GTF comparison script #11
Workflow file for this run
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| 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" | |
| exit 1 | |
| fi | |
| if [ ! -f "Biotypes.tsv" ]; then | |
| echo "Error: Required Biotypes.tsv file not found" | |
| exit 1 | |
| fi | |
| echo "Test files present:" | |
| ls -l test_data/test1.gtf Biotypes.tsv | |
| - name: Run modify_gtf script | |
| env: | |
| PYTHONPATH: ${{ github.workspace }}/3rd-party-tools/build-indices | |
| run: | | |
| python modify_gtf.py \ | |
| -i test_data/test1.gtf \ | |
| -o test_output/modified_test1.gtf \ | |
| -b Biotypes.tsv | |
| if [ ! -f "test_output/modified_test1.gtf" ]; then | |
| echo "Error: Modified GTF was not created" | |
| exit 1 | |
| fi | |
| - name: Run comparison | |
| id: comparison | |
| env: | |
| PYTHONPATH: ${{ github.workspace }}/3rd-party-tools/build-indices | |
| run: | | |
| python compare_gtfs.py \ | |
| test_data/test1.gtf \ | |
| test_output/modified_test1.gtf \ | |
| --output-prefix test_output/comparison_files/comparison | |
| - name: Run unit tests | |
| id: unit_tests | |
| env: | |
| PYTHONPATH: ${{ github.workspace }}/3rd-party-tools/build-indices | |
| run: python -m unittest test_gtf_comparison.py -v | |
| - name: Create comparison summary | |
| if: always() | |
| run: | | |
| { | |
| echo "GTF Comparison Summary" | |
| echo "Generated on: $(date)" | |
| echo | |
| echo "Input GTF: test_data/test1.gtf" | |
| echo "Modified GTF: test_output/modified_test1.gtf" | |
| echo | |
| for diff_type in structural gene attribute; do | |
| echo "=== ${diff_type^} Differences ===" | |
| if [ -f "test_output/comparison_files/comparison_${diff_type}_diff.txt" ]; then | |
| cat "test_output/comparison_files/comparison_${diff_type}_diff.txt" | |
| else | |
| echo "No ${diff_type} differences file found" | |
| fi | |
| echo | |
| done | |
| } > test_output/comparison_files/summary.txt | |
| - name: Zip comparison results | |
| if: always() | |
| run: | | |
| if [ -d "test_output/comparison_files" ] && [ "$(ls -A test_output/comparison_files)" ]; then | |
| cd test_output | |
| zip -r comparison_results.zip comparison_files/ | |
| cd .. | |
| else | |
| echo "No comparison files to zip" | |
| touch test_output/comparison_results.zip | |
| fi | |
| - name: Upload test artifacts | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: gtf-test-results | |
| path: | | |
| 3rd-party-tools/build-indices/test_output/comparison_results.zip | |
| 3rd-party-tools/build-indices/test_output/modified_test1.gtf | |
| compression-level: 9 | |
| - name: Check test results | |
| if: always() | |
| run: | | |
| echo "=== Test Results Summary ===" | |
| TESTS_FAILED=false | |
| # Check unit tests result | |
| if [ "${{ steps.unit_tests.outcome }}" == "success" ]; then | |
| echo "✅ Unit tests passed" | |
| else | |
| echo "❌ Unit tests failed" | |
| TESTS_FAILED=true | |
| fi | |
| # Check comparison results | |
| if [ -f "test_output/comparison_files/comparison_structural_diff.txt" ]; then | |
| if grep -q "differs in" test_output/comparison_files/comparison_structural_diff.txt; then | |
| echo "❌ GTF comparison found differences" | |
| cat test_output/comparison_files/summary.txt | |
| TESTS_FAILED=true | |
| else | |
| echo "✅ GTF comparison passed" | |
| fi | |
| else | |
| echo "❌ GTF comparison failed to generate output" | |
| TESTS_FAILED=true | |
| fi | |
| if [ "$TESTS_FAILED" = true ]; then | |
| exit 1 | |
| fi |