net.sf.basedb.plugins
Class ManualTransformCreator
java.lang.Object
net.sf.basedb.core.plugin.AbstractPlugin
net.sf.basedb.core.plugin.AbstractAnalysisPlugin
net.sf.basedb.plugins.ManualTransformCreator
- 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
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 |
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 |
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 |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
configureJob
private RequestInformation configureJob
configurePlugin
private RequestInformation configurePlugin
toolParameters
private List<PluginParameter<?>> toolParameters
importableFileTypes
private List<String> importableFileTypes
ManualTransformCreator
public ManualTransformCreator()
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 interface Plugin
- Overrides:
supportsConfigurations
in class AbstractPlugin
- Returns:
- TRUE or FALSE
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 interface Plugin
- Overrides:
requiresConfiguration
in class AbstractPlugin
- Returns:
- TRUE or FALSE
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 interface Plugin
- Parameters:
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 null
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 by
InteractivePlugin.getRequestInformation(GuiContext, String)
.
- Specified by:
configure
in interface InteractivePlugin
- Parameters:
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
through
getRequestInformation
public RequestInformation getRequestInformation(GuiContext context,
String command)
throws BaseException
- Description copied from interface:
InteractivePlugin
- This method will return the
RequestInformation
for a given command, i.e.
the list of parameters and some nice help text.
- Specified by:
getRequestInformation
in interface InteractivePlugin
- Parameters:
context
- The current context of the client application,
it is one of the values found in set returned by InteractivePlugin.getGuiContexts()
command
- The command
- Returns:
- The
RequestInformation
for the command
- Throws:
BaseException
- if there is an error
getAnnotationTypes
public ItemQuery<AnnotationType> getAnnotationTypes()
- Return a query that finds annotation types for bioassay sets.
- Specified by:
getAnnotationTypes
in interface AnnotationSetterPlugin
- Returns:
- A query returning annotation types, or null if the current setup doesn't
allow any annotations
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 interface AnnotationSetterPlugin
- Returns:
- A message or null
getConfigureJobParameters
private RequestInformation getConfigureJobParameters(GuiContext context)
getConfigurePluginParameters
private RequestInformation getConfigurePluginParameters(GuiContext context)
getToolParameters
private List<PluginParameter<?>> getToolParameters(List<String> values)
getImportFileType
private String getImportFileType()