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java.lang.Object net.sf.basedb.core.plugin.AbstractPlugin net.sf.basedb.core.plugin.AbstractAnalysisPlugin net.sf.basedb.plugins.ManualTransformCreator
public class ManualTransformCreator
Plug-in that allows a user to manually register an external analysis procedure and to upload files that was generated by it.
Nested Class Summary |
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Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin |
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Plugin.MainType |
Field Summary | |
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private RequestInformation |
configureJob
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private RequestInformation |
configurePlugin
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private List<String> |
importableFileTypes
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private List<PluginParameter<?>> |
toolParameters
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Fields inherited from class net.sf.basedb.core.plugin.AbstractAnalysisPlugin |
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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 |
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annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc |
Constructor Summary | |
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ManualTransformCreator()
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Method Summary | |
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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)
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private RequestInformation |
getConfigurePluginParameters(GuiContext context)
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private String |
getImportFileType()
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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)
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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 |
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getChildDescriptionParameter, getChildNameParameter, getCurrentBioAssaySet, getCurrentExperiment, getGuiContexts, getMainType, getSourceBioAssays, getSourceBioAssaySet, getSourceBioAssaySetParameter, getSourceBioAssaysParameter, getTransformationName, getTransformationNameParameter, isInContext, restrictSource |
Methods inherited from class net.sf.basedb.core.plugin.AbstractPlugin |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface net.sf.basedb.core.plugin.InteractivePlugin |
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getGuiContexts, isInContext |
Methods inherited from interface net.sf.basedb.core.plugin.Plugin |
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done, getMainType, getPermissions, init |
Field Detail |
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private RequestInformation configureJob
private RequestInformation configurePlugin
private List<PluginParameter<?>> toolParameters
private List<String> importableFileTypes
Constructor Detail |
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public ManualTransformCreator()
Method Detail |
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public About getAbout()
Plugin
getAbout
in interface Plugin
About
objectpublic 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 command
RequestInformation
for the command
BaseException
- 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()
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2.17.2: 2011-06-17 | ||||||||
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