Migrate to ODK 1.5

.github/workflows/qc.yml

@@ -19,12 +19,12 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.4
+    container: obolibrary/odkfull:v1.5
 
     # 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
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Run ontology QC checks
         env:

src/ontology/imports/cob_import.owl

@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/ro/imports/cob_import.owl>
-<http://purl.obolibrary.org/obo/ro/releases/2024-02-09/imports/cob_import.owl>
+<http://purl.obolibrary.org/obo/ro/releases/2024-03-02/imports/cob_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/cob/releases/2023-11-16/cob.owl>)
-Annotation(owl:versionInfo "2024-02-09")
+Annotation(owl:versionInfo "2024-03-02")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000016>))
@@ -57,59 +57,43 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000115> "def
 #   Object Properties
 ############################
 
-# Object Property: <http://purl.obolibrary.org/obo/BFO_0000050> (part of)
+# Object Property: <http://purl.obolibrary.org/obo/BFO_0000050> (<http://purl.obolibrary.org/obo/BFO_0000050>)
 
-AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000050> "part of")
 InverseObjectProperties(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/BFO_0000051>)
 TransitiveObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>)
 
-# Object Property: <http://purl.obolibrary.org/obo/BFO_0000051> (has part)
-
-AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000051> "has part")
-
 # Object Property: <http://purl.obolibrary.org/obo/BFO_0000054> (realized in)
 
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000054> "realized in"@en)
 
-# Object Property: <http://purl.obolibrary.org/obo/BFO_0000066> (occurs in)
+# Object Property: <http://purl.obolibrary.org/obo/BFO_0000066> (<http://purl.obolibrary.org/obo/BFO_0000066>)
 
-AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000066> "occurs in")
 InverseObjectProperties(<http://purl.obolibrary.org/obo/BFO_0000066> <http://purl.obolibrary.org/obo/BFO_0000067>)
 ObjectPropertyDomain(<http://purl.obolibrary.org/obo/BFO_0000066> <http://purl.obolibrary.org/obo/BFO_0000015>)
 
 # Object Property: <http://purl.obolibrary.org/obo/BFO_0000067> (contains process)
 
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000067> "contains process"@en)
 
-# Object Property: <http://purl.obolibrary.org/obo/RO_0000052> (characteristic of)
+# Object Property: <http://purl.obolibrary.org/obo/RO_0000052> (<http://purl.obolibrary.org/obo/RO_0000052>)
 
-AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0000052> "characteristic of"@en)
 InverseObjectProperties(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/RO_0000053>)
 
-# Object Property: <http://purl.obolibrary.org/obo/RO_0000053> (has characteristic)
+# Object Property: <http://purl.obolibrary.org/obo/RO_0000053> (<http://purl.obolibrary.org/obo/RO_0000053>)
 
-AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0000053> "has characteristic")
-AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/RO_0000053> "https://github.com/oborel/obo-relations/pull/284")
 InverseFunctionalObjectProperty(<http://purl.obolibrary.org/obo/RO_0000053>)
 ObjectPropertyRange(<http://purl.obolibrary.org/obo/RO_0000053> <http://purl.obolibrary.org/obo/BFO_0000020>)
 
-# Object Property: <http://purl.obolibrary.org/obo/RO_0000056> (participates in)
+# Object Property: <http://purl.obolibrary.org/obo/RO_0000056> (<http://purl.obolibrary.org/obo/RO_0000056>)
 
-AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0000056> "participates in"@en)
 InverseObjectProperties(<http://purl.obolibrary.org/obo/RO_0000056> <http://purl.obolibrary.org/obo/RO_0000057>)
 
-# Object Property: <http://purl.obolibrary.org/obo/RO_0000057> (has participant)
+# Object Property: <http://purl.obolibrary.org/obo/RO_0000057> (<http://purl.obolibrary.org/obo/RO_0000057>)
 
-AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0000057> "has participant")
 ObjectPropertyDomain(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/BFO_0000015>)
 
-# Object Property: <http://purl.obolibrary.org/obo/RO_0000058> (is concretized as)
-
-AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0000058> "is concretized as"@en)
-
-# Object Property: <http://purl.obolibrary.org/obo/RO_0002333> (enabled by)
+# Object Property: <http://purl.obolibrary.org/obo/RO_0002333> (<http://purl.obolibrary.org/obo/RO_0002333>)
 
-AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002333> "enabled by")
 SubObjectPropertyOf(<http://purl.obolibrary.org/obo/RO_0002333> <http://purl.obolibrary.org/obo/RO_0000057>)
 
 

src/ontology/ro-odk.yaml

@@ -1,6 +1,7 @@
 id: ro
 title: "OBO Relations Ontology"
 github_org: oborel
+git_main_branch: master
 repo: obo-relations
 report_fail_on: Error
 edit_format: owl
@@ -18,6 +19,12 @@ namespaces:
   - http://purl.obolibrary.org/obo/BFO_0000050
   - http://purl.obolibrary.org/obo/BFO_0000051
   - http://purl.obolibrary.org/obo/BFO_0000060
+  - http://purl.obolibrary.org/obo/BFO_0000062
+  - http://purl.obolibrary.org/obo/BFO_0000063
+  - http://purl.obolibrary.org/obo/BFO_0000066
+  - http://purl.obolibrary.org/obo/BFO_0000067
+  - http://purl.obolibrary.org/obo/BFO_0000054
+  - http://purl.obolibrary.org/obo/BFO_0000055
 import_group:
   annotation_properties:
         - rdfs:label

src/ontology/ro.Makefile

@@ -53,9 +53,34 @@ $(IMPORTDIR)/cob_import.owl: $(MIRRORDIR)/cob.owl $(IMPORTDIR)/cob_terms_combine
 	if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
     extract -T $(IMPORTDIR)/cob_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \
 	remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/cob_terms_combined.txt --select complement \
+	remove --select "RO:* BFO:0000050* BFO:0000051* BFO:0000060* BFO:0000066*" --axioms "annotation" \
 	query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
 	$(ANNOTATE_CONVERT_FILE); fi
 
+# ========================================
+# Custom imports
+# ========================================
+
+# This filter contains all property characteristic related to RO entities
+# Note: For some reason, IrreflexiveObjectProperty is not supported
+tmp/missing-base.owl: $(EDIT_PREPROCESSED) $(ONTOLOGYTERMS)
+	$(ROBOT) merge -i $(EDIT_PREPROCESSED) \
+		filter -T $(ONTOLOGYTERMS) --trim false --axioms "AsymmetricObjectProperty FunctionalObjectProperty FunctionalDataProperty InverseFunctionalObjectProperty SymmetricObjectProperty TransitiveObjectProperty InverseObjectProperties ObjectPropertyDomain DataPropertyDomain DataPropertyRange ObjectPropertyRange" \
+ -o [email protected] && mv [email protected] $@
+
+# TODO: This goal (and tmp/missing-base.owl) can be removed once https://github.com/ontodev/robot/issues/1108 is resolved
+$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) tmp/missing-base.owl
+	$(ROBOT_RELEASE_IMPORT_MODE) \
+	reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms False \
+	relax \
+	reduce -r ELK \
+	remove --base-iri http://purl.obolibrary.org/obo/RO_ --base-iri http://purl.obolibrary.org/obo/BFO_0000050 --base-iri http://purl.obolibrary.org/obo/BFO_0000051 --base-iri http://purl.obolibrary.org/obo/BFO_0000060 --base-iri http://purl.obolibrary.org/obo/BFO_0000062 --base-iri http://purl.obolibrary.org/obo/BFO_0000063 --base-iri http://purl.obolibrary.org/obo/BFO_0000066 --base-iri http://purl.obolibrary.org/obo/BFO_0000067 --base-iri http://purl.obolibrary.org/obo/BFO_0000054 --base-iri http://purl.obolibrary.org/obo/BFO_0000055 --axioms external --preserve-structure false --trim false \
+	merge -i tmp/missing-base.owl \
+	$(SHARED_ROBOT_COMMANDS) \
+	annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \
+		--ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
+		--output [email protected] && mv [email protected] $@
+
 
 # ========================================
 # DOCUMENTATION

src/ontology/run.sh

@@ -14,6 +14,8 @@
 #
 # See README-editors.md for more details.
 
+set -e
+
 if [ -f run.sh.conf ]; then
     . ./run.sh.conf
 fi
@@ -29,6 +31,22 @@ elif [ -f "$HOME/Library/Application Support/ontology-development-kit/github/tok
     GH_TOKEN=$(cat "$HOME/Library/Application Support/ontology-development-kit/github/token")
 fi
 
+# SSH agent socket
+# On macOS, we cannot use $SSH_AUTH_SOCK directly,
+# we need to use a "magic" socket instead.
+case "$(uname)" in
+Darwin)
+    ODK_SSH_AUTH_SOCKET=/run/host-services/ssh-auth.sock
+    ;;
+*)
+    ODK_SSH_AUTH_SOCKET=$SSH_AUTH_SOCK
+    ;;
+esac
+ODK_SSH_BIND=
+if [ -n "$ODK_SSH_AUTH_SOCKET" ]; then
+    ODK_SSH_BIND=",$ODK_SSH_AUTH_SOCKET:/run/host-services/ssh-auth.sock"
+fi
+
 ODK_IMAGE=${ODK_IMAGE:-odkfull}
 TAG_IN_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $2 }')
 if [ -n "$TAG_IN_IMAGE" ]; then
@@ -40,16 +58,28 @@ ODK_TAG=${ODK_TAG:-latest}
 ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx8G}
 ODK_DEBUG=${ODK_DEBUG:-no}
 
+ODK_USER_ID=${ODK_USER_ID:-$(id -u)}
+ODK_GROUP_ID=${ODK_GROUP_ID:-$(id -g)}
+
+# Convert OWLAPI_* environment variables to the OWLAPI as Java options
+# See http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/model/parameters/ConfigurationOptions.html
+# for a list of allowed options
+OWLAPI_OPTIONS_NAMESPACE=org.semanticweb.owlapi.model.parameters.ConfigurationOptions
+for owlapi_var in $(env | sed -n s/^OWLAPI_//p) ; do
+    ODK_JAVA_OPTS="$ODK_JAVA_OPTS -D$OWLAPI_OPTIONS_NAMESPACE.${owlapi_var%=*}=${owlapi_var#*=}"
+done
+
 TIMECMD=
 if [ x$ODK_DEBUG = xyes ]; then
     # If you wish to change the format string, take care of using
     # non-breaking spaces (U+00A0) instead of normal spaces, to
     # prevent the shell from tokenizing the format string.
-    echo "Running ${IMAGE} with ${ODK_JAVA_OPTS} of memory for ROBOT and Java-based pipeline steps."
+    echo "Running obolibrary/${ODK_IMAGE}:${ODK_TAG} with '${ODK_JAVA_OPTS}' as options for ROBOT and other Java-based pipeline steps."
     TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb"
 fi
+rm -f tmp/debug.log
 
-VOLUME_BIND=$PWD/../../:/work
+VOLUME_BIND=$PWD/../../:/work$ODK_SSH_BIND
 WORK_DIR=/work/src/ontology
 
 if [ -n "$ODK_BINDS" ]; then
@@ -59,14 +89,14 @@ fi
 if [ -n "$USE_SINGULARITY" ]; then
 
     singularity exec --cleanenv $ODK_SINGULARITY_OPTIONS \
-        --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS" \
+        --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS,SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock,ODK_USER_ID=$ODK_USER_ID,ODK_GROUP_ID=$ODK_GROUP_ID,ODK_DEBUG=$ODK_DEBUG" \
         --bind $VOLUME_BIND \
         -W $WORK_DIR \
         docker://obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@"
 else
     BIND_OPTIONS="-v $(echo $VOLUME_BIND | sed 's/,/ -v /')"
     docker run $ODK_DOCKER_OPTIONS $BIND_OPTIONS -w $WORK_DIR \
-        -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" \
+        -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" -e SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock -e ODK_USER_ID=$ODK_USER_ID -e ODK_GROUP_ID=$ODK_GROUP_ID -e ODK_DEBUG=$ODK_DEBUG \
         --rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@"
 fi
 

src/scripts/run-command.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+ODK_DEBUG_FILE=${ODK_DEBUG_FILE:-debug.log}
+echo "Command: sh $@" >> $ODK_DEBUG_FILE
+/usr/bin/time -a -o $ODK_DEBUG_FILE -f "Elapsed time: %E\nPeak memory: %M kb" /bin/sh "$@"

src/scripts/update_repo.sh

@@ -21,10 +21,11 @@ cp target/$OID/src/ontology/run.sh $SRCDIR/ontology/
 cp -r target/$OID/src/sparql/* $SRCDIR/sparql/
 mkdir -p $ROOTDIR/.github
 mkdir -p $ROOTDIR/.github/workflows
-cp -n target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml
+cp target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml
+
 
 
 
 echo "WARNING: These files should be manually migrated: mkdocs.yaml, .gitignore, src/ontology/catalog.xml (if you added a new import or component)"
-echo "WARNING: Your QC workflows have not been updated automatically. Please update the ODK version number(s) in .github/workflows/qc.yml."
+
 echo "Ontology repository update successfully completed."

src/sparql/iri-range-violation.sparql

@@ -13,7 +13,7 @@ WHERE {
     oboInOwl:inSubset
     dcterms:contributor  }
   ?term ?property ?value .
-  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060")))
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000062") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000063") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000066") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000067") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000054") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000055")))
   FILTER (!isIRI(?value))
 }
 

src/sparql/label-with-iri-violation.sparql

@@ -4,6 +4,6 @@ SELECT ?term ?value
 WHERE {
   ?term rdfs:label ?value .
   FILTER (REGEX(?value, "http[s]?[:]"))
-  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060")))
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000062") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000063") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000066") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000067") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000054") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000055")))
 }
 

src/sparql/owldef-self-reference-violation.sparql

@@ -7,6 +7,6 @@ SELECT ?term WHERE {
   { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first ?term ] ] }
     UNION
   { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first [ owl:someValuesFrom ?term ] ] ] }
-  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060")))
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000062") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000063") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000066") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000067") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000054") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000055")))
 }
 

src/sparql/ro_terms.sparql

@@ -3,5 +3,5 @@ WHERE {
   { ?s1 ?p1 ?term . }
   UNION
   { ?term ?p2 ?o2 . }
-  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060")))
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000062") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000063") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000066") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000067") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000054") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000055")))
 }