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

Interface RExecutor

All Known Implementing Classes:

AbstractRExecutor, DockerRExecutor, ProcessRExecutor, RserveRExecutor

public interface RExecutor

This interface define how to prepare, launch and retrieve data of a R analysis.

Since:

2.0

Author:

Laurent Jourdren

Method Summary

Modifier and Type	Method	Description
void	closeConnection()	Close the connection.
void	executeRScript(String rScript, boolean sweave, String sweaveOutput, boolean saveRscript, String description, DataFile workflowOutputDir, String... scriptArguments)	Execute a R script.
void	executeRScript(String code, String description, DataFile workflowOutputDir)	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.
void	putInputFile(DataFile inputFile)	Put a file for the analysis.
void	putInputFile(DataFile inputFile, String outputFilename)	Put a file.
void	removeInputFiles()	Remove input files.
void	writeFile(String content, String outputFilename)	Write a file.

Method Details

getName

String getName()

Get the name of the RExecutor.

Returns:

the name of the RExecutor

openConnection

void openConnection()
             throws IOException

Open the connection.

Throws:

IOException - if an error occurs while opening the connection

closeConnection

void closeConnection()
              throws IOException

Close the connection.

Throws:

IOException - if an error occurs while closing the connection

putInputFile

void putInputFile(DataFile inputFile)
           throws IOException

Put a file for the analysis.

Parameters:

inputFile - the input file

Throws:

IOException - if an error occurs while putting the file

putInputFile

void putInputFile(DataFile inputFile,
 String outputFilename)
           throws IOException

Put a file.

Parameters:

inputFile - the file to put

outputFilename - the output filename

Throws:

IOException - if an exception occurs while putting a file

writeFile

void writeFile(String content,
 String outputFilename)
        throws IOException

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

void executeRScript(String rScript,
 boolean sweave,
 String sweaveOutput,
 boolean saveRscript,
 String description,
 DataFile workflowOutputDir,
 String... scriptArguments)
             throws IOException

Execute a R script.

Parameters:

rScript - the source of the script to execute

sweave - true if the script is a Sweave script

sweaveOutput - Sweave output file

saveRscript - true to keep the R script

description - description of the R script

workflowOutputDir - workflow output directory

scriptArguments - script arguments

Throws:

IOException - if an error occurs while executing the script

executeRScript

void executeRScript(String code,
 String description,
 DataFile workflowOutputDir)
             throws IOException

Execute a R script.

Parameters:

code - code to execute

description - description of the R script

workflowOutputDir - workflow output directory

Throws:

IOException - if an error occurs while executing the script

removeInputFiles

void removeInputFiles()
               throws IOException

Remove input files.

Throws:

IOException - if an error occurs while removing the files

getOutputFiles

void getOutputFiles()
             throws IOException

Get the output files of the analysis

Throws:

IOException - if an error occurs while getting the output files