/*
* 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.data.protocols;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileStatus;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime;
import fr.ens.biologie.genomique.eoulsan.EoulsanRuntime;
import fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime;
import fr.ens.biologie.genomique.eoulsan.data.DataFile;
import fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata;
import fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry;
import fr.ens.biologie.genomique.eoulsan.io.CompressionType;
import fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils;
/**
* This class define an abstract class for DataProtocols based on the Hadoop
* framework Path object.
* @since 1.0
* @author Laurent Jourdren
*/
public abstract class PathDataProtocol extends AbstractDataProtocol {
protected Configuration conf;
/**
* Get Convert a DataFile object to a Path object.
* @param dataFile DataFile to convert
* @return a Path object
*/
public Path getPath(final DataFile dataFile) {
if (dataFile == null) {
throw new NullPointerException("The source is null.");
}
return new Path(dataFile.getSource());
}
@Override
public InputStream getData(final DataFile src) throws IOException {
return PathUtils.createInputStream(getPath(src), this.conf);
}
@Override
public OutputStream putData(final DataFile src) throws IOException {
return PathUtils.createOutputStream(getPath(src), this.conf);
}
@Override
public DataFileMetadata getMetadata(final DataFile src) throws IOException {
if (!exists(src, true)) {
throw new FileNotFoundException("File not found: " + src);
}
final Path path = getPath(src);
final FileStatus status = path.getFileSystem(this.conf).getFileStatus(path);
final SimpleDataFileMetadata result = new SimpleDataFileMetadata();
result.setContentLength(status.getLen());
result.setLastModified(status.getModificationTime());
result.setDataFormat(DataFormatRegistry.getInstance()
.getDataFormatFromFilename(src.getName()));
final CompressionType ct =
CompressionType.getCompressionTypeByFilename(src.getSource());
if (ct != null) {
result.setContentEncoding(ct.getContentEncoding());
}
if (status.isDirectory()) {
result.setDirectory(true);
}
if (status.isSymlink()) {
result.setSymbolicLink(new DataFile(status.getSymlink().toUri()));
}
return result;
}
@Override
public boolean exists(final DataFile src, final boolean followLink) {
final Path path = getPath(src);
try {
final FileSystem fs = path.getFileSystem(conf);
final FileStatus status = fs.getFileStatus(path);
if (status == null) {
return false;
}
if (status.isSymlink()) {
return fs.getFileStatus(fs.getLinkTarget(path)) != null;
}
return true;
} catch (IOException e) {
return false;
}
}
@Override
public boolean canRead() {
return true;
}
@Override
public boolean canWrite() {
return true;
}
//
// Constructor
//
/**
* Constructor.
*/
public PathDataProtocol() {
final AbstractEoulsanRuntime runtime = EoulsanRuntime.getRuntime();
if (!runtime.getMode().isHadoopProtocolMode()
|| !(runtime instanceof HadoopEoulsanRuntime)) {
throw new IllegalStateException(
"Can only create PathDataProtocol in hadoop mode.");
}
final HadoopEoulsanRuntime hadoopRuntime = (HadoopEoulsanRuntime) runtime;
this.conf = hadoopRuntime.getConfiguration();
if (this.conf == null) {
throw new NullPointerException("The Hadoop configuration object is null");
}
}
}