Class BioAssayFactory.Builder

java.lang.Object

ubic.gemma.core.util.test.fixture.BioAssayFactory.Builder

Enclosing class:

BioAssayFactory

public static final class BioAssayFactory.Builder
extends Object

Fluent builder for a BioAssay. All withXxx(...) methods return this for chaining. Single-use; call build() once.

Author:

Phase 3 (Vision section 3 - test-fixture rewrite)

Method Summary

Modifier and Type	Method	Description
BioAssay	build()	Build, persist, and return the BA.
BioAssay	buildTransient()	Build the BA WITHOUT persisting it.
BioAssayFactory.Builder	withAccession(boolean v)
BioAssayFactory.Builder	withArrayDesign(ArrayDesign ad)
BioAssayFactory.Builder	withBioMaterial(BioMaterial bm)
BioAssayFactory.Builder	withIsOutlier(boolean v)
BioAssayFactory.Builder	withName(String n)
BioAssayFactory.Builder	withSequencePairedReads(boolean v)
BioAssayFactory.Builder	withTaxon(Taxon t)	Set the taxon to use when auto-creating the BioMaterial and ArrayDesign defaults.

Methods inherited from class Object

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

Method Details

withName

public BioAssayFactory.Builder withName(String n)

withBioMaterial

public BioAssayFactory.Builder withBioMaterial(BioMaterial bm)

withArrayDesign

public BioAssayFactory.Builder withArrayDesign(ArrayDesign ad)

withTaxon

public BioAssayFactory.Builder withTaxon(Taxon t)

Set the taxon to use when auto-creating the BioMaterial and ArrayDesign defaults. Ignored if both are supplied via withBioMaterial(BioMaterial) and withArrayDesign(ArrayDesign).

withAccession

public BioAssayFactory.Builder withAccession(boolean v)

withIsOutlier

public BioAssayFactory.Builder withIsOutlier(boolean v)

withSequencePairedReads

public BioAssayFactory.Builder withSequencePairedReads(boolean v)

build

public BioAssay build()

Build, persist, and return the BA. The BioMaterial and ArrayDesign are persisted first (no cascade from BA); the BA itself is persisted via SecurableBaseImmutableService.create(BioAssay) so the ACL-creation listener fires.

buildTransient

public BioAssay buildTransient()

Build the BA WITHOUT persisting it. The BioMaterial and ArrayDesign are still persisted (no cascade from BA), and the inverse side BM.bioAssaysUsedIn is updated. The returned BA is transient and ready to be added to an ExpressionExperiment's bioAssays collection (which cascades the persist).

This is the path ExperimentFactory uses when building EE-attached BAs; the EE cascade handles the BA persist.