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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 (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.obo12.parser;
import java.net.URI;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.logging.Logger;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.annotation.Nonnull;
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.OWLAnnotationValue;
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.OWLOntologyID;
import org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLRuntimeException;
import org.semanticweb.owlapi.model.SetOntologyID;
import org.semanticweb.owlapi.model.UnloadableImportException;
import org.semanticweb.owlapi.util.CollectionFactory;
import com.google.common.base.Optional;
/**
* Author: Matthew Horridge
* The University Of Manchester
* Bio-Health Informatics Group
* Date: 10-Jan-2007
*
*/
class OBOConsumer implements OBOParserHandler {
private static final Logger logger = Logger.getLogger(OBOConsumer.class
.getName());
private static final String IMPORT_TAG_NAME = "import";
@Nonnull
private OWLOntologyLoaderConfiguration configuration;
private OWLOntologyManager owlOntologyManager;
@Nonnull
private OWLOntology ontology;
private boolean inHeader;
private String currentId;
private Map handlerMap;
// private String defaultNamespace;
private String defaultNamespaceTagValue = OBOVocabulary.OBO_IRI_BASE;
private String stanzaType;
private boolean termType;
private boolean typedefType;
private boolean instanceType;
@Nonnull
private Set intersectionOfOperands;
@Nonnull
private final Set unionOfOperands = new HashSet<>();
private Map uriCache = new HashMap<>();
private Map symbolicIdCache = new HashMap<>();
private Map tagIRICache = new HashMap<>();
private IDSpaceManager idSpaceManager = new IDSpaceManager();
private String ontologyTagValue = "";
private String dataVersionTagValue = "";
public OBOConsumer(@Nonnull OWLOntology ontology,
@Nonnull OWLOntologyLoaderConfiguration configuration, IRI baseIRI) {
this.configuration = configuration;
owlOntologyManager = ontology.getOWLOntologyManager();
this.ontology = ontology;
intersectionOfOperands = new HashSet<>();
uriCache = new HashMap<>();
for (OBOVocabulary v : OBOVocabulary.values()) {
tagIRICache.put(v.getName(), v.getIRI());
}
ontologyTagValue = getDefaultOntologyTagValue(baseIRI);
loadBuiltinURIs();
setupTagHandlers();
}
private static String getDefaultOntologyTagValue(IRI baseIRI) {
URI baseURI = baseIRI.toURI();
String baseURIPath = baseURI.getPath();
if (baseURIPath == null) {
return baseIRI.toString();
}
int lastSlashIndex = baseURIPath.lastIndexOf("/");
if (lastSlashIndex == -1 || lastSlashIndex + 1 == baseURIPath.length()) {
return baseURIPath;
}
return baseURIPath.substring(lastSlashIndex + 1);
}
public OWLOntologyManager getOWLOntologyManager() {
return owlOntologyManager;
}
@Nonnull
public OWLOntology getOntology() {
return ontology;
}
public String getCurrentId() {
return currentId;
}
public void addSymbolicIdMapping(String symbolicName, IRI fullIRI) {
symbolicIdCache.put(symbolicName, fullIRI);
}
/**
* Sets the value of the default-namespace tag for the current ontology
* being parsed.
*
* @param defaultNamespaceTagValue
* The value of the default-namespace tag.
*/
public void setDefaultNamespaceTagValue(String defaultNamespaceTagValue) {
this.defaultNamespaceTagValue = defaultNamespaceTagValue;
}
/**
* Gets the default-namespace tag value for the current ontology. If not
* default-namespace tag value has been set explicitly then this method
* returns the default value which is equal to
* {@link OBOVocabulary#OBO_IRI_BASE}.
*
* @return The default-namespace tag value. Not null.
*/
public String getDefaultNamespaceTagValue() {
return defaultNamespaceTagValue;
}
/**
* Sets the value of the ontology tag for the current ontology that is being
* parsed. This is used to construct an
* {@link org.semanticweb.owlapi.model.OWLOntologyID} for the current
* ontology once the ontology header has been parsed in its entirety.
*
* @param ontologyTagValue
* The ontology tag value. Ultimately, this will be translated to an
* IRI.
*/
public void setOntologyTagValue(String ontologyTagValue) {
this.ontologyTagValue = ontologyTagValue;
}
/**
* Sets the value of the data-version tag for the current ontology that is
* being parsed. This is used to construct an
* {@link org.semanticweb.owlapi.model.OWLOntologyID} for the current
* ontology once the ontology header has been parsed in its entirety.
*
* @param dataVersionTagValue
* The data-version tag value. Ultimately, this will be translated to
* an IRI.
*/
public void setDataVersionTagValue(String dataVersionTagValue) {
this.dataVersionTagValue = dataVersionTagValue;
}
public void registerIdSpace(String idSpacePrefix, String iriPrefix) {
idSpaceManager.setIRIPrefix(idSpacePrefix, iriPrefix);
}
/**
* Gets a COPY of the {@link IDSpaceManager} held by this OBOConsumer.
*
* @return A copy of the IDSpaceManager held by this consumer.
*/
public IDSpaceManager getIdSpaceManager() {
return idSpaceManager;
}
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<>();
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));
addTagHandler(new XRefTagHandler(this));
addTagHandler(new DefTagValueHandler(this));
addTagHandler(new IsObsoleteTagValueHandler(this));
addTagHandler(new IDSpaceTagValueHandler(this));
addTagHandler(new DataVersionTagValueHandler(this));
addTagHandler(new SynonymTypeDefTagHandler(this));
addTagHandler(new AltIdTagValueHandler(this));
}
private void addTagHandler(TagValueHandler handler) {
handlerMap.put(handler.getTagName(), handler);
}
@Override
public void startHeader() {
inHeader = true;
}
@Override
public void endHeader() {
inHeader = false;
setOntologyId();
}
/**
* Sets the {@link org.semanticweb.owlapi.model.OWLOntologyID} of the
* ontology being parsed from the tag values held by the
* {@link #ontologyTagValue} and {@link #dataVersionTagValue} field. IRIs
* for each field are generated and used to construct the
* {@link org.semanticweb.owlapi.model.OWLOntologyID}.
*/
private void setOntologyId() {
IRI ontologyIRI = IRI.create(idSpaceManager
.getIRIPrefix(ontologyTagValue) + ontologyTagValue);
IRI versionIRI = null;
if (dataVersionTagValue.length() > 0) {
versionIRI = IRI.create(ontologyIRI.toString() + "/"
+ dataVersionTagValue);
}
@SuppressWarnings("null")
OWLOntologyID ontologyID = new OWLOntologyID(
Optional.fromNullable(ontologyIRI),
Optional.fromNullable(versionIRI));
ontology.getOWLOntologyManager().applyChange(
new SetOntologyID(ontology, ontologyID));
}
@Override
public void startFrame(String name) {
currentId = null;
defaultNamespaceTagValue = 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());
}
}
}
@Override
public void endFrame() {
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));
}
@Override
public void handleTagValue(String tag, String value, String qualifierBlock,
String comment) {
try {
TagValueHandler handler = handlerMap.get(tag);
if (handler != null) {
handler.handle(currentId, value, qualifierBlock, comment);
} else if (inHeader) {
if (tag.equals(IMPORT_TAG_NAME)) {
String trim = value.trim();
assert trim != null;
IRI uri = IRI.create(trim);
OWLImportsDeclaration decl = owlOntologyManager
.getOWLDataFactory().getOWLImportsDeclaration(uri);
owlOntologyManager.makeLoadImportRequest(decl,
configuration);
owlOntologyManager
.applyChange(new AddImport(ontology, decl));
} else {
// Ontology annotations
OWLLiteral con = getDataFactory().getOWLLiteral(
unescapeTagValue(value));
OWLAnnotationProperty property = getDataFactory()
.getOWLAnnotationProperty(getIRIFromTagName(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(
unescapeTagValue(value));
IRI annotationPropertyIRI = getIRIFromTagName(tag);
OWLAnnotationProperty property = getDataFactory()
.getOWLAnnotationProperty(annotationPropertyIRI);
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());
}
}
@SuppressWarnings("null")
@Nonnull
public String unescapeTagValue(String value) {
String unquoted;
if (value.startsWith("\"") && value.endsWith("\"")) {
unquoted = value.substring(1, value.length() - 1);
} else {
unquoted = value;
}
StringBuilder sb = new StringBuilder();
for (int i = 0; i < unquoted.length(); i++) {
char ch = unquoted.charAt(i);
if (ch != '\\') {
sb.append(ch);
}
}
return sb.toString();
}
private OWLDataFactory getDataFactory() {
return getOWLOntologyManager().getOWLDataFactory();
}
public OWLClass getCurrentClass() {
return getDataFactory().getOWLClass(getIRI(currentId));
}
public OWLEntity getCurrentEntity() {
if (isTerm()) {
return getCurrentClass();
} else if (isTypedef()) {
// Sometimes, we can have symbolic names e.g. has_part. It's not
// really clear how to tell the difference
IRI propertyIRI = getRelationIRIFromSymbolicIdOrOBOId(currentId);
return getDataFactory().getOWLObjectProperty(propertyIRI);
} else {
return getDataFactory().getOWLNamedIndividual(getIRI(currentId));
}
}
/**
* Gets an IRI from a tag name.
*
* @param tagName
* The tag name.
* @return The IRI for the tag name. For built in tags this is obtained from
* the {@link OBOVocabulary} enum. Not null.
* @throws NullPointerException
* if tagName is null.
*/
@Nonnull
public IRI getIRIFromTagName(String tagName) {
if (tagName == null) {
throw new NullPointerException("tagName must not be null");
}
IRI tagIRI = tagIRICache.get(tagName);
if (tagIRI != null) {
return tagIRI;
} else {
IRI freshTagIRI = IRI.create(OBOVocabulary.OBO_IRI_BASE + tagName);
tagIRICache.put(tagName, freshTagIRI);
return freshTagIRI;
}
}
/**
* Gets an IRI from an OBO ID. The OBO ID may be a canonical OBO ID of the
* form idspace:sequence or it may be a non-canonical ID.
*
* @param oboId
* The OBO ID
* @return An IRI obtained from the translation of the OBO ID.
*/
@Nonnull
public IRI getIRIFromOBOId(String oboId) {
if (oboId == null) {
throw new NullPointerException("oboId must not be null.");
}
return getIRI(oboId);
}
@Nonnull
public IRI getRelationIRIFromSymbolicIdOrOBOId(String symbolicIdOrOBOId) {
IRI fullIRI = symbolicIdCache.get(symbolicIdOrOBOId);
if (fullIRI != null) {
return fullIRI;
}
OBOIdType idType = OBOIdType.getIdType(symbolicIdOrOBOId);
if (idType == null) {
throw new OWLRuntimeException("Invalid ID: " + symbolicIdOrOBOId
+ " in frame " + currentId);
} else {
return idType.getIRIFromOBOId(ontology.getOntologyID(),
idSpaceManager, symbolicIdOrOBOId);
}
}
@Nonnull
private IRI getIRI(String s) {
String trimmed = s.trim();
IRI iri = uriCache.get(trimmed);
if (iri != null) {
return iri;
}
OWLOntologyID ontologyID = getOntology().getOntologyID();
OBOIdType type = OBOIdType.getIdType(trimmed);
if (type == null) {
throw new OWLRuntimeException("Not a valid OBO ID: " + s);
}
IRI freshIRI = type
.getIRIFromOBOId(ontologyID, idSpaceManager, trimmed);
uriCache.put(trimmed, freshIRI);
return freshIRI;
}
private static final Pattern XREF_PATTERN = Pattern
.compile("([^\"]*)\\s*(\"((\\\"|[^\"])*)\")?");
private static final int XREF_ID_GROUP = 1;
private static final int XREF_QUOTED_STRING_GROUP = 3;
public OWLAnnotation parseXRef(@Nonnull String xref) {
Matcher matcher = XREF_PATTERN.matcher(xref);
if (matcher.matches()) {
OWLDataFactory df = getDataFactory();
String xrefQuotedString = matcher.group(XREF_QUOTED_STRING_GROUP);
// the quoted string is a description of the xref. I can't find
// anywhere to put this.
// Just add as a comment for now
@Nonnull
Set xrefDescriptions = new HashSet<>();
if (xrefQuotedString != null) {
xrefDescriptions.add(df.getOWLAnnotation(df.getRDFSComment(),
df.getOWLLiteral(xrefQuotedString)));
}
String xrefId = matcher.group(XREF_ID_GROUP).trim();
assert xrefId != null;
OBOIdType idType = OBOIdType.getIdType(xrefId);
OWLAnnotationValue annotationValue;
if (idType != null) {
annotationValue = getIRIFromOBOId(xrefId);
} else {
annotationValue = getDataFactory().getOWLLiteral(xrefId);
}
OWLAnnotationProperty xrefProperty = df
.getOWLAnnotationProperty(OBOVocabulary.XREF.getIRI());
return df.getOWLAnnotation(xrefProperty, annotationValue,
xrefDescriptions);
} else {
OWLDataFactory df = getDataFactory();
OWLAnnotationProperty xrefProperty = df
.getOWLAnnotationProperty(OBOVocabulary.XREF.getIRI());
return df.getOWLAnnotation(xrefProperty, df.getOWLLiteral(xref));
}
}
}
