ubic.gemma.apps.ArrayDesignMergeCli.java Source code

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Here is the source code for ubic.gemma.apps.ArrayDesignMergeCli.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 java.util.HashSet;

import org.apache.commons.cli.Option;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.lang.StringUtils;

import ubic.gemma.loader.expression.arrayDesign.ArrayDesignMergeService;
import ubic.gemma.model.expression.arrayDesign.ArrayDesign;

/**
 * <ul>
 * <li>make new array design based on others
 * <li>Keep map of relation between new design elements and old ones
 * <li>Store relationship with mergees
 * </ul>
 * <p>
 * Separate operations:
 * <ul>
 * <li>For an EE, Remap DesignElement references to old array designs to new one, and old BioAssay AD refs to new one.
 * </ul>
 * 
 * @author pavlidis
 * @version $Id: ArrayDesignMergeCli.java,v 1.15 2012/11/28 01:55:24 paul Exp $
 */
public class ArrayDesignMergeCli extends ArrayDesignSequenceManipulatingCli {

    public static void main(String[] args) {
        ArrayDesignMergeCli b = new ArrayDesignMergeCli();
        b.doWork(args);
    }

    private HashSet<ArrayDesign> otherArrayDesigns;
    private String newShortName;
    private String newName;
    private ArrayDesignMergeService arrayDesignMergeService;

    private ArrayDesign arrayDesign;

    @Override
    public String getShortDesc() {
        return "Make a new array design that combines the reporters from others.";
    }

    @SuppressWarnings("static-access")
    @Override
    protected void buildOptions() {
        super.buildOptions();
        Option otherArrayDesignOption = OptionBuilder.isRequired().hasArg().withArgName("Other platforms")
                .withDescription(
                        "Short name(s) of arrays to merge with the one given to the -a option, preferably subsumed by it, comma-delimited. "
                                + "If the platform given with -a is already a merged design, these will be added to it if the -add option is given"
                                + "The designs cannot be ones already merged into another design, but they can be mergees.")
                .withLongOpt("other").create('o');

        addOption(otherArrayDesignOption);

        Option newAdName = OptionBuilder.hasArg().withArgName("name")
                .withDescription("Name for new platform, if the given platform is not already a merged design")
                .withLongOpt("name").create('n');
        addOption(newAdName);
        Option newAdShortName = OptionBuilder.hasArg().withArgName("name")
                .withDescription(
                        "Short name for new platform, if the given platform is not already a merged design")
                .withLongOpt("shortname").create('s');
        addOption(newAdShortName);

        Option addOption = OptionBuilder
                .withDescription("If the given platform is already a merged design, add the -o designs to it. "
                        + "Recommended unless there is a specific reason to create a new design.")
                .create("add");
        addOption(addOption);
    }

    @Override
    protected Exception doWork(String[] args) {

        Exception err = processCommandLine("subsumption tester", args);
        if (err != null) {
            bail(ErrorCode.INVALID_OPTION);
            return err;
        }
        arrayDesignMergeService.merge(arrayDesign, otherArrayDesigns, newName, newShortName, this.hasOption("add"));

        return null;
    }

    @Override
    protected void processOptions() {
        super.processOptions();
        if (this.hasOption('o')) {// required
            String otherArrayDesigName = getOptionValue('o');
            String[] names = StringUtils.split(otherArrayDesigName, ',');
            this.otherArrayDesigns = new HashSet<ArrayDesign>();
            for (String string : names) {
                ArrayDesign o = locateArrayDesign(string);
                if (o == null) {
                    throw new IllegalArgumentException("Array design " + string + " not found");
                }
                o = unlazifyArrayDesign(o);
                this.otherArrayDesigns.add(o);
            }
        }

        if (this.arrayDesignsToProcess.size() > 1) {
            throw new IllegalArgumentException(
                    "Cannot be applied to more than one array design given to the '-a' option");
        }

        arrayDesign = this.arrayDesignsToProcess.iterator().next();

        arrayDesign = unlazifyArrayDesign(arrayDesign);

        if (this.hasOption("add")) {
            if (arrayDesign.getMergees().isEmpty()) {
                throw new IllegalArgumentException("The array given must be a merged design when using -add");
            }
        } else {

            if (this.hasOption("n")) {
                this.newName = getOptionValue('n');
            } else {
                throw new IllegalArgumentException("You must provide a name for the new design unless using -add");
            }
            if (this.hasOption("s")) {
                this.newShortName = getOptionValue('s');
            } else {
                throw new IllegalArgumentException(
                        "You must provide a short name for the new design unless using -add");
            }
        }
        arrayDesignMergeService = this.getBean(ArrayDesignMergeService.class);

    }

}