Package ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy

Class AnalysisExecutionServiceGalaxyAsync

java.lang.Object

ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxyAsync

@Async("analysisTaskExecutor")
public class AnalysisExecutionServiceGalaxyAsync
extends java.lang.Object

Service for executing AnalysisSubmission stages within a Galaxy execution manager asynchronously.

Constructor Summary

Constructors

Constructor	Description
AnalysisExecutionServiceGalaxyAsync(AnalysisSubmissionService analysisSubmissionService, AnalysisService analysisService, GalaxyWorkflowService galaxyWorkflowService, AnalysisWorkspaceServiceGalaxy workspaceService, IridaWorkflowsService iridaWorkflowsService, AnalysisSubmissionSampleProcessor analysisSubmissionSampleService)	Builds a new AnalysisExecutionServiceGalaxyAsync with the given information.

Method Summary

Modifier and Type	Method	Description
java.util.concurrent.Future<AnalysisSubmission>	executeAnalysis(AnalysisSubmission analysisSubmission)	Executes the passed prepared AnalysisSubmission in an execution manager.
java.util.concurrent.Future<AnalysisSubmission>	postProcessResults(AnalysisSubmission analysisSubmission)	Calls the AnalysisSubmissionSampleProcessor to perform any post processing required on a given AnalysisSubmission
java.util.concurrent.Future<AnalysisSubmission>	prepareSubmission(AnalysisSubmission analysisSubmission)	Prepares the given AnalysisSubmission to be executed within an execution manager.
java.util.concurrent.Future<AnalysisSubmission>	transferAnalysisResults(AnalysisSubmission submittedAnalysis)	Downloads and saves the results of an AnalysisSubmission that was previously submitted from an execution manager.

Methods inherited from class java.lang.Object

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

Constructor Detail

AnalysisExecutionServiceGalaxyAsync

@Autowired
public AnalysisExecutionServiceGalaxyAsync(AnalysisSubmissionService analysisSubmissionService,
                                           AnalysisService analysisService,
                                           GalaxyWorkflowService galaxyWorkflowService,
                                           AnalysisWorkspaceServiceGalaxy workspaceService,
                                           IridaWorkflowsService iridaWorkflowsService,
                                           AnalysisSubmissionSampleProcessor analysisSubmissionSampleService)

Builds a new AnalysisExecutionServiceGalaxyAsync with the given information.

Parameters:

analysisSubmissionService - A service for analysis submissions.

analysisService - A service for analysis results.

galaxyWorkflowService - A service for Galaxy workflows.

workspaceService - A service for a workflow workspace.

iridaWorkflowsService - A service for loading up IridaWorkflows.

analysisSubmissionSampleService - A service to updating samples associated with a submission with the analysis results.

Method Detail

prepareSubmission

@Transactional
public java.util.concurrent.Future<AnalysisSubmission> prepareSubmission(AnalysisSubmission analysisSubmission)
                                                                  throws IridaWorkflowNotFoundException,
                                                                         java.io.IOException,
                                                                         ExecutionManagerException

Prepares the given AnalysisSubmission to be executed within an execution manager. This will persist the submission within the database.

Parameters:

analysisSubmission - The AnalysisSubmission to prepare.

Returns:

A Future with an AnalysisSubmission for the analysis submitted.

Throws:

IridaWorkflowNotFoundException - If there was an issue getting a workflow.

java.io.IOException - If there was an issue reading the workflow.

ExecutionManagerException - If there was an issue preparing a workspace for the workflow.

executeAnalysis

public java.util.concurrent.Future<AnalysisSubmission> executeAnalysis(AnalysisSubmission analysisSubmission)
                                                                throws ExecutionManagerException,
                                                                       IridaWorkflowException,
                                                                       java.io.IOException

Executes the passed prepared AnalysisSubmission in an execution manager.

Parameters:

analysisSubmission - The AnalysisSubmission to execute.

Returns:

A Future with an AnalysisSubmission for the analysis submitted.

Throws:

ExecutionManagerException - If there was an exception submitting the analysis to the execution manager.

IridaWorkflowException - If there was an issue with the IRIDA workflow.

java.io.IOException - If there was an error reading some of the input files.

transferAnalysisResults

@Transactional
public java.util.concurrent.Future<AnalysisSubmission> transferAnalysisResults(AnalysisSubmission submittedAnalysis)
                                                                        throws ExecutionManagerException,
                                                                               java.io.IOException,
                                                                               IridaWorkflowNotFoundException,
                                                                               IridaWorkflowAnalysisTypeException

Downloads and saves the results of an AnalysisSubmission that was previously submitted from an execution manager.

Parameters:

submittedAnalysis - An AnalysisSubmission that was previously submitted.

Returns:

A Future with an AnalysisSubmission object containing information about the particular analysis.

Throws:

ExecutionManagerException - If there was an issue with the execution manager.

IridaWorkflowNotFoundException - If the workflow for this submission could not be found in IRIDA.

java.io.IOException - If there was an error loading the analysis results from an execution manager.

IridaWorkflowAnalysisTypeException - If there was an issue building an Analysis object.

postProcessResults

@Transactional
public java.util.concurrent.Future<AnalysisSubmission> postProcessResults(AnalysisSubmission analysisSubmission)

Calls the AnalysisSubmissionSampleProcessor to perform any post processing required on a given AnalysisSubmission

Parameters:

analysisSubmission - the AnalysisSubmission to process

Returns:

a Future AnalysisSubmission