Package net.sf.basedb.plugins

Class BfsExporterPlugin

java.lang.Object

net.sf.basedb.core.plugin.AbstractPlugin

net.sf.basedb.plugins.BfsExporterPlugin

All Implemented Interfaces:

InteractivePlugin, Plugin, SignalTarget

public class BfsExporterPlugin
extends AbstractPlugin
implements InteractivePlugin, SignalTarget

Exports bioassay set data to BFS format.

Since:

2.15

Author:

Nicklas

Last modified

$Date: 2019-02-26 11:10:15 +0100 (tis, 26 feb. 2019) $

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	BfsExporterPlugin.ExtendedExportableField

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

Plugin.MainType

Field Summary

Fields

Modifier and Type	Field	Description
private BioAssaySet	bas
private RequestInformation	configureJob
private DbControl	dc
private Map<String,BfsExporterPlugin.ExtendedExportableField>	exportableFields
private static final Set<GuiContext>	guiContexts
static final String	PARAMETER_FILEFORMAT
static final String	PARAMETER_FILENAMEGENERATOR
private ThreadSignalHandler	signalHandler

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

annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc

Constructor Summary

Constructors

Constructor	Description
BfsExporterPlugin()

Method Summary

Modifier and Type	Method	Description
private BfsExporterPlugin.ExtendedExportableField	assayField(String property, String guiTitle, Type type)
protected void	begin(DbControl dc)
void	configure(GuiContext context, Request request, Response response)	Configure the plugin.
private File	createFile(File dir, String name)
private File	createFile(DbControl dc, Directory dir, String name)
protected void	end(boolean success)
private List<BfsExporterPlugin.ExtendedExportableField>	getAssayFields(DbControl dc, BioAssaySet source)
private RequestInformation	getConfigureJobParameters(GuiContext context)
Map<String,BfsExporterPlugin.ExtendedExportableField>	getExportableFields(DbControl dc, BioAssaySet source)
private Collection<BfsExporterPlugin.ExtendedExportableField>	getExtraValueFields(DbControl dc, BioAssaySet source)
static PluginParameter<String>	getFileFormatParameter()	Create a plug-in parameter that asks for the BFS subtype to use in the export.
static PluginParameter<String>	getFileNameGeneratorParameter()	Create a plug-in parameter that asks for the file name generation strategy.
private List<BfsExporterPlugin.ExtendedExportableField>	getFormulaFields(DbControl dc, BioAssaySet source)
Set<GuiContext>	getGuiContexts()	Get a set containing all items that the plugin handles.
Plugin.MainType	getMainType()	Get the type of the plugin.
private List<BfsExporterPlugin.ExtendedExportableField>	getRawdataFields(BioAssaySet source)
static Collection<BfsExporterPlugin.ExtendedExportableField>	getReporterFields()
RequestInformation	getRequestInformation(GuiContext context, String command)	This method will return the RequestInformation for a given command, i.e.
SignalHandler	getSignalHandler()	Get the signal handler that is handling signals on behalf of this object.
private Collection<BfsExporterPlugin.ExtendedExportableField>	getSpotFields(BioAssaySet source)
protected String	getSuccessMessage()
String	isInContext(GuiContext context, Object item)	Check if the plugin can be used on the specified object.
protected void	performExport(ProgressReporter progress)
private BfsExporterPlugin.ExtendedExportableField	rawField(String property, String title, Type type, Formula.AverageMethod averageMethod)
private static BfsExporterPlugin.ExtendedExportableField	reporterField(String property, String guiTitle, Type type, Formula.AverageMethod averageMethod)
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

cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, getPermissions, init, isLogging, log, log, storeValue, storeValue, storeValues, 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

done, getPermissions, init

Field Details

guiContexts

private static final Set<GuiContext> guiContexts

signalHandler

private ThreadSignalHandler signalHandler

configureJob

private RequestInformation configureJob

dc

private DbControl dc

bas

private BioAssaySet bas

exportableFields

private Map<String,BfsExporterPlugin.ExtendedExportableField> exportableFields

PARAMETER_FILEFORMAT

public static final String PARAMETER_FILEFORMAT

See Also:

• Constant Field Values

PARAMETER_FILENAMEGENERATOR

public static final String PARAMETER_FILENAMEGENERATOR

See Also:

• Constant Field Values

Constructor Details

BfsExporterPlugin

public BfsExporterPlugin()

Method Details

getMainType

public Plugin.MainType getMainType()

Description copied from interface: Plugin

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

Specified by:

getMainType in interface Plugin

Returns:

MainType.EXPORT

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

getGuiContexts

public Set<GuiContext> getGuiContexts()

Description copied from interface: InteractivePlugin

Get a set containing all items that the plugin handles. Ie. if the plugin imports reporters, return a set containing Item.REPORTER. This information is used by client applications to put the plugin in the proper place in the user interface.

Specified by:

getGuiContexts in interface InteractivePlugin

Returns:

A Set containing Item:s, or null if the plugin is not concerned about items

isInContext

public String isInContext(GuiContext context,
 Object item)

Description copied from interface: InteractivePlugin

Check if the plugin can be used on the specified object. The item is either a BasicItem or BasicData object, or null if called from a list context. A client application should only call this method for contexts matching one of the contexts in the set returned by the InteractivePlugin.getGuiContexts() method. For GuiContext.Type.ITEM contexts an item of the correct type should be passed as a parameter.

The plug-in can response with a null value indicating success, a warning-level message or throw an exception to indicate an error-level message. Client application should normally only show error-level messages to users, unless the user has requested to see warning messages.

NOTE! Before BASE 2.4 all messages were treated as error-level messages.

Specified by:

isInContext 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()

item - The currently active item, it's type should match the GuiContext.getItem() type, or null if the context is a list context

Returns:

Null if the plugin can use that item, or a warning-level message explaining why the plugin can't be used

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

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 parameters

response - Response object in for the plugin to response through

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 parameters

response - Response object in for the plugin to response through

progress - A ProgressReporter where the plugin can report its progess, can be null

getSignalHandler

public SignalHandler getSignalHandler()

Description copied from interface: SignalTarget

Get the signal handler that is handling signals on behalf of this object. Multiple invokations of this method may receive the same or different objects. Null may be returned if, for some reason, the current object instance doesn't want to receive signals. Returning null is the same as not implementing this interface.

Specified by:

getSignalHandler in interface SignalTarget

Returns:

A SignalHandler object, or null if the current instance doesn't support signals

begin

protected void begin(DbControl dc)

performExport

protected void performExport(ProgressReporter progress)
                      throws IOException

Throws:

IOException

end

protected void end(boolean success)

getSuccessMessage

protected String getSuccessMessage()

getConfigureJobParameters

private RequestInformation getConfigureJobParameters(GuiContext context)

getExportableFields

public Map<String,BfsExporterPlugin.ExtendedExportableField> getExportableFields(DbControl dc,
 BioAssaySet source)

getFormulaFields

private List<BfsExporterPlugin.ExtendedExportableField> getFormulaFields(DbControl dc,
 BioAssaySet source)

getRawdataFields

private List<BfsExporterPlugin.ExtendedExportableField> getRawdataFields(BioAssaySet source)

rawField

private BfsExporterPlugin.ExtendedExportableField rawField(String property,
 String title,
 Type type,
 Formula.AverageMethod averageMethod)

getReporterFields

public static Collection<BfsExporterPlugin.ExtendedExportableField> getReporterFields()

reporterField

private static BfsExporterPlugin.ExtendedExportableField reporterField(String property,
 String guiTitle,
 Type type,
 Formula.AverageMethod averageMethod)

getExtraValueFields

private Collection<BfsExporterPlugin.ExtendedExportableField> getExtraValueFields(DbControl dc,
 BioAssaySet source)

getSpotFields

private Collection<BfsExporterPlugin.ExtendedExportableField> getSpotFields(BioAssaySet source)

getAssayFields

private List<BfsExporterPlugin.ExtendedExportableField> getAssayFields(DbControl dc,
 BioAssaySet source)

assayField

private BfsExporterPlugin.ExtendedExportableField assayField(String property,
 String guiTitle,
 Type type)

createFile

private File createFile(File dir,
 String name)
                 throws IOException

Throws:

IOException

createFile

private File createFile(DbControl dc,
 Directory dir,
 String name)

getFileFormatParameter

public static PluginParameter<String> getFileFormatParameter()

Create a plug-in parameter that asks for the BFS subtype to use in the export.

getFileNameGeneratorParameter

public static PluginParameter<String> getFileNameGeneratorParameter()

Create a plug-in parameter that asks for the file name generation strategy.