GitHub Actions Test Infrastructure #4
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| name: Test CCKP Toolkit Workflow | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| integration-test: | |
| name: Integration Test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Nextflow | |
| run: | | |
| curl -s https://get.nextflow.io | bash | |
| mv nextflow /usr/local/bin/ | |
| nextflow -version | |
| - name: Set up Docker | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Run workflow with test repository | |
| run: | | |
| rm -rf test_results | |
| nextflow run main.nf \ | |
| --repo_url https://github.com/PythonOT/POT.git \ | |
| --output_dir test_results | |
| - name: Run workflow with test fixture | |
| run: | | |
| rm -rf test_results_example | |
| nextflow run main.nf \ | |
| --sample_sheet tests/fixtures/example-input.csv \ | |
| --output_dir test_results_example | |
| - name: Upload test results | |
| uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: integration-test-results | |
| path: | | |
| test_results/ | |
| test_results_example/ | |
| retention-days: 7 | |
| output-validation: | |
| name: Output Validation | |
| needs: integration-test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Download integration test results | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: integration-test-results | |
| path: test_results | |
| - name: Validate outputs | |
| run: | | |
| # Test 1: Check consolidated report | |
| if [ ! -f "test_results/consolidated_report.csv" ] || [ ! -s "test_results/consolidated_report.csv" ]; then | |
| echo "❌ Consolidated report is missing or empty" | |
| exit 1 | |
| fi | |
| echo "✓ Consolidated report exists and is not empty" | |
| # Test 2: Check Almanack results | |
| if [ ! -f "test_results/PythonOT_POT_almanack-results.json" ] || [ ! -s "test_results/PythonOT_POT_almanack-results.json" ]; then | |
| echo "❌ Almanack results are missing or empty" | |
| exit 1 | |
| fi | |
| echo "✓ Almanack results exist and are not empty" | |
| # Test 3: Validate CSV structure | |
| if ! head -n 1 "test_results/consolidated_report.csv" | grep -q "target"; then | |
| echo "❌ CSV header is missing or incorrect" | |
| exit 1 | |
| fi | |
| echo "✓ CSV header is valid" | |
| # Test 4: Check status values | |
| if ! grep -q "PASS\|FAIL" "test_results/consolidated_report.csv"; then | |
| echo "❌ No valid status values found in CSV" | |
| exit 1 | |
| fi | |
| echo "✓ Status values are present" | |
| # Test 5: Check status files | |
| if [ ! -f "test_results/status_repo.txt" ]; then | |
| echo "❌ Repository status file is missing" | |
| exit 1 | |
| fi | |
| echo "✓ Repository status file exists" | |
| if [ ! -f "test_results/status_almanack_POT.txt" ]; then | |
| echo "❌ Almanack status file is missing" | |
| exit 1 | |
| fi | |
| echo "✓ Almanack status file exists" | |
| error-handling: | |
| name: Error Handling | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Nextflow | |
| run: | | |
| curl -s https://get.nextflow.io | bash | |
| mv nextflow /usr/local/bin/ | |
| nextflow -version | |
| - name: Set up Docker | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Test invalid repository URL | |
| run: | | |
| rm -rf error_test_results | |
| if nextflow run main.nf --repo_url "invalid-url" --output_dir error_test_results 2>&1 | grep -q "ERROR: Provide either a sample_sheet or repo_url"; then | |
| echo "✓ Invalid repository URL test passed" | |
| else | |
| echo "❌ Workflow should fail with invalid repository URL" | |
| exit 1 | |
| fi | |
| - name: Test invalid sample sheet | |
| run: | | |
| rm -rf error_test_results | |
| if nextflow run main.nf --sample_sheet "nonexistent.csv" --output_dir error_test_results 2>&1 | grep -q "ERROR: Provide either a sample_sheet or repo_url"; then | |
| echo "✓ Invalid sample sheet test passed" | |
| else | |
| echo "❌ Workflow should fail with invalid sample sheet" | |
| exit 1 | |
| fi | |
| - name: Test conflicting parameters | |
| run: | | |
| rm -rf error_test_results | |
| if nextflow run main.nf \ | |
| --repo_url https://github.com/PythonOT/POT.git \ | |
| --sample_sheet tests/fixtures/example-input.csv \ | |
| --output_dir error_test_results 2>&1 | grep -q "ERROR: Provide either a sample_sheet or repo_url"; then | |
| echo "✓ Conflicting parameters test passed" | |
| else | |
| echo "❌ Workflow should fail when both repo_url and sample_sheet are provided" | |
| exit 1 | |
| fi | |
| - name: Test Synapse parameter validation | |
| run: | | |
| rm -rf error_test_results | |
| # Test that workflow runs without synapse_folder_id when upload_to_synapse is false | |
| if ! nextflow run main.nf \ | |
| --repo_url https://github.com/PythonOT/POT.git \ | |
| --output_dir error_test_results; then | |
| echo "❌ Workflow should run without synapse_folder_id when upload_to_synapse is false" | |
| exit 1 | |
| fi | |
| echo "✓ Workflow runs without synapse_folder_id when upload_to_synapse is false" | |
| # Test that workflow fails without synapse_folder_id when upload_to_synapse is true | |
| if nextflow run main.nf \ | |
| --repo_url https://github.com/PythonOT/POT.git \ | |
| --upload_to_synapse \ | |
| --output_dir error_test_results 2>&1 | grep -q "ERROR: synapse_folder_id must be provided when --upload_to_synapse is true"; then | |
| echo "✓ Workflow fails without synapse_folder_id when upload_to_synapse is true" | |
| else | |
| echo "❌ Workflow should fail without synapse_folder_id when upload_to_synapse is true" | |
| exit 1 | |
| fi | |
| - name: Upload error test results | |
| uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: error-test-results | |
| path: error_test_results/ | |
| retention-days: 7 |