EBI-G2P · seeta-ramaraju · Jul 23, 2026 · Jul 23, 2026 · Jul 29, 2026 · Jul 31, 2026
diff --git a/.dockerignore b/.dockerignore
@@ -0,0 +1,29 @@
+.git
+.github
+.gitlab-ci.yml
+
+__pycache__/
+*.py[cod]
+*$py.class
+
+.pytest_cache/
+.coverage
+htmlcov/
+
+.venv/
+venv/
+env/
+
+.env
+*.env
+config.ini
+
+*.sqlite3
+*.db
+
+staticfiles/
+media/
+
+.DS_Store
+.idea/
+.vscode/
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -10,11 +10,6 @@ jobs:
   test:
     runs-on: ubuntu-latest
 
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ["3.10", "3.11", "3.12"]
-
     services:
       mysql:
         image: mysql:8.0
@@ -24,20 +19,19 @@ jobs:
         ports:
           - 3306:3306
         options: >-
-          --health-cmd="mysqladmin ping -h localhost" --health-interval=10s
-          --health-timeout=5s --health-retries=3
+          --health-cmd="mysqladmin ping -h 127.0.0.1 -uroot -proot"
+          --health-interval=10s --health-timeout=5s --health-retries=10
 
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
 
-      - name: Change to the root directory
-        run: cd /home/runner/work
-
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: "3.12"
+          cache: pip
+          cache-dependency-path: requirements.txt
 
       - name: Install dependencies
         run: |
@@ -48,18 +42,12 @@ jobs:
       - name: Create project config file
         run: |
           echo "# config.ini" > /home/runner/work/config.ini
-          echo "[database]" >> /home/runner/work/config.ini
-          echo "name=test_db" >> /home/runner/work/config.ini
-          echo "user=root" >> /home/runner/work/config.ini
-          echo "password=root" >> /home/runner/work/config.ini
-          echo "host=127.0.0.1" >> /home/runner/work/config.ini
-          echo "port=3306" >> /home/runner/work/config.ini
           echo "[email]" >> /home/runner/work/config.ini
-          echo "from=test_g2p_help@ebi.ac.uk" >>  /home/runner/work/config.ini
-          echo "host=smtp.ebi.ac.uk" >> /home/runner/work/config.ini
-          echo "port=465" >> /home/runner/work/config.ini
-          echo "mailing_list=test_g2p_admin@ebi.ac.uk" >> /home/runner/work/config.ini
-          echo "send_to_mailing_list=True" >>  /home/runner/work/config.ini
+          echo "from=test_email" >>  /home/runner/work/config.ini
+          echo "host=localhost" >> /home/runner/work/config.ini
+          echo "port=25" >> /home/runner/work/config.ini
+          echo "mailing_list=test_email" >> /home/runner/work/config.ini
+          echo "send_to_mailing_list=False" >>  /home/runner/work/config.ini
           echo "[settings]" >> /home/runner/work/config.ini
           echo "DEBUG=True" >> /home/runner/work/config.ini
           echo "ALLOWED_HOSTS=[]" >> /home/runner/work/config.ini
@@ -71,17 +59,24 @@ jobs:
           echo "MAX_DISEASE_NAME_LENGTH=255" >> /home/runner/work/config.ini
           echo "PUBLIC_APP_URL=http://localhost:5173" >> /home/runner/work/config.ini
           echo "[g2p]" >> /home/runner/work/config.ini
-          echo "version=3.0.0" >> /home/runner/work/config.ini
+          echo "version=1.0.0" >> /home/runner/work/config.ini
 
       - name: Run Tests
         run: |
           export SECRET_KEY=$(openssl rand -base64 12)
-          python manage.py makemigrations
-          python manage.py migrate
+          export DB_USERNAME=root
+          export DB_PASSWORD=root
+          export DB_HOST=127.0.0.1
+          export DB_NAME=test_db
+          export DB_PORT=3306
+          export DB_ENGINE=django.db.backends.mysql
+          python manage.py makemigrations --check --dry-run
+          python manage.py migrate --noinput
           python -m coverage run --source=gene2phenotype_app --omit="*/tests/*" manage.py test gene2phenotype_app.tests
           python -m coverage xml -o coverage.cobertura.xml
         env:
           PROJECT_CONFIG_PATH: /home/runner/work/config.ini
+          USE_SQLITE_TEST_DB: "false"
         working-directory: gene2phenotype_project
 
       - name: Code Coverage Summary
@@ -91,4 +86,4 @@ jobs:
           format: markdown
           output: both
           fail_below_min: true
-          thresholds: '80 90'
+          thresholds: "80 90"
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -1,9 +1,164 @@
-# This is a placeholder GitLab CI configuration.
-
 workflow:
   rules:
+    - if: '$CI_PIPELINE_SOURCE == "web" && $CI_COMMIT_TAG'
+      variables:
+        IMAGE_TAG: "$CI_COMMIT_TAG"
+        DOCKER_IMAGE: "$CI_REGISTRY_IMAGE:$CI_COMMIT_TAG"
+      when: always
+    - if: '$CI_PIPELINE_SOURCE == "web" && $CI_COMMIT_BRANCH'
+      variables:
+        IMAGE_TAG: "$CI_COMMIT_REF_SLUG-$CI_PIPELINE_IID-$CI_COMMIT_SHORT_SHA"
+        DOCKER_IMAGE: "$CI_REGISTRY_IMAGE:$CI_COMMIT_REF_SLUG-$CI_PIPELINE_IID-$CI_COMMIT_SHORT_SHA"
+      when: always
     - when: never
 
-hello-world:
+stages:
+  - test
+  - build
+  - deploy
+
+test:
+  stage: test
+  coverage: '/TOTAL.*\s+(\d+%)$/'
+  image: python:3.12-slim-bookworm
+  services:
+    - name: mysql:8.0
+      alias: mysql
+  variables:
+    MYSQL_ROOT_PASSWORD: ci-test-password
+    MYSQL_DATABASE: test_db
+    PROJECT_CONFIG_PATH: "$CI_PROJECT_DIR/config.ini"
+    VIRTUAL_ENV: "$CI_PROJECT_DIR/.venv"
+    DB_USERNAME: root
+    DB_PASSWORD: ci-test-password
+    DB_HOST: mysql
+    DB_NAME: test_db
+    DB_PORT: "3306"
+    DB_ENGINE: django.db.backends.mysql
+    USE_SQLITE_TEST_DB: "false"
+  before_script:
+    - |
+      apt-get update && apt-get install -y --no-install-recommends \
+        default-libmysqlclient-dev \
+        default-mysql-client \
+        build-essential \
+        pkg-config \
+        openssl && \
+      rm -rf /var/lib/apt/lists/*
+    - python -m venv "$VIRTUAL_ENV"
+    - . "$VIRTUAL_ENV/bin/activate"
+    - python -m pip install --upgrade pip
+    - python -m pip install -r requirements.txt
+    - python -m pip install coverage
+    - |
+      for i in $(seq 1 30); do
+        echo "Waiting for MySQL ($i/30)..."
+        if mysqladmin --host="$DB_HOST" --user="$DB_USERNAME" --password="$DB_PASSWORD" --ssl=0 ping; then
+          break
+        fi
+        if [ "$i" -eq 30 ]; then
+          echo "MySQL did not become ready"
+          exit 1
+        fi
+        sleep 2
+      done
+    - |
+      {
+        echo "# config.ini"
+        echo "[email]"
+        echo "from=test_email"
+        echo "host=localhost"
+        echo "port=25"
+        echo "mailing_list=test_email"
+        echo "send_to_mailing_list=False"
+        echo "[settings]"
+        echo "DEBUG=True"
+        echo "ALLOWED_HOSTS=[]"
+        echo "CSRF_TRUSTED_ORIGINS=[]"
+        echo "CORS_ALLOWED_ORIGINS=[]"
+        echo "AUTH_COOKIE_SECURE=False"
+        echo "STATIC_ROOT=/app/staticfiles"
+        echo "STATIC_URL=/static/"
+        echo "MAX_DISEASE_NAME_LENGTH=255"
+        echo "PUBLIC_APP_URL=localhost"
+        echo "[g2p]"
+        echo "version=1.0.0"
+      } > "$PROJECT_CONFIG_PATH"
   script:
-    - echo "Hello, world!"
+    - cd gene2phenotype_project
+    - export SECRET_KEY="$(openssl rand -base64 12)"
+    - python manage.py makemigrations --check --dry-run
+    - python manage.py migrate --noinput
+    - python -m coverage run --source=gene2phenotype_app --omit="*/tests/*" manage.py test --noinput gene2phenotype_app.tests
+    - python -m coverage report --fail-under=80
+    - python -m coverage xml -o coverage.cobertura.xml
+  artifacts:
+    reports:
+      coverage_report:
+        coverage_format: cobertura
+        path: gene2phenotype_project/coverage.cobertura.xml
+    paths:
+      - gene2phenotype_project/coverage.cobertura.xml
+    expire_in: 1 week
+
+build:
+  stage: build
+  needs: ["test"]
+  image: docker:27
+  services:
+    - docker:27-dind
+  before_script:
+    - echo "$CI_REGISTRY_PASSWORD" | docker login "$CI_REGISTRY" -u "$CI_REGISTRY_USER" --password-stdin
+  script:
+    - docker build -t "$DOCKER_IMAGE" .
+    - docker tag "$DOCKER_IMAGE" "$CI_REGISTRY_IMAGE:$CI_COMMIT_SHORT_SHA"
+    - docker push "$DOCKER_IMAGE"
+    - docker push "$CI_REGISTRY_IMAGE:$CI_COMMIT_SHORT_SHA"
+    - docker rmi "$DOCKER_IMAGE" "$CI_REGISTRY_IMAGE:$CI_COMMIT_SHORT_SHA"
+    - docker logout "$CI_REGISTRY"
+
+trigger_k8s_deploy_dev:
+  stage: deploy
+  rules:
+    - if: '$CI_PIPELINE_SOURCE == "web" && $CI_COMMIT_BRANCH'
+      when: manual
+    - when: never
+  environment:
+    name: development
+  trigger:
+    project: "$K8S_MANIFESTS_PROJECT"
+    branch: "$K8S_MANIFESTS_BRANCH"
+    strategy: mirror
+  variables:
+    APP_NAME: g2p-api
+    IMAGE_TAG: "$CI_COMMIT_REF_SLUG-$CI_PIPELINE_IID-$CI_COMMIT_SHORT_SHA"
+    DOCKER_IMAGE: "$CI_REGISTRY_IMAGE:$CI_COMMIT_REF_SLUG-$CI_PIPELINE_IID-$CI_COMMIT_SHORT_SHA"
+    DEPLOY_COMMIT_SHA: "$CI_COMMIT_SHA"
+    DEPLOY_REF: "$CI_COMMIT_REF_NAME"
+    DEPLOY_PIPELINE_URL: "$CI_PIPELINE_URL"
+    DEPLOY_ENV: development
+    KUBE_CONTEXT: "$DEV_AGENT"
+    KUBE_NAMESPACE: "$DEV_NS"
+
+trigger_k8s_deploy_prod:
+  stage: deploy
+  rules:
+    - if: '$CI_PIPELINE_SOURCE == "web" && $CI_COMMIT_TAG'
+      when: manual
+    - when: never
+  environment:
+    name: production
+  trigger:
+    project: "$K8S_MANIFESTS_PROJECT"
+    branch: "$K8S_MANIFESTS_BRANCH"
+    strategy: mirror
+  variables:
+    APP_NAME: g2p-api
+    IMAGE_TAG: "$CI_COMMIT_TAG"
+    DOCKER_IMAGE: "$CI_REGISTRY_IMAGE:$CI_COMMIT_TAG"
+    DEPLOY_COMMIT_SHA: "$CI_COMMIT_SHA"
+    DEPLOY_REF: "$CI_COMMIT_TAG"
+    DEPLOY_PIPELINE_URL: "$CI_PIPELINE_URL"
+    DEPLOY_ENV: production
+    KUBE_CONTEXT: "$PROD_AGENT"
+    KUBE_NAMESPACE: "$PROD_NS"
diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,65 @@
+FROM python:3.12-slim-bookworm AS builder
+
+ENV PYTHONDONTWRITEBYTECODE=1
+ENV PYTHONUNBUFFERED=1
+ENV VIRTUAL_ENV=/opt/venv
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+
+# Build dependencies needed for mysqlclient
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    default-libmysqlclient-dev \
+    build-essential \
+    pkg-config \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /build
+
+# Install dependencies
+COPY requirements.txt .
+RUN python -m venv "$VIRTUAL_ENV" && \
+    pip install --no-cache-dir -r requirements.txt
+
+FROM python:3.12-slim-bookworm AS runtime
+
+ENV PYTHONDONTWRITEBYTECODE=1
+ENV PYTHONUNBUFFERED=1
+ENV VIRTUAL_ENV=/opt/venv
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+ENV DJANGO_SETTINGS_MODULE=gene2phenotype_project.settings
+ENV HOST=0.0.0.0
+ENV PORT=8000
+
+# Runtime dependency for mysqlclient
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    libmariadb3 \
+    && rm -rf /var/lib/apt/lists/* && \
+    useradd -m -u 1000 django && \
+    mkdir -p /app && \
+    chown django:django /app
+
+WORKDIR /app
+
+COPY --from=builder /opt/venv /opt/venv
+
+# Copy application code
+COPY --chown=django:django . .
+
+# Change to the gene2phenotype_project directory
+WORKDIR /app/gene2phenotype_project
+
+USER django
+
+# Collect static files
+RUN SECRET_KEY=dummy-key-for-collectstatic-only \
+    DB_ENGINE=django.db.backends.sqlite3 \
+    DB_NAME=:memory: \
+    DB_USERNAME=dummy \
+    DB_PASSWORD=dummy \
+    DB_HOST=localhost \
+    DB_PORT=5432 \
+    python manage.py collectstatic --noinput --clear
+
+EXPOSE 8000
+
+# Use gunicorn to serve the application
+CMD ["sh", "-c", "exec gunicorn --bind ${HOST}:${PORT} --workers ${GUNICORN_WORKERS:-2} --timeout ${GUNICORN_TIMEOUT:-60} --access-logfile - --error-logfile - gene2phenotype_project.wsgi:application"]