Interface BioMaterialReadService

All Known Implementing Classes:

BioMaterialReadServiceImpl

public interface BioMaterialReadService

Read-only retrieval service for BioMaterial.

Phase 3 of the BioMaterialService decomposition (strangler fig). This service houses the read-side cluster previously implemented directly on the BioMaterialServiceImpl facade: copy, findSubBioMaterials, findSiblings, findByExperiment, findByFactor, loadAndThawOrFail, getExpressionExperiments, and the thaw variants. All methods delegate to BioMaterialDao (and Thaws for eager-loading) with no orchestration of write-side collaborators.

Callers should generally keep using BioMaterialService as the facade — the facade delegates to this service. Direct injection is appropriate where a class would otherwise create a Spring construction cycle through the heavier facade.

ACL / @Secured annotations live on BioMaterialService (the caller-facing facade interface); enforcement happens at the facade proxy boundary, so this interface is intentionally unsecured.

See Also:

• BioMaterialService

Method Summary

Modifier and Type	Method	Description
BioMaterial	copy(BioMaterial bioMaterial)	Copy a BioMaterial.
Collection<BioMaterial>	findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	findByFactor(ExperimentalFactor experimentalFactor)
Collection<BioMaterial>	findSiblings(BioMaterial bioMaterial)	Find the siblings of a given biomaterial (other direct sub-materials of the same source).
Collection<BioMaterial>	findSubBioMaterials(BioMaterial bioMaterial, boolean direct)
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	getExpressionExperiments(BioMaterial bm)	Return the ExpressionExperiment occurrences of a given biomaterial, organized by BioAssay.
<T extends Exception> BioMaterial	loadAndThawOrFail(Long bmId, Function<String,T> exceptionSupplier, String message)	Load a BioMaterial by ID and thaw it eagerly, or throw the supplied exception if no such biomaterial exists.
Collection<BioMaterial>	thaw(Collection<BioMaterial> bioMaterials)	Thaw a collection of BioMaterial for full traversal.
BioMaterial	thaw(BioMaterial bioMaterial)	Thaw a single BioMaterial for full traversal.

Method Details

copy

BioMaterial copy(BioMaterial bioMaterial)

Copy a BioMaterial.

See Also:

• BioMaterialDao.copy(BioMaterial)

findSubBioMaterials

Collection<BioMaterial> findSubBioMaterials(BioMaterial bioMaterial,
 boolean direct)

See Also:

• BioMaterialDao.findSubBioMaterials(BioMaterial, boolean)

findSiblings

Collection<BioMaterial> findSiblings(BioMaterial bioMaterial)

Find the siblings of a given biomaterial (other direct sub-materials of the same source).

findByExperiment

Collection<BioMaterial> findByExperiment(ExpressionExperiment experiment)

See Also:

• BioMaterialDao.findByExperiment(ExpressionExperiment)

findByFactor

Collection<BioMaterial> findByFactor(ExperimentalFactor experimentalFactor)

See Also:

• BioMaterialDao.findByFactor(ExperimentalFactor)

loadAndThawOrFail

<T extends Exception> BioMaterial loadAndThawOrFail(Long bmId,
 Function<String,T> exceptionSupplier,
 String message)
                                             throws T

Load a BioMaterial by ID and thaw it eagerly, or throw the supplied exception if no such biomaterial exists.

Throws:

T

getExpressionExperiments

Map<BioMaterial, Map<BioAssay, ExpressionExperiment>> getExpressionExperiments(BioMaterial bm)

Return the ExpressionExperiment occurrences of a given biomaterial, organized by BioAssay.

See Also:

• BioMaterialDao.getExpressionExperiments(BioMaterial)

thaw

@CheckReturnValue
BioMaterial thaw(BioMaterial bioMaterial)

Thaw a single BioMaterial for full traversal.

thaw

@CheckReturnValue
Collection<BioMaterial> thaw(Collection<BioMaterial> bioMaterials)

Thaw a collection of BioMaterial for full traversal.