public class ManualTransformCreator extends AbstractAnalysisPlugin implements InteractivePlugin, AnnotationSetterPlugin
Plugin.MainType
Modifier and Type | Field and Description |
---|---|
private RequestInformation |
configureJob |
private RequestInformation |
configurePlugin |
private List<String> |
importableFileTypes |
private List<PluginParameter<?>> |
toolParameters |
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 |
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ManualTransformCreator() |
Modifier and Type | Method and Description |
---|---|
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) |
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.
|
getChildDescriptionParameter, getChildNameParameter, getCurrentBioAssaySet, getCurrentDerivedBioAssay, getCurrentExperiment, getGuiContexts, getMainType, getSourceBioAssays, getSourceBioAssaySet, getSourceBioAssaySetParameter, getSourceBioAssaysParameter, getSourceDerivedBioAssay, getSourceDerivedBioAssayParameter, getTransformationName, getTransformationNameParameter, isInContext, restrictSource
cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, getPermissions, init, log, log, storeValue, storeValue, storeValues, validateRequestParameters
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getGuiContexts, isInContext
done, getMainType, getPermissions, init
private RequestInformation configureJob
private RequestInformation configurePlugin
private List<PluginParameter<?>> toolParameters
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 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 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 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 ItemQuery<AnnotationType> getAnnotationTypes()
getAnnotationTypes
in interface AnnotationSetterPlugin
public String getAnnotationMessage()
AnnotationSetterPlugin
getAnnotationMessage
in interface AnnotationSetterPlugin
private RequestInformation getConfigureJobParameters(GuiContext context)
private RequestInformation getConfigurePluginParameters(GuiContext context)
private List<PluginParameter<?>> getToolParameters(List<String> values)
private String getImportFileType()