Add exception handling for XML parsing to FHIR Converter #2397
Workflow file for this run
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| name: Test | |
| on: | |
| workflow_call: | |
| workflow_dispatch: | |
| pull_request: | |
| branches: | |
| - "**" | |
| push: | |
| branches: | |
| - main | |
| paths-ignore: | |
| - pyproject.toml | |
| env: | |
| TEST_RUNNER_PYTHON_VERSION: 3.10.12 | |
| jobs: | |
| postgres-tests: | |
| runs-on: ubuntu-latest | |
| services: | |
| test-db: | |
| image: postgres:13-alpine3.16 | |
| env: | |
| POSTGRES_PASSWORD: pw | |
| POSTGRES_DB: testdb | |
| POSTGRES_USER: postgres | |
| # Set health checks to wait until postgres has started | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| --name testdb | |
| ports: | |
| - 5432:5432 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Setup python ${{env.TEST_RUNNER_PYTHON_VERSION}} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{env.TEST_RUNNER_PYTHON_VERSION}} | |
| cache: pip | |
| - name: Install poetry | |
| run: | | |
| curl -sSL https://install.python-poetry.org | python3 - | |
| echo "${HOME}/.poetry/bin" >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: poetry install | |
| - name: test_postgres_connection | |
| run: poetry run pytest tests/linkage/test_postgres_mpi_connector.py | |
| unit-test-phdi-building-blocks-lib: | |
| runs-on: ubuntu-latest | |
| services: | |
| test-db: | |
| image: postgres:13-alpine3.16 | |
| env: | |
| POSTGRES_PASSWORD: pw | |
| POSTGRES_DB: testdb | |
| POSTGRES_USER: postgres | |
| # Set health checks to wait until postgres has started | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| --name testdb | |
| ports: | |
| - 5432:5432 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Setup python ${{env.TEST_RUNNER_PYTHON_VERSION}} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{env.TEST_RUNNER_PYTHON_VERSION}} | |
| cache: pip | |
| - name: Install poetry | |
| run: | | |
| curl -sSL https://install.python-poetry.org | python3 - | |
| echo "${HOME}/.poetry/bin" >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: poetry install | |
| - name: Run pytest with code coverage output | |
| run: poetry run pytest --cov-report xml --cov=phdi tests/ | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| flags: unit-tests | |
| code-check-python: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Setup python ${{env.TEST_RUNNER_PYTHON_VERSION}} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{env.TEST_RUNNER_PYTHON_VERSION}} | |
| cache: pip | |
| - name: Install dependencies | |
| run: | | |
| pip install -U pip | |
| pip install black flake8 | |
| - name: Check format (black) | |
| run: | | |
| black --check --verbose . | |
| - name: Check style (flake8) | |
| run: | | |
| flake8 | |
| ensure-clean-notebooks: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Check notebook cleanliness | |
| uses: ResearchSoftwareActions/EnsureCleanNotebooksAction@1.1 | |
| list-containers: | |
| uses: ./.github/workflows/listContainers.yaml | |
| unit-test-python-containers: | |
| needs: list-containers | |
| runs-on: ubuntu-latest | |
| services: | |
| test-db: | |
| image: postgres:13-alpine3.16 | |
| env: | |
| POSTGRES_PASSWORD: pw | |
| POSTGRES_DB: testdb | |
| POSTGRES_USER: postgres | |
| # Set health checks to wait until postgres has started | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| --name testdb | |
| ports: | |
| - 5432:5432 | |
| strategy: | |
| matrix: | |
| container-to-test: ${{fromJson(needs.list-containers.outputs.containers)}} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Setup python ${{env.TEST_RUNNER_PYTHON_VERSION}} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{env.TEST_RUNNER_PYTHON_VERSION}} | |
| cache: pip | |
| - name: Install Pytest | |
| run: pip install pytest | |
| - name: Install dependencies | |
| working-directory: ./containers/${{matrix.container-to-test}} | |
| run: | | |
| pip install -r requirements.txt | |
| - name: Run unit tests for containers | |
| env: | |
| MPI_DBNAME: testdb | |
| MPI_PASSWORD: pw | |
| MPI_DB_TYPE: postgres | |
| MPI_HOST: localhost | |
| MPI_USER: postgres | |
| MPI_PORT: 5432 | |
| MPI_PATIENT_TABLE: patient | |
| MPI_PERSON_TABLE: person | |
| working-directory: ./containers/${{matrix.container-to-test}}/tests | |
| run: | | |
| python -m pytest -m "not integration" | |
| integration-test-python-containers: | |
| needs: list-containers | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| directories-to-test: ${{fromJson(needs.list-containers.outputs.integration-dirs)}} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Setup python ${{env.TEST_RUNNER_PYTHON_VERSION}} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{env.TEST_RUNNER_PYTHON_VERSION}} | |
| cache: pip | |
| - name: Install Pytest | |
| run: pip install pytest | |
| - name: Install dependencies | |
| working-directory: ./containers/${{matrix.directories-to-test}} | |
| run: | | |
| pwd | |
| pip install -r requirements.txt | |
| - name: Run integration tests for containers | |
| working-directory: ./containers/${{matrix.directories-to-test}}/tests/integration | |
| run: | | |
| python -m pytest -m "integration" |