/*
* 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.generators;
import static fr.ens.biologie.genomique.eoulsan.EoulsanLogger.getLogger;
import static fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder.singleInputPort;
import static fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder.singleOutputPort;
import static fr.ens.biologie.genomique.eoulsan.data.DataFormats.GENOME_DESC_TXT;
import static fr.ens.biologie.genomique.eoulsan.data.DataFormats.GENOME_FASTA;
import java.io.IOException;
import fr.ens.biologie.genomique.eoulsan.EoulsanRuntime;
import fr.ens.biologie.genomique.eoulsan.Globals;
import fr.ens.biologie.genomique.eoulsan.bio.BadBioEntryException;
import fr.ens.biologie.genomique.eoulsan.bio.GenomeDescription;
import fr.ens.biologie.genomique.eoulsan.core.InputPorts;
import fr.ens.biologie.genomique.eoulsan.core.OutputPorts;
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.Data;
import fr.ens.biologie.genomique.eoulsan.data.DataFile;
import fr.ens.biologie.genomique.eoulsan.data.storages.GenomeDescStorage;
import fr.ens.biologie.genomique.eoulsan.data.storages.SimpleGenomeDescStorage;
import fr.ens.biologie.genomique.eoulsan.modules.AbstractModule;
/**
* This class implements a genome description generator module.
* @since 1.0
* @author Laurent Jourdren
*/
public class GenomeDescriptionGeneratorModule extends AbstractModule {
public static final String MODULE_NAME = "genomedescgenerator";
@Override
public String getName() {
return MODULE_NAME;
}
@Override
public String getDescription() {
return "Generate genome description";
}
@Override
public Version getVersion() {
return Globals.APP_VERSION;
}
@Override
public InputPorts getInputPorts() {
return singleInputPort(GENOME_FASTA);
}
@Override
public OutputPorts getOutputPorts() {
return singleOutputPort(GENOME_DESC_TXT);
}
@Override
public TaskResult execute(final TaskContext context,
final TaskStatus status) {
// Get input and output data
final Data inData = context.getInputData(GENOME_FASTA);
final Data outData = context.getOutputData(GENOME_DESC_TXT, inData);
try {
// Get the genome DataFile
final DataFile genomeDataFile = inData.getDataFile();
// Get the output DataFile
final DataFile genomeDescriptionDataFile = outData.getDataFile();
getLogger().fine("Input genome file: " + genomeDataFile);
getLogger()
.fine("Output genome description file: " + genomeDescriptionDataFile);
// Create genome description DataFile
final GenomeDescription desc = new GenomeDescriptionCreator()
.createGenomeDescription(genomeDataFile);
// Save the genome description in the analysis folder
desc.save(genomeDescriptionDataFile.create());
getLogger().fine("Genome description object: " + desc.toString());
} catch (BadBioEntryException e) {
return status.createTaskResult(e);
} catch (IOException e) {
return status.createTaskResult(e);
}
status.setProgressMessage("Genome description creation");
return status.createTaskResult();
}
/**
* Check if a genome description storage has been defined.
* @return a GenomeDescStorage object if genome storage has been defined or
* null if not
*/
static GenomeDescStorage checkForGenomeDescStore() {
final String genomeDescStoragePath =
EoulsanRuntime.getSettings().getGenomeDescStoragePath();
if (genomeDescStoragePath == null) {
return null;
}
return SimpleGenomeDescStorage
.getInstance(new DataFile(genomeDescStoragePath));
}
}