3.2.1: 2012-12-13

net.sf.basedb.plugins
Class ManualDerivedBioAssayCreator

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.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
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
ManualDerivedBioAssayCreator()
           
 
Method Summary
 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, 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 Detail

configureJob

private RequestInformation configureJob

configurePlugin

private RequestInformation configurePlugin

toolParameters

private List<PluginParameter<?>> toolParameters
Constructor Detail

ManualDerivedBioAssayCreator

public ManualDerivedBioAssayCreator()
Method Detail

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)

3.2.1: 2012-12-13