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

Class RserveRExecutor

java.lang.Object

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

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

All Implemented Interfaces:

RExecutor

public class RserveRExecutor
extends AbstractRExecutor

This class define a RServe RExecutor.

Since:

2.0

Author:

Laurent Jourdren

Field Summary

Fields

Modifier and Type	Field	Description
protected RSConnection	rConnection
static String	REXECUTOR_NAME

Constructor Summary

Constructors

Constructor	Description
RserveRExecutor(File outputDirectory, File temporaryDirectory, String serverName)	Public constructor.

Method Summary

Modifier and Type	Method	Description
void	closeConnection()	Close the connection.
protected void	executeRScript(File rScriptFile, boolean sweave, String sweaveOuput, File workflowOutputDir, String... scriptArguments)	Execute a R script.
String	getName()	Get the name of the RExecutor.
void	getOutputFiles()	Get the output files of the analysis
void	openConnection()	Open the connection.
protected void	putFile(DataFile inputFile, String inputFilename)	Put a file for the analysis.
protected void	removeFile(String filename)	Remove a file of the analysis.
void	writerFile(String content, String outputFilename)	Write a file.

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

executeRScript, getOutputDirectory, getTemporaryDirectory, 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

rConnection

protected RSConnection rConnection

Constructor Detail

RserveRExecutor

public RserveRExecutor(File outputDirectory,
                       File temporaryDirectory,
                       String serverName)
                throws IOException

Public constructor.

Parameters:

outputDirectory - the output directory

temporaryDirectory - the temporary directory

serverName - Rserve server name

Throws:

IOException - if an error occurs

Method Detail

getName

public String getName()

Description copied from interface: RExecutor

Get the name of the RExecutor.

Returns:

the name of the RExecutor

getOutputFiles

public void getOutputFiles()
                    throws IOException

Description copied from interface: RExecutor

Get the output files of the analysis

Specified by:

getOutputFiles in interface RExecutor

Overrides:

getOutputFiles in class AbstractRExecutor

Throws:

IOException - if an error occurs while getting the output files

openConnection

public void openConnection()
                    throws IOException

Description copied from interface: RExecutor

Open the connection.

Specified by:

openConnection in interface RExecutor

Overrides:

openConnection in class AbstractRExecutor

Throws:

IOException - if an error occurs while opening the connection

closeConnection

public void closeConnection()
                     throws IOException

Description copied from interface: RExecutor

Close the connection.

Specified by:

closeConnection in interface RExecutor

Overrides:

closeConnection in class AbstractRExecutor

Throws:

IOException - if an error occurs while closing the connection

removeFile

protected void removeFile(String filename)
                   throws IOException

Description copied from class: AbstractRExecutor

Remove a file of the analysis.

Specified by:

removeFile in class AbstractRExecutor

Parameters:

filename - the filename of the file to remove

Throws:

IOException - if the removing of the file fails

putFile

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

Description copied from class: AbstractRExecutor

Put a file for the analysis.

Specified by:

putFile in class AbstractRExecutor

Parameters:

inputFile - the input file

inputFilename - the output filename

Throws:

IOException - if an error occurs while putting the file

writerFile

public void writerFile(String content,
                       String outputFilename)
                throws IOException

Description copied from interface: RExecutor

Write a file.

Parameters:

content - the content of the file

outputFilename - the output filename

Throws:

IOException - if an exception occurs while writing a file

executeRScript

protected void executeRScript(File rScriptFile,
                              boolean sweave,
                              String sweaveOuput,
                              File workflowOutputDir,
                              String... scriptArguments)
                       throws IOException

Description copied from class: AbstractRExecutor

Execute a R script.

Specified by:

executeRScript in class AbstractRExecutor

Parameters:

rScriptFile - The R script file

sweave - execute the R using Sweave

sweaveOuput - sweave output file

scriptArguments - script arguments

Throws:

IOException - if an error occurs while executing the script