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/* 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 org.semanticweb.owlapi.util;
import static org.semanticweb.owlapi.util.OWLAPIPreconditions.checkNotNull;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Stream;
import org.semanticweb.owlapi.model.AddAxiom;
import org.semanticweb.owlapi.model.AddOntologyAnnotation;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotation;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyChange;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.RemoveAxiom;
import org.semanticweb.owlapi.model.RemoveOntologyAnnotation;
/**
* Renames entities that have a particular IRI. Entities with the specified IRI are renamed
* regardless of whether they are classes, object properties, data properties, individuals or data
* types.
*
* @author Matthew Horridge, The University Of Manchester, Bio-Health Informatics Group
* @since 2.0.0
*/
public class OWLEntityRenamer {
private final OWLOntologyManager m;
private final Collection ontologies;
/**
* @param owlOntologyManager the ontology manager to use
* @param ontologies the ontologies to use
*/
public OWLEntityRenamer(OWLOntologyManager owlOntologyManager,
Collection ontologies) {
m = owlOntologyManager;
this.ontologies = checkNotNull(ontologies, "ontologies cannot be null");
}
private static Stream getAxioms(OWLOntology ont, OWLEntity entity) {
return Stream.of(ont.referencingAxioms(entity), ont.declarationAxioms(entity),
ont.annotationAssertionAxioms(entity.getIRI())).flatMap(x -> x);
}
/**
* Fills a list with ontology changes which will replace a set of axioms with
* duplicated/transformed axioms.
*
* @param changes A list that will be filled with ontology changes which will remove the
* specified axioms from the specified ontology, and add the duplicated/transformed
* version
* @param axioms The axioms to be duplicated/transformed
* @param ont The ontology to which the changed should be applied
* @param duplicator The duplicator that will do the duplicating
*/
private static void fillListWithTransformChanges(List changes,
Stream axioms, OWLOntology ont, OWLObjectDuplicator duplicator) {
axioms.forEach(ax -> {
OWLAxiom dupAx = duplicator.duplicateObject(ax);
if (!dupAx.equals(ax)) {
changes.add(new RemoveAxiom(ont, ax));
changes.add(new AddAxiom(ont, dupAx));
}
});
fillListWithOntologyAnnotationTransformChanges(changes, ont, duplicator);
}
/**
* Fills a list with ontology annotaton changes which will replace ontology annotations.
*
* @param changes A list that will be filled with ontology changes which will remove the
* specified axioms from the specified ontology, and add the duplicated/transformed
* version
* @param ont The ontology to which the changed should be applied
* @param duplicator The duplicator that will do the duplicating
*/
private static void fillListWithOntologyAnnotationTransformChanges(
List changes, OWLOntology ont, OWLObjectDuplicator duplicator) {
ont.annotations().forEach(ax -> {
OWLAnnotation dupAx = duplicator.duplicateObject(ax);
if (!dupAx.equals(ax)) {
changes.add(new RemoveOntologyAnnotation(ont, ax));
changes.add(new AddOntologyAnnotation(ont, dupAx));
}
});
}
/**
* Changes a IRI for another IRI. This creates the appropriate changes to be applied in order to
* change a IRI.
*
* @param iri The IRI to be changed
* @param newIRI The IRI that the IRI should be changed to.
* @return A list of ontology changes that should be applied to change the specified IRI.
*/
public List changeIRI(IRI iri, IRI newIRI) {
checkNotNull(iri, "iri cannot be null");
checkNotNull(newIRI, "newIRI cannot be null");
Map uriMap = new HashMap<>();
uriMap.put(iri, newIRI);
List changes = new ArrayList<>();
OWLObjectDuplicator dup = new OWLObjectDuplicator(m, uriMap,
new RemappingIndividualProvider(false, m.getOWLDataFactory()));
ontologies
.forEach(o -> fillListWithTransformChanges(changes, o.referencingAxioms(iri), o, dup));
return changes;
}
/**
* Changes the IRI of an entity for another IRI.
*
* @param entity The entity whose IRI is to be changed.
* @param newIRI The new IRI
* @return A list of ontology changes that should be applied to change the specified entity IRI.
*/
public List changeIRI(OWLEntity entity, IRI newIRI) {
Map iriMap = new HashMap<>();
iriMap.put(entity, newIRI);
List changes = new ArrayList<>();
OWLObjectDuplicator duplicator = new OWLObjectDuplicator(iriMap, Collections.emptyMap(), m,
new RemappingIndividualProvider(false, m.getOWLDataFactory()));
ontologies.forEach(
o -> fillListWithTransformChanges(changes, getAxioms(o, entity), o, duplicator));
return changes;
}
/**
* @param entity2IRIMap map of IRIs to rename
* @return list of changes
*/
public List changeIRI(Map entity2IRIMap) {
List changes = new ArrayList<>();
OWLObjectDuplicator duplicator =
new OWLObjectDuplicator(entity2IRIMap, Collections.emptyMap(), m,
new RemappingIndividualProvider(false, m.getOWLDataFactory()));
for (OWLOntology ont : ontologies) {
entity2IRIMap.keySet().forEach(
e -> fillListWithTransformChanges(changes, getAxioms(ont, e), ont, duplicator));
}
return changes;
}
}
