Migrated OWLAPI Ontodriver to OWLAPI 5.1.3 (latest).

jopa-owl2java/src/main/java/cz/cvut/kbss/jopa/owl2java/ClassObjectPropertyComputer.java

@@ -23,6 +23,8 @@
 
 import java.util.Collection;
 import java.util.HashSet;
+import java.util.Set;
+import java.util.stream.Collectors;
 
 public class ClassObjectPropertyComputer {
 
@@ -53,15 +55,15 @@ public ClassObjectPropertyComputer(final OWLClass clazz,
             final OWLDataFactory f = merged.getOWLOntologyManager().getOWLDataFactory();
 
             final OWLClass object = filler;
+            final Set<OWLClassExpression> superClasses = EntitySearcher.getSuperClasses(object, merged).collect(
+                    Collectors.toSet());
 
-            if (EntitySearcher.getSuperClasses(object, merged)
-                              .anyMatch(sc -> sc.equals(f.getOWLClass(IRI.create(SequencesVocabulary.c_List))))) {
+            if (superClasses.contains(f.getOWLClass(IRI.create(SequencesVocabulary.c_List)))) {
                 this.filler = new ClassObjectPropertyComputer(object,
                         f.getOWLObjectProperty(IRI.create(SequencesVocabulary.p_element)),
                         set, merged).getFiller();
                 card = Card.LIST;
-            } else if (EntitySearcher.getSuperClasses(object, merged).anyMatch(
-                    sc -> sc.equals(f.getOWLClass(IRI.create(SequencesVocabulary.c_OWLSimpleList))))) {
+            } else if (superClasses.contains(f.getOWLClass(IRI.create(SequencesVocabulary.c_OWLSimpleList)))) {
                 this.filler = new ClassObjectPropertyComputer(object,
                         f.getOWLObjectProperty(IRI.create(SequencesVocabulary.p_hasNext)),
                         set, merged).getFiller();

jopa-owl2java/src/main/java/cz/cvut/kbss/jopa/owl2java/OWL2JavaTransformer.java

@@ -192,8 +192,7 @@ public void generateVocabulary(String context, String pkg, String targetDir, boo
             verifyContextExistence(context);
         }
         ContextDefinition def = (context == null) ? DEFAULT_CONTEXT : contexts.get(context);
-        new JavaTransformer().
-                                     generateVocabulary(ontology, def, pkg, targetDir, withOWLAPI);
+        new JavaTransformer().generateVocabulary(ontology, def, pkg, targetDir, withOWLAPI);
     }
 
     private class ValidContextAnnotationValueVisitor implements OWLAnnotationValueVisitor {

ontodriver-owlapi/pom.xml

@@ -16,7 +16,6 @@
     </parent>
 
     <properties>
-        <net.sourceforge.owlapi.version>4.2.4</net.sourceforge.owlapi.version>
         <cz.cvut.kbss.owl2query.version>0.4.0</cz.cvut.kbss.owl2query.version>
     </properties>
 

ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/EpistemicAxiomRemover.java

@@ -1,11 +1,11 @@
 /**
  * Copyright (C) 2016 Czech Technical University in Prague
- *
+ * <p>
  * This program is free software: you can redistribute it and/or modify it under
  * the terms of the GNU General Public License as published by the Free Software
  * Foundation, either version 3 of the License, or (at your option) any
  * later version.
- *
+ * <p>
  * This program is distributed in the hope that it will be useful, but WITHOUT
  * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
@@ -26,6 +26,7 @@
 
 import java.util.*;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 class EpistemicAxiomRemover {
 
@@ -65,8 +66,7 @@ void remove(AxiomDescriptor descriptor) {
     }
 
     private Collection<OWLOntologyChange> removeClassAssertionAxioms(OWLNamedIndividual individual) {
-        final Collection<OWLClassExpression> types = EntitySearcher.getTypes(individual, ontology);
-        return types.stream().map(cls -> new MutableRemoveAxiom(ontology,
+        return EntitySearcher.getTypes(individual, ontology).map(cls -> new MutableRemoveAxiom(ontology,
                 dataFactory.getOWLClassAssertionAxiom(cls, individual))).collect(Collectors.toList());
     }
 
@@ -81,8 +81,8 @@ private Collection<OWLOntologyChange> removeClassAssertionAxioms(OWLNamedIndivid
     private Collection<? extends OWLOntologyChange> removeDataPropertyAssertions(OWLNamedIndividual individual,
                                                                                  Assertion assertion) {
         final OWLDataProperty dataProperty = dataFactory.getOWLDataProperty(IRI.create(assertion.getIdentifier()));
-        final Collection<OWLLiteral> values = EntitySearcher.getDataPropertyValues(individual, dataProperty, ontology);
-        return values.stream().map(value -> new MutableRemoveAxiom(ontology,
+        final Stream<OWLLiteral> values = EntitySearcher.getDataPropertyValues(individual, dataProperty, ontology);
+        return values.map(value -> new MutableRemoveAxiom(ontology,
                 dataFactory.getOWLDataPropertyAssertionAxiom(dataProperty, individual, value)))
                      .collect(Collectors.toList());
     }
@@ -102,9 +102,8 @@ private Collection<? extends OWLOntologyChange> removeDataPropertyAssertions(OWL
     private Collection<? extends OWLOntologyChange> removeObjectPropertyAssertions(OWLNamedIndividual individual,
                                                                                    Assertion assertion) {
         final OWLObjectProperty objProperty = dataFactory.getOWLObjectProperty(IRI.create(assertion.getIdentifier()));
-        final Collection<OWLIndividual> values = EntitySearcher
-                .getObjectPropertyValues(individual, objProperty, ontology);
-        return values.stream().filter(OWLIndividual::isNamed).map(value -> new MutableRemoveAxiom(ontology,
+        final Stream<OWLIndividual> values = EntitySearcher.getObjectPropertyValues(individual, objProperty, ontology);
+        return values.filter(OWLIndividual::isNamed).map(value -> new MutableRemoveAxiom(ontology,
                 dataFactory.getOWLObjectPropertyAssertionAxiom(objProperty, individual, value)))
                      .collect(Collectors.toList());
     }
@@ -125,9 +124,9 @@ private Collection<? extends OWLOntologyChange> removeAnnotationAssertions(OWLNa
                                                                                Assertion assertion) {
         final OWLAnnotationProperty annProperty = dataFactory
                 .getOWLAnnotationProperty(IRI.create(assertion.getIdentifier()));
-        final Collection<OWLAnnotationAssertionAxiom> values = EntitySearcher
-                .getAnnotationAssertionAxioms(individual.getIRI(), ontology);
-        return values.stream().filter(axiom -> axiom.getProperty().equals(annProperty))
+        final Stream<OWLAnnotationAssertionAxiom> values =
+                EntitySearcher.getAnnotationAssertionAxioms(individual.getIRI(), ontology);
+        return values.filter(axiom -> axiom.getProperty().equals(annProperty))
                      .map(value -> new MutableRemoveAxiom(ontology, value)).collect(Collectors.toList());
     }
 

ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/ExplicitAxiomLoader.java

@@ -24,6 +24,7 @@
 import java.net.URI;
 import java.util.*;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 class ExplicitAxiomLoader implements AxiomLoader {
 
@@ -56,21 +57,18 @@ public Collection<Axiom<?>> loadAxioms(NamedResource subject, Set<Assertion> ass
             axioms.addAll(adapter.getTypesHandler().getTypes(subject, null, false));
         }
         // This involves a lot of filtering, perhaps we should use EntitySearcher and look for values of concrete properties
-        final Collection<OWLDataPropertyAssertionAxiom> dpAssertions = ontology.getDataPropertyAssertionAxioms(
-                individual);
+        final Stream<OWLDataPropertyAssertionAxiom> dpAssertions = ontology.dataPropertyAssertionAxioms(individual);
         axioms.addAll(dataPropertyValuesToAxioms(subject, dpAssertions));
-        final Collection<OWLObjectPropertyAssertionAxiom> opAssertions = ontology.getObjectPropertyAssertionAxioms(
-                individual);
+        final Stream<OWLObjectPropertyAssertionAxiom> opAssertions = ontology.objectPropertyAssertionAxioms(individual);
         axioms.addAll(objectPropertyValuesToAxioms(subject, opAssertions));
-        final Collection<OWLAnnotationAssertionAxiom> apAssertions = ontology.getAnnotationAssertionAxioms(
-                individual.getIRI());
+        final Stream<OWLAnnotationAssertionAxiom> apAssertions = ontology.annotationAssertionAxioms(individual.getIRI());
         axioms.addAll(annotationPropertyValuesToAxioms(subject, apAssertions));
         return axioms;
     }
 
     private Collection<Axiom<?>> dataPropertyValuesToAxioms(NamedResource subject,
-                                                            Collection<OWLDataPropertyAssertionAxiom> axioms) {
-        return axioms.stream().filter(this::shouldLoadDataPropertyValue)
+                                                            Stream<OWLDataPropertyAssertionAxiom> axioms) {
+        return axioms.filter(this::shouldLoadDataPropertyValue)
                      .map(axiom -> axiomAdapter.toAxiom(subject, axiom, false))
                      .collect(Collectors.toList());
     }
@@ -95,16 +93,16 @@ private boolean doesPropertyExist(IRI o) {
     }
 
     private Collection<Axiom<?>> objectPropertyValuesToAxioms(NamedResource subject,
-                                                              Collection<OWLObjectPropertyAssertionAxiom> axioms) {
-        return axioms.stream().filter(axiom ->
+                                                              Stream<OWLObjectPropertyAssertionAxiom> axiomStream) {
+        return axiomStream.filter(axiom ->
                 doesPropertyExist(axiom.getProperty().asOWLObjectProperty().getIRI()))
                      .map(axiom -> axiomAdapter.toAxiom(subject, axiom, false))
                      .collect(Collectors.toList());
     }
 
     private Collection<Axiom<?>> annotationPropertyValuesToAxioms(NamedResource subject,
-                                                                  Collection<OWLAnnotationAssertionAxiom> axioms) {
-        return axioms.stream().filter(this::shouldLoadAnnotationPropertyValue)
+                                                                  Stream<OWLAnnotationAssertionAxiom> axioms) {
+        return axioms.filter(this::shouldLoadAnnotationPropertyValue)
                      .map(axiom -> axiomAdapter.toAxiom(subject, axiom, false))
                      .collect(Collectors.toList());
     }
@@ -127,11 +125,11 @@ private boolean shouldLoadAnnotationPropertyValue(OWLAnnotationAssertionAxiom ax
     public Collection<Axiom<?>> loadPropertyAxioms(NamedResource subject) {
         final OWLNamedIndividual individual = OwlapiUtils.getIndividual(subject, dataFactory);
         final Collection<Axiom<?>> axioms = new ArrayList<>();
-        ontology.getDataPropertyAssertionAxioms(individual)
+        ontology.dataPropertyAssertionAxioms(individual)
                 .forEach(assertion -> axioms.add(axiomAdapter.toAxiom(subject, assertion, false)));
-        ontology.getObjectPropertyAssertionAxioms(individual)
+        ontology.objectPropertyAssertionAxioms(individual)
                 .forEach(assertion -> axioms.add(axiomAdapter.toAxiom(subject, assertion, false)));
-        ontology.getAnnotationAssertionAxioms(individual.getIRI())
+        ontology.annotationAssertionAxioms(individual.getIRI())
                 .forEach(assertion -> axioms.add(axiomAdapter.toAxiom(subject, assertion, false)));
         return axioms;
     }

ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/InferredAxiomLoader.java

@@ -1,11 +1,11 @@
 /**
  * Copyright (C) 2016 Czech Technical University in Prague
- *
+ * <p>
  * This program is free software: you can redistribute it and/or modify it under
  * the terms of the GNU General Public License as published by the Free Software
  * Foundation, either version 3 of the License, or (at your option) any
  * later version.
- *
+ * <p>
  * This program is distributed in the hope that it will be useful, but WITHOUT
  * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
@@ -14,15 +14,16 @@
  */
 package cz.cvut.kbss.ontodriver.owlapi;
 
+import cz.cvut.kbss.ontodriver.model.*;
 import cz.cvut.kbss.ontodriver.owlapi.connector.OntologySnapshot;
 import cz.cvut.kbss.ontodriver.owlapi.exception.ReasonerNotAvailableException;
 import cz.cvut.kbss.ontodriver.owlapi.util.OwlapiUtils;
-import cz.cvut.kbss.ontodriver.model.*;
 import org.semanticweb.owlapi.model.*;
 import org.semanticweb.owlapi.reasoner.OWLReasoner;
 
 import java.util.*;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 public class InferredAxiomLoader implements AxiomLoader {
 
@@ -92,9 +93,9 @@ private OWLDataProperty dataProperty(Assertion dataPropertyAssertion) {
     }
 
     private Collection<Axiom<?>> inferObjectPropertyValues(OWLNamedIndividual individual, Assertion opAssertion) {
-        final Set<OWLNamedIndividual> individuals = reasoner.getObjectPropertyValues(individual,
-                objectProperty(opAssertion)).getFlattened();
-        return individuals.stream().map(
+        final Stream<OWLNamedIndividual> individuals =
+                reasoner.getObjectPropertyValues(individual, objectProperty(opAssertion)).entities();
+        return individuals.map(
                 target -> axiomAdapter.createAxiom(subject, opAssertion, NamedResource.create(target.getIRI().toURI())))
                           .collect(
                                   Collectors.toList());
@@ -108,21 +109,19 @@ private OWLObjectProperty objectProperty(Assertion objectPropertyAssertion) {
     public Collection<Axiom<?>> loadPropertyAxioms(NamedResource subject) {
         final Collection<Axiom<?>> axioms = new ArrayList<>();
         final OWLNamedIndividual individual = OwlapiUtils.getIndividual(subject, dataFactory);
-        for (OWLDataProperty dp : ontology.getDataPropertiesInSignature()) {
+        ontology.dataPropertiesInSignature().forEach(dp -> {
             final Set<OWLLiteral> values = reasoner.getDataPropertyValues(individual, dp);
             for (OWLLiteral literal : values) {
                 axioms.add(axiomAdapter.createAxiom(subject,
                         Assertion.createDataPropertyAssertion(dp.getIRI().toURI(), true), literal));
             }
-        }
-        for (OWLObjectProperty op : ontology.getObjectPropertiesInSignature()) {
-            final Set<OWLNamedIndividual> values = reasoner.getObjectPropertyValues(individual, op).getFlattened();
-            for (OWLNamedIndividual ind : values) {
-                axioms.add(axiomAdapter.createAxiom(subject,
-                        Assertion.createObjectPropertyAssertion(op.getIRI().toURI(), true), NamedResource.create(
-                                ind.getIRI().toURI())));
-            }
-        }
+        });
+        ontology.objectPropertiesInSignature().forEach(op -> {
+            final Assertion opAss = Assertion.createObjectPropertyAssertion(op.getIRI().toURI(), true);
+            reasoner.getObjectPropertyValues(individual, op).entities()
+                    .forEach(ind -> axioms
+                            .add(axiomAdapter.createAxiom(subject, opAss, NamedResource.create(ind.getIRI().toURI()))));
+        });
         return axioms;
     }
 }

ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/TypesHandler.java

@@ -54,7 +54,7 @@ Set<Axiom<URI>> getTypes(NamedResource subject, URI context, boolean includeInfe
     }
 
     private Collection<OWLClassExpression> loadExplicitClasses(NamedResource subject) {
-        return EntitySearcher.getTypes(getIndividual(subject), ontology);
+        return EntitySearcher.getTypes(getIndividual(subject), ontology).collect(Collectors.toSet());
     }
 
     private OWLNamedIndividual getIndividual(NamedResource subject) {
@@ -70,7 +70,7 @@ private Set<Axiom<URI>> owlClassesToAxioms(NamedResource subject, boolean inferr
 
     private Collection<? extends OWLClassExpression> inferClasses(NamedResource subject) {
         final OWLNamedIndividual individual = getIndividual(subject);
-        return reasoner.getTypes(individual, false).getFlattened();
+        return reasoner.getTypes(individual, false).entities().collect(Collectors.toSet());
     }
 
     void addTypes(NamedResource subject, URI context, Set<URI> types) {

ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/list/InferredReferencedListIterator.java

@@ -1,11 +1,11 @@
 /**
  * Copyright (C) 2016 Czech Technical University in Prague
- *
+ * <p>
  * This program is free software: you can redistribute it and/or modify it under
  * the terms of the GNU General Public License as published by the Free Software
  * Foundation, either version 3 of the License, or (at your option) any
  * later version.
- *
+ * <p>
  * This program is distributed in the hope that it will be useful, but WITHOUT
  * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
@@ -14,12 +14,12 @@
  */
 package cz.cvut.kbss.ontodriver.owlapi.list;
 
+import cz.cvut.kbss.ontodriver.descriptor.ReferencedListDescriptor;
+import cz.cvut.kbss.ontodriver.model.NamedResource;
 import cz.cvut.kbss.ontodriver.owlapi.AxiomAdapter;
 import cz.cvut.kbss.ontodriver.owlapi.connector.OntologySnapshot;
 import cz.cvut.kbss.ontodriver.owlapi.exception.ReasonerNotAvailableException;
 import cz.cvut.kbss.ontodriver.owlapi.util.OwlapiUtils;
-import cz.cvut.kbss.ontodriver.descriptor.ReferencedListDescriptor;
-import cz.cvut.kbss.ontodriver.model.NamedResource;
 import org.semanticweb.owlapi.model.OWLIndividual;
 import org.semanticweb.owlapi.model.OWLNamedIndividual;
 import org.semanticweb.owlapi.model.OWLOntologyChange;
@@ -29,6 +29,7 @@
 import java.util.Collections;
 import java.util.List;
 import java.util.NoSuchElementException;
+import java.util.stream.Collectors;
 
 class InferredReferencedListIterator extends ReferencedListIterator {
 
@@ -55,16 +56,18 @@ public boolean hasNext() {
 
     @Override
     void doStep() {
-        final Collection<OWLNamedIndividual> nextNodes = reasoner
-                .getObjectPropertyValues(currentNode, currentNextNodeProperty).getFlattened();
+        final Collection<OWLNamedIndividual> nextNodes =
+                reasoner.getObjectPropertyValues(currentNode, currentNextNodeProperty).entities()
+                        .collect(Collectors.toSet());
         if (nextNodes.isEmpty()) {
             this.next = Collections.emptyList();
             return;
         }
         checkMaxSuccessors(currentNextNodeProperty, nextNodes);
         this.currentNextNodeProperty = hasNextProperty;
         this.currentNode = nextNodes.iterator().next();
-        this.next = reasoner.getObjectPropertyValues(currentNode, hasContentProperty).getFlattened();
+        this.next = reasoner.getObjectPropertyValues(currentNode, hasContentProperty).entities()
+                            .collect(Collectors.toSet());
     }
 
     @Override

ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/list/InferredSimpleListIterator.java

@@ -30,6 +30,7 @@
 import java.util.Collections;
 import java.util.List;
 import java.util.NoSuchElementException;
+import java.util.stream.Collectors;
 
 /**
  * This class differs from the way basic SimpleListIterator iterates over the list. Here, we do step before even calling
@@ -63,7 +64,7 @@ public boolean hasNext() {
     @Override
     void doStep() {
         final NodeSet<OWLNamedIndividual> nodeSet = reasoner.getObjectPropertyValues(currentNode, currentProperty);
-        this.next = nodeSet.isEmpty() ? Collections.emptySet() : nodeSet.getFlattened();
+        this.next = nodeSet.isEmpty() ? Collections.emptySet() : nodeSet.entities().collect(Collectors.toSet());
         this.previousProperty = currentProperty;
         this.currentProperty = hasNextProperty;
         this.previousNode = this.currentNode;

ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/list/ReferencedListHandler.java

@@ -104,7 +104,7 @@ private class ReferencedListNodeGenerator {
         private int index;
         private Assertion property;
 
-        public ReferencedListNodeGenerator(NamedResource baseUri, Assertion nodeContent) {
+        ReferencedListNodeGenerator(NamedResource baseUri, Assertion nodeContent) {
             this.baseUri = baseUri.toString() + "-SEQ_";
             this.changes = new ArrayList<>();
             this.nodeContentProperty = nodeContent;