org.aktin.scripting.r

Class RScript

java.lang.Object

org.aktin.scripting.r.RScript

public class RScript
extends Object

Takes data files from DataExtractor (patient, encounter, etc.) and runs an R script via the command Rscript.

The script should write all generated output (e.g. plots, diagrams, tables) to files in the working directory. The script should not output anything on stdout or stderr. Any output on stdout is treated as warnings, any output on stderr is treated as error messages.

Author:

R.W.Majeed

Constructor Summary

Constructors

Constructor and Description
RScript(Path executable)

Method Summary

Modifier and Type	Method and Description
String	convertStreamToString(InputStream is)
Map<String,String>	getPackageVersions()
String	getVersion()
void	runRscript(Path workingDir, String mainScript, Integer waitMillis) Run the Rscript executable.

Methods inherited from class java.lang.Object

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

Constructor Detail

RScript

public RScript(Path executable)

Method Detail

getVersion

public String getVersion()
                  throws IOException

Throws:

IOException

getPackageVersions

public Map<String,String> getPackageVersions()
                                      throws IOException

Throws:

IOException

runRscript

public void runRscript(Path workingDir,
                       String mainScript,
                       Integer waitMillis)
                throws IOException,
                       TimeoutException,
                       AbnormalTerminationException

Run the Rscript executable. Working directory will be set as specified in the arguments, as well as the main script.

Parameters:

workingDir - Working directory for the Rscript executable. It must contain at least the file specified in the next argument.

mainScript - File name for the main script to be executed in the working directory. The directory must contain the specified file name.

waitMillis - Time to wait for the process to finish. If null the process will wait without limit.

Throws:

IOException - IO error, e.g. with processing the process' output

TimeoutException - the specified timeout elapsed before the process exited

AbnormalTerminationException - process terminated abnormally. the provided script did not execute successfully. For exit code and STDERR output see AbnormalTerminationException.

convertStreamToString

public String convertStreamToString(InputStream is)
                             throws IOException

Throws:

IOException