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

Class PhysicalBioAssayValidator

java.lang.Object

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

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

net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator

All Implemented Interfaces:

NodeValidator<PhysicalBioAssay>

public class PhysicalBioAssayValidator
extends NameableNodeValidator<PhysicalBioAssay>

Validator implementation for physical bioassays. Validation rules:

• Missing item: Validator.MISSING_PHYSICALBIOASSAY
• Access denied: Validator.DENIED_PHYSICALBIOASSAY
• Subtype of parent extract: Validator.INCORRECT_EXTRACT_TYPE

Version:

2.10

Author:

Nicklas

Last modified

$Date: 2015-03-25 08:13:39 +0100 (on, 25 mar 2015) $

Constructor Summary

Constructors

Constructor	Description
PhysicalBioAssayValidator()

Method Summary

Modifier and Type	Method	Description
static void	checkExtractSubtype(DbControl dc, OverviewContext context, Node bioAssayNode, Node extractNode)	Check the subtype of the extract that is the parent to a physical bioassay.
static Set<Extract>	getAllParentExtracts(DbControl dc, OverviewContext context, PhysicalBioAssay bioAssay)	Get all parent extracts that are associated with the given physical bioassay.
protected Fix	getMissingItemFix(DbControl dc, Node parentNode)	Subclasses should override this method if they have a suggessted fix for a missing item problem.
static List<PhysicalBioAssay>	getPhysicalBioAssays(DbControl dc, OverviewContext context, DerivedBioAssay bioAssay)	Get all physical bioassays that are parents to the given derived bioassay.
void	postValidate(DbControl dc, OverviewContext context, Node node, Node parentNode)	Do nothing.

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

getDeniedItemFix, postDeniedItem, postMissingItem, postValidateFolder, preDeniedItem, preMissingItem, preValidate

Methods inherited from class java.lang.Object

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

Constructor Details

PhysicalBioAssayValidator

public PhysicalBioAssayValidator()

Method Details

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<PhysicalBioAssay>

Overrides:

postValidate in class NameableNodeValidator<PhysicalBioAssay>

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

getMissingItemFix

protected Fix getMissingItemFix(DbControl dc,
Node parentNode)

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<PhysicalBioAssay>

Returns:

Always null (since it can never be missing)

checkExtractSubtype

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

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

getPhysicalBioAssays

public static List<PhysicalBioAssay> getPhysicalBioAssays(DbControl dc,
OverviewContext context,
DerivedBioAssay bioAssay)

Get all physical bioassays that are parents to the given derived bioassay. This is a utility method that provides caching support so that queries don't have to be repeated for the same derived bioassay.

Since:

3.2

getAllParentExtracts

public static Set<Extract> getAllParentExtracts(DbControl dc,
OverviewContext context,
PhysicalBioAssay bioAssay)

Get all parent extracts that are associated with the given physical bioassay.

Since:

3.2