examples/.github/workflows/atomic-ehr-codegen-python-us-core-profiles.yaml at main · Aidbox/examples · GitHub

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name: atomic-ehr-codegen-python-us-core-profiles

on:
  push:
    branches:
      - main
    paths:
      - 'developer-experience/atomic-ehr-codegen-python-us-core-profiles/**'
      - '.github/workflows/atomic-ehr-codegen-python-us-core-profiles.yaml'
  pull_request:
    paths:
      - 'developer-experience/atomic-ehr-codegen-python-us-core-profiles/**'
      - '.github/workflows/atomic-ehr-codegen-python-us-core-profiles.yaml'
  workflow_dispatch:

defaults:
  run:
    working-directory: developer-experience/atomic-ehr-codegen-python-us-core-profiles

jobs:
  test:
    runs-on: ubuntu-latest

    services:
      aidbox_db:
        image: healthsamurai/aidboxdb:17
        env:
          POSTGRES_USER: aidbox
          POSTGRES_PASSWORD: aidboxpwd
          POSTGRES_DB: aidbox
        options: >-
          --health-cmd "pg_isready -U aidbox"
          --health-interval 10s
          --health-timeout 5s
          --health-retries 10

      aidbox:
        image: healthsamurai/aidboxone:edge
        ports:
          - 8080:8080
        env:
          AIDBOX_LICENSE: ${{ secrets.AIDBOX_LICENSE }}
          AIDBOX_CLIENT_ID: root
          AIDBOX_CLIENT_SECRET: secret
          AIDBOX_ADMIN_PASSWORD: secret
          AIDBOX_PORT: 8080
          AIDBOX_FHIR_PACKAGES: hl7.fhir.r4.core#4.0.1
          AIDBOX_FHIR_SCHEMA_VALIDATION: true
          BOX_SETTINGS_MODE: read-write
          PGHOST: aidbox_db
          PGPORT: 5432
          PGUSER: aidbox
          PGPASSWORD: aidboxpwd
          PGDATABASE: aidbox

    steps:
      - uses: actions/checkout@v4

      - name: Setup Node.js
        uses: actions/setup-node@v4
        with:
          node-version: '22.12.0'

      - name: Setup Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.12'

      - name: Install Node dependencies
        run: npm install

      - name: Install @atomic-ehr/codegen 0.0.17
        run: npm install --save-dev @atomic-ehr/codegen@0.0.17

      - name: Regenerate fhir_types
        run: npx tsx generate.ts

      - name: Check generated fhir_types are up to date
        run: |
          if [ -n "$(git status --porcelain -- fhir_types)" ]; then
            echo "::error::fhir_types/ changed after regeneration. Run 'npx tsx generate.ts' and commit the result."
            git status --porcelain -- fhir_types
            git diff -- fhir_types
            exit 1
          fi

      - name: Install Python dependencies
        run: pip install -r fhir_types/requirements.txt

      - name: Typecheck
        run: mypy .

      - name: Build bundle
        run: |
          out=$(python load.py)
          echo "$out"
          echo "$out" | grep -qF 'Wrote bundle with 10 entries'

      - name: Compute average BP and check output
        run: |
          out=$(python avg.py)
          echo "$out"
          echo "$out" | grep -qF 'Avg BP: 125.2/82.0 mmHg (n=5)'

      - name: Wait for Aidbox
        run: |
          for i in $(seq 1 60); do
            if curl -fsS http://localhost:8080/health >/dev/null 2>&1; then
              echo "Aidbox is up"; exit 0
            fi
            echo "waiting for Aidbox ($i)"; sleep 3
          done
          echo "Aidbox did not become healthy in time"; exit 1

      - name: POST bundle to Aidbox with fhirpy and read it back
        env:
          AIDBOX_URL: http://localhost:8080/fhir
          AIDBOX_SECRET: secret
        run: |
          out=$(python post.py)
          echo "$out"
          echo "$out" | grep -qF 'Stored BP observations: 5'