Package fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload

Class HadoopUploadModule

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule

fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HadoopUploadModule

All Implemented Interfaces:

Module

public class HadoopUploadModule
extends UploadModule

This class define a module for Hadoop file uploading.

Since:

1.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
HadoopUploadModule(DataFile dest, org.apache.hadoop.conf.Configuration conf)	Public constructor.

Method Summary

Modifier and Type	Method	Description
protected void	copy(Map<DataFile,DataFile> files)	Copy files to destinations.
protected DataFile	getUploadedDataFile(DataFile file)	Generate the DataFile Object for the uploaded DataFile
protected DataFile	getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)	Generate the DataFile Object for the uploaded DataFile

Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule

execute, getDest, getName, getVersion

Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

configure, getChecker, getDescription, getInputPorts, getOutputPorts, getParallelizationMode, getRequiredEoulsanVersion, getRequirements

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

HadoopUploadModule

public HadoopUploadModule(DataFile dest,
                          org.apache.hadoop.conf.Configuration conf)

Public constructor.

Parameters:

dest - destination of the files to upload

conf - Hadoop configuration

Method Detail

getUploadedDataFile

protected DataFile getUploadedDataFile(DataFile file)
                                throws IOException

Description copied from class: UploadModule

Generate the DataFile Object for the uploaded DataFile

Specified by:

getUploadedDataFile in class UploadModule

Parameters:

file - DataFile to upload

Returns:

a new DataFile object with the path to the upload DataFile

Throws:

IOException - if an error occurs while creating the result DataFile

getUploadedDataFile

protected DataFile getUploadedDataFile(DataFile file,
                                       Step step,
                                       Sample sample,
                                       String portName,
                                       DataFormat format,
                                       int fileIndex)
                                throws IOException

Description copied from class: UploadModule

Generate the DataFile Object for the uploaded DataFile

Specified by:

getUploadedDataFile in class UploadModule

Parameters:

file - DataFile to upload

sample - the sample for the source

portName - the port name

format - the format of the file to upload

fileIndex - file index for multifile data

Returns:

a new DataFile object with the path to the upload DataFile

Throws:

IOException - if an error occurs while creating the result DataFile

copy

protected void copy(Map<DataFile,DataFile> files)
             throws IOException

Description copied from class: UploadModule

Copy files to destinations.

Specified by:

copy in class UploadModule

Parameters:

files - map with source and destination for each file

Throws:

IOException - if an error occurs while copying files