Package net.sf.basedb.plugins

Class PlateMappingExporter

java.lang.Object

net.sf.basedb.core.plugin.AbstractPlugin

net.sf.basedb.core.plugin.AbstractExporterPlugin

net.sf.basedb.plugins.PlateMappingExporter

All Implemented Interfaces:

ImmediateDownloadExporter, InteractivePlugin, Plugin, SignalTarget

public class PlateMappingExporter
extends AbstractExporterPlugin
implements InteractivePlugin, SignalTarget

Exporter for plate mappings. It has a fixed file format:

Source plates=1
Source rows=3
Source columns=3
Destination plates=1
Destination rows=3
Destination columns=3
Source plate    Source row      Source column   Destination plate       Destination row Destination column
0       0       0       0       0       0
0       0       1       0       1       0
0       0       2       0       2       0
0       1       0       0       0       1
0       1       1       0       1       1
0       1       2       0       2       1
0       2       0       0       0       2
0       2       1       0       1       2
0       2       2       0       2       2

Version:

2.0

Author:

nicklas

Last modified

$Date: 2012-09-14 09:28:35 +0200 (fr, 14 sep 2012) $

Nested Class Summary

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

Plugin.MainType

Field Summary

Fields

Modifier and Type	Field	Description
private RequestInformation	configureJob
private DbControl	dc
private static final Set<GuiContext>	guiContexts
private PlateMapping	mapping
private static final Set<Permissions>	permissions
private PluginParameter<PlateMapping>	plateMappingParameter
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
PlateMappingExporter()	Create a new importer.

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)	Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.
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)
Set<GuiContext>	getGuiContexts()	Return a set containing the context:s [PLATEMAPPING, ITEM].
Collection<Permissions>	getPermissions()	Request create and write access to File:s and Directory:s and read access to PlateMapping:s and PlateGeometries.
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.
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)	Always null.
protected void	performExport(ExportOutputStream out, ProgressReporter progress)	Perform the export.
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

plateMappingParameter

private PluginParameter<PlateMapping> plateMappingParameter

configureJob

private RequestInformation configureJob

signalHandler

private ThreadSignalHandler signalHandler

dc

private DbControl dc

mapping

private PlateMapping mapping

Constructor Details

PlateMappingExporter

public PlateMappingExporter()

Create a new importer.

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 PlateMapping:s and PlateGeometries.

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()

Return a set containing the context:s [PLATEMAPPING, ITEM].

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)

Always null.

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

configure

public void configure(GuiContext context,
 Request request,
 Response response)

Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.

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

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

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

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

getConfigureJobParameters

private RequestInformation getConfigureJobParameters(GuiContext context,
 Boolean requireFile)