From 8662c1ee3188b8985195ac3874a2fbc1da71cac1 Mon Sep 17 00:00:00 2001 From: Bento007 <1429913+Bento007@users.noreply.github.com> Date: Mon, 1 Apr 2024 00:15:13 +0000 Subject: [PATCH 1/3] chore: update ontology decendant mappings Signed-off-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- ontology-assets/cell_type_descendants.json | 33 ++++++++++++++++++---- ontology-assets/tissue_descendants.json | 4 +++ 2 files changed, 31 insertions(+), 6 deletions(-) diff --git a/ontology-assets/cell_type_descendants.json b/ontology-assets/cell_type_descendants.json index 52009a9e..3fc2850b 100644 --- a/ontology-assets/cell_type_descendants.json +++ b/ontology-assets/cell_type_descendants.json @@ -13,9 +13,12 @@ "CL:1000147", "CL:1000309", "CL:1000311", + "CL:1000409", "CL:1000477", "CL:2000018", - "CL:2000046" + "CL:2000046", + "CL:4030032", + "CL:4030033" ], "CL:0002320": [ "CL:0000057", @@ -162,6 +165,7 @@ "CL:0000216", "CL:0000242", "CL:0000244", + "CL:0000307", "CL:0000312", "CL:0000322", "CL:0000362", @@ -380,6 +384,7 @@ "CL:4030011", "CL:4030018", "CL:4030023", + "CL:4030033", "CL:4030066", "CL:4033044", "CL:4033048" @@ -670,6 +675,7 @@ "CL:0000749", "CL:0000750", "CL:0000751", + "CL:0000752", "CL:0000753", "CL:0000754", "CL:0000756", @@ -784,6 +790,7 @@ "CL:4030063", "CL:4030065", "CL:4030067", + "CL:4033015", "CL:4033019", "CL:4033027", "CL:4033028", @@ -934,6 +941,7 @@ "CL:0000749", "CL:0000750", "CL:0000751", + "CL:0000752", "CL:0000753", "CL:0000754", "CL:0000756", @@ -1028,6 +1036,7 @@ "CL:4030006", "CL:4030027", "CL:4030028", + "CL:4030032", "CL:4030059", "CL:4030061", "CL:4030062", @@ -1108,6 +1117,7 @@ "CL:1000275", "CL:1000278", "CL:1000279", + "CL:1000409", "CL:1000443", "CL:1000477", "CL:1000487", @@ -2110,6 +2120,7 @@ "CL:0000749", "CL:0000750", "CL:0000751", + "CL:0000752", "CL:0000753", "CL:0000754", "CL:0000756", @@ -2189,6 +2200,7 @@ "CL:0000749", "CL:0000750", "CL:0000751", + "CL:0000752", "CL:0000753", "CL:0000754", "CL:0000756", @@ -2254,7 +2266,8 @@ "CL:0002627", "CL:0002629", "CL:0011028", - "CL:0013000" + "CL:0013000", + "CL:4033015" ], "CL:0000101": [ "CL:0000006", @@ -2297,6 +2310,7 @@ "CL:0000006", "CL:0000099", "CL:0000100", + "CL:0000101", "CL:0000103", "CL:0000108", "CL:0000118", @@ -2331,6 +2345,7 @@ "CL:0000749", "CL:0000750", "CL:0000751", + "CL:0000752", "CL:0000753", "CL:0000754", "CL:0000756", @@ -2553,13 +2568,15 @@ "CL:2000016", "CL:2000018", "CL:2000041", - "CL:2000059" + "CL:2000059", + "CL:4030033" ], "CL:0002076": [ "CL:0000155", "CL:0000158", "CL:0000162", "CL:0000209", + "CL:0000307", "CL:0000508", "CL:0000510", "CL:0000577", @@ -2699,7 +2716,8 @@ "CL:2000041", "CL:2000059", "CL:4030009", - "CL:4030011" + "CL:4030011", + "CL:4030033" ], "CL:0011026": [ "CL:0000037", @@ -2954,7 +2972,8 @@ "CL:0002629", "CL:0011028", "CL:0013000", - "CL:4023059" + "CL:4023059", + "CL:4033015" ], "CL:0000098": [ "CL:0000209", @@ -3083,6 +3102,7 @@ "CL:1000275", "CL:1000278", "CL:1000279", + "CL:1000409", "CL:1000443", "CL:1000477", "CL:1000487", @@ -3290,6 +3310,7 @@ "CL:1000698", "CL:1001318", "CL:4028004", - "CL:4028006" + "CL:4028006", + "CL:4030032" ] } \ No newline at end of file diff --git a/ontology-assets/tissue_descendants.json b/ontology-assets/tissue_descendants.json index 1a1fcf17..4c3bc0ca 100644 --- a/ontology-assets/tissue_descendants.json +++ b/ontology-assets/tissue_descendants.json @@ -253,6 +253,7 @@ "UBERON:0000922": [ "UBERON:0000088 (organoid)", "UBERON:0000926", + "UBERON:0001049", "UBERON:0004023", "UBERON:0004024", "UBERON:0004025", @@ -465,6 +466,7 @@ "UBERON:0016530", "UBERON:0016538", "UBERON:0016540", + "UBERON:0018105", "UBERON:0022232", "UBERON:0022352", "UBERON:0023787", @@ -572,6 +574,7 @@ "UBERON:0010032", "UBERON:0010033", "UBERON:0013682", + "UBERON:0018105", "UBERON:0019207" ], "UBERON:0001434": [ @@ -793,6 +796,7 @@ "UBERON:0006761", "UBERON:0007625", "UBERON:0013682", + "UBERON:0018105", "UBERON:0019207" ], "UBERON:0000948": [ From 0b45fa2c68ffecb898fe127083e596927ba617ae Mon Sep 17 00:00:00 2001 From: nayib-jose-gloria Date: Tue, 2 Apr 2024 11:44:06 -0400 Subject: [PATCH 2/3] chore: update tagging for new ontology assets --- .../workflows/generate_decendant_mapping.yml | 18 ++++++-------- .github/workflows/release.yml | 14 ----------- .../workflows/tag-latest-ontology-assets.yml | 24 +++++++++++++++++++ tools/ontology-builder/requirements.txt | 1 + 4 files changed, 32 insertions(+), 25 deletions(-) create mode 100644 .github/workflows/tag-latest-ontology-assets.yml diff --git a/.github/workflows/generate_decendant_mapping.yml b/.github/workflows/generate_decendant_mapping.yml index 030e81a1..8fa19503 100644 --- a/.github/workflows/generate_decendant_mapping.yml +++ b/.github/workflows/generate_decendant_mapping.yml @@ -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 github-actions@github.com - 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 diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 0e2ba13e..6281104a 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -90,17 +90,3 @@ jobs: uses: pypa/gh-action-pypi-publish@release/v1 with: packages-dir: api/python/dist - - 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 diff --git a/.github/workflows/tag-latest-ontology-assets.yml b/.github/workflows/tag-latest-ontology-assets.yml new file mode 100644 index 00000000..45d593a3 --- /dev/null +++ b/.github/workflows/tag-latest-ontology-assets.yml @@ -0,0 +1,24 @@ +name: Tag 'Latest' Ontology Assets + +on: + push: + paths: + - "**/ontology-assets/**.json" + - "**/ontology-assets/**.gz" + 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 diff --git a/tools/ontology-builder/requirements.txt b/tools/ontology-builder/requirements.txt index 336a07b1..06850231 100644 --- a/tools/ontology-builder/requirements.txt +++ b/tools/ontology-builder/requirements.txt @@ -1,3 +1,4 @@ +cellxgene-ontology-guide owlready2==0.45 jsonschema>=4.21.1, <5 semantic-version>=2.10.0, <3 From e05f3d8e5cf8b5a899b37efc6072ee35258382a0 Mon Sep 17 00:00:00 2001 From: nayib-jose-gloria Date: Tue, 2 Apr 2024 15:24:48 -0400 Subject: [PATCH 3/3] pr feedback --- ...decendant_mapping.yml => generate_descendant_mapping.yml} | 0 .github/workflows/tag-latest-ontology-assets.yml | 5 +++-- tools/ontology-builder/requirements.txt | 1 - 3 files changed, 3 insertions(+), 3 deletions(-) rename .github/workflows/{generate_decendant_mapping.yml => generate_descendant_mapping.yml} (100%) diff --git a/.github/workflows/generate_decendant_mapping.yml b/.github/workflows/generate_descendant_mapping.yml similarity index 100% rename from .github/workflows/generate_decendant_mapping.yml rename to .github/workflows/generate_descendant_mapping.yml diff --git a/.github/workflows/tag-latest-ontology-assets.yml b/.github/workflows/tag-latest-ontology-assets.yml index 45d593a3..049b1883 100644 --- a/.github/workflows/tag-latest-ontology-assets.yml +++ b/.github/workflows/tag-latest-ontology-assets.yml @@ -3,8 +3,9 @@ name: Tag 'Latest' Ontology Assets on: push: paths: - - "**/ontology-assets/**.json" - - "**/ontology-assets/**.gz" + - "**/ontology-assets/**descendants.json" + - "**/ontology-assets/**list.json" + - "**/ontology-assets/ontology_info.json" branches: - main diff --git a/tools/ontology-builder/requirements.txt b/tools/ontology-builder/requirements.txt index 06850231..c21c5c55 100644 --- a/tools/ontology-builder/requirements.txt +++ b/tools/ontology-builder/requirements.txt @@ -3,4 +3,3 @@ owlready2==0.45 jsonschema>=4.21.1, <5 semantic-version>=2.10.0, <3 referencing>=0.33 -../../api/python