Update db-xrefs.yaml for #2374 #1451
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| # This is a basic workflow to help you get started with Actions | |
| name: CI | |
| # Controls when the action will run. | |
| on: | |
| # Triggers the workflow on push or pull request events but only for the master branch | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| validate_yaml_and_metadata: | |
| runs-on: ubuntu-latest | |
| container: geneontology/dev-base:latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| # To automatically get bug fixes and new Ruby versions for ruby/setup-ruby, | |
| # change this to (see https://github.com/ruby/setup-ruby#versioning): | |
| # uses: ruby/setup-ruby@v1 | |
| # - name: Set up Ruby | |
| # uses: ruby/setup-ruby@ec106b438a1ff6ff109590de34ddc62c540232e0 | |
| # with: | |
| # ruby-version: 2.2.10 | |
| - name: Install packages | |
| run: apt-get update -qq && apt-get install -y kwalify python3 python3-pip mmv -qq | |
| - name: Install python stuff | |
| run: pip3 install pyyaml typing graphstore/rule-runner linkml==1.7.4 | |
| ## Users. | |
| - name: Test users schema. | |
| run: | | |
| kwalify -E -f metadata/db-xrefs.schema.yaml metadata/db-xrefs.yaml 2>&1 | |
| kwalify -E -f metadata/db-xrefs.schema.yaml metadata/db-xrefs.yaml 2>&1 | grep 'INVALID\|ERROR' > invalid.log || true | |
| test $(stat -c %s invalid.log) -eq 0 | |
| - name: Test users metadata. | |
| run: | | |
| kwalify -E -f metadata/users.schema.yaml metadata/users.yaml 2>&1 | |
| kwalify -E -f metadata/users.schema.yaml metadata/users.yaml 2>&1 | grep 'INVALID\|ERROR' > invalid.log || true | |
| test $(stat -c %s invalid.log) -eq 0 | |
| ## Groups. | |
| - name: Test groups schema. | |
| run: | | |
| kwalify -E -m metadata/groups.schema.yaml 2>&1 | |
| kwalify -E -m metadata/groups.schema.yaml 2>&1 | grep 'INVALID\|ERROR' > invalid.log || true | |
| test $(stat -c %s invalid.log) -eq 0 | |
| - name: Test groups metadata. | |
| run: | | |
| kwalify -E -f metadata/groups.schema.yaml metadata/groups.yaml 2>&1 | |
| kwalify -E -f metadata/groups.schema.yaml metadata/groups.yaml 2>&1 | grep 'INVALID\|ERROR' > invalid.log || true | |
| test $(stat -c %s invalid.log) -eq 0 | |
| ## DB Xrefs. | |
| - name: Test dbxrefs schema. | |
| run: | | |
| kwalify -E -m metadata/db-xrefs.schema.yaml 2>&1 | |
| kwalify -E -m metadata/db-xrefs.schema.yaml 2>&1 | grep 'INVALID\|ERROR' > invalid.log || true | |
| test $(stat -c %s invalid.log) -eq 0 | |
| - name: Test dbxrefs metadata. | |
| run: | | |
| kwalify -E -f metadata/db-xrefs.schema.yaml metadata/db-xrefs.yaml 2>&1 | |
| kwalify -E -f metadata/db-xrefs.schema.yaml metadata/db-xrefs.yaml 2>&1 | grep 'INVALID\|ERROR' > invalid.log || true | |
| test $(stat -c %s invalid.log) -eq 0 | |
| ## Datasets. | |
| - name: Test datasets schema. | |
| run: | | |
| kwalify -E -m metadata/datasets.schema.yaml 2>&1 | |
| kwalify -E -m metadata/datasets.schema.yaml 2>&1 | grep 'INVALID\|ERROR' > invalid.log || true | |
| test $(stat -c %s invalid.log) -eq 0 | |
| - name: Test datasets metadata. | |
| run: | | |
| kwalify -E -f metadata/datasets.schema.yaml metadata/datasets/*.yaml 2>&1 | |
| kwalify -E -f metadata/datasets.schema.yaml metadata/datasets/*.yaml 2>&1 | grep 'INVALID\|ERROR' > invalid.log || true | |
| test $(stat -c %s invalid.log) -eq 0 | |
| ## Extension constraints. | |
| - name: Test extension constraints schema. | |
| run: | | |
| kwalify -E -m metadata/extensions-constraints.schema.yaml 2>&1 | |
| kwalify -E -m metadata/extensions-constraints.schema.yaml 2>&1 | grep 'INVALID\|ERROR' > invalid.log || true | |
| test $(stat -c %s invalid.log) -eq 0 | |
| - name: Test extension constraints metadata. | |
| run: | | |
| kwalify -E -f metadata/extensions-constraints.schema.yaml metadata/extensions-constraints.yaml 2>&1 | |
| kwalify -E -f metadata/extensions-constraints.schema.yaml metadata/extensions-constraints.yaml 2>&1 | grep 'INVALID\|ERROR' > invalid.log || true | |
| test $(stat -c %s invalid.log) -eq 0 | |
| ## GO reference species set. | |
| - name: Test reference species set schema. | |
| run: | | |
| kwalify -E -m metadata/go-reference-species.schema.yaml 2>&1 | |
| kwalify -E -m metadata/go-reference-species.schema.yaml 2>&1 | grep 'INVALID\|ERROR' > invalid.log || true | |
| test $(stat -c %s invalid.log) -eq 0 | |
| - name: Test reference species set metadata. | |
| run: | | |
| kwalify -E -f metadata/go-reference-species.schema.yaml metadata/go-reference-species.yaml 2>&1 | |
| kwalify -E -f metadata/go-reference-species.schema.yaml metadata/go-reference-species.yaml 2>&1 | grep 'INVALID\|ERROR' > invalid.log || true | |
| test $(stat -c %s invalid.log) -eq 0 | |
| - name: Test GO_REF metadata | |
| run: | | |
| linkml-validate -s metadata/gorefs.schema.yaml metadata/gorefs.yaml | |
| ## Cross-test metadata | |
| - name: Cross-test users and groups. | |
| run: python3 ./scripts/sanity-check-users-and-groups.py --verbose --users metadata/users.yaml --groups metadata/groups.yaml | |
| - name: Info | |
| run: which sparta | |
| ## SPARTA | |
| - name: SPARTA. | |
| run: sparta valid --rules metadata/rules/ --schema metadata/rules.schema.yaml | |
| ## Run GO Rule examples | |
| - name: GO Rule example validation | |
| run: pip3 install -r pipeline/requirements.txt && ./scripts/rule-example-validation.sh |