Merge pull request #528 from rcpch/staging

Staging

.github/workflows/autodeploy-to-azure-epilepsy12-development.yml

@@ -16,36 +16,70 @@ on:
 jobs:
   build-and-deploy:
     runs-on: ubuntu-latest
+
+    # this 'environment' refers to GitHub Environments, not environment variables
     environment:
       name: 'development'
       url: ${{ steps.deploy-to-webapp.outputs.webapp-url }}
 
+    # this 'env' refers to environment variables
+    env:
+      DJANGO_CSRF_TRUSTED_ORIGINS: https://localhost,https://0.0.0.0
+      E12_POSTGRES_DB_HOST: 127.0.0.1
+      E12_POSTGRES_DB_NAME: test_db
+      E12_POSTGRES_DB_PASSWORD: postgis
+      E12_POSTGRES_DB_PORT: 5432
+      E12_POSTGRES_DB_USER: postgis
+      POSTCODES_IO_API_URL: https://api.postcodes.io
+      RCPCH_CENSUS_PLATFORM_TOKEN: ${{ secrets.RCPCH_CENSUS_PLATFORM_TOKEN }}
+      RCPCH_CENSUS_PLATFORM_URL: https://api.rcpch.ac.uk/deprivation/v1
+      RCPCH_HERMES_SERVER_URL: http://rcpch-hermes.uksouth.azurecontainer.io:8080/v1/snomed
+
+    # Sets up a Postgis container for the test db
+    services:
+      postgis:
+        image: postgis/postgis:15-3.3
+        env:
+          POSTGRES_USER: postgis
+          POSTGRES_PASSWORD: postgis
+          POSTGRES_DB: test_db
+        ports:
+          - 5432:5432
+        # needed because the postgis container does not provide a healthcheck
+        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
+
     steps:
       - uses: actions/checkout@v3
-
-      - name: List all files
-        run: ls -al
-
+
       - name: Set up Python version
         uses: actions/setup-python@v4
         with:
           python-version: '3.10'
-          
+
       - name: Install PostGIS dependencies
         run: sudo apt-get install -y binutils libproj-dev gdal-bin libgdal-dev python3-gdal
 
       - name: Create and start virtual environment
         run: |
           python -m venv venv
           source venv/bin/activate
-      
+
       # python dependencies
       - name: Install dependencies
-        run: pip install -r requirements.txt
-
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      # run migrations
+      - name: Run migrations
+        run: python manage.py migrate
+
       - name: collect static files
         run: python manage.py collectstatic --noinput
 
+      - name: Pytest Suite
+        run: pytest -rP
+
       # Deploy to Azure
       - name: 'Deploy to Azure Web App'
         uses: azure/webapps-deploy@v2

.github/workflows/autodeploy-to-azure-epilepsy12-staging.yml

@@ -14,55 +14,77 @@ on:
   workflow_dispatch:
 
 jobs:
-  build:
+  build-and-deploy:
     runs-on: ubuntu-latest
 
+    # this 'environment' refers to GitHub Environments, not environment variables
+    environment:
+      name: 'staging'
+      url: ${{ steps.deploy-to-webapp.outputs.webapp-url }}
+
+    # this 'env' refers to environment variables
+    env:
+      DJANGO_CSRF_TRUSTED_ORIGINS: https://localhost,https://0.0.0.0
+      E12_POSTGRES_DB_HOST: 127.0.0.1
+      E12_POSTGRES_DB_NAME: test_db
+      E12_POSTGRES_DB_PASSWORD: postgis
+      E12_POSTGRES_DB_PORT: 5432
+      E12_POSTGRES_DB_USER: postgis
+      POSTCODES_IO_API_URL: https://api.postcodes.io
+      RCPCH_CENSUS_PLATFORM_TOKEN: ${{ secrets.RCPCH_CENSUS_PLATFORM_TOKEN }}
+      RCPCH_CENSUS_PLATFORM_URL: https://api.rcpch.ac.uk/deprivation/v1
+      RCPCH_HERMES_SERVER_URL: http://rcpch-hermes.uksouth.azurecontainer.io:8080/v1/snomed
+
+    # Sets up a Postgis container for the test db
+    services:
+      postgis:
+        image: postgis/postgis:15-3.3
+        env:
+          POSTGRES_USER: postgis
+          POSTGRES_PASSWORD: postgis
+          POSTGRES_DB: test_db
+        ports:
+          - 5432:5432
+        # needed because the postgis container does not provide a healthcheck
+        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
+
     steps:
       - uses: actions/checkout@v3
 
       - name: Set up Python version
         uses: actions/setup-python@v4
         with:
           python-version: '3.10'
-              
+
       - name: Install PostGIS dependencies
         run: sudo apt-get install -y binutils libproj-dev gdal-bin libgdal-dev python3-gdal
 
       - name: Create and start virtual environment
         run: |
           python -m venv venv
           source venv/bin/activate
-      
+
+      # python dependencies
       - name: Install dependencies
-        run: pip install -r requirements.txt
-
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
       - name: collect static files
         run: python manage.py collectstatic --noinput
-
-      # Optional: Add step to run tests here (PyTest, Django test suites, etc.)
-
+
+      - name: Pytest Suite
+        run: pytest -rP
+
       - name: Upload artifact for deployment jobs
         uses: actions/upload-artifact@v3
         with:
           name: python-app
           path: |
-            . 
+            .
             !venv/
 
-  deploy:
-    runs-on: ubuntu-latest
-    needs: build
-    environment:
-      name: 'staging'
-      url: ${{ steps.deploy-to-webapp.outputs.webapp-url }}
-
-    steps:
-      - name: Download artifact from build job
-        uses: actions/download-artifact@v3
-        with:
-          name: python-app
-          path: .
-
+        # Deploy to Azure
       - name: 'Deploy to Azure Web App'
         uses: azure/webapps-deploy@v2
         id: deploy-to-webapp

.github/workflows/test-workflow-temp.yml

@@ -0,0 +1,80 @@
+name: Temp workflow to test Pytest Suite
+
+on:
+  push:
+    branches:
+      - "add-cicd-auto-pytest"
+  workflow_dispatch:
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+
+    # this 'env' refers to environment variables
+    env:
+        DJANGO_CSRF_TRUSTED_ORIGINS: https://localhost,https://0.0.0.0
+        E12_POSTGRES_DB_HOST: 127.0.0.1
+        E12_POSTGRES_DB_NAME: test_db
+        E12_POSTGRES_DB_PASSWORD: postgis
+        E12_POSTGRES_DB_PORT: 5432
+        E12_POSTGRES_DB_USER: postgis
+        POSTCODES_IO_API_URL: https://api.postcodes.io
+        RCPCH_CENSUS_PLATFORM_TOKEN: ${{ secrets.RCPCH_CENSUS_PLATFORM_TOKEN }}
+        RCPCH_CENSUS_PLATFORM_URL: https://api.rcpch.ac.uk/deprivation/v1
+        RCPCH_HERMES_SERVER_URL: http://rcpch-hermes.uksouth.azurecontainer.io:8080/v1/snomed
+
+    # this 'environment' refers to GitHub Environments, not environment variables
+    environment:
+      name: "development"
+      url: ${{ steps.deploy-to-webapp.outputs.webapp-url }}
+
+    services:
+      postgis:
+        image: postgis/postgis:15-3.3
+        env:
+          POSTGRES_USER: postgis
+          POSTGRES_PASSWORD: postgis
+          POSTGRES_DB: test_db
+        ports:
+          - 5432:5432
+        # needed because the postgis container does not provide a healthcheck
+        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: List all files
+        run: ls -al
+
+      - name: Set up Python version
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install PostGIS dependencies
+        run: sudo apt-get install -y binutils libproj-dev gdal-bin libgdal-dev python3-gdal
+
+      - name: Create and start virtual environment
+        run: |
+          python -m venv venv
+          source venv/bin/activate
+
+      # python dependencies
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      # run migrations
+      - name: Run migrations
+        run: python manage.py migrate
+
+      - name: collect static files
+        run: python manage.py collectstatic --noinput
+
+      # Run Pytest Suite
+      - name: print settings for debugging  purposes
+        run: python manage.py diffsettings --all
+
+      - name: Pytest Suite
+        run: pytest -rP

docker-compose.dev-init.yml

@@ -25,7 +25,7 @@ services:
       - DEBUG=True
       - DJANGO_ALLOWED_HOSTS=0.0.0.0
       - DJANGO_CSRF_TRUSTED_ORIGINS=https://localhost,https://0.0.0.0
-      - POSTCODES_IO_API_URL=https://api.postcodes.io/postcodes
+      - POSTCODES_IO_API_URL=https://api.postcodes.io
       - RCPCH_CENSUS_PLATFORM_URL=https://api.rcpch.ac.uk/deprivation/v1 # live
       # - RCPCH_CENSUS_PLATFORM_URL=http://0.0.0.0:8001 # development
       - RCPCH_HERMES_SERVER_URL=http://rcpch-hermes.uksouth.azurecontainer.io:8080/v1/snomed 
@@ -43,15 +43,15 @@ services:
     command: >
       sh -c "python manage.py collectstatic --noinput &&
             python manage.py migrate &&
-            python manage.py seed --mode=seed_dummy_cases &&
+            python manage.py seed --mode=cases --cases 100 &&
             python manage.py seed --mode=seed_registrations &&
             python manage.py seed --mode=seed_groups_and_permissions &&
             python manage.py createsuperuser --noinput &&
             echo 'DEV SETUP SCRIPT: Development superuser email: [email protected]' &&
             echo 'DEV SETUP SCRIPT: Development superuser password: pw' &&
             python manage.py runserver 0.0.0.0:8000"
 
-  # db container - runs postgres
+  # db container - runs postgis
   db:
     image: postgis/postgis:15-3.3
     volumes:

docker-compose.dev.yml

@@ -36,6 +36,8 @@ services:
     # ensures that docker compose always displays log output
     tty: true
     stdin_open: true
+    env_file:
+      - .env # env file with the token for RCPCH Census Platform, not committed to Git
 
   # db container - runs postgres
   db: