2.17.2: 2011-06-17

net.sf.basedb.plugins
Class JepExtraValueCalculator

java.lang.Object
  extended by net.sf.basedb.core.plugin.AbstractPlugin
      extended by net.sf.basedb.core.plugin.AbstractAnalysisPlugin
          extended by 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: 2010-11-08 14:49:35 +0100 (Mon, 08 Nov 2010) $

Nested Class Summary
 
Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin
Plugin.MainType
 
Field Summary
private static About about
          Plugin description
private  RequestInformation configureJob
           
private static PluginParameter<String> expressionParameter
           
private  PluginParameter<ExtraValueType> extraValueTypeParameter
           
private static Set<GuiContext> guiContexts
           
private static Set<Permissions> permissions
           
private  ThreadSignalHandler signalHandler
           
 
Fields inherited from class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
CHILD_DESCRIPTION, CHILD_NAME, CONTEXT_BIOASSAYS, CONTEXT_BIOASSAYSET, defaultGuiContexts, nameType, optionalNameType, SOURCE_BIOASSAYS, SOURCE_BIOASSAYSET, TRANSFORMATION_NAME
 
Fields inherited from class net.sf.basedb.core.plugin.AbstractPlugin
annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc
 
Constructor Summary
JepExtraValueCalculator()
           
 
Method Summary
 void configure(GuiContext context, Request request, Response response)
          Configure the plugin.
 About getAbout()
          Get information about the plugin, such as name, version, authors, etc.
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 and that the logged in user has permission to use the current experiment.
 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, getCurrentExperiment, getMainType, getSourceBioAssays, getSourceBioAssaySet, getSourceBioAssaySetParameter, getSourceBioAssaysParameter, getTransformationName, getTransformationNameParameter, restrictSource
 
Methods inherited from class net.sf.basedb.core.plugin.AbstractPlugin
checkInterrupted, cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, init, 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 Detail

about

private static final About about
Plugin description


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 Detail

JepExtraValueCalculator

public JepExtraValueCalculator()
Method Detail

getAbout

public About getAbout()
Description copied from interface: Plugin
Get information about the plugin, such as name, version, authors, etc.

Specified by:
getAbout in interface Plugin
Returns:
An About object

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 and that the logged in user has permission to use the current experiment.

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 bioassayset, 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()

2.17.2: 2011-06-17