owlapi-version5/compatibility/src/main/java/org/coode/owlapi/obo12/parser/OWLOBO12Parser.java
/*
 * 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 static org.semanticweb.owlapi.util.OWLAPIPreconditions.verifyNotNull;

import java.io.IOException;
import java.io.Reader;
import java.util.List;
import org.semanticweb.owlapi.io.AbstractOWLParser;
import org.semanticweb.owlapi.io.DocumentSources;
import org.semanticweb.owlapi.io.OWLOntologyDocumentSource;
import org.semanticweb.owlapi.io.OWLOntologyInputSourceException;
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 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, verifyNotNull(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 OWLDocumentFormat parse(OWLOntologyDocumentSource source, OWLOntology ontology,
        OWLOntologyLoaderConfiguration config) {
        RawFrameHandler rawFrameHandler = new RawFrameHandler();
        OBOConsumer oboConsumer = new OBOConsumer(ontology, config, source.getDocumentIRI());
        try (Reader r = DocumentSources.wrapInputAsReader(source, config)) {
            OBOParser parser = new OBOParser(new StreamProvider(r));
            parser.setHandler(rawFrameHandler);
            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();
                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 | OWLOntologyInputSourceException | IOException e) {
            throw new OWLParserException(e);
        }
        OBO12DocumentFormat format = new OBO12DocumentFormat();
        format.setIDSpaceManager(oboConsumer.getIdSpaceManager());
        return format;
    }

    @Override
    public OWLDocumentFormatFactory getSupportedFormat() {
        return new OBO12DocumentFormatFactory();
    }
}
