Schema Version Bump Workflow #5
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| name: Schema Version Bump Workflow | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| is-major-schema-bump: | |
| description: "Set to 'true' to kickoff major schema update; otherwise trigger a minor schema update" | |
| required: true | |
| default: 'false' | |
| permissions: | |
| id-token: write | |
| contents: write | |
| pull-requests: write | |
| jobs: | |
| ontology-dry-run: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: 3.8 | |
| - name: Python cache | |
| uses: actions/cache@v1 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install dependencies | |
| run: | | |
| pip install -r scripts/schema_bump_dry_run_ontologies/requirements.txt | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v2 | |
| with: | |
| aws-region: us-west-2 | |
| role-to-assume: ${{ secrets.AWS_PROD_ROLE_TO_ASSUME }} | |
| role-duration-seconds: 2700 | |
| - name: Pull AWS Secrets | |
| uses: aws-actions/aws-secretsmanager-get-secrets@v1 | |
| with: | |
| secret-ids: | |
| AUTH0_SECRETS, corpora/backend/prod/auth0-secret | |
| - name: Run Dry-Run Script | |
| if: steps.changed-files.outputs.any_changed == 'true' | |
| run: python3 -m scripts.schema_bump_dry_run_ontologies.ontology_bump_dry_run | |
| env: | |
| corpus_env: "prod" | |
| - name: Store JSON with Replaced By Ontology Term Mappings | |
| uses: actions/cache/save@v3 | |
| with: | |
| path: "./replaced-by.json" | |
| key: replaced-by-map | |
| - name: upload dry run to slack | |
| run: | | |
| curl -F [email protected] -F "initial_comment=Ontology Dry Run Report" -F channels=${{secrets.SLACK_CURATOR_REPORTING_CHANNEL}} -H "Authorization: Bearer ${{secrets.SLACK_CURATOR_REPORTING_APP_AUTH}}" https://slack.com/api/files.upload | |
| gencode-dry-run: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: 3.9 | |
| - name: Python cache | |
| uses: actions/cache@v1 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install dependencies | |
| run: | | |
| pip install -r scripts/schema_bump_dry_run_genes/requirements.txt | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v2 | |
| with: | |
| aws-region: us-west-2 | |
| role-to-assume: ${{ secrets.AWS_PROD_ROLE_TO_ASSUME }} | |
| role-duration-seconds: 2700 | |
| - name: Pull AWS Secrets | |
| uses: aws-actions/aws-secretsmanager-get-secrets@v1 | |
| with: | |
| secret-ids: | |
| AUTH0_SECRETS, corpora/backend/prod/auth0-secret | |
| - name: Check if any GENCODE csv files have changed | |
| id: changed-files | |
| uses: tj-actions/changed-files@v36 | |
| with: | |
| files: cellxgene_schema_cli/cellxgene_schema/ontology_files/*.csv.gz | |
| - name: Run Dry-Run Script | |
| if: steps.changed-files.outputs.any_changed == 'true' | |
| run: python3 -m scripts.schema_bump_dry_run_genes.gene_bump_dry_run | |
| env: | |
| corpus_env: "prod" | |
| - name: upload to slack | |
| if: steps.changed-files.outputs.any_changed == 'true' | |
| run: | | |
| curl -F [email protected] -F "initial_comment=Gene Dry Run Report" -F channels=${{secrets | |
| .SLACK_CURATOR_REPORTING_CHANNEL}} -H "Authorization: Bearer ${{secrets.SLACK_CURATOR_REPORTING_APP_AUTH}}" https://slack.com/api/files.upload | |
| publish-to-pypi: | |
| name: Build and publish Python distributions to PyPI | |
| runs-on: ubuntu-latest | |
| if: "${{ github.event.inputs.is-major-schema-bump == 'false' }}" | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.x" | |
| - name: setup git | |
| run: | | |
| git config user.name github-actions | |
| git config user.email [email protected] | |
| # - name: Bump and tag release version | |
| # run: | | |
| # pip install bumpversion | |
| # pip install wheel | |
| # bumpversion --config-file .bumpversion.cfg minor --allow-dirty | |
| # bumpversion --config-file .bumpversion.cfg prerel --allow-dirty --tag | |
| # - name: Build dist | |
| # run: >- | |
| # make pydist | |
| # - name: Publish distribution to Test PyPI | |
| # uses: pypa/gh-action-pypi-publish@release/v1 | |
| # with: | |
| # password: ${{ secrets.TEST_PYPI_API_TOKEN }} | |
| # repository-url: https://test.pypi.org/legacy/ | |
| # packages-dir: cellxgene_schema_cli/dist/ | |
| # - name: Install and Test Package from Test PyPI | |
| # run: | | |
| # pip install -r cellxgene_schema_cli/requirements.txt | |
| # pip install --index-url https://test.pypi.org/simple/ cellxgene-schema | |
| # cellxgene-schema validate cellxgene_schema_cli/tests/fixtures/h5ads/example_valid.h5ad | |
| # - name: Publish distribution to PyPI | |
| # uses: pypa/gh-action-pypi-publish@release/v1 | |
| # with: | |
| # password: ${{ secrets.PYPI_API_TOKEN }} | |
| # packages-dir: cellxgene_schema_cli/dist/ | |
| # - name: Push tags | |
| # run: | | |
| # git push origin --follow-tags | |
| # - name: Trigger rebuild of Data Portal Processing Image | |
| # run: | | |
| # curl -X POST https://api.github.com/repos/chanzuckerberg/single-cell-data-portal/dispatches \ | |
| # -H 'Accept: application/vnd.github.everest-preview+json' \ | |
| # --header 'authorization: Bearer ${{ secrets.CZIBUILDBOT_GITHUB_TOKEN }}' \ | |
| # --data '{"event_type": "rebuild-processing"}' | |
| update-ontology-mappings: | |
| runs-on: macos-latest | |
| steps: | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v2 | |
| with: | |
| aws-region: us-west-2 | |
| role-to-assume: ${{ secrets.AWS_PROD_ROLE_TO_ASSUME }} | |
| role-duration-seconds: 1800 | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: 3.11 | |
| - name: Python cache | |
| uses: actions/cache@v1 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: install homebrew requirements | |
| run: brew install graphviz | |
| - name: install requirements | |
| run: | | |
| pip install -r scripts/compute_mappings/requirements.txt | |
| - name: Generate Ontology Scripts | |
| run: | | |
| ./scripts/compute_mappings/compute_tissue_and_cell_type_mappings.py | |
| ./scripts/compute_mappings/compute_ancestor_mapping.py | |
| - name: Push Updated Ontology Mappings to S3 | |
| run: | | |
| aws s3 sync --exclude="*" --include="*ontology_mapping.json" scripts/compute_mappings s3://cellxgene-schema-ref-files-prod/ontology-mappings/backend | |
| aws s3 sync --exclude="*" --include="*descendants.json" scripts/compute_mappings s3://cellxgene-schema-ref-files-prod/ontology-mappings/frontend | |
| aws s3 sync --exclude="*" --include="*.gz" cellxgene_schema_cli/cellxgene_schema/ontology_files s3://cellxgene-schema-ref-files-prod/ontology-mappings/gzips | |
| - name: Trigger Data Portal to pull latest ontology mappings | |
| run: | | |
| curl -X POST https://api.github.com/repos/chanzuckerberg/single-cell-data-portal/dispatches \ | |
| -H 'Accept: application/vnd.github.everest-preview+json' \ | |
| --header 'authorization: Bearer ${{ secrets.CZIBUILDBOT_GITHUB_TOKEN }}' \ | |
| --data '{"event_type": "pull-ontology-mappings"}' | |
| generate-conversion-script: | |
| runs-on: ubuntu-latest | |
| needs: [ontology-dry-run, publish-to-pypi] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.event.pull_request.head.ref }} # checking out the last commit to this branch | |
| - name: Set up Python | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: 3.11 | |
| - name: Python cache | |
| uses: actions/cache@v1 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install dependencies | |
| run: | | |
| pip install -r scripts/migration_assistant/requirements.txt | |
| - name: Retrieve Replaced By Ontology Term Mapping | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: ./replaced-by.json | |
| key: replaced-by-map | |
| - name: Run Conversion Script Generator | |
| run: | | |
| make generate-conversion-script | |
| - name: Get Version | |
| id: get_version | |
| run: | | |
| echo "old_version=$(make show-current-version)" >> $GITHUB_ENV | |
| - name: setup git | |
| run: | | |
| git config user.name github-actions | |
| git config user.email [email protected] | |
| - name: remove diff files | |
| run: | | |
| git rm --ignore-unmatch ./cellxgene_schema_cli/cellxgene_schema/ontology_files/*_diff.txt | |
| - name: Bump Patch Version | |
| if: ${{ github.event.inputs.is-major-schema-bump }} == 'false' | |
| run: | | |
| pip install bumpversion | |
| pip install wheel | |
| bumpversion --config-file .bumpversion.cfg patch --allow-dirty | |
| bumpversion --config-file .bumpversion.cfg prerel --allow-dirty --tag | |
| echo "new_version=$(make show-current-version)" >> $GITHUB_ENV | |
| - name: Bump RC to Major Version | |
| if: ${{ github.event.inputs.is-major-schema-bump }} == 'true' | |
| run: | | |
| pip install bumpversion | |
| pip install wheel | |
| bumpversion --config-file .bumpversion.cfg prerel --allow-dirty --tag | |
| echo "new_version=$(make show-current-version)" >> $GITHUB_ENV | |
| - name: Create Pull Request | |
| uses: peter-evans/create-pull-request@v5 | |
| with: | |
| commit-message: 'AUTO: update migrate.py schema_version ${{ env.old_version }}->${{ env.new_version }}' | |
| title: 'AUTO: update migrate.py schema_version ${{ env.old_version }}->${{ env.new_version }}' | |
| body: 'This is an automated PR to update migrate.py from schema_version ${{ env.old_version }}->${{ env.new_version }}.' | |
| branch: auto/update-convert-py-to-${{ env.new_version }} | |
| base: main | |
| reviewers: ${{ vars.MIGRATION_REVIEWERS }} | |
| add-paths: | | |
| cellxgene_schema_cli/setup.py | |
| cellxgene_schema_cli/cellxgene_schema/__init__.py | |
| cellxgene_schema_cli/cellxgene_schema/migrate.py | |
| .bumpversion.cfg |