ci.yml

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: build

on:
  push:
    branches: [main, develop, 'GEN*', 'gen*']
    paths-ignore:
      - '**.md'                            # All Markdown files
      - '**/docs/**'                       # Documentation directory
      - '.github/workflows/codeql.yml'     # Code scanner
      - '.github/workflows/build_docs.yml' # mkdocs GH workflow

  pull_request:
      types:
        - opened
        - reopened

  release:
    types:
      - created

env:
  REGISTRY: ghcr.io
  IMAGE_NAME: ${{ github.repository }}
  TEST_PROJECT_SYNID: syn7208886

jobs:

  determine-changes:
    runs-on: ubuntu-latest
    outputs:
      non-test-changes: ${{ steps.get-changes.outputs.non-test-changes }}
    steps:
      - name: Checkout Code
        uses: actions/checkout@v3
        with:
          fetch-depth: 0

      - name: Determine Changes
        id: get-changes
        run: |
          if [ "${{ github.event_name }}" == "push" ]; then
            echo "Handling a push event..."
            ALL_CHANGED_FILES=$(git diff --name-only HEAD^ HEAD)
          elif [ "${{ github.event_name }}" == "pull_request" ]; then
            echo "Handling a pull request event..."
            git fetch origin ${{ github.base_ref }}
            ALL_CHANGED_FILES=$(git diff --name-only origin/${{ github.base_ref }} HEAD)
          fi
          echo "All Changed Files: $ALL_CHANGED_FILES"
          NON_TEST_CHANGES=$(echo "$ALL_CHANGED_FILES" | grep -v '^tests/' || true)
          echo "Non-Test Changes: $NON_TEST_CHANGES"
          echo "::set-output name=non-test-changes::$NON_TEST_CHANGES"

  test:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.8, 3.9]
    steps:
    - uses: actions/checkout@v4
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        sudo apt-get install -y bedtools
        python -m pip install --upgrade pip
        pip install flake8 pytest pytest-cov cython
        pip install .
        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
    # - name: Lint with flake8
    #   run: |
    #     # stop the build if there are Python syntax errors or undefined names
    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
    #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
    - name: Test with pytest
      run: |
        pytest tests/ --cov=genie --cov=genie_registry --cov-report=html
    - name: Upload pytest test results
      uses: actions/upload-artifact@v4
      with:
        name: pytest-results-${{ matrix.python-version }}
        path: htmlcov
      # Use always() to always run this step to publish test results when there are test failures
      if: ${{ always() }}


  lint:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: psf/black@stable
        with:
            version: "~=23.12"

  build-container:
    needs: [test, lint]
    runs-on: ubuntu-latest
    permissions:
      contents: read
      packages: write

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Setup Docker buildx
        uses: docker/setup-buildx-action@v3

      - name: Log into registry ${{ env.REGISTRY }}
        uses: docker/#-action@v3
        with:
          registry: ${{ env.REGISTRY }}
          username: ${{ github.actor }}
          password: ${{ secrets.GITHUB_TOKEN }}

      - name: Extract Docker metadata
        id: meta
        uses: docker/metadata-action@v5
        with:
          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
      
      - name: Format tags as registry refs
        id: registry_refs
        env:
          TAGS: ${{ steps.meta.outputs.json }}
        run: |
          echo tags=$(echo $TAGS | jq '.tags[] | "type=registry,ref=" + . + "_cache"| @text') >> $GITHUB_OUTPUT

      - name: Build and push Docker image
        id: build-and-push
        uses: docker/build-push-action@v5
        if: github.event_name != 'pull_request'
        with:
          context: .
          push: true
          provenance: false
          tags: ${{ steps.meta.outputs.tags }}
          labels: ${{ steps.meta.outputs.labels }}
          cache-from: ${{ steps.registry_refs.outputs.tags }},mode=max
          cache-to: ${{ steps.registry_refs.outputs.tags }},mode=max

  integration-tests:
    needs: [determine-changes, lint, test, build-container]
    runs-on: ubuntu-latest
    if: ${{ needs.determine-changes.outputs.non-test-changes }}
    steps:
    - name: Checkout repository
      uses: actions/checkout@v4

    - name: Extract Branch Name
      run: |
        if [ "$GITHUB_HEAD_REF" != "" ]; then
          echo "BRANCH_NAME=$GITHUB_HEAD_REF" >> $GITHUB_ENV
        else
          echo "BRANCH_NAME=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV
        fi

    - name: Pull Public Docker Image from GHCR
      run: |
        docker pull ghcr.io/sage-bionetworks/genie:${{ env.BRANCH_NAME }}

    - name: Start Docker Container
      run: |
        docker run -d --name genie-container \
          -e SYNAPSE_AUTH_TOKEN="${{ secrets.SYNAPSE_AUTH_TOKEN }}" \
          ghcr.io/sage-bionetworks/genie:${{ env.BRANCH_NAME }} \
          sh -c "while true; do sleep 1; done"
    
    - name: Run validation in test pipeline
      run: |
        docker exec genie-container \
        python3 /root/Genie/bin/input_to_database.py \
            mutation \
            --project_id ${{ env.TEST_PROJECT_SYNID }} \
            --onlyValidate \
            --genie_annotation_pkg /root/annotation-tools
    
    - name: Run processing on mutation data in test pipeline
      run: |
        docker exec genie-container \
        python3 /root/Genie/bin/input_to_database.py mutation \
            --project_id ${{ env.TEST_PROJECT_SYNID }} \
            --genie_annotation_pkg /root/annotation-tools \
            --createNewMafDatabase

    - name: Run processing on non-mutation data in test pipeline
      run: |
        docker exec genie-container \
        python3 /root/Genie/bin/input_to_database.py main \
            --project_id ${{ env.TEST_PROJECT_SYNID }}

    - name: Run consortium release in test pipeline
      run: |
        docker exec genie-container \
        python3 /root/Genie/bin/database_to_staging.py Jan-2017 ../cbioportal TEST --test

    - name: Run public release in test pipeline
      run: |
        docker exec genie-container \
        python3 /root/Genie/bin/consortium_to_public.py Jan-2017 ../cbioportal TEST --test

    - name: Stop and Remove Docker Container
      run: docker stop genie-container && docker rm genie-container

  deploy:
    needs: [test, lint, build-container, integration-tests]
    runs-on: ubuntu-latest
    if: github.event_name == 'release'
    permissions:
      id-token: write
    steps:
    - uses: actions/checkout@v4
    - name: Set up Python
      uses: actions/setup-python@v5
      with:
        python-version: '3.x'
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install setuptools wheel build
    - name: Build distributions
      run: python -m build
    - name: Publish to pypi
      uses: pypa/gh-action-pypi-publish@release/v1