ubic.gemma.core.apps.PazarLoaderCli.java Source code

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Here is the source code for ubic.gemma.core.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.core.apps;

import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.lang3.StringUtils;
import ubic.gemma.core.apps.GemmaCLI.CommandGroup;
import ubic.gemma.core.loader.pazar.PazarLoader;
import ubic.gemma.core.util.AbstractCLI;
import ubic.gemma.core.util.AbstractCLIContextCLI;
import ubic.gemma.persistence.service.association.TfGeneAssociationService;

import java.io.File;

/**
 * @author paul
 * @deprecated
 */
@Deprecated
public class PazarLoaderCli extends AbstractCLIContextCLI {

    private File file = null;

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

    @Override
    public String getCommandName() {
        return "loadPazar";
    }

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

    @Override
    protected Exception doWork(String[] args) {
        Exception e = super.processCommandLine(args);
        if (e != null)
            return e;

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

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

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

        return null;
    }

    @Override
    public String getShortDesc() {
        return "Loads Pazar records into the database";
    }

    @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);
            }
        }
    }

    @Override
    public CommandGroup getCommandGroup() {
        return CommandGroup.MISC;
    }

}