added new scripts to BuildIndices docker for marmoset #18
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |