ubic.gemma.apps.ExpressionExperimentDataFileGeneratorCli.java Source code

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Here is the source code for ubic.gemma.apps.ExpressionExperimentDataFileGeneratorCli.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.ArrayList;
import java.util.Collection;
import java.util.concurrent.ArrayBlockingQueue;
import java.util.concurrent.BlockingQueue;

import org.apache.commons.cli.Option;
import org.apache.commons.cli.OptionBuilder;
import org.springframework.security.core.context.SecurityContext;
import org.springframework.security.core.context.SecurityContextHolder;

import ubic.gemma.analysis.service.ExpressionDataFileService;
import ubic.gemma.model.common.auditAndSecurity.AuditTrailService;
import ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType;
import ubic.gemma.model.common.auditAndSecurity.eventType.CommentedEvent;
import ubic.gemma.model.expression.experiment.BioAssaySet;
import ubic.gemma.model.expression.experiment.ExpressionExperiment;

/**
 * @author paul
 * @version $Id: ExpressionExperimentDataFileGeneratorCli.java,v 1.13 2012/06/05 18:29:46 paul Exp $
 */
public class ExpressionExperimentDataFileGeneratorCli extends ExpressionExperimentManipulatingCLI {

    /**
     * @param args
     */
    public static void main(String[] args) {
        ExpressionExperimentDataFileGeneratorCli p = new ExpressionExperimentDataFileGeneratorCli();
        Exception e = p.doWork(args);
        if (e != null) {
            log.fatal(e, e);
        }
    }

    private boolean force_write = false;

    ExpressionDataFileService expressionDataFileService;

    private String DESCRIPTION = "Generate Flat data files (diff expression, co-expression) for a given set of experiments";

    @Override
    public String getShortDesc() {
        return DESCRIPTION;
    }

    /*
     * (non-Javadoc)
     * 
     * @see ubic.gemma.util.AbstractCLI#buildOptions()
     */
    @SuppressWarnings("static-access")
    @Override
    protected void buildOptions() {
        super.buildOptions();

        Option forceWriteOption = OptionBuilder.hasArg().withArgName("ForceWrite")
                .withDescription("Overwrites exsiting files if this option is set").withLongOpt("forceWrite")
                .create('w');

        addThreadsOption();
        addOption(forceWriteOption);
    }

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

        Exception exp = processCommandLine(DESCRIPTION, args);
        if (exp != null) {
            return exp;
        }

        BlockingQueue<BioAssaySet> queue = new ArrayBlockingQueue<BioAssaySet>(expressionExperiments.size());

        // Add the Experiments to the queue for processing
        for (BioAssaySet ee : expressionExperiments) {
            if (ee instanceof ExpressionExperiment) {
                try {
                    queue.put(ee);
                } catch (InterruptedException ie) {
                    log.info(ie);
                }
            } else {
                throw new UnsupportedOperationException("Can't handle non-EE BioAssaySets yet");
            }

        }

        // Inner class for processing the experiments
        class Worker extends Thread {
            BlockingQueue<BioAssaySet> q;
            SecurityContext context;

            Worker(BlockingQueue<BioAssaySet> q, SecurityContext context) {
                this.context = context;
                this.q = q;
            }

            @Override
            public void run() {

                SecurityContextHolder.setContext(this.context);

                while (true) {
                    BioAssaySet ee = q.poll();
                    if (ee == null) {
                        break;
                    }
                    log.info("Processing Experiment: " + ee.getName());
                    processExperiment((ExpressionExperiment) ee);

                }

            }
        }

        final SecurityContext context = SecurityContextHolder.getContext();

        Collection<Thread> threads = new ArrayList<Thread>();

        for (int i = 1; i <= this.numThreads; i++) {
            Worker worker = new Worker(queue, context);
            threads.add(worker);
            log.info("Starting thread " + i);
            worker.start();
        }

        waitForThreadPoolCompletion(threads);

        summarizeProcessing();

        return null;

    }

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

        if (hasOption(THREADS_OPTION)) {
            this.numThreads = this.getIntegerOptionValue("threads");
        }

        if (hasOption('w')) {
            this.force_write = true;
        }

        expressionDataFileService = this.getBean(ExpressionDataFileService.class);
    }

    private void processExperiment(ExpressionExperiment ee) {

        try {
            ee = this.eeService.thawLite(ee);

            AuditTrailService ats = this.getBean(AuditTrailService.class);
            AuditEventType type = CommentedEvent.Factory.newInstance();

            expressionDataFileService.writeOrLocateCoexpressionDataFile(ee, force_write);
            expressionDataFileService.writeOrLocateDiffExpressionDataFiles(ee, force_write);

            ats.addUpdateEvent(ee, type, "Generated Flat data files for downloading");
            super.successObjects
                    .add("Success:  generated data file for " + ee.getShortName() + " ID=" + ee.getId());

        } catch (Exception e) {
            log.info("Caught runtime error: " + e);
            super.errorObjects.add(
                    "FAILED: for ee: " + ee.getShortName() + " ID= " + ee.getId() + " Error: " + e.getMessage());
        }
    }

}