Package ca.corefacility.bioinformatics.irida.config.workflow

Class IridaWorkflowsConfig

java.lang.Object

ca.corefacility.bioinformatics.irida.config.workflow.IridaWorkflowsConfig

@Configuration
@Import({IridaPluginConfig.class,IridaAnalysisTypesServiceConfig.class})
public class IridaWorkflowsConfig
extends java.lang.Object

Class used to load up test workflows.

Constructor Summary

Constructors

Constructor	Description
IridaWorkflowsConfig()

Method Summary

Modifier and Type	Method	Description
IridaWorkflowIdSet	defaultIridaWorkflows()	A set of workflow ids to use as defaults.
AnalysisTypeSet	disabledAnalysisTypes()	Builds a AnalysisTypeSet of AnalysisTypes which are to be disabled from the UI.
java.lang.String	iridaPipelinePluginStyle()	Gets a String containing pipeline plugin styles (CSS).
IridaWorkflowLoaderService	iridaWorkflowLoaderService()	Constructs a service for loading up workflows for IRIDA.
IridaWorkflowSet	iridaWorkflows(java.nio.file.Path iridaWorkflowTypesPath)	Builds a set of workflows to load up into IRIDA.
IridaWorkflowsService	iridaWorkflowsService(IridaWorkflowSet iridaWorkflows, IridaWorkflowIdSet defaultIridaWorkflows, AnalysisTypeSet disabledAnalysisTypes)	Builds a new IridaWorkflowsService.
java.nio.file.Path	iridaWorkflowTypesPath()	Gets the Path for all IRIDA workflow types.
org.springframework.oxm.Unmarshaller	workflowDescriptionUnmarshaller()	Sets up an Unmarshaller for workflow objects.

Methods inherited from class java.lang.Object

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

Constructor Detail

IridaWorkflowsConfig

public IridaWorkflowsConfig()

Method Detail

iridaWorkflowTypesPath

@Bean
public java.nio.file.Path iridaWorkflowTypesPath()
                                          throws java.net.URISyntaxException

Gets the Path for all IRIDA workflow types.

Returns:

The Path for all IRIDA workflow types.

Throws:

java.net.URISyntaxException - if the path is not a valid uri.

iridaPipelinePluginStyle

@Bean(name="iridaPipelinePluginStyle")
public java.lang.String iridaPipelinePluginStyle()

Gets a String containing pipeline plugin styles (CSS).

Returns:

A CSS String containing pipeline plugin styles.

iridaWorkflows

@Bean
public IridaWorkflowSet iridaWorkflows(java.nio.file.Path iridaWorkflowTypesPath)
                                throws java.io.IOException,
                                       IridaWorkflowLoadException,
                                       IridaPluginException

Builds a set of workflows to load up into IRIDA.

Parameters:

iridaWorkflowTypesPath - The parent directory containing sub-directories for all IRIDA workflow types.

Returns:

A set of workflows to load into IRIDA.

Throws:

java.io.IOException - If an I/O error occured.

IridaWorkflowLoadException - If there was an issue loading a specific workflow.

IridaPluginException - If there was an issue when loading pipeline plugin workflows.

defaultIridaWorkflows

@Bean
public IridaWorkflowIdSet defaultIridaWorkflows()

A set of workflow ids to use as defaults.

Returns:

A set of workflow ids to use as defaults.

workflowDescriptionUnmarshaller

@Bean
public org.springframework.oxm.Unmarshaller workflowDescriptionUnmarshaller()

Sets up an Unmarshaller for workflow objects.

Returns:

An Unmarshaller for workflow objects.

iridaWorkflowLoaderService

@Bean
public IridaWorkflowLoaderService iridaWorkflowLoaderService()

Constructs a service for loading up workflows for IRIDA.

Returns:

A service for loading workflows for IRIDA.

disabledAnalysisTypes

@Bean
public AnalysisTypeSet disabledAnalysisTypes()

Builds a AnalysisTypeSet of AnalysisTypes which are to be disabled from the UI.

Returns:

A AnalysisTypeSet of AnalysisTypes which are to be disabled from the UI.

iridaWorkflowsService

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

Builds a new IridaWorkflowsService.

Parameters:

iridaWorkflows - The set of IridaWorkflows to use.

defaultIridaWorkflows - The set of ids for default workflows to use.

disabledAnalysisTypes - The set of disabled AnalysisTypes.

Returns:

A new IridaWorkflowsService.

Throws:

IridaWorkflowException - If there was an error loading a workflow.