Minor id schema fix #478
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| name: test_modules | |
| on: | |
| push: | |
| branches: "**" | |
| pull_request_target: | |
| types: [opened, reopened, synchronize] | |
| branches: "**" | |
| jobs: | |
| security_check: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Get User Permission | |
| id: checkAccess | |
| uses: actions-cool/check-user-permission@v2 | |
| with: | |
| require: write | |
| username: ${{ github.triggering_actor }} | |
| - name: Check User Permission | |
| if: steps.checkAccess.outputs.require-result == 'false' | |
| run: | | |
| echo "${{ github.triggering_actor }} does not have permissions on this repo." | |
| echo "Current permission level is ${{ steps.checkAccess.outputs.user-permission }}" | |
| echo "Job originally triggered by ${{ github.actor }}" | |
| exit 1 | |
| test_map: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 2 | |
| matrix: | |
| map_args: ["-d 'ENA' -f relecov_tools/schema/ena_schema.json", "-d 'GISAID' -f relecov_tools/schema/gisaid_schema.json"] | |
| steps: | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.12' | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| fetch-depth: 0 | |
| - name: Install package and dependencies | |
| run: | | |
| pip install -r requirements.txt | |
| pip install . | |
| - name: Run each module tests | |
| run: | | |
| relecov-tools map -j tests/data/map_validate/processed_metadata_lab_test.json -p relecov_tools/schema/relecov_schema.json ${{ matrix.map_args }} -o . | |
| env: | |
| OUTPUT_LOCATION: ${{ github.workspace }}/tests/ | |
| - name: Upload output file | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: test-output | |
| path: output.txt | |
| test_all_modules: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 4 | |
| matrix: | |
| modules: | |
| - "read-lab-metadata" | |
| - "read-bioinfo-metadata" | |
| - "validate" | |
| - "build-schema" | |
| env: | |
| OUTPUT_LOCATION: ${{ github.workspace }}/tests/ | |
| steps: | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.12' | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| fetch-depth: 0 | |
| - name: Install package and dependencies | |
| run: | | |
| pip install -r requirements.txt | |
| pip install . | |
| - name: Run read-lab-metadata module | |
| if: matrix.modules == 'read-lab-metadata' | |
| run: | | |
| relecov-tools read-lab-metadata \ | |
| -m tests/data/read_lab_metadata/metadata_lab_test.xlsx \ | |
| -s tests/data/read_lab_metadata/samples_data_test.json \ | |
| -o $OUTPUT_LOCATION | |
| - name: Run read-bioinfo-metadata module | |
| if: matrix.modules == 'read-bioinfo-metadata' | |
| run: | | |
| relecov-tools read-bioinfo-metadata \ | |
| --json_file tests/data/read_bioinfo_metadata/validated_samples.json \ | |
| --input_folder tests/data/read_bioinfo_metadata/analysis_folder/ \ | |
| --software_name viralrecon \ | |
| --soft_validation \ | |
| -o $OUTPUT_LOCATION | |
| - name: Run validate module with upload files (default) | |
| if: matrix.modules == 'validate' | |
| run: | | |
| python3 tests/test_validate.py \ | |
| -j tests/data/map_validate/processed_metadata_lab_test.json \ | |
| -m tests/data/map_validate/metadata_lab_test.xlsx \ | |
| --upload_files \ | |
| -o tests/data/map_validate/ \ | |
| -s relecov_tools/schema/relecov_schema.json \ | |
| -l tests/data/map_validate/previous_processes_log_summary.json | |
| env: | |
| TEST_USER: ${{ secrets.TEST_USER }} | |
| TEST_PASSWORD: ${{ secrets.TEST_PASSWORD }} | |
| TEST_PORT: ${{ secrets.TEST_PORT }} | |
| GITHUB_WORKSPACE: ${{ github.workspace }} | |
| - name: Run build-schema module | |
| if: matrix.modules == 'build-schema' | |
| run: | | |
| relecov-tools build-schema \ | |
| -i tests/data/build_schema/metadata_mapping_file.xlsx \ | |
| --version $SCHEMA_DEFAULT_VERSION \ | |
| --project $PROJECT_NAME \ | |
| --non-interactive \ | |
| -o $OUTPUT_LOCATION | |
| env: | |
| SCHEMA_DEFAULT_VERSION: "3.0.0" | |
| PROJECT_NAME: "relecov" | |
| - name: Upload output file | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: test-output | |
| path: ${{ github.workspace }}/output.txt |