Package net.sf.basedb.plugins

Class JepExtraValueCalculator

java.lang.Object

net.sf.basedb.core.plugin.AbstractPlugin

net.sf.basedb.core.plugin.AbstractAnalysisPlugin

net.sf.basedb.plugins.JepExtraValueCalculator

All Implemented Interfaces:

InteractivePlugin, Plugin, SignalTarget

public class JepExtraValueCalculator
extends AbstractAnalysisPlugin
implements InteractivePlugin, SignalTarget

This plugin caluclates extra values from a bioassayset using mathematical formulas entered by the user.

Version:

2.0

Author:

nicklas

Last modified

$Date: 2012-09-14 09:28:35 +0200 (fr, 14 sep 2012) $

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 static final PluginParameter<String>	expressionParameter
private PluginParameter<ExtraValueType>	extraValueTypeParameter
private static final Set<GuiContext>	guiContexts
private static final Set<Permissions>	permissions
private ThreadSignalHandler	signalHandler

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
JepExtraValueCalculator()

Method Summary

Modifier and Type	Method	Description
void	configure(GuiContext context, Request request, Response response)	Configure the plugin.
private RequestInformation	getConfigureJobParameters()
Set<GuiContext>	getGuiContexts()	Get a set containing all items that the plugin handles.
Collection<Permissions>	getPermissions()	Request use access to Experiment:s and ExtraValueType:s and read access to Job:s.
RequestInformation	getRequestInformation(GuiContext context, String command)	This method will return the RequestInformation for a given command, i.e.
SignalHandler	getSignalHandler()	Get the signal handler that is handling signals on behalf of this object.
String	isInContext(GuiContext context, Object item)	Check that the item is a bioassayset/derived bioassay and that the logged in user has permission to use the current item.
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, 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, init

Field Details

permissions

private static final Set<Permissions> permissions

guiContexts

private static final Set<GuiContext> guiContexts

expressionParameter

private static final PluginParameter<String> expressionParameter

signalHandler

private ThreadSignalHandler signalHandler

configureJob

private RequestInformation configureJob

extraValueTypeParameter

private PluginParameter<ExtraValueType> extraValueTypeParameter

Constructor Details

JepExtraValueCalculator

public JepExtraValueCalculator()

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

getPermissions

public Collection<Permissions> getPermissions()

Request use access to Experiment:s and ExtraValueType:s and read access to Job:s.

Specified by:

getPermissions in interface Plugin

Overrides:

getPermissions in class AbstractPlugin

Returns:

A collection of permissions or null to not use permissions

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)

Description copied from class: AbstractAnalysisPlugin

Check that the item is a bioassayset/derived bioassay and that the logged in user has permission to use the current item.

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

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

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

getSignalHandler

public SignalHandler getSignalHandler()

Description copied from interface: SignalTarget

Get the signal handler that is handling signals on behalf of this object. Multiple invokations of this method may receive the same or different objects. Null may be returned if, for some reason, the current object instance doesn't want to receive signals. Returning null is the same as not implementing this interface.

Specified by:

getSignalHandler in interface SignalTarget

Returns:

A SignalHandler object, or null if the current instance doesn't support signals

getConfigureJobParameters

private RequestInformation getConfigureJobParameters()