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

Class CopyInputDataModule

java.lang.Object

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

fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule

All Implemented Interfaces:

Module

public class CopyInputDataModule
extends AbstractModule

Copy input files of a format in another location or in different compression format.

Since:

2.0

Author:

Laurent Jourdren

Field Summary

Fields

Modifier and Type	Field	Description
static String	FORMAT_PARAMETER
static String	MODULE_NAME
static String	OUTPUT_COMPRESSION_PARAMETER
static String	OUTPUT_COMPRESSIONS_ALLOWED_PARAMETER

Constructor Summary

Constructors

Constructor	Description
CopyInputDataModule()

Method Summary

Modifier and Type	Method	Description
void	configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the module.
static String	encodeAllowedCompressionsParameterValue(EnumSet<fr.ens.biologie.genomique.kenetre.io.CompressionType> outputCompressionAllowed)	Method to encode an EnumSet of the allowed compressions parameter in a string.
TaskResult	execute(TaskContext context, TaskStatus status)	Execute a task step.
InputPorts	getInputPorts()	Get the input data format.
String	getName()	Get the name of the module.
OutputPorts	getOutputPorts()	Get the output data format.
fr.ens.biologie.genomique.kenetre.util.Version	getVersion()	Get version of the Module.

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

getChecker, getDescription, getParallelizationMode, getRequiredEoulsanVersion, getRequirements

Methods inherited from class java.lang.Object

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

Field Detail

MODULE_NAME

public static final String MODULE_NAME

See Also:

Constant Field Values

FORMAT_PARAMETER

public static final String FORMAT_PARAMETER

See Also:

Constant Field Values

OUTPUT_COMPRESSION_PARAMETER

public static final String OUTPUT_COMPRESSION_PARAMETER

See Also:

Constant Field Values

OUTPUT_COMPRESSIONS_ALLOWED_PARAMETER

public static final String OUTPUT_COMPRESSIONS_ALLOWED_PARAMETER

See Also:

Constant Field Values

Constructor Detail

CopyInputDataModule

public CopyInputDataModule()

Method Detail

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

getInputPorts

public InputPorts getInputPorts()

Description copied from interface: Module

Get the input data format.

Specified by:

getInputPorts in interface Module

Overrides:

getInputPorts in class AbstractModule

Returns:

a set with DataFormat or null if the module does not any need input format

getOutputPorts

public OutputPorts getOutputPorts()

Description copied from interface: Module

Get the output data format.

Specified by:

getOutputPorts in interface Module

Overrides:

getOutputPorts in class AbstractModule

Returns:

an set with DataFormat or null if the module does not produce any output data

configure

public void configure(StepConfigurationContext context,
                      Set<Parameter> stepParameters)
               throws EoulsanException

Description copied from interface: Module

Set the parameters of the step to configure the module.

Specified by:

configure in interface Module

Overrides:

configure in class AbstractModule

Parameters:

context - configuration context. The context can be null for generator steps

stepParameters - parameters of the step

Throws:

EoulsanException - if a parameter is invalid

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

encodeAllowedCompressionsParameterValue

public static String encodeAllowedCompressionsParameterValue(EnumSet<fr.ens.biologie.genomique.kenetre.io.CompressionType> outputCompressionAllowed)

Method to encode an EnumSet of the allowed compressions parameter in a string.

Parameters:

outputCompressionAllowed - the EnumSet to encode

Returns:

a string with the EnumSet encoded