ubic.gemma.apps.PazarLoaderCli.java Source code

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

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/*
 * The Gemma project
 * 
 * Copyright (c) 2010 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.OptionBuilder;
import org.apache.commons.lang.StringUtils;
import ubic.gemma.loader.pazar.PazarLoader;
import ubic.gemma.model.association.TfGeneAssociationService;
import ubic.gemma.util.AbstractCLIContextCLI;

import java.io.File;

/**
 * @author paul
 * @version $Id: PazarLoaderCli.java,v 1.3 2013/02/18 18:36:44 anton Exp $
 */
public class PazarLoaderCli extends AbstractCLIContextCLI {

    private File file = null;

    @SuppressWarnings("static-access")
    @Override
    protected void buildOptions() {
        super.addOption(OptionBuilder.isRequired().withLongOpt("file").hasArg().create('f'));
    }

    @Override
    protected Exception doWork(String[] args) {
        super.processCommandLine("Load Pazar data", args);

        TfGeneAssociationService tfs = this.getBean(TfGeneAssociationService.class);
        tfs.removeAll();

        PazarLoader l = this.getBean(PazarLoader.class);

        try {
            l.load(file);
        } catch (Exception e) {
            return e;
        }

        return null;
    }

    @Override
    protected void processOptions() {
        super.processOptions();
        if (this.hasOption('f')) {
            String fileName = this.getOptionValue('f');
            if (StringUtils.isBlank(fileName)) {
                throw new IllegalArgumentException("file name required");
            }
            this.file = new File(fileName);
            if (!file.canRead()) {
                throw new IllegalArgumentException("Cannot read from " + file);
            }
        }
    }

    public static void main(String[] args) {
        PazarLoaderCli c = new PazarLoaderCli();
        Exception e = c.doWork(args);
        if (e != null) {
            log.fatal(e);
        }
    }

}