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

Interface AnalysisExecutionService

All Known Implementing Classes:

AnalysisExecutionServiceGalaxy

public interface AnalysisExecutionService

Service for submission of AnalysisSubmissions to an execution manager.

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.

Method Detail

prepareSubmission

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 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

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

getWorkflowStatus

GalaxyWorkflowStatus getWorkflowStatus(AnalysisSubmission submittedAnalysis)
                                throws ExecutionManagerException

Gets the status for the given submitted analysis.

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.

transferAnalysisResults

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

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

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

Parameters:

analysisSubmission - the AnalysisSubmission to process

Returns:

a Future AnalysisSubmission

cleanupSubmission

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

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

Parameters:

analysisSubmission - The AnalysisSubmission to clean.

Returns:

The cleaned-up AnalysisSubmission.

Throws:

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

getCapacity

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.

Returns:

the number of available slots for running jobs