3.0.4: 2012-03-05

net.sf.basedb.util.affymetrix
Class CelValidationAction

java.lang.Object
  extended by net.sf.basedb.util.fileset.SingleFileValidationAction
      extended by net.sf.basedb.util.affymetrix.CelValidationAction
All Implemented Interfaces:
Action, ValidationAction

public class CelValidationAction
extends SingleFileValidationAction

Action for validation of CEL files in a file set. The CEL file must be connected with a RawBioAssay. The raw bioassay should have an ArrayDesign that has a CDF file matching the chip type.

This class is just a wrapper for CelValidator so that we can hook the validation into the extensions system.

Since:
3.0
Author:
Nicklas
Last modified
$Date: 2011-08-11 11:09:06 +0200 (Thu, 11 Aug 2011) $

Field Summary
private  DbControl dc
           
private  RawBioAssay rba
           
private  CelValidator validator
           
 
Constructor Summary
CelValidationAction(DbControl dc, RawBioAssay rba)
          Create a new action.
 
Method Summary
 void resetMetadata()
          Reset all metadata that this class normally can set.
 void validateAndExtractMetadata()
          Validate and extract metadata from the file(s) that has been added to this validator.
 
Methods inherited from class net.sf.basedb.util.fileset.SingleFileValidationAction
acceptFile, getAcceptedFile
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

dc

private final DbControl dc

rba

private final RawBioAssay rba

validator

private final CelValidator validator
Constructor Detail

CelValidationAction

public CelValidationAction(DbControl dc,
                           RawBioAssay rba)
Create a new action.

Parameters:
dc - An open DbControl
rba - The raw bioassay the CEL file is connected with
Method Detail

validateAndExtractMetadata

public void validateAndExtractMetadata()
                                throws InvalidDataException,
                                       InvalidRelationException
Description copied from interface: ValidationAction
Validate and extract metadata from the file(s) that has been added to this validator. If the ValidationAction.acceptFile(FileSetMember) method returns Accept.VALIDATE_IMMEDIATELY this method is called and the validator should work on the last accepted file.

This method is also called after all files has been processed if at least one file returned Accept.VALIDATE_LATER.

This method is recommended to throw an InvalidDataException or a subclass if the file is not a valid file. PermissionDeniedException:s are ignored by the core and will not change the validation status. An exception of type InvalidRelationException can be thrown if the file itself is valid, but a related file that it depends on is not. The core will still mark the file as invalid and store the error message, but extracted metadata will not be reset.

Throws:
InvalidDataException - If the validator detects an invalid file
InvalidRelationException - If the validator detects that the file is valid but another file that it depends on is not, metadata extract will still happen

resetMetadata

public void resetMetadata()
Description copied from interface: ValidationAction
Reset all metadata that this class normally can set. This method is called if the validation of a file failed or if a file is removed from the file set. Any previous metadata that may signal that a valid file is present should be reset.


3.0.4: 2012-03-05