Package net.sf.basedb.util.affymetrix

Class CelValidationAction

java.lang.Object

net.sf.basedb.util.fileset.SingleFileValidationAction

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 (to, 11 aug 2011) $

Field Summary

Fields

Modifier and Type	Field	Description
private final DbControl	dc
private final RawBioAssay	rba
private final CelValidator	validator

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
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 Details

dc

private final DbControl dc

rba

private final RawBioAssay rba

validator

private final CelValidator validator

Constructor Details

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 Details

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.