ci.yml

name: LAPIS-SILO

on:
  push:

concurrency:
  group: ci-${{ github.ref }}
  cancel-in-progress: true

env:
  DOCKER_DEPENDENCY_IMAGE_NAME: ghcr.io/genspectrum/lapis-silo-dependencies
  DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis-silo

jobs:
  formatting-check:
    name: Formatting Check
    runs-on: ubuntu-latest
    strategy:
      matrix:
        path:
          - check: 'src'
          - check: 'include'
            exclude: '(PerfEvent.hpp)'
    steps:
      - uses: actions/checkout@v4
      - name: Run clang-format style check
        uses: jidicula/clang-format-action@v4.14.0
        with:
          clang-format-version: '17'
          check-path: ${{ matrix.path['check'] }}
          exclude-regex: ${{ matrix.path['exclude'] }}

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

      - name: Generate dependency files hash
        id: files-hash
        run: |
          DIR_HASH=$(echo -n ${{ hashFiles('conanfile.py', 'conanprofile.docker', '.github/workflows/ci.yml', './Dockerfile_dependencies') }})
          echo "DIR_HASH=$DIR_HASH" >> $GITHUB_ENV

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

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

      - name: Check if image exists
        id: check-image
        run: |
          EXISTS=$(docker manifest inspect ${{ env.DOCKER_DEPENDENCY_IMAGE_NAME }}:${{ env.DIR_HASH }} > /dev/null 2>&1 && echo "true" || echo "false")
          echo "CACHE_HIT=$EXISTS" >> $GITHUB_ENV

      - name: Set up Docker Buildx
        if: env.CACHE_HIT == 'false'
        uses: docker/setup-buildx-action@v3

      - name: Build and push image if input files changed
        if: env.CACHE_HIT == 'false'
        uses: docker/build-push-action@v6
        with:
          context: .
          file: Dockerfile_dependencies
          push: true
          tags: ${{ steps.dockerMetadata.outputs.tags }}
          cache-from: type=gha,ref=builder-image-cache-${{ hashFiles('conanfile.py', 'Dockerfile') }}
          cache-to: type=gha,mode=min,ref=builder-image-cache-${{ hashFiles('conanfile.py', 'Dockerfile') }}
          platforms: linux/amd64,linux/arm64

      - name: Retag and push existing image if cache hit
        if: env.CACHE_HIT == 'true'
        run: |
          TAGS=(${{ steps.dockerMetadata.outputs.tags }})
          for TAG in "${TAGS[@]}"; do
            docker buildx imagetools create --tag $TAG ${{ env.DOCKER_DEPENDENCY_IMAGE_NAME }}:${{ env.DIR_HASH }}
          done

  dockerImageUnitTests:
    name: Build Docker Image and Run Unit Tests
    runs-on: ubuntu-latest
    needs: dependencyImage
    permissions:
      packages: write
    steps:
      - uses: actions/checkout@v4

      - name: Generate dependency files hash
        id: files-hash
        run: |
          DIR_HASH=$(echo -n ${{ hashFiles('conanfile.py', 'conanprofile.docker', '.github/workflows/ci.yml', './Dockerfile_dependencies') }})
          echo "DIR_HASH=$DIR_HASH" >> $GITHUB_ENV

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

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

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

      - name: Build unit test image
        uses: docker/build-push-action@v6
        with:
          context: .
          target: builder
          tags: builder
          load: true
          cache-from: type=gha,ref=${{ github.ref_name }}-image-cache
          cache-to: type=gha,mode=min,ref=${{ github.ref_name }}-image-cache
          build-args: |
            DEPENDENCY_IMAGE=ghcr.io/genspectrum/lapis-silo-dependencies:${{ env.DIR_HASH }}

      - name: Run tests
        uses: addnab/docker-run-action@v3
        with:
          image: builder
          run: ./silo_test

      - name: Build and push production image
        if: ${{ github.event_name == 'push' }}
        uses: docker/build-push-action@v6
        with:
          context: .
          push: true
          platforms: ${{ github.ref == 'refs/heads/main' && 'linux/amd64,linux/arm64' || 'linux/amd64' }}
          tags: ${{ steps.dockerMetadata.outputs.tags }}
          build-args: |
            DEPENDENCY_IMAGE=ghcr.io/genspectrum/lapis-silo-dependencies:${{ env.DIR_HASH }}

  endToEndTests:
    name: Run End To End Tests
    needs: dockerImageUnitTests
    runs-on: ubuntu-latest
    strategy:
      matrix:
        preprocessing-docker-compose: [
          docker-compose-for-tests-preprocessing-from-ndjson.yml
        ]
    steps:
      - uses: actions/checkout@v4

      - name: Use Node.js ${{ matrix.node-version }}
        uses: actions/setup-node@v4
        with:
          node-version: 18.x

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

      - name: npm install
        run: cd endToEndTests && npm ci

      - name: Check Format
        run: cd endToEndTests && npm run check-format

      - name: Docker Metadata
        id: dockerMetadata
        uses: docker/metadata-action@v5
        with:
          images: ${{ env.DOCKER_IMAGE_NAME }}
          tags: type=ref,event=branch

      - name: Start Docker Container and preprocess data
        run: docker compose -f ${{ matrix.preprocessing-docker-compose }} up
        env:
          SILO_IMAGE: ${{ steps.dockerMetadata.outputs.tags }}

      - name: Start Docker Container and run api
        run: docker compose -f docker-compose-for-tests-api.yml up -d --wait
        env:
          SILO_IMAGE: ${{ steps.dockerMetadata.outputs.tags }}

      - name: Run Tests
        run: cd endToEndTests && SILO_URL=localhost:8080 npm run test