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

Class SampleValidator

java.lang.Object

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

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

net.sf.basedb.util.overview.validator.SampleValidator

All Implemented Interfaces:

NodeValidator<Sample>

public class SampleValidator
extends NameableNodeValidator<Sample>

Validator implementation for sample. Validation rules:

• Missing item: Validator.MISSING_SAMPLE
• Access denied: Validator.DENIED_SAMPLE
• Subtype of parent sample: Validator.INCORRECT_SAMPLE_TYPE
• Subtype of parent biosource: Validator.INCORRECT_BIOSOURCE_TYPE

Version:

2.10

Author:

Nicklas

Last modified

$Date: 2012-04-03 09:31:52 +0200 (ti, 03 apr 2012) $

Constructor Summary

Constructors

Constructor	Description
SampleValidator()

Method Summary

Modifier and Type	Method	Description
static void	checkParentBioSourceSubtype(DbControl dc, OverviewContext context, Node sampleNode, Node bioSourceNode)	Check the subtype of the biosurce that is the parent to a sample.
static void	checkParentSampleSubtype(DbControl dc, OverviewContext context, Node childNode, Node parentNode)	Check the subtype of the sample that is the parent to another sample.
protected Fix	getMissingItemFix(DbControl dc, Node parentNode)	The suggested fix is to add a parent sample to the extract or one or more samples to the pooled sample.
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

SampleValidator

public SampleValidator()

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<Sample>

Overrides:

postValidate in class NameableNodeValidator<Sample>

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)

The suggested fix is to add a parent sample to the extract or one or more samples to the pooled sample.

Specified by:

getMissingItemFix in class BasicNodeValidator<Sample>

checkParentBioSourceSubtype

public static void checkParentBioSourceSubtype(DbControl dc,
 OverviewContext context,
 Node sampleNode,
 Node bioSourceNode)

Check the subtype of the biosurce that is the parent to a sample. Given that the sample has a non-null subtype, which has a related BIOSOURCE subtype, this method checks if the parent biosource has the same subtype. If there is no related subtype for the sample, any subtype for the parent is accepted.

Since:

3.0

checkParentSampleSubtype

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

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

Since:

3.0