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

Class ProcessRExecutor

java.lang.Object

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

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

All Implemented Interfaces:

RExecutor

Direct Known Subclasses:

DockerRExecutor

public class ProcessRExecutor
extends AbstractRExecutor

This class define a standard RExecutor using a system process.

Since:

2.0

Author:

Laurent Jourdren

Field Summary

Fields

Modifier and Type	Field	Description
protected static String	DEFAULT_R_LANG
protected static String	LANG_ENVIRONMENT_VARIABLE
static String	REXECUTOR_NAME
static String	RSCRIPT_EXECUTABLE

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	ProcessRExecutor(File outputDirectory, File temporaryDirectory)	Constructor.

Method Summary

Modifier and Type	Method	Description
protected static File	changeFileExtension(File file, String newExtension)	Change the extendsion of a file
void	closeConnection()	Close the connection.
protected List<String>	createCommand(File rScriptFile, boolean sweave, String sweaveOuput, String... scriptArguments)	Create R command.
protected fr.ens.biologie.genomique.kenetre.util.process.SimpleProcess	createSimpleProcess()	Create the process that will execute the R Script.
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.
protected static boolean	isSameLocalPath(DataFile a, DataFile b)	Check if two file have the same local path
protected void	putFile(DataFile inputFile, String outputFilename)	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, 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

RSCRIPT_EXECUTABLE

public static final String RSCRIPT_EXECUTABLE

See Also:

Constant Field Values

LANG_ENVIRONMENT_VARIABLE

protected static final String LANG_ENVIRONMENT_VARIABLE

See Also:

Constant Field Values

DEFAULT_R_LANG

protected static final String DEFAULT_R_LANG

See Also:

Constant Field Values

Constructor Detail

ProcessRExecutor

protected ProcessRExecutor(File outputDirectory,
                           File temporaryDirectory)
                    throws IOException

Constructor.

Parameters:

outputDirectory - the output directory

temporaryDirectory - the temporary directory

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.

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.

Specified by:

putFile in class AbstractRExecutor

Parameters:

inputFile - the input file

outputFilename - 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

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

createCommand

protected List<String> createCommand(File rScriptFile,
                                     boolean sweave,
                                     String sweaveOuput,
                                     String... scriptArguments)

Create R command.

Parameters:

rScriptFile - the R script file to execute

sweave - true if the script is a Sweave file

scriptArguments - script arguments

Returns:

the R command as a list

createSimpleProcess

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

Create the process that will execute the R Script.

Returns:

a SimpleProcess object

Throws:

IOException - if an error occurs when creation the process object

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

changeFileExtension

protected static File changeFileExtension(File file,
                                          String newExtension)

Change the extendsion of a file

Parameters:

file - the file

newExtension - the new extension of the file

Returns:

a file object

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

isSameLocalPath

protected static boolean isSameLocalPath(DataFile a,
                                         DataFile b)

Check if two file have the same local path

Parameters:

a - first file

b - second file

Returns:

true if the file have the same local file