Package ca.corefacility.bioinformatics.irida.service.workflow

Class IridaWorkflowsService

java.lang.Object

ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService

@Service
public class IridaWorkflowsService
extends java.lang.Object

Class used to load up installed workflows in IRIDA.

Constructor Summary

Constructors

Constructor	Description
IridaWorkflowsService(IridaWorkflowSet iridaWorkflows, IridaWorkflowIdSet defaultIridaWorkflows)	Builds a new IridaWorkflowsService for loading up installed workflows.
IridaWorkflowsService(IridaWorkflowSet iridaWorkflows, IridaWorkflowIdSet defaultIridaWorkflows, AnalysisTypeSet disabledAnalysisTypes)	Builds a new IridaWorkflowsService for loading up installed workflows.

Method Summary

Modifier and Type	Method	Description
java.util.Map<AnalysisType,IridaWorkflow>	getAllDefaultWorkflowsByType(java.util.Set<AnalysisType> analysisTypes)	Gets all of the default workflows for a given Set of AnalysisTypes.
java.util.Set<IridaWorkflow>	getAllWorkflowsByType(AnalysisType analysisType)	Gets all the workflows for a given AnalysisType.
IridaWorkflow	getDefaultWorkflowByType(AnalysisType analysisType)	Gets the default workflow for a given type of analysis.
IridaWorkflow	getDisplayableIridaWorkflow(java.util.UUID workflowId)	Returns a workflow with the given id that is displayable.
java.util.Set<AnalysisType>	getDisplayableWorkflowTypes()	Gets a Set of disabled AnalysisTypes.
IridaWorkflow	getIridaWorkflow(java.util.UUID workflowId)	Returns a workflow with the given id.
IridaWorkflow	getIridaWorkflowOrUnknown(AnalysisSubmission analysisSubmission)	Returns a workflow associated with the given AnalysisSubmission, attempting to fill in as many details as possible if the workflow can't be found.
IridaWorkflow	getIridaWorkflowOrUnknown(java.util.UUID iridaWorkflowId)	Returns a workflow associated with the given UUID, attempting to fill in as many details as possible if the workflow can't be found.
java.util.List<java.lang.String>	getOutputNames(java.util.UUID workflowId)	Get list of workflow output names.
java.util.Set<IridaWorkflow>	getRegisteredWorkflows()	Gets a Set of all installed workflows.
java.util.Set<AnalysisType>	getRegisteredWorkflowTypes()	Gets a Set of all registered AnalysisType for all workflows.
java.util.Set<java.util.UUID>	getSingleSampleWorkflows()	Get all registered single-sample workflow UUIDs for retrieving AnalysisOutputFile info with a 1-to-1 mapping to a Sample
void	registerWorkflow(IridaWorkflow iridaWorkflow)	Registers the given workflow with this service.
void	registerWorkflows(java.util.Set<IridaWorkflow> iridaWorkflows)	Registers the set of workflows with IRIDA.
void	setDefaultWorkflow(java.util.UUID workflowId)	Sets the given workflow as a default workflow for it's analysis type.
void	setDefaultWorkflows(java.util.Set<java.util.UUID> defaultWorkflows)	Sets the given set of workflow ids as default workflows.

Methods inherited from class java.lang.Object

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

Constructor Detail

IridaWorkflowsService

public IridaWorkflowsService(IridaWorkflowSet iridaWorkflows,
                             IridaWorkflowIdSet defaultIridaWorkflows)
                      throws IridaWorkflowException

Builds a new IridaWorkflowsService for loading up installed workflows.

Parameters:

iridaWorkflows - A IridaWorkflowSet of IridaWorkflows to use in IRIDA.

defaultIridaWorkflows - A IridaWorkflowIdSet of UUIDs to use as the default workflows.

Throws:

IridaWorkflowException - If there was an issue when attempting to register the workflows.

IridaWorkflowsService

@Autowired
public IridaWorkflowsService(IridaWorkflowSet iridaWorkflows,
                             IridaWorkflowIdSet defaultIridaWorkflows,
                             AnalysisTypeSet disabledAnalysisTypes)
                      throws IridaWorkflowException

Builds a new IridaWorkflowsService for loading up installed workflows.

Parameters:

iridaWorkflows - A IridaWorkflowSet of IridaWorkflows to use in IRIDA.

defaultIridaWorkflows - A IridaWorkflowIdSet of UUIDs to use as the default workflows.

disabledAnalysisTypes - A Set of disabled AnalysisTypes.

Throws:

IridaWorkflowException - If there was an issue when attempting to register the workflows.

Method Detail

setDefaultWorkflow

public void setDefaultWorkflow(java.util.UUID workflowId)
                        throws IridaWorkflowNotFoundException,
                               IridaWorkflowDefaultException

Sets the given workflow as a default workflow for it's analysis type.

Parameters:

workflowId - The workflow id to set as default.

Throws:

IridaWorkflowNotFoundException - If the given workflow cannot be found.

IridaWorkflowDefaultException - If the corresponding workflow type already has a default workflow set.

setDefaultWorkflows

public void setDefaultWorkflows(java.util.Set<java.util.UUID> defaultWorkflows)
                         throws IridaWorkflowNotFoundException,
                                IridaWorkflowDefaultException

Sets the given set of workflow ids as default workflows.

Parameters:

defaultWorkflows - The set of workflow ids to set as defaults.

Throws:

IridaWorkflowNotFoundException - If one of the workflow ids has no corresponding workflow.

IridaWorkflowDefaultException - If there was an issue setting a default workflow.

registerWorkflows

public void registerWorkflows(java.util.Set<IridaWorkflow> iridaWorkflows)
                       throws IridaWorkflowException

Registers the set of workflows with IRIDA.

Parameters:

iridaWorkflows - The set of workflows to register.

Throws:

IridaWorkflowException - If there was an issue registering a workflow.

registerWorkflow

public void registerWorkflow(IridaWorkflow iridaWorkflow)
                      throws IridaWorkflowException

Registers the given workflow with this service.

Parameters:

iridaWorkflow - The workflow to register.

Throws:

IridaWorkflowException - If there was an issue when registering the workflow.

getDefaultWorkflowByType

public IridaWorkflow getDefaultWorkflowByType(AnalysisType analysisType)
                                       throws IridaWorkflowNotFoundException

Gets the default workflow for a given type of analysis.

Parameters:

analysisType - The type of analysis to search for.

Returns:

An IridaWorkflow for this analysis type.

Throws:

IridaWorkflowNotFoundException - if the workflow could not be found for the specified analysis type.

getAllDefaultWorkflowsByType

public java.util.Map<AnalysisType,IridaWorkflow> getAllDefaultWorkflowsByType(java.util.Set<AnalysisType> analysisTypes)
                                                                             throws IridaWorkflowNotFoundException

Gets all of the default workflows for a given Set of AnalysisTypes.

Parameters:

analysisTypes - A Set of AnalysisTypes.

Returns:

A Map of AnalysisType to IridaWorkflow all the passed analysis types.

Throws:

IridaWorkflowNotFoundException - If one of the analysis types does not have any associated workflows.

getAllWorkflowsByType

public java.util.Set<IridaWorkflow> getAllWorkflowsByType(AnalysisType analysisType)
                                                   throws IridaWorkflowNotFoundException

Gets all the workflows for a given AnalysisType.

Parameters:

analysisType - The AnalysisType to search for workflows.

Returns:

A Set of IridaWorkflows for this analysis type.

Throws:

IridaWorkflowNotFoundException - If not corresponding workflows could not be found.

getRegisteredWorkflowTypes

public java.util.Set<AnalysisType> getRegisteredWorkflowTypes()

Gets a Set of all registered AnalysisType for all workflows.

Returns:

A Set of all the types of all installed workflows.

getDisplayableWorkflowTypes

public java.util.Set<AnalysisType> getDisplayableWorkflowTypes()

Gets a Set of disabled AnalysisTypes.

Returns:

A Set of disabled AnalysisTypes.

getIridaWorkflow

public IridaWorkflow getIridaWorkflow(java.util.UUID workflowId)
                               throws IridaWorkflowNotFoundException

Returns a workflow with the given id.

Parameters:

workflowId - The identifier of the workflow to get.

Returns:

An IridaWorkflow with the given identifier.

Throws:

IridaWorkflowNotFoundException - If no workflow with the given identifier was found.

getDisplayableIridaWorkflow

public IridaWorkflow getDisplayableIridaWorkflow(java.util.UUID workflowId)
                                          throws IridaWorkflowNotDisplayableException,
                                                 IridaWorkflowNotFoundException

Returns a workflow with the given id that is displayable.

Parameters:

workflowId - The identifier of the workflow to get.

Returns:

An IridaWorkflow with the given identifier that is displayable.

Throws:

IridaWorkflowNotDisplayableException - If no workflow with the given identifier is not displayable.

IridaWorkflowNotFoundException - If the workflow was not found.

getOutputNames

public java.util.List<java.lang.String> getOutputNames(java.util.UUID workflowId)
                                                throws IridaWorkflowNotFoundException

Get list of workflow output names.

Parameters:

workflowId - Workflow UUID.

Returns:

List of workflow output names.

Throws:

IridaWorkflowNotFoundException - if no workflow with the given UUID found.

getRegisteredWorkflows

public java.util.Set<IridaWorkflow> getRegisteredWorkflows()

Gets a Set of all installed workflows.

Returns:

A Set of all installed workflows.

getSingleSampleWorkflows

public java.util.Set<java.util.UUID> getSingleSampleWorkflows()

Get all registered single-sample workflow UUIDs for retrieving AnalysisOutputFile info with a 1-to-1 mapping to a Sample

Since all automated analyses and many other pipelines at this time produce results that map 1-to-1 to a Sample and it is trivial to download multi-sample, collection-type AnalysisOutputFiles (they are zipped and contain all output for all Sample inputs), we want to enable easy retrieval of results for single-sample pipelines for batch download.

Returns:

UUIDs for single-sample workflows

getIridaWorkflowOrUnknown

public IridaWorkflow getIridaWorkflowOrUnknown(java.util.UUID iridaWorkflowId)

Returns a workflow associated with the given UUID, attempting to fill in as many details as possible if the workflow can't be found.

Parameters:

iridaWorkflowId - The UUID object to search for a workflow.

Returns:

An IridaWorkflow with the given submission, or an 'unknown' workflow object if the associated workflow is not found.

getIridaWorkflowOrUnknown

public IridaWorkflow getIridaWorkflowOrUnknown(AnalysisSubmission analysisSubmission)

Returns a workflow associated with the given AnalysisSubmission, attempting to fill in as many details as possible if the workflow can't be found.

Parameters:

analysisSubmission - The AnalysisSubmission object to search for a workflow.

Returns:

An IridaWorkflow with the given submission, or an 'unknown' workflow object if the associated workflow is not found.