com.b2international.snowowl.snomed.reasoner.server.ontology.SnomedOntologyService.java Source code

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Here is the source code for com.b2international.snowowl.snomed.reasoner.server.ontology.SnomedOntologyService.java

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/*
 * Copyright 2011-2015 B2i Healthcare Pte Ltd, http://b2i.sg
 * 
 * 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 com.b2international.snowowl.snomed.reasoner.server.ontology;

import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.text.MessageFormat;
import java.util.List;
import java.util.concurrent.atomic.AtomicLong;

import org.protege.owlapi.concurrent.SynchronizedOWLDataFactoryImpl;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyChange;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyFormat;
import org.semanticweb.owlapi.model.OWLOntologyID;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import com.b2international.snowowl.core.api.IBranchPath;
import com.b2international.snowowl.snomed.reasoner.exceptions.OntologyException;
import com.b2international.snowowl.snomed.reasoner.model.SnomedOntologyUtils;
import com.b2international.snowowl.snomed.reasoner.net4j.SnomedOntologyExportType;
import com.google.common.base.Stopwatch;
import com.google.common.io.Closeables;

/**
 * Provides a common entry point for creating {@link OWLOntology OWLOntologies} containing the OWL representation of an entire branch.
 *
 */
public class SnomedOntologyService {

    private static final Logger LOGGER = LoggerFactory.getLogger(SnomedOntologyService.class);

    private final AtomicLong uniqueSuffix = new AtomicLong();

    private final OWLOntologyManager manager;

    public SnomedOntologyService() {
        manager = OWLManager.createOWLOntologyManager(SynchronizedOWLDataFactoryImpl.getInstance());
        manager.addOntologyFactory(new DelegateOntologyFactory());
    }

    private IRI getOntologyIRI(final IBranchPath branchPath) {
        return SnomedOntologyUtils.BASE_IRI.resolve(branchPath.getPath());
    }

    /**
     * 
     * @param branchPath
     * @return
     */
    public OWLOntology getOntologyIfExists(final IBranchPath branchPath) {
        return manager.getOntology(new OWLOntologyID(getOntologyIRI(branchPath)));
    }

    /**
     * 
     * @param branchPath
     * @return
     * @throws IOException
     * @throws OWLOntologyCreationException
     */
    public OWLOntology createOntology(final IBranchPath branchPath)
            throws IOException, OWLOntologyCreationException {
        return createOntology(branchPath, false);
    }

    public OWLOntology createOntology(final IBranchPath branchPath, final boolean shared)
            throws OWLOntologyCreationException {
        final IRI ontologyIRI = getOntologyIRI(branchPath);
        final IRI versionIRI = shared ? null
                : ontologyIRI.resolve("#" + System.currentTimeMillis() + "_" + uniqueSuffix.getAndIncrement());
        return createOntology(ontologyIRI, versionIRI);
    }

    private OWLOntology createOntology(final IRI ontologyIRI, final IRI versionIRI)
            throws OWLOntologyCreationException {
        final Stopwatch stopwatch = Stopwatch.createStarted();
        LOGGER.info(MessageFormat.format(">>> Creating ontology ''{0}''", ontologyIRI));

        OWLOntology ontology = null;
        final OWLOntologyID ontologyID = new OWLOntologyID(ontologyIRI, versionIRI);
        ontology = manager.getOntology(ontologyID);

        if (null != ontology) {
            LOGGER.info(MessageFormat.format("<<< Creating ontology ''{0}'' [cached] [{1}]", ontologyIRI,
                    stopwatch.toString()));
            return ontology;
        }

        ontology = manager.createOntology(ontologyID);

        LOGGER.info(MessageFormat.format("<<< Creating ontology ''{0}'' [built] [{1}]", ontologyIRI,
                stopwatch.toString()));
        return ontology;
    }

    /**
     * 
     * @param ontology
     */
    public void removeOntology(final OWLOntology ontology) {
        final OWLOntologyID ontologyID = ontology.getOntologyID();
        LOGGER.info(MessageFormat.format("Unloading ontology ''{0}''.", ontologyID));

        if (ontology instanceof DelegateOntology) {
            ((DelegateOntology) ontology).dispose();
        } else {
            manager.removeOntology(ontology);
        }
    }

    /**
     * 
     * @param ontology
     * @param exportType
     * @param outputFile
     * @throws IOException 
     */
    public void saveOntology(final OWLOntology ontology, final SnomedOntologyExportType exportType,
            final File outputFile) throws IOException {
        OutputStream outputStream = null;

        try {
            final OWLOntologyFormat ontologyFormat = exportType.getFormat();
            if (ontologyFormat.isPrefixOWLOntologyFormat()) {
                ontologyFormat.asPrefixOWLOntologyFormat()
                        .copyPrefixesFrom(SnomedOntologyUtils.createPrefixManager(ontology));
            }

            outputStream = new FileOutputStream(outputFile);
            outputStream = new BufferedOutputStream(outputStream);
            manager.saveOntology(ontology, ontologyFormat, outputStream);
        } catch (final IOException e) {
            throw new OntologyException(e);
        } catch (final OWLOntologyStorageException e) {
            throw new OntologyException(e);
        } finally {
            Closeables.close(outputStream, true);
        }
    }

    /**
     * 
     * @param branchPath
     * @param changes 
     */
    public void applyChanges(final OWLOntology ontology, final List<OWLOntologyChange> changes) {
        // Don't apply if the ontology was already removed from the manager
        if (!manager.contains(ontology.getOntologyID())) {
            return;
        }

        manager.applyChanges(changes);
    }
}