org.broadinstitute.hellbender.utils.runtime

Class ScriptExecutor

java.lang.Object

org.broadinstitute.hellbender.utils.runtime.ScriptExecutor

Direct Known Subclasses:

PythonExecutorBase, RScriptExecutor

public abstract class ScriptExecutor
extends java.lang.Object

Base class for executors that find and run scripts in an external script engine process (R, Python, etc). Subclasses must implement: getApproximateCommandLine() getScriptException(java.lang.String)

Field Summary

Fields

Modifier and Type	Field and Description
protected java.lang.String	externalScriptExecutableName
protected boolean	ignoreExceptions

Constructor Summary

Constructors

Constructor and Description
ScriptExecutor(java.lang.String externalScriptExecutableName)

Method Summary

Modifier and Type	Method and Description
protected void	executableMissing()
protected boolean	executeCuratedArgs(java.lang.String[] commandLineArguments) Execute the script represented by the arguments in commandLineArguments.
boolean	externalExecutableExists()
abstract java.lang.String	getApproximateCommandLine() Return a (not necessarily executable) string representing the command line for this executor for error reporting purposes.
abstract ScriptExecutorException	getScriptException(java.lang.String message) Called by the script executor when error is encountered.
void	setIgnoreExceptions(boolean ignoreExceptions) Set to true to have the ScriptExecutor catch and ignore GATK exceptions.

Methods inherited from class java.lang.Object

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

Field Detail

externalScriptExecutableName

protected final java.lang.String externalScriptExecutableName

ignoreExceptions

protected boolean ignoreExceptions

Constructor Detail

ScriptExecutor

public ScriptExecutor(java.lang.String externalScriptExecutableName)

Parameters:

externalScriptExecutableName - Name of the script engine to run (i.e. "RScript" or "python")

Method Detail

externalExecutableExists

public boolean externalExecutableExists()

Returns:

true if the executable exists and can be found on the path

setIgnoreExceptions

public void setIgnoreExceptions(boolean ignoreExceptions)

Set to true to have the ScriptExecutor catch and ignore GATK exceptions.

Parameters:

ignoreExceptions -

getApproximateCommandLine

public abstract java.lang.String getApproximateCommandLine()

Return a (not necessarily executable) string representing the command line for this executor for error reporting purposes.

Returns:

Command line string.

executableMissing

protected void executableMissing()

getScriptException

public abstract ScriptExecutorException getScriptException(java.lang.String message)

Called by the script executor when error is encountered. Subclasses should override and return an exception that is a subclass of ScriptExecutorException.

Parameters:

message - String with the cause of the exception.

Returns:

a {#ScriptExecutorException}-derived exception object

executeCuratedArgs

protected boolean executeCuratedArgs(java.lang.String[] commandLineArguments)

Execute the script represented by the arguments in commandLineArguments.

Parameters:

commandLineArguments -

Returns:

true if the command executed successfully, otherwise false