Merge branch 'main' into user_removal_mme_check

.github/workflows/build_and_publish.yml

@@ -47,14 +47,23 @@ jobs:
     - name: Check out git repository
       uses: actions/checkout@v2
 
-    - name: Build and publish to Docker Hub
+    - name: Publish main image (Dockerfile) to Registry
       uses: elgohr/Publish-Docker-Github-Action@master
       with:
         name: clinicalgenomics/scout
         username: ${{ secrets.DOCKER_USERNAME }}
         password: ${{ secrets.DOCKER_PASSWORD }}
         tags: "latest,${{ github.event.release.tag_name }}"
 
+    - name: Publish server image (Dockerfile-server) to Registry
+      uses: elgohr/Publish-Docker-Github-Action@master
+      with:
+        name: clinicalgenomics/scout-server
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+        dockerfile: Dockerfile-server
+        tags: "latest,${{ github.event.release.tag_name }}"
+
  deploy-docs:
    name: Deploy Docs to GitHubIO
    runs-on: ubuntu-latest
@@ -69,4 +78,3 @@ jobs:
       run: pip install mkdocs mkdocs-material markdown-include
     - name: Deploy documentation
       run: mkdocs gh-deploy --force
-

.github/workflows/server_stage_docker_push.yml

@@ -0,0 +1,37 @@
+name: Publish to Docker stage
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  docker-stage-push:
+    name: Create staging docker image
+    runs-on: ubuntu-latest
+    steps:
+     - name: Check out git repository
+       uses: actions/checkout@v2
+
+     - name: Get branch name
+       id: branch-name
+       uses: tj-actions/branch-names@v5
+
+     - name: Login to Docker Hub
+       uses: docker/login-action@v1
+       with:
+         username: ${{ secrets.DOCKER_USERNAME }}
+         password: ${{ secrets.DOCKER_PASSWORD }}
+
+     - name: Set up Docker Buildx
+       id: buildx
+       uses: docker/setup-buildx-action@v1
+
+     - name: Build and push
+       if: steps.branch-name.outputs.is_default == 'false'
+       uses: docker/build-push-action@v2
+       with:
+         context: ./
+         file: ./Dockerfile-server
+         push: true
+         tags: "clinicalgenomics/scout-server-stage:${{steps.branch-name.outputs.current_branch}}, clinicalgenomics/scout-server-stage:latest"

CHANGELOG.md

@@ -4,8 +4,20 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
+
 ## []
 ### Added
+- Created a Dockefile to be used to serve the dockerized app in production
+- Modified the code to collect database params specified as env vars
+- Created a GitHub action that pushes the Dockerfile-server image to Docker Hub (scout-server-stage) every time a PR is opened
+- Created a GitHub action that pushes the Dockerfile-server image to Docker Hub (scout-server) every time a new release is created
+### Changed
+- Updated the python config file documentation in admin guide
+### Fixed
+
+
+## [4.45]
+### Added
 ### Changed
 - Start Scout also when loqusdbapi is not reachable
 - Clearer definition of manual standard and custom inheritance models in gene panels

Dockerfile

@@ -9,7 +9,7 @@ WORKDIR /app
 
 # Install Scout dependencies
 COPY requirements.txt .
-RUN pip install --no-cache-dir -r requirements.txt gunicorn
+RUN pip install --no-cache-dir -r requirements.txt
 
 
 #########
@@ -35,7 +35,7 @@ ENV PATH="/venv/bin:$PATH"
 RUN echo export PATH="/venv/bin:\$PATH" > /etc/profile.d/venv.sh
 
 # Create a non-root user to run commands
-RUN groupadd --gid 10001 worker && useradd -g worker --uid 10001 --shell /usr/sbin/nologin --create-home worker
+RUN groupadd --gid 1000 worker && useradd -g worker --uid 1000 --shell /usr/sbin/nologin --create-home worker
 
 # Copy virtual environment from builder
 COPY --chown=worker:worker --from=python-builder /venv /venv

Dockerfile-server

@@ -0,0 +1,67 @@
+###########
+# BUILDER #
+###########
+FROM clinicalgenomics/python3.8-cyvcf2-venv:1.0 AS python-builder
+
+ENV PATH="/venv/bin:$PATH"
+
+WORKDIR /app
+
+# Install Scout dependencies
+COPY requirements.txt .
+RUN pip install --no-cache-dir -r requirements.txt gunicorn
+
+#########
+# FINAL #
+#########
+FROM python:3.8-slim
+
+LABEL about.home="https://github.com/Clinical-Genomics/scout"
+LABEL about.documentation="https://clinical-genomics.github.io/scout"
+LABEL about.tags="WGS,WES,Rare diseases,VCF,variants,SNP,Next generation sequencing"
+LABEL about.license="MIT License (MIT)"
+
+# Install base dependencies
+RUN apt-get update && \
+     apt-get -y upgrade && \
+     apt-get -y install -y --no-install-recommends libpango-1.0-0 libpangocairo-1.0-0 && \
+     apt-get clean && \
+     rm -rf /var/lib/apt/lists/*
+
+# Do not upgrade to the latest pip version to ensure more reproducible builds
+ENV PIP_DISABLE_PIP_VERSION_CHECK=1
+ENV PATH="/venv/bin:$PATH"
+RUN echo export PATH="/venv/bin:\$PATH" > /etc/profile.d/venv.sh
+
+# Create a non-root user to run commands
+RUN groupadd --gid 1000 worker && useradd -g worker --uid 1000 --shell /usr/sbin/nologin --create-home worker
+
+# Copy virtual environment from builder
+COPY --chown=worker:worker --from=python-builder /venv /venv
+
+WORKDIR /home/worker/app
+COPY . /home/worker/app
+
+# Install only Scout app
+RUN pip install --no-cache-dir --editable .[coverage]
+
+# Run the app as non-root user
+USER worker
+
+ENV GUNICORN_WORKERS=1
+ENV GUNICORN_THREADS=1
+ENV GUNICORN_BIND="0.0.0.0:8000"
+ENV GUNICORN_TIMEOUT=400
+
+CMD gunicorn \
+    --workers=$GUNICORN_WORKERS \
+    --bind=$GUNICORN_BIND  \
+    --threads=$GUNICORN_THREADS \
+    --timeout=$GUNICORN_TIMEOUT \
+    --proxy-protocol \
+    --forwarded-allow-ips="10.0.2.100,127.0.0.1" \
+    --log-syslog \
+    --access-logfile - \
+    --error-logfile - \
+    --log-level="debug" \
+    scout.server.auto:app

README.md

@@ -36,9 +36,9 @@ The repository includes a Makefile with common shortcuts to simplify setting up
 This demo is consisting of 3 containers:
 - a MongoDB instance, on the default port 27017 in the container, mapped to host port 27013
 - scout-cli --> the Scout command line, connected to the database. Populates the database with demo data
-- scout-web --> the Scout web app, that serves the app on localhost, port 5000.
+- scout-web --> the Scout web app, that serves the app on localhost, port 8000.
 
-Once the server has started you and open the app in the web browser at the following address: http://localhost:5000/
+Once the server has started you and open the app in the web browser at the following address: http://localhost:8000/
 
 The command to stop the demo are either `docker-compose down` or `make down`.
 

docker-compose.yml

@@ -28,13 +28,21 @@ services:
       - mongodb
 
   scout-web:
-    build: .
-    container_name: scout-web
+    build:
+      context: .
+      dockerfile: Dockerfile-server
     expose:
-      - '5000'
+      - '8000'
     ports:
-      - '5000:5000'
-    command: scout --host mongodb --demo serve --host 0.0.0.0
+      - '8000:8000'
+    environment:
+      SCOUT_CONFIG: /home/worker/app/scout/server/config.py
+      MONGO_HOST: mongodb
+      MONGO_DBNAME: scout-demo
+      GUNICORN_WORKERS: 1
+      GUNICORN_TREADS: 1
+      GUNICORN_BIND: 0.0.0.0:8000
+      GUNICORN_TIMEOUT: 400
     volumes:
       - ./scout:/home/worker/app/scout
     networks: