net.sf.basedb.plugins
Class GalExporter

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

All Implemented Interfaces:

ImmediateDownloadExporter, InteractivePlugin, Plugin, SignalTarget

public class GalExporter
extends AbstractExporterPlugin
implements SignalTarget, InteractivePlugin

Exports an array design with features to a GAL file. The exporter only works for array desigs that has stored the features in a database. For a description of the GAL format see http://www.moleculardevices.com/pages/software/gn_genepix_file_formats.html#gal

Version:

2.7

Author:

nicklas

Last modified

$Date: 2010-11-08 14:49:35 +0100 (Mon, 08 Nov 2010) $

Nested Class Summary

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

Plugin.MainType

Field Summary

private static About	about
private RequestInformation	configureJob
private DbControl	dc
private static Set<GuiContext>	guiContexts
private long	numExported
private static Set<Permissions>	permissions
private ThreadSignalHandler	signalHandler
private static Pattern	unsafe

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

GalExporter()

Method Summary

protected void	begin(DbControl dc) Called just before the export starts.
void	configure(GuiContext context, Request request, Response response) Configure the plugin.
protected void	createBlockHeaders(List<String> headers, ArrayDesign design, Integer featureDiameter, List<ArrayDesignBlock> blocks) Create header entries for each block in the array design.
protected String	createHeader(String name, Object value) Create a properly formatted GAL header.
protected void	createStandardHeaders(List<String> headers, ArrayDesign design, List<ArrayDesignBlock> blocks) Create the standard headers that are required by the GAL format or that are useful to have in the GAL file.
protected void	end(boolean success) Called just after everything has been committed to the database, or immediately after an error has ocurred.
void	exportGal(DbControl dc, ArrayDesign design, Integer featureDiameter, PrintWriter writer, ProgressReporter progress) Exports an array design with features to a GAL file.
void	exportGal(DbControl dc, ArrayDesign design, PrintWriter writer, ProgressReporter progress) Deprecated. Use exportGal(DbControl, ArrayDesign, Integer, PrintWriter, ProgressReporter) instead
About	getAbout() Get information about the plugin, such as name, version, authors, etc.
private RequestInformation	getConfigureJobParameters(Boolean requireFile)
Set<GuiContext>	getGuiContexts() Get a set containing all items that the plugin handles.
Collection<Permissions>	getPermissions() Request create and write access to File:s, Directory:s and ArrayDesign:s read access to User:s and forced read access to DataFileType:s.
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) Check if the plugin can be used on the specified object.
protected String	makeSafeHeaderValue(String value) Removes "unsafe" characters in the value.
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.
protected void	writeDataHeader(PrintWriter writer) Write the data header.
protected void	writeFeature(PrintWriter writer, FeatureData feature, ArrayDesignBlock block) Write feature data.
protected void	writeHeaders(PrintWriter writer, List<String> headers) Write the headers of the GAL file, including the two first lines with the "ATF 1.0" line and the second line with the number of header lines and the number of data columns.
protected void	writeMissingFeature(PrintWriter writer, FeatureCoordinate missing) Write a missing features.

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

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, getMainType, init, run

Field Detail

about

private static final About about

guiContexts

private static final Set<GuiContext> guiContexts

permissions

private static final Set<Permissions> permissions

signalHandler

private ThreadSignalHandler signalHandler

configureJob

private RequestInformation configureJob

dc

private DbControl dc

numExported

private long numExported

unsafe

private static final Pattern unsafe

Constructor Detail

GalExporter

public GalExporter()

Method Detail

getAbout

public About getAbout()

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

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, Directory:s and ArrayDesign:s read access to User:s and forced read access to DataFileType: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

exportGal

public void exportGal(DbControl dc,
                      ArrayDesign design,
                      PrintWriter writer,
                      ProgressReporter progress)
               throws IOException

Deprecated. Use exportGal(DbControl, ArrayDesign, Integer, PrintWriter, ProgressReporter) instead

Throws:

IOException

exportGal

public void exportGal(DbControl dc,
                      ArrayDesign design,
                      Integer featureDiameter,
                      PrintWriter writer,
                      ProgressReporter progress)
               throws IOException

Exports an array design with features to a GAL file. The array must have features in the database.

Parameters:

dc - The DbControl to use for database access

design - The array design to export

featureDiameter - The expected feature diameter (in µm) of spots, or null to use the values from the database

writer - The stream to write to

progress - An optional progress reporter

Throws:

IOException

Since:

2.8

createStandardHeaders

protected void createStandardHeaders(List<String> headers,
                                     ArrayDesign design,
                                     List<ArrayDesignBlock> blocks)

Create the standard headers that are required by the GAL format or that are useful to have in the GAL file.

Parameters:

headers - Add the created headers to this list; use createHeader(String, Object) to create a properly formatted header

design - The current array design

blocks - A list with all blocks in the array design

createBlockHeaders

protected void createBlockHeaders(List<String> headers,
                                  ArrayDesign design,
                                  Integer featureDiameter,
                                  List<ArrayDesignBlock> blocks)

Create header entries for each block in the array design.

Parameters:

headers - Add the created headers to this list; use createHeader(String, Object) to create a properly formatted header

design - The current array design

featureDiameter - The expected feature diameter (µm), or null to use ArrayDesignBlock.getFeatureDiameter()

blocks - A list with all blocks in the array design

createHeader

protected String createHeader(String name,
                              Object value)

Create a properly formatted GAL header. The typical format is "name=value". We assume that the header name has no strange characters in it, but use makeSafeHeaderValue(String) for the value.

Parameters:

name - The name of the header

value - The value of the header

Returns:

A properly formatted header

makeSafeHeaderValue

protected String makeSafeHeaderValue(String value)

Removes "unsafe" characters in the value. Unsafe characers are:

• quote (")
• newline (\n, \r)

Parameters:

value - The value to check

Returns:

The checked value

writeHeaders

protected void writeHeaders(PrintWriter writer,
                            List<String> headers)

Write the headers of the GAL file, including the two first lines with the "ATF 1.0" line and the second line with the number of header lines and the number of data columns.

Parameters:

writer - The writer to print to

headers - The list with all headers

writeDataHeader

protected void writeDataHeader(PrintWriter writer)

Write the data header. The column headers must match the data written by writeFeature(PrintWriter, FeatureData, ArrayDesignBlock) and writeMissingFeature(PrintWriter, FeatureCoordinate).

Parameters:

writer - The writer to print to

writeFeature

protected void writeFeature(PrintWriter writer,
                            FeatureData feature,
                            ArrayDesignBlock block)

Write feature data. The data that is written must match the column headers written by writeDataHeader(PrintWriter). Features that doesn't have a reporter should get ID and Name = empty.

Parameters:

writer - The writer to print to

feature - The feature

block - The block on which the feature is located

writeMissingFeature

protected void writeMissingFeature(PrintWriter writer,
                                   FeatureCoordinate missing)

Write a missing features. The data that is written must match the column headers written by writeDataHeader(PrintWriter). The ID and Name should be empty.

Parameters:

writer - The writer to print to

missing - The feature

getConfigureJobParameters

private RequestInformation getConfigureJobParameters(Boolean requireFile)