ubic.gemma.apps.OwlOntologyLoadCli.java Source code

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Here is the source code for ubic.gemma.apps.OwlOntologyLoadCli.java

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/*
 * The Gemma project
 * 
 * Copyright (c) 2007 Columbia University
 * 
 * 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 ubic.gemma.apps;

import java.io.File;
import java.io.IOException;

import org.apache.commons.cli.OptionBuilder;

import ubic.basecode.ontology.OntologyLoader;
import ubic.gemma.util.AbstractCLI;

/**
 * Load an Ontology into the persistent store. Simple tool to initialize OWL ontologies locally.
 * 
 * @author Paul
 * @version $Id: OwlOntologyLoadCli.java,v 1.7 2009/12/20 07:50:08 paul Exp $
 */
public class OwlOntologyLoadCli extends AbstractCLI {

    public static void main(String[] args) {
        OwlOntologyLoadCli p = new OwlOntologyLoadCli();
        Exception e = p.doWork(args);
        if (e != null)
            log.error(e, e);
    }

    private String url;
    private File file;
    private boolean force;

    @Override
    public String getShortDesc() {
        return "Load an Ontology into the persistent store";
    }

    /*
     * (non-Javadoc)
     * @see ubic.gemma.util.AbstractCLI#buildOptions()
     */
    @SuppressWarnings("static-access")
    @Override
    protected void buildOptions() {
        addOption(OptionBuilder.isRequired().hasArg().withArgName("url")
                .withDescription("Base URL for the OWL file").withLongOpt("url").create("o"));

        addOption(OptionBuilder.withDescription("Force reloading of Ontology in Database").withLongOpt("force")
                .create("f"));

        addOption(OptionBuilder.withDescription("Load from file").withLongOpt("file").create("l"));

    }

    /*
     * (non-Javadoc)
     * @see ubic.gemma.util.AbstractCLI#doWork(java.lang.String[])
     */
    @Override
    protected Exception doWork(String[] args) {
        Exception exception = processCommandLine("Load OWL ontology", args);

        if (exception != null)
            return exception;

        try {
            if (file != null) {
                OntologyLoader.loadFromFile(file, url);
            } else {
                OntologyLoader.loadPersistentModel(url, force);
            }

            // log.info( "Loaded " + values.size() + " terms" );

            // if ( log.isDebugEnabled() ) {
            // for ( OntologyResource term : values ) {
            // log.debug( term );
            //
            // if ( !( term instanceof OntologyTerm ) ) continue;
            //
            // Collection<OntologyTerm> superClasses = ( ( OntologyTerm ) term ).getParents( true );
            // for ( OntologyTerm o : superClasses ) {
            // log.debug( " isa: " + o );
            // }
            //
            // Collection<AnnotationProperty> annotations = ( ( OntologyTerm ) term ).getAnnotations();
            //
            // for ( AnnotationProperty o : annotations ) {
            // log.debug( " Annot: " + o );
            // }
            //
            // }
            // }
        } catch (IOException e) {
            return e;
        }

        return null;
    }

    /*
     * (non-Javadoc)
     * @see ubic.gemma.util.AbstractCLI#processOptions()
     */
    @Override
    protected void processOptions() {
        this.url = this.getOptionValue('o');
        this.force = this.hasOption('f');

        if (this.getOptionValue('l') != null)
            this.file = new File(this.getOptionValue('l'));
    }

}