Merge branch 'master' into switch-fma-bridge-to-official-purls

.github/workflows/auto-pr-ontobot.yml

@@ -6,7 +6,30 @@ on:
     types: [ opened, edited ]
 
 jobs:
+  check:
+    runs-on: ubuntu-latest
+    outputs:
+      phraseExists: ${{ steps.check-body.outputs.result }}
+    steps:
+      - name: Check if issue body contains 'Hey ontobot'
+        id: check-body
+        uses: actions/github-script@v6
+        with:
+          script: |
+            const issue = await github.rest.issues.get({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: context.issue.number
+            });
+            if (!issue.data.body) {
+              console.log('Issue body is empty or null');
+              return false;
+            }
+            return issue.data.body.toLowerCase().includes('hey ontobot');
+  
   build:
+    needs: check
+    if: needs.check.outputs.phraseExists == 'true'
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:

.github/workflows/diff.yml

@@ -20,7 +20,7 @@ jobs:
           trigger: '#gogoeditdiff'
         env:
           GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
-      - uses: docker-practice/actions-setup-docker@master
+      - uses: better0fdead/actions-setup-docker@better0fdead/increase-timeout
         if: steps.check.outputs.triggered == 'true'
       - run: |
           set -x
@@ -30,7 +30,7 @@ jobs:
         run: docker pull obolibrary/odklite
         if: steps.check.outputs.triggered == 'true'
       # Checks-out current branch
-      - uses: xt0rted/pull-request-comment-branch@v1
+      - uses: xt0rted/pull-request-comment-branch@v2.0.0
         id: comment-branch
       - uses: actions/checkout@v3
         if: steps.check.outputs.triggered == 'true'
@@ -92,12 +92,11 @@ jobs:
         if: steps.check.outputs.triggered == 'true'
       - name: Post reasoned comment
         if: steps.check.outputs.triggered == 'true'
-        env:
-          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
-        uses: NejcZdovc/[email protected]
+        uses: NejcZdovc/[email protected]
         with:
           file: "../../comment.md"
           identifier: "REASONED"
+          github_token: ${{secrets.GITHUB_TOKEN}}
       - uses: actions/checkout@v3
         if: steps.check.outputs.triggered == 'true'
       - name: Download edit diff
@@ -110,12 +109,11 @@ jobs:
         if: steps.check.outputs.triggered == 'true'
       - name: Post comment
         if: steps.check.outputs.triggered == 'true'
-        env:
-          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
-        uses: NejcZdovc/[email protected]
+        uses: NejcZdovc/[email protected]
         with:
           file: "../../edit-comment.md"
           identifier: "UNREASONED"
+          github_token: ${{secrets.GITHUB_TOKEN}}
 
 
 

.github/workflows/qc.yml

@@ -7,8 +7,12 @@ on:
   # Triggers the workflow on push or pull request events but only for the master branch
   push:
     branches: [ master ]
+    paths:
+      - 'src/**'
   pull_request:
     branches: [ master ]
+    paths:
+      - 'src/**'
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
@@ -20,7 +24,9 @@ jobs:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
     container: obolibrary/odkfull:v1.4.3
-
+    permissions:
+      contents: read
+      pull-requests: write
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it

.gitignore

@@ -194,6 +194,7 @@ composite-metazoan.*
 composite-metazoan-basic.*
 composite-vertebrate.*
 composite-vertebrate-basic.*
+collected-metazoan.*
 ext.json
 ext.obo
 ext.owl
@@ -215,4 +216,4 @@ src/ontology/subsets/*.json
 src/ontology/subsets/*.obo
 src/ontology/subsets/*.owl
 src/ontology/subsets/*.tsv
-src/ontology/imports/*_import.owl
+src/ontology/imports/*_import.owl

src/ontology/Makefile

@@ -51,7 +51,7 @@ OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
 VERSION=                    $(TODAY)
 ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
 ANNOTATE_CONVERT_FILE =     annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@
-OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/mappings.owl $(COMPONENTSDIR)/in-subset.owl $(COMPONENTSDIR)/hra_subset.owl $(COMPONENTSDIR)/vasculature_class.owl $(COMPONENTSDIR)/hra_depiction_3d_images.owl 
+OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/disjoint_union_over.owl $(COMPONENTSDIR)/mappings.owl $(COMPONENTSDIR)/in-subset.owl $(COMPONENTSDIR)/hra_subset.owl $(COMPONENTSDIR)/vasculature_class.owl $(COMPONENTSDIR)/hra_depiction_3d_images.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 PATTERNDIR=                 ../patterns
@@ -62,7 +62,7 @@ PATTERN_RELEASE_FILES=      $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.
 
 FORMATS = $(sort  owl obo json owl)
 FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
-RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic basic composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy )
+RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic basic collected-metazoan composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy )
 
 # ----------------------------------------
 # Top-level targets
@@ -402,6 +402,7 @@ $(COMPONENTSDIR)/%: | $(COMPONENTSDIR)
 
 
 
+
 # ----------------------------------------
 # Mirroring upstream ontologies
 # ----------------------------------------
@@ -706,6 +707,12 @@ basic.json: basic.owl
 	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
 		convert --check false -f json -o $@.tmp.json &&\
 		mv $@.tmp.json $@
+collected-metazoan.obo: collected-metazoan.owl
+	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
+collected-metazoan.json: collected-metazoan.owl
+	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
+		convert --check false -f json -o $@.tmp.json &&\
+		mv $@.tmp.json $@
 composite-metazoan.obo: composite-metazoan.owl
 	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
 composite-metazoan.json: composite-metazoan.owl
@@ -810,6 +817,9 @@ $(ONT)-basic.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(KEEPRELATION
 basic.owl:
 	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
 
+collected-metazoan.owl:
+	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
+
 composite-metazoan.owl:
 	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
 

src/ontology/bridge/bridges.rules.m4

@@ -6,15 +6,15 @@ prefix BFO:       <http://purl.obolibrary.org/obo/BFO_>
 prefix BSPO:      <http://purl.obolibrary.org/obo/BSPO_>
 prefix CARO:      <http://purl.obolibrary.org/obo/CARO_>
 prefix CL:        <http://purl.obolibrary.org/obo/CL_>
-prefix DHBA:      <http://purl.obolibrary.org/obo/DHBA_>
+prefix DHBA:      <https://purl.brain-bican.org/ontology/dhbao/DHBA_>
 prefix EHDAA2:    <http://purl.obolibrary.org/obo/EHDAA2_>
 prefix EMAPA:     <http://purl.obolibrary.org/obo/EMAPA_>
 prefix FBbt:      <http://purl.obolibrary.org/obo/FBbt_>
 prefix FBdv:      <http://purl.obolibrary.org/obo/FBdv_>
 prefix FMA:       <http://purl.org/sig/ont/fma/fma>
 prefix GO:        <http://purl.obolibrary.org/obo/GO_>
 prefix HAO:       <http://purl.obolibrary.org/obo/HAO_>
-prefix HBA:       <http://purl.obolibrary.org/obo/HBA_>
+prefix HBA:       <https://purl.brain-bican.org/ontology/hbao/HBA_>
 prefix HsapDv:    <http://purl.obolibrary.org/obo/HsapDv_>
 prefix IAO:       <http://purl.obolibrary.org/obo/IAO_>
 prefix KUPO:      <http://purl.obolibrary.org/obo/KUPO_>
@@ -25,7 +25,7 @@ prefix NCIT:      <http://purl.obolibrary.org/obo/NCIT_>
 prefix OG:        <http://purl.obolibrary.org/obo/OG_>
 prefix OGES:      <http://purl.obolibrary.org/obo/OGES_>
 prefix OIO:       <http://www.geneontology.org/formats/oboInOwl#>
-prefix PBA:       <http://purl.obolibrary.org/obo/PBA_>
+prefix PBA:       <https://purl.brain-bican.org/ontology/pbao/PBA_>
 prefix RO:        <http://purl.obolibrary.org/obo/RO_>
 prefix SCTID:     <http://purl.obolibrary.org/obo/SCTID_>
 prefix SPD:       <http://purl.obolibrary.org/obo/SPD_>