Merge pull request #232 from CODEX-CELIDA/dependabot/pip/main/depende… #742
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - main | |
| tags: | |
| - v* | |
| pull_request: | |
| branches: | |
| - master | |
| - main | |
| - dev | |
| jobs: | |
| pytest: | |
| runs-on: ubuntu-latest | |
| env: | |
| POSTGRES_USER: postgres | |
| POSTGRES_PASSWORD: postgres | |
| POSTGRES_DB: ohdsi | |
| services: | |
| postgres: | |
| image: postgres | |
| env: # Set the environment variables for the service container - not sure why job-level env doesn't work here | |
| POSTGRES_USER: ${{ env.POSTGRES_USER }} | |
| POSTGRES_PASSWORD: ${{ env.POSTGRES_PASSWORD }} | |
| POSTGRES_DB: ${{ env.POSTGRES_DB }} | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| ports: | |
| - 5432:5432 | |
| recommendation-server: | |
| image: glichtner/celida-recommendation-server:main | |
| env: | |
| GH_REPOSITORY: https://github.com/CODEX-CELIDA/celida-recommendations | |
| options: >- | |
| --health-cmd "curl -f -s http://localhost:80/health || exit 1" | |
| --health-interval 30s | |
| --health-timeout 10s | |
| --health-retries 5 | |
| --health-start-period 30s | |
| ports: | |
| - 8000:80 | |
| strategy: | |
| matrix: | |
| python-version: ["3.11"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| token: ${{ secrets.SUBMODULE_PERSONAL_ACCESS_TOKEN }} | |
| - name: Test Recommendation Server | |
| run: | | |
| curl http://localhost:8000/fhir/ActivityDefinition?url=https://www.netzwerk-universitaetsmedizin.de/fhir/codex-celida/guideline/covid19-inpatient-therapy/recommended-action/drug-administration-action/antithrombotic-prophylaxis-tinzaparin-administration | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| - name: Setup requirements | |
| run: | | |
| pip install -r requirements.txt | |
| pip install -r requirements-dev.txt | |
| - name: Build Cython extension | |
| run: python setup.py build_ext --inplace | |
| - name: Test with pytest | |
| env: | |
| CELIDA_EE_FHIR_BASE_URL: http://localhost:8000/fhir | |
| CELIDA_EE_FHIR_TERMINOLOGY_SERVER_URL: http://tx.fhir.org/r4 | |
| CELIDA_EE_TIMEZONE: Europe/Berlin | |
| CELIDA_EE_OMOP__USER: ${{ env.POSTGRES_USER }} | |
| CELIDA_EE_OMOP__PASSWORD: ${{ env.POSTGRES_PASSWORD }} | |
| CELIDA_EE_OMOP__HOST: localhost | |
| CELIDA_EE_OMOP__PORT: 5432 | |
| CELIDA_EE_OMOP__DATABASE: ${{ env.POSTGRES_DB }} | |
| CELIDA_EE_OMOP__DATA_SCHEMA: cds_cdm | |
| CELIDA_EE_OMOP__RESULT_SCHEMA: celida | |
| CELIDA_EE_EPISODE_OF_CARE_VISIT_DETAIL: 0 | |
| CELIDA_EE_MULTIPROCESSING_USE: 0 | |
| CELIDA_EE_MULTIPROCESSING_POOL_SIZE: -1 | |
| run: | | |
| pytest \ | |
| --color=yes \ | |
| --cov=execution_engine \ | |
| --cov-report=xml \ | |
| --postgresql-host=$CELIDA_EE_OMOP__HOST \ | |
| --postgresql-port=$CELIDA_EE_OMOP__PORT \ | |
| --postgresql-user=$CELIDA_EE_OMOP__USER \ | |
| --postgresql-password=$CELIDA_EE_OMOP__PASSWORD \ | |
| --run-slow-tests \ | |
| --run-recommendation-tests | |
| - name: Coverage | |
| uses: codecov/codecov-action@v4 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |