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uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl Maven / Gradle / Ivy
/* This file is part of the OWL API.
* The contents of this file are subject to the LGPL License, Version 3.0.
* Copyright 2014, The University of Manchester
*
* 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.
* 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 details.
* You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
*
* Alternatively, the contents of this file may be used under the terms of the Apache License, Version 2.0 in which case, the provisions of the Apache License Version 2.0 are applicable instead of those above.
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
* Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. */
package uk.ac.manchester.cs.owl.owlapi;
import static org.semanticweb.owlapi.model.parameters.Imports.EXCLUDED;
import static org.semanticweb.owlapi.util.OWLAPIPreconditions.checkNotNull;
import static org.semanticweb.owlapi.util.OWLAPIPreconditions.verifyNotNull;
import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.asList;
import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.asSet;
import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.empty;
import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.streamFromSorted;
import java.io.Serializable;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.util.function.Function;
import java.util.function.Predicate;
import java.util.stream.Stream;
import javax.annotation.Nullable;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.EntityType;
import org.semanticweb.owlapi.model.HasSignature;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotation;
import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.semanticweb.owlapi.model.OWLAnonymousIndividual;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLAxiomCollection;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLClassAxiom;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLDataProperty;
import org.semanticweb.owlapi.model.OWLDataPropertyAxiom;
import org.semanticweb.owlapi.model.OWLDatatype;
import org.semanticweb.owlapi.model.OWLDatatypeDefinitionAxiom;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLImportsDeclaration;
import org.semanticweb.owlapi.model.OWLIndividual;
import org.semanticweb.owlapi.model.OWLIndividualAxiom;
import org.semanticweb.owlapi.model.OWLLiteral;
import org.semanticweb.owlapi.model.OWLLogicalAxiom;
import org.semanticweb.owlapi.model.OWLNamedIndividual;
import org.semanticweb.owlapi.model.OWLObject;
import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLObjectPropertyAxiom;
import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyID;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLPrimitive;
import org.semanticweb.owlapi.model.parameters.AxiomAnnotations;
import org.semanticweb.owlapi.model.parameters.Imports;
import org.semanticweb.owlapi.model.parameters.Navigation;
import org.semanticweb.owlapi.util.OWLAPIStreamUtils;
import org.semanticweb.owlapi.util.OWLAxiomSearchFilter;
import org.semanticweb.owlapi.vocab.OWL2Datatype;
import com.github.benmanes.caffeine.cache.LoadingCache;
/**
* @author Matthew Horridge, The University Of Manchester, Bio-Health Informatics Group
* @since 2.0.0
*/
public class OWLImmutableOntologyImpl extends OWLAxiomIndexImpl
implements OWLOntology, Serializable {
// @formatter:off
protected static LoadingCache> ontsignatures =
build(OWLImmutableOntologyImpl::build);
protected static LoadingCache> ontanonCaches = build(key -> asList(key.ints.get(OWLAnonymousIndividual.class, OWLAxiom.class).get().keySet().distinct().sorted()));
protected static LoadingCache> ontclassesSignatures = build(key -> asList(key.ints.get(OWLClass.class, OWLAxiom.class).get().keySet().distinct().sorted()));
protected static LoadingCache> ontdataPropertySignatures = build(key -> asList(key.ints.get(OWLDataProperty.class, OWLAxiom.class).get().keySet().distinct().sorted()));
protected static LoadingCache> ontobjectPropertySignatures = build(key -> asList(key.ints.get(OWLObjectProperty.class, OWLAxiom.class).get().keySet().distinct().sorted()));
protected static LoadingCache> ontdatatypeSignatures = build(key -> asList(key.ints.get(OWLDatatype.class, OWLAxiom.class).get().keySet().distinct().sorted()));
protected static LoadingCache> ontindividualSignatures = build(key -> asList(key.ints.get(OWLNamedIndividual.class, OWLAxiom.class).get().keySet().distinct().sorted()));
protected static LoadingCache> ontannotationPropertiesSignatures = build(key -> asList(Stream.concat(key.ints.get(OWLAnnotationProperty.class, OWLAxiom.class, Navigation.IN_SUB_POSITION).get().keySet(),key.ints.getOntologyAnnotations().flatMap(a->a.annotationPropertiesInSignature())).distinct().sorted()));
// @formatter:on
protected static void invalidateOntologyCaches(OWLImmutableOntologyImpl o) {
ontsignatures.invalidate(o);
ontanonCaches.invalidate(o);
ontclassesSignatures.invalidate(o);
ontdataPropertySignatures.invalidate(o);
ontobjectPropertySignatures.invalidate(o);
ontdatatypeSignatures.invalidate(o);
ontindividualSignatures.invalidate(o);
ontannotationPropertiesSignatures.invalidate(o);
}
private static Set build(OWLImmutableOntologyImpl key) {
Stream stream =
Stream
.of(key.classesInSignature(), key.objectPropertiesInSignature(),
key.dataPropertiesInSignature(), key.individualsInSignature(),
key.datatypesInSignature(), key.annotationPropertiesInSignature())
.flatMap(x -> x);
return asSet(stream.distinct().sorted());
}
@Nullable
protected OWLOntologyManager manager;
protected OWLDataFactory df;
protected OWLOntologyID ontologyID;
/**
* @param manager ontology manager
* @param ontologyID ontology id
*/
public OWLImmutableOntologyImpl(OWLOntologyManager manager, OWLOntologyID ontologyID) {
this.manager = checkNotNull(manager, "manager cannot be null");
this.ontologyID = checkNotNull(ontologyID, "ontologyID cannot be null");
df = manager.getOWLDataFactory();
}
private static void add(Set punned, Set test, OWLEntity e) {
if (!test.add(e.getIRI())) {
punned.add(e.getIRI());
}
}
@Override
public String toString() {
StringBuilder sb = new StringBuilder(100);
sb.append("Ontology(").append(ontologyID).append(") [Axioms: ").append(ints.getAxiomCount())
.append(" Logical Axioms: ").append(ints.getLogicalAxiomCount())
.append("] First 20 axioms: {");
ints.getAxioms().limit(20).forEach(a -> sb.append(a).append(' '));
sb.append('}');
return sb.toString();
}
@Override
public OWLOntologyManager getOWLOntologyManager() {
OWLOntologyManager m = manager;
if (m == null) {
throw new IllegalStateException("Manager on ontology " + getOntologyID()
+ " is null; the ontology is no longer associated to a manager. Ensure the ontology is not being used after being removed from its manager.");
}
return verifyNotNull(m, "manager cannot be null at this stage");
}
@Override
public void setOWLOntologyManager(@Nullable OWLOntologyManager manager) {
this.manager = manager;
}
@Override
public OWLOntologyID getOntologyID() {
return ontologyID;
}
@Override
public boolean isAnonymous() {
return ontologyID.isAnonymous();
}
@Override
public boolean isEmpty() {
return ints.isEmpty();
}
@Override
public int getAxiomCount(AxiomType axiomType) {
return ints.getAxiomCount(axiomType);
}
@Override
public int getAxiomCount() {
return ints.getAxiomCount();
}
@Override
public boolean containsAxiom(OWLAxiom axiom) {
return Internals.contains(ints.getAxiomsByType(), axiom.getAxiomType(), axiom);
}
@Override
public Stream axioms() {
return ints.getAxioms();
}
@Override
@SuppressWarnings("unchecked")
public Stream axioms(AxiomType axiomType) {
return (Stream) ints.getAxiomsByType().getValues(axiomType);
}
@Override
public Stream logicalAxioms() {
return ints.getLogicalAxioms();
}
@Override
public int getLogicalAxiomCount() {
return ints.getLogicalAxiomCount();
}
@Override
public int getAxiomCount(AxiomType axiomType, Imports imports) {
return imports.stream(this).mapToInt(o -> o.getAxiomCount(axiomType)).sum();
}
@Override
public int getAxiomCount(Imports imports) {
return imports.stream(this).mapToInt(OWLAxiomCollection::getAxiomCount).sum();
}
@Override
public Stream tboxAxioms(Imports imports) {
return AxiomType.TBoxAxiomTypes.stream().flatMap(t -> axioms(t, imports));
}
@Override
public Stream aboxAxioms(Imports imports) {
return AxiomType.ABoxAxiomTypes.stream().flatMap(t -> axioms(t, imports));
}
@Override
public Stream rboxAxioms(Imports imports) {
return AxiomType.RBoxAxiomTypes.stream().flatMap(t -> axioms(t, imports));
}
@Override
public int getLogicalAxiomCount(Imports imports) {
return imports.stream(this).mapToInt(OWLAxiomCollection::getLogicalAxiomCount).sum();
}
@Override
public Stream annotations() {
return ints.getOntologyAnnotations().sorted();
}
@Override
public List annotationsAsList() {
return asList(annotations());
}
@Override
public Stream generalClassAxioms() {
return ints.getGeneralClassAxioms();
}
@Override
public boolean containsAxiom(OWLAxiom axiom, Imports imports,
AxiomAnnotations ignoreAnnotations) {
return imports.stream(this).anyMatch(o -> ignoreAnnotations.contains(o, axiom));
}
@Override
public Stream axiomsIgnoreAnnotations(OWLAxiom axiom) {
return axioms(axiom.getAxiomType()).map(x -> (OWLAxiom) x)
.filter(ax -> ax.equalsIgnoreAnnotations(axiom));
}
@Override
public boolean containsAxiomIgnoreAnnotations(OWLAxiom axiom) {
if (containsAxiom(axiom)) {
return true;
}
return axioms(axiom.getAxiomType()).anyMatch(ax -> ax.equalsIgnoreAnnotations(axiom));
}
@Override
public Stream axiomsIgnoreAnnotations(OWLAxiom axiom, Imports imports) {
return imports.stream(this).flatMap(o -> o.axiomsIgnoreAnnotations(axiom));
}
@Override
public boolean containsClassInSignature(IRI iri, Imports imports) {
return imports.stream(this).anyMatch(o -> o.containsClassInSignature(iri));
}
@Override
public boolean containsObjectPropertyInSignature(IRI iri, Imports imports) {
return imports.stream(this).anyMatch(o -> o.containsObjectPropertyInSignature(iri));
}
@Override
public boolean containsDataPropertyInSignature(IRI iri, Imports imports) {
return imports.stream(this).anyMatch(o -> o.containsDataPropertyInSignature(iri));
}
@Override
public boolean containsAnnotationPropertyInSignature(IRI iri, Imports imports) {
boolean result =
imports.stream(this).anyMatch(o -> o.containsAnnotationPropertyInSignature(iri));
if (result) {
return result;
}
return checkOntologyAnnotations(df.getOWLAnnotationProperty(iri));
}
private boolean checkOntologyAnnotations(OWLAnnotationProperty p) {
return ints.getOntologyAnnotations().anyMatch(ann -> ann.getProperty().equals(p));
}
@Override
public boolean containsIndividualInSignature(IRI iri, Imports imports) {
return imports.stream(this).anyMatch(o -> o.containsIndividualInSignature(iri));
}
@Override
public boolean containsDatatypeInSignature(IRI iri, Imports imports) {
return imports.stream(this).anyMatch(o -> o.containsDatatypeInSignature(iri));
}
@Override
public boolean containsEntitiesOfTypeInSignature(EntityType type) {
return ints.anyEntities(type);
}
@Override
public Stream entitiesInSignature(IRI iri) {
return unsortedSignature()
.filter((Predicate) c -> c.getIRI().equals(iri)).sorted();
}
@Override
public Stream unsortedSignature() {
return Stream
.of(ints.get(OWLClass.class, OWLAxiom.class).get().keySet(),
ints.get(OWLObjectProperty.class, OWLAxiom.class).get().keySet(),
ints.get(OWLDataProperty.class, OWLAxiom.class).get().keySet(),
ints.get(OWLNamedIndividual.class, OWLAxiom.class).get().keySet(),
ints.get(OWLDatatype.class, OWLAxiom.class).get().keySet(),
ints.get(OWLAnnotationProperty.class, OWLAxiom.class, Navigation.IN_SUB_POSITION)
.get().keySet(),
ints.getOntologyAnnotations().map(OWLAnnotation::getProperty))
.flatMap(Function.identity());
}
@Override
public Set getPunnedIRIs(Imports includeImportsClosure) {
Set punned = new HashSet<>();
Set test = new HashSet<>();
includeImportsClosure.stream(this).flatMap(HasSignature::unsortedSignature)
.forEach(e -> add(punned, test, e));
if (punned.isEmpty()) {
return Collections.emptySet();
}
return punned;
}
@Override
public boolean containsReference(OWLEntity entity, Imports includeImportsClosure) {
if (includeImportsClosure == EXCLUDED) {
return ints.containsReference(entity);
}
return importsClosure().anyMatch(o -> o.containsReference(entity, EXCLUDED));
}
@Override
public boolean isDeclared(OWLEntity owlEntity) {
return ints.isDeclared(owlEntity);
}
@Override
public boolean containsEntityInSignature(OWLEntity owlEntity) {
return ontsignatures.get(this).contains(owlEntity);
}
@Override
public Stream signature() {
return streamFromSorted(ontsignatures.get(this));
}
@Override
public Stream anonymousIndividuals() {
return streamFromSorted(ontanonCaches.get(this));
}
@Override
public Stream classesInSignature() {
return streamFromSorted(ontclassesSignatures.get(this));
}
@Override
public Stream dataPropertiesInSignature() {
return streamFromSorted(ontdataPropertySignatures.get(this));
}
@Override
public Stream objectPropertiesInSignature() {
return streamFromSorted(ontobjectPropertySignatures.get(this));
}
@Override
public Stream individualsInSignature() {
return streamFromSorted(ontindividualSignatures.get(this));
}
@Override
public Stream datatypesInSignature() {
return streamFromSorted(ontdatatypeSignatures.get(this));
}
@Override
public Stream referencedAnonymousIndividuals() {
return anonymousIndividuals();
}
@Override
public Stream annotationPropertiesInSignature() {
return streamFromSorted(ontannotationPropertiesSignatures.get(this));
}
@Override
public Stream importsDeclarations() {
return ints.getImportsDeclarations();
}
@Override
public Stream directImportsDocuments() {
return ints.getImportsDeclarations().map(OWLImportsDeclaration::getIRI);
}
@Override
public Stream imports() {
return getOWLOntologyManager().imports(this);
}
@Override
public Stream directImports() {
return getOWLOntologyManager().directImports(this);
}
@Override
public Stream importsClosure() {
return getOWLOntologyManager().importsClosure(this);
}
@Override
public Stream axioms(OWLClass cls) {
return ints.get(OWLClass.class, OWLClassAxiom.class).get().values(cls, OWLClassAxiom.class);
}
@Override
public Stream axioms(OWLObjectPropertyExpression property) {
return Stream.of(asymmetricObjectPropertyAxioms(property),
reflexiveObjectPropertyAxioms(property), symmetricObjectPropertyAxioms(property),
irreflexiveObjectPropertyAxioms(property), transitiveObjectPropertyAxioms(property),
inverseFunctionalObjectPropertyAxioms(property),
functionalObjectPropertyAxioms(property), inverseObjectPropertyAxioms(property),
objectPropertyDomainAxioms(property), equivalentObjectPropertiesAxioms(property),
disjointObjectPropertiesAxioms(property), objectPropertyRangeAxioms(property),
objectSubPropertyAxiomsForSubProperty(property)).flatMap(x -> x);
}
@Override
public Stream axioms(OWLDataProperty property) {
return Stream.of(dataPropertyDomainAxioms(property),
equivalentDataPropertiesAxioms(property), disjointDataPropertiesAxioms(property),
dataPropertyRangeAxioms(property), functionalDataPropertyAxioms(property),
dataSubPropertyAxiomsForSubProperty(property)).flatMap(x -> x);
}
@Override
public Stream axioms(OWLIndividual individual) {
return Stream.of(classAssertionAxioms(individual),
objectPropertyAssertionAxioms(individual), dataPropertyAssertionAxioms(individual),
negativeObjectPropertyAssertionAxioms(individual),
negativeDataPropertyAssertionAxioms(individual), sameIndividualAxioms(individual),
differentIndividualAxioms(individual)).flatMap(x -> x);
}
@Override
public Stream axioms(OWLDatatype datatype) {
return datatypeDefinitions(datatype);
}
@Override
public Stream referencingAxioms(OWLPrimitive owlEntity) {
if (owlEntity instanceof OWLEntity) {
return ints.getReferencingAxioms((OWLEntity) owlEntity);
} else if (owlEntity instanceof OWLAnonymousIndividual) {
return ints.get(OWLAnonymousIndividual.class, OWLAxiom.class).get()
.values((OWLAnonymousIndividual) owlEntity, OWLAxiom.class);
} else if (owlEntity.isIRI()) {
Set axioms = new HashSet<>();
String iriString = owlEntity.toString();
// axioms referring entities with this IRI, data property assertions
// with IRI as subject, annotations with IRI as subject or object.
entitiesInSignature((IRI) owlEntity)
.forEach(e -> OWLAPIStreamUtils.add(axioms, referencingAxioms(e)));
axioms(AxiomType.DATA_PROPERTY_ASSERTION)
.filter(ax -> OWL2Datatype.XSD_ANY_URI.matches(ax.getObject().getDatatype()))
.filter(ax -> ax.getObject().getLiteral().equals(iriString)).forEach(axioms::add);
axioms(AxiomType.ANNOTATION_ASSERTION)
.forEach(ax -> examineAssertion(owlEntity, axioms, ax));
return axioms.stream();
} else if (owlEntity instanceof OWLLiteral) {
Set axioms = new HashSet<>();
axioms(AxiomType.DATA_PROPERTY_ASSERTION).filter(ax -> ax.getObject().equals(owlEntity))
.forEach(axioms::add);
axioms(AxiomType.ANNOTATION_ASSERTION)
.filter(ax -> owlEntity.equals(ax.getValue().asLiteral().orElse(null)))
.forEach(axioms::add);
AxiomType.AXIOM_TYPES.stream().flatMap(this::axioms)
.filter(ax -> hasLiteralInAnnotations(owlEntity, ax)).forEach(axioms::add);
return axioms.stream();
}
return empty();
}
protected boolean hasLiteralInAnnotations(OWLPrimitive owlEntity, OWLAxiom ax) {
return ax.annotations().anyMatch(a -> a.getValue().equals(owlEntity));
}
protected void examineAssertion(OWLPrimitive owlEntity, Set axioms,
OWLAnnotationAssertionAxiom ax) {
if (ax.getSubject().equals(owlEntity)) {
axioms.add(ax);
} else {
ax.getValue().asLiteral().ifPresent(lit -> {
if (OWL2Datatype.XSD_ANY_URI.matches(lit.getDatatype())
&& lit.getLiteral().equals(owlEntity.toString())) {
axioms.add(ax);
}
});
}
}
// OWLAxiomIndex
@Override
@SuppressWarnings("unchecked")
public Stream axioms(Class type,
Class explicitClass, OWLObject entity, Navigation forSubPosition) {
Optional> optional =
ints.get((Class) explicitClass, type, forSubPosition);
if (optional.isPresent()) {
return optional.get().values(entity, type);
}
if (!(entity instanceof OWLEntity)) {
return empty();
}
return axioms(AxiomType.getTypeForClass(type))
.filter(a -> a.containsEntityInSignature((OWLEntity) entity));
}
@SuppressWarnings("unchecked")
@Override
public Stream axioms(OWLAxiomSearchFilter filter, Object key,
Imports imports) {
return imports.stream(this).flatMap(o -> (Stream) o.axioms(filter, key));
}
@SuppressWarnings("unchecked")
@Override
public Stream axioms(OWLAxiomSearchFilter filter, Object key) {
Collection c = (Collection) ints.filterAxioms(filter, key);
return c.stream();
}
@Override
public boolean contains(OWLAxiomSearchFilter filter, Object key) {
return ints.contains(filter, key);
}
@Override
public boolean contains(OWLAxiomSearchFilter filter, Object key, Imports imports) {
return imports.stream(this).anyMatch(o -> o.contains(filter, key));
}
@Override
public boolean containsDatatypeInSignature(IRI iri) {
return ints.containsDatatypeInSignature(iri);
}
@Override
public boolean containsClassInSignature(IRI iri) {
return ints.containsClassInSignature(iri);
}
@Override
public boolean containsObjectPropertyInSignature(IRI iri) {
return ints.containsObjectPropertyInSignature(iri);
}
@Override
public boolean containsDataPropertyInSignature(IRI iri) {
return ints.containsDataPropertyInSignature(iri);
}
@Override
public boolean containsAnnotationPropertyInSignature(IRI iri) {
return ints.containsAnnotationPropertyInSignature(iri);
}
@Override
public boolean containsIndividualInSignature(IRI iri) {
return ints.containsIndividualInSignature(iri);
}
@Override
public boolean containsReference(OWLEntity entity) {
return ints.containsReference(entity);
}
}
