ZFIN · matentzn · Feb 20, 2023
diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
@@ -19,7 +19,7 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.3.0
+    container: obolibrary/odkfull:v1.4
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
diff --git a/src/ontology/run.sh b/src/ontology/run.sh
@@ -8,18 +8,70 @@
 # The assumption is that you are working in the src/ontology folder;
 # we therefore map the whole repo (../..) to a docker volume.
 #
+# To use singularity instead of docker, please issue
+# export USE_SINGULARITY=<any-value>
+# before running this script.
+#
 # See README-editors.md for more details.
 
-IMAGE=${IMAGE:-odkfull}
+if [ -f run.sh.conf ]; then
+    . ./run.sh.conf
+fi
 
+# Look for a GitHub token
+if [ -n "$GH_TOKEN" ]; then
+    :
+elif [ -f ../../.github/token.txt ]; then
+    GH_TOKEN=$(cat ../../.github/token.txt)
+elif [ -f $XDG_CONFIG_HOME/ontology-development-kit/github/token ]; then
+    GH_TOKEN=$(cat $XDG_CONFIG_HOME/ontology-development-kit/github/token)
+elif [ -f "$HOME/Library/Application Support/ontology-development-kit/github/token" ]; then
+    GH_TOKEN=$(cat "$HOME/Library/Application Support/ontology-development-kit/github/token")
+fi
+
+ODK_IMAGE=${ODK_IMAGE:-odkfull}
+TAG_IN_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $2 }')
+if [ -n "$TAG_IN_IMAGE" ]; then
+  # Override ODK_TAG env var if IMAGE already includes a tag
+  ODK_TAG=$TAG_IN_IMAGE
+  ODK_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $1 }')
+fi
+ODK_TAG=${ODK_TAG:-latest}
+ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx8G}
 ODK_DEBUG=${ODK_DEBUG:-no}
 
 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."
     TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb"
 fi
 
-docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx8G' -e JAVA_OPTS='-Xmx8G' --rm -ti obolibrary/$IMAGE $TIMECMD "$@"
+VOLUME_BIND=$PWD/../../:/work
+WORK_DIR=/work/src/ontology
+
+if [ -n "$ODK_BINDS" ]; then
+    VOLUME_BIND="$VOLUME_BIND,$ODK_BINDS"
+fi
+
+if [ -n "$USE_SINGULARITY" ]; then
+
+    singularity exec --cleanenv $ODK_SINGULARITY_OPTIONS \
+        --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS" \
+        --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="$ODK_JAVA_OPTS" \
+        --rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@"
+fi
+
+case "$@" in
+*update_repo*|*release*)
+    echo "Please remember to update your ODK image from time to time: https://oboacademy.github.io/obook/howto/odk-update/."
+    ;;
+esac
diff --git a/src/scripts/update_repo.sh b/src/scripts/update_repo.sh
@@ -24,5 +24,7 @@ mkdir -p $ROOTDIR/.github/workflows
 cp -n target/$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 "Update successfully completed."
+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."
diff --git a/src/sparql/edges.sparql b/src/sparql/edges.sparql
@@ -1,4 +1,3 @@
-prefix obo: <http://purl.obolibrary.org/obo/> 
 prefix owl: <http://www.w3.org/2002/07/owl#>
 prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

diff --git a/src/sparql/inject-subset-declaration.ru b/src/sparql/inject-subset-declaration.ru
@@ -7,5 +7,5 @@ INSERT { ?y rdfs:subPropertyOf <http://www.geneontology.org/formats/oboInOwl#Sub
 WHERE {
   ?x <http://www.geneontology.org/formats/oboInOwl#inSubset>  ?y .
   FILTER(isIRI(?y))
-  FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)"))
+  FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)") || regex(str(?y),"^(http://purl.obolibrary.org/obo)"))
 }
diff --git a/src/sparql/inject-synonymtype-declaration.ru b/src/sparql/inject-synonymtype-declaration.ru
@@ -0,0 +1,11 @@
+PREFIX : <http://www.test.com/ns/test#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+INSERT { ?y rdfs:subPropertyOf <http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty> . }
+
+WHERE {
+  ?x <http://www.geneontology.org/formats/oboInOwl#hasSynonymType>  ?y .
+  FILTER(isIRI(?y))
+  FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)") || regex(str(?y),"^(http://purl.obolibrary.org/obo)"))
+}
diff --git a/src/sparql/iri-range-violation.sparql b/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/ZFA_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/ZFA_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/zfa.owl") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/ZFS_")))
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/ZFA_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/zfa.owl") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/ZFS_")))
   FILTER (!isIRI(?value))
 }
 
diff --git a/src/sparql/label-with-iri-violation.sparql b/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/ZFA_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/ZFA_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/zfa.owl") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/ZFS_")))
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/ZFA_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/zfa.owl") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/ZFS_")))
 }
 
diff --git a/src/sparql/multiple-replaced_by-violation.sparql b/src/sparql/multiple-replaced_by-violation.sparql
@@ -0,0 +1,12 @@
+PREFIX replaced_by: <http://purl.obolibrary.org/obo/IAO_0100001>
+
+SELECT DISTINCT ?entity ?property ?value WHERE {
+  VALUES ?property {
+    replaced_by:
+  }
+  ?entity ?property ?value1 .
+  ?entity ?property ?value2 .
+  FILTER(?value1!=?value2)
+  BIND(CONCAT(str(?value1), CONCAT("|", str(?value2))) as ?value)
+}
+
diff --git a/src/sparql/owldef-self-reference-violation.sparql b/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/ZFA_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/ZFA_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/zfa.owl") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/ZFS_")))
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/ZFA_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/zfa.owl") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/ZFS_")))
 }
 
diff --git a/src/sparql/simple-seed.sparql b/src/sparql/simple-seed.sparql
@@ -1,5 +1,4 @@
 prefix owl: <http://www.w3.org/2002/07/owl#>
-prefix obo: <http://purl.obolibrary.org/obo/>
 
 SELECT DISTINCT ?cls WHERE
 {

diff --git a/src/sparql/subsets-labeled.sparql b/src/sparql/subsets-labeled.sparql
@@ -1,5 +1,4 @@
 prefix oio: <http://www.geneontology.org/formats/oboInOwl#>
-prefix def: <http://purl.obolibrary.org/obo/IAO_0000115>
 prefix owl: <http://www.w3.org/2002/07/owl#>
 prefix inSubset: <http://www.geneontology.org/formats/oboInOwl#inSubset>
 prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>

diff --git a/src/sparql/zfa_terms.sparql b/src/sparql/zfa_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/ZFA_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/ZFA_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/zfa.owl") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/ZFS_")))
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/ZFA_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/zfa.owl") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/ZFS_")))
 }