compbio.engine.cluster.drmaa
Class JobRunner

java.lang.Object
  compbio.engine.cluster.drmaa.JobRunner

All Implemented Interfaces:

SyncExecutor

public class JobRunner
extends Object
implements SyncExecutor

Single cluster job runner class

Author:

pvtroshin

Constructor Summary

JobRunner(ConfiguredExecutable<?> confExec)

Method Summary

boolean	cancelJob() Stops running job.
boolean	cleanup() Clean up after the job
boolean	deepClean()
void	executeJob() Execute the job
static JobRunner	getInstance(ConfiguredExecutable<?> executable)
org.ggf.drmaa.JobInfo	getJobInfo() This method will block before the calculation has completed and then return the object containing a job execution statistics
JobStatus	getJobStatus() Query the status of the job by its id.
String	getWorkDirectory()
ConfiguredExecutable<?>	waitForResult() Call to this method block for as long as it is required for an executable to finish its job.

Methods inherited from class java.lang.Object

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

Constructor Detail

JobRunner

public JobRunner(ConfiguredExecutable<?> confExec)
          throws JobSubmissionException

Throws:

JobSubmissionException

Method Detail

deepClean

public boolean deepClean()

cleanup

public boolean cleanup()

Description copied from interface: SyncExecutor

Clean up after the job

Specified by:

cleanup in interface SyncExecutor

Returns:

true if all the files created by this job have been removed successfully, false otherwise

cancelJob

public boolean cancelJob()

Description copied from interface: SyncExecutor

Stops running job. Clean up is not performed.

Specified by:

cancelJob in interface SyncExecutor

Returns:

true if job was cancelled successfully, false otherwise

getWorkDirectory

public String getWorkDirectory()

Specified by:

getWorkDirectory in interface SyncExecutor

Returns:

working directory if the task

executeJob

public void executeJob()
                throws JobSubmissionException

Description copied from interface: SyncExecutor

Execute the job

Specified by:

executeJob in interface SyncExecutor

Throws:

JobSubmissionException - if submission fails

getJobInfo

public org.ggf.drmaa.JobInfo getJobInfo()
                                 throws JobExecutionException

This method will block before the calculation has completed and then return the object containing a job execution statistics

Returns:

Throws:

JobExecutionException

waitForResult

public ConfiguredExecutable<?> waitForResult()
                                      throws JobExecutionException

Description copied from interface: SyncExecutor

Call to this method block for as long as it is required for an executable to finish its job. If the calculation has been completed already, the this method returns results immediately. This could return the result directly, but that would be type unsafe

Specified by:

waitForResult in interface SyncExecutor

Returns:

object from wich the result can be obtained

Throws:

JobExecutionException

getJobStatus

public JobStatus getJobStatus()

Description copied from interface: SyncExecutor

Query the status of the job by its id.

Specified by:

getJobStatus in interface SyncExecutor

Returns:

- JobStatus

getInstance

public static JobRunner getInstance(ConfiguredExecutable<?> executable)
                             throws JobSubmissionException

Throws:

JobSubmissionException