ubic.gemma.apps.ArrayDesignProbeRenamerCli.java Source code

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Here is the source code for ubic.gemma.apps.ArrayDesignProbeRenamerCli.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.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;

import org.apache.commons.cli.OptionBuilder;

import ubic.gemma.loader.expression.arrayDesign.ArrayDesignProbeRenamingService;
import ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignProbeRenamingEvent;
import ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType;
import ubic.gemma.model.expression.arrayDesign.ArrayDesign;

/**
 * Put new names on probes. This is needed in some cases where probes were given generic names that weren't helpful for
 * matching them to sequences.
 * 
 * @author pavlidis
 * @version $Id: ArrayDesignProbeRenamerCli.java,v 1.8 2012/06/05 18:29:45 paul Exp $
 */
public class ArrayDesignProbeRenamerCli extends ArrayDesignSequenceManipulatingCli {

    public static void main(String[] args) {
        ArrayDesignProbeRenamerCli a = new ArrayDesignProbeRenamerCli();
        try {
            Exception e = a.doWork(args);
            if (e != null) {
                log.fatal(e, e);
            }
        } catch (RuntimeException e) {
            log.fatal(e, e);
        }
    }

    private String fileName;

    @SuppressWarnings("static-access")
    @Override
    protected void buildOptions() {
        super.buildOptions();
        addOption(OptionBuilder.isRequired().hasArg().withArgName("file")
                .withDescription("Two-column file with old and new identifiers (additional columns ignored)")
                .create('f'));
    }

    @Override
    protected Exception doWork(String[] args) {
        Exception e = processCommandLine("replace array design probe names", args);
        if (e != null) {
            return e;
        }

        if (fileName == null) {
            throw new IllegalArgumentException("filename cannot be null");
        }

        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);

        ArrayDesignProbeRenamingService arrayDesignProbeRenamingService = this
                .getBean(ArrayDesignProbeRenamingService.class);

        try {
            File file = new File(fileName);
            if (!file.canRead()) {
                throw new IOException("Cannot read from " + fileName);
            }
            InputStream newIdFile = new FileInputStream(file);
            arrayDesignProbeRenamingService.reName(arrayDesign, newIdFile);
            newIdFile.close();
            audit(arrayDesign, "Probes renamed using file " + fileName);
        } catch (Exception ex) {
            return ex;
        }

        return null;
    }

    @Override
    protected void processOptions() {
        super.processOptions();

        this.fileName = getOptionValue('f');

    }

    /**
     * @param arrayDesign
     */
    private void audit(ArrayDesign arrayDesign, String note) {
        super.arrayDesignReportService.generateArrayDesignReport(arrayDesign.getId());
        AuditEventType eventType = ArrayDesignProbeRenamingEvent.Factory.newInstance();
        auditTrailService.addUpdateEvent(arrayDesign, eventType, note);
    }

}