2.17.2: 2011-06-17

net.sf.basedb.plugins
Class CdfFileReporterImporter

java.lang.Object
  extended by net.sf.basedb.core.plugin.AbstractPlugin
      extended by 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 Affymetrix 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: 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
          Plugin description
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.
 About getAbout()
          Get information about the plugin, such as name, version, authors, etc.
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
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
 

Field Detail

about

private static final About about
Plugin description


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

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

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)

2.17.2: 2011-06-17