ubic.gemma.apps.ArrayDesignSubsumptionTesterCli.java Source code

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Here is the source code for ubic.gemma.apps.ArrayDesignSubsumptionTesterCli.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.Collection;
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.model.common.auditAndSecurity.eventType.ArrayDesignSubsumeCheckEvent;
import ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType;
import ubic.gemma.model.expression.arrayDesign.ArrayDesign;

/**
 * Test two array designs to see if one subsumes the other, and if so update their information.
 * 
 * @author pavlidis
 * @version $Id: ArrayDesignSubsumptionTesterCli.java,v 1.11 2012/06/08 16:30:36 paul Exp $
 */
public class ArrayDesignSubsumptionTesterCli extends ArrayDesignSequenceManipulatingCli {

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

    private Collection<String> otherArrayDesignNames;

    @SuppressWarnings("static-access")
    @Override
    protected void buildOptions() {
        super.buildOptions();
        Option otherArrayDesignOption = OptionBuilder.isRequired().hasArg().withArgName("Other platform")
                .withDescription("Short name(s) of platforms to compare to the first one, comma-delimited")
                .withLongOpt("other").create('o');

        addOption(otherArrayDesignOption);
    }

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

        Exception err = processCommandLine("subsumption tester", args);
        if (err != null) {
            bail(ErrorCode.INVALID_OPTION);
            return err;
        }

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

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

        for (String otherArrayDesigName : otherArrayDesignNames) {
            ArrayDesign otherArrayDesign = locateArrayDesign(otherArrayDesigName);

            if (arrayDesign.equals(otherArrayDesign)) {
                continue;
            }

            if (otherArrayDesign == null) {
                log.error("No arrayDesign " + otherArrayDesigName + " found");
                bail(ErrorCode.INVALID_OPTION);
            }

            otherArrayDesign = unlazifyArrayDesign(otherArrayDesign);

            Boolean aSubsumeso = this.arrayDesignService.updateSubsumingStatus(arrayDesign, otherArrayDesign);

            if (!aSubsumeso) {
                // test other way around, but only if first way failed (to avoid cycles)
                this.arrayDesignService.updateSubsumingStatus(otherArrayDesign, arrayDesign);
            }
            audit(otherArrayDesign, "Tested to see if it is subsumed by " + arrayDesign);
        }

        audit(arrayDesign, "Tested to see if it subsumes: " + StringUtils.join(otherArrayDesignNames, ','));

        return null;
    }

    @Override
    protected void processOptions() {
        super.processOptions();
        if (this.hasOption('o')) {
            String otherArrayDesigName = getOptionValue('o');
            String[] names = StringUtils.split(otherArrayDesigName, ',');
            this.otherArrayDesignNames = new HashSet<String>();
            for (String string : names) {
                this.otherArrayDesignNames.add(string);
            }
        }
    }

    private void audit(ArrayDesign arrayDesign, String note) {
        AuditEventType eventType = ArrayDesignSubsumeCheckEvent.Factory.newInstance();
        auditTrailService.addUpdateEvent(arrayDesign, eventType, note);
    }

}