gtf_tests.yml

name: GTF Comparison Tests

on:
  pull_request:
    branches: [ "develop", "master" ]
    paths:
      - '3rd-party-tools/build-indices/**'

jobs:
  test:
    runs-on: ubuntu-latest
    
    defaults:
      run:
        working-directory: 3rd-party-tools/build-indices

    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 pandas

    - name: Create output directories
      run: |
        mkdir -p test_output/comparison_files
        mkdir -p test_data/reference_outputs

    - name: Verify test data
      run: |
        if [ ! -f "test_data/test1.gtf" ]; then
          echo "Error: Required test file test_data/test1.gtf not found"
          ls -la test_data/
          exit 1
        fi
        if [ ! -f "Biotypes.tsv" ]; then
          echo "Error: Required Biotypes.tsv file not found"
          ls -la
          exit 1
        fi
        echo "Test files present:"
        ls -l test_data/test1.gtf Biotypes.tsv

    - name: Run GTF modification and comparison
      id: gtf_tests
      env:
        PYTHONPATH: ${{ github.workspace }}/3rd-party-tools/build-indices
      run: |
        # Run the unit tests
        python -m unittest test_gtf_comparison.py -v
      continue-on-error: true

    - name: Prepare artifacts
      if: always()
      run: |
        # Create directory for all artifacts
        mkdir -p artifact_output
        
        # Copy test input files
        cp test_data/test1.gtf artifact_output/
        cp Biotypes.tsv artifact_output/
        
        # Copy test outputs if they exist
        if [ -d "test_output" ]; then
          cp -r test_output/* artifact_output/
        fi
        
        # Copy reference outputs if they exist
        if [ -d "test_data/reference_outputs" ]; then
          mkdir -p artifact_output/reference_outputs
          cp -r test_data/reference_outputs/* artifact_output/reference_outputs/
        fi
        
        # Create manifest
        {
          echo "GTF Test Artifacts"
          echo "Generated: $(date)"
          echo ""
          echo "Test Input Files:"
          ls -l artifact_output/test1.gtf artifact_output/Biotypes.tsv
          echo ""
          echo "Test Outputs:"
          ls -R artifact_output/test_output/ 2>/dev/null || echo "No test outputs found"
          echo ""
          echo "Reference Outputs:"
          ls -R artifact_output/reference_outputs/ 2>/dev/null || echo "No reference outputs found"
        } > artifact_output/manifest.txt

    - name: Upload test artifacts
      if: always()
      uses: actions/upload-artifact@v4
      with:
        name: gtf-test-results
        path: |
          3rd-party-tools/build-indices/artifact_output/**/*
          3rd-party-tools/build-indices/test_output/**/*
          3rd-party-tools/build-indices/test_data/reference_outputs/**/*
        compression-level: 9
        retention-days: 14

    - name: Check test results
      if: always()
      run: |
        echo "=== Test Results Summary ==="
        
        # Check unit test results
        if [ "${{ steps.gtf_tests.outcome }}" == "success" ]; then
          echo "✅ GTF tests passed"
        else
          echo "❌ GTF tests failed"
          
          # Display difference report if it exists
          if [ -f "test_output/comparison_files/difference_report.txt" ]; then
            echo ""
            echo "Differences found:"
            cat test_output/comparison_files/difference_report.txt
          fi
          
          # Display test summary if it exists
          if [ -f "test_output/comparison_files/test_summary.txt" ]; then
            echo ""
            echo "Test Summary:"
            cat test_output/comparison_files/test_summary.txt
          fi
          
          exit 1
        fi