Package net.sf.basedb.plugins
Class ManualTransformCreator
- java.lang.Object
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- net.sf.basedb.core.plugin.AbstractPlugin
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- net.sf.basedb.core.plugin.AbstractAnalysisPlugin
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- net.sf.basedb.plugins.ManualTransformCreator
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin
Plugin.MainType
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Field Summary
Fields Modifier and Type Field Description private RequestInformation
configureJob
private RequestInformation
configurePlugin
private List<String>
importableFileTypes
private List<PluginParameter<?>>
toolParameters
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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
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Fields inherited from class net.sf.basedb.core.plugin.AbstractPlugin
annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc
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Constructor Summary
Constructors Constructor Description ManualTransformCreator()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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 theRequestInformation
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, getCurrentDerivedBioAssay, getCurrentExperiment, getGuiContexts, getMainType, getSourceBioAssays, getSourceBioAssaySet, getSourceBioAssaySetParameter, getSourceBioAssaysParameter, getSourceDerivedBioAssay, getSourceDerivedBioAssayParameter, getTransformationName, getTransformationNameParameter, isInContext, restrictSource
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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
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface net.sf.basedb.core.plugin.InteractivePlugin
getGuiContexts, isInContext
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Methods inherited from interface net.sf.basedb.core.plugin.Plugin
done, getMainType, getPermissions, init
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Field Detail
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configureJob
private RequestInformation configureJob
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configurePlugin
private RequestInformation configurePlugin
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toolParameters
private List<PluginParameter<?>> toolParameters
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Method Detail
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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
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 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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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 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
public ItemQuery<AnnotationType> 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
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 interfaceAnnotationSetterPlugin
- Returns:
- A message or null
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getConfigureJobParameters
private RequestInformation getConfigureJobParameters(GuiContext context)
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getConfigurePluginParameters
private RequestInformation getConfigurePluginParameters(GuiContext context)
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getToolParameters
private List<PluginParameter<?>> getToolParameters(List<String> values)
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getImportFileType
private String getImportFileType()
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