Package org.broadinstitute.hellbender.utils.python

Class PythonExecutorBase

java.lang.Object

org.broadinstitute.hellbender.utils.runtime.ScriptExecutor

org.broadinstitute.hellbender.utils.python.PythonExecutorBase

Direct Known Subclasses:

PythonScriptExecutor, StreamingPythonScriptExecutor

public abstract class PythonExecutorBase
extends ScriptExecutor

Base class for services for executing Python Scripts.

• All tools that use PythonScriptExecutor must have a Java-based front-end, with standard GATK (Barclay-based) arguments.
• Minimize the amount of code written in Python -- as much of each tool's work as possible should be done in Java. In particular, reading/writing final inputs and outputs should happen in Java. This is important to ensure the goal of universal GCS support, consistent Google authentication handling, etc.
• The names of any files that are created by Python code should be passed in to the python code from Java.
• All dependencies (Python and native) of Python libraries used should be clearly documented, and included in the default GATK docker image.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	PythonExecutorBase.PythonExecutableName	Enum of possible executables that can be launched by this executor.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	PYTHON_EXTENSION

Fields inherited from class org.broadinstitute.hellbender.utils.runtime.ScriptExecutor

externalScriptExecutableName, ignoreExceptions

Constructor Summary

Constructors

Constructor	Description
PythonExecutorBase(boolean ensureExecutableExists)
PythonExecutorBase(PythonExecutorBase.PythonExecutableName pythonExecutableName, boolean ensureExecutableExists)

Method Summary

Modifier and Type	Method	Description
abstract String	getApproximateCommandLine()	Return a (not necessarily executable) string representing the current command line for this executor for error reporting purposes.
ScriptExecutorException	getScriptException(String message)	Return an exception specific to this executor type, to be thrown on error conditions.

Methods inherited from class org.broadinstitute.hellbender.utils.runtime.ScriptExecutor

executableMissing, executeCuratedArgs, executeCuratedArgsAndGetOutput, externalExecutableExists, getExceptionMessageFromScriptError, setIgnoreExceptions

Methods inherited from class java.lang.Object

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

Field Details

PYTHON_EXTENSION

public static final String PYTHON_EXTENSION

See Also:

• Constant Field Values

Constructor Details

PythonExecutorBase

public PythonExecutorBase(boolean ensureExecutableExists)

Parameters:

ensureExecutableExists - throw if the python executable cannot be located

PythonExecutorBase

public PythonExecutorBase(PythonExecutorBase.PythonExecutableName pythonExecutableName,
 boolean ensureExecutableExists)

Parameters:

pythonExecutableName - name of the python executable to start

ensureExecutableExists - throw if the python executable cannot be found

Method Details

getScriptException

public ScriptExecutorException getScriptException(String message)

Return an exception specific to this executor type, to be thrown on error conditions.

Specified by:

getScriptException in class ScriptExecutor

Parameters:

message -

Returns:

a {#ScriptExecutorException}-derived exception object

getApproximateCommandLine

public abstract String getApproximateCommandLine()

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

Specified by:

getApproximateCommandLine in class ScriptExecutor

Returns:

Command line string.