org.molgenis.util

Class RScript

java.lang.Object

org.molgenis.util.RScript

public class RScript
extends Object

This class provides an handle to an R script

• it has a static path to the R command
• it can start the script
• it can create a temp file

Author:

P219083

Field Summary

Fields

Modifier and Type	Field and Description
String	R_COMMAND command to run R

Constructor Summary

Constructors

Constructor and Description
RScript() Construct an R script object

Method Summary

Methods

Modifier and Type	Method and Description
void	append(String command) Add a command to the r script.
void	append(String command, Object... args) Add a command to the r script as a template
void	copyFile(String fromPath, String toPath) Helper function to copy a file
void	deleteFile(String path) Helper function to delete a file
String	execute() Execute the R script.
String	execute(String scriptPathName) Execute the R script.
String	getErrors()
String	getOutput()
String	getR_COMMAND()
String	getResult()
void	setR_COMMAND(String r_COMMAND)
String	toString() Show the contents of the R script that has been created

Methods inherited from class java.lang.Object

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

Field Detail

R_COMMAND

public String R_COMMAND

command to run R

Constructor Detail

RScript

public RScript()

Construct an R script object

Method Detail

getErrors

public String getErrors()

getOutput

public String getOutput()

getResult

public String getResult()

getR_COMMAND

public String getR_COMMAND()

setR_COMMAND

public void setR_COMMAND(String r_COMMAND)

append

public void append(String command)

Add a command to the r script.

Parameters:

command -

append

public void append(String command,
          Object... args)

Add a command to the r script as a template

Parameters:

command -

args - a variable list of arguments

execute

public String execute()
               throws RScriptException

Execute the R script.

Returns:

the output of the script

Throws:

RScriptException

execute

public String execute(String scriptPathName)
               throws RScriptException

Execute the R script. Extra parameter for specifying file name.

Returns:

the output of the script

Throws:

RScriptException

copyFile

public void copyFile(String fromPath,
            String toPath)
              throws Exception

Helper function to copy a file

Throws:

Exception

deleteFile

public void deleteFile(String path)
                throws Exception

Helper function to delete a file

Throws:

Exception

toString

public String toString()

Show the contents of the R script that has been created

Overrides:

toString in class Object