ubic.gemma.apps.PubMedLoaderCli.java Source code

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

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/*
 * The Gemma project
 * 
 * Copyright (c) 2007 University of British Columbia
 * 
 * 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 org.apache.commons.cli.Option;
import org.apache.commons.cli.OptionBuilder;
import ubic.gemma.loader.entrez.pubmed.PubMedService;
import ubic.gemma.util.AbstractCLIContextCLI;

import java.io.File;

/**
 * Load PubMed files from XML files -- not used routinely!
 * 
 * @author pavlidis
 * @version $Id: PubMedLoaderCli.java,v 1.4 2013/02/18 18:36:45 anton Exp $
 */
public class PubMedLoaderCli extends AbstractCLIContextCLI {

    /**
     * @param args
     */
    public static void main(String[] args) {
        PubMedLoaderCli p = new PubMedLoaderCli();
        Exception exception = p.doWork(args);
        if (exception != null) {
            log.error(exception, exception);
        }
    }

    private String directory;

    @Override
    public String getShortDesc() {
        return "Loads PubMed records into the database from XML files";
    }

    @SuppressWarnings("static-access")
    @Override
    protected void buildOptions() {
        Option fileOption = OptionBuilder.isRequired().hasArg().withArgName("Directory")
                .withDescription("Directory of PubMed XML files to load").withLongOpt("dir").create('d');
        this.addOption(fileOption);

    }

    @Override
    protected Exception doWork(String[] args) {
        processCommandLine("Load PubMed records", args);
        PubMedService pms = this.getBean(PubMedService.class);
        pms.loadFromDirectory(new File(directory));
        return null;
    }

    @Override
    protected void processOptions() {
        super.processOptions();
        if (this.hasOption('d')) {
            this.directory = this.getOptionValue('d');
        }
    }

}