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build.yml
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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: Wait for MIABIS Blaze
run: .github/scripts/wait-for-url.sh http://localhost:5432/health
- name: Docker Logs
run: docker logs test-blaze
- name: Docker Logs
run: docker logs miabis-blaze
- name: Docker Logs
run: sleep 20 && docker logs fhir-module
- name: Verify upload succeeded for blaze
run: .github/scripts/check-patient-exists.sh http://localhost:8080/fhir
- name: Verify upload succeeded for MIABIS blaze
run: .github/scripts/check-patient-exists.sh http://localhost:5432/fhir
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: Wait for MIABIS Blaze
run: .github/scripts/wait-for-url.sh http://localhost:5432/health
- name: Docker Logs
run: docker logs test-blaze
- name: Docker Logs
run: docker logs miabis-blaze
- name: Docker Logs
run: sleep 20 && docker logs fhir-module
- name: Verify upload succeeded
run: .github/scripts/check-patient-exists.sh http://localhost:8080/fhir
- name: Verify upload succeeded for MIABIS blaze
run: .github/scripts/check-patient-exists.sh http://localhost:5432/fhir
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