/* * 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.modules.mgmt.upload; import static fr.ens.biologie.genomique.eoulsan.EoulsanLogger.getLogger; import static fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule.DATAFORMATS_TO_DOWNLOAD_SETTING; import java.util.HashSet; import java.util.Set; import fr.ens.biologie.genomique.eoulsan.EoulsanException; import fr.ens.biologie.genomique.eoulsan.Globals; import fr.ens.biologie.genomique.eoulsan.Settings; import fr.ens.biologie.genomique.eoulsan.annotations.HadoopCompatible; import fr.ens.biologie.genomique.eoulsan.core.Parameter; import fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext; import fr.ens.biologie.genomique.eoulsan.core.TaskContext; import fr.ens.biologie.genomique.eoulsan.core.TaskResult; import fr.ens.biologie.genomique.eoulsan.core.TaskStatus; import fr.ens.biologie.genomique.eoulsan.core.Version; import fr.ens.biologie.genomique.eoulsan.data.DataFormat; import fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry; import fr.ens.biologie.genomique.eoulsan.modules.AbstractModule; /** * This Step allow to define the list of the formats of the files to download at * the end of a Hadoop execution. * @since 1.0 * @author Laurent Jourdren */ @HadoopCompatible public class DefineDataFormatToDownload extends AbstractModule { protected static final String STEP_NAME = "defineformatstodownload"; private DataFormat[] inFormats; @Override public String getName() { return STEP_NAME; } @Override public String getDescription() { return "define the list of the formats of the files to download " + "at the end of a Hadoop execution"; } @Override public Version getVersion() { return Globals.APP_VERSION; } @Override public void configure(final StepConfigurationContext context, final Set<Parameter> stepParameters) throws EoulsanException { String formatNames = null; for (Parameter p : stepParameters) { if ("formats".equals(p.getName())) { formatNames = p.getStringValue(); } else { throw new EoulsanException( "Unknown parameter for " + getName() + " step: " + p.getName()); } } if (formatNames == null) { throw new EoulsanException("No format to download set."); } final String[] fields = formatNames.split(","); final Set<DataFormat> formats = new HashSet<>(); final DataFormatRegistry registry = DataFormatRegistry.getInstance(); for (String format : fields) { if ("".equals(format.trim())) { continue; } final DataFormat df = registry.getDataFormatFromName(format.trim()); if (df == null) { throw new EoulsanException("Format not found : " + format.trim()); } formats.add(df); } this.inFormats = formats.toArray(new DataFormat[formats.size()]); } @Override public TaskResult execute(final TaskContext context, final TaskStatus status) { final StringBuilder sb = new StringBuilder(); boolean first = true; for (DataFormat df : this.inFormats) { if (first) { first = false; } else { sb.append(','); } sb.append(df.getName()); } final String formats = sb.toString(); getLogger().info("Format to download: " + formats); // Save the list of the DataFormat to download in the settings final Settings settings = context.getRuntime().getSettings(); settings.setSetting(DATAFORMATS_TO_DOWNLOAD_SETTING, formats, false); status.setProgressMessage("Formats to download: " + formats); return status.createTaskResult(); } }