Refactor of read-bioinfo-metadata module for tool compatibility expansion #15
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| name: Python Package using Conda | |
| on: | |
| push: | |
| branches: "**" | |
| pull_request_target: | |
| types: [opened, reopened, synchronize, closed] | |
| 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_sftp_handle: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 1 | |
| matrix: | |
| download_options: ["download_only", "download_clean", "delete_only"] | |
| target_folders: ["", "-t COD-test-1"] | |
| steps: | |
| - name: Set up Python 3.9.16 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.9.16' | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| with: | |
| path: . | |
| - name: Install package and dependencies | |
| run: | | |
| pip install -r requirements.txt | |
| pip install . | |
| - name: Run sftp_handle tests | |
| run: | | |
| python3 tests/test_sftp_handle.py --download_option ${{ matrix.download_options }} ${{ matrix.target_folders }} | |
| env: | |
| TEST_USER: ${{ secrets.TEST_USER }} | |
| TEST_PASSWORD: ${{ secrets.TEST_PASSWORD }} | |
| TEST_PORT: ${{ secrets.TEST_PORT }} | |
| OUTPUT_LOCATION: ${{ github.workspace }}/tests/ | |
| 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 3.9.16 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.9.16' | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| with: | |
| path: . | |
| - 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: ${{ github.workspace }}/tests/ | |
| - name: Upload output file | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: test-output | |
| path: output.txt | |
| test_all_modules: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 3 | |
| matrix: | |
| modules: ["read-lab-metadata", "read-bioinfo-metadata", "validate"] | |
| steps: | |
| - name: Set up Python 3.9.16 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.9.16' | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| with: | |
| path: . | |
| - name: Install package and dependencies | |
| run: | | |
| pip install -r requirements.txt | |
| pip install . | |
| - name: Run each module tests | |
| run: | | |
| if [ "${{ matrix.modules }}" == "read-lab-metadata" ]; then | |
| 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 $OUTPUT_LOCATION | |
| elif [ "${{ matrix.modules }}" == "validate" ]; then | |
| relecov-tools validate -j tests/data/map_validate/processed_metadata_lab_test.json -s relecov_tools/schema/relecov_schema.json -m tests/data/map_validate/metadata_lab_test.xlsx -o $OUTPUT_LOCATION | |
| fi | |
| env: | |
| OUTPUT_LOCATION: ${{ github.workspace }}/tests/ | |
| - name: Upload output file | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: test-output | |
| path: output.txt |