ci.yml

name: LAPIS-SILO

on:
  pull_request:
  push:
    branches:
      - main

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

      - 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: Determine HEAD_SHA
        run: |
          if [[ "${{ github.event_name }}" == "pull_request" ]]; then
            echo "HEAD_SHA=${{ github.event.pull_request.head.sha }}" >> $GITHUB_ENV
          else
            echo "HEAD_SHA=${{ github.sha }}" >> $GITHUB_ENV
          fi

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

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

      - name: Determine platforms for build
        run: |
          echo "PLATFORMS=amd64 " >> $GITHUB_ENV

          # Write the current labels to a file
          cat <<EOF > event.json
          ${{ toJSON(github.event.pull_request.labels) }}
          EOF

          # Check if we are on main or the PR has the label 'arm-image'
          if [[ "$GITHUB_REF" == "refs/heads/main" ]] || jq -e '.[] | select(.name == "arm-image")' event.json > /dev/null; then
            echo "PLATFORMS+=arm64" >> $GITHUB_ENV
            EXISTS=$(docker manifest inspect \
              ${{ env.DOCKER_DEPENDENCY_IMAGE_NAME }}:filehash-${{ env.DIR_HASH }} \
              | jq '.manifests | map(.platform.architecture) | contains(["arm64"])') > /dev/null 2>&1 && echo "true" || echo "false"
            echo "CACHE_HIT=$EXISTS" >> $GITHUB_ENV
          fi

      - 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: ${{ env.DOCKER_DEPENDENCY_IMAGE_NAME }}:filehash-${{ env.DIR_HASH }}
          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: ${{ env.PLATFORMS }}

      - name: Tag dependency image with commit hash
        run: |
          docker buildx imagetools create \
            --tag ${{ env.DOCKER_DEPENDENCY_IMAGE_NAME }}:commit-${{ env.HEAD_SHA }} \
            ${{ env.DOCKER_DEPENDENCY_IMAGE_NAME }}:filehash-${{ env.DIR_HASH }}

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

      - name: Build and push production image
        uses: docker/build-push-action@v6
        with:
          context: .
          push: true
          platforms: ${{ env.PLATFORMS }}
          cache-from: type=gha,ref=${{ github.ref_name }}-image-cache
          cache-to: type=gha,mode=min,ref=${{ github.ref_name }}-image-cache
          tags: ${{ steps.dockerMetadataImage.outputs.tags }}
          build-args: |
            DEPENDENCY_IMAGE=${{ env.DOCKER_DEPENDENCY_IMAGE_NAME }}:commit-${{ env.HEAD_SHA }}

      - 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=${{ env.DOCKER_DEPENDENCY_IMAGE_NAME }}:commit-${{ env.HEAD_SHA }}

      - name: Run unit tests
        run: |
          docker run \
            --entrypoint "./silo_test" \
            builder

  endToEndTests:
    name: Run End To End Tests
    needs: dockerImage
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

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

      - name: Determine HEAD_SHA
        run: |
          if [[ "${{ github.event_name }}" == "pull_request" ]]; then
            echo "HEAD_SHA=${{ github.event.pull_request.head.sha }}" >> $GITHUB_ENV
          else
            echo "HEAD_SHA=${{ github.sha }}" >> $GITHUB_ENV
          fi

      - 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: Start Docker Container and preprocess data
        run: docker compose -f docker-compose-for-tests-preprocessing-from-ndjson.yml up
        env:
          SILO_IMAGE: ${{ env.DOCKER_IMAGE_NAME }}:commit-${{ env.HEAD_SHA }}

      - name: Start Docker Container and run api
        run: docker compose -f docker-compose-for-tests-api.yml up -d --wait
        env:
          SILO_IMAGE: ${{ env.DOCKER_IMAGE_NAME }}:commit-${{ env.HEAD_SHA }}

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

  linterChanges:
    name: Build/Run linter on changed files
    needs: dockerImage
    if: github.event_name == 'pull_request'
    runs-on: ubuntu-latest
    env:
      PR_NUMBER: ${{ github.event.number }}
    container:
      image: ghcr.io/genspectrum/lapis-silo-dependencies:commit-${{ github.event.pull_request.head.sha }}
    steps:
      - uses: actions/checkout@v4

      - shell: bash
        name: Configure and run clang-tidy on changed files
        run: |
          mv /src/build .
          cmake -DBUILD_WITH_CLANG_TIDY=on -D CMAKE_BUILD_TYPE=Debug -B build/Debug
          echo "Successfully configured cmake"
          files=""
          PAGE=1  
          while true; do
            page_files=$(curl -s \
           "https://api.github.com/repos/${{ github.repository }}/pulls/${PR_NUMBER}/files?per_page=100&page=$PAGE" \
           | jq -r '.[] | select(.status != "removed") | .filename')
            # If there are no more files, break the loop
            if [[ -z "$page_files" ]]; then
              break
            fi
            files+="$page_files"$'\n'
            PAGE=$((PAGE + 1))
          done
          
          echo "Changed files of this PR:"
          echo "$files"
          IFS=$'\n'
          for file in $files; do
            echo "Check ending for file: $file"
            if [[ $file == *.cpp ]]; then
              echo "Now linting the file: $file"
              echo "cmake --build build/Debug --target ${file%.cpp}.o"
              cmake --build build/Debug --target ${file%.cpp}.o
            fi
          done