Show summary if no sequencing groups / assays exist (#564) #650
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| name: Deploy | |
| on: | |
| # Building on manual dispatch, and pushes to dev / main. But restricting | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - main | |
| - dev | |
| permissions: | |
| id-token: write | |
| contents: read | |
| jobs: | |
| deploy: | |
| runs-on: ubuntu-latest | |
| env: | |
| DOCKER_BUILDKIT: 1 | |
| BUILDKIT_PROGRESS: plain | |
| CLOUDSDK_CORE_DISABLE_PROMPTS: 1 | |
| # used for generating API | |
| SM_DOCKER: australia-southeast1-docker.pkg.dev/sample-metadata/images/server:${{ github.sha }} | |
| SM_API_DOCKER: australia-southeast1-docker.pkg.dev/cpg-common/images/sm-api | |
| defaults: | |
| run: | |
| shell: bash -eo pipefail -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - id: "google-cloud-auth" | |
| name: "Authenticate to Google Cloud" | |
| uses: "google-github-actions/auth@v1" | |
| with: | |
| workload_identity_provider: "projects/774248915715/locations/global/workloadIdentityPools/gh-deploy-pool/providers/gh-provider" | |
| service_account: "[email protected]" | |
| - id: "google-cloud-sdk-setup" | |
| name: "Set up Cloud SDK" | |
| uses: google-github-actions/setup-gcloud@v1 | |
| - name: "gcloud docker auth" | |
| run: | | |
| gcloud auth configure-docker australia-southeast1-docker.pkg.dev | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - uses: actions/setup-java@v3 | |
| with: | |
| distribution: "temurin" # See 'Supported distributions' for available options | |
| java-version: "17" | |
| - name: Setup build env | |
| run: | | |
| pip install -r requirements-dev.txt | |
| pip install -r requirements.txt | |
| wget https://repo1.maven.org/maven2/org/openapitools/openapi-generator-cli/5.3.0/openapi-generator-cli-5.3.0.jar -O openapi-generator-cli.jar | |
| - name: prepare-deployment | |
| run: | | |
| if [[ $GITHUB_REF == 'refs/heads/main' ]]; then | |
| echo DEPLOYMENT_TYPE=prod >> $GITHUB_ENV | |
| echo SM_ENVIRONMENT=production >> $GITHUB_ENV | |
| else | |
| echo DEPLOYMENT_TYPE=dev >> $GITHUB_ENV | |
| echo SM_ENVIRONMENT=development >> $GITHUB_ENV | |
| pip install bump2version | |
| # add | |
| bump2version patch \ | |
| --no-commit --allow-dirty \ | |
| --new-version $(cat deploy/python/version.txt)dev$(echo $(git rev-parse HEAD) | cut -c1-7) | |
| fi | |
| # we have to build the image first without the web files to | |
| # generate the openapi file to then generate the documentation | |
| - name: "build image" | |
| run: | | |
| docker build \ | |
| --build-arg SM_ENVIRONMENT=$SM_ENVIRONMENT \ | |
| --tag $SM_DOCKER \ | |
| -f deploy/api/Dockerfile \ | |
| . | |
| - name: "build deployable API" | |
| run: | | |
| export OPENAPI_COMMAND="java -jar openapi-generator-cli.jar" | |
| python regenerate_api.py | |
| ls -lGh metamist | |
| # also copies build artifacts to api/public | |
| - name: "build web front-end" | |
| run: | | |
| set -eo pipefail | |
| pushd web | |
| # installs package-lock, not what it thinks it should be | |
| npm ci | |
| npm run build | |
| popd | |
| # rebuild docker image now that front-end files are in the right place | |
| - name: "build image II" | |
| run: | | |
| docker build --tag $SM_DOCKER -f deploy/api/Dockerfile . | |
| - name: Build python package | |
| run: python setup.py sdist | |
| - name: "push server image" | |
| run: | | |
| docker push $SM_DOCKER | |
| - name: "deploy to Cloud Run" | |
| run: | | |
| if [[ $GITHUB_REF == 'refs/heads/main' ]]; then | |
| gcloud_deploy_name=sample-metadata-api | |
| else | |
| gcloud_deploy_name=sample-metadata-api-dev | |
| fi | |
| gcloud run deploy \ | |
| $gcloud_deploy_name --image $SM_DOCKER \ | |
| --region australia-southeast1 --no-allow-unauthenticated \ | |
| --platform managed | |
| - name: Publish package | |
| if: github.ref == 'refs/heads/main' | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| packages-dir: dist/ | |
| skip-existing: true |