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java.lang.Objectnet.sf.basedb.core.plugin.AbstractPlugin
net.sf.basedb.core.plugin.AbstractAnalysisPlugin
net.sf.basedb.plugins.ManualDerivedBioAssayCreator
public class ManualDerivedBioAssayCreator
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.
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<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, CONTEXT_DERIVEDBIOASSAY, defaultGuiContexts, nameType, optionalNameType, SOURCE_BIOASSAYS, SOURCE_BIOASSAYSET, SOURCE_DERIVEDBIOASSAY, 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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ManualDerivedBioAssayCreator()
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Method Summary | |
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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)
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private RequestInformation |
getConfigurePluginParameters(GuiContext context)
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Set<GuiContext> |
getGuiContexts()
Get a set containing all items that the plugin handles. |
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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String |
isInContext(GuiContext context,
Object item)
Adds check of the item subtype. |
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.AbstractPlugin |
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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.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
Constructor Detail |
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public ManualDerivedBioAssayCreator()
Method Detail |
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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 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)
isInContext
in interface InteractivePlugin
isInContext
in class AbstractAnalysisPlugin
context
- Current guicontextitem
- The item to check.
public 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)
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3.2.1: 2012-12-13 | ||||||||
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