org.coode.owlapi.obo12.parser.OWLOBO12Parser Maven / Gradle / Ivy

/*
 * 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

 * The University Of Manchester

 * Bio-Health Informatics Group

 * Date: 10-Jan-2007

 * 

 */
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 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();
    }
}