ontapi: [#55] support raw signature*,containsInSignature*,referencedAnonymousIndividuals with imports

Author: sszuev

src/main/java/com/github/owlcs/ontapi/BaseOntologyModelImpl.java

@@ -282,23 +282,31 @@ public Stream<OWLClassExpression> nestedClassExpressions() {
 
     @Override
     public Stream<OWLAnonymousIndividual> anonymousIndividuals() {
-        return base.listOWLAnonymousIndividuals();
+        return base.listComponentOWLAnonymousIndividuals();
     }
 
     @Override
     public Stream<OWLAnonymousIndividual> referencedAnonymousIndividuals() {
         return anonymousIndividuals();
     }
 
+    @Override
+    public Stream<OWLAnonymousIndividual> referencedAnonymousIndividuals(Imports imports) {
+        if (imports == Imports.INCLUDED && !config.useComponentCache()) {
+            return getFullGraphModel().listGraphOWLAnonymousIndividuals();
+        }
+        return imports.stream(this).flatMap(OWLOntology::referencedAnonymousIndividuals).distinct().sorted();
+    }
+
     @Override
     public Stream<OWLNamedIndividual> individualsInSignature() {
-        return base.listOWLNamedIndividuals();
+        return base.listComponentOWLNamedIndividuals();
     }
 
     @Override
     public Stream<OWLNamedIndividual> individualsInSignature(Imports imports) {
         if (imports == Imports.INCLUDED && !config.useComponentCache()) {
-            return getFullGraphModel().listOWLNamedIndividuals();
+            return getFullGraphModel().listGraphOWLNamedIndividuals();
         }
         return imports.stream(this).flatMap(OWLOntology::individualsInSignature).distinct().sorted();
     }
@@ -996,31 +1004,49 @@ public boolean contains(OWLAxiomSearchFilter filter, Object key) {
 
     @Override
     public boolean containsClassInSignature(IRI iri, Imports imports) {
+        if (imports == Imports.INCLUDED && !config.useComponentCache()) {
+            return getFullGraphModel().containsOWLEntity(getDataFactory().getOWLClass(iri));
+        }
         return imports.stream(this).anyMatch(o -> o.containsClassInSignature(iri));
     }
 
     @Override
     public boolean containsObjectPropertyInSignature(IRI iri, Imports imports) {
+        if (imports == Imports.INCLUDED && !config.useComponentCache()) {
+            return getFullGraphModel().containsOWLEntity(getDataFactory().getOWLObjectProperty(iri));
+        }
         return imports.stream(this).anyMatch(o -> o.containsObjectPropertyInSignature(iri));
     }
 
     @Override
     public boolean containsDataPropertyInSignature(IRI iri, Imports imports) {
+        if (imports == Imports.INCLUDED && !config.useComponentCache()) {
+            return getFullGraphModel().containsOWLEntity(getDataFactory().getOWLDataProperty(iri));
+        }
         return imports.stream(this).anyMatch(o -> o.containsDataPropertyInSignature(iri));
     }
 
     @Override
     public boolean containsAnnotationPropertyInSignature(IRI iri, Imports imports) {
+        if (imports == Imports.INCLUDED && !config.useComponentCache()) {
+            return getFullGraphModel().containsOWLEntity(getDataFactory().getOWLAnnotationProperty(iri));
+        }
         return imports.stream(this).anyMatch(o -> o.containsAnnotationPropertyInSignature(iri));
     }
 
     @Override
     public boolean containsDatatypeInSignature(IRI iri, Imports imports) {
+        if (imports == Imports.INCLUDED && !config.useComponentCache()) {
+            return getFullGraphModel().containsOWLEntity(getDataFactory().getOWLDatatype(iri));
+        }
         return imports.stream(this).anyMatch(o -> o.containsDatatypeInSignature(iri));
     }
 
     @Override
     public boolean containsIndividualInSignature(IRI iri, Imports imports) {
+        if (imports == Imports.INCLUDED && !config.useComponentCache()) {
+            return getFullGraphModel().containsOWLEntity(getDataFactory().getOWLNamedIndividual(iri));
+        }
         return imports.stream(this).anyMatch(o -> o.containsIndividualInSignature(iri));
     }
 

src/main/java/com/github/owlcs/ontapi/internal/InternalGraphModel.java

@@ -99,18 +99,44 @@ public interface InternalGraphModel extends OntModel, OntEnhGraph, HasOntologyID
     Stream<OWLClassExpression> listOWLClassExpressions();
 
     /**
-     * Lists all anonymous individuals in the form of OWL-API objects.
+     * Lists all (component) anonymous individuals in the form of OWL-API objects.
+     * The difference with the method {@link #listGraphOWLAnonymousIndividuals()} is that
+     * this method retrieves individuals from components' cache collected from base graph,
+     * while the method {@link #listGraphOWLAnonymousIndividuals()} uses {@link OntModel#individuals()}.
      *
      * @return a {@code Stream} of {@link OWLAnonymousIndividual}s
      */
-    Stream<OWLAnonymousIndividual> listOWLAnonymousIndividuals();
+    Stream<OWLAnonymousIndividual> listComponentOWLAnonymousIndividuals();
 
     /**
-     * Lists all named individuals in the form of OWL-API objects.
+     * Lists all (graph) anonymous individuals in the form of OWL-API objects.
+     * This method uses {@link OntModel#individuals()} method,
+     * while the method {@link #listComponentOWLAnonymousIndividuals()} parses individuals from components'
+     * cache collected from base graph.
      *
      * @return a {@code Stream} of {@link OWLNamedIndividual}s
      */
-    Stream<OWLNamedIndividual> listOWLNamedIndividuals();
+    Stream<OWLAnonymousIndividual> listGraphOWLAnonymousIndividuals();
+
+    /**
+     * Lists all (component) named individuals in the form of OWL-API objects.
+     * The difference with the method {@link #listGraphOWLNamedIndividuals()} is that
+     * this method retrieves individuals from components' cache collected from base graph,
+     * while the method {@link #listGraphOWLNamedIndividuals()} uses {@link OntModel#individuals()}.
+     *
+     * @return a {@code Stream} of {@link OWLNamedIndividual}s
+     */
+    Stream<OWLNamedIndividual> listComponentOWLNamedIndividuals();
+
+    /**
+     * Lists all (graph) named individuals in the form of OWL-API objects.
+     * This method uses {@link OntModel#individuals()} method,
+     * while the method {@link #listComponentOWLNamedIndividuals()} parses individuals from components'
+     * cache collected from base graph.
+     *
+     * @return a {@code Stream} of {@link OWLNamedIndividual}s
+     */
+    Stream<OWLNamedIndividual> listGraphOWLNamedIndividuals();
 
     /**
      * Lists all OWL classes in the form of OWL-API objects.

src/main/java/com/github/owlcs/ontapi/internal/InternalReadGraphModel.java

@@ -462,19 +462,37 @@ public boolean containsOWLDeclaration(OWLEntity e) {
         return listOWLAxioms(OWLDeclarationAxiom.class).anyMatch(x -> x.getEntity().equals(e));
     }
 
-    public Stream<OWLAnonymousIndividual> listOWLAnonymousIndividuals() {
+    public Stream<OWLAnonymousIndividual> listComponentOWLAnonymousIndividuals() {
         return listComponents(OWLComponentType.ANONYMOUS_INDIVIDUAL);
     }
 
+    public Stream<OWLAnonymousIndividual> listGraphOWLAnonymousIndividuals() {
+        ModelObjectFactory factory = getObjectFactory();
+        InternalConfig config = getConfig();
+        return individuals()
+                .filter(RDFNode::isAnon)
+                .map(it -> (OWLAnonymousIndividual) (factory.getIndividual(it).getOWLObject()))
+                .map(it -> strip(it, config));
+    }
+
     public Stream<OWLClassExpression> listOWLClassExpressions() {
         return ModelIterators.reduceDistinct(selectContentObjects(OWLComponentType.CLASS_EXPRESSION)
                 .flatMap(OWLObject::nestedClassExpressions), getConfig());
     }
 
-    public Stream<OWLNamedIndividual> listOWLNamedIndividuals() {
+    public Stream<OWLNamedIndividual> listComponentOWLNamedIndividuals() {
         return listComponents(OWLComponentType.NAMED_INDIVIDUAL);
     }
 
+    public Stream<OWLNamedIndividual> listGraphOWLNamedIndividuals() {
+        ModelObjectFactory factory = getObjectFactory();
+        InternalConfig config = getConfig();
+        return individuals()
+                .filter(RDFNode::isURIResource)
+                .map(it -> (OWLNamedIndividual) (factory.getIndividual(it).getOWLObject()))
+                .map(it -> strip(it, config));
+    }
+
     public Stream<OWLClass> listOWLClasses() {
         return listComponents(OWLComponentType.CLASS);
     }

src/test/java/com/github/owlcs/ontapi/tests/internal/InternalGraphModelTest.java

@@ -167,8 +167,8 @@ public void testFoafEntities() {
 
         test(OWLClass.class, jena.listOWLClasses(), owl.classesInSignature());
         test(OWLDatatype.class, jena.listOWLDatatypes(), owl.datatypesInSignature());
-        test(OWLNamedIndividual.class, jena.listOWLNamedIndividuals(), owl.individualsInSignature());
-        test(OWLAnonymousIndividual.class, jena.listOWLAnonymousIndividuals(), owl.anonymousIndividuals());
+        test(OWLNamedIndividual.class, jena.listComponentOWLNamedIndividuals(), owl.individualsInSignature());
+        test(OWLAnonymousIndividual.class, jena.listComponentOWLAnonymousIndividuals(), owl.anonymousIndividuals());
         Set<OWLAnnotationProperty> expectedAnnotationProperties = owl.annotationPropertiesInSignature()
                 .collect(Collectors.toSet());
         Set<OWLDataProperty> expectedDataProperties = owl.dataPropertiesInSignature().collect(Collectors.toSet());
@@ -228,8 +228,8 @@ private void testEntities(String file, OntFormat format) {
         debugPrint(jena, owl);
         test(OWLClass.class, jena.listOWLClasses(), owl.classesInSignature());
         test(OWLDatatype.class, jena.listOWLDatatypes(), owl.datatypesInSignature());
-        test(OWLNamedIndividual.class, jena.listOWLNamedIndividuals(), owl.individualsInSignature());
-        test(OWLAnonymousIndividual.class, jena.listOWLAnonymousIndividuals(), owl.anonymousIndividuals());
+        test(OWLNamedIndividual.class, jena.listComponentOWLNamedIndividuals(), owl.individualsInSignature());
+        test(OWLAnonymousIndividual.class, jena.listComponentOWLAnonymousIndividuals(), owl.anonymousIndividuals());
         test(OWLAnnotationProperty.class, jena.listOWLAnnotationProperties(), owl.annotationPropertiesInSignature());
         test(OWLObjectProperty.class, jena.listOWLObjectProperties(), owl.objectPropertiesInSignature());
         test(OWLDataProperty.class, jena.listOWLDataProperties(), owl.dataPropertiesInSignature());