Merge pull request #1187 from ontodev/issue1108-characteristicsmissin…

…gfrombase Extend RelatedObjectsHelper.getAxiomSubjects() to missing property axiom types
ontodev · May 1, 2024 · 8452b42 · 8452b42
2 parents e76c16e + 663a25f
commit 8452b42
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Handle IRIs that are not entities in export [#1168]
 - Fix integration tests [#1181]
 - Invalid Xrefs test has been fixed to recognise invalid CURIEs correctly [#1127]
+- Fix issue with correctly determining base entities [#1108]
 
 ## [1.9.5] - 2023-09-20
 
@@ -399,7 +400,9 @@ First official release of ROBOT!
 [#1152]: https://github.com/ontodev/robot/issues/1152
 [#1148]: https://github.com/ontodev/robot/pull/1148
 [#1135]: https://github.com/ontodev/robot/pull/1135
+[#1127]: https://github.com/ontodev/robot/pull/1127
 [#1119]: https://github.com/ontodev/robot/pull/1119
+[#1108]: https://github.com/ontodev/robot/pull/1108
 [#1104]: https://github.com/ontodev/robot/pull/1104
 [#1100]: https://github.com/ontodev/robot/pull/1100
 [#1091]: https://github.com/ontodev/robot/issues/1091

diff --git a/docs/examples/template-base-filter.owl b/docs/examples/template-base-filter.owl
@@ -58,6 +58,15 @@
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weight of a mouse or rat in kilograms (kg).</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rebecca C Jackson</obo:IAO_0000117>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">weight in kilograms</rdfs:label>
+        <rdfs:domain>
+            <owl:Class>
+                <owl:unionOf rdf:parseType="Collection">
+                    <rdf:Description rdf:about="http://example.com/B6C3F1"/>
+                    <rdf:Description rdf:about="http://example.com/F344N"/>
+                </owl:unionOf>
+            </owl:Class>
+        </rdfs:domain>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#decimal"/>
     </owl:DatatypeProperty>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://example.com/propery-1"/>

diff --git a/docs/examples/template-base.owl b/docs/examples/template-base.owl
@@ -58,6 +58,15 @@
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weight of a mouse or rat in kilograms (kg).</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rebecca C Jackson</obo:IAO_0000117>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">weight in kilograms</rdfs:label>
+        <rdfs:domain>
+            <owl:Class>
+                <owl:unionOf rdf:parseType="Collection">
+                    <rdf:Description rdf:about="http://example.com/B6C3F1"/>
+                    <rdf:Description rdf:about="http://example.com/F344N"/>
+                </owl:unionOf>
+            </owl:Class>
+        </rdfs:domain>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#decimal"/>
     </owl:DatatypeProperty>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://example.com/propery-1"/>

diff --git a/docs/examples/template-drop-axiom-filter.owl b/docs/examples/template-drop-axiom-filter.owl
@@ -52,6 +52,15 @@
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weight of a mouse or rat in kilograms (kg).</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rebecca C Jackson</obo:IAO_0000117>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">weight in kilograms</rdfs:label>
+        <rdfs:domain>
+            <owl:Class>
+                <owl:unionOf rdf:parseType="Collection">
+                    <rdf:Description rdf:about="http://example.com/B6C3F1"/>
+                    <rdf:Description rdf:about="http://example.com/F344N"/>
+                </owl:unionOf>
+            </owl:Class>
+        </rdfs:domain>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#decimal"/>
     </owl:DatatypeProperty>
 
 
@@ -126,5 +135,5 @@
 
 
 
-<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
 
diff --git a/docs/examples/template-drop-axiom-remove.owl b/docs/examples/template-drop-axiom-remove.owl
@@ -52,6 +52,15 @@
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weight of a mouse or rat in kilograms (kg).</obo:IAO_0000115>
         <obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rebecca C Jackson</obo:IAO_0000117>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">weight in kilograms</rdfs:label>
+        <rdfs:domain>
+            <owl:Class>
+                <owl:unionOf rdf:parseType="Collection">
+                    <rdf:Description rdf:about="http://example.com/B6C3F1"/>
+                    <rdf:Description rdf:about="http://example.com/F344N"/>
+                </owl:unionOf>
+            </owl:Class>
+        </rdfs:domain>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#decimal"/>
     </owl:DatatypeProperty>
 
 

diff --git a/robot-core/src/main/java/org/obolibrary/robot/RelatedObjectsHelper.java b/robot-core/src/main/java/org/obolibrary/robot/RelatedObjectsHelper.java
@@ -1417,6 +1417,14 @@ private static Set<IRI> getAxiomSubjects(OWLAxiom axiom) {
       } else {
         iris.addAll(getIRIsFromEntities(subject.getSignature()));
       }
+    } else if (axiom instanceof OWLSubAnnotationPropertyOfAxiom) {
+      OWLSubAnnotationPropertyOfAxiom spAxiom = (OWLSubAnnotationPropertyOfAxiom) axiom;
+      OWLAnnotationProperty subject = spAxiom.getSubProperty();
+      if (!subject.isAnonymous()) {
+        return Sets.newHashSet(subject.asOWLAnnotationProperty().getIRI());
+      } else {
+        iris.addAll(getIRIsFromEntities(subject.getSignature()));
+      }
     } else if (axiom instanceof OWLEquivalentDataPropertiesAxiom) {
       OWLEquivalentDataPropertiesAxiom eqAxiom = (OWLEquivalentDataPropertiesAxiom) axiom;
       for (OWLSubDataPropertyOfAxiom spAxiom : eqAxiom.asSubDataPropertyOfAxioms()) {
@@ -1492,6 +1500,54 @@ private static Set<IRI> getAxiomSubjects(OWLAxiom axiom) {
       for (OWLObjectPropertyExpression expr : spcAxiom.getPropertyChain()) {
         iris.addAll(getIRIsFromEntities(expr.getSignature()));
       }
+    } else if (axiom instanceof OWLObjectPropertyCharacteristicAxiom) {
+      OWLObjectPropertyCharacteristicAxiom chAxiom = (OWLObjectPropertyCharacteristicAxiom) axiom;
+      OWLObjectPropertyExpression subject = chAxiom.getProperty();
+      if (!subject.isAnonymous()) {
+        return Sets.newHashSet(subject.asOWLObjectProperty().getIRI());
+      } else {
+        iris.addAll(getIRIsFromEntities(subject.getSignature()));
+      }
+    } else if (axiom instanceof OWLObjectPropertyDomainAxiom) {
+      OWLObjectPropertyDomainAxiom domainAxiom = (OWLObjectPropertyDomainAxiom) axiom;
+      OWLObjectPropertyExpression subject = domainAxiom.getProperty();
+      if (!subject.isAnonymous()) {
+        return Sets.newHashSet(subject.asOWLObjectProperty().getIRI());
+      } else {
+        iris.addAll(getIRIsFromEntities(subject.getSignature()));
+      }
+    } else if (axiom instanceof OWLObjectPropertyRangeAxiom) {
+      OWLObjectPropertyRangeAxiom rangeAxiom = (OWLObjectPropertyRangeAxiom) axiom;
+      OWLObjectPropertyExpression subject = rangeAxiom.getProperty();
+      if (!subject.isAnonymous()) {
+        return Sets.newHashSet(subject.asOWLObjectProperty().getIRI());
+      } else {
+        iris.addAll(getIRIsFromEntities(subject.getSignature()));
+      }
+    } else if (axiom instanceof OWLDataPropertyDomainAxiom) {
+      OWLDataPropertyDomainAxiom domainAxiom = (OWLDataPropertyDomainAxiom) axiom;
+      OWLDataPropertyExpression subject = domainAxiom.getProperty();
+      if (!subject.isAnonymous()) {
+        return Sets.newHashSet(subject.asOWLDataProperty().getIRI());
+      } else {
+        iris.addAll(getIRIsFromEntities(subject.getSignature()));
+      }
+    } else if (axiom instanceof OWLDataPropertyRangeAxiom) {
+      OWLDataPropertyRangeAxiom rangeAxiom = (OWLDataPropertyRangeAxiom) axiom;
+      OWLDataPropertyExpression subject = rangeAxiom.getProperty();
+      if (!subject.isAnonymous()) {
+        return Sets.newHashSet(subject.asOWLDataProperty().getIRI());
+      } else {
+        iris.addAll(getIRIsFromEntities(subject.getSignature()));
+      }
+    } else if (axiom instanceof OWLInverseObjectPropertiesAxiom) {
+      OWLInverseObjectPropertiesAxiom iopAxiom = (OWLInverseObjectPropertiesAxiom) axiom;
+      OWLObjectPropertyExpression subject = iopAxiom.getFirstProperty();
+      if (!subject.isAnonymous()) {
+        return Sets.newHashSet(subject.asOWLObjectProperty().getIRI());
+      } else {
+        iris.addAll(getIRIsFromEntities(subject.getSignature()));
+      }
     } else {
       logger.warn("Axiom type not supported: " + axiom.getClass().toString());
     }