net.sf.basedb.core.plugin
Class AbstractAnalysisPlugin

java.lang.Object
  net.sf.basedb.core.plugin.AbstractPlugin
      net.sf.basedb.core.plugin.AbstractAnalysisPlugin

All Implemented Interfaces:

Plugin

Direct Known Subclasses:

Base1PluginExecuter, ExternalProgramExecutor, FormulaFilter, JepExtraValueCalculator, JepIntensityTransformer, LowessNormalization, ManualTransformCreator, MedianRatioNormalization

public abstract class AbstractAnalysisPlugin
extends AbstractPlugin

This is a base class that is useful for all analysis type plugins. It has helper methods for generating some common parameter types needed by many plugins, such as the source bioassay set and child bioassay set name and description, etc.

Version:

2.0

Author:

nicklas

Last modified

$Date: 2010-08-13 12:48:17 +0200 (Fri, 13 Aug 2010) $

Nested Class Summary

Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin

Plugin.MainType

Field Summary

protected static String	CHILD_DESCRIPTION The name of the parameter that asks for the description of the child bioassay set.
protected static String	CHILD_NAME The name of the parameter that asks for the name of the child bioassay set.
protected static GuiContext	CONTEXT_BIOASSAYS GuiContext = [Item.BIOASSAY, GuiContext.Type.LIST]
protected static GuiContext	CONTEXT_BIOASSAYSET GuiContext = [Item.BIOASSAYSET, GuiContext.Type.ITEM]
protected static Set<GuiContext>	defaultGuiContexts The default gui contexts where it makes sense to use an analysis plugin.
private static StringParameterType	descriptionType A parameter type for description parameters.
protected static StringParameterType	nameType A parameter type for name parameters which are required and must have a value.
protected static StringParameterType	optionalNameType A parameter type for name parameters which are optional.
protected static String	SOURCE_BIOASSAYS
protected static String	SOURCE_BIOASSAYSET
private static ItemParameterType<BioAssaySet>	sourceBioAssaySetType The parameter type for the source bioassay set.
private PluginParameter<BioAssaySet>	sourceParameter The source parameter.
private PluginParameter<BioAssay>	sourceSubSetParameter The bioAssays subset parameter.
protected static String	TRANSFORMATION_NAME The name of the parameter that asks for the name of the transformation.

Fields inherited from class net.sf.basedb.core.plugin.AbstractPlugin

annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc

Constructor Summary

protected

AbstractAnalysisPlugin() Create a new AbstractAnalysisPlugin.

Method Summary

protected PluginParameter<String>	getChildDescriptionParameter(String label, String description, String defaultValue) Create a plugin parameter that asks for the description of the child bioassay set.
protected PluginParameter<String>	getChildNameParameter(String label, String description, String defaultValue) Create a plugin parameter that asks for the name of the child bioassay set.
protected BioAssaySet	getCurrentBioAssaySet(DbControl dc) Get the current source bioassay set.
protected Experiment	getCurrentExperiment(DbControl dc) Get the current experiment from information in the current context: SessionControl.getCurrentContext(Item.EXPERIMENT).
Set<GuiContext>	getGuiContexts()
Plugin.MainType	getMainType() Get the type of the plugin.
protected List<BioAssay>	getSourceBioAssays(DbControl dc) Gets a list of bioassays that were selected from the current bioassay set, to use for the analysis.
protected BioAssaySet	getSourceBioAssaySet(DbControl dc) Get the bioassay set that is used as the source for the plugin.
protected PluginParameter<BioAssaySet>	getSourceBioAssaySetParameter(String label, String description) Get a plugin parameter that asks for a bioassay set to use as data source for the plugin.
protected PluginParameter<BioAssay>	getSourceBioAssaysParameter(String label, String description) Gets a plugin parameter that asks for a subset of bioassays to use as data source for the plugin.
protected String	getTransformationName(DbControl dc) Generate a name for the transformation based on the plugin and it's configuration.
protected PluginParameter<String>	getTransformationNameParameter(String label, String description, String defaultValue) Create a plugin parameter that asks for the name of the transformation.
String	isInContext(GuiContext context, Object item) Check that the item is a bioassayset and that the logged in user has permission to use the current experiment.
protected DynamicSpotQuery	restrictSource(DynamicSpotQuery query, List<BioAssay> bioAssays) Restricts a query to only include values from listed bioassays

Methods inherited from class net.sf.basedb.core.plugin.AbstractPlugin

checkInterrupted, cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, getPermissions, init, log, log, requiresConfiguration, storeValue, storeValue, storeValues, supportsConfigurations, 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

getAbout, run

Field Detail

CONTEXT_BIOASSAYSET

protected static final GuiContext CONTEXT_BIOASSAYSET

GuiContext = [Item.BIOASSAYSET, GuiContext.Type.ITEM]

Since:

2.4

CONTEXT_BIOASSAYS

protected static final GuiContext CONTEXT_BIOASSAYS

GuiContext = [Item.BIOASSAY, GuiContext.Type.LIST]

Since:

2.4

defaultGuiContexts

protected static final Set<GuiContext> defaultGuiContexts

The default gui contexts where it makes sense to use an analysis plugin. Override for the InteractivePlugin.getGuiContexts() method to specify other contexts. This set can't be modified. This set only includes the CONTEXT_BIOASSAYSET.

nameType

protected static final StringParameterType nameType

A parameter type for name parameters which are required and must have a value.

optionalNameType

protected static final StringParameterType optionalNameType

A parameter type for name parameters which are optional.

descriptionType

private static final StringParameterType descriptionType

A parameter type for description parameters.

sourceBioAssaySetType

private static final ItemParameterType<BioAssaySet> sourceBioAssaySetType

The parameter type for the source bioassay set.

sourceParameter

private PluginParameter<BioAssaySet> sourceParameter

The source parameter.

See Also:

getSourceBioAssaySetParameter(String, String)

sourceSubSetParameter

private PluginParameter<BioAssay> sourceSubSetParameter

The bioAssays subset parameter. To use when working on subset of bioassays in a bioAssaySet

See Also:

getSourceBioAssaysParameter(String, String)

SOURCE_BIOASSAYSET

protected static final String SOURCE_BIOASSAYSET

See Also:

Constant Field Values

SOURCE_BIOASSAYS

protected static final String SOURCE_BIOASSAYS

See Also:

Constant Field Values

CHILD_NAME

protected static final String CHILD_NAME

The name of the parameter that asks for the name of the child bioassay set.

See Also:

getChildNameParameter(String, String, String), Constant Field Values

CHILD_DESCRIPTION

protected static final String CHILD_DESCRIPTION

The name of the parameter that asks for the description of the child bioassay set.

See Also:

getChildDescriptionParameter(String, String, String), Constant Field Values

TRANSFORMATION_NAME

protected static final String TRANSFORMATION_NAME

The name of the parameter that asks for the name of the transformation.

See Also:

getTransformationNameParameter(String, String, String), Constant Field Values

Constructor Detail

AbstractAnalysisPlugin

protected AbstractAnalysisPlugin()

Create a new AbstractAnalysisPlugin.

Method Detail

getMainType

public Plugin.MainType getMainType()

Description copied from interface: Plugin

Get the type of the plugin. This method must always return the same value.

Returns:

Plugin.MainType.ANALYZE

getGuiContexts

public Set<GuiContext> getGuiContexts()

isInContext

public String isInContext(GuiContext context,
                          Object item)

Check that the item is a bioassayset and that the logged in user has permission to use the current experiment.

Parameters:

context - Current guicontext

item - The item to check.

Returns:

null if the item is a bioassayset, an error message otherwise

Throws:

PermissionDeniedException - If the logged in user dosen't have permission to use the Experiment

getSourceBioAssaySetParameter

protected PluginParameter<BioAssaySet> getSourceBioAssaySetParameter(String label,
                                                                     String description)

Get a plugin parameter that asks for a bioassay set to use as data source for the plugin. Calling this method multiple times return the same plugin parameter object. The label and description for the first call is always used.

Parameters:

label - The parameter label, or null to use the default (Source bioasay set)

description - The parameter description, or null to use the default (The bioassay set that is used as the data source for this job.)

getSourceBioAssaysParameter

protected PluginParameter<BioAssay> getSourceBioAssaysParameter(String label,
                                                                String description)

Gets a plugin parameter that asks for a subset of bioassays to use as data source for the plugin.

Parameters:

label - The parameter's label. Uses a default value if null.

description - Description of the parameter. Uses a default value if null.

Returns:

A plugin parameter

Since:

2.4

getChildNameParameter

protected PluginParameter<String> getChildNameParameter(String label,
                                                        String description,
                                                        String defaultValue)

Create a plugin parameter that asks for the name of the child bioassay set.

Parameters:

label - The label to use for the parameter or null to use the default label (Child name)

description - The description to use for the parameter or null to use the default description (The name of the child bioassay set)

defaultValue - The default value for the child name or null to use the default value (New bioassay set)

Returns:

A plugin parameter

getChildDescriptionParameter

protected PluginParameter<String> getChildDescriptionParameter(String label,
                                                               String description,
                                                               String defaultValue)

Create a plugin parameter that asks for the description of the child bioassay set.

Parameters:

label - The label to use for the parameter or null to use the default label (Child description)

description - The description to use for the parameter or null to use the default description (An optional description of the child bioassay set)

defaultValue - The default value for the child name or null to not use any default value

Returns:

A plugin parameter

getTransformationNameParameter

protected PluginParameter<String> getTransformationNameParameter(String label,
                                                                 String description,
                                                                 String defaultValue)

Create a plugin parameter that asks for the name of the transformation.

Parameters:

label - The label to use for the parameter or null to use the default label (Transformation name)

description - The description to use for the parameter or null to use the default description (The name of the transformation)

defaultValue - The default value for the transformation name or null to not use any default

Returns:

A plugin parameter

getCurrentExperiment

protected Experiment getCurrentExperiment(DbControl dc)

Get the current experiment from information in the current context: SessionControl.getCurrentContext(Item.EXPERIMENT). Note that this information is normally only available during the configuration phase of a plugin, not during the execution phase.

Parameters:

dc - The DbControl to use for database access

Returns:

The current experiment or null

getCurrentBioAssaySet

protected BioAssaySet getCurrentBioAssaySet(DbControl dc)

Get the current source bioassay set. We first check the job's parameter values with the getSourceBioAssaySet(DbControl) method. If this returns null we check the information in the current context: SessionControl.getCurrentContext(Item.BIOASSAYSET). Note that this information is normally only available during the configuration phase of a plugin, not during the execution phase.

Parameters:

dc - The DbControl to use for database access

Returns:

The current bioassay set or null

See Also:

getSourceBioAssaySet(DbControl)

getSourceBioAssaySet

protected BioAssaySet getSourceBioAssaySet(DbControl dc)

Get the bioassay set that is used as the source for the plugin. The source bioassay set is only available in the execution phase if the plugin has saved it as a job parameter during the configuration of a job.

Returns:

The source bioassay set or null

See Also:

getSourceBioAssaySetParameter(String, String)

getSourceBioAssays

protected List<BioAssay> getSourceBioAssays(DbControl dc)

Gets a list of bioassays that were selected from the current bioassay set, to use for the analysis.

Parameters:

dc - The DbControl to access the database with

Returns:

A list with bioassays or null.

Since:

2.4

getTransformationName

protected String getTransformationName(DbControl dc)

Generate a name for the transformation based on the plugin and it's configuration. The name is created by taking the name of the plugin from the About.getName() method and combine it with the configuration used. If no configuration is used only the plugin name is used.

Parameters:

dc - The DbControl to use for database access

Returns:

A name for the transformation

restrictSource

protected DynamicSpotQuery restrictSource(DynamicSpotQuery query,
                                          List<BioAssay> bioAssays)

Restricts a query to only include values from listed bioassays

Parameters:

query - The query to set restriction on

bioAssays - A list with bioassays the restriction should include

Returns:

A DynamicSpotQuery object. The query parameter is restricted if bioAssays holds item(s), otherwise it will it will be the same

Since:

2.4