public class ExtractLoader extends BasicItemNodeLoader<Extract>
Sample
:s -> Extract
:s ->
PhysicalBioAssay
:s. The reverse-loading direction is the opposite
direction. In both cases we also need to consider pooled extracts.ALLOW_ROOT_NODE, allowAsRootNode, DENY_ROOT_NODE, factoryKey, nameGenerator
Constructor and Description |
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ExtractLoader() |
Modifier and Type | Method and Description |
---|---|
Node |
createForwardNode(DbControl dc,
OverviewContext context,
Node parentNode)
Create forward-loading extract nodes from a given parent sample
or extract.
|
private Node |
createForwardNode(Extract parentExtract,
DbControl dc,
OverviewContext context,
Node parentNode,
boolean onlyPushAnnotationTypes)
Create forward-loading extract nodes for the (pooled) extract that has a given
extract among their parents.
|
private Node |
createForwardNode(Sample sample,
DbControl dc,
OverviewContext context,
Node parentNode,
boolean onlyPushAnnotationTypes)
Create forward-loading extract nodes for the extracts that has a given
sample as their parent.
|
private Node |
createPooledReverseNode(Extract product,
DbControl dc,
OverviewContext context,
Node parentNode)
Create reverse-loading extract nodes of a pooled extract.
|
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 extracts+physical bioassays with the
ItemSubtype.getPushAnnotations()
flag set. |
Node |
createReverseNode(DbControl dc,
OverviewContext context,
Node parentNode)
The parent node can be one of:
Physical bioassay: Load the source extract(s) and return a folder-type node
Extract: Load the parent extracts and return either a folder-type or
item-type node depending on the number of parents
Raw bioassay: Load the parent extract and return an item-type node
Derived bioassay: Load the parent extract and return an item-type node
|
private Node |
createReverseNode(DerivedBioAssay bioAssay,
DbControl dc,
OverviewContext context,
Node bioAssayNode) |
private Node |
createReverseNode(PhysicalBioAssay bioAssay,
DbControl dc,
OverviewContext context,
Node bioAssayNode)
Create reverse-loading extract nodes from a physical bioassay.
|
private Node |
createReverseNode(RawBioAssay raw,
DbControl dc,
OverviewContext context,
Node rawNode) |
private Node |
createSingleParentReverseNode(Extract bioMaterial,
DbControl dc,
OverviewContext context,
Node parentNode)
Create a reverse-loading extract node from an extract.
|
private Set<Integer> |
getAllChildren(DbControl dc,
Set<Integer> parents) |
private Set<Integer> |
getExtractChain(Node node) |
protected void |
loadForwardChildNodes(DbControl dc,
OverviewContext context,
Node extractNode)
Loads the child extracts and physical bioassays that has been created from
this extract.
|
protected void |
loadPropertyChildNodes(DbControl dc,
OverviewContext context,
Node extractNode)
Loads property nodes of an extract.
|
protected void |
loadReverseChildNodes(DbControl dc,
OverviewContext context,
Node extractNode)
Load either the parent sample or extract(s) and child extracts+physical bioassays
with a subtype that has
ItemSubtype.getPushAnnotations() flag set. |
createItemNode, createRootNode, getNodeFactory, getNodeFactory, getNodeLoader, getNodeLoaderFactory, getNodeNameGenerator, getNodeValidator, getNodeValidatorFactory, postValidateFolder
loadChildNodes, loadChildNodesOfFolderNode, loadChildNodesOfItemNode
public Node createForwardNode(DbControl dc, OverviewContext context, Node parentNode)
createForwardNode
in interface NodeLoader<Extract>
createForwardNode
in class AbstractNodeLoader<Extract>
dc
- The DbControl to use for database accesscontext
- The overview contextparentNode
- The parent nodepublic Node createReverseNode(DbControl dc, OverviewContext context, Node parentNode)
createReverseNode
in interface NodeLoader<Extract>
createReverseNode
in class AbstractNodeLoader<Extract>
dc
- The DbControl to use for database accesscontext
- The overview contextparentNode
- The child nodepublic Node createPropertyNode(DbControl dc, OverviewContext context, Node parentNode)
ItemSubtype.getPushAnnotations()
flag set. The parent node should be a sample or extract node.createPropertyNode
in interface NodeLoader<Extract>
createPropertyNode
in class AbstractNodeLoader<Extract>
dc
- The DbControl to use for database accesscontext
- The overview contextparentNode
- The parent nodeprotected void loadPropertyChildNodes(DbControl dc, OverviewContext context, Node extractNode)
AnnotationLoader.createPropertyNode(DbControl, OverviewContext, Node)
BioPlateLoader.createPropertyNode(DbControl, OverviewContext, Node)
ProtocolLoader.createPropertyNode(DbControl, OverviewContext, Node)
KitLoader.createPropertyNode(DbControl, OverviewContext, Node)
HardwareLoader.createPropertyNode(DbControl, OverviewContext, Node)
TagLoader.createPropertyNode(DbControl, OverviewContext, Node)
loadPropertyChildNodes
in class AbstractNodeLoader<Extract>
protected void loadForwardChildNodes(DbControl dc, OverviewContext context, Node extractNode)
loadForwardChildNodes
in class AbstractNodeLoader<Extract>
createForwardNode(DbControl, OverviewContext, Node)
,
PhysicalBioAssayLoader.createForwardNode(DbControl, OverviewContext, Node)
,
DerivedBioAssayLoader.createForwardNode(DbControl, OverviewContext, Node)
,
RawBioAssayLoader.createForwardNode(DbControl, OverviewContext, Node)
protected void loadReverseChildNodes(DbControl dc, OverviewContext context, Node extractNode)
ItemSubtype.getPushAnnotations()
flag set.private Node createPooledReverseNode(Extract product, DbControl dc, OverviewContext context, Node parentNode)
private Node createSingleParentReverseNode(Extract bioMaterial, DbControl dc, OverviewContext context, Node parentNode)
private Node createReverseNode(PhysicalBioAssay bioAssay, DbControl dc, OverviewContext context, Node bioAssayNode)
private Node createReverseNode(DerivedBioAssay bioAssay, DbControl dc, OverviewContext context, Node bioAssayNode)
private Node createReverseNode(RawBioAssay raw, DbControl dc, OverviewContext context, Node rawNode)
private Node createForwardNode(Sample sample, DbControl dc, OverviewContext context, Node parentNode, boolean onlyPushAnnotationTypes)
private Node createForwardNode(Extract parentExtract, DbControl dc, OverviewContext context, Node parentNode, boolean onlyPushAnnotationTypes)
ItemSubtype.getPushAnnotations()
set.