main.yml

name: CI/CD

on:
  push:
    branches:
      - main
  pull_request:
    types: [opened, reopened, ready_for_review, synchronize]

jobs:
  test:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2
    - uses: r-lib/actions/setup-r@v2
    - name: Install lintr
      run: Rscript -e 'install.packages("lintr", repos = "https://cloud.r-project.org")'
    - name: Run linter
      run: make lint
    - name: Check that tests have been run successfully
      env:
        BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
      run: |
        if [ ! -f tests/testing_complete.txt ]; then
          echo "Tests have not been run successfully,  please run Rscript tests/testthat/run_tests.R and commit the results"
          exit 1
        fi
        if [ "$BRANCH_NAME" != "main" ] && ! grep -q "$BRANCH_NAME" tests/testing_complete.txt; then
          echo "Tests have not been run successfully for branch: $BRANCH_NAME, please run Rscript tests/testthat/run_tests.R and commit the results"
          exit 1
        fi

  build:
    runs-on: ubuntu-latest
    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
    steps:
    - uses: actions/checkout@v2
    
    - name: Set up Docker Buildx
      uses: docker/setup-buildx-action@v2
    
    - name: Clean up Docker system and free up space
      run: |
        docker system prune -af --volumes || true
        docker builder prune -af || true
        sudo rm -rf /usr/share/dotnet
        sudo rm -rf /usr/local/lib/android
        sudo rm -rf /opt/ghc
        sudo rm -rf "/usr/local/share/boost"
        sudo rm -rf "$AGENT_TOOLSDIRECTORY"
        df -h
    
    - name: Set up SSH Key
      run: |
        mkdir -p ~/.ssh
        echo "${{ secrets.ORACLE_SSH_PRIVATE_KEY }}" > ~/.ssh/oracle_gpmap.key
        chmod 600 ~/.ssh/oracle_gpmap.key
        ssh-keyscan -H "${{ secrets.ORACLE_SERVER }}" >> ~/.ssh/known_hosts

    - name: Login to Docker Hub
      uses: docker/login-action@v1
      with:
        username: ${{ secrets.DOCKER_USERNAME }}
        password: ${{ secrets.DOCKER_PASSWORD }}

    - name: Build and push API image
      uses: docker/build-push-action@v4
      with:
        file: docker/uploadDockerfile
        context: .
        push: true
        load: false
        no-cache: true
        provenance: false
        cache-from: ""
        cache-to: ""
        tags: |
          mrcieu/genotype-phenotype-upload:latest
          mrcieu/genotype-phenotype-upload:${{ github.sha }}
        platforms: linux/amd64
    
    - name: Clean up Docker after build
      if: always()
      run: |
        docker system prune -af --volumes || true
        docker builder prune -af || true
        # Remove the base image if it's taking up space
        docker rmi mrcieu/genotype-phenotype-map:1.0.0 || true
        df -h

    - name: Populate .env files and copy deployment files to server
      env:
        ORACLE_SERVER: ${{ secrets.ORACLE_SERVER }}
      run: |
        FILES=".env.pipeline_worker"
        scp -i ~/.ssh/oracle_gpmap.key $FILES opc@${ORACLE_SERVER}:/home/opc/genotype-phenotype-api/