test.yml

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@v5
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}