CI build #255
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name: CI build | |
on: | |
schedule: | |
- cron: '0 10 * * *' # every day at 10am | |
push: | |
branches: | |
- main | |
pull_request: | |
jobs: | |
py-lint: | |
name: Lint | |
continue-on-error: true | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout code | |
uses: actions/checkout@v3 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: '3.11' | |
cache: 'pip' | |
- name: Install python dependencies | |
run: | | |
python -m pip install --upgrade pip | |
pip install -r requirements.txt | |
- name: Run pylint | |
run: pylint --recursive=y . | |
unit-tests: | |
name: Unit tests | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout code | |
uses: actions/checkout@v3 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: '3.11' | |
cache: 'pip' | |
- name: Run unit tests | |
run: make test | |
- name: Upload coverage to Codecov | |
uses: codecov/codecov-action@v3 | |
with: | |
flags: unit | |
integration-tests: | |
needs: unit-tests | |
name: Integration tests | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout code | |
uses: actions/checkout@v3 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: '3.11' | |
cache: 'pip' | |
- name: Run integration tests | |
run: make validate | |
- name: Upload coverage to Codecov | |
uses: codecov/codecov-action@v3 | |
with: | |
flags: integration | |
build-image: | |
name: Docker image build | |
needs: [ integration-tests ] | |
runs-on: ubuntu-latest | |
steps: | |
- name: Check out Git repository | |
uses: actions/checkout@v3 | |
- name: Set up QEMU | |
uses: docker/setup-qemu-action@v2 | |
- name: Set up Docker Buildx | |
uses: docker/setup-buildx-action@v2 | |
- name: Build image | |
uses: docker/build-push-action@v4 | |
with: | |
context: . | |
tags: ghcr.io/bbmri-cz/fhir-module:latest | |
outputs: type=docker,dest=/tmp/fhir-module.tar | |
cache-from: type=gha | |
cache-to: type=gha,mode=max | |
- name: Upload FHIR-Module Image | |
uses: actions/upload-artifact@v3 | |
with: | |
name: fhir-module-image | |
path: /tmp/fhir-module.tar | |
system-test: | |
name: System test | |
needs: [ build-image ] | |
runs-on: ubuntu-latest | |
steps: | |
- name: Check out Git repository | |
uses: actions/checkout@v3 | |
- name: Install jq | |
run: sudo apt-get install -y jq | |
- name: Download artifact | |
uses: actions/download-artifact@v3 | |
with: | |
name: fhir-module-image | |
path: /tmp | |
- name: Load FHIR-Module Image | |
run: docker load --input /tmp/fhir-module.tar | |
- name: Create docker network | |
run: docker network create system-test | |
- name: Run sandbox in dev env | |
run: docker compose --profile dev up -d | |
- name: Wait for Blaze | |
run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
- name: Docker Logs | |
run: docker logs blaze | |
- name: Docker Logs | |
run: sleep 20 && docker logs fhir-module | |
- name: Verify upload succeeded | |
run: .github/scripts/check-patient-exists.sh | |
system-test-csv: | |
name: System test csv files | |
needs: [ system-test ] | |
runs-on: ubuntu-latest | |
steps: | |
- name: Check out Git repository | |
uses: actions/checkout@v3 | |
- name: Install jq | |
run: sudo apt-get install -y jq | |
- name: Download artifact | |
uses: actions/download-artifact@v3 | |
with: | |
name: fhir-module-image | |
path: /tmp | |
- name: Load FHIR-Module Image | |
run: docker load --input /tmp/fhir-module.tar | |
- name: Create docker network | |
run: docker network create system-test | |
- name: Run sandbox in dev env (use compose.override.yaml to work with csv files) | |
run: docker compose -f compose.yaml -f .github/comp_override/compose.override.yaml --profile dev up -d | |
- name: Wait for Blaze | |
run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
- name: Docker Logs | |
run: docker logs blaze | |
- name: Docker Logs | |
run: sleep 20 && docker logs fhir-module | |
- name: Verify upload succeeded | |
run: .github/scripts/check-patient-exists.sh | |
build-push-image: | |
name: Publish docker image | |
needs: [ system-test-csv ] | |
runs-on: ubuntu-latest | |
steps: | |
- name: Check out Git repository | |
uses: actions/checkout@v3 | |
- name: Set up QEMU | |
uses: docker/setup-qemu-action@v2 | |
- name: Set up Docker Buildx | |
uses: docker/setup-buildx-action@v2 | |
- name: Login to GitHub Container Registry | |
uses: docker/login-action@v2 | |
with: | |
registry: ghcr.io | |
username: ${{ github.repository_owner }} | |
password: ${{ secrets.GITHUB_TOKEN }} | |
- name: Docker meta | |
id: docker-meta | |
uses: docker/metadata-action@v4 | |
with: | |
images: | | |
ghcr.io/${{ github.repository_owner }}/fhir-module | |
tags: | | |
type=schedule | |
type=ref,event=branch | |
type=ref,event=pr | |
type=semver,pattern={{version}} | |
type=semver,pattern={{major}}.{{minor}} | |
type=raw,value=latest,enable=${{ github.ref == format('refs/heads/{0}', 'main') }} | |
- name: Build and push image | |
uses: docker/build-push-action@v4 | |
with: | |
context: . | |
platforms: linux/amd64,linux/arm64 | |
push: true | |
tags: ${{ steps.docker-meta.outputs.tags }} | |
labels: ${{ steps.docker-meta.outputs.labels }} | |
cache-from: type=gha | |
cache-to: type=gha,mode=max |