/*
* 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.io.IOException;
import java.io.InputStream;
import java.io.Reader;
import org.semanticweb.owlapi.io.AbstractOWLParser;
import org.semanticweb.owlapi.io.OWLOntologyDocumentSource;
import org.semanticweb.owlapi.io.OWLParserException;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException;
import org.semanticweb.owlapi.model.OWLOntologyChangeException;
import org.semanticweb.owlapi.model.OWLOntologyFormat;
import org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration;
import org.semanticweb.owlapi.model.UnloadableImportException;
/**
* Author: Matthew Horridge<br>
* The University Of Manchester<br>
* Bio-Health Informatics Group<br>
* Date: 10-Jan-2007<br><br>
*/
public class OWLOBOParser extends AbstractOWLParser {
public OWLOntologyFormat parse(OWLOntologyDocumentSource documentSource, OWLOntology ontology) throws OWLParserException, IOException, UnloadableImportException {
return parse(documentSource, ontology, new OWLOntologyLoaderConfiguration());
}
public OWLOntologyFormat parse(OWLOntologyDocumentSource documentSource, OWLOntology ontology, OWLOntologyLoaderConfiguration configuration) throws OWLParserException, IOException, OWLOntologyChangeException, UnloadableImportException {
OBOParser parser;
Reader reader = null;
InputStream is = null;
if (documentSource.isReaderAvailable()) {
// parser = new OBOParser(documentSource.getReader());
reader = documentSource.getReader();
parser = new OBOParser(reader);
}
else if (documentSource.isInputStreamAvailable()) {
//parser = new OBOParser(documentSource.getInputStream());
is = documentSource.getInputStream();
parser = new OBOParser(is);
}
else {
//parser = new OBOParser(getInputStream(documentSource.getDocumentIRI()));
is = getInputStream(documentSource.getDocumentIRI());
parser = new OBOParser(is);
}
parser.setHandler(new OBOConsumer(ontology, configuration));
try {
parser.parse();
}
catch (ParseException e) {
if(e.getCause()!=null && e.getCause() instanceof OWLOntologyChangeException) {
throw (OWLOntologyChangeException)e.getCause();
}
if(e.getCause()!=null && e.getCause() instanceof OWLOntologyAlreadyExistsException) {
OWLOntologyAlreadyExistsException ex=(OWLOntologyAlreadyExistsException)e.getCause();
throw new UnloadableImportException(ex, ontology.getOWLOntologyManager().getOWLDataFactory().getOWLImportsDeclaration(ex.getOntologyID().getOntologyIRI()));
}
Token currentToken = e.currentToken;
if (currentToken != null) {
int beginLine = currentToken.beginLine;
int beginColumn = currentToken.beginColumn;
throw new OWLParserException(e, beginLine, beginColumn);
}
else {
throw new OWLParserException(e);
}
}
catch(TokenMgrError e) {
throw new OWLParserException(e);
} finally {
if (is != null) {
is.close();
} else if (reader != null) {
reader.close();
}
}
return new OBOOntologyFormat();
}
}