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

Class RSConnection

java.lang.Object

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

public class RSConnection
extends Object

This class define an enhanced connection to RServe.

Since:

1.2

Author:

Laurent Jourdren, Marion Gaussen

Constructor Summary

Constructors

Constructor	Description
RSConnection()	Default constructor.
RSConnection(String serverName)	Public constructor.

Method Summary

Modifier and Type	Method	Description
void	disConnect()	Destroy the connection to the Rserve server.
void	executeRCode(String source)	Execute a R code.
void	executeRnwCode(String source)	Execute a R Sweave code.
void	executeRnwCode(String source, String latexOutput)	Execute a R Sweave code.
void	getAllFiles(File outPath)	Get all the file on the Rserve server.
void	getFile(String rServeFilename, File outputFile)	Get a file from the RServer.
byte[]	getFileAsArray(String filename)	Get a file as a byte array.
InputStream	getFileInputStream(String filename)	Create an inputStream on a file on RServer.
OutputStream	getFileOutputStream(String filename)	Create an outputStream on a file on RServer.
void	getFilesIntoZip(List<String> rServeFilenames, File zipFile)	Get a list of files from the RServer.
org.rosuda.REngine.Rserve.RConnection	getRConnection()	Get the R connection.
String	getServerName()	Get the name of the Rserve server.
List<String>	listFiles()	List files on Rserve server.
Image	loadImage(String filename)	Load an image.
org.rosuda.REngine.Rserve.RFileInputStream	openFile(String filename)	Open a file to read on Rserve server.
void	putFile(File inputFile, String rServeFilename)	Put a file from the RServer.
void	putFile(InputStream is, String rServeFilename)	Put a file from the RServer.
void	removeAllFiles()	Remove all the files of the working directory.
void	removeFile(String filename)	Remove a file on the RServer.
void	setCommandArgs(List<String> arguments)	Override the commandArg() R function.
void	writeStringAsFile(String outputFilename, String value)	Write a file to the RServer.

Methods inherited from class java.lang.Object

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

Constructor Detail

RSConnection

public RSConnection()

Default constructor. Connect to the localhost.

RSConnection

public RSConnection(String serverName)

Public constructor.

Parameters:

serverName - RServe server to use

Method Detail

getRConnection

public org.rosuda.REngine.Rserve.RConnection getRConnection()
                                                     throws org.rosuda.REngine.REngineException

Get the R connection.

Returns:

Returns the RConnection

Throws:

org.rosuda.REngine.REngineException - if an error occurs while connecting to the server

getServerName

public String getServerName()

Get the name of the Rserve server.

Returns:

the name of the Rserve server

writeStringAsFile

public void writeStringAsFile(String outputFilename,
                              String value)
                       throws org.rosuda.REngine.REngineException

Write a file to the RServer.

Parameters:

outputFilename - the filename

value - The content of the file

Throws:

org.rosuda.REngine.REngineException - if an error occurs while writing the file

getFileInputStream

public InputStream getFileInputStream(String filename)
                               throws org.rosuda.REngine.REngineException

Create an inputStream on a file on RServer.

Parameters:

filename - Name of the file on RServer to load

Returns:

an inputStream

Throws:

org.rosuda.REngine.REngineException - if an exception occurs while reading file

getFileOutputStream

public OutputStream getFileOutputStream(String filename)
                                 throws org.rosuda.REngine.REngineException

Create an outputStream on a file on RServer.

Parameters:

filename - Name of the file on RServer to write

Returns:

an outputStream

Throws:

org.rosuda.REngine.REngineException - if an exception occurs while reading file

putFile

public void putFile(File inputFile,
                    String rServeFilename)
             throws org.rosuda.REngine.REngineException

Put a file from the RServer.

Parameters:

inputFile - input file of the file to put

rServeFilename - filename of the file to put

Throws:

org.rosuda.REngine.REngineException - if an error occurs while downloading the file

putFile

public void putFile(InputStream is,
                    String rServeFilename)
             throws org.rosuda.REngine.REngineException

Put a file from the RServer.

Parameters:

is - input stream of the file to put

rServeFilename - filename of the file to put

Throws:

org.rosuda.REngine.REngineException - if an error occurs while downloading the file

getFile

public void getFile(String rServeFilename,
                    File outputFile)
             throws org.rosuda.REngine.REngineException

Get a file from the RServer.

Parameters:

rServeFilename - filename of the file to retrieve

outputFile - output file of the file to retrieve

Throws:

org.rosuda.REngine.REngineException - if an error occurs while downloading the file

getFilesIntoZip

public void getFilesIntoZip(List<String> rServeFilenames,
                            File zipFile)
                     throws org.rosuda.REngine.REngineException

Get a list of files from the RServer.

Parameters:

rServeFilenames - list of filenames of the files to retrieve

zipFile - zip output file for the files to retrieve

Throws:

org.rosuda.REngine.REngineException - if an error occurs while downloading the file

removeFile

public void removeFile(String filename)
                throws org.rosuda.REngine.REngineException

Remove a file on the RServer.

Parameters:

filename - File to remove

Throws:

org.rosuda.REngine.REngineException

removeAllFiles

public void removeAllFiles()
                    throws org.rosuda.REngine.REngineException,
                           org.rosuda.REngine.REXPMismatchException

Remove all the files of the working directory.

Throws:

org.rosuda.REngine.REngineException - if an error occurs while removing the file

org.rosuda.REngine.REXPMismatchException - if an error occurs while removing the file

setCommandArgs

public void setCommandArgs(List<String> arguments)
                    throws org.rosuda.REngine.REngineException

Override the commandArg() R function.

Parameters:

arguments - the arguments

Throws:

org.rosuda.REngine.REngineException - if an error occurs while executing R code

executeRCode

public void executeRCode(String source)
                  throws org.rosuda.REngine.REngineException

Execute a R code.

Parameters:

source - code to execute

Throws:

org.rosuda.REngine.REngineException - if an error while executing the code

executeRnwCode

public void executeRnwCode(String source)
                    throws org.rosuda.REngine.REngineException

Execute a R Sweave code.

Parameters:

source - code to execute

Throws:

org.rosuda.REngine.REngineException - if an error while executing the code

executeRnwCode

public void executeRnwCode(String source,
                           String latexOutput)
                    throws org.rosuda.REngine.REngineException

Execute a R Sweave code.

Parameters:

source - code to execute

latexOutput - output latex filename

Throws:

org.rosuda.REngine.REngineException - if an error while executing the code

loadImage

public Image loadImage(String filename)
                throws org.rosuda.REngine.REngineException

Load an image.

Parameters:

filename - filename of the image on the server

Returns:

an Image object

Throws:

org.rosuda.REngine.REngineException - if an error while loading the image

getFileAsArray

public byte[] getFileAsArray(String filename)
                      throws org.rosuda.REngine.REngineException

Get a file as a byte array.

Parameters:

filename - filename of the file on the server

Returns:

a byte array

Throws:

org.rosuda.REngine.REngineException - if an error while loading the file

openFile

public org.rosuda.REngine.Rserve.RFileInputStream openFile(String filename)
                                                    throws org.rosuda.REngine.REngineException

Open a file to read on Rserve server.

Parameters:

filename - the filename

Returns:

an input stream

Throws:

org.rosuda.REngine.REngineException - if an error occurs while creating the input stream

getAllFiles

public void getAllFiles(File outPath)
                 throws org.rosuda.REngine.REngineException,
                        org.rosuda.REngine.REXPMismatchException

Get all the file on the Rserve server.

Parameters:

outPath - the output path

Throws:

org.rosuda.REngine.REngineException - if an error occurs while retrieving the files

org.rosuda.REngine.REXPMismatchException - if an error occurs while retrieving the files

listFiles

public List<String> listFiles()
                       throws org.rosuda.REngine.REngineException,
                              org.rosuda.REngine.REXPMismatchException

List files on Rserve server.

Returns:

files a String list of files names

Throws:

org.rosuda.REngine.REngineException - if an error occurs with the server

org.rosuda.REngine.REXPMismatchException - if an error occurs with the server

disConnect

public void disConnect()

Destroy the connection to the Rserve server.