major(release): demo-review-staging (#1763)

Co-authored-by: ieuans <ieuanscanlon@hotmail.co.uk>
Co-authored-by: alexcoldea <alexcoldea3@gmail.com>
Co-authored-by: Alex Coldea <32749167+alexcoldea@users.noreply.github.com>
Co-authored-by: Muhammad A Elmessary <33552352+elmessary@users.noreply.github.com>
Co-authored-by: Arthur zinnurov <zinnurov_2012@mail.ru>
Co-authored-by: elmessary <muhammad.elmessary@swansea.ac.uk>
Co-authored-by: roshantoby@gmail.com <R0$#@n1995>
Co-authored-by: roshantoby <roshantoby@gmail.com>

.github/workflows/code_ref_gh_pages_generate.yml

@@ -2,60 +2,58 @@ name: Codebase Sphinx Documentation
 
 on:
   push:
-    branches: [ gh-pages]
+    branches: [ gh-pages ]
+
 jobs:
   build_docs_job:
     name: Code Reference Generator
     runs-on: windows-latest
-    env: 
+    env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - name: Checkout 
         uses: actions/checkout@v2
         with:
-              token: ${{ secrets.GITHUB_TOKEN }}
+          token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Set up Python
         uses: actions/setup-python@v2
         with: 
-              python-version: 3.9.0
+          python-version: 3.10.0
 
       - name: Install dependencies
         run: |
-              python -m pip install -U sphinx
-              python -m pip install furo
-              python -m pip install django
-              python -m pip install mock
-              pip install sphinxjp.themes.basicstrap
-              cd requirements
-              pip install python_ldap-3.3.1-cp39-cp39-win_amd64.whl
-              pip install sphinxjp
-              pip install -r base.txt
+          python -m pip install -U sphinx
+          python -m pip install furo
+          python -m pip install django
+          python -m pip install mock
+          pip install sphinxjp.themes.basicstrap
+          cd docker/requirements
+          pip install ./wheels/python_ldap-3.4.4-cp310-cp310-win_amd64.whl
+          pip install -r base.txt
+          pip install sphinxjp
 
       - name: Make the Codebase Reference sphinx docs
         run: |
-              cd docs/codebase_docs/
-              sphinx-apidoc -o source ../../CodeListLibrary_project  
-              cd source
-              del "clinicalcode.migrations.rst"
-              cd ..
-              sphinx-build -b html source ..
+          cd docs/codebase_docs/
+          sphinx-apidoc -o source ../../CodeListLibrary_project  
+          cd source
+          del "clinicalcode.migrations.rst"
+          cd ..
+          sphinx-build -b html source ..
 
       - name: Init new codebase docs repo
         run: |
-              touch .nojekyll
-              git add -A
-              git config --local user.email "action@github.com"
-              git config --local user.name "GitHub Action"
-              git commit -m "deployed documentation"
-
+          touch .nojekyll
+          git add -A
+          git config --local user.email "action@github.com"
+          git config --local user.name "GitHub Action"
+          git commit -m "deployed documentation"
 
       - name: Push to destination branch
         uses: ad-m/github-push-action@master
-        with: 
-            github_token: ${{ secrets.GITHUB_TOKEN }}
-            branch: gh-pages
-            force: true
-
-
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: gh-pages
+          force: true

.github/workflows/issues_close_projects.yml

@@ -15,7 +15,7 @@ jobs:
     steps:
       - uses: dessant/issue-states@v2
         with:
-            github-token: ${{ github.token }}
-            open-issue-columns: ''
-            closed-issue-columns: 'Done / Deployed'
-            log-output: false
+          github-token: ${{ github.token }}
+          open-issue-columns: ''
+          closed-issue-columns: 'Done / Deployed'
+          log-output: false

.github/workflows/on-pr-update.yaml

@@ -25,6 +25,7 @@ jobs:
         concept-library-container:
           - './.github/workflows/on-pr-update.yaml'
           - './CodeListLibrary_project/**'
+          - './engagelens/**'
           - './docker/**'
 
     secrets:
@@ -44,7 +45,7 @@ jobs:
       cosign-public-key: ${{ vars.COSIGN_PUBLIC_KEY }}
       slack-channel: ${{ vars.SLACK_CHANNEL }}
       build-command: |
-        docker build -t $IMAGE -f "docker/production/build.Dockerfile" --build-arg server_name="conceptlibrary.saildatabank.com" .
+        docker build -t $IMAGE -f "docker/app/app.Dockerfile" --build-arg server_name="conceptlibrary.saildatabank.com" .
     secrets:
       cosign-private-key: ${{ secrets.COSIGN_PRIVATE_KEY }}
       cosign-password: ${{ secrets.COSIGN_PASSWORD }}

.github/workflows/on-release.yaml

@@ -25,6 +25,7 @@ jobs:
         concept-library-container:
           - './.github/workflows/on-release.yaml'
           - './CodeListLibrary_project/**'
+          - './engagelens/**'
           - './docker/**'
 
     secrets:
@@ -46,7 +47,7 @@ jobs:
       cosign-public-key: ${{ vars.COSIGN_PUBLIC_KEY }}
       slack-channel: ${{ vars.SLACK_CHANNEL }}
       build-command: |
-        docker build -t $IMAGE -f "docker/production/build.Dockerfile" --build-arg server_name="conceptlibrary.saildatabank.com" .
+        docker build -t $IMAGE -f "docker/app/app.Dockerfile" --build-arg server_name="conceptlibrary.saildatabank.com" .
     secrets:
       cosign-private-key: ${{ secrets.COSIGN_PRIVATE_KEY }}
       cosign-password: ${{ secrets.COSIGN_PASSWORD }}

.github/workflows/testing-pipline.yml

@@ -50,7 +50,7 @@ jobs:
       - uses: actions/cache@v3
         with:
           path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('docker/requirements/test-requirements.txt') }}
+          key: ${{ runner.os }}-pip-${{ hashFiles('docker/requirements/test.txt') }}
           restore-keys: |
             ${{ runner.os }}-pip-
 
@@ -66,7 +66,7 @@ jobs:
       - name: Install Dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install --upgrade --upgrade-strategy eager --default-timeout 100  -r docker/requirements/test-requirements.txt
+          pip install --upgrade --upgrade-strategy eager --default-timeout 100  -r docker/requirements/test.txt
 
       - name: Prepare Selenium
         uses: nanasess/setup-chromedriver@v2
@@ -82,17 +82,15 @@ jobs:
 
       - name: Run application
         run: |
-          export $(grep -v '^#' docker/selenium-testing/env/remotetest.compose.env | xargs)
+          export $(grep -v '^#' docker/.env/remote.test.env | xargs)
           cd CodeListLibrary_project
-          python manage.py makemigrations
-          python manage.py migrate
           python manage.py runserver 0.0.0.0:8000 > /dev/null &
 
       - name: Run tests
         run: |
-          export $(grep -v '^#' docker/selenium-testing/env/remotetest.compose.env | xargs)
+          export $(grep -v '^#' docker/.env/remote.test.env | xargs)
           cd CodeListLibrary_project
-          pytest -vv -s --cov-report xml --cov . --html=report.html --self-contained-html --alluredir=./clinicalcode/tests/allure-results
+          pytest -vv -s --random-order --cov-report xml --cov . --html=report.html --self-contained-html --alluredir=./clinicalcode/tests/allure-results
         env:
           DISPLAY: ":99"
 

.gitignore

@@ -1,27 +1,60 @@
+# Py artefacts
 *.pyc
 __pycache__
+
+# Py env
+**/env/
+**/.env/
+**/venv/
+**/.venv/
+
+# IDE
+.vscode
 .project
 .pydevproject
-.DS_Store
-CodeListLibrary_project/.settings/org.eclipse.core.resources.prefs
-.settings/org.eclipse.ltk.core.refactoring.prefs
-requirements/base - Django2.txt
-docs/~$plication Guide.docx
-**/docker/**/backup
-*.backup
-git.token
-CodeListLibrary_project/debug.log
-.vscode
-.settings/org.eclipse.core.resources.prefs
-venv
+**/.settings/
+**/base - Django2.txt
+
+# Ignore secrets
+**/*.token
+
+# Disallow prod env
+**/env_vars.*
+
+# Allow example secrets
+!docker/**/db/example.git.token
+
+# Dumps
+**/*.backup
 **/dump.rdb
-CodeListLibrary_project/staticroot/*
+
+# Deployment artefacts
 CodeListLibrary_project/media/*
-docker/development/db/postgresql.conf
-docker/CodeListLibrary_project
+CodeListLibrary_project/staticroot/*
 
-# macOS system files
-.DS_Stores
+# Testing artefacts
+**/.pytest_cache/
+**/tests/**/allure*/
+
+# Docker
+**/cl_log/
+**/docker/**/backup/
+**/docker/development/db/*.sql
+**/docker/development/db/postgresql.conf
+**/docker/CodeListLibrary_project
+
+# Engagelens
+**/engagelens/.env
+
+# Allow docker env directory
+!**/docker/.env/
+!**/docker/**/env/
+
+# Platform / OS files
 .idea
+.DS_Stores
+
+# Misc. files
+docs/~$plication Guide.docx
+CodeListLibrary_project/debug.log
 
-CodeListLibrary_project/clinicalcode/tests/allure-results/