Package net.sf.basedb.plugins
Class ManualDerivedBioAssayCreator
java.lang.Object
net.sf.basedb.core.plugin.AbstractPlugin
net.sf.basedb.core.plugin.AbstractAnalysisPlugin
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
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Nested Class Summary
Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin
Plugin.MainType
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Field Summary
Modifier and TypeFieldDescriptionprivate RequestInformation
private RequestInformation
private List<PluginParameter<?>>
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
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionvoid
configure
(GuiContext context, Request request, Response response) Configure the plugin.Get a message that explains what the plug-in does with the annotations it has.Return a query that finds annotation types for bioassay sets.private RequestInformation
getConfigureJobParameters
(GuiContext context) private RequestInformation
getConfigurePluginParameters
(GuiContext context) Get a set containing all items that the plugin handles.getRequestInformation
(GuiContext context, String command) This method will return theRequestInformation
for a given command, i.e.private List<PluginParameter<?>>
getToolParameters
(List<String> values) isInContext
(GuiContext context, Object item) Adds check of the item subtype.boolean
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
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, isLogging, 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
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Field Details
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configureJob
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configurePlugin
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toolParameters
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Constructor Details
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ManualDerivedBioAssayCreator
public ManualDerivedBioAssayCreator()
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Method Details
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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 interfacePlugin
- Overrides:
supportsConfigurations
in classAbstractPlugin
- Returns:
- TRUE or FALSE
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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 interfacePlugin
- Overrides:
requiresConfiguration
in classAbstractPlugin
- Returns:
- TRUE or FALSE
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run
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 interfacePlugin
- Parameters:
request
- Request object with the command and parametersresponse
- Response object in for the plugin to response throughprogress
- AProgressReporter
where the plugin can report its progess, can be null
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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 containingItem.REPORTER
. This information is used by client applications to put the plugin in the proper place in the user interface.- Specified by:
getGuiContexts
in interfaceInteractivePlugin
- Overrides:
getGuiContexts
in classAbstractAnalysisPlugin
- Returns:
- A
Set
containingItem
:s, or null if the plugin is not concerned about items
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isInContext
Adds check of the item subtype.- Specified by:
isInContext
in interfaceInteractivePlugin
- Overrides:
isInContext
in classAbstractAnalysisPlugin
- Parameters:
context
- Current guicontextitem
- The item to check.- Returns:
- null if the item is a valid item, an error message otherwise
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configure
Description copied from interface:InteractivePlugin
Configure the plugin. Hopefully the client is supplying values for the parameters specified byInteractivePlugin.getRequestInformation(GuiContext, String)
.- Specified by:
configure
in interfaceInteractivePlugin
- Parameters:
context
- The current context of the client application, it is one of the values found in set returned byInteractivePlugin.getGuiContexts()
request
- Request object with the command and parametersresponse
- Response object in for the plugin to response through
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getRequestInformation
public RequestInformation getRequestInformation(GuiContext context, String command) throws BaseException Description copied from interface:InteractivePlugin
This method will return theRequestInformation
for a given command, i.e. the list of parameters and some nice help text.- Specified by:
getRequestInformation
in interfaceInteractivePlugin
- Parameters:
context
- The current context of the client application, it is one of the values found in set returned byInteractivePlugin.getGuiContexts()
command
- The command- Returns:
- The
RequestInformation
for the command - Throws:
BaseException
- if there is an error
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getAnnotationTypes
Return a query that finds annotation types for bioassay sets.- Specified by:
getAnnotationTypes
in interfaceAnnotationSetterPlugin
- Returns:
- A query returning annotation types, or null if the current setup doesn't allow any annotations
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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 interfaceAnnotationSetterPlugin
- Returns:
- A message or null
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getConfigureJobParameters
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getConfigurePluginParameters
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getToolParameters
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