Package net.sf.basedb.plugins

Class BaseFileExporterPlugin

java.lang.Object

net.sf.basedb.core.plugin.AbstractPlugin

net.sf.basedb.core.plugin.AbstractExporterPlugin

net.sf.basedb.plugins.BaseFileExporterPlugin

All Implemented Interfaces:

ImmediateDownloadExporter, InteractivePlugin, Plugin, SignalTarget

public class BaseFileExporterPlugin
extends AbstractExporterPlugin
implements InteractivePlugin, SignalTarget

Exports bioassay set data as serial or matrix BASEfile:s.

Version:

2.12

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	BaseFileExporterPlugin.ExtendedDynamicField

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,BaseFileExporterPlugin.ExtendedDynamicField>	exportableFields
private static final String	FORMAT_BASEFILE_MATRIX
private static final String	FORMAT_BASEFILE_SERIAL
private static final Set<GuiContext>	guiContexts
static final String	PARAMETER_FILEFORMAT
private static final Set<Permissions>	permissions
private ThreadSignalHandler	signalHandler

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

optionalSaveAsType, OVERWRITE, overwriteType, requiredSaveAsType, SAVE_AS

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

annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc

Constructor Summary

Constructors

Constructor	Description
BaseFileExporterPlugin()

Method Summary

Modifier and Type	Method	Description
protected void	begin(DbControl dc)	Called just before the export starts.
void	configure(GuiContext context, Request request, Response response)	Configure the plugin.
protected void	end(boolean success)	Called just after everything has been committed to the database, or immediately after an error has ocurred.
private RequestInformation	getConfigureJobParameters(GuiContext context, Boolean requireFile)
Map<String,BaseFileExporterPlugin.ExtendedDynamicField>	getExportableFields(DbControl dc, BioAssaySet source)
private Collection<BaseFileExporterPlugin.ExtendedDynamicField>	getExtraValueFields(DbControl dc, BioAssaySet source)
static PluginParameter<String>	getFileFormatParameter()	Create a plug-in parameter that asks for the BASEFile subtype to use in the export.
private List<BaseFileExporterPlugin.ExtendedDynamicField>	getFormulaFields(DbControl dc, BioAssaySet source)
Set<GuiContext>	getGuiContexts()	Get a set containing all items that the plugin handles.
Collection<Permissions>	getPermissions()	Request create and write access to File:s and Directory:s and read access to Experiment:s and User:s.
private List<BaseFileExporterPlugin.ExtendedDynamicField>	getRawdataFields(BioAssaySet source)
private Collection<BaseFileExporterPlugin.ExtendedDynamicField>	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<BaseFileExporterPlugin.ExtendedDynamicField>	getSpotFields(BioAssaySet source)
protected String	getSuccessMessage()	Called if the export was successful to let the subclass generate a simple message that is sent back to the core and user interface.
String	isInContext(GuiContext context, Object item)	Check if the plugin can be used on the specified object.
protected void	performExport(ExportOutputStream out, ProgressReporter progress)	Perform the export.
private BaseFileExporterPlugin.ExtendedDynamicField	rawField(String property, String guiTitle, Type type, Formula.AverageMethod averageMethod)
private BaseFileExporterPlugin.ExtendedDynamicField	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.
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.AbstractExporterPlugin

doExport, getMainType, getOverwrite, getOverwriteParameter, getSaveAsParameter, getSaveAsPath, getSaveTo, pathCanBeUsed, run

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

cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, 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, getMainType, init, run

Field Details

guiContexts

private static final Set<GuiContext> guiContexts

permissions

private static final Set<Permissions> permissions

FORMAT_BASEFILE_SERIAL

private static final String FORMAT_BASEFILE_SERIAL

See Also:

• Constant Field Values

FORMAT_BASEFILE_MATRIX

private static final String FORMAT_BASEFILE_MATRIX

See Also:

• Constant Field Values

signalHandler

private ThreadSignalHandler signalHandler

configureJob

private RequestInformation configureJob

dc

private DbControl dc

bas

private BioAssaySet bas

exportableFields

private Map<String,BaseFileExporterPlugin.ExtendedDynamicField> exportableFields

PARAMETER_FILEFORMAT

public static final String PARAMETER_FILEFORMAT

See Also:

• Constant Field Values

Constructor Details

BaseFileExporterPlugin

public BaseFileExporterPlugin()

Method Details

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

getPermissions

public Collection<Permissions> getPermissions()

Request create and write access to File:s and Directory:s and read access to Experiment:s and User:s.

Specified by:

getPermissions in interface Plugin

Overrides:

getPermissions in class AbstractPlugin

Returns:

A collection of permissions or null to not use permissions

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

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)

Description copied from class: AbstractExporterPlugin

Called just before the export starts. A subclass may override this method if it needs to initialise some resources.

Overrides:

begin in class AbstractExporterPlugin

Parameters:

dc - The DbControl that is used to write to the database. A subclass may use this read from the database as well

See Also:

• AbstractExporterPlugin.end(boolean)

performExport

protected void performExport(ExportOutputStream out,
 ProgressReporter progress)
                      throws IOException

Description copied from class: AbstractExporterPlugin

Perform the export. This method replaces the ImmediateDownloadExporter.doExport(ExportOutputStream, ProgressReporter) method.

Specified by:

performExport in class AbstractExporterPlugin

Parameters:

out - Output stream to write the exported data to

progress - An optional progress reporter

Throws:

IOException

end

protected void end(boolean success)

Description copied from class: AbstractExporterPlugin

Called just after everything has been committed to the database, or immediately after an error has ocurred. A subclass should clean up any resources aquired in the AbstractExporterPlugin.begin(DbControl) method here.

Overrides:

end in class AbstractExporterPlugin

Parameters:

success - TRUE if the file was parsed successfully, FALSE otherwise

See Also:

• AbstractExporterPlugin.begin(DbControl)

getSuccessMessage

protected String getSuccessMessage()

Description copied from class: AbstractExporterPlugin

Called if the export was successful to let the subclass generate a simple message that is sent back to the core and user interface. An example message might by: 178 reporters exported successfully. The default implementation always return null.

Overrides:

getSuccessMessage in class AbstractExporterPlugin

getFileFormatParameter

public static PluginParameter<String> getFileFormatParameter()

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

getConfigureJobParameters

private RequestInformation getConfigureJobParameters(GuiContext context,
 Boolean requireFile)

getExportableFields

public Map<String,BaseFileExporterPlugin.ExtendedDynamicField> getExportableFields(DbControl dc,
 BioAssaySet source)

getFormulaFields

private List<BaseFileExporterPlugin.ExtendedDynamicField> getFormulaFields(DbControl dc,
 BioAssaySet source)

getRawdataFields

private List<BaseFileExporterPlugin.ExtendedDynamicField> getRawdataFields(BioAssaySet source)

rawField

private BaseFileExporterPlugin.ExtendedDynamicField rawField(String property,
 String guiTitle,
 Type type,
 Formula.AverageMethod averageMethod)

getReporterFields

private Collection<BaseFileExporterPlugin.ExtendedDynamicField> getReporterFields()

reporterField

private BaseFileExporterPlugin.ExtendedDynamicField reporterField(String property,
 String guiTitle,
 Type type,
 Formula.AverageMethod averageMethod)

getExtraValueFields

private Collection<BaseFileExporterPlugin.ExtendedDynamicField> getExtraValueFields(DbControl dc,
 BioAssaySet source)

getSpotFields

private Collection<BaseFileExporterPlugin.ExtendedDynamicField> getSpotFields(BioAssaySet source)