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* comparison script updated * added tests * added yaml for testing * removed extra gtf tester * updated when to run test * upgratde actions/upload-artifact@v3 * fixed paths for pytests * fixed python path for pytest * fixed python path for pytest * updated the script to run off Marmoset gtf file * updated the unittest to run modify_gtf script and saved an example output from previous run * updated yml to run all analysis * updated yml to run all analysis * updated yml to run all analysis * bug fix * bug fixes * improved comparisons * added readme * added readme
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,133 @@ | ||
| name: GTF Comparison Tests | ||
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| on: | ||
| pull_request: | ||
| branches: [ "develop", "master" ] | ||
| paths: | ||
| - '3rd-party-tools/build-indices/**' | ||
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||
| jobs: | ||
| test: | ||
| runs-on: ubuntu-latest | ||
|
|
||
| defaults: | ||
| run: | ||
| working-directory: 3rd-party-tools/build-indices | ||
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| steps: | ||
| - uses: actions/checkout@v4 | ||
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|
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| - name: Set up Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: '3.x' | ||
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| - 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 | ||
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|
||
| - 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 |
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