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+ + + + + + + + + + + + +
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+ + + +
+ +

+ +compbio.engine.cluster.drmaa +
+Class JobRunner

+
+java.lang.Object
+  extended by 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
+ booleancancelJob() + +
+          Stops running job.
+ booleancleanup() + +
+          Clean up after the job
+ booleandeepClean() + +
+           
+ voidexecuteJob() + +
+          Execute the job
+static JobRunnergetInstance(ConfiguredExecutable<?> executable) + +
+           
+ org.ggf.drmaa.JobInfogetJobInfo() + +
+          This method will block before the calculation has completed and then + return the object containing a job execution statistics
+ JobStatusgetJobStatus() + +
+          Query the status of the job by its id.
+ StringgetWorkDirectory() + +
+           
+ 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
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + +