2.17.2: 2011-06-17

net.sf.basedb.plugins
Class ManualTransformCreator

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.ManualTransformCreator
All Implemented Interfaces:
AnnotationSetterPlugin, InteractivePlugin, Plugin

public class ManualTransformCreator
extends AbstractAnalysisPlugin
implements InteractivePlugin, AnnotationSetterPlugin

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

Since:
2.12
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<String> importableFileTypes
           
private  List<PluginParameter<?>> toolParameters
           
 
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
ManualTransformCreator()
           
 
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.
 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)
           
private  String getImportFileType()
           
 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)
           
 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, getGuiContexts, getMainType, getSourceBioAssays, getSourceBioAssaySet, getSourceBioAssaySetParameter, getSourceBioAssaysParameter, getTransformationName, getTransformationNameParameter, isInContext, restrictSource
 
Methods inherited from class net.sf.basedb.core.plugin.AbstractPlugin
checkInterrupted, 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.InteractivePlugin
getGuiContexts, isInContext
 
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

importableFileTypes

private List<String> importableFileTypes
Constructor Detail

ManualTransformCreator

public ManualTransformCreator()
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

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

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)

getImportFileType

private String getImportFileType()

2.17.2: 2011-06-17