Merge 7b32b5b into 3f626b7

.github/workflows/build_container_pull.yml

@@ -0,0 +1,29 @@
+---
+
+name: Build container for stage testing
+on: [push]
+
+jobs:
+  docker-image-ci:
+    name: Docker Image CI
+    runs-on: ubuntu-latest
+    steps:
+
+      - name: Check out git repository
+        uses: actions/checkout@v1
+
+      - name: Get branch name
+        uses: nelonoel/branch-name@v1.0.1
+
+      - name: Modify illegal docker names
+        id: get_branch_name
+        shell: bash
+        run: echo "##[set-output name=branch;]$(echo "$(tr "/" "-" <<<$BRANCH_NAME)")"
+
+      - name: Build and publish to Docker Hub
+        uses: elgohr/Publish-Docker-Github-Action@master
+        with:
+          name: clinicalgenomics/niptool-stage
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+          tags: "${{ steps.get_branch_name.outputs.branch }}"

.github/workflows/build_container_release.yml

@@ -0,0 +1,24 @@
+---
+
+name: Build container from latest release
+on:
+  release:
+    types:
+      - created
+
+jobs:
+  docker-image-CI:
+    name: Docker Image CI
+    runs-on: ubuntu-latest
+    steps:
+
+      - name: Check out git repository
+        uses: actions/checkout@v2
+
+      - name: Build and publish to Docker Hub
+        uses: elgohr/Publish-Docker-Github-Action@master
+        with:
+          name: clinicalgenomics/niptool
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+          tags: "${{ github.event.release.tag_name }}, latest"

Dockerfile

@@ -4,6 +4,17 @@ LABEL base_image="python:3.8-slim"
 LABEL about.home="https://github.com/Clinical-Genomics/NIPTool"
 LABEL about.tags="NIPT,statistics,Non Invasive Prenatal Test,python"
 
+
+ENV GUNICORN_WORKERS=1
+ENV GUNICORN_THREADS=1
+ENV GUNICORN_BIND="0.0.0.0:8000"
+ENV GUNICORN_TIMEOUT=400
+ENV DB_URI="mongodb://localhost:27017/nipt-demo"
+ENV DB_NAME="nipt-demo"
+ENV SERVICE_SCOPE="external"
+
+EXPOSE 8000
+
 WORKDIR /home/worker/app
 COPY . /home/worker/app
 
@@ -13,7 +24,10 @@ RUN pip install -r requirements.txt
 # Install app
 RUN pip install -e .
 
-# Create and switch to a new non-root user
-RUN useradd worker
-RUN chown worker:worker -R /home/worker
-USER worker
+CMD gunicorn \
+    --workers=$GUNICORN_WORKERS \
+    --bind=$GUNICORN_BIND  \
+    --threads=$GUNICORN_THREADS \
+    --timeout=$GUNICORN_TIMEOUT \
+    --worker-class=uvicorn.workers.UvicornWorker \
+    NIPTool.main:$SERVICE_SCOPE\_app

NIPTool/commands/base.py

@@ -26,7 +26,7 @@
 @click.group()
 @click.pass_context
 def cli(context: click.Context):
-    """ Main entry point """
+    """Main entry point"""
     logging.basicConfig(level=logging.INFO)
     context.obj = {}
 
@@ -41,9 +41,7 @@ def serve_command(reload: bool, api: str):
 
     This command will serve the user interface (external) as default
     """
-    app = "NIPTool.main:external_app"
-    if api == "internal":
-        app = "NIPTool.main:internal_app"
+    app = f"NIPTool.main:{api}_app"
     LOG.info("Running %s api on host:%s and port:%s", api, settings.host, settings.port)
     uvicorn.run(app=app, host=settings.host, port=settings.port, reload=reload)
 

NIPTool/config.py

@@ -21,7 +21,7 @@ class Settings(BaseSettings):
     port: int = 8000
 
     class Config:
-        from_file = str(ENV_FILE)
+        env_file = str(ENV_FILE)
 
 
 settings = Settings()

requirements.txt

@@ -15,4 +15,5 @@ jinja2
 passlib
 fastapi
 uvicorn
+gunicorn
 python-jose