/*
* 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.hadoop;
import static fr.ens.biologie.genomique.eoulsan.EoulsanLogger.getLogger;
import java.io.IOException;
import java.util.Set;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import fr.ens.biologie.genomique.eoulsan.CommonHadoop;
import fr.ens.biologie.genomique.eoulsan.EoulsanException;
import fr.ens.biologie.genomique.eoulsan.EoulsanRuntime;
import fr.ens.biologie.genomique.eoulsan.Globals;
import fr.ens.biologie.genomique.eoulsan.annotations.HadoopOnly;
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.design.Design;
import fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignWriter;
import fr.ens.biologie.genomique.eoulsan.modules.AbstractModule;
import fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils;
/**
* This module copy design and workflow file to output directory.
* @since 1.0
* @author Laurent Jourdren
*/
@HadoopOnly
public class CopyDesignAndWorkflowFilesToOutputModule extends AbstractModule {
/** Module name. */
public static final String MODULE_NAME = "_copy_design_params_to_output";
private Configuration conf;
//
// Module methods
//
@Override
public String getName() {
return MODULE_NAME;
}
@Override
public String getDescription() {
return "Copy design and workflow file to output path.";
}
@Override
public Version getVersion() {
return Globals.APP_VERSION;
}
@Override
public void configure(final StepConfigurationContext context,
final Set<Parameter> stepParameters) throws EoulsanException {
this.conf = CommonHadoop.createConfiguration(EoulsanRuntime.getSettings());
}
@Override
public TaskResult execute(final TaskContext context,
final TaskStatus status) {
final Configuration conf = this.conf;
final Path designPath = new Path(context.getDesignFile().getSource());
final Path workflowPath = new Path(context.getWorkflowFile().getSource());
final Path outputPath = new Path(context.getOutputDirectory().getSource());
final Path outputDesignPath = new Path(outputPath, designPath.getName());
final Path outputWorkflowPath =
new Path(outputPath, workflowPath.getName());
// Copy design file
try {
if (!PathUtils.exists(outputDesignPath, conf)) {
final FileSystem outputDesignFs = outputDesignPath.getFileSystem(conf);
final Design design = context.getWorkflow().getDesign();
new Eoulsan1DesignWriter(outputDesignFs.create(outputDesignPath))
.write(design);
}
} catch (IOException e) {
getLogger().severe("Unable to copy design file to output path.");
}
// Copy workflow file
try {
if (!PathUtils.exists(outputWorkflowPath, conf)) {
PathUtils.copy(designPath, outputWorkflowPath, conf);
}
} catch (IOException e) {
getLogger().severe("Unable to copy design file to output path.");
}
return status.createTaskResult();
}
}