/*
* 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.io.CompressionType.BZIP2;
import static fr.ens.biologie.genomique.eoulsan.io.CompressionType.removeCompressionExtension;
import static fr.ens.biologie.genomique.eoulsan.util.StringUtils.compressionExtension;
import java.io.IOException;
import java.util.Map;
import fr.ens.biologie.genomique.eoulsan.annotations.LocalOnly;
import fr.ens.biologie.genomique.eoulsan.core.Step;
import fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile;
import fr.ens.biologie.genomique.eoulsan.data.DataFile;
import fr.ens.biologie.genomique.eoulsan.data.DataFormat;
import fr.ens.biologie.genomique.eoulsan.data.DataFormatConverter;
import fr.ens.biologie.genomique.eoulsan.design.Sample;
import fr.ens.biologie.genomique.eoulsan.io.CompressionType;
/**
* This class define a Step for local mode file uploading.
* @since 1.0
* @author Laurent Jourdren
*/
@LocalOnly
public class LocalUploadModule extends UploadModule {
@Override
protected DataFile getUploadedDataFile(final DataFile file)
throws IOException {
final String filename;
if (file.getName().endsWith(".zip")
|| file.getName().endsWith(".jar") || file.getName().endsWith(".xml")
|| file.getName().endsWith(".txt")) {
filename = file.getName();
} else {
filename = CompressionType.removeCompressionExtension(file.getName())
+ CompressionType.BZIP2.getExtension();
}
return new DataFile(getDest(), filename);
}
@Override
protected DataFile getUploadedDataFile(final DataFile file, final Step step,
final Sample sample, final String portName, final DataFormat format,
final int fileIndex) throws IOException {
final String filename;
if (sample == null || format == null) {
if (file == null) {
throw new IOException("Input file is null.");
}
filename = file.getName();
} else {
filename = StepOutputDataFile.newStandardFilename(step, portName, format,
sample, fileIndex, CompressionType.NONE);
}
// Don't compress ZIP files
if (".zip".equals(compressionExtension(filename))) {
return new DataFile(getDest(), filename);
}
return new DataFile(getDest(),
removeCompressionExtension(filename) + BZIP2.getExtension());
}
@Override
protected void copy(final Map<DataFile, DataFile> files) throws IOException {
if (files == null) {
throw new NullPointerException("The files argument is null.");
}
for (Map.Entry<DataFile, DataFile> e : files.entrySet()) {
final DataFile src = e.getKey();
final DataFile dest = e.getValue();
if (src == null || dest == null) {
continue;
}
getLogger().info("Convert " + src + " to " + dest);
new DataFormatConverter(src, dest).convert();
}
}
//
// Constructor
//
/**
* Public constructor.
* @param dest destination of the files to upload
*/
public LocalUploadModule(final DataFile dest) {
super(dest);
}
}