Package ca.corefacility.bioinformatics.irida.plugins

Interface IridaPlugin

All Superinterfaces:

org.pf4j.ExtensionPoint

public interface IridaPlugin
extends org.pf4j.ExtensionPoint

Interface describing the methods which must be exposed by an IRIDA pipeline plugin

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	PLUGIN_API_VERSION	Defines the particular IRIDA Plugin API version.

Method Summary

Modifier and Type	Method	Description
AnalysisType	getAnalysisType()	Gets the particular AnalysisType of the workflow to load.
default java.util.Optional<java.lang.String>	getAnalysisViewer()	Get the name of the viewer to use for this pipeline
default java.util.Optional<java.awt.Color>	getBackgroundColor()	Gets an optional Color object used to modify the background color in the "Select a Pipeline" page.
java.util.UUID	getDefaultWorkflowUUID()	Gets the UUID of the default implementation of the workflow to use.
default java.util.Optional<java.awt.Color>	getTextColor()	Gets an optional Color object used to modify the text color in the "Select a Pipeline" page.
default java.util.Optional<AnalysisSampleUpdater>	getUpdater(MetadataTemplateService metadataTemplateService, SampleService sampleService, IridaWorkflowsService iridaWorkflowsService)	Get the AnalysisSampleUpdater if available for this analysis pipeline
default java.nio.file.Path	getWorkflowsPath()	Gets a Path to a directory containing the workflows to load.

Field Detail

PLUGIN_API_VERSION

static final java.lang.String PLUGIN_API_VERSION

Defines the particular IRIDA Plugin API version.

Please use this version in your plugin's pom.xml file as:

     <Plugin-Requires>1.0.0</Plugin-Requires>
 

If there are breaking changes to the IRIDA Plugin API this version will change, giving you an indication of when to update your plugin.

See Also:

Constant Field Values

Method Detail

getUpdater

default java.util.Optional<AnalysisSampleUpdater> getUpdater(MetadataTemplateService metadataTemplateService,
                                                             SampleService sampleService,
                                                             IridaWorkflowsService iridaWorkflowsService)
                                                      throws IridaPluginException

Get the AnalysisSampleUpdater if available for this analysis pipeline

Parameters:

metadataTemplateService - a MetadataTemplateService for getting metadata fields

sampleService - a SampleService for updating samples

iridaWorkflowsService - The IridaWorkflowsService for getting information about a workflow.

Returns:

An Optional AnalysisSampleUpdater if one is available for this pipeline

Throws:

IridaPluginException - if an error occurs when loading the AnalysisSampleUpdater

getAnalysisType

AnalysisType getAnalysisType()

Gets the particular AnalysisType of the workflow to load.

Returns:

The AnalysisType of the workflow.

getDefaultWorkflowUUID

java.util.UUID getDefaultWorkflowUUID()

Gets the UUID of the default implementation of the workflow to use.

Returns:

The UUID of the workflow.

getAnalysisViewer

default java.util.Optional<java.lang.String> getAnalysisViewer()

Get the name of the viewer to use for this pipeline

Returns:

The name of the viewer if it's available

getBackgroundColor

default java.util.Optional<java.awt.Color> getBackgroundColor()

Gets an optional Color object used to modify the background color in the "Select a Pipeline" page.

Returns:

The color for the pipeline in the "Select a Pipeline" page.

getTextColor

default java.util.Optional<java.awt.Color> getTextColor()

Gets an optional Color object used to modify the text color in the "Select a Pipeline" page.

Returns:

The text color for the pipeline in the "Select a Pipeline" page.

getWorkflowsPath

default java.nio.file.Path getWorkflowsPath()
                                     throws IridaPluginException

Gets a Path to a directory containing the workflows to load.

Returns:

The workflows path.

Throws:

IridaPluginException - If there was an exception getting the workflow paths.