Package net.sf.basedb.util.overview.validator

Class DerivedBioAssayValidator

java.lang.Object

net.sf.basedb.util.overview.validator.BasicNodeValidator<I>

net.sf.basedb.util.overview.validator.NameableNodeValidator<DerivedBioAssay>

net.sf.basedb.util.overview.validator.DerivedBioAssayValidator

All Implemented Interfaces:

NodeValidator<DerivedBioAssay>

public class DerivedBioAssayValidator
extends NameableNodeValidator<DerivedBioAssay>

Validator implementation for derived bioassays. Validation rules:

• Missing item: Validator.MISSING_DERIVEDBIOASSAY
• Access denied: Validator.DENIED_DERIVEDBIOASSAY
• Parent extract mismatch: Validator.PARENT_EXTRACT_MISMATCH
• Incorrect related subtypes: Validator.INCORRECT_DERIVEDBIOASSAY_TYPE, Validator.INCORRECT_PHYSICALBIOASSAY_TYPE, Validator.INCORRECT_EXTRACT_TYPE

Version:

2.10

Author:

Nicklas

Last modified

$Date: 2009-02-16 20:29:47 +0100 (må, 16 feb 2009) $

Constructor Summary

Constructors

Constructor	Description
DerivedBioAssayValidator()

Method Summary

Modifier and Type	Method	Description
static void	checkDerivedBioAssaySubtype(DbControl dc, OverviewContext context, Node childNode, Node parentNode)	Check the subtype of the derived bioassay that is the parent to a child derived bioassay.
static void	checkExtractSubtype(DbControl dc, OverviewContext context, Node bioAssayNode, Node extractNode)	Check the subtype of the extract that is the linked with a derived bioassay.
static void	checkPhysicalBioAssaySubtype(DbControl dc, OverviewContext context, Node derivedBioAssayNode, Node physicalBioAssayNode)	Check the subtype of the physical bioassay that is the parent to a derived bioassay.
protected Fix	getMissingItemFix(DbControl dc, Node rawBioAssayNode)	Subclasses should override this method if they have a suggessted fix for a missing item problem.
void	postValidate(DbControl dc, OverviewContext context, Node node, Node parentNode)	Do nothing.
boolean	preMissingItem(DbControl dc, OverviewContext context, Node parentNode)	If the parent raw bioassay has a link to an extract, we ignore the missing derived bioassay.

Methods inherited from class net.sf.basedb.util.overview.validator.BasicNodeValidator

getDeniedItemFix, postDeniedItem, postMissingItem, postValidateFolder, preDeniedItem, preValidate

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

DerivedBioAssayValidator

public DerivedBioAssayValidator()

Method Details

preMissingItem

public boolean preMissingItem(DbControl dc,
 OverviewContext context,
 Node parentNode)

If the parent raw bioassay has a link to an extract, we ignore the missing derived bioassay.

Specified by:

preMissingItem in interface NodeValidator<DerivedBioAssay>

Overrides:

preMissingItem in class BasicNodeValidator<DerivedBioAssay>

Parameters:

dc - A DbControl to use if the validation needs to access the database

context - The current overview context

parentNode - The parent node that is missing the item

Returns:

Always false

Since:

3.0

getMissingItemFix

protected Fix getMissingItemFix(DbControl dc,
 Node rawBioAssayNode)

Description copied from class: BasicNodeValidator

Subclasses should override this method if they have a suggessted fix for a missing item problem. The default implementation does nothing, but the following template may be usable by most subclasses:

                new Fix("Add item to parent", parentNode.getItem())
                

Specified by:

getMissingItemFix in class BasicNodeValidator<DerivedBioAssay>

Returns:

Suggested fix is to add a derived bioassay as parent to the raw bioassay.

postValidate

public void postValidate(DbControl dc,
 OverviewContext context,
 Node node,
 Node parentNode)

Description copied from class: BasicNodeValidator

Do nothing. Subclasses should override this method if they need more validation for an existing and accessible item.

Specified by:

postValidate in interface NodeValidator<DerivedBioAssay>

Overrides:

postValidate in class NameableNodeValidator<DerivedBioAssay>

Parameters:

dc - A DbControl to use if the validation needs to access the database

context - The current overview context

node - The node object that represents item

parentNode - The parent node that is linked with the item

checkPhysicalBioAssaySubtype

public static void checkPhysicalBioAssaySubtype(DbControl dc,
 OverviewContext context,
 Node derivedBioAssayNode,
 Node physicalBioAssayNode)

Check the subtype of the physical bioassay that is the parent to a derived bioassay. Given that the derived bioassay has a non-null subtype, which has a related PHYISICALBIOASSAY subtype, this method checks if the physical bioassay has the same subtype. If there is no related subtype for the derived bioassay, any subtype for the physical bioassay is accepted.

checkDerivedBioAssaySubtype

public static void checkDerivedBioAssaySubtype(DbControl dc,
 OverviewContext context,
 Node childNode,
 Node parentNode)

Check the subtype of the derived bioassay that is the parent to a child derived bioassay. Given that the child bioassay has a non-null subtype, which has a related DERIVEDBIOASSAY subtype, this method checks if the parent bioassay has the same subtype. If there is no related subtype for the child bioassay, any subtype for the parent bioassay is accepted.

checkExtractSubtype

public static void checkExtractSubtype(DbControl dc,
 OverviewContext context,
 Node bioAssayNode,
 Node extractNode)

Check the subtype of the extract that is the linked with a derived bioassay. Given that the bioassay has a non-null subtype, which has a related EXTRACT subtype, this method checks if the extract has the same subtype. If there is no related subtype for the bioassay, any subtype for the extract is accepted.