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

Interface AnalysisWorkspaceService

All Known Implementing Classes:

AnalysisWorkspaceServiceGalaxy

public interface AnalysisWorkspaceService

Defines a service used to perform the tasks for execution of a workflow.

Method Summary

Modifier and Type	Method	Description
Analysis	getAnalysisResults(AnalysisSubmission analysisSubmission)	Gets an Analysis object containing the results for this analysis.
boolean	outputFilesExist(AnalysisSubmission analysisSubmission)	Checks if all output files from a given AnalysisSubmission are available on galaxy.
PreparedWorkflowGalaxy	prepareAnalysisFiles(AnalysisSubmission analysisSubmission)	Uploads and prepares the files and other necessary data structures of a workflow for an analysis given an analysis submission.
java.lang.String	prepareAnalysisWorkspace(AnalysisSubmission analysisSubmission)	Prepares the workspace for an analysis given an analysis submission.

Method Detail

prepareAnalysisWorkspace

java.lang.String prepareAnalysisWorkspace(AnalysisSubmission analysisSubmission)
                                   throws ExecutionManagerException

Prepares the workspace for an analysis given an analysis submission. This provides a remote location where files can be stored for analysis (creates a Galaxy History).

Parameters:

analysisSubmission - The submission used to perform an analysis.

Returns:

A String identifying the analysis workspace.

Throws:

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

prepareAnalysisFiles

PreparedWorkflowGalaxy prepareAnalysisFiles(AnalysisSubmission analysisSubmission)
                                     throws ExecutionManagerException,
                                            IridaWorkflowException,
                                            java.io.IOException

Uploads and prepares the files and other necessary data structures of a workflow for an analysis given an analysis submission.

Parameters:

analysisSubmission - The submission used to perform an analysis.

Returns:

A PreparedWorkflow which can be submitted.

Throws:

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

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

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

getAnalysisResults

Analysis getAnalysisResults(AnalysisSubmission analysisSubmission)
                     throws ExecutionManagerException,
                            IridaWorkflowNotFoundException,
                            java.io.IOException,
                            IridaWorkflowAnalysisTypeException

Gets an Analysis object containing the results for this analysis. This object is not persisted in the database.

Parameters:

analysisSubmission - The submission to get the results for.

Returns:

An Analysis object containing the results.

Throws:

ExecutionManagerException - If there was an error getting the results.

IridaWorkflowNotFoundException - If the workflow passed to this analysis submission could not be found.

java.io.IOException - If there was an error when loading the results of an analysis from Galaxy to a local file.

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

outputFilesExist

boolean outputFilesExist(AnalysisSubmission analysisSubmission)
                  throws IridaWorkflowNotFoundException,
                         ExecutionManagerException

Checks if all output files from a given AnalysisSubmission are available on galaxy.

Parameters:

analysisSubmission - The AnalysisSubmission.

Returns:

boolean

Throws:

ExecutionManagerException - If there was an error getting the results.

IridaWorkflowNotFoundException - If the workflow passed to this analysis submission could not be found.