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

Class AnalysisExecutionServiceGalaxy

java.lang.Object

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

All Implemented Interfaces:

AnalysisExecutionService

public class AnalysisExecutionServiceGalaxy
extends java.lang.Object
implements AnalysisExecutionService

Service for performing analyses within a Galaxy execution manager.

Constructor Summary

Constructors

Constructor	Description
AnalysisExecutionServiceGalaxy(AnalysisSubmissionService analysisSubmissionService, GalaxyHistoriesService galaxyHistoriesService, AnalysisExecutionServiceGalaxyAsync analysisExecutionServiceGalaxyAsync, AnalysisExecutionServiceGalaxyCleanupAsync analysisExecutionServiceGalaxyCleanupAsync)	Builds a new AnalysisExecutionServiceGalaxy with the given information.

Method Summary

Modifier and Type	Method	Description
java.util.concurrent.Future<AnalysisSubmission>	cleanupSubmission(AnalysisSubmission analysisSubmission)	Cleans up any intermediate files in the execution manager for this submission.
java.util.concurrent.Future<AnalysisSubmission>	executeAnalysis(AnalysisSubmission analysisSubmission)	Executes the passed prepared AnalysisSubmission in an execution manager.
int	getCapacity()	Get the AnalysisExecutionService capacity for running new jobs.
GalaxyWorkflowStatus	getWorkflowStatus(AnalysisSubmission submittedAnalysis)	Gets the status for the given submitted analysis.
java.util.concurrent.Future<AnalysisSubmission>	postProcessResults(AnalysisSubmission analysisSubmission)	Performs any post processing required for an 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

AnalysisExecutionServiceGalaxy

@Autowired
public AnalysisExecutionServiceGalaxy(AnalysisSubmissionService analysisSubmissionService,
                                      GalaxyHistoriesService galaxyHistoriesService,
                                      AnalysisExecutionServiceGalaxyAsync analysisExecutionServiceGalaxyAsync,
                                      AnalysisExecutionServiceGalaxyCleanupAsync analysisExecutionServiceGalaxyCleanupAsync)

Builds a new AnalysisExecutionServiceGalaxy with the given information.

Parameters:

analysisSubmissionService - A service for analysis submissions.

galaxyHistoriesService - A service for Galaxy histories.

analysisExecutionServiceGalaxyAsync - An AnalysisExecutionServiceGalaxyAsync for executing the tasks asynchronously.

analysisExecutionServiceGalaxyCleanupAsync - A service for cleaning up files in Galaxy.

Method Detail

prepareSubmission

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.

Specified by:

prepareSubmission in interface AnalysisExecutionService

Parameters:

analysisSubmission - The AnalysisSubmission to prepare.

Returns:

A Future of type AnalysisSubmission which can be used to access the prepared submission.

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.

Specified by:

executeAnalysis in interface AnalysisExecutionService

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

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.

Specified by:

transferAnalysisResults in interface AnalysisExecutionService

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.

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

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

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

postProcessResults

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

Performs any post processing required for an AnalysisSubmission. Usually this will be a sample updater implementation.

Specified by:

postProcessResults in interface AnalysisExecutionService

Parameters:

analysisSubmission - the AnalysisSubmission to process

Returns:

a Future AnalysisSubmission

getWorkflowStatus

public GalaxyWorkflowStatus getWorkflowStatus(AnalysisSubmission submittedAnalysis)
                                       throws ExecutionManagerException

Gets the status for the given submitted analysis.

Specified by:

getWorkflowStatus in interface AnalysisExecutionService

Parameters:

submittedAnalysis - The AnalysisSubmission to check the status in the execution manager.

Returns:

A WorkflowStatus object containing the status of the analysis.

Throws:

ExecutionManagerException - If there was an issue checking the status.

cleanupSubmission

public java.util.concurrent.Future<AnalysisSubmission> cleanupSubmission(AnalysisSubmission analysisSubmission)
                                                                  throws ExecutionManagerException

Cleans up any intermediate files in the execution manager for this submission.

Specified by:

cleanupSubmission in interface AnalysisExecutionService

Parameters:

analysisSubmission - The AnalysisSubmission to clean.

Returns:

The cleaned-up AnalysisSubmission.

Throws:

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

getCapacity

public int getCapacity()

Get the AnalysisExecutionService capacity for running new jobs. This will return the number of open slots for running new workflows. NOTE: This is not a hard limit. It just reports the number running vs configured maximum requested.

Specified by:

getCapacity in interface AnalysisExecutionService

Returns:

the number of available slots for running jobs