Class BioAssayServiceImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractService<BioAssay>

ubic.gemma.persistence.service.AbstractFilteringVoEnabledService<BioAssay, BioAssayValueObject>

ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl

All Implemented Interfaces:

BaseImmutableService<BioAssay>, BaseReadOnlyService<BioAssay>, BaseService<BioAssay>, BaseVoEnabledService<BioAssay, BioAssayValueObject>, SecurableBaseImmutableService<BioAssay>, SecurableBaseReadOnlyService<BioAssay>, SecurableBaseService<BioAssay>, SecurableBaseVoEnabledService<BioAssay, BioAssayValueObject>, SecurableFilteringVoEnabledService<BioAssay, BioAssayValueObject>, BioAssayService, FilteringService<BioAssay>, FilteringVoEnabledService<BioAssay, BioAssayValueObject>

@Service
public class BioAssayServiceImpl
extends AbstractFilteringVoEnabledService<BioAssay, BioAssayValueObject>
implements BioAssayService

Author:

pavlidis, keshav, joseph

See Also:

• BioAssayService

Field Summary

Fields inherited from class AbstractService

log

Constructor Summary

Constructors

Constructor	Description
BioAssayServiceImpl(BioAssayDao bioAssayDao, BioMaterialDao bioMaterialDao)

Method Summary

Modifier and Type	Method	Description
void	addBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial)	Associates a bioMaterial with a specified bioAssay.
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)	Cursor-mode counterpart to the legacy unpaginated BioAssayDao EE-scoped sample listing — see CURSOR_PAGINATION_STEP1_PLAN.md step 1k.
CursorPage<BioAssayValueObject>	loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet subset, Cursor cursor, int limit)	Cursor-mode counterpart to the legacy unpaginated subset-scoped sample listing — see CURSOR_PAGINATION_STEP1_PLAN.md step 1u.
void	removeBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial)	Removes the association between a specific bioMaterial and a bioAssay.
Collection<BioAssay>	thaw(Collection<BioAssay> bioAssays)
BioAssay	thaw(BioAssay ba)

Methods inherited from class AbstractFilteringVoEnabledService

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, load, load, loadAllValueObjects, loadIds, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjects, loadValueObjects, loadValueObjectsByCursor, loadValueObjectsByIds

Methods inherited from class AbstractService

countAll, create, create, ensureInSession, ensureInSession, find, findOrCreate, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, remove, remove, save, save, streamAll, streamAll, update, update

Methods inherited from class Object

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

Methods inherited from interface BaseReadOnlyService

countAll, getElementClass, loadOrFail, loadOrFail

Methods inherited from interface FilteringService

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery

Methods inherited from interface FilteringVoEnabledService

loadValueObjectsByCursor

Methods inherited from interface SecurableBaseImmutableService

create, create, findOrCreate, remove, remove

Methods inherited from interface SecurableBaseReadOnlyService

find, findOrFail, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

Methods inherited from interface SecurableBaseService

save, save, update, update

Methods inherited from interface SecurableBaseVoEnabledService

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface SecurableFilteringVoEnabledService

load, load, loadIds, loadValueObjects, loadValueObjects

Constructor Details

BioAssayServiceImpl

@Autowired
public BioAssayServiceImpl(BioAssayDao bioAssayDao,
 BioMaterialDao bioMaterialDao)

Method Details

addBioMaterialAssociation

@Transactional
public void addBioMaterialAssociation(BioAssay bioAssay,
 BioMaterial bioMaterial)

Description copied from interface: BioAssayService

Associates a bioMaterial with a specified bioAssay.

Specified by:

addBioMaterialAssociation in interface BioAssayService

Parameters:

bioAssay - bio assay

bioMaterial - bio material

removeBioMaterialAssociation

@Transactional
public void removeBioMaterialAssociation(BioAssay bioAssay,
 BioMaterial bioMaterial)

Description copied from interface: BioAssayService

Removes the association between a specific bioMaterial and a bioAssay.

Specified by:

removeBioMaterialAssociation in interface BioAssayService

Parameters:

bioAssay - bio assay

bioMaterial - bio material

See Also:

• BioAssayService.removeBioMaterialAssociation(BioAssay, ubic.gemma.model.expression.biomaterial.BioMaterial)

findBioAssayDimensions

public Collection<BioAssayDimension> findBioAssayDimensions(BioAssay bioAssay)

Description copied from interface: BioAssayService

Locate all BioAssayDimensions in which the selected BioAssay occurs

Specified by:

findBioAssayDimensions in interface BioAssayService

Parameters:

bioAssay - bio assay

Returns:

bio assay dimensions

See Also:

• BioAssayService.findBioAssayDimensions(BioAssay)

findByShortName

public BioAssay findByShortName(String shortName)

Specified by:

findByShortName in interface BioAssayService

findByAccession

public Collection<BioAssay> findByAccession(String accession)

Specified by:

findByAccession in interface BioAssayService

Parameters:

accession - eg GSM12345.

Returns:

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

findSubBioAssays

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

Specified by:

findSubBioAssays in interface BioAssayService

See Also:

• BioMaterialService.findSubBioMaterials(BioMaterial, boolean)

findSiblings

public Collection<BioAssay> findSiblings(BioAssay bioAssay)

Specified by:

findSiblings in interface BioAssayService

getBioAssaySets

public Collection<BioAssaySet> getBioAssaySets(BioAssay bioAssay)

Description copied from interface: BioAssayService

Obtain all the BioAssaySet that contain the given BioAssay.

Specified by:

getBioAssaySets in interface BioAssayService

thaw

public BioAssay thaw(BioAssay ba)

Specified by:

thaw in interface BioAssayService

thaw

public Collection<BioAssay> thaw(Collection<BioAssay> bioAssays)

Specified by:

thaw in interface BioAssayService

loadValueObjects

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

Specified by:

loadValueObjects in interface BioAssayService

See Also:

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

loadValueObjectsByCursorForExpressionExperiment

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

Description copied from interface: BioAssayService

Cursor-mode counterpart to the legacy unpaginated BioAssayDao EE-scoped sample listing — see CURSOR_PAGINATION_STEP1_PLAN.md step 1k. Always sorts by ascending id (primary key, indexed and unique); the cursor DAO restricts cursors to single-component id sorts until the index audit lands.

Specified by:

loadValueObjectsByCursorForExpressionExperiment in interface BioAssayService

See Also:

• BioAssayDao.loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment, Cursor, int)

loadValueObjectsByCursorForSubSet

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

Description copied from interface: BioAssayService

Cursor-mode counterpart to the legacy unpaginated subset-scoped sample listing — see CURSOR_PAGINATION_STEP1_PLAN.md step 1u. Always sorts by ascending id (primary key, indexed and unique). The service layer is responsible for populating any assay2sourceAssayMap the caller wants surfaced on the returned BioAssayValueObjects after this call returns (the DAO does not build it).

Specified by:

loadValueObjectsByCursorForSubSet in interface BioAssayService

See Also:

• BioAssayDao.loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet, Cursor, int)