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chore: update ontology decendant mappings #162
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8662c1e
chore: update ontology decendant mappings
Bento007 cd52ab1
Merge branch 'main' into update-ontology-decendant-mappings
nayib-jose-gloria 0b45fa2
chore: update tagging for new ontology assets
nayib-jose-gloria e05f3d8
pr feedback
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| #This is a github actions that run every monday at 12am. It will run generate_decendant_mapping.py off the main | ||
| # github branch and open a pull request to commit the new ontology_decendant files to cellxgene-ontology-guide | ||
|
|
||
| name: Generate Ontology Decendant Mappings | ||
| name: Generate Ontology Descendant Mappings | ||
| on: | ||
| schedule: | ||
| - cron: "0 0 * * 1" | ||
|
|
@@ -20,7 +20,7 @@ permissions: | |
| pull-requests: write | ||
|
|
||
| jobs: | ||
| generate-ontology-decendant-mappings: | ||
| generate-ontology-descendant-mappings: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout main | ||
|
|
@@ -45,13 +45,9 @@ jobs: | |
| git config user.email [email protected] | ||
| - name: install requirements | ||
| run: | | ||
| cd ./tools/ontology-builder/ | ||
| cd ./tools/ontology-builder/ | ||
| pip install -r requirements.txt | ||
| - name: install local cellxgene-ontology-guide api version #TODO: this or the pypi version? | ||
| run: | | ||
| cd ./api/python | ||
| make install | ||
| - name: generate ontology decendant mappings | ||
| - name: generate ontology descendant mappings | ||
| run: | | ||
| python3 tools/ontology-builder/src/descendent_mapping_generator.py | ||
| - name: Create Pull Request | ||
|
|
@@ -60,9 +56,9 @@ jobs: | |
| token: ${{ secrets.GITHUB_TOKEN }} | ||
| add-paths: | | ||
| ./ontology-assets/*.json | ||
| commit-message: "chore: update ontology decendant mappings" | ||
| title: "chore: update ontology decendant mappings" | ||
| branch: update-ontology-decendant-mappings | ||
| commit-message: "chore: update ontology descendant mappings" | ||
| title: "chore: update ontology descendant mappings" | ||
| branch: update-ontology-descendant-mappings | ||
| base: main | ||
| signoff: true | ||
| draft: false | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| name: Tag 'Latest' Ontology Assets | ||
|
|
||
| on: | ||
| push: | ||
| paths: | ||
| - "**/ontology-assets/**descendants.json" | ||
| - "**/ontology-assets/**list.json" | ||
| - "**/ontology-assets/ontology_info.json" | ||
| branches: | ||
| - main | ||
|
|
||
| jobs: | ||
| tag-latest-release: | ||
| runs-on: [ubuntu-latest] | ||
| needs: publish-pypi-package | ||
| steps: | ||
| - name: Checkout main branch | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| ref: main | ||
| fetch-depth: 0 | ||
| - name: Reassign 'latest' tag | ||
| run: | | ||
| git tag -f latest | ||
| git push origin latest |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,5 @@ | ||
| cellxgene-ontology-guide | ||
| owlready2==0.45 | ||
| jsonschema>=4.21.1, <5 | ||
| semantic-version>=2.10.0, <3 | ||
| referencing>=0.33 | ||
| ../../api/python | ||
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The last line of this file should install cellxgene-ontology-guide from the current branch. If that isn't what we want then remove it.