fix: prefer loinc codes for procedure names (#2950) #1066
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| name: Create New Release | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - main | |
| # Run all tests before making a release | |
| jobs: | |
| # Only make a release if commit contains [RELEASE] | |
| check-commit-message: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| contains_release: ${{ steps.commit_check.outputs.contains_release }} | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v4 | |
| - name: Check commit message for [RELEASE] | |
| id: commit_check | |
| run: | | |
| if [[ "${{ github.event.head_commit.message }}" == *"[RELEASE]"* ]]; then | |
| echo "contains_release=true" >> $GITHUB_OUTPUT | |
| else | |
| echo "contains_release=false" >> $GITHUB_OUTPUT | |
| fi | |
| list-containers: | |
| needs: check-commit-message | |
| if: ${{ needs.check-commit-message.outputs.contains_release == 'true' }} | |
| uses: ./.github/workflows/listContainers.yaml | |
| test-for-release: | |
| needs: | |
| - check-commit-message | |
| - list-containers | |
| if: ${{ needs.check-commit-message.outputs.contains_release == 'true' }} | |
| strategy: | |
| matrix: | |
| container: ${{fromJson(needs.list-containers.outputs.all-containers)}} | |
| uses: ./.github/workflows/run-container-workflow.yaml | |
| with: | |
| container: ${{ matrix.container }} | |
| secrets: inherit | |
| tag-release: | |
| name: Update phdi init version number | |
| needs: test-for-release | |
| permissions: | |
| contents: write | |
| outputs: | |
| version: ${{ steps.get_version.outputs.version }} | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: "0" | |
| ref: "main" | |
| - name: Install poetry and dependencies | |
| run: | | |
| pip install poetry | |
| # update the version number in the phdi/__init.py__ file | |
| - name: Get PHDI Version | |
| id: get_version | |
| run: | | |
| VERSION_WITH_PHDI=$(poetry version) | |
| echo "version=${VERSION_WITH_PHDI:5}" >> $GITHUB_OUTPUT | |
| # Create new release tag | |
| - name: Set up Git user | |
| run: | | |
| git config --local user.email "action@github.com" | |
| git config --local user.name "GitHub Action" | |
| - name: Tag Release | |
| uses: EndBug/latest-tag@latest | |
| with: | |
| ref: ${{ steps.get_version.outputs.version }} | |
| # Generate release notes | |
| - name: Generate release notes | |
| id: release_notes | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| latest_release_date=$(gh api "/repos/$GITHUB_REPOSITORY/releases?per_page=1" | jq ".[0].created_at") | |
| prs=$(gh pr list --base main --state closed --json title,number,url,closedAt -q ".[] | select(.closedAt > $latest_release_date) | select(.title | contains(\"RELEASE\") | not)") | |
| echo "# Release Notes" > release-notes.md | |
| echo "" >> release-notes.md | |
| echo "" >> release-notes.md | |
| while IFS= read -r pr; do | |
| pr_title=$(echo "$pr" | jq -r ".title") | |
| pr_number=$(echo "$pr" | jq -r ".number") | |
| pr_url=$(echo "$pr" | jq -r ".url") | |
| line_text="- $pr_title ([#$pr_number]($pr_url))" | |
| echo $line_text >> release-notes.md | |
| done < <(printf '%s' "$prs") | |
| # Create new release based upon the latest created tag | |
| - name: Create Release | |
| id: create_release | |
| uses: actions/create-release@v1.1.4 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| tag_name: ${{ steps.get_version.outputs.version }} | |
| release_name: ${{ steps.get_version.outputs.version }} | |
| body_path: release-notes.md | |
| release-to-pypi: | |
| name: Build and publish PHDI to PyPI | |
| needs: tag-release | |
| runs-on: ubuntu-latest | |
| permissions: | |
| id-token: write | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: "0" | |
| ref: ${{ needs.tag-release.outputs.version }} | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.x" | |
| - name: Install pypa/build | |
| run: >- | |
| python -m | |
| pip install | |
| build | |
| --user | |
| - name: Build a binary wheel and a source tarball | |
| run: >- | |
| python -m | |
| build | |
| --sdist | |
| --wheel | |
| --outdir dist/ | |
| . | |
| - name: Publish distribution 📦 to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| # Rebuild all containers for the new release | |
| build-containers-for-release: | |
| needs: | |
| - tag-release | |
| - release-to-pypi | |
| permissions: | |
| contents: read | |
| packages: write | |
| id-token: write | |
| uses: ./.github/workflows/buildReleaseContainers.yaml | |
| with: | |
| container-tag: ${{ needs.tag-release.outputs.version }} | |
| # Create updated PHDI docs for the latest release | |
| generate-and-update-phdi-docs: | |
| needs: | |
| - tag-release | |
| - build-containers-for-release | |
| permissions: | |
| contents: write | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: "0" | |
| ref: ${{ needs.tag-release.outputs.version }} | |
| - name: Install poetry and dependencies | |
| run: | | |
| pip install poetry | |
| poetry install | |
| - name: Set environment variable for pdoc | |
| run: echo "PDOC_ALLOW_EXEC=1" >> $GITHUB_ENV | |
| - name: Clear Poetry Cache | |
| run: | | |
| poetry cache clear pypi --all | |
| poetry cache clear virtualenvs --all | |
| - name: Generate docs and move to docs branch | |
| run: | | |
| poetry run pdoc ./phdi -o ./docs/${{ needs.tag-release.outputs.version }}/sdk | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: phdi-docs | |
| path: ./docs/${{ needs.tag-release.outputs.version }}/sdk | |
| # Create updated container docs for the latest release | |
| generate-and-update-container-docs: | |
| needs: | |
| - tag-release | |
| - list-containers | |
| - generate-and-update-phdi-docs | |
| permissions: | |
| contents: write | |
| runs-on: ubuntu-latest | |
| services: | |
| test-db: | |
| image: postgres:13-alpine3.16 | |
| env: | |
| POSTGRES_PASSWORD: pw | |
| POSTGRES_DB: testdb | |
| POSTGRES_USER: postgres | |
| # Set health checks to wait until postgres has started | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| --name testdb | |
| ports: | |
| - 5432:5432 | |
| strategy: | |
| matrix: | |
| container: ${{fromJson(needs.list-containers.outputs.python-containers)}} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: "0" | |
| ref: ${{ needs.tag-release.outputs.version }} | |
| - name: Update Container Documentation | |
| env: | |
| MPI_DBNAME: testdb | |
| MPI_PASSWORD: pw | |
| MPI_DB_TYPE: postgres | |
| MPI_HOST: localhost | |
| MPI_USER: postgres | |
| MPI_PORT: 5432 | |
| MPI_PATIENT_TABLE: patient | |
| MPI_PERSON_TABLE: person | |
| run: | | |
| npm i -g redoc-cli | |
| CONTAINER=${{ matrix.container }} | |
| cd $GITHUB_WORKSPACE/containers/$CONTAINER | |
| cp $GITHUB_WORKSPACE/utils/make_openapi_json.py . | |
| pip install -r requirements.txt | |
| python make_openapi_json.py | |
| redoc-cli build -o $GITHUB_WORKSPACE/docs/${{ needs.tag-release.outputs.version }}/containers/$CONTAINER.html openapi.json | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: container-docs | |
| path: ./docs/${{ needs.tag-release.outputs.version }}/containers | |
| commit-docs: | |
| needs: | |
| - tag-release | |
| - generate-and-update-phdi-docs | |
| - generate-and-update-container-docs | |
| permissions: | |
| contents: write | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: docs | |
| - name: Download phdi docs from artifacts | |
| uses: actions/download-artifact@v4.1.7 | |
| with: | |
| name: phdi-docs | |
| path: ./docs/${{ needs.tag-release.outputs.version }}/sdk | |
| - name: Download container docs from artifacts | |
| uses: actions/download-artifact@v4.1.7 | |
| with: | |
| name: container-docs | |
| path: ./docs/${{ needs.tag-release.outputs.version }}/containers | |
| - name: Copy to latest folder | |
| run: | | |
| rm -rf ./docs/latest | |
| mkdir -p ./docs/latest/sdk | |
| mkdir -p ./docs/latest/containers | |
| cp -r ./docs/${{ needs.tag-release.outputs.version }}/sdk/* ./docs/latest/sdk | |
| cp -r ./docs/${{ needs.tag-release.outputs.version }}/containers/* ./docs/latest/containers | |
| - name: Commit New Documentation | |
| uses: EndBug/add-and-commit@v9 | |
| with: | |
| add: docs | |
| message: Automated update of docs for ${{ needs.tag-release.outputs.version }} release. |