chibi.gemmaanalysis.cli.deprecated.AddExperimentalDesignCLI.java Source code

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Here is the source code for chibi.gemmaanalysis.cli.deprecated.AddExperimentalDesignCLI.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 chibi.gemmaanalysis.cli.deprecated;

import java.util.HashSet;

import org.apache.commons.lang3.time.StopWatch;

import ubic.gemma.expression.experiment.service.ExpressionExperimentService;
import ubic.gemma.model.common.description.Characteristic;
import ubic.gemma.model.expression.experiment.ExperimentalDesign;
import ubic.gemma.model.expression.experiment.ExperimentalFactor;
import ubic.gemma.model.expression.experiment.ExpressionExperiment;
import ubic.gemma.util.AbstractSpringAwareCLI;

/**
 * @author klc
 * @version $Id$
 */
@Deprecated
public class AddExperimentalDesignCLI extends AbstractSpringAwareCLI {

    // These were the previous EE ids that had no experimentalDesign
    // The easiest way to get this set is to use a sql query like: select ee.id from expression_experiment as ee where
    // ee.experimental_design is null
    // private static final long[] EEwithNoED = { 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215,
    // 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 620, 670, 671, 672,
    // 673, 675 };

    private static final long[] EEwithNoED = {};

    ExpressionExperimentService eeService;

    /*
     * (non-Javadoc)
     * 
     * @see ubic.gemma.util.AbstractCLI#buildOptions()
     */
    @Override
    protected void buildOptions() {

    }

    /*
     * (non-Javadoc)
     * 
     * @see ubic.gemma.util.AbstractSpringAwareCLI#processOptions()
     */
    @Override
    protected void processOptions() {
        super.processOptions();
        this.eeService = getBean(ExpressionExperimentService.class);
    }

    /**
     * @param args
     */
    public static void main(String[] args) {
        AddExperimentalDesignCLI p = new AddExperimentalDesignCLI();
        StopWatch watch = new StopWatch();
        watch.start();
        try {
            Exception ex = p.doWork(args);
            if (ex != null) {
                ex.printStackTrace();
            }
            watch.stop();
            log.info("Total run time: " + watch.getTime());
        } catch (Exception e) {
            throw new RuntimeException(e);
        }
    }

    /*
     * (non-Javadoc)
     * 
     * @see ubic.gemma.util.AbstractCLI#doWork(java.lang.String[])
     */
    @Override
    protected Exception doWork(String[] args) {
        Exception err = processCommandLine(args);
        if (err != null) {
            return err;
        }
        try {

            for (Long eeId : EEwithNoED) {
                log.info("Adding experimental design to ee: " + eeId);
                addEd2EE(eeId);
            }

        } catch (Exception e) {
            log.error(e);
            return e;
        }
        return null;
    }

    private void addEd2EE(Long eeID) {

        ExpressionExperiment ee = eeService.load(eeID);

        // Is this necessary to test?
        if (ee.getExperimentalDesign() != null)
            return;

        ExperimentalDesign ed = ExperimentalDesign.Factory.newInstance();
        ed.setExperimentalFactors(new HashSet<ExperimentalFactor>());
        ed.setName(ee.getName() + " Experimental Design");
        ed.setTypes(new HashSet<Characteristic>());

        ee.setExperimentalDesign(ed);
        eeService.update(ee);

    }

    /*
     * (non-Javadoc)
     * 
     * @see ubic.gemma.util.AbstractCLI#getCommandName()
     */
    @Override
    public String getCommandName() {
        return null;
    }

}