/* * 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'École normale supérieure 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() { } }