Interface BioAssayReadService

All Known Implementing Classes:

BioAssayReadServiceImpl

public interface BioAssayReadService

Read-only retrieval service for BioAssay.

Phase 3 of the BioAssayService decomposition (strangler fig). This service houses the DAO-bound read cluster previously implemented directly on the BioAssayServiceImpl facade: findBioAssayDimensions, findByShortName, findByAccession, findSubBioAssays, findSiblings, getBioAssaySets, thaw (x2), loadValueObjects, loadValueObjectsByCursorForExpressionExperiment, and loadValueObjectsByCursorForSubSet. All methods delegate to BioAssayDao (and read-side collaborators) and orchestrate no writes.

Write-side methods (addBioMaterialAssociation, removeBioMaterialAssociation, plus the inherited BaseService mutators) stay on the BioAssayService facade.

Callers should generally keep using BioAssayService as the facade -- the facade delegates to this service. Direct injection is appropriate where a class is logically read-only (REST endpoints, CLIs, browser controllers, intra-core readers).

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

See Also:

• BioAssayService

Method Summary

Modifier and Type	Method	Description
Collection<BioAssayDimension>	findBioAssayDimensions(BioAssay bioAssay)	Locate all BioAssayDimensions in which the selected BioAssay occurs.
Collection<BioAssay>	findByAccession(String accession)
BioAssay	findByShortName(String shortName)
Collection<BioAssay>	findSiblings(BioAssay bioAssay)
Collection<BioAssay>	findSubBioAssays(BioAssay bioAssay, boolean direct)
Collection<BioAssaySet>	getBioAssaySets(BioAssay bioAssay)	Obtain all the BioAssaySet that contain the given BioAssay.
List<BioAssayValueObject>	loadValueObjects(Collection<BioAssay> entities, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
CursorPage<BioAssayValueObject>	loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment ee, Cursor cursor, int limit)
CursorPage<BioAssayValueObject>	loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet subset, Cursor cursor, int limit)
Collection<BioAssay>	thaw(Collection<BioAssay> bioAssays)
BioAssay	thaw(BioAssay bioAssay)

Method Details

findBioAssayDimensions

Collection<BioAssayDimension> findBioAssayDimensions(BioAssay bioAssay)

Locate all BioAssayDimensions in which the selected BioAssay occurs.

findByShortName

@Nullable
BioAssay findByShortName(String shortName)

findByAccession

Collection<BioAssay> findByAccession(String accession)

Parameters:

accession - eg GSM12345.

Returns:

BioAssays that match based on the plain accession (unconstrained by ExternalDatabase).

findSubBioAssays

Collection<BioAssay> findSubBioAssays(BioAssay bioAssay,
 boolean direct)

findSiblings

Collection<BioAssay> findSiblings(BioAssay bioAssay)

getBioAssaySets

Collection<BioAssaySet> getBioAssaySets(BioAssay bioAssay)

Obtain all the BioAssaySet that contain the given BioAssay.

thaw

@CheckReturnValue
BioAssay thaw(BioAssay bioAssay)

thaw

@CheckReturnValue
Collection<BioAssay> thaw(Collection<BioAssay> bioAssays)

loadValueObjects

List<BioAssayValueObject> loadValueObjects(Collection<BioAssay> entities,
 @Nullable
 Map<BioAssay,BioAssay> assay2sourceAssayMap,
 boolean basic,
 boolean allFactorValues)

See Also:

• BioAssayDao.loadValueObjects(Collection, Map, Map, boolean, boolean)

loadValueObjectsByCursorForExpressionExperiment

CursorPage<BioAssayValueObject> loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment ee,
 @Nullable
 Cursor cursor,
 int limit)

See Also:

• BioAssayDao.loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment, Cursor, int)

loadValueObjectsByCursorForSubSet

CursorPage<BioAssayValueObject> loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet subset,
 @Nullable
 Cursor cursor,
 int limit)

See Also:

• BioAssayDao.loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet, Cursor, int)