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

Class UploadModule

java.lang.Object

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

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

All Implemented Interfaces:

Module

Direct Known Subclasses:

HadoopUploadModule, LocalUploadModule

public abstract class UploadModule
extends AbstractModule

This class define a abstract module class for files uploading.

Since:

1.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
UploadModule(DataFile destination)	Public constructor.

Method Summary

Modifier and Type	Method	Description
protected abstract void	copy(Map<DataFile,DataFile> files)	Copy files to destinations.
TaskResult	execute(TaskContext context, TaskStatus status)	Execute a task step.
protected DataFile	getDest()
String	getName()	Get the name of the module.
protected abstract DataFile	getUploadedDataFile(DataFile file)	Generate the DataFile Object for the uploaded DataFile
protected abstract DataFile	getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)	Generate the DataFile Object for the uploaded DataFile
fr.ens.biologie.genomique.kenetre.util.Version	getVersion()	Get version of the Module.

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

UploadModule

public UploadModule(DataFile destination)

Public constructor.

Parameters:

destination - destination of the uploaded files

Method Detail

getDest

protected DataFile getDest()

execute

public TaskResult execute(TaskContext context,
                          TaskStatus status)

Description copied from interface: Module

Execute a task step.

Parameters:

context - Execution context

status - of the task

getName

public String getName()

Description copied from interface: Module

Get the name of the module.

Returns:

the name of the module

getVersion

public fr.ens.biologie.genomique.kenetre.util.Version getVersion()

Description copied from interface: Module

Get version of the Module.

Returns:

a Version object with the version of the Module

getUploadedDataFile

protected abstract DataFile getUploadedDataFile(DataFile file)
                                         throws IOException

Generate the DataFile Object for the uploaded DataFile

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

Generate the DataFile Object for the uploaded DataFile

Parameters:

file - DataFile to upload

portName - the port name

format - the format of the file to upload

sample - the sample for the source

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

Copy files to destinations.

Parameters:

files - map with source and destination for each file

Throws:

IOException - if an error occurs while copying files