Dockerhub stage

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,29 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+Thank you for taking the time to contribute an issue! 
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem in the current program to new available techology or software? Please describe and add links/citations if appropriate.**
+A clear and concise description of what the problem is or what the advance you would like us to incorporate is. Ex. when triaging structural variantS, I would like to [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/other-issue.md

@@ -0,0 +1,10 @@
+---
+name: Other issue
+about: Describe your issue, request or question here
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+Try to be as clear and precise as possible, adding sufficient detail and context.

.github/workflows/build_and_publish.yml

@@ -0,0 +1,25 @@
+name: Publish to Docker Hub
+
+on:
+ release:
+  types:
+   - created
+
+jobs:
+ docker-image-CI:
+   name: Docker Image CI
+   runs-on: ubuntu-latest
+   steps:
+
+    - name: Check out git repository
+      uses: actions/checkout@v4
+      with:
+        submodules: 'recursive'
+
+    - name: Publish main image (Dockerfile) to Registry
+      uses: elgohr/Publish-Docker-Github-Action@v5
+      with:
+        name: clinicalgenomics/phenopacket-api
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+        tags: "latest,${{ github.event.release.tag_name }}"

.github/workflows/keep_a_changelog.yml

@@ -0,0 +1,15 @@
+name: "Changelog Reminder"
+on:
+  pull_request:
+      types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
+
+jobs:
+  # Enforces the update of a changelog file on every pull request
+  changelog:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: dangoslen/changelog-enforcer@v3
+      with:
+        changeLogPath: 'CHANGELOG.md'
+        skipLabels: 'Skip-Changelog'

.github/workflows/push_build_latest_docker.yml

@@ -0,0 +1,26 @@
+name: Publish to Docker Hub
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+ docker-image-CI:
+   name: Docker Image CI
+   runs-on: ubuntu-latest
+   steps:
+
+    - name: Check out git repository
+      uses: actions/checkout@v4
+      with:
+        submodules: 'recursive'
+
+
+    - name: Publish main image (Dockerfile) to Registry
+      uses: elgohr/Publish-Docker-Github-Action@v5
+      with:
+        name: clinicalgenomics/phenopacket-api-stage
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+        tags: "latest, ${{steps.branch-name.outputs.current_branch}}"

.github/workflows/woke.yml

@@ -0,0 +1,15 @@
+name: woke
+on:
+  - pull_request
+jobs:
+  woke:
+    name: Non-inclusive language check with woke
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: woke
+        uses: get-woke/woke-action@v0
+        with:
+          fail-on-error: false

CHANGELOG.md

@@ -0,0 +1,16 @@
+# Changelog
+
+## [unreleased]
+### Changed
+- Allow configuring multiple trusted CORS origins
+- CG production Docker automation
+- CG stage Docker automation
+- More recent docker base image
+
+## Legacy version history
+
+## 1.1.0
+- Generate password for customformdata
+- Backend status
+## 1.0.0
+- Initial release

Dockerfile

@@ -1,4 +1,4 @@
-FROM node:16-alpine as base
+FROM node:22-alpine as base
 # Create app directory
 WORKDIR /usr/src/app
 COPY package*.json ./
@@ -11,14 +11,18 @@ FROM base as build-stage
 RUN npm run build
 
 # # stage 2 - copy from buildstage to "prod image"
-FROM node:16-alpine as production-stage
+FROM node:22-alpine as production-stage
 WORKDIR /app
 RUN chown node:node .
 USER node
 COPY package*.json ./
 COPY tsconfig.json ./
+COPY apischema.json ./
+
 RUN npm ci --only=production
 COPY --from=build-stage /usr/src/app/dist ./dist
 
+COPY ./phenopacket-schema ./phenopacket-schema
+
 EXPOSE 3000
-CMD ["node", "/app/dist/index.js"]
+CMD ["node", "/app/dist/index.js"]

README.md

@@ -43,14 +43,3 @@ Express + Typescript + MongoDB stack for storing Phenopackets.
 `npm install -g protobuf2swagger`
 
 `protobuf2swagger`
-
-## Version history
-
-### 1.0.0
-
-- Initial release
-
-### 1.1.0
-
-- Generate password for customformdata
-- Backend status

src/index.ts

@@ -14,7 +14,7 @@ app.use(express.json({ limit: "100mb" }));
 app.use(express.urlencoded({ extended: true }));
 app.use(
   cors({
-    origin: process.env.ALLOWED_ORIGIN,
+    origin: process.env.ALLOWED_ORIGIN.split(";"),
   })
 );