/*
* 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.io.IOException;
import java.io.InputStream;
import java.io.Reader;
import java.util.List;
import org.semanticweb.owlapi.io.AbstractOWLParser;
import org.semanticweb.owlapi.io.OWLOntologyDocumentSource;
import org.semanticweb.owlapi.io.OWLParserException;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLDocumentFormat;
import org.semanticweb.owlapi.model.OWLDocumentFormatFactory;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException;
import org.semanticweb.owlapi.model.OWLOntologyChangeException;
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>
*/
class OWLOBO12Parser extends AbstractOWLParser {
private static final long serialVersionUID = 40000L;
@SuppressWarnings("resource")
@Override
public OWLDocumentFormat parse(OWLOntologyDocumentSource documentSource,
OWLOntology ontology, OWLOntologyLoaderConfiguration configuration)
throws OWLParserException, IOException, OWLOntologyChangeException,
UnloadableImportException {
OBOParser parser;
Reader reader = null;
InputStream is = null;
if (documentSource.isReaderAvailable()) {
reader = documentSource.getReader();
parser = new OBOParser(reader);
} else if (documentSource.isInputStreamAvailable()) {
is = documentSource.getInputStream();
parser = new OBOParser(is);
} else {
is = getInputStream(documentSource.getDocumentIRI(), configuration);
parser = new OBOParser(is);
}
RawFrameHandler rawFrameHandler = new RawFrameHandler();
OBOConsumer oboConsumer = new OBOConsumer(ontology, configuration,
documentSource.getDocumentIRI());
parser.setHandler(rawFrameHandler);
try {
parser.parse();
parseFrames(rawFrameHandler, oboConsumer);
} 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();
IRI importedOntologyIRI = ex.getOntologyID().getOntologyIRI()
.get();
assert importedOntologyIRI != null;
throw new UnloadableImportException(ex, ontology
.getOWLOntologyManager().getOWLDataFactory()
.getOWLImportsDeclaration(importedOntologyIRI));
}
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();
}
}
OBO12DocumentFormat format = new OBO12DocumentFormat();
format.setIDSpaceManager(oboConsumer.getIdSpaceManager());
return format;
}
private static void parseFrames(RawFrameHandler rawFrameHandler,
OBOConsumer oboConsumer) {
parseHeaderFrame(rawFrameHandler, oboConsumer);
parseFrames(oboConsumer, rawFrameHandler.getTypeDefFrames());
parseFrames(oboConsumer, rawFrameHandler.getNonTypeDefFrames());
}
private static void parseHeaderFrame(RawFrameHandler rawFrameHandler,
OBOConsumer consumer) {
consumer.startHeader();
parseFrameTagValuePairs(consumer, rawFrameHandler.getHeaderFrame());
consumer.endHeader();
}
private static void parseFrames(OBOConsumer oboConsumer,
List<OBOFrame> frames) {
for (OBOFrame frame : frames) {
parseFrame(oboConsumer, frame);
}
}
private static void parseFrame(OBOConsumer oboConsumer, OBOFrame frame) {
oboConsumer.startFrame(frame.getFrameType());
parseFrameTagValuePairs(oboConsumer, frame);
oboConsumer.endFrame();
}
private static void parseFrameTagValuePairs(OBOConsumer oboConsumer,
OBOFrame frame) {
for (OBOTagValuePair tagValuePair : frame.getTagValuePairs()) {
oboConsumer.handleTagValue(tagValuePair.getTagName(),
tagValuePair.getValue(), tagValuePair.getQualifier(),
tagValuePair.getComment());
}
}
@Override
public OWLDocumentFormatFactory getSupportedFormat() {
return new OBO12DocumentFormatFactory();
}
}