Package ca.corefacility.bioinformatics.irida.service.impl

Class AnalysisExecutionScheduledTaskImpl

java.lang.Object

ca.corefacility.bioinformatics.irida.service.impl.AnalysisExecutionScheduledTaskImpl

All Implemented Interfaces:

AnalysisExecutionScheduledTask

public class AnalysisExecutionScheduledTaskImpl
extends java.lang.Object
implements AnalysisExecutionScheduledTask

Implementation of analysis execution tasks. This will scan for AnalysisSubmissions and execute the Analysis defined by the submissions.

Constructor Summary

Constructors

Constructor	Description
AnalysisExecutionScheduledTaskImpl(AnalysisSubmissionRepository analysisSubmissionRepository, AnalysisExecutionService analysisExecutionServiceGalaxy, CleanupAnalysisSubmissionCondition cleanupCondition, GalaxyJobErrorsService galaxyJobErrorsService, JobErrorRepository jobErrorRepository, EmailController emailController, AnalysisWorkspaceService analysisWorkspaceService)	Builds a new AnalysisExecutionScheduledTaskImpl with the given service classes.

Method Summary

Modifier and Type	Method	Description
java.util.Set<java.util.concurrent.Future<AnalysisSubmission>>	cleanupAnalysisSubmissions()	Cycle through any completed or errored AnalysisSubmissions and delete intermediate files in the execution manager.
java.util.Set<java.util.concurrent.Future<AnalysisSubmission>>	executeAnalyses()	Cycle through any outstanding AnalysisSubmissions and execute them.
java.util.Set<java.util.concurrent.Future<AnalysisSubmission>>	monitorRunningAnalyses()	Cycle through any AnalysisSubmissions currently running and mark as complete any completed analyses.
java.util.Set<java.util.concurrent.Future<AnalysisSubmission>>	postProcessResults()	Cycle through any transferred AnalysisSubmissions and perform post processing as necessary
java.util.Set<java.util.concurrent.Future<AnalysisSubmission>>	prepareAnalyses()	Cycle through new AnalysisSubmissions and prepare them for execution.
java.util.Set<java.util.concurrent.Future<AnalysisSubmission>>	transferAnalysesResults()	Cycle through any completed AnalysisSubmissions and transfer the results to IRIDA.

Methods inherited from class java.lang.Object

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

Constructor Detail

AnalysisExecutionScheduledTaskImpl

@Autowired
public AnalysisExecutionScheduledTaskImpl(AnalysisSubmissionRepository analysisSubmissionRepository,
                                          AnalysisExecutionService analysisExecutionServiceGalaxy,
                                          CleanupAnalysisSubmissionCondition cleanupCondition,
                                          GalaxyJobErrorsService galaxyJobErrorsService,
                                          JobErrorRepository jobErrorRepository,
                                          EmailController emailController,
                                          AnalysisWorkspaceService analysisWorkspaceService)

Builds a new AnalysisExecutionScheduledTaskImpl with the given service classes.

Parameters:

analysisSubmissionRepository - A repository for AnalysisSubmissions.

analysisExecutionServiceGalaxy - A service for executing AnalysisSubmissions.

cleanupCondition - The condition defining when an AnalysisSubmission should be cleaned up.

galaxyJobErrorsService - GalaxyJobErrorsService for getting JobError objects

jobErrorRepository - JobErrorRepository for JobError objects

emailController - EmailController for sending completion/error emails for AnalysisSubmissions

analysisWorkspaceService - AnalysisWorkspaceService

Method Detail

prepareAnalyses

public java.util.Set<java.util.concurrent.Future<AnalysisSubmission>> prepareAnalyses()

Cycle through new AnalysisSubmissions and prepare them for execution.

Specified by:

prepareAnalyses in interface AnalysisExecutionScheduledTask

Returns:

A Set of Future AnalysisSubmissions reflecting the changes in this submission along each of the stages.

executeAnalyses

public java.util.Set<java.util.concurrent.Future<AnalysisSubmission>> executeAnalyses()

Cycle through any outstanding AnalysisSubmissions and execute them.

Specified by:

executeAnalyses in interface AnalysisExecutionScheduledTask

Returns:

A Set of Future AnalysisSubmissions reflecting the changes in this submission along each of the stages.

monitorRunningAnalyses

public java.util.Set<java.util.concurrent.Future<AnalysisSubmission>> monitorRunningAnalyses()

Cycle through any AnalysisSubmissions currently running and mark as complete any completed analyses.

Specified by:

monitorRunningAnalyses in interface AnalysisExecutionScheduledTask

Returns:

A Set of Future AnalysisSubmissions reflecting the changes in this submission along each of the stages.

transferAnalysesResults

public java.util.Set<java.util.concurrent.Future<AnalysisSubmission>> transferAnalysesResults()

Cycle through any completed AnalysisSubmissions and transfer the results to IRIDA.

Specified by:

transferAnalysesResults in interface AnalysisExecutionScheduledTask

Returns:

A Set of Future AnalysisSubmissions reflecting the changes in this submission along each of the stages.

postProcessResults

public java.util.Set<java.util.concurrent.Future<AnalysisSubmission>> postProcessResults()

Cycle through any transferred AnalysisSubmissions and perform post processing as necessary

Specified by:

postProcessResults in interface AnalysisExecutionScheduledTask

Returns:

a Set of Future AnalysisSubmissions

cleanupAnalysisSubmissions

public java.util.Set<java.util.concurrent.Future<AnalysisSubmission>> cleanupAnalysisSubmissions()

Cycle through any completed or errored AnalysisSubmissions and delete intermediate files in the execution manager.

Specified by:

cleanupAnalysisSubmissions in interface AnalysisExecutionScheduledTask

Returns:

A Set of Future AnalysisSubmissions for all the analyses that were cleaned.