galaxyproject/brc-analytics (opens in new tab)

name: Check pull request title
on:
  pull_request:
    types: [edited, opened, synchronize, reopened]

jobs:
  check-pr-title:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-node@v4
        with:
          node-version: "22.12.0"
      - name: Cache npm cache
        uses: actions/cache@v4
        with:
          path: ~/.npm
          key: ${{ runner.os }}-node-${{ hashFiles('package-lock.json') }}
      - name: Install dependencies
        run: npm ci
      - name: Check pull request title for Conventional Commits format and GitHub issue number
        uses: ./.github/actions/check-input-commit-message
        with:
          message: ${{ github.event.pull_request.title }}

name: Deploy to S3 and CloudFront

on:
  push:
    branches: [main]
permissions:
  id-token: write
  contents: read

concurrency:
  group: dev-deploy
  cancel-in-progress: false

jobs:
  build-and-deploy:
    if: github.repository == 'galaxyproject/brc-analytics'
    runs-on: ubuntu-latest

    steps:
      - name: Checkout Code
        uses: actions/checkout@v3
        with:
          fetch-depth: 0

      - name: Setup Node.js
        uses: actions/setup-node@v3
        with:
          node-version: "22.12.0"

      - name: Install Dependencies
        run: npm ci

      - name: Build Next.js Site
        env:
          NEXT_PUBLIC_BASE_PATH: ""
        run: npm run build:dev

      - name: Configure AWS Credentials
        uses: aws-actions/configure-aws-credentials@v4
        with:
          role-to-assume: arn:aws:iam::${{ secrets.DEV_AWS_ACCOUNT_ID }}:role/${{ secrets.DEV_AWS_ROLE_NAME }}
          role-session-name: ${{ secrets.DEV_ROLE_SESSION_NAME }}
          aws-region: ${{ secrets.DEV_AWS_REGION }}

      - name: Sync to S3
        env:
          SRCDIR: out/
        run: |
          aws s3 sync $SRCDIR s3://${{ secrets.DEV_S3_BUCKET_NAME }} --delete

      - name: Invalidate CloudFront Cache
        run: |
          aws cloudfront create-invalidation --distribution-id ${{ secrets.DEV_CLOUDFRONT_DISTRIBUTION_ID }} --paths "/*"

name: Publish Release

on:
  workflow_dispatch:
    inputs:
      release_id:
        description: "Tag name of the draft release to publish (e.g., v0.19.0)"
        required: true

permissions:
  actions: write
  contents: write
  pull-requests: write

jobs:
  publish-release:
    if: github.repository == 'galaxyproject/brc-analytics'
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@v4
        with:
          fetch-depth: 0

      - name: Setup Node.js
        uses: actions/setup-node@v4
        with:
          node-version: "22.12.0"

      - name: Configure git
        run: |
          git config user.name github-actions
          git config user.email github-actions@github.com

      - name: Get release info
        id: get_release
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          RELEASE_ID: ${{ github.event.inputs.release_id }}
        run: |
          RELEASE_TAG=$(gh release view $RELEASE_ID --json tagName -q '.tagName')
          VERSION=${RELEASE_TAG#v}
          echo "tag=$RELEASE_TAG" >> $GITHUB_OUTPUT
          echo "version=$VERSION" >> $GITHUB_OUTPUT

      - name: Merge main to production
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        run: |
          # Fetch all branches
          git fetch origin main production

          # Checkout production and merge main
          git checkout production
          git merge origin/main -m "Release ${{ steps.get_release.outputs.tag }}: merge main to production"

          # Move the release tag to point to this merge commit so git describe
          # shows the correct version (e.g., "v0.21.0" not "v0.21.0-1-gXXX")
          git tag -f ${{ steps.get_release.outputs.tag }}

          # Push production branch and updated tag
          git push origin production
          git push origin ${{ steps.get_release.outputs.tag }} --force

      - name: Trigger production deploy
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        run: |
          # GITHUB_TOKEN pushes don't trigger workflows, so we manually trigger the deploy
          gh workflow run publish.yml --ref production

      - name: Publish release
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          RELEASE_ID: ${{ github.event.inputs.release_id }}
        run: |
          gh release edit "$RELEASE_ID" --draft=false

      - name: Bump main to next development version
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        run: |
          CURRENT_VERSION="${{ steps.get_release.outputs.version }}"

          # Parse version components
          IFS='.' read -r MAJOR MINOR PATCH <<< "$CURRENT_VERSION"

          # Always do minor bump: 0.19.0 → 0.20.0
          NEXT_VERSION="${MAJOR}.$((MINOR + 1)).0"

          echo "Bumping from $CURRENT_VERSION to $NEXT_VERSION"

          BRANCH_NAME="release/bump-to-$NEXT_VERSION"

          # Create branch from main
          git checkout main
          git pull origin main
          git checkout -b "$BRANCH_NAME"

          # Update version
          npm version $NEXT_VERSION --no-git-tag-version

          # Commit changes
          git add package.json package-lock.json
          git commit -m "chore: bump version to $NEXT_VERSION for next development cycle [skip ci]"

          # Push branch
          git push -u origin "$BRANCH_NAME"

          # Create PR
          gh pr create \
            --title "chore: bump version to $NEXT_VERSION" \
            --body "Automated version bump after release ${{ steps.get_release.outputs.tag }}.

          - \`production\` branch = ${{ steps.get_release.outputs.version }} (stable)
          - \`main\` branch = $NEXT_VERSION (development)" \
            --head "$BRANCH_NAME" \
            --base main

name: Deploy to S3 and CloudFront

on:
  push:
    branches:
      # - main  # todo, consolidate auth approach and merge dev-deploy into this.
      - production
  workflow_dispatch:
    branches:
      - production

concurrency:
  group: prod-deploy
  cancel-in-progress: false

jobs:
  build-and-deploy:
    if: github.repository == 'galaxyproject/brc-analytics'
    runs-on: ubuntu-latest
    environment: ${{ github.ref == 'refs/heads/production' && 'production' || 'development' }}

    steps:
      - name: Checkout Code
        uses: actions/checkout@v3
        with:
          fetch-depth: 0

      - name: Setup Node.js
        uses: actions/setup-node@v3
        with:
          node-version: "22.12.0"

      - name: Install Dependencies
        run: npm ci

      - name: Build Next.js Site
        env:
          NEXT_PUBLIC_BASE_PATH: ""
        run: npm run build:prod

      - name: Configure AWS Credentials
        uses: aws-actions/configure-aws-credentials@v3
        with:
          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
          aws-region: ${{ secrets.AWS_REGION }}

      - name: Sync to S3
        env:
          SRCDIR: out/
        run: |
          aws s3 sync $SRCDIR s3://${{ secrets.S3_BUCKET_NAME }} --delete

      - name: Invalidate CloudFront Cache
        run: |
          aws cloudfront create-invalidation --distribution-id ${{ secrets.CLOUDFRONT_DISTRIBUTION_ID }} --paths "/*"

name: Release Drafter

on:
  push:
    branches:
      - main
  pull_request_target:
    types: [opened, reopened, synchronize]
  workflow_dispatch:
    inputs:
      version:
        description: "Release version"
        required: true

permissions:
  contents: read

jobs:
  update_release_draft:
    permissions:
      contents: write
      pull-requests: write
    if: github.repository == 'galaxyproject/brc-analytics'
    runs-on: ubuntu-latest
    steps:
      - uses: release-drafter/release-drafter@v6
        with:
          config-name: release-drafter.yml
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

name: Run checks
on: [pull_request]

jobs:
  e2e-tests:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-node@v4
        with:
          node-version: "22.12.0"
      - name: Cache npm cache
        uses: actions/cache@v4
        with:
          path: ~/.npm
          key: ${{ runner.os }}-node-${{ hashFiles('package-lock.json') }}
      - name: Install dependencies
        run: npm ci
      - name: Build production bundle
        run: npm run build:local
      - name: Install Playwright browsers
        run: npx playwright install --with-deps
      - name: Run e2e tests
        run: npm run test:e2e
      - name: Upload test results
        uses: actions/upload-artifact@v4
        if: failure()
        with:
          name: playwright-report
          path: playwright-report/
          retention-days: 7

  run-checks:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-node@v4
        with:
          node-version: "22.12.0"
      - name: Cache npm cache
        uses: actions/cache@v4
        with:
          path: ~/.npm
          key: ${{ runner.os }}-node-${{ hashFiles('package-lock.json') }}
      - name: Install dependencies
        run: npm ci
      - name: Run Prettier
        run: npm run check-format
      - name: Run Linter (ESLint)
        run: npm run lint
      - name: Type Check
        run: npx tsc --noEmit

      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.12.4"
          cache: "pip"
          cache-dependency-path: "./catalog/build/py/requirements.txt"
      - name: Install Python dependencies
        run: pip install -r ./catalog/build/py/requirements.txt
      - name: Run linkml-lint
        # Run linting on the LinkML schemas, to enforce conventions such as in naming, and to catch simple errors.
        run: npm run lint-schema
      - name: Test LinkML Python generation
        # Generate Python code from the main LinkML schemas, discarding the output; this will catch more subtle errors such as references to nonexistent elements.
        run: npm run test-gen-python
      - name: Validate BRC catalog files
        # Validate the catalog source files against their corresponding LinkML schemas.
        run: npm run validate-brc-catalog
      - name: Validate GA2 catalog files
        # Validate the GA2 catalog source files.
        run: npm run validate-ga2-catalog
      - name: poetry lint
        # Validate the GA2 catalog source files.
        run: poetry check -P catalog/py_package/

  api-tests:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v6

      - name: Set up Python
        uses: actions/setup-python@v6
        with:
          python-version: "3.12"

      - name: Install uv
        uses: astral-sh/setup-uv@v7

      - name: Create backend .env file
        run: cp backend/api/.env.example backend/api/.env

      - name: Build catalog data
        run: |
          npm ci
          npm run build-brc-db

      - name: Start backend services
        run: |
          cd backend
          docker compose up -d --build
          docker compose logs

      - name: Wait for services to be healthy
        run: |
          timeout 60 bash -c 'until curl -s http://localhost:8080/api/v1/health | grep -q healthy; do sleep 2; done'

      - name: Run API smoke tests
        run: |
          cd backend/api
          uv run --extra dev pytest tests/ -v

      - name: Show logs on failure
        if: failure()
        run: |
          cd backend
          docker compose logs

      - name: Stop backend services
        if: always()
        run: |
          cd backend
          docker compose down -v

name: Update brc data catalog

on:
  schedule:
    # At 10:00 on Sunday
    - cron: "0 10 * * 0"

  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:

jobs:
  update-catalog:
    if: github.repository == 'galaxyproject/brc-analytics'
    permissions:
      contents: write
      pull-requests: write
    runs-on: ubuntu-latest
    steps:
      - uses: actions/setup-python@v5
        with:
          python-version: "3.12"
          architecture: "x64"
      - name: Checkout
        uses: actions/checkout@v4
      - name: Install python dependencies
        run: pip install -r ./catalog/build/py/requirements.txt
      - name: Install npm dependencies
        run: npm ci
      - name: Run catalog script
        run: npm run build-brc-from-ncbi
      - name: Get current date
        id: date
        run: echo "date=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
      - name: Create Pull Request
        uses: peter-evans/create-pull-request@v7
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          title: "chore: update data catalog ${{ steps.date.outputs.date }}"
          commit-message: "chore: update data catalog ${{ steps.date.outputs.date }}"