/*
* This file is part of the OWL API.
*
* The contents of this file are subject to the LGPL License, Version 3.0.
*
* Copyright (C) 2011, 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.
*
* Copyright 2011, University of Manchester
*
* 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.coode.owlapi.obo.parser;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.logging.Logger;
import org.semanticweb.owlapi.model.AddAxiom;
import org.semanticweb.owlapi.model.AddImport;
import org.semanticweb.owlapi.model.AddOntologyAnnotation;
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.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLDeclarationAxiom;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLImportsDeclaration;
import org.semanticweb.owlapi.model.OWLLiteral;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.UnloadableImportException;
import org.semanticweb.owlapi.util.CollectionFactory;
/**
* Author: Matthew Horridge<br>
* The University Of Manchester<br>
* Bio-Health Informatics Group<br>
* Date: 10-Jan-2007<br><br>
*/
public class OBOConsumer implements OBOParserHandler {
private static final Logger logger = Logger.getLogger(OBOConsumer.class.getName());
private static final String IMPORT_TAG_NAME = "import";
private OWLOntologyLoaderConfiguration configuration;
private OWLOntologyManager owlOntologyManager;
private OWLOntology ontology;
private boolean inHeader;
private String currentId;
private Map<String, TagValueHandler> handlerMap;
private String defaultNamespace;
private String currentNamespace;
private String stanzaType;
private boolean termType;
private boolean typedefType;
private boolean instanceType;
private Set<OWLClassExpression> intersectionOfOperands;
private Set<OWLClassExpression> unionOfOperands;
private Map<String, IRI> uriCache;
@SuppressWarnings("deprecation")
public OBOConsumer(OWLOntology ontology, OWLOntologyLoaderConfiguration configuration) {
this.configuration = configuration;
this.owlOntologyManager = ontology.getOWLOntologyManager();
this.ontology = ontology;
defaultNamespace = OBOVocabulary.ONTOLOGY_URI_BASE;
intersectionOfOperands = new HashSet<OWLClassExpression>();
unionOfOperands = new HashSet<OWLClassExpression>();
uriCache = new HashMap<String, IRI>();
loadBuiltinURIs();
setupTagHandlers();
}
public OBOConsumer(OWLOntologyManager owlOntologyManager, OWLOntology ontology, OWLOntologyLoaderConfiguration configuration) {
this(ontology, configuration);
}
public OWLOntologyManager getOWLOntologyManager() {
return owlOntologyManager;
}
public OWLOntology getOntology() {
return ontology;
}
public String getCurrentId() {
return currentId;
}
public String getDefaultNamespace() {
return defaultNamespace;
}
public void setDefaultNamespace(String defaultNamespace) {
this.defaultNamespace = defaultNamespace;
}
public String getCurrentNamespace() {
return currentNamespace;
}
public void setCurrentNamespace(String currentNamespace) {
this.currentNamespace = currentNamespace;
}
public void setCurrentId(String currentId) {
this.currentId = currentId;
}
public void addUnionOfOperand(OWLClassExpression classExpression) {
unionOfOperands.add(classExpression);
}
public void addIntersectionOfOperand(OWLClassExpression classExpression) {
intersectionOfOperands.add(classExpression);
}
public String getStanzaType() {
return stanzaType;
}
public boolean isTerm() {
return termType;
}
public boolean isTypedef() {
return typedefType;
}
public boolean isInstanceType() {
return instanceType;
}
private void loadBuiltinURIs() {
for (OBOVocabulary v : OBOVocabulary.values()) {
uriCache.put(v.getName(), v.getIRI());
}
}
private void setupTagHandlers() {
handlerMap = new HashMap<String, TagValueHandler>();
addTagHandler(new OntologyTagValueHandler(this));
addTagHandler(new IDTagValueHandler(this));
addTagHandler(new NameTagValueHandler(this));
addTagHandler(new IsATagValueHandler(this));
addTagHandler(new PartOfTagValueHandler(this));
addTagHandler(new TransitiveTagValueHandler(this));
addTagHandler(new SymmetricTagValueHandler(this));
addTagHandler(new RelationshipTagValueHandler(this));
addTagHandler(new UnionOfHandler(this));
addTagHandler(new IntersectionOfHandler(this));
addTagHandler(new DisjointFromHandler(this));
addTagHandler(new AsymmetricHandler(this));
addTagHandler(new InverseHandler(this));
addTagHandler(new ReflexiveHandler(this));
addTagHandler(new TransitiveOverHandler(this));
addTagHandler(new DefaultNamespaceTagValueHandler(this));
addTagHandler(new SynonymTagValueHandler(this));
}
private void addTagHandler(TagValueHandler handler) {
handlerMap.put(handler.getTag(), handler);
}
public void startHeader() {
inHeader = true;
}
public void endHeader() {
inHeader = false;
}
public void startStanza(String name) {
currentId = null;
currentNamespace = null;
stanzaType = name;
termType = stanzaType.equals(OBOVocabulary.TERM.getName());
typedefType = false;
instanceType = false;
if (!termType) {
typedefType = stanzaType.equals(OBOVocabulary.TYPEDEF.getName());
if (!typedefType) {
instanceType = stanzaType.equals(OBOVocabulary.INSTANCE.getName());
}
}
}
public void endStanza() {
if (!unionOfOperands.isEmpty()) {
createUnionEquivalentClass();
unionOfOperands.clear();
}
if (!intersectionOfOperands.isEmpty()) {
createIntersectionEquivalentClass();
intersectionOfOperands.clear();
}
}
private void createUnionEquivalentClass() {
OWLClassExpression equivalentClass;
if (unionOfOperands.size() == 1) {
equivalentClass = unionOfOperands.iterator().next();
}
else {
equivalentClass = getDataFactory().getOWLObjectUnionOf(unionOfOperands);
}
createEquivalentClass(equivalentClass);
}
private void createIntersectionEquivalentClass() {
OWLClassExpression equivalentClass;
if (intersectionOfOperands.size() == 1) {
equivalentClass = intersectionOfOperands.iterator().next();
}
else {
equivalentClass = getDataFactory().getOWLObjectIntersectionOf(intersectionOfOperands);
}
createEquivalentClass(equivalentClass);
}
private void createEquivalentClass(OWLClassExpression classExpression) {
OWLAxiom ax = getDataFactory().getOWLEquivalentClassesAxiom(CollectionFactory.createSet(getCurrentClass(), classExpression));
getOWLOntologyManager().applyChange(new AddAxiom(ontology, ax));
}
public void handleTagValue(String tag, String value, String comment) {
try {
TagValueHandler handler = handlerMap.get(tag);
if (handler != null) {
handler.handle(currentId, value, comment);
}
else if (inHeader) {
if (tag.equals(IMPORT_TAG_NAME)) {
IRI uri = IRI.create(value.trim());
OWLImportsDeclaration decl = owlOntologyManager.getOWLDataFactory().getOWLImportsDeclaration(uri);
owlOntologyManager.makeLoadImportRequest(decl, configuration);
owlOntologyManager.applyChange(new AddImport(ontology, decl));
}
else {
// Ontology annotations
OWLLiteral con = getDataFactory().getOWLLiteral(value);
OWLAnnotationProperty property = getDataFactory().getOWLAnnotationProperty(getIRI(tag));
OWLAnnotation anno = getDataFactory().getOWLAnnotation(property, con);
owlOntologyManager.applyChange(new AddOntologyAnnotation(ontology, anno));
}
}
else if (currentId != null) {
// Add as annotation
if (configuration.isLoadAnnotationAxioms()) {
IRI subject = getIRI(currentId);
OWLLiteral con = getDataFactory().getOWLLiteral(value, "");
OWLAnnotationProperty property = getDataFactory().getOWLAnnotationProperty(getIRI(tag));
OWLAnnotation anno = getDataFactory().getOWLAnnotation(property, con);
OWLAnnotationAssertionAxiom ax = getDataFactory().getOWLAnnotationAssertionAxiom(subject, anno);
owlOntologyManager.addAxiom(ontology, ax);
OWLDeclarationAxiom annotationPropertyDeclaration = getDataFactory().getOWLDeclarationAxiom(property);
owlOntologyManager.addAxiom(ontology, annotationPropertyDeclaration);
}
}
}
catch (UnloadableImportException e) {
logger.severe(e.getMessage());
}
}
private OWLDataFactory getDataFactory() {
return getOWLOntologyManager().getOWLDataFactory();
}
public OWLClass getCurrentClass() {
return getDataFactory().getOWLClass(getIRI(currentId));
}
public OWLEntity getCurrentEntity() {
if (isTerm()) {
return getCurrentClass();
}
else if (isTypedef()) {
return getDataFactory().getOWLObjectProperty(getIRI(currentId));
}
else {
return getDataFactory().getOWLNamedIndividual(getIRI(currentId));
}
}
public IRI getTagIRI(String tagName) {
return getIRI(tagName);
}
public IRI getIdIRI(String identifier) {
if(identifier == null) {
Thread.dumpStack();
}
if(identifier.indexOf(":") != -1) {
return getIRI(identifier);
}
else {
StringBuilder sb = new StringBuilder();
sb.append(defaultNamespace);
sb.append(":");
sb.append(identifier);
return getIRI(sb.toString());
}
}
private IRI getIRI(String s) {
IRI iri = uriCache.get(s);
if (iri != null) {
return iri;
}
String escapedString = s.replace(" ", "%20");
iri = OBOVocabulary.ID2IRI(escapedString);
uriCache.put(s, iri);
return iri;
}
}