version bumps #166
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - main | |
| tags: | |
| - v* | |
| pull_request: | |
| 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_RELEASE_BASE: https://github.com/CODEX-CELIDA/celida-recommendations/releases | |
| PACKAGE_NAME_TEMPLATE: recommendations.celida.codex.netzwerk-universitaetsmedizin.de-{version}.tgz | |
| 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 | |
| - name: Clone Submodule | |
| run: | | |
| mkdir -p $HOME/.ssh | |
| echo '${{ secrets.SUBMODULE_REPO_DEPLOY_KEY }}' > $HOME/.ssh/ssh.key | |
| chmod 600 $HOME/.ssh/ssh.key | |
| export GIT_SSH_COMMAND="ssh -i $HOME/.ssh/ssh.key" | |
| git submodule set-url tests/omop_cdm git@github.com:CODEX-CELIDA/omop-test-vocabulary.git | |
| git submodule update --init --recursive | |
| git submodule set-url tests/omop_cdm https://github.com/CODEX-CELIDA/omop-test-vocabulary.git | |
| unset GIT_SSH_COMMAND | |
| - 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/no-antithrombotic-prophylaxis-nadroparin-administration-low-weight | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| - name: Setup requirements | |
| run: | | |
| pip install -r requirements.txt | |
| pip install -r requirements-dev.txt | |
| mv sample.env .env | |
| - name: Test with pytest | |
| env: | |
| FHIR_BASE_URL: http://localhost:8000/fhir | |
| FHIR_TERMINOLOGY_SERVER_URL: http://tx.fhir.org/r4 | |
| CELIDA_EE_TIMEZONE: Europe/Berlin | |
| OMOP__USER: ${{ env.POSTGRES_USER }} | |
| OMOP__PASSWORD: ${{ env.POSTGRES_PASSWORD }} | |
| OMOP__HOST: localhost | |
| OMOP__PORT: 5432 | |
| OMOP__DATABASE: ${{ env.POSTGRES_DB }} | |
| OMOP__SCHEMA: cds_cdm | |
| run: | | |
| pytest \ | |
| --color=yes \ | |
| --cov=execution_engine \ | |
| --cov-report=xml \ | |
| --postgresql-host=$OMOP__HOST \ | |
| --postgresql-port=$OMOP__PORT \ | |
| --postgresql-user=$OMOP__USER \ | |
| --postgresql-password=$OMOP__PASSWORD \ | |
| --run-slow-tests \ | |
| --run-recommendation-tests | |
| - name: Coverage | |
| uses: codecov/codecov-action@v3 |