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
static final String	REXECUTOR_NAME
static final String	RSCRIPT_EXECUTABLE

Method Summary

Modifier and Type	Method	Description
void	closeConnection()	Close the connection.
void	executeR(String code, File workflowOutputDir)
String	getName()	Get the name of the RExecutor.
void	writeFile(String content, String outputFilename)	Write a file.

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

executeRScript, executeRScript, getOutputFiles, openConnection, putInputFile, putInputFile, removeInputFiles

Methods inherited from class java.lang.Object

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

Field Details

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

Method Details

getName

public String getName()

Description copied from interface: RExecutor

Get the name of the RExecutor.

Returns:

the name of the RExecutor

writeFile

public void writeFile(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

executeR

public void executeR(String code,
 File workflowOutputDir)
              throws IOException

Throws:

IOException

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