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

Class ExtractValidator

java.lang.Object

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

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

net.sf.basedb.util.overview.validator.ExtractValidator

All Implemented Interfaces:

NodeValidator<Extract>

public class ExtractValidator
extends NameableNodeValidator<Extract>

Validator implementation for extracts. Validation rules:

• Missing item: Validator.MISSING_EXTRACT
• Access denied: Validator.DENIED_EXTRACT
• Subtype of parent extract: Validator.INCORRECT_EXTRACT_TYPE
• Subtype of parent sample: Validator.INCORRECT_SAMPLE_TYPE
• Different tag than parent: Validator.DIFFERENT_TAG
• Parent is tagged, but child is not: Validator.TAGGED_PARENT
• Duplicates of same tag+position on bioassay: Validator.NONUNIQUE_TAG
• Incorrect position on bioassay: Validator.INCORRECT_BIOASSAY_POSITION

Version:

2.10

Author:

Nicklas

Last modified

$Date: 2019-02-26 11:10:15 +0100 (tis, 26 feb. 2019) $

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) static class	ExtractValidator.TagPosition

Constructor Summary

Constructors

Constructor	Description
ExtractValidator()

Method Summary

Modifier and Type	Method	Description
private void	checkExtractOnBioAssay(DbControl dc, OverviewContext context, Node extractNode, Node bioAssayNode)
static void	checkExtractTag(DbControl dc, OverviewContext context, Node childNode, Node parentNode)	Check the tag of the child extract in relation to a parent extract.
static void	checkParentExtractSubtype(DbControl dc, OverviewContext context, Node childNode, Node parentNode)	Check the subtype of the extract that is the parent to another extract.
static void	checkParentSampleSubtype(DbControl dc, OverviewContext context, Node extractNode, Node sampleNode)	Check the subtype of the sample that is the parent to an extract.
protected Fix	getMissingItemFix(DbControl dc, Node parentNode)	The suggested fix is to add parent extracts to the physical bioassay or one or more extracts to the pooled extract.
static boolean	isRelated(DbControl dc, OverviewContext context, Extract parent, Extract child)	Check if two given extracts have a parent-child relationship.
void	postValidate(DbControl dc, OverviewContext context, Node node, Node parentNode)	Do nothing.
void	postValidateFolder(DbControl dc, OverviewContext context, Node folderNode, Node parentNode)	If the parent is a physical bioassay, check that extracts on the same position has different tags.
boolean	preMissingItem(DbControl dc, OverviewContext context, Node parentNode)	Do not report missing items if the parent node is a derived or (root) raw bioassay.

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

getDeniedItemFix, postDeniedItem, postMissingItem, preDeniedItem, preValidate

Methods inherited from class java.lang.Object

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

Constructor Details

ExtractValidator

public ExtractValidator()

Method Details

preMissingItem

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

Do not report missing items if the parent node is a derived or (root) raw bioassay.

Specified by:

preMissingItem in interface NodeValidator<Extract>

Overrides:

preMissingItem in class BasicNodeValidator<Extract>

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

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<Extract>

Overrides:

postValidate in class NameableNodeValidator<Extract>

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 parent extracts to the physical bioassay or one or more extracts to the pooled extract.

Specified by:

getMissingItemFix in class BasicNodeValidator<Extract>

postValidateFolder

public void postValidateFolder(DbControl dc,
OverviewContext context,
Node folderNode,
Node parentNode)

If the parent is a physical bioassay, check that extracts on the same position has different tags.

Specified by:

postValidateFolder in interface NodeValidator<Extract>

Overrides:

postValidateFolder in class BasicNodeValidator<Extract>

Parameters:

dc - A DbControl to use for database access

context - The current overview context

folderNode - The folder node, or null if no folder has been created

parentNode - The parent node (never null)

checkParentSampleSubtype

public static void checkParentSampleSubtype(DbControl dc,
OverviewContext context,
Node extractNode,
Node sampleNode)

Check the subtype of the sample that is the parent to an extract. Given that the extract 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 extract, any subtype for the parent is accepted.

Since:

3.0

checkParentExtractSubtype

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

Check the subtype of the extract that is the parent to another extract. Given that the child extract 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 child extract, any subtype for the parent is accepted.

Since:

3.0

checkExtractTag

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

Check the tag of the child extract in relation to a parent extract. If the parent extract has a tag, the child must have the same tag. If the parent is not tagged, then the child may have any tag or no tag.

Since:

3.0

isRelated

public static boolean isRelated(DbControl dc,
OverviewContext context,
Extract parent,
Extract child)

Check if two given extracts have a parent-child relationship.

Since:

3.2

checkExtractOnBioAssay

private void checkExtractOnBioAssay(DbControl dc,
OverviewContext context,
Node extractNode,
Node bioAssayNode)