org.broadinstitute.hellbender.utils.python

Class PythonScriptExecutor

java.lang.Object

org.broadinstitute.hellbender.utils.runtime.ScriptExecutor

org.broadinstitute.hellbender.utils.python.PythonExecutorBase

org.broadinstitute.hellbender.utils.python.PythonScriptExecutor

public class PythonScriptExecutor
extends PythonExecutorBase

Generic service 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.

NOTE: Serial executions on the same PythonScriptExecutor are each run in a new process. No python state is retained between command/script/module execution. Using -i doesn't buy you anything (for this version of the executor, at least) since the process is terminated after each command completes.

Nested Class Summary

Nested classes/interfaces inherited from class org.broadinstitute.hellbender.utils.python.PythonExecutorBase

PythonExecutorBase.PythonExecutableName

Field Summary

Fields inherited from class org.broadinstitute.hellbender.utils.python.PythonExecutorBase

PYTHON_EXTENSION

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

externalScriptExecutableName, ignoreExceptions

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
static void	checkPythonEnvironmentForPackage(java.lang.String packageName)
boolean	executeArgs(java.util.List<java.lang.String> rawArgs) Executes the Python executor using the values in rawArgs
boolean	executeCommand(java.lang.String command, java.util.List<java.lang.String> pythonProcessArgs, java.util.List<java.lang.String> scriptArgs) Execute a python command (-c).
boolean	executeModule(java.lang.String moduleName, java.util.List<java.lang.String> pythonProcessArgs, java.util.List<java.lang.String> scriptArgs) Execute a python module (-m).
boolean	executeScript(Resource scriptResource, java.util.List<java.lang.String> pythonProcessArgs, java.util.List<java.lang.String> scriptArgs) Execute a python script from a Resource file.
boolean	executeScript(java.lang.String scriptName, java.util.List<java.lang.String> pythonProcessArgs, java.util.List<java.lang.String> scriptArgs) Execute a python script.
java.lang.String	getApproximateCommandLine() Return a (not necessarily executable) string representing the current command line for this executor for error reporting purposes.

Methods inherited from class org.broadinstitute.hellbender.utils.python.PythonExecutorBase

getScriptException

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

executableMissing, executeCuratedArgs, externalExecutableExists, setIgnoreExceptions

Methods inherited from class java.lang.Object

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

Constructor Detail

PythonScriptExecutor

public PythonScriptExecutor(boolean ensureExecutableExists)

Parameters:

ensureExecutableExists - throw if the python executable cannot be located

PythonScriptExecutor

public PythonScriptExecutor(PythonExecutorBase.PythonExecutableName pythonExecutableName,
                            boolean ensureExecutableExists)

Parameters:

pythonExecutableName - name of the python executable to start

ensureExecutableExists - throw if the python executable cannot be found

Method Detail

executeCommand

public boolean executeCommand(java.lang.String command,
                              java.util.List<java.lang.String> pythonProcessArgs,
                              java.util.List<java.lang.String> scriptArgs)

Execute a python command (-c). No intermediate shell is created.

Parameters:

command - python command to be executed

pythonProcessArgs - args to be passed to the python process

scriptArgs - args to be passed to the python code

Returns:

true if the command succeeds, otherwise false

executeModule

public boolean executeModule(java.lang.String moduleName,
                             java.util.List<java.lang.String> pythonProcessArgs,
                             java.util.List<java.lang.String> scriptArgs)

Execute a python module (-m). Modules must be on sys.path

Parameters:

moduleName - name of the module to execute

pythonProcessArgs - args to be passed to the python process

scriptArgs - args to be passed to the python code

Returns:

true if the command succeeds, otherwise false

executeScript

public boolean executeScript(Resource scriptResource,
                             java.util.List<java.lang.String> pythonProcessArgs,
                             java.util.List<java.lang.String> scriptArgs)

Execute a python script from a Resource file.

Parameters:

scriptResource - Resource for the script to execute

pythonProcessArgs - args to be passed to the python process

scriptArgs - args to be passed to the python code

Returns:

true if the command succeeds, otherwise false

executeScript

public boolean executeScript(java.lang.String scriptName,
                             java.util.List<java.lang.String> pythonProcessArgs,
                             java.util.List<java.lang.String> scriptArgs)

Execute a python script.

Parameters:

scriptName - full path name of the script to execute

pythonProcessArgs - args to be passed to the python process

scriptArgs - args to be passed to the python code

Returns:

true if the command succeeds

executeArgs

public boolean executeArgs(java.util.List<java.lang.String> rawArgs)

Executes the Python executor using the values in rawArgs

Parameters:

rawArgs - raw command line arguments to be passed to the Python process

Returns:

true if the command succeeds, otherwise false

getApproximateCommandLine

public java.lang.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 PythonExecutorBase

Returns:

Command line string.

checkPythonEnvironmentForPackage

public static void checkPythonEnvironmentForPackage(java.lang.String packageName)