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

Class IridaWorkflowLoaderService

java.lang.Object

ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowLoaderService

@Service
public class IridaWorkflowLoaderService
extends java.lang.Object

Used to load up IRIDA workflows.

Constructor Summary

Constructors

Constructor	Description
IridaWorkflowLoaderService(org.springframework.oxm.Unmarshaller workflowDescriptionUnmarshaller, AnalysisTypesService analysisTypesService)	Builds a new IridaWorkflowLoaderService with the given unmarshaller.

Method Summary

Modifier and Type	Method	Description
java.util.Set<IridaWorkflow>	loadAllWorkflowImplementations(java.nio.file.Path workflowDirectory)	Loads up a set of IridaWorkflows from the given directory.
IridaWorkflow	loadIridaWorkflow(java.nio.file.Path descriptionFile, java.nio.file.Path structureFile)	Loads up an IridaWorkflow from the given information files.
IridaWorkflow	loadIridaWorkflowFromDirectory(java.nio.file.Path workflowDirectory)	Loads up a workflow from the given directory.
IridaWorkflowDescription	loadWorkflowDescription(java.nio.file.Path descriptionFile)	Loads up the workflow description from the given file.
IridaWorkflowStructure	loadWorkflowStructure(java.nio.file.Path structureFile)	Loads up the structure of the workflow given the file.

Methods inherited from class java.lang.Object

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

Constructor Detail

IridaWorkflowLoaderService

@Autowired
public IridaWorkflowLoaderService(org.springframework.oxm.Unmarshaller workflowDescriptionUnmarshaller,
                                  AnalysisTypesService analysisTypesService)

Builds a new IridaWorkflowLoaderService with the given unmarshaller.

Parameters:

workflowDescriptionUnmarshaller - The unmarshaller to use.

analysisTypesService - The AnalysisTypesService to use.

Method Detail

loadAllWorkflowImplementations

public java.util.Set<IridaWorkflow> loadAllWorkflowImplementations(java.nio.file.Path workflowDirectory)
                                                            throws java.io.IOException,
                                                                   IridaWorkflowLoadException

Loads up a set of IridaWorkflows from the given directory.

Parameters:

workflowDirectory - The directory containing the different workflow implementations and files.

Returns:

A set of IridaWorkflows for all implementations.

Throws:

java.io.IOException - If there was an issue reading one of the workflow files.

IridaWorkflowLoadException - If there was an issue when loading up the workflows.

loadIridaWorkflowFromDirectory

public IridaWorkflow loadIridaWorkflowFromDirectory(java.nio.file.Path workflowDirectory)
                                             throws java.io.IOException,
                                                    IridaWorkflowLoadException

Loads up a workflow from the given directory.

Parameters:

workflowDirectory - The directory containing a single version of a workflow.

Returns:

An IridaWorkflow from this directory.

Throws:

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

IridaWorkflowLoadException - If there was an issue loading up the workflow.

loadIridaWorkflow

public IridaWorkflow loadIridaWorkflow(java.nio.file.Path descriptionFile,
                                       java.nio.file.Path structureFile)
                                throws java.io.IOException,
                                       IridaWorkflowLoadException

Loads up an IridaWorkflow from the given information files.

Parameters:

descriptionFile - The description file for the workflow.

structureFile - The file describing the structure of a workflow.

Returns:

An IridaWorkflow object for this workflow.

Throws:

java.io.IOException - If there was an issue reading the passed file.

IridaWorkflowLoadException - If there was an issue loading up the workflow.

loadWorkflowDescription

public IridaWorkflowDescription loadWorkflowDescription(java.nio.file.Path descriptionFile)
                                                 throws java.io.IOException,
                                                        IridaWorkflowLoadException

Loads up the workflow description from the given file.

Parameters:

descriptionFile - The file to load up a workflow description.

Returns:

An IridaWorkflowDescription object.

Throws:

java.io.IOException - If there was an issue reading the passed file.

IridaWorkflowLoadException - If there was an issue loading up the workflow description.

loadWorkflowStructure

public IridaWorkflowStructure loadWorkflowStructure(java.nio.file.Path structureFile)
                                             throws java.io.FileNotFoundException

Loads up the structure of the workflow given the file.

Parameters:

structureFile - The file to load up.

Returns:

An IridaWorkflowStructure defining the structure of the workflow.

Throws:

java.io.FileNotFoundException - If the structure file could not be found.