Package net.sf.basedb.util.overview.loader

Class SampleLoader

java.lang.Object

net.sf.basedb.util.overview.loader.AbstractNodeLoader<I>

net.sf.basedb.util.overview.loader.BasicItemNodeLoader<Sample>

net.sf.basedb.util.overview.loader.SampleLoader

All Implemented Interfaces:

NodeLoader<Sample>

public class SampleLoader
extends BasicItemNodeLoader<Sample>

Node loader implementation for samples. The forward-loading direction goes from BioSource:s -> Sample:s -> Extract:s. The reverse-loading direction is the opposite direction. In both cases we also need to consider pooled samples.

Version:

2.10

Author:

Nicklas

Last modified

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

Field Summary

Fields inherited from class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

ALLOW_ROOT_NODE, allowAsRootNode, DENY_ROOT_NODE, factoryKey, nameGenerator

Constructor Summary

Constructors

Constructor	Description
SampleLoader()

Method Summary

Modifier and Type	Method	Description
private Node	createForwardNode(BioSource bioSource, DbControl dc, OverviewContext context, Node parentNode, boolean onlyPushAnnotationTypes)	Create forward-loading sample nodes for the samples that has a given biosource as their parent.
Node	createForwardNode(DbControl dc, OverviewContext context, Node parentNode)	Create forward-loading sample nodes from a given parent biosource or sample.
private Node	createForwardNode(Sample parentSample, DbControl dc, OverviewContext context, Node parentNode, boolean onlyPushAnnotationTypes)	Create forward-loading sample nodes for the (pooled) samples that has a given sample as their parent.
private Node	createPooledReverseNode(Sample product, DbControl dc, OverviewContext context, Node parentNode)	Create reverse-loading samples nodes of a sample with other sample(s) as parent items.
Node	createPropertyNode(DbControl dc, OverviewContext context, Node parentNode)	A property node is created when moving in the reverse direction so that we can load child samples+extracts with the ItemSubtype.getPushAnnotations() flag set.
Node	createReverseNode(DbControl dc, OverviewContext context, Node parentNode)	Create reverse-loading sample nodes from an extract node or from a pooled sample.
private Node	createSingleParentReverseNode(MeasuredBioMaterial bioMaterial, DbControl dc, OverviewContext context, Node parentNode)	Create a reverse-loading sample node from an extract or sample.
protected void	loadForwardChildNodes(DbControl dc, OverviewContext context, Node sampleNode)	Loads the pooled samples and extracts that has been created from this sample.
protected void	loadPropertyChildNodes(DbControl dc, OverviewContext context, Node sampleNode)	Loads property nodes of a sample.
protected void	loadReverseChildNodes(DbControl dc, OverviewContext context, Node sampleNode)	If the sample is a pooled sample, loads the parent samples that it was pooled from.

Methods inherited from class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

createItemNode, createRootNode, getNodeFactory, getNodeFactory, getNodeLoader, getNodeLoaderFactory, getNodeNameGenerator, getNodeValidator, getNodeValidatorFactory, postValidateFolder

Methods inherited from class net.sf.basedb.util.overview.loader.AbstractNodeLoader

loadChildNodes, loadChildNodesOfFolderNode, loadChildNodesOfItemNode

Methods inherited from class java.lang.Object

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

Constructor Details

SampleLoader

public SampleLoader()

Method Details

createForwardNode

public Node createForwardNode(DbControl dc,
OverviewContext context,
Node parentNode)

Create forward-loading sample nodes from a given parent biosource or sample. In both cases the returned node is a folder-type node that contains the child samples. It can also create all-loading node from a biomaterial list for the member samples.

Specified by:

createForwardNode in interface NodeLoader<Sample>

Overrides:

createForwardNode in class AbstractNodeLoader<Sample>

Parameters:

dc - The DbControl to use for database access

context - The overview context

parentNode - The parent node

Returns:

The folder node for the samples (or null if used with a list)

createReverseNode

public Node createReverseNode(DbControl dc,
OverviewContext context,
Node parentNode)

Create reverse-loading sample nodes from an extract node or from a pooled sample. In the first case, the returned node is an item-type node with the parent sample. In the second case, the returned node is a folder-type node with the pooled samples.

Specified by:

createReverseNode in interface NodeLoader<Sample>

Overrides:

createReverseNode in class AbstractNodeLoader<Sample>

Parameters:

dc - The DbControl to use for database access

context - The overview context

parentNode - The child node

Returns:

A folder-type or item-type node

createPropertyNode

public Node createPropertyNode(DbControl dc,
OverviewContext context,
Node parentNode)

A property node is created when moving in the reverse direction so that we can load child samples+extracts with the ItemSubtype.getPushAnnotations() flag set. The parent node should be a biosource or sample node.

Specified by:

createPropertyNode in interface NodeLoader<Sample>

Overrides:

createPropertyNode in class AbstractNodeLoader<Sample>

Parameters:

dc - The DbControl to use for database access

context - The overview context

parentNode - The parent node

Returns:

A node (may be a folder-type node with many subnodes), or null

Since:

3.1

loadPropertyChildNodes

protected void loadPropertyChildNodes(DbControl dc,
OverviewContext context,
Node sampleNode)

Loads property nodes of a sample.

• Annotations: AnnotationLoader.createPropertyNode(DbControl, OverviewContext, Node)
• Bioplate/well: BioPlateLoader.createPropertyNode(DbControl, OverviewContext, Node)
• Protocol: ProtocolLoader.createPropertyNode(DbControl, OverviewContext, Node)
• Kit: KitLoader.createPropertyNode(DbControl, OverviewContext, Node)

Overrides:

loadPropertyChildNodes in class AbstractNodeLoader<Sample>

loadForwardChildNodes

protected void loadForwardChildNodes(DbControl dc,
OverviewContext context,
Node sampleNode)

Loads the pooled samples and extracts that has been created from this sample.

Overrides:

loadForwardChildNodes in class AbstractNodeLoader<Sample>

See Also:

ExtractLoader.createForwardNode(DbControl, OverviewContext, Node), createForwardNode(DbControl, OverviewContext, Node)

loadReverseChildNodes

protected void loadReverseChildNodes(DbControl dc,
OverviewContext context,
Node sampleNode)

If the sample is a pooled sample, loads the parent samples that it was pooled from. Otherwise load the parent biosource. Also load any child samples or extracts that have a subtype with the ItemSubtype.getPushAnnotations() flag set.

Overrides:

loadReverseChildNodes in class AbstractNodeLoader<Sample>

See Also:

createReverseNode(DbControl, OverviewContext, Node), BioSourceLoader.createReverseNode(DbControl, OverviewContext, Node)

createPooledReverseNode

private Node createPooledReverseNode(Sample product,
DbControl dc,
OverviewContext context,
Node parentNode)

Create reverse-loading samples nodes of a sample with other sample(s) as parent items. Eg. the child nodes are the source sample(s) that was used to create the given product.

createSingleParentReverseNode

private Node createSingleParentReverseNode(MeasuredBioMaterial bioMaterial,
DbControl dc,
OverviewContext context,
Node parentNode)

Create a reverse-loading sample node from an extract or sample. Eg. the child node is the sample that is the parent of the (non-pooled) extract/sample.

createForwardNode

private Node createForwardNode(BioSource bioSource,
DbControl dc,
OverviewContext context,
Node parentNode,
boolean onlyPushAnnotationTypes)

Create forward-loading sample nodes for the samples that has a given biosource as their parent.

createForwardNode

private Node createForwardNode(Sample parentSample,
DbControl dc,
OverviewContext context,
Node parentNode,
boolean onlyPushAnnotationTypes)

Create forward-loading sample nodes for the (pooled) samples that has a given sample as their parent.