Package net.sf.basedb.plugins

Class ManualDerivedBioAssayCreator

java.lang.Object

net.sf.basedb.core.plugin.AbstractPlugin

net.sf.basedb.core.plugin.AbstractAnalysisPlugin

net.sf.basedb.plugins.ManualDerivedBioAssayCreator

All Implemented Interfaces:

AnnotationSetterPlugin, InteractivePlugin, Plugin

public class ManualDerivedBioAssayCreator
extends AbstractAnalysisPlugin
implements InteractivePlugin, AnnotationSetterPlugin

Plug-in that allows a user to manually register an external analysis procedure for derived bioassays and to upload files that was generated by it.

Since:

3.0

Author:

Nicklas

Nested Class Summary

Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin

Plugin.MainType

Field Summary

Fields

Modifier and Type	Field	Description
private RequestInformation	configureJob
private RequestInformation	configurePlugin
private List<PluginParameter<?>>	toolParameters

Fields inherited from class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

CHILD_DESCRIPTION, CHILD_NAME, CONTEXT_BIOASSAYS, CONTEXT_BIOASSAYSET, CONTEXT_DERIVEDBIOASSAY, defaultGuiContexts, nameType, optionalNameType, SOURCE_BIOASSAYS, SOURCE_BIOASSAYSET, SOURCE_DERIVEDBIOASSAY, TRANSFORMATION_NAME

Fields inherited from class net.sf.basedb.core.plugin.AbstractPlugin

annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc

Constructor Summary

Constructors

Constructor	Description
ManualDerivedBioAssayCreator()

Method Summary

Modifier and Type	Method	Description
void	configure(GuiContext context, Request request, Response response)	Configure the plugin.
String	getAnnotationMessage()	Get a message that explains what the plug-in does with the annotations it has.
ItemQuery<AnnotationType>	getAnnotationTypes()	Return a query that finds annotation types for bioassay sets.
private RequestInformation	getConfigureJobParameters(GuiContext context)
private RequestInformation	getConfigurePluginParameters(GuiContext context)
Set<GuiContext>	getGuiContexts()	Get a set containing all items that the plugin handles.
RequestInformation	getRequestInformation(GuiContext context, String command)	This method will return the RequestInformation for a given command, i.e.
private List<PluginParameter<?>>	getToolParameters(List<String> values)
String	isInContext(GuiContext context, Object item)	Adds check of the item subtype.
boolean	requiresConfiguration()	Returns FALSE, since that is how the plugins used to work before this method was introduced.
void	run(Request request, Response response, ProgressReporter progress)	Run the plugin.
boolean	supportsConfigurations()	Returns TRUE, since that is how the plugins used to work before this method was introduced.

Methods inherited from class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

getChildDescriptionParameter, getChildNameParameter, getCurrentBioAssaySet, getCurrentDerivedBioAssay, getCurrentExperiment, getMainType, getSourceBioAssays, getSourceBioAssaySet, getSourceBioAssaySetParameter, getSourceBioAssaysParameter, getSourceDerivedBioAssay, getSourceDerivedBioAssayParameter, getTransformationName, getTransformationNameParameter, restrictSource

Methods inherited from class net.sf.basedb.core.plugin.AbstractPlugin

cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, getPermissions, init, isLogging, log, log, storeValue, storeValue, storeValues, validateRequestParameters

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.sf.basedb.core.plugin.Plugin

done, getMainType, getPermissions, init

Field Details

configureJob

private RequestInformation configureJob

configurePlugin

private RequestInformation configurePlugin

toolParameters

private List<PluginParameter<?>> toolParameters

Constructor Details

ManualDerivedBioAssayCreator

public ManualDerivedBioAssayCreator()

Method Details

supportsConfigurations

public boolean supportsConfigurations()

Description copied from class: AbstractPlugin

Returns TRUE, since that is how the plugins used to work before this method was introduced.

Specified by:

supportsConfigurations in interface Plugin

Overrides:

supportsConfigurations in class AbstractPlugin

Returns:

TRUE or FALSE

requiresConfiguration

public boolean requiresConfiguration()

Description copied from class: AbstractPlugin

Returns FALSE, since that is how the plugins used to work before this method was introduced.

Specified by:

requiresConfiguration in interface Plugin

Overrides:

requiresConfiguration in class AbstractPlugin

Returns:

TRUE or FALSE

run

public void run(Request request,
 Response response,
 ProgressReporter progress)

Description copied from interface: Plugin

Run the plugin. If a progress reporter object is passed it is recommended that the plugin makes use of it.

Specified by:

run in interface Plugin

Parameters:

request - Request object with the command and parameters

response - Response object in for the plugin to response through

progress - A ProgressReporter where the plugin can report its progess, can be null

getGuiContexts

public Set<GuiContext> getGuiContexts()

Description copied from interface: InteractivePlugin

Get a set containing all items that the plugin handles. Ie. if the plugin imports reporters, return a set containing Item.REPORTER. This information is used by client applications to put the plugin in the proper place in the user interface.

Specified by:

getGuiContexts in interface InteractivePlugin

Overrides:

getGuiContexts in class AbstractAnalysisPlugin

Returns:

A Set containing Item:s, or null if the plugin is not concerned about items

isInContext

public String isInContext(GuiContext context,
 Object item)

Adds check of the item subtype.

Specified by:

isInContext in interface InteractivePlugin

Overrides:

isInContext in class AbstractAnalysisPlugin

Parameters:

context - Current guicontext

item - The item to check.

Returns:

null if the item is a valid item, an error message otherwise

configure

public void configure(GuiContext context,
 Request request,
 Response response)

Description copied from interface: InteractivePlugin

Configure the plugin. Hopefully the client is supplying values for the parameters specified by InteractivePlugin.getRequestInformation(GuiContext, String).

Specified by:

configure in interface InteractivePlugin

Parameters:

context - The current context of the client application, it is one of the values found in set returned by InteractivePlugin.getGuiContexts()

request - Request object with the command and parameters

response - Response object in for the plugin to response through

getRequestInformation

public RequestInformation getRequestInformation(GuiContext context,
 String command)
                                         throws BaseException

Description copied from interface: InteractivePlugin

This method will return the RequestInformation for a given command, i.e. the list of parameters and some nice help text.

Specified by:

getRequestInformation in interface InteractivePlugin

Parameters:

context - The current context of the client application, it is one of the values found in set returned by InteractivePlugin.getGuiContexts()

command - The command

Returns:

The RequestInformation for the command

Throws:

BaseException - if there is an error

getAnnotationTypes

public ItemQuery<AnnotationType> getAnnotationTypes()

Return a query that finds annotation types for bioassay sets.

Specified by:

getAnnotationTypes in interface AnnotationSetterPlugin

Returns:

A query returning annotation types, or null if the current setup doesn't allow any annotations

getAnnotationMessage

public String getAnnotationMessage()

Description copied from interface: AnnotationSetterPlugin

Get a message that explains what the plug-in does with the annotations it has.

Specified by:

getAnnotationMessage in interface AnnotationSetterPlugin

Returns:

A message or null

getConfigureJobParameters

private RequestInformation getConfigureJobParameters(GuiContext context)

getConfigurePluginParameters

private RequestInformation getConfigurePluginParameters(GuiContext context)

getToolParameters

private List<PluginParameter<?>> getToolParameters(List<String> values)