Class BioAssayFactory

java.lang.Object

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

@Component
public class BioAssayFactory
extends Object

Typed factory for persistent BioAssay test fixtures.

Phase 3 split-out from the inline BA construction inside ExperimentFactory.Builder.build(). Use this factory when a test needs an isolated, persistent BioAssay (not necessarily attached to an ExpressionExperiment); for the EE-attached case keep using ExperimentFactory.

Usage:

  // Fresh BA with auto-created BioMaterial + ArrayDesign on mouse
  BioAssay ba = bioAssayFactory.builder().build();

  // BA wired to a specific BM and AD
  BioAssay ba = bioAssayFactory.builder()
                     .withBioMaterial(bm)
                     .withArrayDesign(ad)
                     .build();

  // Named BA
  BioAssay ba = bioAssayFactory.builder()
                     .withName("GSM12345_ba")
                     .build();

Design notes (HB6-relevant):

• The BA mapping does NOT cascade from BioAssay to sampleUsed / arrayDesignUsed. Both must be persistent before SecurableBaseImmutableService.create(BioAssay) is called. This factory pre-persists both via their respective services so the production code path fires (ACL listeners on the BM and AD).
• BioMaterial.getBioAssaysUsedIn().add(ba) is the collection mutation that keeps the inverse side in sync. We do this BEFORE the BA persist so subsequent loads see the relationship.
• A transient GEO DatabaseEntry accession is attached to every BA - mirrors the inline pattern in ExperimentFactory and satisfies tests that filter on accession.
• BioMaterialFactory does not yet exist as a separate component; until it lands, this factory inlines BM creation (same shape as ExperimentFactory's inline BM block). The BioAssayFactory.Builder.withBioMaterial(BioMaterial) hook is the seam to swap in once BioMaterialFactory lands.

Author:

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

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static final class	BioAssayFactory.Builder	Fluent builder for a BioAssay.

Constructor Summary

Constructors

Constructor	Description
BioAssayFactory()

Method Summary

Modifier and Type	Method	Description
BioAssayFactory.Builder	builder()	Start building a BioAssay.

Methods inherited from class Object

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

Constructor Details

BioAssayFactory

public BioAssayFactory()

Method Details

builder

public BioAssayFactory.Builder builder()

Start building a BioAssay. All defaults can be overridden via withXxx(...) methods.