Package fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters

Class AbstractExecutorInterpreter

java.lang.Object

fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.AbstractExecutorInterpreter

All Implemented Interfaces:

ExecutorInterpreter

Direct Known Subclasses:

DefaultExecutorInterpreter, DockerExecutorInterpreter, GenericExecutorInterpreter

public abstract class AbstractExecutorInterpreter
extends Object
implements ExecutorInterpreter

This class define an abstract executor interpreter that contains the default implementation of the execute() method that use a ProcessBuilder.

Since:

2.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
AbstractExecutorInterpreter()

Method Summary

Modifier and Type	Method	Description
ToolExecutorResult	execute(List<String> commandLine, File executionDirectory, File temporaryDirectory, File stdoutFile, File stderrFile, File... filesUsed)	Execute a command line.
protected fr.ens.biologie.genomique.kenetre.util.process.SimpleProcess	newSimpleProcess()	Create a new SimpleProcess that will be use to launch the command.

Methods inherited from class java.lang.Object

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

Methods inherited from interface fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.ExecutorInterpreter

createCommandLine, getName

Constructor Detail

AbstractExecutorInterpreter

public AbstractExecutorInterpreter()

Method Detail

newSimpleProcess

protected fr.ens.biologie.genomique.kenetre.util.process.SimpleProcess newSimpleProcess()
                                                                                 throws IOException

Create a new SimpleProcess that will be use to launch the command.

Returns:

a new SimpleProcess object

Throws:

IOException - if an error occurs while creating the process

execute

public ToolExecutorResult execute(List<String> commandLine,
                                  File executionDirectory,
                                  File temporaryDirectory,
                                  File stdoutFile,
                                  File stderrFile,
                                  File... filesUsed)
                           throws IOException

Description copied from interface: ExecutorInterpreter

Execute a command line.

Specified by:

execute in interface ExecutorInterpreter

Parameters:

commandLine - the command line to execute

executionDirectory - execution directory

temporaryDirectory - temporary directory

stdoutFile - stdout file

stderrFile - stderr file

filesUsed - files used

Returns:

a ToolExecutor object

Throws:

IOException - if an error occurs while executing the command