net.sf.basedb.plugins
Class BioAssaySetExporter

java.lang.Object
  net.sf.basedb.core.plugin.AbstractPlugin
      net.sf.basedb.core.plugin.AbstractExporterPlugin
          net.sf.basedb.plugins.BioAssaySetExporter

All Implemented Interfaces:

ImmediateDownloadExporter, InteractivePlugin, Plugin, SignalTarget

Deprecated. In 2.12. Use: SerialBaseFileExporter or MatrixBaseFileExporter for BASEfile export and the extension package at http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev for MeV export

public class BioAssaySetExporter
extends AbstractExporterPlugin
implements InteractivePlugin, SignalTarget

Exporter for bioassay sets. Supported formats: - Tab Delimited, Multiple Sample Files (TDMS Format) for use in MeV (available from http://www.tm4.org). - BASEfile. - Plain Matrix, see documentation for exportPlainMatrix method for a description of the format.

Version:

2.1

Author:

enell, jari, peter

Last modified

$Date: 2010-08-13 10:50:27 +0200 (Fri, 13 Aug 2010) $

Nested Class Summary

static class	BioAssaySetExporter.QueryItem Deprecated.
private static class	BioAssaySetExporter.QueryItemTitleComparator Deprecated.

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

Plugin.MainType

Field Summary

private static About	about Deprecated.
private BioAssaySet	bas Deprecated.
private PluginParameter<BioAssaySet>	bioAssaySetParameter Deprecated.
private static String	COMMAND_CONFIGURE_BASEFILE Deprecated.
private RequestInformation	configureJob Deprecated.
private RequestInformation	configureJobBasefile Deprecated.
private DbControl	dc Deprecated.
private static String	FORMAT_BASEFILE_MATRIX Deprecated.
private static String	FORMAT_BASEFILE_SERIAL Deprecated.
private static Set<String>	FORMAT_BASEFILES Deprecated.
private static String	FORMAT_MEV_TDMS Deprecated.
private static String	FORMAT_PLAIN_MATRIX Deprecated.
private PluginParameter<String>	formatParameter Deprecated.
private PluginParameter<Boolean>	geneAveragesParameter Deprecated.
private static Set<GuiContext>	guiContexts Deprecated.
private static Set<Permissions>	permissions Deprecated.
private ThreadSignalHandler	signalHandler Deprecated.
private PluginParameter<String>	usedColumnsParameter Deprecated.
private PluginParameter<String>	usedFieldsParameter Deprecated.

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

BioAssaySetExporter()
Deprecated.

Method Summary

protected void	begin(DbControl dc) Deprecated. Called just before the export starts.
void	configure(GuiContext context, Request request, Response response) Deprecated. Configure the plugin.
protected void	end(boolean success) Deprecated. Called just after everything has been committed to the database, or immediately after an error has ocurred.
void	exportBaseFileMatrix(BioAssaySet bas, File file, Map<String,String> parameters, List<String> reporterFields, List<String> spotFields, Boolean mergeReporters) Deprecated. In 2.11 and 2.12, use MatrixBaseFileExporter instead
void	exportBaseFileMatrix(BioAssaySet bas, File file, Map<String,String> parameters, List<String> reporterFields, List<String> spotFields, Boolean mergeReporters, ProgressReporter progress) Deprecated. In 2.12, use MatrixBaseFileExporter instead
void	exportBaseFileMatrix(BioAssaySet bas, OutputStream os, Map<String,String> parameters, List<String> reporterFields, List<String> spotFields, boolean mergeReporters) Deprecated. In 2.11 and 2.12, use MatrixBaseFileExporter instead.
void	exportBaseFileMatrix(BioAssaySet bas, OutputStream os, Map<String,String> parameters, List<String> reporterFields, List<String> spotFields, boolean mergeReporters, ProgressReporter progress) Deprecated. In 2.11 and 2.12, use MatrixBaseFileExporter instead.
private void	exportBaseFileSectionAssays(PrintWriter out, DbControl dc, BioAssaySet bas) Deprecated.
private void	exportBaseFileSectionHead(PrintWriter out, Map<String,String> parameters) Deprecated.
private void	exportBaseFileSectionSpots(PrintWriter out, DbControl dc, BioAssaySet bas, DynamicSpotQuery query, List<String> reporterFields, List<String> spotFields, List<BioAssay> assays, Map<String,BioAssaySetExporter.QueryItem> qi, long count, boolean mergeOnReporters, Map<Integer,String> reporterLine, ProgressReporter progress) Deprecated.
void	exportBaseFileSerial(BioAssaySet bas, File file, Map<String,String> parameters, List<String> reporterFields, List<String> spotFields, Boolean mergeReporters) Deprecated. In 2.11 and 2.12, use SerialBaseFileExporter instead.
void	exportBaseFileSerial(BioAssaySet bas, File file, Map<String,String> parameters, List<String> reporterFields, List<String> spotFields, Boolean mergeReporters, ProgressReporter progress) Deprecated. In 2.12, use SerialBaseFileExporter instead.
void	exportBaseFileSerial(BioAssaySet bas, OutputStream os, Map<String,String> parameters, List<String> reporterFields, List<String> spotFields, boolean mergeReporters) Deprecated. In 2.11 and 2.12, use SerialBaseFileExporter instead.
void	exportBaseFileSerial(BioAssaySet bas, OutputStream os, Map<String,String> parameters, List<String> reporterFields, List<String> spotFields, boolean mergeReporters, ProgressReporter progress) Deprecated. In 2.12, use SerialBaseFileExporter instead.
void	exportMeV(BioAssaySet bioassayset, OutputStream to, ProgressReporter progress) Deprecated. In 2.12, use extension package found at http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev instead
void	exportPlainMatrix(BioAssaySet bioassayset, OutputStream os, ProgressReporter progress) Deprecated. In 2.12, no direct replacement, write a subclass of AbstractBioAssaySetExporter instead
About	getAbout() Deprecated. Get information about the plugin, such as name, version, authors, etc.
private List<BioAssaySetExporter.QueryItem>	getBaseFileExtraQI(DbControl dc, BioAssaySet bas) Deprecated.
private List<BioAssaySetExporter.QueryItem>	getBaseFileFormulaQI(DbControl dc, BioAssaySet bas) Deprecated.
private Map<String,BioAssaySetExporter.QueryItem>	getBaseFileQIMap(DbControl dc, BioAssaySet bas) Deprecated.
private List<BioAssaySetExporter.QueryItem>	getBaseFileRawQI(BioAssaySet bas) Deprecated.
private Map<Integer,String>	getBaseFileReporterFields(DbControl dc, BioAssaySet bas, DynamicPositionQuery query, Map<String,BioAssaySetExporter.QueryItem> queryMap, List<String> reporterFields, boolean mergeOnReporters) Deprecated.
private List<BioAssaySetExporter.QueryItem>	getBaseFileReporterQI() Deprecated.
private List<BioAssaySetExporter.QueryItem>	getBaseFileSpotQI(BioAssaySet bas) Deprecated.
private long	getBaseFileSpotSectionCount(DbControl dc, DynamicSpotQuery count, boolean mergeReporters) Deprecated.
private RequestInformation	getConfigureBasefileParameters(GuiContext context) Deprecated.
private RequestInformation	getConfigureJobParameters(GuiContext context, Boolean requireFile) Deprecated.
List<AnnotationType>	getExperimentalFactors(DbControl dc, BioAssaySet bas) Deprecated.
Set<GuiContext>	getGuiContexts() Deprecated. Get a set containing all items that the plugin handles.
Plugin.MainType	getMainType() Deprecated. Get the type of the plugin.
Collection<Permissions>	getPermissions() Deprecated. Request create and write access to File:s and Directory:s and read access to Experiment:s and User:s.
RequestInformation	getRequestInformation(GuiContext context, String command) Deprecated. This method will return the RequestInformation for a given command, i.e.
SignalHandler	getSignalHandler() Deprecated. Get the signal handler that is handling signals on behalf of this object.
protected String	getSuccessMessage() Deprecated. 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) Deprecated. Check if the plugin can be used on the specified object.
protected void	performExport(ExportOutputStream out, ProgressReporter progress) Deprecated. Perform the export.
boolean	requiresConfiguration() Deprecated. Returns FALSE, since that is how the plugins used to work before this method was introduced.
boolean	supportsConfigurations() Deprecated. 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, getOverwrite, getOverwriteParameter, getSaveAsParameter, getSaveAsPath, getSaveTo, pathCanBeUsed, run

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

checkInterrupted, cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, 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

Methods inherited from interface net.sf.basedb.core.plugin.Plugin

done, init, run

Field Detail

signalHandler

private ThreadSignalHandler signalHandler

Deprecated.

dc

private DbControl dc

Deprecated.

bas

private BioAssaySet bas

Deprecated.

about

private static final About about

Deprecated.

configureJob

private RequestInformation configureJob

Deprecated.

configureJobBasefile

private RequestInformation configureJobBasefile

Deprecated.

guiContexts

private static final Set<GuiContext> guiContexts

Deprecated.

permissions

private static final Set<Permissions> permissions

Deprecated.

bioAssaySetParameter

private PluginParameter<BioAssaySet> bioAssaySetParameter

Deprecated.

formatParameter

private PluginParameter<String> formatParameter

Deprecated.

geneAveragesParameter

private PluginParameter<Boolean> geneAveragesParameter

Deprecated.

usedFieldsParameter

private PluginParameter<String> usedFieldsParameter

Deprecated.

usedColumnsParameter

private PluginParameter<String> usedColumnsParameter

Deprecated.

COMMAND_CONFIGURE_BASEFILE

private static final String COMMAND_CONFIGURE_BASEFILE

Deprecated.

See Also:

Constant Field Values

FORMAT_BASEFILE_SERIAL

private static final String FORMAT_BASEFILE_SERIAL

Deprecated.

See Also:

Constant Field Values

FORMAT_BASEFILE_MATRIX

private static final String FORMAT_BASEFILE_MATRIX

Deprecated.

See Also:

Constant Field Values

FORMAT_MEV_TDMS

private static final String FORMAT_MEV_TDMS

Deprecated.

See Also:

Constant Field Values

FORMAT_PLAIN_MATRIX

private static final String FORMAT_PLAIN_MATRIX

Deprecated.

See Also:

Constant Field Values

FORMAT_BASEFILES

private static final Set<String> FORMAT_BASEFILES

Deprecated.

Constructor Detail

BioAssaySetExporter

public BioAssaySetExporter()

Deprecated.

Method Detail

configure

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

Deprecated.

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()

Deprecated.

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

exportBaseFileMatrix

public void exportBaseFileMatrix(BioAssaySet bas,
                                 File file,
                                 Map<String,String> parameters,
                                 List<String> reporterFields,
                                 List<String> spotFields,
                                 Boolean mergeReporters)
                          throws IOException,
                                 SQLException

Deprecated. In 2.11 and 2.12, use MatrixBaseFileExporter instead

Throws:

IOException

SQLException

exportBaseFileMatrix

public void exportBaseFileMatrix(BioAssaySet bas,
                                 File file,
                                 Map<String,String> parameters,
                                 List<String> reporterFields,
                                 List<String> spotFields,
                                 Boolean mergeReporters,
                                 ProgressReporter progress)
                          throws IOException,
                                 SQLException

Deprecated. In 2.12, use MatrixBaseFileExporter instead

Export the data from a bioassayset as a serial BASEfile. The reporterFields and spotFields parameter must identify the data to export.

The reporterFields parameter supports the following:

rep.<property>

The reporter property with the specified name, for example: rep.externalId, rep.symbol or a property defined in the extended properties file.

The spotFields parameter supports the following:

intensityN	The intensity in channel N
position	The position number for this spot in the data matrix
raw.<property>	The raw data property with the specified name, for example: raw.x, raw.row or a property defined by the raw data type.
frm.<id>	The value of the formula with the specified ID.
xtra.<externalId>	The value of the extra value with the specified external ID.

Parameters:

bas - The bioassayset to export

file - The file to export to

parameters - Header information that should go at the top of the BASEfile

reporterFields - The reporter fields that should be exportered

spotFields - The spot fields that should be exported

mergeReporters - TRUE to merge spot data having the same reporter (currently not supported)

progress - An optional progress reporter

Throws:

IOException - If there is an IO error

SQLException - If there is an error reading from the database

Since:

2.11

exportBaseFileMatrix

public void exportBaseFileMatrix(BioAssaySet bas,
                                 OutputStream os,
                                 Map<String,String> parameters,
                                 List<String> reporterFields,
                                 List<String> spotFields,
                                 boolean mergeReporters)
                          throws IOException,
                                 SQLException

Deprecated. In 2.11 and 2.12, use MatrixBaseFileExporter instead.

Throws:

IOException

SQLException

exportBaseFileMatrix

public void exportBaseFileMatrix(BioAssaySet bas,
                                 OutputStream os,
                                 Map<String,String> parameters,
                                 List<String> reporterFields,
                                 List<String> spotFields,
                                 boolean mergeReporters,
                                 ProgressReporter progress)
                          throws IOException,
                                 SQLException

Deprecated. In 2.11 and 2.12, use MatrixBaseFileExporter instead.

Throws:

IOException

SQLException

Since:

2.11

exportBaseFileSectionAssays

private void exportBaseFileSectionAssays(PrintWriter out,
                                         DbControl dc,
                                         BioAssaySet bas)

Deprecated.

exportBaseFileSectionHead

private void exportBaseFileSectionHead(PrintWriter out,
                                       Map<String,String> parameters)

Deprecated.

exportBaseFileSerial

public void exportBaseFileSerial(BioAssaySet bas,
                                 File file,
                                 Map<String,String> parameters,
                                 List<String> reporterFields,
                                 List<String> spotFields,
                                 Boolean mergeReporters)
                          throws IOException,
                                 SQLException

Deprecated. In 2.11 and 2.12, use SerialBaseFileExporter instead.

Throws:

IOException

SQLException

exportBaseFileSerial

public void exportBaseFileSerial(BioAssaySet bas,
                                 File file,
                                 Map<String,String> parameters,
                                 List<String> reporterFields,
                                 List<String> spotFields,
                                 Boolean mergeReporters,
                                 ProgressReporter progress)
                          throws IOException,
                                 SQLException

Deprecated. In 2.12, use SerialBaseFileExporter instead.

Export the data from a bioassayset as a serial BASEfile. See exportBaseFileMatrix(BioAssaySet, File, Map, List, List, Boolean) for information about the naming of parameters.

Parameters:

bas - The bioassayset to export

file - The file to export to

parameters - Header information that should go at the top of the BASEfile

reporterFields - The reporter fields that should be exportered

spotFields - The spot fields that should be exported

mergeReporters - TRUE to merge spot data having the same reporter (currently not supported)

progress - An optional progress reporter

Throws:

IOException - If there is an IO error

SQLException - If there is an error reading from the database

Since:

2.11

exportBaseFileSerial

public void exportBaseFileSerial(BioAssaySet bas,
                                 OutputStream os,
                                 Map<String,String> parameters,
                                 List<String> reporterFields,
                                 List<String> spotFields,
                                 boolean mergeReporters)
                          throws IOException,
                                 SQLException

Deprecated. In 2.11 and 2.12, use SerialBaseFileExporter instead.

Throws:

IOException

SQLException

exportBaseFileSerial

public void exportBaseFileSerial(BioAssaySet bas,
                                 OutputStream os,
                                 Map<String,String> parameters,
                                 List<String> reporterFields,
                                 List<String> spotFields,
                                 boolean mergeReporters,
                                 ProgressReporter progress)
                          throws IOException,
                                 SQLException

Deprecated. In 2.12, use SerialBaseFileExporter instead.

Throws:

IOException

SQLException

Since:

2.11

exportBaseFileSectionSpots

private void exportBaseFileSectionSpots(PrintWriter out,
                                        DbControl dc,
                                        BioAssaySet bas,
                                        DynamicSpotQuery query,
                                        List<String> reporterFields,
                                        List<String> spotFields,
                                        List<BioAssay> assays,
                                        Map<String,BioAssaySetExporter.QueryItem> qi,
                                        long count,
                                        boolean mergeOnReporters,
                                        Map<Integer,String> reporterLine,
                                        ProgressReporter progress)
                                 throws SQLException

Deprecated.

Throws:

SQLException

exportMeV

public void exportMeV(BioAssaySet bioassayset,
                      OutputStream to,
                      ProgressReporter progress)
               throws IOException,
                      SQLException

Deprecated. In 2.12, use extension package found at http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev instead

Export bioassayset data in MeV format. The export includes all reporter information and all experimental factor information. If the expriment is a two-channel experiment the ch1/ch2 ratio (non-log value!) is exported as the expression value otherwise the raw intensity of channel 1 is exported.

Parameters:

bioassayset - The bioassayset to export

to - The stream to write the exported data to

progress - An optional progress reporter

Throws:

IOException - If there is an IO error

SQLException - If there is an error reading from the database

exportPlainMatrix

public void exportPlainMatrix(BioAssaySet bioassayset,
                              OutputStream os,
                              ProgressReporter progress)
                       throws IOException,
                              SQLException

Deprecated. In 2.12, no direct replacement, write a subclass of AbstractBioAssaySetExporter instead

Export bioassayset data in plain matrix format. Plain matrix format is simply a matrix with no header nor reporter information. Each column in the matrix corresponds to an assay, and each row corresponds to a reporter. Missing values are reported as entries with no number and 'NaN' is reported for undefined values (such as division with zero). Note, reporters with no measurement within a bioassay set are not reported at all, i.e., a row is not exported with misssing values only. To be clear, we state this once more: Rows (reporters) are only exported if one or more columns (assays) have a value. The value can be 'NaN'. The data exported depends on the underlying microarray platform; - 1-channel: raw ch1 intensity - 2-channel: the fraction ch1/ch2, note! non-log value The justification for exporting non-log values for 2-channel data is to follow the MeV export format where non-log data is exported for 2-channel data. 'NaN' is returned for zero ch2 values. The plug-in or user that uses this method must keep track of the row and column information themselves. The row is sorted in ascending position order, the columns are sorted in ascending column order.

Parameters:

bioassayset - The bioassayset to export

os - The stream to write the exported data to

progress - An optional progress reporter

Throws:

IOException - If there is an IO error

SQLException - If there is an error reading from the database

getAbout

public About getAbout()

Deprecated.

Description copied from interface: Plugin

Get information about the plugin, such as name, version, authors, etc.

Specified by:

getAbout in interface Plugin

Returns:

An About object

getBaseFileSpotSectionCount

private long getBaseFileSpotSectionCount(DbControl dc,
                                         DynamicSpotQuery count,
                                         boolean mergeReporters)

Deprecated.

getBaseFileReporterFields

private Map<Integer,String> getBaseFileReporterFields(DbControl dc,
                                                      BioAssaySet bas,
                                                      DynamicPositionQuery query,
                                                      Map<String,BioAssaySetExporter.QueryItem> queryMap,
                                                      List<String> reporterFields,
                                                      boolean mergeOnReporters)
                                               throws SQLException

Deprecated.

Throws:

SQLException

getBaseFileExtraQI

private List<BioAssaySetExporter.QueryItem> getBaseFileExtraQI(DbControl dc,
                                                               BioAssaySet bas)

Deprecated.

getBaseFileFormulaQI

private List<BioAssaySetExporter.QueryItem> getBaseFileFormulaQI(DbControl dc,
                                                                 BioAssaySet bas)

Deprecated.

getBaseFileQIMap

private Map<String,BioAssaySetExporter.QueryItem> getBaseFileQIMap(DbControl dc,
                                                                   BioAssaySet bas)

Deprecated.

getBaseFileRawQI

private List<BioAssaySetExporter.QueryItem> getBaseFileRawQI(BioAssaySet bas)

Deprecated.

getBaseFileReporterQI

private List<BioAssaySetExporter.QueryItem> getBaseFileReporterQI()

Deprecated.

getBaseFileSpotQI

private List<BioAssaySetExporter.QueryItem> getBaseFileSpotQI(BioAssaySet bas)

Deprecated.

getConfigureBasefileParameters

private RequestInformation getConfigureBasefileParameters(GuiContext context)

Deprecated.

getConfigureJobParameters

private RequestInformation getConfigureJobParameters(GuiContext context,
                                                     Boolean requireFile)

Deprecated.

getExperimentalFactors

public List<AnnotationType> getExperimentalFactors(DbControl dc,
                                                   BioAssaySet bas)

Deprecated.

getGuiContexts

public Set<GuiContext> getGuiContexts()

Deprecated.

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

getMainType

public Plugin.MainType getMainType()

Deprecated.

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

Overrides:

getMainType in class AbstractExporterPlugin

Returns:

MainType.EXPORT

getPermissions

public Collection<Permissions> getPermissions()

Deprecated.

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

getRequestInformation

public RequestInformation getRequestInformation(GuiContext context,
                                                String command)
                                         throws BaseException

Deprecated.

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

isInContext

public String isInContext(GuiContext context,
                          Object item)

Deprecated.

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

requiresConfiguration

public boolean requiresConfiguration()

Deprecated.

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

begin

protected void begin(DbControl dc)

Deprecated.

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

Deprecated.

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)

Deprecated.

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()

Deprecated.

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

supportsConfigurations

public boolean supportsConfigurations()

Deprecated.

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