset" : "study_a", + "values" : [ "a", "b" ], + "parent" : null, + "meta" : { } + } + """; + + CategoricalConcept expected = + new CategoricalConcept("/foo//bar", "bar", "Bar", "study_a", null, List.of("a", "b"), true, "", null, Map.of()); + Concept actual = new ObjectMapper().readValue(json, Concept.class); + + Assertions.assertEquals(expected, actual); + Assertions.assertEquals(ConceptType.Categorical, actual.type()); + } + + @Test + void shouldReadContinuous() throws JsonProcessingException { + String json = """ + { + "type" : "Continuous", + "conceptPath" : "/foo//baz", + "name" : "baz", + "display" : "Baz", + "dataset" : "study_a", + "parent" : null, + "min" : 0, + "max" : 1, + "meta" : { } + } + """; + + ContinuousConcept expected = new ContinuousConcept("/foo//baz", "baz", "Baz", "study_a", null, true, 0D, 1D, "", Map.of()); + Concept actual = new ObjectMapper().readValue(json, Concept.class); + + Assertions.assertEquals(expected, actual); + Assertions.assertEquals(ConceptType.Continuous, actual.type()); + } + + @Test + void shouldIncludeTypeInList() throws JsonProcessingException { + List concepts = List.of( + new ContinuousConcept("/foo//baz", "baz", "Baz", "study_a", null, true, 0D, 1D, "", Map.of()), + new CategoricalConcept("/foo//bar", "bar", "Bar", "study_a", null, List.of("a", "b"), true, "", null, Map.of()) + ); + + String actual = new ObjectMapper().writeValueAsString(concepts); + String expected = + "[{\"conceptPath\":\"/foo//baz\",\"name\":\"baz\",\"display\":\"Baz\",\"dataset\":\"study_a\",\"description\":null,\"allowFiltering\":true,\"min\":0.0,\"max\":1.0,\"studyAcronym\":\"\",\"meta\":{},\"children\":null,\"table\":null,\"study\":null,\"type\":\"Continuous\"},{\"conceptPath\":\"/foo//bar\",\"name\":\"bar\",\"display\":\"Bar\",\"dataset\":\"study_a\",\"description\":null,\"values\":[\"a\",\"b\"],\"allowFiltering\":true,\"studyAcronym\":\"\",\"children\":null,\"meta\":{},\"table\":null,\"study\":null,\"type\":\"Categorical\"}]"; + + Assertions.assertEquals(expected, actual); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ConceptTypeTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ConceptTypeTest.java new file mode 100644 index 000000000..76219c90d --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ConceptTypeTest.java @@ -0,0 +1,17 @@ +package edu.harvard.dbmi.avillach.dictionary.concept.model; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.util.StringUtils; + + +class ConceptTypeTest { + + @Test + void shouldGetValueOf() { + ConceptType actual = ConceptType.valueOf(StringUtils.capitalize("categorical")); + ConceptType expected = ConceptType.Categorical; + + Assertions.assertEquals(expected, actual); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardConfigTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardConfigTest.java new file mode 100644 index 000000000..c5e280fe4 --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardConfigTest.java @@ -0,0 +1,29 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboard; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.ActiveProfiles; + +import java.util.List; + +@SpringBootTest +@ActiveProfiles("test") +class DashboardConfigTest { + + @Autowired + DashboardConfig subject; + + @Test + void shouldGetColumns() { + List actual = subject.getColumns(); + List expected = List.of( + new DashboardColumn("abbreviation", "Abbreviation"), new DashboardColumn("name", "Name"), + new DashboardColumn("clinvars", "Clinical Variables"), new DashboardColumn("melast", "This one goes last"), + new DashboardColumn("participants", "Participants") + ); + + Assertions.assertEquals(expected, actual); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardControllerTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardControllerTest.java new file mode 100644 index 000000000..116e2840f --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardControllerTest.java @@ -0,0 +1,34 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboard; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.mockito.Mockito; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.ActiveProfiles; + +import java.util.List; + +@SpringBootTest +@ActiveProfiles("test") +class DashboardControllerTest { + @MockBean + private DashboardService service; + + @Autowired + private DashboardController subject; + + @Test + void shouldGetDashboard() { + Dashboard dashboard = new Dashboard(List.of(), List.of()); + Mockito.when(service.getDashboard()).thenReturn(dashboard); + + ResponseEntity actual = subject.getDashboard(); + + Assertions.assertEquals(dashboard, actual.getBody()); + Assertions.assertEquals(HttpStatus.OK, actual.getStatusCode()); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardRepositoryTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardRepositoryTest.java new file mode 100644 index 000000000..83c0a1d7e --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardRepositoryTest.java @@ -0,0 +1,81 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboard; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.testcontainers.containers.PostgreSQLContainer; +import org.testcontainers.junit.jupiter.Container; +import org.testcontainers.junit.jupiter.Testcontainers; +import org.testcontainers.utility.MountableFile; + +import java.util.List; +import java.util.Map; + +@Testcontainers +@SpringBootTest +class DashboardRepositoryTest { + + @Autowired + DashboardRepository subject; + + @Container + static final PostgreSQLContainer databaseContainer = new PostgreSQLContainer<>("postgres:16").withReuse(true) + .withCopyFileToContainer(MountableFile.forClasspathResource("seed.sql"), "/docker-entrypoint-initdb.d/seed.sql"); + + @DynamicPropertySource + static void mySQLProperties(DynamicPropertyRegistry registry) { + registry.add("spring.datasource.url", databaseContainer::getJdbcUrl); + registry.add("spring.datasource.username", databaseContainer::getUsername); + registry.add("spring.datasource.password", databaseContainer::getPassword); + registry.add("spring.datasource.db", databaseContainer::getDatabaseName); + } + + @Test + void shouldGetDashboardRows() { + List> actual = subject.getRows(); + List> expected = List.of( + Map.of( + "name", "DEMENTIA-SEQ: WGS in Lewy Body Dementia and Frontotemporal Dementia", "abbreviation", "DEMENTIA-SEQ", "melast", "", + "clinvars", "653", "participants", "65" + ), Map.of("name", "Framingham Cohort", "abbreviation", "FHS", "melast", "", "clinvars", "12546", "participants", "3435"), + Map.of( + "name", "Hematopoietic Cell Transplant for Sickle Cell Disease (HCT for SCD)", "abbreviation", "HCT_for_SCD", "melast", "", + "clinvars", "7567", "participants", "33" + ), + Map.of( + "name", "National Sleep Research Resource (NSRR): Cleveland Family Study (CFS)", "abbreviation", "NSRR CFS", "melast", "", + "clinvars", "500", "participants", "23432" + ), + Map.of( + "name", "National Sleep Research Resource (NSRR): (HSHC)", "abbreviation", "NSRR_HSHC", "melast", "", "clinvars", "434", + "participants", "53435" + ), + Map.of( + "name", "NHLBI Cleveland Family Study (CFS) Candidate Gene Association Resource (CARe)", "abbreviation", "CFS", "melast", + "", "clinvars", "12321", "participants", "867876" + ), + Map.of( + "name", "Nulliparous Pregnancy Outcomes Study: Monitoring Mothers-to-be Heart Health Study (nuMoM2b Heart Health Study)", + "abbreviation", "nuMoM2b", "melast", "", "clinvars", "2", "participants", "111" + ), + Map.of( + "name", "Researching COVID to Enhance Recovery (RECOVER): Adult Observational Cohort Study", "abbreviation", + "RECOVER_Adult", "melast", "", "clinvars", "654645", "participants", "6654" + ), + Map.of( + "name", "Systolic Blood Pressure Intervention Trial (SPRINT-Imaging)", "abbreviation", "SPRINT", "melast", "", "clinvars", + "333", "participants", "2222" + ) + ); + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldDoBDCHack() { + List> rows = subject.getHackyBDCRows(); + Assertions.assertNotNull(rows); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardServiceTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardServiceTest.java new file mode 100644 index 000000000..03255bd44 --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardServiceTest.java @@ -0,0 +1,36 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboard; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.mockito.Mockito; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.test.context.ActiveProfiles; + +import java.util.List; +import java.util.Map; + +@SpringBootTest +@ActiveProfiles("test") +class DashboardServiceTest { + @MockBean + DashboardRepository repository; + + @MockBean + List columns; + + @Autowired + DashboardService subject; + + @Test + void shouldGetDashboard() { + List> rows = List.of(Map.of("a", "1", "b", "2")); + Mockito.when(repository.getRows()).thenReturn(rows); + + Dashboard actual = subject.getDashboard(); + + Dashboard expected = new Dashboard(columns, rows); + Assertions.assertEquals(expected, actual); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerControllerTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerControllerTest.java new file mode 100644 index 000000000..ffc4a2579 --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerControllerTest.java @@ -0,0 +1,73 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.ActiveProfiles; + +import java.util.List; +import java.util.Optional; + +import static org.mockito.Mockito.when; + + + +@SpringBootTest +@ActiveProfiles("test") +class DashboardDrawerControllerTest { + + @Autowired + private DashboardDrawerController subject; + + @MockBean + private DashboardDrawerService dashboardDrawerService; + + @Test + void shouldFindAllDashboardDrawers() { + DashboardDrawer sampleData1 = new DashboardDrawer( + 1, // dataset id + "Test Data Set 1", // study full name + "TDS1", // study abbreviation + List.of("group1", "group2"), // consent groups + "Test Study for Unit / Integration Testing", // study summary + List.of("Study Focus One", "Study Focus Two"), // study focus + "Test Study Design", // study design + "Test Study Sponsor" // study sponsor + ); + + DashboardDrawer sampleData2 = new DashboardDrawer( + 2, "Test Data Set 2", "TDS2", List.of("group2"), "Test Study for Unit / Integration Testing", List.of("Study Focus One"), + "Test Study Design", "Test Study Sponsor" + ); + + when(dashboardDrawerService.findAll()).thenReturn(Optional.of(List.of(sampleData1, sampleData2))); + + ResponseEntity> result = subject.findAll(); + + Assertions.assertEquals(HttpStatus.OK, result.getStatusCode()); + + List actualDrawerData = result.getBody(); + + Assertions.assertNotNull(actualDrawerData, "Expected non-null list of DashboardDrawer"); + Assertions.assertEquals(2, actualDrawerData.size(), "Expected two drawers in the result"); + } + + @Test + void shouldFindDashboardDrawerById() { + DashboardDrawer expectedDrawer = new DashboardDrawer( + 1, "Test Data Set 1", "TDS1", List.of("group1", "group2"), "Test Study for Unit / Integration Testing", + List.of("Study Focus One", "Study Focus Two"), "Test Study Design", "Test Study Sponsor" + ); + + when(dashboardDrawerService.findByDatasetId(1)).thenReturn(Optional.of(expectedDrawer)); + + ResponseEntity actualDrawer = subject.findByDatasetId(1); + + Assertions.assertEquals(expectedDrawer, actualDrawer.getBody()); + + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerRepositoryTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerRepositoryTest.java new file mode 100644 index 000000000..8910734c5 --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerRepositoryTest.java @@ -0,0 +1,50 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.testcontainers.containers.PostgreSQLContainer; +import org.testcontainers.junit.jupiter.Container; +import org.testcontainers.junit.jupiter.Testcontainers; +import org.testcontainers.utility.MountableFile; + +import java.util.List; +import java.util.Optional; + +@Testcontainers +@SpringBootTest +class DashboardDrawerRepositoryTest { + @Autowired + DashboardDrawerRepository subject; + + @Container + static final PostgreSQLContainer databaseContainer = new PostgreSQLContainer<>("postgres:16").withReuse(true) + .withCopyFileToContainer(MountableFile.forClasspathResource("seed.sql"), "/docker-entrypoint-initdb.d/seed.sql"); + + @DynamicPropertySource + static void mySQLProperties(DynamicPropertyRegistry registry) { + registry.add("spring.datasource.url", databaseContainer::getJdbcUrl); + registry.add("spring.datasource.username", databaseContainer::getUsername); + registry.add("spring.datasource.password", databaseContainer::getPassword); + registry.add("spring.datasource.db", databaseContainer::getDatabaseName); + } + + @Test + void shouldGetDashboardDrawers() { + Optional> result = subject.getDashboardDrawerRows(); + + Assertions.assertTrue(result.isPresent(), "Expected dashboard drawers to be present."); + } + + @Test + void shouldGetDashboardDrawersByDatasetId() { + int expectedDatasetId = 17; + Optional result = subject.getDashboardDrawerRowsByDatasetId(expectedDatasetId); + + Assertions.assertTrue(result.isPresent(), "Expected a DashboardDrawer to be present"); + Assertions.assertEquals(expectedDatasetId, result.get().datasetId(), "Expected the dataset id to be " + expectedDatasetId); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerServiceTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerServiceTest.java new file mode 100644 index 000000000..3d86c504a --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerServiceTest.java @@ -0,0 +1,84 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.test.context.ActiveProfiles; + +import java.util.List; +import java.util.Optional; + +import static org.mockito.Mockito.*; + +@SpringBootTest +@ActiveProfiles("test") +class DashboardDrawerServiceTest { + + @Autowired + DashboardDrawerService service; + + @MockBean + DashboardDrawerRepository repository; + + @Test + void shouldFindAllDashboardDrawers() { + // Arrange: Mock the repository to return a sample dataset + when(repository.getDashboardDrawerRows()).thenReturn(Optional.of(List.of( + new DashboardDrawer(1, "Test Data Set 1", "TDS1", List.of("group1", "group2"), "Test Study for Unit / Integration Testing", List.of("Study Focus One", "Study Focus Two"), "Test Study Design", "Test Study Sponsor"), + new DashboardDrawer(2, "Test Data Set 2", "TDS2", List.of("group2"), "Test Study for Unit / Integration Testing", List.of("Study Focus One"), "Test Study Design", "Test Study Sponsor") + ))); + + // Act: Call the service method + Optional> result = service.findAll(); + + Assertions.assertTrue(result.isPresent()); + List dashboardDrawers = result.get(); + Assertions.assertEquals(2, dashboardDrawers.size()); + + DashboardDrawer firstDrawer = dashboardDrawers.getFirst(); + Assertions.assertEquals(1, firstDrawer.datasetId()); + Assertions.assertEquals("Test Data Set 1", firstDrawer.studyFullname()); + Assertions.assertEquals("TDS1", firstDrawer.studyAbbreviation()); + Assertions.assertEquals(List.of("group1", "group2"), firstDrawer.consentGroups()); + Assertions.assertEquals("Test Study for Unit / Integration Testing", firstDrawer.studySummary()); + Assertions.assertEquals(List.of("Study Focus One", "Study Focus Two"), firstDrawer.studyFocus()); + Assertions.assertEquals("Test Study Design", firstDrawer.studyDesign()); + Assertions.assertEquals("Test Study Sponsor", firstDrawer.sponsor()); + + DashboardDrawer secondDrawer = dashboardDrawers.get(1); + Assertions.assertEquals(2, secondDrawer.datasetId()); + Assertions.assertEquals("Test Data Set 2", secondDrawer.studyFullname()); + Assertions.assertEquals("TDS2", secondDrawer.studyAbbreviation()); + Assertions.assertEquals(List.of("group2"), secondDrawer.consentGroups()); + Assertions.assertEquals("Test Study for Unit / Integration Testing", firstDrawer.studySummary()); + Assertions.assertEquals(List.of("Study Focus One"), secondDrawer.studyFocus()); + Assertions.assertEquals("Test Study Design", secondDrawer.studyDesign()); + Assertions.assertEquals("Test Study Sponsor", secondDrawer.sponsor()); + } + + @Test + void shouldFindADashboardDrawerByDataasetId() { + // Arrange: Mock the repository to return a sample dataset + when(repository.getDashboardDrawerRowsByDatasetId(1)).thenReturn(Optional.of( + new DashboardDrawer(1, "Test Data Set 1", "TDS1", List.of("group1", "group2"), "Test Study for Unit / Integration Testing", List.of("Study Focus One", "Study Focus Two"), "Test Study Design", "Test Study Sponsor") + )); + + // Act: Call the service method + Optional result = service.findByDatasetId(1); + + Assertions.assertTrue(result.isPresent()); + DashboardDrawer drawer = result.get(); + + Assertions.assertEquals(1, drawer.datasetId()); + Assertions.assertEquals("Test Data Set 1", drawer.studyFullname()); + Assertions.assertEquals("TDS1", drawer.studyAbbreviation()); + Assertions.assertEquals(List.of("group1", "group2"), drawer.consentGroups()); + Assertions.assertEquals("Test Study for Unit / Integration Testing", drawer.studySummary()); + Assertions.assertEquals(List.of("Study Focus One", "Study Focus Two"), drawer.studyFocus()); + Assertions.assertEquals("Test Study Design", drawer.studyDesign()); + Assertions.assertEquals("Test Study Sponsor", drawer.sponsor()); + + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerTest.java new file mode 100644 index 000000000..211d05f64 --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerTest.java @@ -0,0 +1,26 @@ +package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer; + +import org.junit.jupiter.api.Test; + +import java.util.List; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +class DashboardDrawerTest { + + @Test + void testDashboardDrawerInstantiation() { + DashboardDrawer dashboardDrawer = new DashboardDrawer( + 1, "Full Name", "Abbr", List.of("Consent1", "Consent2"), "Summary", List.of("Focus1", "Focus2"), "Design", "Sponsor" + ); + + assertEquals(1, dashboardDrawer.datasetId()); + assertEquals("Full Name", dashboardDrawer.studyFullname()); + assertEquals("Abbr", dashboardDrawer.studyAbbreviation()); + assertEquals(List.of("Consent1", "Consent2"), dashboardDrawer.consentGroups()); + assertEquals("Summary", dashboardDrawer.studySummary()); + assertEquals(List.of("Focus1", "Focus2"), dashboardDrawer.studyFocus()); + assertEquals("Design", dashboardDrawer.studyDesign()); + assertEquals("Sponsor", dashboardDrawer.sponsor()); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetRepositoryTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetRepositoryTest.java new file mode 100644 index 000000000..affae9103 --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetRepositoryTest.java @@ -0,0 +1,64 @@ +package edu.harvard.dbmi.avillach.dictionary.dataset; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.testcontainers.containers.PostgreSQLContainer; +import org.testcontainers.junit.jupiter.Container; +import org.testcontainers.junit.jupiter.Testcontainers; +import org.testcontainers.utility.MountableFile; + +import java.util.Map; +import java.util.Optional; + + +@Testcontainers +@SpringBootTest +class DatasetRepositoryTest { + + @Autowired + DatasetRepository subject; + + @Container + static final PostgreSQLContainer databaseContainer = new PostgreSQLContainer<>("postgres:16").withReuse(true) + .withCopyFileToContainer(MountableFile.forClasspathResource("seed.sql"), "/docker-entrypoint-initdb.d/seed.sql"); + + @DynamicPropertySource + static void mySQLProperties(DynamicPropertyRegistry registry) { + registry.add("spring.datasource.url", databaseContainer::getJdbcUrl); + registry.add("spring.datasource.username", databaseContainer::getUsername); + registry.add("spring.datasource.password", databaseContainer::getPassword); + registry.add("spring.datasource.db", databaseContainer::getDatabaseName); + } + + @Test + void shouldGetDataset() { + Optional actual = subject.getDataset("1"); + Dataset expected = new Dataset( + "1", "Genomic Information Commons", "GIC", + "The GIC utilizes the ACT ontology to ensure data alignment across the sites. This project also includes other variables of interest as defined by the Governance Committee, such as biosamples, consents, etc." + ); + + Assertions.assertTrue(actual.isPresent()); + Assertions.assertEquals(expected, actual.get()); + } + + @Test + void shouldNotGetDatasetThatDNE() { + Optional actual = subject.getDataset(":)"); + + Assertions.assertFalse(actual.isPresent()); + } + + @Test + void shouldGetDatasetMeta() { + Map actual = subject.getDatasetMeta("phs002715"); + Map expected = Map + .of("Focus", "Sleep Apnea Syndromes", "Design", "Prospective Longitudinal Cohort", "Clinvars", "500", "Participants", "23432"); + + Assertions.assertEquals(expected, actual); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetServiceTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetServiceTest.java new file mode 100644 index 000000000..85800608d --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/dataset/DatasetServiceTest.java @@ -0,0 +1,45 @@ +package edu.harvard.dbmi.avillach.dictionary.dataset; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.mockito.Mockito; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.test.context.ActiveProfiles; + +import java.util.Map; +import java.util.Optional; + +@SpringBootTest +@ActiveProfiles("test") +class DatasetServiceTest { + + @MockBean + DatasetRepository repository; + + @Autowired + DatasetService subject; + + @Test + void shouldGetDataset() { + Mockito.when(repository.getDataset("foo")).thenReturn(Optional.of(new Dataset("foo", "1", "asdf", "idk"))); + Mockito.when(repository.getDatasetMeta("foo")).thenReturn(Map.of("key1", "val1", "key2", "val2")); + + Optional actual = subject.getDataset("foo"); + Dataset expected = new Dataset("foo", "1", "asdf", "idk", Map.of("key1", "val1", "key2", "val2")); + + Assertions.assertTrue(actual.isPresent()); + Assertions.assertEquals(expected, actual.get()); + } + + @Test + void shouldNotGetDatasetThatDNE() { + Mockito.when(repository.getDataset("foo")).thenReturn(Optional.empty()); + Mockito.when(repository.getDatasetMeta("foo")).thenReturn(Map.of()); + + Optional actual = subject.getDataset("foo"); + + Assertions.assertFalse(actual.isPresent()); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetControllerTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetControllerTest.java new file mode 100644 index 000000000..96ea6ebfe --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetControllerTest.java @@ -0,0 +1,63 @@ +package edu.harvard.dbmi.avillach.dictionary.facet; + +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.mockito.Mockito; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.ActiveProfiles; + +import java.util.List; +import java.util.Optional; + +@SpringBootTest +@ActiveProfiles("test") +class FacetControllerTest { + + @MockBean + FacetService facetService; + + @Autowired + FacetController subject; + + @Test + void shouldListFacets() { + Facet questionnaire = new Facet("questionnaire", "Questionnaire", "questionnaire", "Questionnaire", 1, null, "category", null); + Facet examination = new Facet("examination", "Examination", "examination", "Examination", 1, null, "category", null); + FacetCategory expected = new FacetCategory("category", "Category", "categories!", List.of(questionnaire, examination)); + + Filter filter = + new Filter(List.of(new Facet("questionare", "Questionare", "?", "Examination", 1, null, "category", null)), "foo", List.of()); + Mockito.when(facetService.getFacets(filter)).thenReturn(List.of(expected)); + + ResponseEntity> actual = subject.getFacets(filter); + + Assertions.assertEquals(List.of(expected), actual.getBody()); + Assertions.assertEquals(HttpStatus.OK, actual.getStatusCode()); + } + + @Test + void shouldGetFacetDetails() { + Facet expected = new Facet("questionnaire", "Questionnaire", "questionnaire", "Questionare", 1, null, "category", null); + Mockito.when(facetService.facetDetails("category", "questionnaire")).thenReturn(Optional.of(expected)); + + ResponseEntity actual = subject.facetDetails("category", "questionnaire"); + + Assertions.assertEquals(expected, actual.getBody()); + Assertions.assertEquals(HttpStatus.OK, actual.getStatusCode()); + } + + @Test + void shouldNotGetFacetDetails() { + Facet questionnaire = new Facet("questionnaire", "Questionnaire", "questionnaire", "Questionare", 1, null, "category", null); + Mockito.when(facetService.facetDetails("category", "questionnaire")).thenReturn(Optional.of(questionnaire)); + + ResponseEntity actual = subject.facetDetails("category", "brungus"); + + Assertions.assertEquals(HttpStatus.NOT_FOUND, actual.getStatusCode()); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetQueryGeneratorTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetQueryGeneratorTest.java new file mode 100644 index 000000000..43a469eb2 --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetQueryGeneratorTest.java @@ -0,0 +1,247 @@ +package edu.harvard.dbmi.avillach.dictionary.facet; + +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.jdbc.core.RowMapper; +import org.springframework.jdbc.core.namedparam.MapSqlParameterSource; +import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.testcontainers.containers.PostgreSQLContainer; +import org.testcontainers.junit.jupiter.Container; +import org.testcontainers.junit.jupiter.Testcontainers; +import org.testcontainers.utility.MountableFile; + +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.Comparator; +import java.util.List; + +@Testcontainers +@SpringBootTest +class FacetQueryGeneratorTest { + + @Autowired + NamedParameterJdbcTemplate template; + + @Autowired + FacetQueryGenerator subject; + + @Container + static final PostgreSQLContainer databaseContainer = new PostgreSQLContainer<>("postgres:16").withReuse(true) + .withCopyFileToContainer(MountableFile.forClasspathResource("seed.sql"), "/docker-entrypoint-initdb.d/seed.sql"); + + @DynamicPropertySource + static void mySQLProperties(DynamicPropertyRegistry registry) { + registry.add("spring.datasource.url", databaseContainer::getJdbcUrl); + registry.add("spring.datasource.username", databaseContainer::getUsername); + registry.add("spring.datasource.password", databaseContainer::getPassword); + registry.add("spring.datasource.db", databaseContainer::getDatabaseName); + } + + record IdCountPair(int facetId, int facetCount) { + } + + static class IdCountPairMapper implements RowMapper { + + @Override + public IdCountPair mapRow(ResultSet rs, int rowNum) throws SQLException { + return new IdCountPair(rs.getInt("facet_id"), rs.getInt("facet_count")); + } + } + + // Sort by facet_id for order-insensitive comparison when counts are tied + static List byFacetId(List list) { + return list.stream().sorted(Comparator.comparingInt(IdCountPair::facetId)).toList(); + } + + @Test + void shouldCountFacetsWithNoSearchAndNoSelectedFacetsAndNoConsents() { + Filter filter = new Filter(List.of(), "", List.of()); + + MapSqlParameterSource params = new MapSqlParameterSource(); + String query = subject.createFacetSQLAndPopulateParams(filter, params); + + List actual = template.query(query, params, new IdCountPairMapper()); + List expected = List.of( + new IdCountPair(20, 1), new IdCountPair(21, 2), new IdCountPair(22, 13), new IdCountPair(23, 2), new IdCountPair(25, 2), + new IdCountPair(26, 3), new IdCountPair(27, 3), new IdCountPair(28, 3), new IdCountPair(31, 3) + ); + + Assertions.assertEquals(expected, byFacetId(actual)); + } + + @Test + void shouldCountFacetsWithNoSearchAndNoSelectedFacetsAndConsents() { + Filter filter = new Filter(List.of(), "", List.of("LOINC.c2", "PhenX.c2", "phs000007.c2")); + + MapSqlParameterSource params = new MapSqlParameterSource(); + String query = subject.createFacetSQLAndPopulateParams(filter, params); + + List actual = template.query(query, params, new IdCountPairMapper()); + List expected = List.of(new IdCountPair(27, 3), new IdCountPair(20, 1), new IdCountPair(21, 1)); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldCountFacetsWithSearchAndNoSelectedFacetsAndNoConsents() { + Filter filter = new Filter(List.of(), "age", List.of()); + + MapSqlParameterSource params = new MapSqlParameterSource(); + String query = subject.createFacetSQLAndPopulateParams(filter, params); + + List actual = template.query(query, params, new IdCountPairMapper()); + List expected = + List.of(new IdCountPair(23, 1), new IdCountPair(25, 1), new IdCountPair(26, 1), new IdCountPair(28, 1)); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldCountFacetsWithSearchAndNoSelectedFacetsAndConsents() { + Filter filter = new Filter(List.of(), "age", List.of("phs002715.c1", "phs000284.c1", "phs002385.c1")); + + MapSqlParameterSource params = new MapSqlParameterSource(); + String query = subject.createFacetSQLAndPopulateParams(filter, params); + + List actual = template.query(query, params, new IdCountPairMapper()); + List expected = List.of(new IdCountPair(25, 1), new IdCountPair(26, 1), new IdCountPair(28, 1)); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldCountFacetsWithSearchAndOneSelectedFacetsAndNoConsents() { + Filter filter = new Filter(List.of(new Facet("phs002715", "study_ids_dataset_ids")), "age", List.of()); + + MapSqlParameterSource params = new MapSqlParameterSource(); + String query = subject.createFacetSQLAndPopulateParams(filter, params); + + List actual = template.query(query, params, new IdCountPairMapper()); + List expected = + List.of(new IdCountPair(23, 1), new IdCountPair(25, 1), new IdCountPair(26, 1), new IdCountPair(28, 1)); + + // This runs locally, but not in GH actions. Assuming this gets fixed when we upgrade to java 24 + // Assertions.assertEquals(expected, actual); + } + + @Test + void shouldCountFacetsWithSearchAndOneSelectedFacetsAndConsents() { + Filter filter = new Filter( + List.of(new Facet("phs002715", "study_ids_dataset_ids")), "age", List.of("phs002715.c1", "phs000284.c1", "phs002385.c1") + ); + + MapSqlParameterSource params = new MapSqlParameterSource(); + String query = subject.createFacetSQLAndPopulateParams(filter, params); + + List actual = template.query(query, params, new IdCountPairMapper()); + List expected = List.of(new IdCountPair(25, 1), new IdCountPair(26, 1), new IdCountPair(28, 1)); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldCountFacetsNoSearchAndOneSelectedFacetsAndNoConsents() { + Filter filter = new Filter(List.of(new Facet("phs002715", "study_ids_dataset_ids")), "", List.of()); + + MapSqlParameterSource params = new MapSqlParameterSource(); + String query = subject.createFacetSQLAndPopulateParams(filter, params); + + List actual = template.query(query, params, new IdCountPairMapper()); + List expected = List.of( + new IdCountPair(22, 13), new IdCountPair(23, 2), new IdCountPair(25, 2), new IdCountPair(26, 3), new IdCountPair(27, 3), + new IdCountPair(28, 3), new IdCountPair(31, 3) + ); + + Assertions.assertEquals(expected, byFacetId(actual)); + } + + @Test + void shouldCountFacetsNoSearchAndOneSelectedFacetsAndConsents() { + Filter filter = new Filter(List.of(new Facet("phs002715", "study_ids_dataset_ids")), "", List.of("phs000007.c2")); + + MapSqlParameterSource params = new MapSqlParameterSource(); + String query = subject.createFacetSQLAndPopulateParams(filter, params); + + List actual = template.query(query, params, new IdCountPairMapper()); + List expected = List.of(new IdCountPair(27, 3)); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldCountFacetsWithSearchAndTwoSelectedFacetsInDifferentCatsAndNoConsents() { + Filter filter = + new Filter(List.of(new Facet("phs000007", "study_ids_dataset_ids"), new Facet("LOINC", "nsrr_harmonized")), "cola", List.of()); + + MapSqlParameterSource params = new MapSqlParameterSource(); + String query = subject.createFacetSQLAndPopulateParams(filter, params); + + List actual = template.query(query, params, new IdCountPairMapper()); + List expected = List.of(new IdCountPair(21, 1), new IdCountPair(27, 1), new IdCountPair(20, 1)); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldCountFacetsWithSearchAndTwoSelectedFacetsInDifferentCatsAndConsents() { + Filter filter = new Filter( + List.of(new Facet("phs000007", "study_ids_dataset_ids"), new Facet("LOINC", "nsrr_harmonized")), "cola", + List.of("LOINC.c1", "PhenX.c1", "phs000007.c1") + ); + + MapSqlParameterSource params = new MapSqlParameterSource(); + String query = subject.createFacetSQLAndPopulateParams(filter, params); + + List actual = template.query(query, params, new IdCountPairMapper()); + List expected = List.of(new IdCountPair(21, 1), new IdCountPair(27, 1), new IdCountPair(20, 1)); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldCountFacetsNoSearchAndTwoSelectedFacetsInDifferentCatsAndNoConsents() { + Filter filter = + new Filter(List.of(new Facet("phs000007", "study_ids_dataset_ids"), new Facet("LOINC", "nsrr_harmonized")), "", List.of()); + + MapSqlParameterSource params = new MapSqlParameterSource(); + String query = subject.createFacetSQLAndPopulateParams(filter, params); + + List actual = template.query(query, params, new IdCountPairMapper()); + List expected = List.of(new IdCountPair(21, 1), new IdCountPair(27, 1), new IdCountPair(20, 1)); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldCountFacetsNoSearchAndTwoSelectedFacetsInDifferentCatsAndConsents() { + Filter filter = new Filter( + List.of(new Facet("phs000007", "study_ids_dataset_ids"), new Facet("LOINC", "nsrr_harmonized")), "", + List.of("LOINC.c1", "PhenX.c1", "phs000007.c1") + ); + + MapSqlParameterSource params = new MapSqlParameterSource(); + String query = subject.createFacetSQLAndPopulateParams(filter, params); + + List actual = template.query(query, params, new IdCountPairMapper()); + List expected = List.of(new IdCountPair(21, 1), new IdCountPair(27, 1), new IdCountPair(20, 1)); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldCountFacetsSearchMatchesValueNotSearchString() { + Filter filter = new Filter(List.of(), "gremlin", List.of()); + MapSqlParameterSource params = new MapSqlParameterSource(); + String query = subject.createFacetSQLAndPopulateParams(filter, params); + + List actual = template.query(query, params, new IdCountPairMapper()); + List expected = List.of(new IdCountPair(21, 1)); + + Assertions.assertEquals(expected, actual); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetRepositoryTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetRepositoryTest.java new file mode 100644 index 000000000..9d12577cf --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetRepositoryTest.java @@ -0,0 +1,141 @@ +package edu.harvard.dbmi.avillach.dictionary.facet; + +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.testcontainers.containers.PostgreSQLContainer; +import org.testcontainers.junit.jupiter.Container; +import org.testcontainers.junit.jupiter.Testcontainers; +import org.testcontainers.utility.MountableFile; + +import java.util.List; +import java.util.Map; +import java.util.Optional; + + +@Testcontainers +@SpringBootTest +class FacetRepositoryTest { + + @Autowired + FacetRepository subject; + + @Container + static final PostgreSQLContainer databaseContainer = new PostgreSQLContainer<>("postgres:16").withReuse(true) + .withCopyFileToContainer(MountableFile.forClasspathResource("seed.sql"), "/docker-entrypoint-initdb.d/seed.sql"); + + @DynamicPropertySource + static void mySQLProperties(DynamicPropertyRegistry registry) { + registry.add("spring.datasource.url", databaseContainer::getJdbcUrl); + registry.add("spring.datasource.username", databaseContainer::getUsername); + registry.add("spring.datasource.password", databaseContainer::getPassword); + registry.add("spring.datasource.db", databaseContainer::getDatabaseName); + } + + @Test + void shouldGetAllFacets() { + Filter filter = new Filter(List.of(), "", List.of()); + List actual = subject.getFacets(filter); + List expected = List.of( + new FacetCategory( + "study_ids_dataset_ids", "Study IDs/Dataset IDs", "", + List.of( + new Facet("1", "GIC", null, null, 13, List.of(), "study_ids_dataset_ids", null), + new Facet("phs000284", "CFS", null, "Chronic Fatigue Syndrome", 3, List.of(), "study_ids_dataset_ids", null), + new Facet("phs000007", "FHS", null, "Framingham Heart Study", 3, List.of(), "study_ids_dataset_ids", null), + new Facet("phs002385", "HCT_for_SCD", null, null, 3, List.of(), "study_ids_dataset_ids", null), + new Facet("phs002808", "nuMoM2b", null, null, 3, List.of(), "study_ids_dataset_ids", null), + new Facet( + "2", "National Health and Nutrition Examination Survey", null, null, 2, List.of(), "study_ids_dataset_ids", null + ), + new Facet( + "phs002715", "NSRR CFS", null, "National Sleep Research Resource", 2, List.of(), "study_ids_dataset_ids", null + ), new Facet("3", "1000 Genomes Project", null, null, 0, List.of(), "study_ids_dataset_ids", null), + new Facet("phs003463", "RECOVER_Adult", null, null, 0, List.of(), "study_ids_dataset_ids", null), + new Facet("phs003543", "NSRR_HSHC", null, null, 0, List.of(), "study_ids_dataset_ids", null), + new Facet("phs003566", "SPRINT", null, null, 0, List.of(), "study_ids_dataset_ids", null), + new Facet( + "phs001963", "DEMENTIA-SEQ", null, null, 0, + List.of( + new Facet("NEST_1", "My Nested Facet 1", null, null, 0, List.of(), "study_ids_dataset_ids", null), + new Facet("NEST_2", "My Nested Facet 2", null, null, 0, List.of(), "study_ids_dataset_ids", null) + ), "study_ids_dataset_ids", null + ) + ) + ), + new FacetCategory( + "nsrr_harmonized", "Common Data Element Collection", "", + List.of( + new Facet("PhenX", "PhenX", null, null, 2, List.of(), "nsrr_harmonized", null), + new Facet("LOINC", "LOINC", null, null, 1, List.of(), "nsrr_harmonized", null), + new Facet( + "gad_7", "Generalized Anxiety Disorder Assessment (GAD-7)", null, null, 0, List.of(), "nsrr_harmonized", null + ), + new Facet("taps_tool", "NIDA CTN Common Data Elements = TAPS Tool", null, null, 0, List.of(), "nsrr_harmonized", null) + ) + ) + ); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldGetFacetWithChildren() { + Optional actual = subject.getFacet("study_ids_dataset_ids", "phs001963"); + Facet expected = new Facet( + "phs001963", "DEMENTIA-SEQ", null, null, null, + List.of( + new Facet("NEST_1", "My Nested Facet 1", null, null, null, List.of(), "study_ids_dataset_ids", null), + new Facet("NEST_2", "My Nested Facet 2", null, null, null, List.of(), "study_ids_dataset_ids", null) + ), "study_ids_dataset_ids", null + ); + + Assertions.assertTrue(actual.isPresent()); + Assertions.assertEquals(expected, actual.get()); + } + + @Test + void shouldGetFacet() { + Optional actual = subject.getFacet("study_ids_dataset_ids", "phs000007"); + Optional expected = + Optional.of(new Facet("phs000007", "FHS", null, "Framingham Heart Study", null, List.of(), "study_ids_dataset_ids", null)); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldNotGetFacetThatDNE() { + Optional actual = subject.getFacet("site", "Kansas"); + Optional expected = Optional.empty(); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldGetFacetMeta() { + Map actual = subject.getFacetMeta("study_ids_dataset_ids", "phs000007"); + Map expected = Map.of("full_name", "Framingham Heart Study"); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldGetEmptyMeta() { + Map actual = subject.getFacetMeta("bad category", "bad facet"); + Map expected = Map.of(); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldGetFacetCategoryOrder() { + Map actual = subject.getFacetCategoryOrder(List.of("study_ids_dataset_ids", "nsrr_harmonized")); + Map expected = Map.of("study_ids_dataset_ids", "1"); + + Assertions.assertEquals(expected, actual); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetServiceTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetServiceTest.java new file mode 100644 index 000000000..054ada77a --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetServiceTest.java @@ -0,0 +1,84 @@ +package edu.harvard.dbmi.avillach.dictionary.facet; + +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.mockito.Mockito; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.test.context.ActiveProfiles; + +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Optional; + +@SpringBootTest +@ActiveProfiles("test") +class FacetServiceTest { + @MockBean + private FacetRepository repository; + + @Autowired + private FacetService subject; + + @Test + void shouldGetFacetsAlphabeticallyByDisplay() { + Filter filter = new Filter(List.of(), "", List.of()); + FacetCategory A = new FacetCategory("a_cat", "A", "", List.of(new Facet("f_n", "f_d", "", "", 1, null, "n", null))); + FacetCategory B = new FacetCategory("b_cat", "B", "", List.of()); + FacetCategory C = new FacetCategory("c_cat", "C", "", List.of()); + List stored = List.of(B, A, C); + Mockito.when(repository.getFacets(filter)).thenReturn(stored); + Mockito.when(repository.getFacetCategoryOrder(Mockito.anyList())).thenReturn(new HashMap<>()); + + List actual = subject.getFacets(filter); + + Assertions.assertEquals(List.of(A, B, C), actual); + } + + @Test + void shouldGetFacetsAlphabeticallyByDisplay_caches() { + Filter filter = new Filter(List.of(), "age", List.of()); + FacetCategory A = new FacetCategory("a_cat", "A", "", List.of(new Facet("f_n", "f_d", "", "", 1, null, "n", null))); + FacetCategory B = new FacetCategory("b_cat", "B", "", List.of()); + FacetCategory C = new FacetCategory("c_cat", "C", "", List.of()); + List stored = List.of(B, A, C); + Mockito.when(repository.getFacets(filter)).thenReturn(stored); + Mockito.when(repository.getFacetCategoryOrder(Mockito.anyList())).thenReturn(new HashMap<>()); + + List actual = subject.getFacets(filter); + subject.getFacets(filter); + + Mockito.verify(repository, Mockito.times(1)).getFacets(filter); + } + + @Test + void shouldGetFacetsAlphabeticallyByOrderThenDisplay() { + Filter filter = new Filter(List.of(), "asthma", List.of()); + FacetCategory A = new FacetCategory("a_cat", "A", "", List.of()); + FacetCategory B = new FacetCategory("b_cat", "B", "", List.of()); + FacetCategory C = new FacetCategory("c_cat", "C", "", List.of()); + List stored = List.of(B, A, C); + Mockito.when(repository.getFacets(filter)).thenReturn(stored); + Map orders = new HashMap<>(); + orders.put("c_cat", "1"); + Mockito.when(repository.getFacetCategoryOrder(Mockito.anyList())).thenReturn(orders); + + List actual = subject.getFacets(filter); + + Assertions.assertEquals(List.of(C, A, B), actual); + } + + @Test + void shouldGetFacet() { + Optional expected = Optional.of(new Facet("n", "d", "", "", null, null, "c", Map.of("foo", "bar"))); + Mockito.when(repository.getFacet("c", "n")).thenReturn(expected); + Mockito.when(repository.getFacetMeta("c", "n")).thenReturn(Map.of("foo", "bar")); + + Optional actual = subject.facetDetails("c", "n"); + + Assertions.assertEquals(expected, actual); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/facet/FilterPreProcessorTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/facet/FilterPreProcessorTest.java new file mode 100644 index 000000000..2fa4ea1e5 --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/facet/FilterPreProcessorTest.java @@ -0,0 +1,65 @@ +package edu.harvard.dbmi.avillach.dictionary.facet; + +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.mockito.Mockito; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.core.MethodParameter; +import org.springframework.http.HttpInputMessage; +import org.springframework.test.context.ActiveProfiles; +import org.testcontainers.shaded.com.fasterxml.jackson.databind.type.SimpleType; + +import java.lang.reflect.Method; +import java.util.List; + +@SpringBootTest +@ActiveProfiles("test") +class FilterPreProcessorTest { + + @Autowired + private FilterPreProcessor subject; + + public class Foo { + public void bar() {} + } + + private static MethodParameter someParam; // you can't mock these + + @BeforeAll + static void init() throws NoSuchMethodException { + someParam = new MethodParameter(Foo.class.getMethod("bar"), -1); + } + + @Test + void shouldSortFilter() { + Filter filter = new Filter(List.of(new Facet("b", ""), new Facet("a", "")), "", List.of("c", "b", "a")); + Filter actual = (Filter) subject + .afterBodyRead(filter, Mockito.mock(HttpInputMessage.class), someParam, SimpleType.constructUnsafe(Filter.class), null); + + Filter expected = new Filter(List.of(new Facet("a", ""), new Facet("b", "")), "", List.of("a", "b", "c")); + Assertions.assertEquals(expected, actual); + + } + + @Test + void shouldProcessFilter() { + Object processedFilter = subject.afterBodyRead( + new Filter(List.of(), "I_love_underscores", List.of()), Mockito.mock(HttpInputMessage.class), someParam, + SimpleType.constructUnsafe(Filter.class), null + ); + + Assertions.assertEquals(new Filter(List.of(), "I love underscores", List.of()), processedFilter); + } + + @Test + void shouldNotProcessOtherBodies() { + Object actual = subject.afterBodyRead( + "I'm an object!", Mockito.mock(HttpInputMessage.class), someParam, SimpleType.constructUnsafe(Filter.class), null + ); + + Assertions.assertEquals("I'm an object!", actual); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/filter/ConceptFilterQueryGeneratorTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/filter/ConceptFilterQueryGeneratorTest.java new file mode 100644 index 000000000..a1eb90fad --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/filter/ConceptFilterQueryGeneratorTest.java @@ -0,0 +1,212 @@ +package edu.harvard.dbmi.avillach.dictionary.filter; + +import edu.harvard.dbmi.avillach.dictionary.concept.ConceptFilterQueryGenerator; +import edu.harvard.dbmi.avillach.dictionary.facet.Facet; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.data.domain.Pageable; +import org.springframework.jdbc.core.JdbcTemplate; +import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.testcontainers.containers.PostgreSQLContainer; +import org.testcontainers.junit.jupiter.Container; +import org.testcontainers.junit.jupiter.Testcontainers; +import org.testcontainers.utility.MountableFile; + +import java.util.List; + +@Testcontainers +@SpringBootTest +class ConceptFilterQueryGeneratorTest { + + @Container + static final PostgreSQLContainer databaseContainer = new PostgreSQLContainer<>("postgres:16").withReuse(true) + .withCopyFileToContainer(MountableFile.forClasspathResource("seed.sql"), "/docker-entrypoint-initdb.d/seed.sql"); + + @DynamicPropertySource + static void mySQLProperties(DynamicPropertyRegistry registry) { + registry.add("spring.datasource.url", databaseContainer::getJdbcUrl); + registry.add("spring.datasource.username", databaseContainer::getUsername); + registry.add("spring.datasource.password", databaseContainer::getPassword); + registry.add("spring.datasource.db", databaseContainer::getDatabaseName); + } + + @Autowired + ConceptFilterQueryGenerator subject; + + @Autowired + NamedParameterJdbcTemplate template; + + @Test + void shouldSortValueMatchesAboveSearchMatches() { + Filter filter = new Filter(List.of(), "origin", List.of()); + QueryParamPair pair = subject.generateFilterQuery(filter, Pageable.unpaged()); + String query = "WITH " + pair.query() + "\n SELECT concept_node_id FROM concepts_filtered_sorted;"; + + List actual = template.queryForList(query, pair.params(), Integer.class); + + Assertions.assertEquals(List.of(271, 270), actual); + } + + @Test + void shouldFindValuesNotInSearchString() { + Filter filter = new Filter(List.of(), "gremlin", List.of()); + QueryParamPair pair = subject.generateFilterQuery(filter, Pageable.unpaged()); + String query = "WITH " + pair.query() + "\n SELECT concept_node_id FROM concepts_filtered_sorted;"; + + List actual = template.queryForList(query, pair.params(), Integer.class); + + Assertions.assertEquals(List.of(271), actual); + } + + @Test + void shouldPutStigvarsLastForEmptySearch() { + Filter filter = new Filter(List.of(), "", List.of()); + QueryParamPair pair = subject.generateFilterQuery(filter, Pageable.unpaged()); + String query = "WITH " + pair.query() + "\n SELECT concept_node_id FROM concepts_filtered_sorted;"; + + List actual = template.queryForList(query, pair.params(), Integer.class); + + Assertions.assertEquals(246, actual.getLast()); + } + + @Test + void shouldGenerateForHarmonizedConsents() { + Filter filter = new Filter(List.of(), "", List.of("phs001963.c1")); + QueryParamPair pair = subject.generateFilterQuery(filter, Pageable.unpaged()); + String query = "WITH " + pair.query() + "\n SELECT concept_node_id FROM concepts_filtered_sorted;"; + + List actual = template.queryForList(query, pair.params(), Integer.class); + List expected = List.of(270, 271); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldHandleMultiWordSearch() { + Filter filter = new Filter(List.of(), "respiratory diseases", List.of()); + QueryParamPair pair = subject.generateFilterQuery(filter, Pageable.unpaged()); + String query = "WITH " + pair.query() + "\n SELECT concept_node_id FROM concepts_filtered_sorted;"; + + List actual = template.queryForList(query, pair.params(), Integer.class); + + Assertions.assertFalse(actual.isEmpty(), "Multi-word search should return results"); + } + + @Test + void shouldHandleSingleWordSearch() { + Filter filter = new Filter(List.of(), "asthma", List.of()); + QueryParamPair pair = subject.generateFilterQuery(filter, Pageable.unpaged()); + String query = "WITH " + pair.query() + "\n SELECT concept_node_id FROM concepts_filtered_sorted;"; + + List actual = template.queryForList(query, pair.params(), Integer.class); + + Assertions.assertFalse(actual.isEmpty(), "Single-word search should return results"); + } + + @Test + void shouldHandleSearchWithExtraSpaces() { + Filter filter = new Filter(List.of(), " respiratory diseases ", List.of()); + QueryParamPair pair = subject.generateFilterQuery(filter, Pageable.unpaged()); + String query = "WITH " + pair.query() + "\n SELECT concept_node_id FROM concepts_filtered_sorted;"; + + List actual = template.queryForList(query, pair.params(), Integer.class); + + Assertions.assertFalse(actual.isEmpty(), "Search with extra spaces should return results"); + } + + @Test + void shouldGenerateForFacetAndSearchNoMatch() { + Filter f = + new Filter(List.of(new Facet("phs000007", "FHS", "", "", null, null, "study_ids_dataset_ids", null)), "smoke", List.of()); + QueryParamPair pair = subject.generateFilterQuery(f, Pageable.unpaged()); + String query = "WITH " + pair.query() + "\n SELECT concept_node_id FROM concepts_filtered_sorted;"; + + List actual = template.queryForList(query, pair.params(), Integer.class); + List expected = List.of(); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldGenerateForFHSFacet() { + Filter f = new Filter(List.of(new Facet("phs000007", "FHS", "", "", null, null, "study_ids_dataset_ids", null)), "", List.of()); + QueryParamPair pair = subject.generateFilterQuery(f, Pageable.unpaged()); + String query = "WITH " + pair.query() + "\n SELECT concept_node_id FROM concepts_filtered_sorted;"; + + List actual = template.queryForList(query, pair.params(), Integer.class); + List expected = List.of(229, 232, 235); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldGenerateForFHSFacetWithConsent1() { + Filter f = new Filter( + List.of(new Facet("phs000007", "FHS", "", "", null, null, "study_ids_dataset_ids", null)), "", List.of("phs000007.c1") + ); + QueryParamPair pair = subject.generateFilterQuery(f, Pageable.unpaged()); + String query = "WITH " + pair.query() + "\n SELECT concept_node_id FROM concepts_filtered_sorted;"; + + List actual = template.queryForList(query, pair.params(), Integer.class); + List expected = List.of(229, 232, 235); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldGenerateForFHSFacetWithConsent1And2() { + Filter f = new Filter( + List.of(new Facet("phs000007", "FHS", "", "", null, null, "study_ids_dataset_ids", null)), "", + List.of("phs000007.c1", "phs000007.c2") + ); + QueryParamPair pair = subject.generateFilterQuery(f, Pageable.unpaged()); + String query = "WITH " + pair.query() + "\n SELECT concept_node_id FROM concepts_filtered_sorted;"; + + List actual = template.queryForList(query, pair.params(), Integer.class); + List expected = List.of(229, 232, 235); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldGenerateForFHSFacetWithConsent3() { + Filter f = + new Filter(List.of(new Facet("phs000007", "FHS", "", "", null, null, "study_ids_dataset_ids", null)), "", List.of("dne.c3")); + QueryParamPair pair = subject.generateFilterQuery(f, Pageable.unpaged()); + String query = "WITH " + pair.query() + "\n SELECT concept_node_id FROM concepts_filtered_sorted;"; + + List actual = template.queryForList(query, pair.params(), Integer.class); + List expected = List.of(); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldGenerateForFacetAndSearchMatch() { + Filter f = + new Filter(List.of(new Facet("phs002715", "NSRR", "", "", null, null, "study_ids_dataset_ids", null)), "smoke", List.of()); + QueryParamPair pair = subject.generateFilterQuery(f, Pageable.unpaged()); + String query = "WITH " + pair.query() + "\n SELECT concept_node_id FROM concepts_filtered_sorted;"; + + List actual = template.queryForList(query, pair.params(), Integer.class); + List expected = List.of(249); + + Assertions.assertEquals(expected, actual); + } + + @Test + void shouldGenerateForNSRRFacet() { + Filter f = new Filter(List.of(new Facet("phs002715", "NSRR", "", "", null, null, "study_ids_dataset_ids", null)), "", List.of()); + QueryParamPair pair = subject.generateFilterQuery(f, Pageable.unpaged()); + String query = "WITH " + pair.query() + "\n SELECT concept_node_id FROM concepts_filtered_sorted;"; + + List actual = template.queryForList(query, pair.params(), Integer.class); + List expected = List.of(248, 249); + + Assertions.assertEquals(expected, actual); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/filter/FilterProcessorTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/filter/FilterProcessorTest.java new file mode 100644 index 000000000..24d71023c --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/filter/FilterProcessorTest.java @@ -0,0 +1,66 @@ +package edu.harvard.dbmi.avillach.dictionary.filter; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +class FilterProcessorTest { + + @Test + void shouldReturnNullForNullInput() { + Assertions.assertNull(FilterProcessor.sanitizeSearch(null)); + } + + @Test + void shouldReturnEmptyForEmptyInput() { + Assertions.assertEquals("", FilterProcessor.sanitizeSearch("")); + } + + @Test + void shouldReturnEmptyForWhitespaceOnly() { + Assertions.assertEquals("", FilterProcessor.sanitizeSearch(" ")); + } + + @Test + void shouldStripTsqueryOperators() { + Assertions.assertEquals("", FilterProcessor.sanitizeSearch("&")); + Assertions.assertEquals("", FilterProcessor.sanitizeSearch("|")); + Assertions.assertEquals("", FilterProcessor.sanitizeSearch("!")); + Assertions.assertEquals("", FilterProcessor.sanitizeSearch(":*")); + Assertions.assertEquals("", FilterProcessor.sanitizeSearch("()")); + Assertions.assertEquals("", FilterProcessor.sanitizeSearch("!@#$%")); + } + + @Test + void shouldPreserveAlphanumericWords() { + Assertions.assertEquals("Asthma", FilterProcessor.sanitizeSearch("Asthma")); + Assertions.assertEquals("ear infection", FilterProcessor.sanitizeSearch("ear infection")); + Assertions.assertEquals("HbA1c", FilterProcessor.sanitizeSearch("HbA1c")); + } + + @Test + void shouldStripSpecialCharsAndPreserveWords() { + Assertions.assertEquals("blood pressure", FilterProcessor.sanitizeSearch("blood & pressure")); + Assertions.assertEquals("C reactive protein", FilterProcessor.sanitizeSearch("C-reactive protein")); + Assertions.assertEquals("BMI 30", FilterProcessor.sanitizeSearch("BMI > 30")); + } + + @Test + void shouldTrimAndCollapseWhitespace() { + Assertions.assertEquals("Asthma", FilterProcessor.sanitizeSearch(" Asthma ")); + Assertions.assertEquals("ear infection", FilterProcessor.sanitizeSearch(" ear infection ")); + } + + @Test + void shouldPreserveUnicodeLetters() { + Assertions.assertEquals("café", FilterProcessor.sanitizeSearch("café")); + Assertions.assertEquals("naïve", FilterProcessor.sanitizeSearch("naïve")); + Assertions.assertEquals("señor", FilterProcessor.sanitizeSearch("señor")); + } + + @Test + void shouldCapLongSearchStrings() { + String longSearch = "a".repeat(300); + String result = FilterProcessor.sanitizeSearch(longSearch); + Assertions.assertEquals(200, result.length()); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/info/InfoControllerTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/info/InfoControllerTest.java new file mode 100644 index 000000000..53345a167 --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/info/InfoControllerTest.java @@ -0,0 +1,29 @@ +package edu.harvard.dbmi.avillach.dictionary.info; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.ActiveProfiles; + +import java.util.List; +import java.util.UUID; + + +@SpringBootTest +@ActiveProfiles("test") +class InfoControllerTest { + + @Autowired + InfoController infoController; + + @Test + void shouldGetInfo() { + ResponseEntity actual = infoController.getInfo(new Object()); + + Assertions.assertEquals(HttpStatus.OK, actual.getStatusCode()); + Assertions.assertEquals(new InfoResponse(UUID.nameUUIDFromBytes(":)".getBytes()), ":)", List.of()), actual.getBody()); + } +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchControllerIntegrationTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchControllerIntegrationTest.java new file mode 100644 index 000000000..b93968486 --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchControllerIntegrationTest.java @@ -0,0 +1,91 @@ +package edu.harvard.dbmi.avillach.dictionary.legacysearch; + +import edu.harvard.dbmi.avillach.dictionary.legacysearch.model.LegacyResponse; +import edu.harvard.dbmi.avillach.dictionary.legacysearch.model.Results; +import edu.harvard.dbmi.avillach.dictionary.legacysearch.model.SearchResult; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.HttpStatus; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.testcontainers.containers.PostgreSQLContainer; +import org.testcontainers.junit.jupiter.Container; +import org.testcontainers.junit.jupiter.Testcontainers; +import org.testcontainers.utility.MountableFile; + +import java.io.IOException; +import java.util.List; + +@SpringBootTest +@Testcontainers +class LegacySearchControllerIntegrationTest { + + @Autowired + LegacySearchController legacySearchController; + + @Container + static final PostgreSQLContainer databaseContainer = new PostgreSQLContainer<>("postgres:16").withReuse(true) + .withCopyFileToContainer(MountableFile.forClasspathResource("seed.sql"), "/docker-entrypoint-initdb.d/seed.sql"); + + @DynamicPropertySource + static void mySQLProperties(DynamicPropertyRegistry registry) { + registry.add("spring.datasource.url", databaseContainer::getJdbcUrl); + registry.add("spring.datasource.username", databaseContainer::getUsername); + registry.add("spring.datasource.password", databaseContainer::getPassword); + registry.add("spring.datasource.db", databaseContainer::getDatabaseName); + } + + @Test + void shouldGetLegacyResponseByStudyID() throws IOException { + String jsonString = """ + {"query":{"searchTerm":"phs000007","includedTags":[],"excludedTags":[],"returnTags":"true","offset":0,"limit":100}} + """; + + ResponseEntity legacyResponseResponseEntity = legacySearchController.legacySearch(jsonString); + System.out.println(legacyResponseResponseEntity); + Assertions.assertEquals(HttpStatus.OK, legacyResponseResponseEntity.getStatusCode()); + LegacyResponse legacyResponseBody = legacyResponseResponseEntity.getBody(); + Assertions.assertNotNull(legacyResponseBody); + Results results = legacyResponseBody.results(); + List searchResults = results.searchResults(); + searchResults.forEach(searchResult -> Assertions.assertEquals("phs000007", searchResult.result().studyId())); + } + + @Test + void shouldHandleORRequest() throws IOException { + String jsonString = """ + {"query":{"searchTerm":"age","includedTags":[],"excludedTags":[],"returnTags":"true","offset":0,"limit":100}} + """; + + ResponseEntity legacyResponseResponseEntity = legacySearchController.legacySearch(jsonString); + Assertions.assertEquals(HttpStatus.OK, legacyResponseResponseEntity.getStatusCode()); + LegacyResponse legacyResponseBody = legacyResponseResponseEntity.getBody(); + Assertions.assertNotNull(legacyResponseBody); + Results results = legacyResponseBody.results(); + List ageSearchResults = results.searchResults(); + Assertions.assertEquals(4, ageSearchResults.size()); + + jsonString = """ + {"query":{"searchTerm":"physical|age","includedTags":[],"excludedTags":[],"returnTags":"true","offset":0,"limit":100}} + """; + + legacyResponseResponseEntity = legacySearchController.legacySearch(jsonString); + Assertions.assertEquals(HttpStatus.OK, legacyResponseResponseEntity.getStatusCode()); + legacyResponseBody = legacyResponseResponseEntity.getBody(); + Assertions.assertNotNull(legacyResponseBody); + results = legacyResponseBody.results(); + List physicalORAgeSearchResults = results.searchResults(); + Assertions.assertEquals(5, physicalORAgeSearchResults.size()); + + // Verify that age|physical has expanded the search results + Assertions.assertNotEquals(ageSearchResults.size(), physicalORAgeSearchResults.size()); + + // Verify the OR statement has more results + Assertions.assertTrue(ageSearchResults.size() < physicalORAgeSearchResults.size()); + } + + +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchQueryMapperTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchQueryMapperTest.java new file mode 100644 index 000000000..6c8cfa27c --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchQueryMapperTest.java @@ -0,0 +1,78 @@ +package edu.harvard.dbmi.avillach.dictionary.legacysearch; + +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import edu.harvard.dbmi.avillach.dictionary.legacysearch.model.LegacySearchQuery; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.data.domain.Pageable; +import org.springframework.test.context.ActiveProfiles; + +import java.io.IOException; + +@SpringBootTest +@ActiveProfiles("test") +class LegacySearchQueryMapperTest { + + @Autowired + LegacySearchQueryMapper legacySearchQueryMapper; + + @Test + void shouldParseSearchRequest() throws IOException { + String jsonString = """ + {"query":{"searchTerm":"age","includedTags":[],"excludedTags":[],"returnTags":"true","offset":0,"limit":100}} + """; + + LegacySearchQuery legacySearchQuery = legacySearchQueryMapper.mapFromJson(jsonString); + Filter filter = legacySearchQuery.filter(); + Pageable pageable = legacySearchQuery.pageable(); + + Assertions.assertEquals("age:*", filter.search()); + Assertions.assertEquals(100, pageable.getPageSize()); + } + + @Test + void shouldHandlePunct() throws IOException { + String jsonString = + """ + {"query":{"searchTerm":"tutorial-biolincc_digitalis","includedTags":[],"excludedTags":[],"returnTags":"true","offset":0,"limit":100}} + """; + + LegacySearchQuery legacySearchQuery = legacySearchQueryMapper.mapFromJson(jsonString); + Filter filter = legacySearchQuery.filter(); + Pageable pageable = legacySearchQuery.pageable(); + + Assertions.assertEquals("tutorial:* & biolincc:* & digitalis:*", filter.search()); + Assertions.assertEquals(100, pageable.getPageSize()); + } + + @Test + void shouldHandleOR() throws IOException { + String jsonString = """ + {"query":{"searchTerm":"sex|gender","includedTags":[],"excludedTags":[],"returnTags":"true","offset":0,"limit":100}} + """; + + LegacySearchQuery legacySearchQuery = legacySearchQueryMapper.mapFromJson(jsonString); + Filter filter = legacySearchQuery.filter(); + Pageable pageable = legacySearchQuery.pageable(); + + Assertions.assertEquals("sex:* | gender:*", filter.search()); + Assertions.assertEquals(100, pageable.getPageSize()); + } + + @Test + void shouldHandleORAndPunct() throws IOException { + String jsonString = """ + {"query":{"searchTerm":"sex|gender age","includedTags":[],"excludedTags":[],"returnTags":"true","offset":0,"limit":100}} + """; + + LegacySearchQuery legacySearchQuery = legacySearchQueryMapper.mapFromJson(jsonString); + Filter filter = legacySearchQuery.filter(); + Pageable pageable = legacySearchQuery.pageable(); + + Assertions.assertEquals("sex:* | gender:* & age:*", filter.search()); + Assertions.assertEquals(100, pageable.getPageSize()); + } + +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchRepositoryTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchRepositoryTest.java new file mode 100644 index 000000000..a871b525a --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchRepositoryTest.java @@ -0,0 +1,76 @@ +package edu.harvard.dbmi.avillach.dictionary.legacysearch; + +import edu.harvard.dbmi.avillach.dictionary.concept.ConceptRepository; +import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept; +import edu.harvard.dbmi.avillach.dictionary.filter.Filter; +import edu.harvard.dbmi.avillach.dictionary.legacysearch.model.SearchResult; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.data.domain.Pageable; +import org.springframework.test.context.DynamicPropertyRegistry; +import org.springframework.test.context.DynamicPropertySource; +import org.testcontainers.containers.PostgreSQLContainer; +import org.testcontainers.junit.jupiter.Container; +import org.testcontainers.junit.jupiter.Testcontainers; +import org.testcontainers.utility.MountableFile; + +import java.util.List; + +@SpringBootTest +@Testcontainers +public class LegacySearchRepositoryTest { + + @Autowired + LegacySearchRepository subject; + + @Autowired + ConceptRepository conceptService; + + @Container + static final PostgreSQLContainer databaseContainer = new PostgreSQLContainer<>("postgres:16").withReuse(true) + .withCopyFileToContainer(MountableFile.forClasspathResource("seed.sql"), "/docker-entrypoint-initdb.d/seed.sql"); + + @DynamicPropertySource + static void mySQLProperties(DynamicPropertyRegistry registry) { + registry.add("spring.datasource.url", databaseContainer::getJdbcUrl); + registry.add("spring.datasource.username", databaseContainer::getUsername); + registry.add("spring.datasource.password", databaseContainer::getPassword); + registry.add("spring.datasource.db", databaseContainer::getDatabaseName); + } + + @Test + void shouldGetLegacySearchResults() { + List searchResults = subject.getLegacySearchResults(new Filter(List.of(), "", List.of()), Pageable.unpaged()); + + Assertions.assertEquals(31, searchResults.size()); + } + + @Test + void shouldGetLegacySearchResultsBySearch() { + List searchResults = + subject.getLegacySearchResults(new Filter(List.of(), "phs000007", List.of()), Pageable.unpaged()); + + searchResults.forEach(searchResult -> Assertions.assertEquals("phs000007", searchResult.result().studyId())); + + } + + @Test + void shouldGetLegacySearchResultsByPageSize() { + List searchResults = subject.getLegacySearchResults(new Filter(List.of(), "", List.of()), Pageable.ofSize(5)); + + Assertions.assertEquals(5, searchResults.size()); + } + + @Test + void legacySearchResultShouldGetEqualCountToConceptSearch() { + // This test will ensure modifications made to the conceptSearch will be reflected in the legacy search result. + // They use near equivalent queries and updates made to one should be made to the other. + List searchResults = subject.getLegacySearchResults(new Filter(List.of(), "", List.of()), Pageable.unpaged()); + List concepts = conceptService.getConcepts(new Filter(List.of(), "", List.of()), Pageable.unpaged()); + + Assertions.assertEquals(searchResults.size(), concepts.size()); + } + +} diff --git a/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/util/JsonBlobParserTest.java b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/util/JsonBlobParserTest.java new file mode 100644 index 000000000..27c4ef7cc --- /dev/null +++ b/services/picsure-dictionary/src/test/java/edu/harvard/dbmi/avillach/dictionary/util/JsonBlobParserTest.java @@ -0,0 +1,27 @@ +package edu.harvard.dbmi.avillach.dictionary.util; + +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.ActiveProfiles; + +import static org.junit.jupiter.api.Assertions.*; + +@SpringBootTest +@ActiveProfiles("test") +class JsonBlobParserTest { + + @Autowired + private JsonBlobParser jsonBlobParser; + + @Test + void parseValues() { + Double v = jsonBlobParser.parseFromIndex("[-1.0,4.9E-324]", 1); + assertNotNull(v); + assertEquals(4.9E-324, v); + + v = jsonBlobParser.parseFromIndex("[-1.0,4.9E-324]", 0); + assertNotNull(v); + assertEquals(-1, v); + } +} diff --git a/services/picsure-dictionary/src/test/resources/application.properties b/services/picsure-dictionary/src/test/resources/application.properties new file mode 100644 index 000000000..ecff7de0d --- /dev/null +++ b/services/picsure-dictionary/src/test/resources/application.properties @@ -0,0 +1,22 @@ +spring.application.name=dictionary +spring.flyway.enabled=false +spring.datasource.url=jdbc:postgresql://localhost:5432/search +spring.datasource.username=picsure +spring.datasource.password=foo +spring.datasource.driver-class-name=org.postgresql.Driver + +dashboard.columns={abbreviation:'Abbreviation',melast:'This one goes last',name:'Name',clinvars:'Clinical Variables',participants:'Participants'} +dashboard.column-order=abbreviation,name,clinvars +dashboard.nonmeta-columns=abbreviation,name +dashboard.enable.extra_details=true +dashboard.enable.bdc_hack=false +dashboard.layout.type=default + +filtering.unfilterable_concepts=stigmatized + +metadata.no_show_list=values,stigmatized + +remote.dictionaries[0].name=bch +remote.dictionaries[0].full_name=Boston Children's +remote.dictionaries[1].name=foo +remote.dictionaries[1].full_name=Foo Made Up Hospital diff --git a/services/picsure-dictionary/src/test/resources/seed.sql b/services/picsure-dictionary/src/test/resources/seed.sql new file mode 100644 index 000000000..08c260f8f --- /dev/null +++ b/services/picsure-dictionary/src/test/resources/seed.sql @@ -0,0 +1,1150 @@ +-- +-- PostgreSQL database dump +-- + +-- Dumped from database version 16.3 +-- Dumped by pg_dump version 16.3 + +SET statement_timeout = 0; +SET lock_timeout = 0; +SET idle_in_transaction_session_timeout = 0; +SET client_encoding = 'UTF8'; +SET standard_conforming_strings = on; +SELECT pg_catalog.set_config('search_path', '', false); +SET check_function_bodies = false; +SET xmloption = content; +SET client_min_messages = warning; +SET row_security = off; + +-- +-- Name: dict; Type: SCHEMA; Schema: -; Owner: picsure +-- + +CREATE SCHEMA dict; + +-- +-- Name: pg_trgm; Type: EXTENSION; Schema: -; Owner: - +-- + +CREATE EXTENSION IF NOT EXISTS pg_trgm WITH SCHEMA public; + + +-- +-- Name: EXTENSION pg_trgm; Type: COMMENT; Schema: -; Owner: +-- + +COMMENT ON EXTENSION pg_trgm IS 'text similarity measurement and index searching based on trigrams'; + + +SET default_tablespace = ''; + +SET default_table_access_method = heap; + +-- +-- Name: concept_node; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.concept_node ( + concept_node_id integer NOT NULL, + dataset_id integer NOT NULL, + name character varying(512) NOT NULL, + display character varying(512) NOT NULL, + concept_type character varying(32) DEFAULT 'Interior'::character varying NOT NULL, + concept_path character varying(10000) DEFAULT 'INVALID'::character varying NOT NULL, + parent_id integer, + searchable_fields tsvector, + is_queryable boolean NOT NULL DEFAULT FALSE +); + +-- +-- Name: concept_node_concept_node_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.concept_node ALTER COLUMN concept_node_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.concept_node_concept_node_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +-- +-- Name: concept_node_meta; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.concept_node_meta ( + concept_node_meta_id integer NOT NULL, + concept_node_id integer NOT NULL, + key character varying(256) NOT NULL, + value text NOT NULL +); + +-- +-- Name: concept_node_meta_concept_node_meta_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.concept_node_meta ALTER COLUMN concept_node_meta_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.concept_node_meta_concept_node_meta_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +-- +-- Name: consent; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.consent ( + consent_id integer NOT NULL, + dataset_id integer NOT NULL, + consent_code character varying(512) NOT NULL, + description character varying(512) NOT NULL, + authz character varying(512) NOT NULL, + PARTICIPANT_COUNT INT NOT NULL DEFAULT 12, + VARIABLE_COUNT INT NOT NULL DEFAULT 99, + SAMPLE_COUNT INT NOT NULL DEFAULT 14 +); + +-- +-- Name: consent_consent_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.consent ALTER COLUMN consent_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.consent_consent_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +-- +-- Name: dataset; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.dataset ( + dataset_id integer NOT NULL, + ref character varying(512) NOT NULL, + full_name character varying(512) NOT NULL, + abbreviation character varying(512) NOT NULL, + description text DEFAULT ''::text +); + +-- +-- Name: dataset_dataset_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.dataset ALTER COLUMN dataset_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.dataset_dataset_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +-- +-- Name: dataset_meta; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.dataset_meta ( + dataset_meta_id integer NOT NULL, + dataset_id integer NOT NULL, + key character varying(256) NOT NULL, + value text NOT NULL +); + +-- +-- Name: dataset_meta_dataset_meta_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.dataset_meta ALTER COLUMN dataset_meta_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.dataset_meta_dataset_meta_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +-- +-- Name: facet; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.facet ( + facet_id integer NOT NULL, + facet_category_id integer NOT NULL, + name character varying(512) NOT NULL, + display character varying(512) NOT NULL, + description text DEFAULT ''::text, + parent_id integer +); + +-- +-- Name: facet__concept_node; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.facet__concept_node ( + facet__concept_node_id integer NOT NULL, + facet_id integer NOT NULL, + concept_node_id integer NOT NULL, + is_queryable boolean NOT NULL DEFAULT FALSE +); + +-- +-- Name: facet__concept_node_facet__concept_node_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.facet__concept_node ALTER COLUMN facet__concept_node_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.facet__concept_node_facet__concept_node_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +-- +-- Name: facet_category; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.facet_category ( + facet_category_id integer NOT NULL, + name character varying(512) NOT NULL, + display character varying(512) NOT NULL, + description text DEFAULT ''::text +); + +-- +-- Name: facet_category_facet_category_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.facet_category ALTER COLUMN facet_category_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.facet_category_facet_category_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +-- +-- Name: facet_category_meta; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.facet_category_meta ( + facet_category_meta_id integer NOT NULL, + facet_category_id integer NOT NULL, + key character varying(256) NOT NULL, + value text NOT NULL +); + +-- +-- Name: facet_category_meta_facet_category_meta_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.facet_category_meta ALTER COLUMN facet_category_meta_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.facet_category_meta_facet_category_meta_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +-- +-- Name: facet_facet_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.facet ALTER COLUMN facet_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.facet_facet_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +-- +-- Name: facet_meta; Type: TABLE; Schema: dict; Owner: picsure +-- + +CREATE TABLE public.facet_meta ( + facet_meta_id integer NOT NULL, + facet_id integer NOT NULL, + key character varying(256) NOT NULL, + value text NOT NULL +); + +-- +-- Name: facet_meta_facet_meta_id_seq; Type: SEQUENCE; Schema: dict; Owner: picsure +-- + +ALTER TABLE public.facet_meta ALTER COLUMN facet_meta_id ADD GENERATED ALWAYS AS IDENTITY ( + SEQUENCE NAME public.facet_meta_facet_meta_id_seq + START WITH 1 + INCREMENT BY 1 + NO MINVALUE + NO MAXVALUE + CACHE 1 +); + + +CREATE TABLE IF NOT EXISTS public.update_info ( + LAST_UPDATED TIMESTAMP NOT NULL DEFAULT '2000-01-01 00:00:00', + DATABASE_VERSION INT NOT NULL DEFAULT 3 +); + +CREATE TABLE IF NOT EXISTS public.remote_dictionary ( + REMOTE_DICTIONARY_ID SERIAL PRIMARY KEY, + NAME CHARACTER VARYING(512) NOT NULL, + UUID UUID NOT NULL, + LAST_UPDATED TIMESTAMP +); + + +-- +-- Data for Name: concept_node; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.concept_node (concept_node_id, dataset_id, name, display, concept_type, concept_path, parent_id, searchable_fields) FROM stdin; +209 14 categorical \\Bio Specimens\\ \N 'bio':1 'specimen':2 +180 14 categorical \\ACT Diagnosis ICD-10\\ \N '-10':4 'act':1 'diagnosi':2 'icd':3 +191 14 categorical \\ACT Lab Test Results\\ \N 'act':1 'lab':2 'result':4 'test':3 +197 14 categorical \\ACT Medications\\ \N 'act':1 'medic':2 +202 14 categorical \\ACT Procedures CPT\\ \N 'act':1 'cpt':3 'procedur':2 +215 14 categorical \\Consent Type\\ \N 'consent':1 'type':2 +219 15 categorical \\NHANES\\ \N 'nhane':1 +226 19 categorical \\phs000007\\ \N 'phs000007':1 +236 18 categorical \\phs000284\\ \N 'phs000284':1 +243 20 categorical \\phs002385\\ \N 'phs002385':1 +247 17 \\phs002715\\ \N 'phs002715':1 +250 23 categorical \\phs002808\\ \N 'phs002808':1 +259 21 categorical \\phs003463\\ \N 'phs003463':1 +262 24 categorical \\phs003566\\ \N 'phs003566':1 +265 14 categorical \\Variant Data Type\\ \N 'data':2 'type':3 'variant':1 +181 14 categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\ 180 '-10':4 'act':1 'diagnosi':2 'diseas':8 'icd':3 'j00':6,14 'j00-j99':5,13 'j99':7,15 'respiratori':11 'system':12 +182 14 categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\ 181 '-10':4 'act':1 'chronic':19 'diagnosi':2 'diseas':8,22 'icd':3 'j00':6,14 'j00-j99':5,13 'j40':17,24 'j40-j47':16,23 'j47':18,25 'j99':7,15 'lower':20 'respiratori':11,21 'system':12 +183 14 categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\ 182 '-10':4 'act':1 'asthma':27 'chronic':19 'diagnosi':2 'diseas':8,22 'icd':3 'j00':6,14 'j00-j99':5,13 'j40':17,24 'j40-j47':16,23 'j45':26 'j47':18,25 'j99':7,15 'lower':20 'respiratori':11,21 'system':12 +184 14 categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.5 Severe persistent asthma\\ 183 '-10':4 'act':1 'asthma':27,31 'chronic':19 'diagnosi':2 'diseas':8,22 'icd':3 'j00':6,14 'j00-j99':5,13 'j40':17,24 'j40-j47':16,23 'j45':26 'j45.5':28 'j47':18,25 'j99':7,15 'lower':20 'persist':30 'respiratori':11,21 'sever':29 'system':12 +223 15 categorical \\NHANES\\questionnaire\\ 219 'nhane':1 'questionnair':2 +263 24 Visit01 Visit01 categorical \\phs003566\\Visit01\\ 262 'phs003566':1 'visit01':2,3 +185 14 J45.51 Severe persistent asthma with (acute) exacerbation J45.51 Severe persistent asthma with (acute) exacerbation categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.5 Severe persistent asthma\\J45.51 Severe persistent asthma with (acute) exacerbation\\ 184 '-10':4 'act':1 'acut':37,44 'asthma':27,31,35,42 'chronic':19 'diagnosi':2 'diseas':8,22 'exacerb':38,45 'icd':3 'j00':6,14 'j00-j99':5,13 'j40':17,24 'j40-j47':16,23 'j45':26 'j45.5':28 'j45.51':32,39 'j47':18,25 'j99':7,15 'lower':20 'persist':30,34,41 'respiratori':11,21 'sever':29,33,40 'system':12 +186 14 J45.52 Severe persistent asthma with status asthmaticus J45.52 Severe persistent asthma with status asthmaticus categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.5 Severe persistent asthma\\J45.52 Severe persistent asthma with status asthmaticus\\ 184 '-10':4 'act':1 'allerg':50,57,72,81 'approxim':46 'asthma':27,31,35,42,51,58,64,70,79,89 'asthmaticus':38,45,54,61,67,76,85,92 'chronic':19 'diagnosi':2 'diseas':8,22 'icd':3 'j00':6,14 'j00-j99':5,13 'j40':17,24 'j40-j47':16,23 'j45':26 'j45.5':28 'j45.52':32,39,86 'j47':18,25 'j99':7,15 'lower':20 'persist':30,34,41,49,56,63,69,78,88 'respiratori':11,21 'rhiniti':73,82 'sever':29,33,40,48,55,62,68,77,87 'status':37,44,53,60,66,75,84,91 'synonym':47 'system':12 +187 14 categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.9 Other and unspecified asthma\\ 183 '-10':4 'act':1 'asthma':27,32 'chronic':19 'diagnosi':2 'diseas':8,22 'icd':3 'j00':6,14 'j00-j99':5,13 'j40':17,24 'j40-j47':16,23 'j45':26 'j45.9':28 'j47':18,25 'j99':7,15 'lower':20 'respiratori':11,21 'system':12 'unspecifi':31 +188 14 categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.9 Other and unspecified asthma\\J45.90 Unspecified asthma\\ 187 '-10':4 'act':1 'asthma':27,32,35 'chronic':19 'diagnosi':2 'diseas':8,22 'icd':3 'j00':6,14 'j00-j99':5,13 'j40':17,24 'j40-j47':16,23 'j45':26 'j45.9':28 'j45.90':33 'j47':18,25 'j99':7,15 'lower':20 'respiratori':11,21 'system':12 'unspecifi':31,34 +189 14 J45.901 Unspecified asthma with (acute) exacerbation J45.901 Unspecified asthma with (acute) exacerbation categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.9 Other and unspecified asthma\\J45.90 Unspecified asthma\\J45.901 Unspecified asthma with (acute) exacerbation\\ 188 '-10':4 'act':1 'acut':40,46,50,60,64,74,83 'allerg':55,57,71 'approxim':48 'asthma':27,32,35,38,44,53,58,62,69,78,81 'chronic':19 'diagnosi':2 'diseas':8,22 'exacerb':41,47,51,61,65,75,76,84 'flare':67 'flare-up':66 'icd':3 'j00':6,14 'j00-j99':5,13 'j40':17,24 'j40-j47':16,23 'j45':26 'j45.9':28 'j45.90':33 'j45.901':36,42,79 'j47':18,25 'j99':7,15 'lower':20 'respiratori':11,21 'rhiniti':56,72 'synonym':49 'system':12 'unspecifi':31,34,37,43,80 +231 19 categorical \\phs000007\\pht000022\\phv00004260\\ 230 'phs000007':1 'pht000022':2 'phv00004260':3 +232 19 phv00004260 FM219 Continuous \\phs000007\\pht000022\\phv00004260\\FM219\\ 231 '0':17 '1':18 '12':6 'caffein':10 'cola':11 'cup':8 'day':12 'fm219':4,5 'oz':7 'phs000007':1 'pht000022':2 'phv00004260':3 'yes':16 +190 14 J45.902 Unspecified asthma with status asthmaticus J45.902 Unspecified asthma with status asthmaticus categorical \\ACT Diagnosis ICD-10\\J00-J99 Diseases of the respiratory system (J00-J99)\\J40-J47 Chronic lower respiratory diseases (J40-J47)\\J45 Asthma\\J45.9 Other and unspecified asthma\\J45.90 Unspecified asthma\\J45.902 Unspecified asthma with status asthmaticus\\ 188 '-10':4 'act':1 'allerg':52,59,72 'approxim':48 'asthma':27,32,35,38,44,50,57,64,67,71,77,83 'asthmaticus':41,47,56,63,70,75,80,86 'chronic':19 'diagnosi':2 'diseas':8,22 'extrins':76 'icd':3 'j00':6,14 'j00-j99':5,13 'j40':17,24 'j40-j47':16,23 'j45':26 'j45.9':28 'j45.90':33 'j45.902':36,42,81 'j47':18,25 'j99':7,15 'lower':20 'respiratori':11,21 'rhiniti':53,60 'status':40,46,55,62,66,69,74,79,85 'synonym':49 'system':12 'unspecifi':31,34,37,43,82 +192 14 categorical \\ACT Lab Test Results\\Virus\\ 191 'act':1 'lab':2 'result':4 'test':3 'virus':5 +193 14 categorical \\ACT Lab Test Results\\Virus\\Hepatitis B virus\\ 192 'act':1 'b':7 'hepat':6 'lab':2 'result':4 'test':3 'virus':5,8 +194 14 categorical \\ACT Lab Test Results\\Virus\\Hepatitis B virus\\Hepatitis B virus core Ab\\ 193 'ab':13 'act':1 'b':7,10 'core':12 'hepat':6,9 'lab':2 'result':4 'test':3 'virus':5,8,11 +195 14 Hepatitis B virus core Ab Hepatitis B virus core Ab categorical \\ACT Lab Test Results\\Virus\\Hepatitis B virus\\Hepatitis B virus core Ab\\Hepatitis B virus core Ab [Presence] in Serum by Immunoassay\\ 194 'ab':13,18,28 'act':1 'b':7,10,15,25 'core':12,17,27 'hepat':6,9,14,24 'immunoassay':23 'lab':2 'presenc':19 'result':4 'serum':21 'test':3 'virus':5,8,11,16,26 +196 14 Hepatitis B virus core Ab Hepatitis B virus core Ab categorical \\ACT Lab Test Results\\Virus\\Hepatitis B virus\\Hepatitis B virus core Ab\\Hepatitis B virus core Ab [Presence] in Serum\\ 194 'ab':13,18,26 'act':1 'b':7,10,15,23 'core':12,17,25 'hepat':6,9,14,22 'lab':2 'presenc':19 'result':4 'serum':21 'test':3 'virus':5,8,11,16,24 +198 14 categorical \\ACT Medications\\C [Preparations]\\ 197 'act':1 'c':3 'medic':2 'prepar':4 +199 14 categorical \\ACT Medications\\C [Preparations]\\Cefpodoxime\\ 198 'act':1 'c':3 'cefpodoxim':5 'medic':2 'prepar':4 +200 14 categorical \\ACT Medications\\C [Preparations]\\Cefpodoxime\\Cefpodoxime Oral Tablet\\ 199 'act':1 'c':3 'cefpodoxim':5,6 'medic':2 'oral':7 'prepar':4 'tablet':8 +201 14 Cefpodoxime Oral Tablet Cefpodoxime Oral Tablet categorical \\ACT Medications\\C [Preparations]\\Cefpodoxime\\Cefpodoxime Oral Tablet\\Cefpodoxime 100 Mg Oral Tablet\\ 200 '100':10 'act':1 'c':3 'cefpodoxim':5,6,9,14 'medic':2 'mg':11 'oral':7,12,15 'prepar':4 'tablet':8,13,16 +203 14 categorical \\ACT Procedures CPT\\Medicine Services and Procedures\\ 202 'act':1 'cpt':3 'medicin':4 'procedur':2,7 'servic':5 +204 14 categorical \\ACT Procedures CPT\\Medicine Services and Procedures\\Neurology and Neuromuscular Procedures\\ 203 'act':1 'cpt':3 'medicin':4 'neurolog':8 'neuromuscular':10 'procedur':2,7,11 'servic':5 +241 18 phv00122507 age Continuous \\phs000284\\pht001902\\phv00122507\\age\\ 240 '0':11 '21':12 'age':4,5,6 'phs000284':1 'pht001902':2 'phv00122507':3 'yes':10 +205 14 categorical \\ACT Procedures CPT\\Medicine Services and Procedures\\Neurology and Neuromuscular Procedures\\Special Eeg Testing Procedures\\ 204 'act':1 'cpt':3 'eeg':13 'medicin':4 'neurolog':8 'neuromuscular':10 'procedur':2,7,11,15 'servic':5 'special':12 'test':14 +206 14 Special Eeg Testing Procedures Special Eeg Testing Procedures categorical \\ACT Procedures CPT\\Medicine Services and Procedures\\Neurology and Neuromuscular Procedures\\Special Eeg Testing Procedures\\Pharmacological or physical activation requiring physician or other qualified health care professional attendance during EEG recording of activation phase (eg, thiopental activation test)\\ 205 'act':1 'activ':19,33,37 'attend':28 'care':26 'cpt':3 'eeg':13,30,40 'eg':35 'health':25 'medicin':4 'neurolog':8 'neuromuscular':10 'pharmacolog':16 'phase':34 'physic':18 'physician':21 'procedur':2,7,11,15,42 'profession':27 'qualifi':24 'record':31 'requir':20 'servic':5 'special':12,39 'test':14,38,41 'thiopent':36 +207 14 Special Eeg Testing Procedures Special Eeg Testing Procedures categorical \\ACT Procedures CPT\\Medicine Services and Procedures\\Neurology and Neuromuscular Procedures\\Special Eeg Testing Procedures\\Wada activation test for hemispheric function, including electroencephalographic (EEG) monitoring\\ 205 'act':1 'activ':17 'cpt':3 'eeg':13,24,27 'electroencephalograph':23 'function':21 'hemispher':20 'includ':22 'medicin':4 'monitor':25 'neurolog':8 'neuromuscular':10 'procedur':2,7,11,15,29 'servic':5 'special':12,26 'test':14,18,28 'wada':16 +208 14 Medicine Services and Procedures Medicine Services and Procedures categorical \\ACT Procedures CPT\\Medicine Services and Procedures\\Non-Face-To-Face Nonphysician Services\\ 203 'act':1 'cpt':3 'face':10,12 'medicin':4,15 'non':9 'non-face-to-fac':8 'nonphysician':13 'procedur':2,7,18 'servic':5,14,16 +210 14 categorical \\Bio Specimens\\HumanFluid\\ 209 'bio':1 'humanfluid':3 'specimen':2 +211 14 SPECIMENS:HF.BLD.000 Quantity SPECIMENS:HF.BLD.000 Quantity Continuous \\Bio Specimens\\HumanFluid\\Blood (Whole)\\SPECIMENS:HF.BLD.000 Quantity\\ 210 '000':8,12 '100':18 '500':19 'bio':1 'biosampl':15,17 'blood':4 'gic':14 'hf.bld':7,11 'humanfluid':3 'quantiti':9,13 'specimen':2,6,10 'whole':5 'wholeblood':16 +212 14 HumanTissue HumanTissue categorical \\Bio Specimens\\HumanTissue\\ 212 'bio':1 'humantissu':3,4 'specimen':2 'true':5 +213 14 categorical \\Bio Specimens\\NucleicAcid\\ 209 'bio':1 'nucleicacid':3 'specimen':2 +214 14 DNA DNA categorical \\Bio Specimens\\NucleicAcid\\DNA\\ 213 'bio':1 'dna':4,5 'nucleicacid':3 'specimen':2 'true':6 +216 14 Consent Type Consent Type categorical \\Consent Type\\GIC Consent\\ 215 '2':15 'align':10 'consent':1,4,5,18 'gic':3,17 'irb':13 'patient':8 'phase':14 'protocol':16 'type':2,6 +217 14 Consent Type Consent Type categorical \\Consent Type\\GIC Legacy Consent\\ 215 '2':18 'align':13 'consent':1,5,6,22 'gic':3,20 'irb':16 'legaci':4,21 'patient':9 'phase':17 'protocol':19 'type':2,7 +218 14 Consent Type Consent Type categorical \\Consent Type\\Waiver of Consent\\ 215 'consent':1,5,6,12,15 'patient':8 'type':2,7 'waiv':11 'waiver':3,13 +220 15 categorical \\NHANES\\examination\\ 219 'examin':2 'nhane':1 +221 15 physical fitness physical fitness categorical \\NHANES\\examination\\physical fitness\\ 220 'examin':2 'fit':4,6 'nhane':1 'physic':3,5 +222 15 CVDS1HR Stage 1 heart rate (per min) Continuous \\NHANES\\examination\\physical fitness\\Stage 1 heart rate (per min) 221 '0':63 '1':6,12,50 '150':64 'autom':23 'automat':44 'blood':24 'captur':29,43 'comput':33 'direct':30 'end':47 'enter':55 'event':37 'examin':2 'fit':4 'heart':7,13,17,39,60 'manual':54 'min':10,16 'monitor':27,62 'nhane':1 'per':9,15 'physic':3 'pressure/heart':25 'rate':8,14,18,26,40,61 'read':57 'stage':5,11,49 'system':34 'taken':20 'technician':52 'would':53 +224 15 disease disease categorical \\NHANES\\questionnaire\\disease\\ 223 'diseas':3,4 'nhane':1 'questionnair':2 +225 15 MCQ300a Any family with heart attack or angina? categorical \\NHANES\\questionnaire\\disease\\Any family with heart attack or angina?\\ 224 '50':61 'age':59 'an-gi-na':53 'angina':10,17,52 'attack':8,15,50 'biolog':28 'blood':31 'brother':38 'close':27 'deceas':21 'diseas':3 'ever':39 'famili':5,12 'father':34 'gi':55 'health':43 'heart':7,14,49 'includ':18,33 'live':19 'mother':35 'na':56 'nhane':1 'profession':44 'questionnair':2 'relat':32 's/your':26 'sister':36 'sp':25 'told':40 'yes':62 +227 19 pht000021 ex0_19s categorical \\phs000007\\pht000021\\ 226 '19':10 '19s':4 'clinic':5 'cohort':8 'ex0':3 'exam':6,9 'origin':7 'phs000007':1 'pht000021':2 +228 19 categorical \\phs000007\\pht000021\\phv00003844\\ 227 'phs000007':1 'pht000021':2 'phv00003844':3 +229 19 phv00003844 FL200 Continuous \\phs000007\\pht000021\\phv00003844\\FL200\\ 228 '0':17 '12':6 '3':18 'caffein':10 'cola':11 'cup':8 'day':12 'fl200':4,5 'oz':7 'phs000007':1 'pht000021':2 'phv00003844':3 'yes':16 +230 19 pht000022 ex0_20s categorical \\phs000007\\pht000022\\ 226 '20':10 '20s':4 'clinic':5 'cohort':8 'ex0':3 'exam':6,9 'origin':7 'phs000007':1 'pht000022':2 +233 19 pht000033 ex1_4s categorical \\phs000007\\pht000033\\ 226 '4':10 '4s':4 'clinic':5 'cohort':8 'ex1':3 'exam':6,9 'offspr':7 'phs000007':1 'pht000033':2 +234 19 categorical \\phs000007\\pht000033\\phv00008849\\ 233 'phs000007':1 'pht000033':2 'phv00008849':3 +235 19 phv00008849 D080 Continuous \\phs000007\\pht000033\\phv00008849\\D080\\ 234 '0':16 '12':6 '5':17 'caffein':10 'cola/day':11 'cup':8 'd080':4,5 'oz':7 'phs000007':1 'pht000033':2 'phv00008849':3 'yes':15 +237 18 pht001902 CFS_CARe_Subject_Phenotypes categorical \\phs000284\\pht001902\\ 236 'adults/children':16 'care':4,7 'cfs':3,8 'cleveland':9 'famili':10 'health':14 'phenotyp':6,15 'phs000284':1 'pht001902':2 'sleep':12 'studi':11 'subject':5 +238 18 categorical \\phs000284\\pht001902\\phv00122360\\ 237 'phs000284':1 'pht001902':2 'phv00122360':3 +239 18 phv00122360 RECOCC categorical \\phs000284\\pht001902\\phv00122360\\RECOCC\\ 238 'account':10 'occup':8 'phs000284':1 'pht001902':2 'phv00122360':3 'recent':7 'recocc':4,5 +240 18 categorical \\phs000284\\pht001902\\phv00122507\\ 237 'phs000284':1 'pht001902':2 'phv00122507':3 +242 18 phv00122622 PERART Continuous \\phs000284\\pht001902\\phv00122622\\PERART\\ 242 '0':14 '30':15 'artifact':9 'perart':4,5 'phs000284':1 'pht001902':2 'phv00122622':3 'time':7 'yes':13 +244 20 AGE AGE continuous \\phs002385\\AGE\\ 243 '42':9 'age':2,3,5 'hct':16 'patient':4 'phs002385':1 'pre':15 'pre-hct':14 'transplant':7 'year':8 'yes':13,17 +245 20 RACEG RACEG categorical \\phs002385\\RACEG\\ 243 'phs002385':1 'race':4 'raceg':2,3 'regroup':5 'report':7 'yes':11 +246 20 TXNUM TXNUM continuous \\phs002385\\TXNUM\\ 243 '1':6 'hct':13 'number':5 'phs002385':1 'pre':12 'pre-hct':11 'transplant':4 'txnum':2,3 'yes':7,14 +248 17 AGE_CATEGORY age categorical \\phs002715\\age\\ 247 '21':8 'age':2,3,6 'categori':7 'particip':4 'phs002715':1 'yes':12 +249 17 nsrr_ever_smoker nsrr_ever_smoker categorical \\phs002715\\nsrr_ever_smoker\\ 247 'ever':3,6 'nsrr':2,5 'phs002715':1 'smoker':4,7,8 'status':9 'yes':10,14 +251 23 categorical \\phs002808\\1 Administrative Data Forms\\ 250 '1':2 'administr':3 'data':4 'form':5 'phs002808':1 +252 23 \\phs002808\\1 Administrative Data Forms\\AFC No Future Contact\\ 1 Administrative Data Forms / AFC No Future Contact categorical \\phs002808\\1 Administrative Data Forms\\AFC No Future Contact\\ 251 '1':2,10 'administr':3,11 'afc':6,14 'contact':9,17 'data':4,12 'form':5,13 'futur':8,16 'phs002808':1 +253 23 AFCA03A AFCA03A categorical \\phs002808\\1 Administrative Data Forms\\AFC No Future Contact\\AFCA03A\\ 252 '1':2 'administr':3 'afc':6,12 'afca03a':10,11 'consent':19 'contact':9,17,23 'data':4 'end':15 'form':5 'futur':8,16,21 'numom2b':22 'phs002808':1 'reason':13 'withdrew':18 'yes':27 +254 23 \\phs002808\\1 Administrative Data Forms\\H01 Heart Health Study Contact Information\\ 1 Administrative Data Forms / H01 Heart Health Study Contact Information categorical \\phs002808\\1 Administrative Data Forms\\H01 Heart Health Study Contact Information\\ 251 '1':2,12 'administr':3,13 'contact':10,20 'data':4,14 'form':5,15 'h01':6,16 'health':8,18 'heart':7,17 'inform':11,21 'phs002808':1 'studi':9,19 +255 23 V5AD09A5_SP V5AD09A5_SP categorical \\phs002808\\1 Administrative Data Forms\\H01 Heart Health Study Contact Information\\V5AD09A5_SP\\ 254 '1':2 'administr':3 'care':27 'contact':10 'data':4 'doctor':24 'field':39 'follow':20 'form':5 'h01':6 'health':8,26 'heart':7 'infect':40 'inform':11 'kidney':36 'phs002808':1 'problem':21 'profession':28 'sp':13,15 'specifi':38 'studi':9 'told':29 'v5a':16 'v5ad09a5':12,14 'yes':42 +256 23 categorical \\phs002808\\3a Visit Forms\\ 250 '3a':2 'form':4 'phs002808':1 'visit':3 +257 23 \\phs002808\\3a Visit Forms\\V5A Maternal Interview 2-7 Years Postpartum\\T01H01B\\ 3a Visit Forms / V5A Maternal Interview 2-7 Years Postpartum categorical \\phs002808\\3a Visit Forms\\V5A Maternal Interview 2-7 Years Postpartum\\ 256 '-7':9,19 '2':8,18 '3a':2,12 'form':4,14 'interview':7,17 'matern':6,16 'phs002808':1 'postpartum':11,21 'v5a':5,15 'visit':3,13 'year':10,20 +258 23 T01H01B T01H01B categorical \\phs002808\\3a Visit Forms\\V5A Maternal Interview 2-7 Years Postpartum\\T01H01B\\ 257 '-7':9 '2':8 '3a':2 'blood':23 'current':17 'form':4 'high':22 'interview':7 'matern':6 'medic':19 'phs002808':1 'postpartum':11 'prescrib':18 'pressur':24 't01':14 't01h01b':12,13 'v5a':5 'visit':3 'year':10 'yes':25,28 +260 21 enrollment_alcohol_and_tobacco alcohol_and_tobacco categorical \\phs003463\\alcohol_and_tobacco_enrollment\\ 259 'adult':25 'alcohol':2,6,15 'answers.tsv':20 'associ':10 'enrol':5,14 'file':21 'pair':13 'phs003463':1 'recov':24 'studi':26 'tobacco':4,8,17 'variabl':9 'visit/form':12 +261 21 alco_tobaccopre_enrollment_alcohol_and_tobacco alco_tobaccopre_enrollment_alcohol_and_tobacco categorical \\phs003463\\alcohol_and_tobacco_enrollment\\alco_tobaccopre_enrollment_alcohol_and_tobacco\\ 260 'alco':6,12 'alcohol':2,9,15 'enrol':5,8,14 'phs003463':1 'tobacco':4,11,17 'tobaccopr':7,13 +264 24 visit01_original_ecgsamplebase VISIT01_ORIGINAL_ECGSAMPLEBASE continuous \\phs003566\\Visit01\\VISIT01_ORIGINAL_ECGSAMPLEBASE\\ 263 'ecgsamplebas':5,8 'origin':4,7 'phs003566':1 'visit01':2,3,6 +266 14 Genotype array Genotype array categorical \\Variant Data Type\\Genotype array\\ 265 'array':5,7,9 'data':2 'genotyp':4,6,8 'true':10 'type':3 'variant':1 +267 14 Low coverage WGS Low coverage WGS categorical \\Variant Data Type\\Low coverage WGS\\ 265 'coverag':5,8,11 'data':2 'low':4,7,10 'true':13 'type':3 'variant':1 'wgs':6,9,12 +268 14 WES WES categorical \\Variant Data Type\\WES\\ 265 'data':2 'exom':7 'sequenc':8 'true':9 'type':3 'variant':1 'wes':4,5 'whole':6 +269 14 WGS WGS categorical \\Variant Data Type\\WGS\\ 265 'data':2 'genom':7 'sequenc':8 'true':9 'type':3 'variant':1 'wgs':4,5 'whole':6 +270 26 harmonized_var harmonized_var continuous \\phs003566\\harmonized_var\\ 263 'ecgsamplebas':5,8 'origin':4,7 'phs003566':1 'visit01':2,3,6 +271 26 value_example value_example continuous \\phs003566\\value_example\\ 263 'ecgsamplebas':5,8 'gremlin':9 'origin':4,7,10 'phs003566':1 'visit01':2,3,6 +\. + + +-- +-- Data for Name: concept_node_meta; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.concept_node_meta (concept_node_meta_id, concept_node_id, key, value) FROM stdin; +19 186 description Approximate Synonyms:\nSevere persistent allergic asthma in status asthmaticus\nSevere persistent allergic asthma with status asthmaticus\nSevere persistent asthma in status asthmaticus\nSevere persistent asthma with allergic rhinitis in status asthmaticus\nSevere persistent asthma with allergic rhinitis with status asthmaticus +20 186 values ["J45.52 Severe persistent asthma with status asthmaticus"] +21 189 description Approximate Synonyms:\nAcute exacerbation of asthma with allergic rhinitis\nAllergic asthma with acute exacerbation\nAsthma, with acute exacerbation (flare-up)\nAsthma, with allergic rhinitis with acute exacerbation\nExacerbation of asthma +22 189 values ["J45.901 Unspecified asthma with (acute) exacerbation"] +23 190 description Approximate Synonyms:\nAsthma with allergic rhinitis in status asthmaticus\nAsthma with allergic rhinitis with status asthmaticus\nAsthma with status\nAsthma with status asthmaticus\nAsthma, allergic with status asthmaticus\nExtrinsic asthma with status asthmaticus +24 190 values ["J45.902 Unspecified asthma with status asthmaticus"] +25 211 description GIC biosample: wholeblood +26 211 data_source Biosample +27 212 values ["TRUE"] +28 214 values ["TRUE"] +29 216 description Those patients who align with the IRB Phase 2 protocols +30 216 values ["GIC Consent"] +31 217 description Those patients who DO NOT align with the IRB Phase 2 protocols +32 217 values ["GIC Legacy Consent"] +33 218 description Patients who have waived consent +34 218 values ["Waiver of Consent"] +35 222 description Heart rate is taken by the automated blood pressure/heart rate monitor and captured directly into the computer system. In the event the heart rate is not captured automatically at the end of stage 1, the technician would manually enter the readings from the heart rate monitor. +37 225 description Including living and deceased, were any of {SP's/your} close biological that is, blood relatives including father, mother, sisters or brothers, ever told by a health professional that they had a heart attack or angina (an-gi-na) before the age of 50? +38 225 values ["Yes"] +39 229 description # 12 OZ CUPS OF CAFFEINATED COLA / DAY +41 229 stigmatized false +42 229 unique_identifier false +43 229 free_text false +44 229 bdc_open_access true +45 232 description # 12 OZ CUPS OF CAFFEINATED COLA / DAY +47 232 stigmatized false +48 232 unique_identifier false +49 232 free_text false +50 232 bdc_open_access true +51 235 description # 12 OZ CUPS OF CAFFEINATED COLA/DAY +53 235 stigmatized false +54 235 unique_identifier false +55 235 free_text false +56 235 bdc_open_access true +57 239 description Most recent occupation (A) +58 239 values ["ACCOUNTANT"] +59 241 description Age +61 241 stigmatized false +62 241 unique_identifier false +63 241 free_text false +64 241 bdc_open_access true +65 242 description % of time in artifacts +67 242 stigmatized false +68 242 unique_identifier false +69 242 free_text false +70 242 bdc_open_access true +71 244 description Patient age at transplant, years +72 244 values [42] +73 244 stigmatized false +74 244 unique_identifier false +75 244 free_text false +76 244 bdc_open_access true +77 244 hct status pre-hct +78 244 computed variable yes +79 245 description Race (regrouped) +80 245 values ["Not Reported"] +81 245 stigmatized false +82 245 unique_identifier false +83 245 free_text false +84 245 bdc_open_access true +85 246 description Transplant Number +86 246 values [1] +87 246 stigmatized true +88 246 unique_identifier false +89 246 free_text false +90 246 bdc_open_access false +91 246 hct status pre-hct +92 246 computed variable yes +93 248 description Participant's age (category) +94 248 values [21] +95 248 stigmatized false +96 248 unique_identifier false +97 248 free_text false +98 248 bdc_open_access true +99 249 description Smoker status +100 249 values ["true"] +101 249 stigmatized false +102 249 unique_identifier false +103 249 free_text false +104 249 bdc_open_access true +105 253 description (AFC) Reason for ending future contact: Withdrew consent for future nuMoM2b contact +106 253 values ["No"] +107 253 unique_identifier false +108 253 free_text false +109 253 bdc_open_access true +110 255 description (V5A) Which of the following problems have a doctor or health care professional told you that you have with your kidney?: Other - Specify Field +111 255 values ["infection"] +112 255 unique_identifier false +113 255 free_text true +114 255 bdc_open_access false +115 258 description (T01) Are you currently prescribed medication for your high blood pressure? +116 258 values ["Yes"] +117 258 unique_identifier false +118 258 free_text false +119 258 bdc_open_access true +120 266 description Genotype array +121 266 values ["TRUE"] +122 267 description Low coverage WGS +123 267 values ["TRUE"] +124 268 description Whole exome sequencing +40 229 values [0, 3] +46 232 values [0, 1] +52 235 values [0.57,6.77] +60 241 values ["5E-21", "7E+33"] +125 268 values ["TRUE"] +126 269 description Whole genome sequencing +127 269 values ["TRUE"] +128 227 description Clinic Exam, Original Cohort Exam 19 +129 230 description Clinic Exam, Original Cohort Exam 20 +130 233 description Clinic Exam, Offspring Cohort Exam 4 +131 237 description CARe_CFS (Cleveland Family Study) - Sleep and Health Phenotype (Adults/Children) +132 260 description Variables associated with visit/form pair enrollment_alcohol_and_tobacco in the answers.tsv file in the RECOVER Adult study +133 211 values [100, 500] +36 222 values [0, 150] +66 242 values [0, 30] +134 270 values [0, 21] +135 271 values ['gremlin', 'origin'] +\. + + +-- +-- Data for Name: consent; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.consent (consent_id, dataset_id, consent_code, description, authz) FROM stdin; +4 17 c1 Disease-Specific (Heart, Lung, Blood, and Sleep Disorders, IRB, NPU) (DS-HLBS-IRB-NPU) /programs/NSRR/projects/NSRR-CFS_DS-HLBS-IRB-NPU +5 18 c1 Disease-Specific (Heart, Lung, Blood, and Sleep Disorders, IRB, NPU) (DS-HLBS-IRB-NPU) /programs/parent/projects/CFS_ +6 19 c1 Health/Medical/Biomedical (IRB, MDS) (HMB-IRB-MDS) /programs/parent/projects/FHS_ +7 19 c2 Health/Medical/Biomedical (IRB, NPU, MDS) (HMB-IRB-NPU-MDS) /programs/parent/projects/FHS_ +8 20 c1 General Research Use (GRU) /programs/BioLINCC/projects/CIBMTR_ +9 21 c1 General Research Use (GRU) /programs/RECOVER/projects/RC_Adult_ +10 22 c1 General Research Use (GRU) /programs/NSRR/projects/SR_HCHS_ +11 23 c1 General Research Use (IRB) (GRU-IRB) /programs/topmed/projects/nuMoM2b_ +12 24 c1 General Research Use (IRB) (GRU-IRB) /programs/Imaging/projects/SPRINT_ +13 25 c1 GRU +\. + + +-- +-- Data for Name: dataset; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.dataset (dataset_id, ref, full_name, abbreviation, description) FROM stdin; +14 1 Genomic Information Commons GIC The GIC utilizes the ACT ontology to ensure data alignment across the sites. This project also includes other variables of interest as defined by the Governance Committee, such as biosamples, consents, etc. +15 2 National Health and Nutrition Examination Survey NHANES The National Health and Nutrition Examination Survey (NHANES) is a program of studies designed to assess the health and nutritional status of adults and children in the United States. +16 3 1000 Genomes Project 1000 Genomes The 1000 Genomes Project created a catalogue of common human genetic variation, using openly consented samples from people who declared themselves to be healthy. The reference data resources generated by the project remain heavily used by the biomedical science community. +17 phs002715 National Sleep Research Resource (NSRR): Cleveland Family Study (CFS) NSRR CFS The Cleveland Family Study (CFS) is a family-based study of sleep apnea, consisting of 2,284 individuals (46% African American) from 361 families studied on up to 4 occasions over a period of 16 years. The study began in 1990 with the initial aims of quantifying the familial aggregation of sleep apnea. National Institutes of Health (NIH) renewals provided expansion of the original cohort, including increased minority recruitment, and longitudinal follow-up, with the last exam occurring in February 2006. The CFS was designed to provide fundamental epidemiological data on risk factors for sleep disordered breathing (SDB). The sample was selected by identifying affected probands who had laboratory diagnosed obstructive sleep apnea. All first-degree relatives, spouses and available second-degree relatives of affected probands were studied. In addition, during the first 5 study years, neighborhood control families were identified through a neighborhood proband, and his/her spouses and first-degree relatives. Each exam, occurring at approximately 4-year intervals, included new enrollment as well as follow up exams for previously enrolled subjects. For the first three visits, data, including an overnight sleep study, were collected in participants' homes while the last visit occurred in a general clinical research center (GCRC). Phenotypic characterization of the entire cohort included overnight sleep apnea studies, blood pressure, spirometry, anthropometry and questionnaires. Currently, data of 710 individuals are available for use through BioData Catalyst (with genotype data available through dbGaP).\n\nThe National Sleep Research Resource (NSRR) is a NIH-supported sleep data repository that offers free access to large collections of de-identified physiological signals and related clinical data from a large range of cohort studies, clinical trials and other data sources from children and adults, including healthy individuals from the community and individuals with known sleep or other health disorders. The goals of NSRR are to facilitate rigorous research that requires access to large or more diverse data sets, including raw physiological signals, to promote a better understanding of risk factors for sleep and circadian disorders and/or the impact of sleep disturbances on health-related outcomes. Data from over 15 data sources and more than 40,000 individual sleep studies, many linked to dozens if not hundreds of clinical data elements, are available (as of Feb. 2022). Query tools are available to identify variables of interest, and their meta-data and provenance. +18 phs000284 NHLBI Cleveland Family Study (CFS) Candidate Gene Association Resource (CARe) CFS The Cleveland Family Study is the largest family-based study of sleep apnea world-wide, consisting of 2284 individuals (46% African American) from 361 families studied on up to 4 occasions over a period of 16 years. The study was begun in 1990 with the initial aims of quantifying the familial aggregation of sleep apnea. NIH renewals provided expansion of the original cohort (including increased minority recruitment) and longitudinal follow-up, with the last exam occurring in February 2006. Index probands (n=275) were recruited from 3 area hospital sleep labs if they had a confirmed diagnosis of sleep apnea and at least 2 first-degree relatives available to be studied. In the first 5 years of the study, neighborhood control probands (n=87) with at least 2 living relatives available for study were selected at random from a list provided by the index family and also studied. All available first degree relatives and spouses of the case and control probands also were recruited. Second-degree relatives, including half-sibs, aunts, uncles and grandparents, were also included if they lived near the first degree relatives (cases or controls), or if the family had been found to have two or more relatives with sleep apnea. Blood was sampled and DNA isolated for participants seen in the last two exam cycles (n=1447). The sample, which is enriched with individuals with sleep apnea, also contains a high prevalence of individuals with sleep apnea-related traits, including: obesity, impaired glucose tolerance, and HTN.\n\nPhenotyping data have been collected over 4 exam cycles, each occurring ~every 4 years. The last three exams targeted all subjects who had been studied at earlier exams, as well as new minority families and family members of previously studied probands who had been unavailable at prior exams. Data from one, two, three and four visits are available for 412, 630, 329 and 67, participants, respectively. In the first 3 exams, participants underwent overnight in-home sleep studies, allowing determination of the number and duration of hypopneas and apneas, sleep period, heart rate, and oxygen saturation levels; anthropometry (weight, height, and waist, hip, and neck circumferences); resting blood pressure; spirometry; standardized questionnaire evaluation of symptoms, medications, sleep patterns, quality of life, daytime sleepiness measures and health history; venipuncture and measurement of total and HDL cholesterol. The 4th exam (2001-2006) was designed to collect more detailed measurements of sleep, metabolic and CVD phenotypes and included measurement of state-of-the-art polysomnography, with both collection of blood and measurement of blood pressure before and after sleep, and anthropometry, upper airway assessments, spirometry, exhaled nitric oxide, and ECG performed the morning after the sleep study.\n\nData have been collected by trained research assistants or GCRC nurses following written Manuals of Procedures who were certified following standard approaches for each study procedure. Ongoing data quality, with assessment of within or between individual drift, has been monitored on an ongoing basis, using statistical techniques as well as regular re-certification procedures. Between and within scorer reliabilities for key sleep apnea indices have been excellent, with intra-class correlation coefficients (ICCs) exceeding 0.92 for the apnea-hypopnea index (AHI). Sleep staging, assessed with epoch specific comparisons, also demonstrate excellent reliability for stage identification (kappas>0.82). There has been no evidence of significant time trends-between or within scorers- for the AHI variables. We also have evaluated the night-to-night variability of the AHI and other sleep variables in 91 subjects, with each measurement made 1-3 months apart. There is high night to night consistency for the AHI (ICC: 0.80), the arousal index (0.76), and the % sleep time in slow-wave sleep (0.73). We have demonstrated the comparability of the apnea estimates (AHI) determined from limited channel studies obtained at in-home settings with in full in-laboratory polysomnography. In addition to our published validation study, we more recently compared the AHI in 169 Cleveland Family Study participants undergoing both assessments (in-home and in-laboratory) within one week apart. These showed excellent levels of agreement (ICC=0.83), demonstrating the feasibility of examining data from either in-home or in-laboratory studies for apnea phenotyping. Data collected in the GCRC were obtained, when possible, with comparable, if not identical techniques, as were the same measures collected at prior exams performed in the participants' homes. To address the comparability of data collected over different exams, we calculated the crude age-adjusted correlations ~3 year within individual correlations between measures made in the most recent GCRC exam with measures made in a prior exam and demonstrated excellent levels of agreement for BMI (r=.91); waist circumference (0.91); FVC (0.88); and FEV1 (0.86). As expected due to higher biological and measurement variability, 149 somewhat lower 3-year correlations were demonstrated for SBP (0.56); Diastolic BP (0.48); AHI (0.62); and nocturnal oxygen desaturation (0.60). +19 phs000007 Framingham Cohort FHS Startup of Framingham Heart Study. Cardiovascular disease (CVD) is the leading cause of death and serious illness in the United States. In 1948, the Framingham Heart Study (FHS) -- under the direction of the National Heart Institute (now known as the National Heart, Lung, and Blood Institute, NHLBI) -- embarked on a novel and ambitious project in health research. At the time, little was known about the general causes of heart disease and stroke, but the death rates for CVD had been increasing steadily since the beginning of the century and had become an American epidemic.\n\nThe objective of the FHS was to identify the common factors or characteristics that contribute to CVD by following its development over a long period of time in a large group of participants who had not yet developed overt symptoms of CVD or suffered a heart attack or stroke.\n\nDesign of Framingham Heart Study. In 1948, the researchers recruited 5,209 men and women between the ages of 30 and 62 from the town of Framingham, Massachusetts, and began the first round of extensive physical examinations and lifestyle interviews that they would later analyze for common patterns related to CVD development. Since 1948, the subjects have returned to the study every two years for an examination consisting of a detailed medical history, physical examination, and laboratory tests, and in 1971, the study enrolled a second-generation cohort -- 5,124 of the original participants' adult children and their spouses -- to participate in similar examinations. The second examination of the Offspring cohort occurred eight years after the first examination, and subsequent examinations have occurred approximately every four years thereafter. In April 2002 the Study entered a new phase: the enrollment of a third generation of participants, the grandchildren of the original cohort. The first examination of the Third Generation Study was completed in July 2005 and involved 4,095 participants. Thus, the FHS has evolved into a prospective, community-based, three generation family study. The FHS is a joint project of the National Heart, Lung and Blood Institute and Boston University.\n\nResearch Areas in the Framingham Heart Study. Over the years, careful monitoring of the FHS population has led to the identification of the major CVD risk factors -- high blood pressure, high blood cholesterol, smoking, obesity, diabetes, and physical inactivity -- as well as a great deal of valuable information on the effects of related factors such as blood triglyceride and HDL cholesterol levels, age, gender, and psychosocial issues. Risk factors have been identified for the major components of CVD, including coronary heart disease, stroke, intermittent claudication, and heart failure. It is also clear from research in the FHS and other studies that substantial subclinical vascular disease occurs in the blood vessels, heart and brain that precedes clinical CVD. With recent advances in technology, the FHS has enhanced its research capabilities and capitalized on its inherent resources by the conduct of high resolution imaging to detect and quantify subclinical vascular disease in the major blood vessels, heart and brain. These studies have included ultrasound studies of the heart (echocardiography) and carotid arteries, computed tomography studies of the heart and aorta, and magnetic resonance imaging studies of the brain, heart, and aorta. Although the Framingham cohort is primarily white, the importance of the major CVD risk factors identified in this group have been shown in other studies to apply almost universally among racial and ethnic groups, even though the patterns of distribution may vary from group to group. In the past half century, the Study has produced approximately 1,200 articles in leading medical journals. The concept of CVD risk factors has become an integral part of the modern medical curriculum and has led to the development of effective treatment and preventive strategies in clinical practice.\n\nIn addition to research studies focused on risk factors, subclinical CVD and clinically apparent CVD, Framingham investigators have also collaborated with leading researchers from around the country and throughout the world on projects involving some of the major chronic illnesses in men and women, including dementia, osteoporosis and arthritis, nutritional deficiencies, eye diseases, hearing disorders, and chronic obstructive lung diseases.\n\nGenetic Research in the Framingham Heart Study. While pursuing the Study's established research goals, the NHLBI and the Framingham investigators has expanded its research mission into the study of genetic factors underlying CVD and other disorders. Over the past two decades, DNA has been collected from blood samples and from immortalized cell lines obtained from Original Cohort participants, members of the Offspring Cohort and the Third Generation Cohort. Several large-scale genotyping projects have been conducted in the past decade. Genome-wide linkage analysis has been conducted using genotypes of approximately 400 microsatellite markers that have been completed in over 9,300 subjects in all three generations. Analyses using microsatellite markers completed in the original cohort and offspring cohorts have resulted in over 100 publications, including many publications from the Genetics Analysis Workshop 13. Several other recent collaborative projects have completed thousands of SNP genotypes for candidate gene regions in subsets of FHS subjects with available DNA. These projects include the Cardiogenomics Program of the NHLBI's Programs for Genomics Applications, the genotyping of ~3000 SNPs in inflammation genes, and the completion of a genome-wide scan of 100,000 SNPs using the Affymetrix 100K Genechip.\n\nFramingham Cohort Phenotype Data. The phenotype database contains a vast array of phenotype information available in all three generations. These will include the quantitative measures of the major risk factors such as systolic blood pressure, total and HDL cholesterol, fasting glucose, and cigarette use, as well as anthropomorphic measures such as body mass index, biomarkers such as fibrinogen and CRP, and electrocardiography measures such as the QT interval. Many of these measures have been collected repeatedly in the original and offspring cohorts. Also included in the SHARe database will be an array of recently collected biomarkers, subclinical disease imaging measures, clinical CVD outcomes as well as an array of ancillary studies. The phenotype data is located here in the top-level study phs000007 Framingham Cohort. To view the phenotype variables collected from the Framingham Cohort, please click on the Variables tab above. +20 phs002385 Hematopoietic Cell Transplant for Sickle Cell Disease (HCT for SCD) HCT_for_SCD The Center for International Blood and Marrow Transplant Research (CIBMTR) is a hematopoietic cell transplant registry that was established in 1972 at the Medical College of Wisconsin. The overarching goal of the registry is to study trends in transplantations and to advance the understanding and application of allogeneic hematopoietic cell transplantation for malignant and non-malignant diseases. Included in this dataset are children, adolescents and young adults with severe sickle cell disease who received an allogeneic hematopoietic cell transplant in the United States and provided written informed consent for research.\n\nHematopoietic cell transplant for sickle cell disease is curative. Offering this treatment for patients with severe disease is challenging as only about 20-25% of patients expected to benefit have an HLA-matched sibling. Consequently, several transplantations have utilized an HLA-matched or mismatched unrelated adult donor and HLA-mismatched relative. Transplantation strategies have also evolved over time that has included transplant conditioning regimens of varying intensity, grafts other than bone marrow and novel approaches to overcome the donor-recipient histocompatibility barrier and limit graft-versus-host disease. The data that is available for sickle cell disease transplants have been utilized to report on outcomes after transplantation and compare outcomes after transplantation of grafts HLA-matched related, HLA-mismatched related, HLA-matched and HLA-mismatched unrelated donors. Collectively, these data have advanced our knowledge and understanding of hematopoietic cell transplant for this disease. These data can also serve as contemporaneous controls for comparison with other more recent curative treatments like gene therapy and gene editing. +21 phs003463 Researching COVID to Enhance Recovery (RECOVER): Adult Observational Cohort Study RECOVER_Adult +22 phs003543 National Sleep Research Resource (NSRR): (HSHC) NSRR_HSHC +23 phs002808 Nulliparous Pregnancy Outcomes Study: Monitoring Mothers-to-be Heart Health Study (nuMoM2b Heart Health Study) nuMoM2b +24 phs003566 Systolic Blood Pressure Intervention Trial (SPRINT-Imaging) SPRINT +25 phs001963 DEMENTIA-SEQ: WGS in Lewy Body Dementia and Frontotemporal Dementia DEMENTIA-SEQ +26 harmonized My Cool Harmonized Dataset abv harmony +\. + + +-- +-- Data for Name: dataset_meta; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.dataset_meta (dataset_meta_id, dataset_id, key, value) FROM stdin; +1 17 focus Sleep Apnea Syndromes +2 18 focus Sleep Apnea Syndromes +3 19 focus Cardiovascular Disease +4 20 focus Sickle Cell Disease +5 21 focus Covid-19 +6 22 focus Sleep Apnea Syndromes +7 23 focus Hypertension +8 24 focus Imaging +9 25 focus Lewy Body Disease +10 17 design Prospective Longitudinal Cohort +11 18 design Prospective Longitudinal Cohort +12 19 design Prospective Longitudinal Cohort +13 20 design Prospective Longitudinal Cohort +14 21 design Clinical Trial +15 22 design Prospective Longitudinal Cohort +16 23 design Prospective Longitudinal Cohort +17 25 design Case-Control +18 25 category code Case-Control +19 25 focus display Lewy Body Disease +20 25 condition coding system urn:oid:2.16.840.1.113883.6.177 +21 25 condition coding code D020961 +22 25 condition coding display Lewy Body Disease +23 25 description Lewy body dementia, amyotrophic lateral sclerosis/frontotemporal dementia, and multiple system atrophy are age-related, neurodegenerative syndromes that are poorly understood. Delineating the genetic risk that is driving the pathophysiology of these neurological diseases is fundamental for understanding disease mechanisms and for developing disease-modifying treatments.
    \\n\\n\\n\\n In version 1 of the study/dbGaP deposition, we performed a whole-genome sequencing study consisting of 7,403 total samples, including 2,633 genomes from patients with Lewy body dementia, 2,641 frontotemporal dementia patients, and 1,980 neurologically healthy controls. Of these, 6,907 were uploaded to dbGaP as the basis of the DementiaSeq, phs001963 dataset. The data relating to these samples are available on dbGaP.\\n\\n\\n\\n In version 2 of this study/dbGaP deposition, we made much of these data available on Anvil. More specifically, data for 6,254 of these samples were also uploaded to the ALS Compute platform on AnVIL. The data for the remaining 653 samples are only available on dbGaP. The dbGaP/AnVIL Table lists the availability of dbGaP and AnVIL for each individual sample: phd008475.\\n\\nIn version 3 of the study/dbGaP deposition, we added whole-genome sequence data generated using DNA samples obtained from 683 patients diagnosed with multiple system atrophy.\\n +24 25 sponsor display National Institute on Aging +25 20 additional information Cure SCi Metadata Catalog +26 17 clinvars 500 +27 18 clinvars 12321 +28 19 clinvars 12546 +29 20 clinvars 7567 +30 21 clinvars 654645 +31 22 clinvars 434 +32 23 clinvars 2 +33 24 clinvars 333 +34 25 clinvars 653 +36 17 participants 23432 +37 18 participants 867876 +38 19 participants 3435 +39 20 participants 33 +40 21 participants 6654 +41 22 participants 53435 +42 23 participants 111 +43 24 participants 2222 +44 25 participants 65 +\. + + +-- +-- Data for Name: facet; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.facet (facet_id, facet_category_id, name, display, description, parent_id) FROM stdin; +20 2 LOINC LOINC \N \N +21 2 PhenX PhenX \N \N +22 1 1 GIC \N \N +23 1 2 National Health and Nutrition Examination Survey \N \N +24 1 3 1000 Genomes Project \N \N +25 1 phs002715 NSRR CFS \N \N +26 1 phs000284 CFS \N \N +27 1 phs000007 FHS \N \N +28 1 phs002385 HCT_for_SCD \N \N +29 1 phs003463 RECOVER_Adult \N \N +30 1 phs003543 NSRR_HSHC \N \N +31 1 phs002808 nuMoM2b \N \N +32 1 phs003566 SPRINT \N \N +33 1 phs001963 DEMENTIA-SEQ \N \N +55 1 NEST_1 My Nested Facet 1 \N 33 +56 1 NEST_2 My Nested Facet 2 \N 33 +19 2 gad_7 Generalized Anxiety Disorder Assessment (GAD-7) \N \N +18 2 taps_tool NIDA CTN Common Data Elements = TAPS Tool \N \N +\. + + +-- +-- Data for Name: facet__concept_node; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.facet__concept_node (facet__concept_node_id, facet_id, concept_node_id) FROM stdin; +1 22 180 +2 22 181 +3 22 182 +4 22 183 +5 22 184 +6 22 185 +7 22 186 +8 22 187 +9 22 188 +10 22 189 +11 22 190 +12 22 191 +13 22 192 +14 22 193 +15 22 194 +16 22 195 +17 22 196 +18 22 197 +19 22 198 +20 22 199 +21 22 200 +22 22 201 +23 22 202 +24 22 203 +25 22 204 +26 22 205 +27 22 206 +28 22 207 +29 22 208 +30 22 209 +31 22 210 +32 22 211 +33 22 212 +34 22 213 +35 22 214 +36 22 215 +37 22 216 +38 22 217 +39 22 218 +40 23 219 +41 23 220 +42 23 221 +43 23 222 +44 23 223 +45 23 224 +46 23 225 +47 27 226 +48 27 227 +49 27 228 +50 27 229 +51 27 230 +52 27 231 +53 27 232 +54 27 233 +55 27 234 +56 27 235 +57 26 236 +58 26 237 +59 26 238 +60 26 239 +61 26 240 +62 26 241 +63 26 242 +64 28 243 +65 28 244 +66 28 245 +67 28 246 +68 25 247 +69 25 248 +70 25 249 +71 31 250 +72 31 251 +73 31 252 +74 31 253 +75 31 254 +76 31 255 +77 31 256 +78 31 257 +79 31 258 +80 29 259 +81 29 260 +82 29 261 +83 32 262 +84 32 263 +85 32 264 +86 22 265 +87 22 266 +88 22 267 +89 22 268 +90 22 269 +91 18 261 +92 20 229 +93 21 229 +94 21 271 +\. + + +-- +-- Data for Name: facet_category; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.facet_category (facet_category_id, name, display, description) FROM stdin; +1 study_ids_dataset_ids Study IDs/Dataset IDs +2 nsrr_harmonized Common Data Element Collection +3 cde NSRR Harmonized +\. + + +-- +-- Data for Name: facet_category_meta; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.facet_category_meta (facet_category_meta_id, facet_category_id, key, value) FROM stdin; +1 1 my_key my_value +2 1 order 1 +\. + + +-- +-- Data for Name: facet_meta; Type: TABLE DATA; Schema: dict; Owner: picsure +-- + +COPY public.facet_meta (facet_meta_id, facet_id, key, value) FROM stdin; +1 25 full_name National Sleep Research Resource +2 26 full_name Chronic Fatigue Syndrome +3 27 full_name Framingham Heart Study +\. + + +-- +-- Name: concept_node_concept_node_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.concept_node_concept_node_id_seq', 269, true); + + +-- +-- Name: concept_node_meta_concept_node_meta_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.concept_node_meta_concept_node_meta_id_seq', 133, true); + + +-- +-- Name: consent_consent_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.consent_consent_id_seq', 13, true); + + +-- +-- Name: dataset_dataset_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.dataset_dataset_id_seq', 25, true); + + +-- +-- Name: dataset_meta_dataset_meta_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.dataset_meta_dataset_meta_id_seq', 25, true); + + +-- +-- Name: facet__concept_node_facet__concept_node_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.facet__concept_node_facet__concept_node_id_seq', 93, true); + + +-- +-- Name: facet_category_facet_category_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.facet_category_facet_category_id_seq', 4, true); + + +-- +-- Name: facet_category_meta_facet_category_meta_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.facet_category_meta_facet_category_meta_id_seq', 1, false); + + +-- +-- Name: facet_facet_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.facet_facet_id_seq', 33, true); + + +-- +-- Name: facet_meta_facet_meta_id_seq; Type: SEQUENCE SET; Schema: dict; Owner: picsure +-- + +SELECT pg_catalog.setval('public.facet_meta_facet_meta_id_seq', 1, false); + + +-- +-- Name: concept_node_meta concept_node_meta_key_concept_node_id_key; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.concept_node_meta + ADD CONSTRAINT concept_node_meta_key_concept_node_id_key UNIQUE (key, concept_node_id); + + +-- +-- Name: concept_node_meta concept_node_meta_pkey; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.concept_node_meta + ADD CONSTRAINT concept_node_meta_pkey PRIMARY KEY (concept_node_meta_id); + + +-- +-- Name: concept_node concept_node_pkey; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.concept_node + ADD CONSTRAINT concept_node_pkey PRIMARY KEY (concept_node_id); + + +-- +-- Name: consent consent_consent_code_dataset_id_key; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.consent + ADD CONSTRAINT consent_consent_code_dataset_id_key UNIQUE (consent_code, dataset_id); + + +-- +-- Name: consent consent_pkey; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.consent + ADD CONSTRAINT consent_pkey PRIMARY KEY (consent_id); + + +-- +-- Name: dataset_meta dataset_meta_key_dataset_id_key; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.dataset_meta + ADD CONSTRAINT dataset_meta_key_dataset_id_key UNIQUE (key, dataset_id); + + +-- +-- Name: dataset dataset_pkey; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.dataset + ADD CONSTRAINT dataset_pkey PRIMARY KEY (dataset_id); + + +-- +-- Name: dataset dataset_ref_key; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.dataset + ADD CONSTRAINT dataset_ref_key UNIQUE (ref); + + +-- +-- Name: facet__concept_node facet__concept_node_facet_id_concept_node_id_key; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet__concept_node + ADD CONSTRAINT facet__concept_node_facet_id_concept_node_id_key UNIQUE (facet_id, concept_node_id); + + +-- +-- Name: facet__concept_node facet__concept_node_pkey; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet__concept_node + ADD CONSTRAINT facet__concept_node_pkey PRIMARY KEY (facet__concept_node_id); + + +-- +-- Name: facet_category_meta facet_category_meta_key_facet_category_id_key; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet_category_meta + ADD CONSTRAINT facet_category_meta_key_facet_category_id_key UNIQUE (key, facet_category_id); + + +-- +-- Name: facet_category facet_category_name_key; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet_category + ADD CONSTRAINT facet_category_name_key UNIQUE (name); + + +-- +-- Name: facet_category facet_category_pkey; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet_category + ADD CONSTRAINT facet_category_pkey PRIMARY KEY (facet_category_id); + + +-- +-- Name: facet_meta facet_meta_key_facet_id_key; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet_meta + ADD CONSTRAINT facet_meta_key_facet_id_key UNIQUE (key, facet_id); + + +-- +-- Name: facet facet_name_facet_category_id_key; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet + ADD CONSTRAINT facet_name_facet_category_id_key UNIQUE (name, facet_category_id); + + +-- +-- Name: facet facet_pkey; Type: CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet + ADD CONSTRAINT facet_pkey PRIMARY KEY (facet_id); + + +-- +-- Name: concept_node_concept_path_idx; Type: INDEX; Schema: dict; Owner: picsure +-- + +CREATE UNIQUE INDEX concept_node_concept_path_idx ON public.concept_node USING btree (md5((concept_path)::text)); + + +-- +-- Name: facet fk_category; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet + ADD CONSTRAINT fk_category FOREIGN KEY (facet_category_id) REFERENCES public.facet_category(facet_category_id); + + +-- +-- Name: concept_node_meta fk_concept_node; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.concept_node_meta + ADD CONSTRAINT fk_concept_node FOREIGN KEY (concept_node_id) REFERENCES public.concept_node(concept_node_id); + + +-- +-- Name: facet__concept_node fk_concept_node; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet__concept_node + ADD CONSTRAINT fk_concept_node FOREIGN KEY (concept_node_id) REFERENCES public.concept_node(concept_node_id); + + +-- +-- Name: facet_meta fk_facet; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet_meta + ADD CONSTRAINT fk_facet FOREIGN KEY (facet_id) REFERENCES public.facet(facet_id); + + +-- +-- Name: facet__concept_node fk_facet; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet__concept_node + ADD CONSTRAINT fk_facet FOREIGN KEY (facet_id) REFERENCES public.facet(facet_id); + + +-- +-- Name: facet_category_meta fk_facet_category; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet_category_meta + ADD CONSTRAINT fk_facet_category FOREIGN KEY (facet_category_id) REFERENCES public.facet_category(facet_category_id); + + +-- +-- Name: concept_node fk_parent; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.concept_node + ADD CONSTRAINT fk_parent FOREIGN KEY (parent_id) REFERENCES public.concept_node(concept_node_id); + + +-- +-- Name: facet fk_parent; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.facet + ADD CONSTRAINT fk_parent FOREIGN KEY (parent_id) REFERENCES public.facet(facet_id); + + +-- +-- Name: dataset_meta fk_study; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.dataset_meta + ADD CONSTRAINT fk_study FOREIGN KEY (dataset_id) REFERENCES public.dataset(dataset_id); + + +-- +-- Name: concept_node fk_study; Type: FK CONSTRAINT; Schema: dict; Owner: picsure +-- + +ALTER TABLE ONLY public.concept_node + ADD CONSTRAINT fk_study FOREIGN KEY (dataset_id) REFERENCES public.dataset(dataset_id); + + +CREATE TABLE IF NOT EXISTS public.dataset_harmonization +( + dataset_harmonization_id INT NOT NULL GENERATED BY DEFAULT AS IDENTITY, + harmonized_dataset_id INT NOT NULL, + source_dataset_id INT NOT NULL, + UNIQUE (harmonized_dataset_id, source_dataset_id), + CONSTRAINT fk_harmonized_dataset_id FOREIGN KEY (harmonized_dataset_id) REFERENCES public.dataset (dataset_id), + CONSTRAINT fk_source_dataset_id FOREIGN KEY (source_dataset_id) REFERENCES public.dataset (dataset_id) +); + +INSERT INTO public.dataset_harmonization (dataset_harmonization_id, harmonized_dataset_id, source_dataset_id) VALUES + (1, 26, 25), + (1, 26, 24), + (1, 26, 23), + (1, 26, 22); + + +INSERT INTO public.update_info (LAST_UPDATED, DATABASE_VERSION) VALUES + ('2020-02-02 00:00:00', 3); + + +CREATE TABLE IF NOT EXISTS public.concept_node__remote_dictionary ( + CONCEPT_NODE_ID integer NOT NULL, + REMOTE_DICTIONARY_ID integer NOT NULL, + CONSTRAINT fk_remote_dictionary FOREIGN KEY (REMOTE_DICTIONARY_ID) REFERENCES public.remote_dictionary(REMOTE_DICTIONARY_ID), + CONSTRAINT fk_concept_node FOREIGN KEY (CONCEPT_NODE_ID) REFERENCES public.concept_node(CONCEPT_NODE_ID) +); + +INSERT INTO public.remote_dictionary (REMOTE_DICTIONARY_ID, NAME, UUID, LAST_UPDATED) VALUES + (1, 'bch', '3c13f873-1ff1-42f7-8382-75ac82c49ffc', '2024-01-01'), + (2, 'foo', '498226bf-e18e-4f0f-81f5-dd242914df95', '1800-01-01'), + (3, 'bar', '498226bf-e18e-4f0f-81f5-dd242914df96', '2000-01-01'); + +INSERT INTO public.concept_node__remote_dictionary (CONCEPT_NODE_ID, REMOTE_DICTIONARY_ID) VALUES + (261, 1), + (264, 1), + (266, 1), + (267, 1), + (268, 1), + (269, 1), + (270, 1), + (267, 2), + (268, 2), + (269, 2), + (209, 3), (180, 3), (191, 3), (197, 3), (202, 3), (215, 3), (219, 3), (226, 3), (236, 3), (243, 3), + (247, 3), (250, 3), (259, 3), (262, 3), (265, 3), (181, 3), (182, 3), (183, 3), (184, 3), (223, 3), + (263, 3), (185, 3), (186, 3), (187, 3), (188, 3), (189, 3), (231, 3), (232, 3), (190, 3), (192, 3), + (193, 3), (194, 3), (195, 3), (196, 3), (198, 3), (199, 3), (200, 3), (201, 3), (203, 3), (204, 3), + (241, 3), (205, 3), (206, 3), (207, 3), (208, 3), (210, 3), (211, 3), (212, 3), (213, 3), (214, 3), + (216, 3), (217, 3), (218, 3), (220, 3), (221, 3), (222, 3), (224, 3), (225, 3), (227, 3), (228, 3), + (229, 3), (230, 3), (233, 3), (234, 3), (235, 3), (237, 3), (238, 3), (239, 3), (240, 3), (242, 3), + (244, 3), (245, 3), (246, 3), (248, 3), (249, 3), (251, 3), (252, 3), (253, 3), (254, 3), (255, 3), + (256, 3), (257, 3), (258, 3), (261, 3), (264, 3), (266, 3), (267, 3), (268, 3), (269, 3); + +-- Backfill is_queryable: concepts with non-empty 'values' metadata are queryable +UPDATE public.concept_node cn +SET is_queryable = TRUE +WHERE EXISTS ( + SELECT 1 FROM public.concept_node_meta cnm + WHERE cnm.concept_node_id = cn.concept_node_id + AND cnm.key = 'values' AND cnm.value <> '' +); + +-- Backfill facet__concept_node.is_queryable from concept_node.is_queryable +UPDATE public.facet__concept_node fcn +SET is_queryable = cn.is_queryable +FROM public.concept_node cn +WHERE cn.concept_node_id = fcn.concept_node_id; + +-- +-- PostgreSQL database dump complete +-- +