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cbe65b4
build: establish monorepo aggregator + pic-sure-bom scaffold
Gcolon021 Jul 10, 2026
89d53c9
Add 'libs/pic-sure-logging-client/' from commit 'a26baf432f263b8a7efd…
Gcolon021 Jul 10, 2026
acf3785
Add 'libs/pic-sure-commons/' from commit '8fc524f5c8a995f0b14a245c73a…
Gcolon021 Jul 10, 2026
afafdec
build: vendor pic-sure-commons + pic-sure-logging-client (subtree imp…
Gcolon021 Jul 10, 2026
9ee2d71
feat(spring-commons): shared exception/audit/identity/actuator-securi…
Gcolon021 Jul 10, 2026
f7a322a
feat(gateway): Spring Cloud Gateway module scaffold, config, docker
Gcolon021 Jul 10, 2026
c1356d1
feat(gateway): DB-free auth/audit filter chain + security config
Gcolon021 Jul 10, 2026
b131c85
feat(gateway): route definitions + system health composition
Gcolon021 Jul 10, 2026
e9e7e55
test(gateway): route, filter-chain, and health tests
Gcolon021 Jul 10, 2026
c907cbb
build(gateway): register module in aggregator
Gcolon021 Jul 10, 2026
d9d2431
feat(operations-service): add Configuration/NamedDataset/Query JPA en…
Gcolon021 Jul 10, 2026
fdbce88
feat(operations-service): add config/dataset/internal-query service a…
Gcolon021 Jul 10, 2026
2b6001d
test(operations-service): add unit and integration tests for config/d…
Gcolon021 Jul 10, 2026
2d8a648
build(operations-service): register module in aggregator
Gcolon021 Jul 10, 2026
7b7e15e
feat(hpds-model): add v1->v3 query translation
Gcolon021 Jul 10, 2026
eaf4970
test(api-model): update QueryRequestTest for v3 query shape
Gcolon021 Jul 10, 2026
c177fb6
feat(hpds-query-service): add query/search service and controller sur…
Gcolon021 Jul 10, 2026
ea2cc5f
feat(hpds-query-service): add aggregate query and obfuscation surfaces
Gcolon021 Jul 10, 2026
8d013b0
test(hpds-query-service): add unit and integration tests for query/se…
Gcolon021 Jul 10, 2026
366191e
build(hpds-query-service): register module in aggregator
Gcolon021 Jul 10, 2026
53d3a5a
feat(audit): record adapter caller (X-Client-Type) in shared audit ev…
Gcolon021 Jul 10, 2026
24738ce
build: restore full module aggregator + CI (post-legacy)
Gcolon021 Jul 10, 2026
b462f2e
chore!: remove legacy pic-sure modules (superseded by gateway + servi…
Gcolon021 Jul 10, 2026
c3f06a2
chore(import): import PIC-SURE-Visualization at 1988897e2 as services…
Gcolon021 Jul 11, 2026
2f9a32c
chore(import): import pic-sure-auth-microapp at 114e56b77 as services…
Gcolon021 Jul 11, 2026
85d2487
chore(import): import PIC-SURE-Logging at 0ed1c26c3 as services/pic-s…
Gcolon021 Jul 11, 2026
0aaa1f4
chore(import): import pic-sure-hpds at 3f89e144c as services/pic-sure…
Gcolon021 Jul 11, 2026
7b39dbc
chore(import): import pic-sure-services at c8620b323 as services/pic-…
Gcolon021 Jul 11, 2026
5762d17
chore(import): import picsure-dictionary at 84c788f58 as services/pic…
Gcolon021 Jul 11, 2026
b86ebe3
feat(visualization): adopt parent+BOM, RestClient+HC5 via detect(); a…
Gcolon021 Jul 11, 2026
a902181
style(visualization): spotless-normalize (mechanical, repo formatter)
Gcolon021 Jul 11, 2026
f491c78
feat(pic-sure-services): adopt parent+BOM for info-service + uploader…
Gcolon021 Jul 11, 2026
52fc3c7
style(pic-sure-services): spotless-normalize (mechanical, repo format…
Gcolon021 Jul 11, 2026
9bd5ea8
feat(dictionary): adopt parent+BOM (3 modules), Java 25, RestClient+H…
Gcolon021 Jul 11, 2026
ef0fdc4
style(dictionary): spotless-normalize (mechanical, repo formatter)
Gcolon021 Jul 11, 2026
0d2ba54
feat(logging): adopt parent+BOM, Java 25 (stays Javalin; Jetty 11 BOM…
Gcolon021 Jul 11, 2026
c2a6dce
style(logging): spotless-normalize (mechanical, repo formatter)
Gcolon021 Jul 11, 2026
ebdd656
feat(psama): adopt parent+BOM, Java 25, RestClient over HC5; drop JUn…
Gcolon021 Jul 11, 2026
e1d3ecf
feat(hpds): adopt parent+BOM across 8 modules (HTTP convergence defer…
Gcolon021 Jul 11, 2026
689cf0b
style(hpds): spotless-normalize (mechanical, repo formatter)
Gcolon021 Jul 11, 2026
bf31c12
build: activate dependency-convergence + duplicate-responsibility bans
Gcolon021 Jul 14, 2026
ce77e3b
build: Spring Boot 3.5.9 -> 3.5.16 (root + platform lockstep)
Gcolon021 Jul 14, 2026
292e2ef
build: add Maven wrapper (Maven 3.9.9)
Gcolon021 Jul 14, 2026
94b8742
ci: workflows run ./mvnw; catch-all gains dependency caching
Gcolon021 Jul 14, 2026
4f7d9c3
build: spotless Eclipse formatter 4.26 -> 4.35 (no reactor reformat)
Gcolon021 Jul 16, 2026
55797fc
ci(secrets): gitleaks PR scan workflow, pre-push hook, .gitleaksignor…
Gcolon021 Jul 14, 2026
3a49b31
ci(deps): consolidated root dependabot.yml (maven reactor + actions)
Gcolon021 Jul 14, 2026
9db9d34
fix(hooks): pre-push gitleaks reads /dev/null, not the hook's ref lis…
Gcolon021 Jul 14, 2026
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11 changes: 11 additions & 0 deletions .github/dependabot.yml
Original file line number Diff line number Diff line change
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version: 2
updates:
- package-ecosystem: maven
directory: "/"
schedule:
interval: weekly
open-pull-requests-limit: 5
- package-ecosystem: github-actions
directory: "/"
schedule:
interval: weekly
20 changes: 20 additions & 0 deletions .github/release.yml
Original file line number Diff line number Diff line change
@@ -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:
- "*"
23 changes: 23 additions & 0 deletions .github/workflows/github-actions-deploy-snapshots.yml
Original file line number Diff line number Diff line change
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name: Maven Deploy Snapshots

on:
push:
branches:
- 'master'
- '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: Build with Maven
run: mvn --update-snapshots deploy
env:
GITHUB_TOKEN: ${{ github.token }}
20 changes: 20 additions & 0 deletions .github/workflows/github-actions-test.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
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'
cache: maven
- name: Test with Maven
run: ./mvnw --update-snapshots test
env:
GITHUB_TOKEN: ${{ github.token }}
21 changes: 21 additions & 0 deletions .github/workflows/label-checker.yml
Original file line number Diff line number Diff line change
@@ -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 }}

22 changes: 22 additions & 0 deletions .github/workflows/pic-sure-auth-microapp-test.yml
Original file line number Diff line number Diff line change
@@ -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 }}
22 changes: 22 additions & 0 deletions .github/workflows/pic-sure-hpds-test.yml
Original file line number Diff line number Diff line change
@@ -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 }}
22 changes: 22 additions & 0 deletions .github/workflows/pic-sure-logging-test.yml
Original file line number Diff line number Diff line change
@@ -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 }}
22 changes: 22 additions & 0 deletions .github/workflows/pic-sure-services-test.yml
Original file line number Diff line number Diff line change
@@ -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 }}
22 changes: 22 additions & 0 deletions .github/workflows/picsure-dictionary-test.yml
Original file line number Diff line number Diff line change
@@ -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: ${{ github.token }}
19 changes: 19 additions & 0 deletions .github/workflows/secrets-scan.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
name: secrets scan
on:
pull_request:
jobs:
gitleaks:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd #v6.0.2
with:
fetch-depth: 0
- name: Install gitleaks 8.30.1 (checksum-verified)
run: |
curl -sSfL -o /tmp/gitleaks.tar.gz https://github.com/gitleaks/gitleaks/releases/download/v8.30.1/gitleaks_8.30.1_linux_x64.tar.gz
echo "551f6fc83ea457d62a0d98237cbad105af8d557003051f41f3e7ca7b3f2470eb /tmp/gitleaks.tar.gz" | sha256sum -c -
tar -xzf /tmp/gitleaks.tar.gz -C /tmp gitleaks
- name: Scan PR commits
run: >
/tmp/gitleaks git --redact --no-banner
--log-opts="${{ github.event.pull_request.base.sha }}..${{ github.event.pull_request.head.sha }}" .
22 changes: 22 additions & 0 deletions .github/workflows/visualization-service-test.yml
Original file line number Diff line number Diff line change
@@ -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 }}
38 changes: 38 additions & 0 deletions .gitignore
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@@ -0,0 +1,38 @@
target/
pom.xml.tag
pom.xml.releaseBackup
pom.xml.versionsBackup
pom.xml.next
release.properties
dependency-reduced-pom.xml
.flattened-pom.xml
buildNumber.properties
.mvn/timing.properties
log/

#Eclipse
.project
.settings/
.classpath

#Intellij
.idea/
*.iml
*.iws

#Mac
.DS_Store


# Avoid ignoring Maven wrapper jar file (.jar files are usually ignored)
!/.mvn/wrapper/maven-wrapper.jar

# Claude Code: local-only files, never commit (plans, specs, reviews, tickets, settings)
.claude/
**/.claude/
docs/superpowers/
*.http

# TODO: Remove once development is complete
george_development_notes.md
fable-master-handoff.md
4 changes: 4 additions & 0 deletions .gitleaksignore
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@@ -0,0 +1,4 @@
# gitleaks false-positive fingerprints — one per line:
# <commit>:<file>:<rule-id>:<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.
3 changes: 3 additions & 0 deletions .mvn/wrapper/maven-wrapper.properties
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@@ -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
1 change: 1 addition & 0 deletions .sdkmanrc
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
java=25.0.3-tem
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