Merge pull request #71 from Clinical-Genomics/container

Docker file (minor)

 ### Added
- Docker file
- commit template
- dockerhub push to stage - on pulrequest
- dockerhub push to prod - on new release
- bump version - on merge to master 
- updating test coverage - on merge to master
- dockerhub push to stage - on merge to master

.github/commit_template.txt

@@ -0,0 +1,9 @@
+
+ ### Added
+ -
+
+ ### Changed
+ -
+
+ ### Fixed
+ -

.github/workflows/dockerhub_push.yml

@@ -0,0 +1,35 @@
+
+name: Push cg_lims image to Docker Hub on push event
+
+on: [pull_request]
+
+jobs:
+  docker-image-push:
+    runs-on: ubuntu-latest
+    steps:
+     - name: Check out git repository
+       uses: actions/checkout@v2
+
+     - name: Extract branch name and remove illegal chars
+       id: get_branch_name
+       shell: bash
+       run: echo "##[set-output name=branch;]$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")"
+
+     - name: Login to Docker Hub
+       uses: docker/login-action@v1
+       with:
+         username: ${{ secrets.DOCKER_USERNAME }}
+         password: ${{ secrets.DOCKER_PASSWORD }}
+
+     - name: Set up Docker Buildx
+       id: buildx
+       uses: docker/setup-buildx-action@v1
+
+     - name: Build and push
+       id: docker_build
+       uses: docker/build-push-action@v2
+       with:
+         context: ./
+         file: ./Dockerfile
+         push: true
+         tags: "clinicalgenomics/cg_lims-stage:${{steps.get_branch_name.outputs.branch}}, clinicalgenomics/cg_lims-stage:latest"

.github/workflows/dockerhub_push_release.yml

@@ -0,0 +1,35 @@
+
+name: Push to Docker Hub on new release event
+
+on:
+ release:
+  types:
+   - created
+
+jobs:
+  docker-image-release_push:
+    # Push to Docker Hub when a new release is created
+    runs-on: ubuntu-latest
+    steps:
+
+     - name: Check Out Repo
+       uses: actions/checkout@v2
+
+     - name: Login to Docker Hub
+       uses: docker/login-action@v1
+       with:
+         username: ${{ secrets.DOCKER_USERNAME }}
+         password: ${{ secrets.DOCKER_PASSWORD }}
+
+     - name: Set up Docker Buildx
+       id: buildx
+       uses: docker/setup-buildx-action@v1
+
+     - name: Build and push
+       id: docker_build
+       uses: docker/build-push-action@v2
+       with:
+         context: ./
+         file: ./Dockerfile
+         push: true
+         tags: "clinicalgenomics/cg_lims:${{github.event.release.tag_name}}, clinicalgenomics/cg_lims:latest"

.github/workflows/merge_master_ci.yml

@@ -0,0 +1,92 @@
+name: 'Merge-master-CI'
+on:
+  push:
+    branches:
+      - 'master'
+      - 'main'
+
+jobs:
+  bump-version:
+    runs-on: ubuntu-latest
+    name: Bump version and push tags to master
+    steps:
+      - name: Bump version
+        uses: Clinical-Genomics/bump2version-ci@master
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_REPOSITORY: ${{ github.repository }}
+          GITHUB_ACTOR: ${{ github.actor }}
+        with:
+          release_pat: ${{ secrets.BUMPVERSION_TOKEN }}
+
+  docker-image-push:
+    runs-on: ubuntu-latest
+    name: Push staging docker image to dockerhub
+    steps:
+      - name: Check out git repository
+        uses: actions/checkout@v2
+
+      - name: Extract branch name and remove illegal chars
+        id: get_branch_name
+        shell: bash
+        run: echo "##[set-output name=branch;]$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")"
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v2
+        with:
+          context: ./
+          file: ./Dockerfile
+          push: true
+          tags: "clinicalgenomics/cg_lims-stage:${{steps.get_branch_name.outputs.branch}}, clinicalgenomics/cg_lims-stage:latest"
+
+  tests-coverage:
+    runs-on: ubuntu-latest
+    name: Test and coveralls
+    steps:
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Check out limsmock
+        uses: actions/checkout@v2
+        with:
+          repository: "Clinical-Genomics/limsmock"
+
+      - name: Install limsmock dependencies
+        run: |
+          python -m pip install --upgrade pip==21.1.2
+          pip install -r requirements.txt -r requirements-dev.txt .
+
+      - name: Check out cg_lims
+        uses: actions/checkout@v2
+        with:
+          repository: "Clinical-Genomics/cg_lims"
+
+      - name: Install cg_lims dependencies
+        run: |
+          pip install -r requirements.txt -r requirements-dev.txt .
+
+      - name: Install coveralls dependencies
+        run: |
+          pip install pytest-cov coveralls
+
+      - name: Test with pytest & Coveralls
+        run: |
+          pytest --cov=cg_lims/
+          coveralls
+        env:
+          GITHUB: 1
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}

Dockerfile

@@ -0,0 +1,42 @@
+FROM python:3.8-slim
+
+LABEL base_image="python:3.8-slim"
+LABEL about.home="https://github.com/Clinical-Genomics/cg_lims"
+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 BASEURI="https://clinical-lims-stage.scilifelab.se"
+ENV HOST="clinical-lims-stage.scilifelab.se"
+ENV USERNAME="apiuser"
+ENV PASSWORD="??"
+ENV CG_URL="https://clinical-api.scilifelab.se/api/v1"
+ENV CG_LIMS_HOST="localhost"
+ENV CG_LIMS_PORT=8000
+
+EXPOSE 8000
+
+WORKDIR /home/worker/app
+COPY . /home/worker/app
+
+# Install app requirements
+RUN pip install -r requirements.txt
+
+# Install app
+RUN pip install -e .
+
+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 - \
+    --log-level="debug" \
+    --worker-class=uvicorn.workers.UvicornWorker \
+    cg_lims.app.api.api_v1.api:app

requirements.txt

@@ -3,4 +3,6 @@ click
 PyYAML
 pydantic
 fastapi
-pandas
+pandas
+gunicorn
+uvicorn