public class JepExtraValueCalculator extends AbstractAnalysisPlugin implements InteractivePlugin, SignalTarget
Plugin.MainType
Modifier and Type | Field and 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 |
CHILD_DESCRIPTION, CHILD_NAME, CONTEXT_BIOASSAYS, CONTEXT_BIOASSAYSET, CONTEXT_DERIVEDBIOASSAY, defaultGuiContexts, nameType, optionalNameType, SOURCE_BIOASSAYS, SOURCE_BIOASSAYSET, SOURCE_DERIVEDBIOASSAY, TRANSFORMATION_NAME
annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc
Constructor and Description |
---|
JepExtraValueCalculator() |
Modifier and Type | Method and 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.
|
getChildDescriptionParameter, getChildNameParameter, getCurrentBioAssaySet, getCurrentDerivedBioAssay, getCurrentExperiment, getMainType, getSourceBioAssays, getSourceBioAssaySet, getSourceBioAssaySetParameter, getSourceBioAssaysParameter, getSourceDerivedBioAssay, getSourceDerivedBioAssayParameter, getTransformationName, getTransformationNameParameter, restrictSource
cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, init, log, log, storeValue, storeValue, storeValues, validateRequestParameters
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
done, getMainType, init
private static final Set<Permissions> permissions
private static final Set<GuiContext> guiContexts
private static final PluginParameter<String> expressionParameter
private ThreadSignalHandler signalHandler
private RequestInformation configureJob
private PluginParameter<ExtraValueType> extraValueTypeParameter
public boolean supportsConfigurations()
AbstractPlugin
supportsConfigurations
in interface Plugin
supportsConfigurations
in class AbstractPlugin
public boolean requiresConfiguration()
AbstractPlugin
requiresConfiguration
in interface Plugin
requiresConfiguration
in class AbstractPlugin
public Collection<Permissions> getPermissions()
getPermissions
in interface Plugin
getPermissions
in class AbstractPlugin
public void run(Request request, Response response, ProgressReporter progress)
Plugin
run
in interface Plugin
request
- Request object with the command and parametersresponse
- Response object in for the plugin to response
throughprogress
- A ProgressReporter
where the plugin can report
its progess, can be nullpublic Set<GuiContext> getGuiContexts()
InteractivePlugin
Item.REPORTER
.
This information is used by client applications to put the plugin
in the proper place in the user interface.getGuiContexts
in interface InteractivePlugin
getGuiContexts
in class AbstractAnalysisPlugin
Set
containing Item
:s, or null
if the plugin is not concerned about itemspublic String isInContext(GuiContext context, Object item)
AbstractAnalysisPlugin
isInContext
in interface InteractivePlugin
isInContext
in class AbstractAnalysisPlugin
context
- Current guicontextitem
- The item to check.public RequestInformation getRequestInformation(GuiContext context, String command) throws BaseException
InteractivePlugin
RequestInformation
for a given command, i.e.
the list of parameters and some nice help text.getRequestInformation
in interface InteractivePlugin
context
- The current context of the client application,
it is one of the values found in set returned by InteractivePlugin.getGuiContexts()
command
- The commandRequestInformation
for the commandBaseException
- if there is an errorpublic void configure(GuiContext context, Request request, Response response)
InteractivePlugin
InteractivePlugin.getRequestInformation(GuiContext, String)
.configure
in interface InteractivePlugin
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 parametersresponse
- Response object in for the plugin to response
throughpublic SignalHandler getSignalHandler()
SignalTarget
getSignalHandler
in interface SignalTarget
private RequestInformation getConfigureJobParameters()