Package fr.ens.biologie.genomique.eoulsan.util.r

Class DockerRExecutor

java.lang.Object

fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor

fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor

fr.ens.biologie.genomique.eoulsan.util.r.DockerRExecutor

All Implemented Interfaces:

RExecutor

public class DockerRExecutor
extends ProcessRExecutor

This class define a Docker RExecutor.

Since:

2.0

Author:

Laurent Jourdren

Field Summary

Fields

Modifier and Type	Field	Description
static String	REXECUTOR_NAME

Fields inherited from class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor

DEFAULT_R_LANG, LANG_ENVIRONMENT_VARIABLE, RSCRIPT_EXECUTABLE

Constructor Summary

Constructors

Constructor	Description
DockerRExecutor(File outputDirectory, File temporaryDirectory, String dockerImage)	Constructor.

Method Summary

Modifier and Type	Method	Description
protected fr.ens.biologie.genomique.kenetre.util.process.SimpleProcess	createSimpleProcess()	Create the process that will execute the R Script.
String	getName()	Get the name of the RExecutor.
protected void	putFile(DataFile inputFile, String outputFilename)	Put a file for the analysis.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor

changeFileExtension, closeConnection, createCommand, executeRScript, isSameLocalPath, removeFile, writerFile

Methods inherited from class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor

executeRScript, getOutputDirectory, getOutputFiles, getTemporaryDirectory, openConnection, putInputFile, putInputFile, removeInputFiles

Methods inherited from class java.lang.Object

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

Field Detail

REXECUTOR_NAME

public static final String REXECUTOR_NAME

See Also:

Constant Field Values

Constructor Detail

DockerRExecutor

public DockerRExecutor(File outputDirectory,
                       File temporaryDirectory,
                       String dockerImage)
                throws IOException

Constructor.

Parameters:

outputDirectory - the output directory

temporaryDirectory - the temporary directory

dockerImage - docker image to use

Throws:

IOException - if an error occurs while creating the object

Method Detail

getName

public String getName()

Description copied from interface: RExecutor

Get the name of the RExecutor.

Specified by:

getName in interface RExecutor

Overrides:

getName in class ProcessRExecutor

Returns:

the name of the RExecutor

putFile

protected void putFile(DataFile inputFile,
                       String outputFilename)
                throws IOException

Description copied from class: AbstractRExecutor

Put a file for the analysis.

Overrides:

putFile in class ProcessRExecutor

Parameters:

inputFile - the input file

outputFilename - the output filename

Throws:

IOException - if an error occurs while putting the file

createSimpleProcess

protected fr.ens.biologie.genomique.kenetre.util.process.SimpleProcess createSimpleProcess()
                                                                                    throws IOException

Description copied from class: ProcessRExecutor

Create the process that will execute the R Script.

Overrides:

createSimpleProcess in class ProcessRExecutor

Returns:

a SimpleProcess object

Throws:

IOException - if an error occurs when creation the process object