lapis.yml

name: LAPIS

on: [ push ]

env:
  DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis

jobs:
  Tests:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Set up JDK
        uses: actions/setup-java@v4
        with:
          java-version: '21'
          distribution: 'adopt'
      - name: Setup Gradle
        uses: gradle/actions/setup-gradle@v4
      - name: Execute Tests
        working-directory: lapis
        run: ./gradlew test
      - name: Check Format And Lint
        working-directory: lapis
        run: ./gradlew ktlintCheck

  dockerImage:
    name: Build Docker Image
    runs-on: ubuntu-latest
    permissions:
      packages: write
    steps:
      - uses: actions/checkout@v4

      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v3

      - name: Login to GitHub Container Registry
        uses: docker/login-action@v3
        with:
          registry: ghcr.io
          username: ${{ github.actor }}
          password: ${{ secrets.GITHUB_TOKEN }}

      - name: Docker metadata
        id: dockerMetadata
        uses: docker/metadata-action@v5
        with:
          images: ${{ env.DOCKER_IMAGE_NAME }}
          tags: |
            type=ref,event=branch,enable=${{ github.ref != format('refs/heads/{0}', 'main') }}
            type=raw,value=latest,enable=${{ github.ref == format('refs/heads/{0}', 'main') }}

      - name: Build application image
        uses: docker/build-push-action@v6
        with:
          context: ./lapis
          tags: ${{ steps.dockerMetadata.outputs.tags }}
          cache-from: type=gha,scope=lapis-${{ github.ref }}
          cache-to: type=gha,mode=max,scope=lapis-${{ github.ref }}
          platforms: ${{ github.ref == 'refs/heads/main' && 'linux/amd64,linux/arm64' || 'linux/amd64' }}
          push: false

      - name: Build and push versioned image
        uses: docker/build-push-action@v6
        with:
          context: ./lapis
          file: ./lapis/Dockerfile_versionSupplier
          tags: ${{ steps.dockerMetadata.outputs.tags }}
          platforms: ${{ github.ref == 'refs/heads/main' && 'linux/amd64,linux/arm64' || 'linux/amd64' }}
          push: true
          build-args: |
            BASE_IMAGE=${{ steps.dockerMetadata.outputs.tags }}
            VERSION=${{ github.sha }}

  endToEndTests:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Set up JDK
        uses: actions/setup-java@v4
        with:
          java-version: '21'
          distribution: 'adopt'

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

      - name: Setup Gradle
        uses: gradle/actions/setup-gradle@v4

      - name: Build OpenAPI Spec
        working-directory: lapis
        run: ./gradlew generateOpenApiDocs

      - name: Build OpenAPI Spec Protected
        working-directory: lapis
        run: ./gradlew generateOpenApiDocs -PopennessLevel=protected

      - name: Build OpenAPI Spec Multi segmented
        working-directory: lapis
        run: ./gradlew generateOpenApiDocs -Psegmented=true

      - name: Cache .npm
        uses: actions/cache@v4
        with:
          path: ~/.npm
          key: ${{ runner.os }}-node-${{ hashFiles('lapis-e2e/**/package-lock.json') }}

      - name: Prepare Tests
        run: npm ci
        working-directory: lapis-e2e

      - name: Generate Lapis Client
        run: npm run generateLapisClient
        working-directory: lapis-e2e

      - name: Generate Lapis Client Protected
        run: npm run generateLapisClientProtected
        working-directory: lapis-e2e

      - name: Generate Lapis Client Multi Segmented
        run: npm run generateLapisClientMultiSegmented
        working-directory: lapis-e2e

      - name: Check Format
        run: npm run check-format
        working-directory: lapis-e2e

      - name: Docker metadata
        id: dockerMetadata
        uses: docker/metadata-action@v5
        with:
          images: ${{ env.DOCKER_IMAGE_NAME }}
          tags: |
            type=ref,event=branch,enable=${{ github.ref != 'refs/heads/main' }}
            type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' }}

      - name: Get LAPIS Branch Tag
        id: lapisBranchTag
        env:
          TAG: ${{ steps.dockerMetadata.outputs.tags }}
        run: echo "lapisTag=${TAG##*:}" >> $GITHUB_OUTPUT

      - name: Wait for Docker Image
        uses: lewagon/wait-on-check-action@v1.3.4
        with:
          ref: ${{ github.ref }}
          check-name: Build Docker Image
          repo-token: ${{ secrets.GITHUB_TOKEN }}

      - name: Start SILO and LAPIS and Run Tests
        run: |
          docker compose -f lapis/docker-compose.yml pull
          docker compose -f lapis/docker-compose.yml up -d --wait
          cd lapis-e2e && npm run test
        env:
          SILO_TAG: latest
          LAPIS_TAG: ${{ steps.lapisBranchTag.outputs.lapisTag }}

      - name: Store Logs
        if: ${{ always() }}
        run: |
          cd lapis
          mkdir p e2e-logs
          docker compose logs silo > e2e-logs/silo.log
          docker compose logs siloPreprocessing > e2e-logs/siloPreprocessing.log
          docker compose logs siloMultisegmented > e2e-logs/siloMultisegmented.log
          docker compose logs siloPreprocessingMultisegmented > e2e-logs/siloPreprocessingMultisegmented.log
          docker compose logs lapisOpen > e2e-logs/lapisOpen.log
          docker compose logs lapisProtected > e2e-logs/lapisProtected.log
          docker compose logs lapisMultiSegmented > e2e-logs/lapisMultiSegmented.log
        env:
          SILO_TAG: latest
          LAPIS_TAG: ${{ steps.lapisBranchTag.outputs.lapisTag }}

      - name: Upload logs
        if: ${{ always() }}
        uses: actions/upload-artifact@v4
        with:
          name: logs
          path: lapis/e2e-logs