fr.ens.biologie.genomique.eoulsan.util.hadoop.MapReduceUtils.java Source code

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Here is the source code for fr.ens.biologie.genomique.eoulsan.util.hadoop.MapReduceUtils.java

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/*
 *                  Eoulsan development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public License version 2.1 or
 * later and CeCILL-C. This should be distributed with the code.
 * If you do not have a copy, see:
 *
 *      http://www.gnu.org/licenses/lgpl-2.1.txt
 *      http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt
 *
 * Copyright for this code is held jointly by the Genomic platform
 * of the Institut de Biologie de l'cole normale suprieure and
 * the individual authors. These should be listed in @author doc
 * comments.
 *
 * For more information on the Eoulsan project and its aims,
 * or to join the Eoulsan Google group, visit the home page
 * at:
 *
 *      http://outils.genomique.biologie.ens.fr/eoulsan
 *
 */

package fr.ens.biologie.genomique.eoulsan.util.hadoop;

import java.io.IOException;

import org.apache.hadoop.mapreduce.Job;

import fr.ens.biologie.genomique.eoulsan.EoulsanException;
import fr.ens.biologie.genomique.eoulsan.core.TaskStatus;

/**
 * This class contains utility method to easily manipulate the new Hadoop
 * MapReduce API.
 * @since 1.0
 * @author Laurent Jourdren
 */
public final class MapReduceUtils {

    /**
     * Wait the completion of a job.
     * @param job the job to submit
     * @param jobDescription the description of the job
     * @param waitTimeInMillis waiting time between 2 checks of the completion of
     *          jobs
     * @param status step status
     * @param counterGroup group of the counter to log
     * @throws EoulsanException if the job fail or if an exception occurs while
     *           submitting or waiting the end of the job
     */
    public static void submitAndWaitForJob(final Job job, final String jobDescription, final int waitTimeInMillis,
            final TaskStatus status, final String counterGroup) throws EoulsanException {

        if (job == null) {
            throw new NullPointerException("The job is null");
        }

        if (jobDescription == null) {
            throw new NullPointerException("The jobDescription is null");
        }

        try {

            // Set the description of the context
            status.setDescription(job.getJobName());

            // Submit the job
            job.submit();

            // Add the Hadoop job to the list of job to kill if workflow fails
            HadoopJobEmergencyStopTask.addHadoopJobEmergencyStopTask(job);

            // Job the completion of the job (non verbose mode)
            job.waitForCompletion(false);

            // Remove the Hadoop job to the list of job to kill if workflow fails
            HadoopJobEmergencyStopTask.removeHadoopJobEmergencyStopTask(job);

            // Check if the job has been successfully executed
            if (!job.isSuccessful()) {

                status.setProgressMessage("FAILED");

                throw new EoulsanException("Fail of the Hadoop job: " + job.getJobFile());
            }

            // Set the counters
            status.setCounters(new HadoopReporter(job.getCounters()), counterGroup);

        } catch (ClassNotFoundException | InterruptedException | IOException e) {
            throw new EoulsanException(e);
        }
    }

    //
    // Constructor
    //

    private MapReduceUtils() {
    }

}