net.sf.basedb.plugins
Class CdfFileReporterImporter

java.lang.Object
  net.sf.basedb.core.plugin.AbstractPlugin
      net.sf.basedb.plugins.CdfFileReporterImporter

All Implemented Interfaces:

AutoDetectingImporter, InteractivePlugin, Plugin, SignalTarget

public class CdfFileReporterImporter
extends AbstractPlugin
implements InteractivePlugin, AutoDetectingImporter, SignalTarget

This plug-in can import probesets from Affymetrix CDF files as reporters. The plug-in uses the CdfValidator class for the actual work.

Version:

2.4

Author:

nicklas

Developer info

In order to support the AutoDetectingImporter interface we needed to duplicate the file format checks from the Fusion SDK in this class. See isImportable(InputStream).

Last modified

$Date: 2011-09-02 15:01:58 +0200 (Fri, 02 Sep 2011) $

Nested Class Summary

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

Plugin.MainType

Field Summary

private RequestInformation	configureJob
private static Set<GuiContext>	guiContexts
private static Set<Permissions>	permissions
private ThreadSignalHandler	signalHandler

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

annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc

Constructor Summary

CdfFileReporterImporter()
Constructor should be empty.

Method Summary

void	configure(GuiContext context, Request request, Response response) Configure the plugin.
void	doImport(InputStream in, ProgressReporter progress) Import the data from the given InputStream.
private RequestInformation	getConfigureJobParameters(GuiContext context)
Set<GuiContext>	getGuiContexts() Get a set containing all items that the plugin handles.
Plugin.MainType	getMainType() Get the type of the plugin.
Collection<Permissions>	getPermissions() Request create and write access to Reporter:s and read access to File:s ArrayDesign:s, ReporterType:s, Platform:s and 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.
private int	importFromCdf(DbControl dc, affymetrix.fusion.cdf.FusionCDFData cdf, ProgressReporter progress)
boolean	isImportable(InputStream in) Check if the given InputStream can be imported by this plugin.
String	isInContext(GuiContext context, Object item) If used from an array design context, verify that the array design is an affymetrix chip.
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, 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

Field Detail

guiContexts

private static final Set<GuiContext> guiContexts

permissions

private static final Set<Permissions> permissions

configureJob

private RequestInformation configureJob

signalHandler

private ThreadSignalHandler signalHandler

Constructor Detail

CdfFileReporterImporter

public CdfFileReporterImporter()

Constructor should be empty.

Method Detail

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

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:

One of the defined types

getPermissions

public Collection<Permissions> getPermissions()

Request create and write access to Reporter:s and read access to File:s ArrayDesign:s, ReporterType:s, Platform:s and DataFileType:s

Specified by:

getPermissions in interface Plugin

Overrides:

getPermissions in class AbstractPlugin

Returns:

A collection of permissions or null to not use permissions

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

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)

If used from an array design context, verify that the array design is an affymetrix chip.

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

isImportable

public final boolean isImportable(InputStream in)
                           throws BaseException

Description copied from interface: AutoDetectingImporter

Check if the given InputStream can be imported by this plugin.

Specified by:

isImportable in interface AutoDetectingImporter

Parameters:

in - The input stream to check

Returns:

TRUE if the stream can be imported, FALSE otherwise

Throws:

BaseException - If something goes wrong

doImport

public void doImport(InputStream in,
                     ProgressReporter progress)
              throws BaseException

Description copied from interface: AutoDetectingImporter

Import the data from the given InputStream.

Specified by:

doImport in interface AutoDetectingImporter

Parameters:

in - The input stream to read from

progress - Progress reporter used by the caller to keep track of the progress. Null is allowed

Throws:

BaseException - If something goes wrong

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)

importFromCdf

private int importFromCdf(DbControl dc,
                          affymetrix.fusion.cdf.FusionCDFData cdf,
                          ProgressReporter progress)