Package ubic.gemma.persistence.service.expression.bioAssay

Interface BioAssayService

All Superinterfaces:

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

All Known Implementing Classes:

BioAssayServiceImpl

@Service
public interface BioAssayService
extends SecurableBaseService<BioAssay>, SecurableFilteringVoEnabledService<BioAssay,BioAssayValueObject>

Author:

kelsey

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)
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 bioAssay)

Methods inherited from interface ubic.gemma.persistence.service.BaseReadOnlyService

countAll, getElementClass, loadOrFail, loadOrFail

Methods inherited from interface ubic.gemma.persistence.service.FilteringService

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

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseImmutableService

create, create, findOrCreate, remove, remove

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService

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

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService

save, save, update, update

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService

load, load, loadIds, loadValueObjects, loadValueObjects

Method Details

addBioMaterialAssociation

@PreAuthorize("hasPermission(#bioAssay, \'write\') or hasPermission(#bioAssay, \'administration\')")
void addBioMaterialAssociation(BioAssay bioAssay,
 BioMaterial bioMaterial)

Associates a bioMaterial with a specified bioAssay.

Parameters:

bioAssay - bio assay

bioMaterial - bio material

findBioAssayDimensions

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<BioAssayDimension> findBioAssayDimensions(BioAssay bioAssay)

Locate all BioAssayDimensions in which the selected BioAssay occurs

Parameters:

bioAssay - bio assay

Returns:

bio assay dimensions

findByShortName

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
BioAssay findByShortName(String shortName)

findByAccession

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<BioAssay> findByAccession(String accession)

Parameters:

accession - eg GSM12345.

Returns:

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

findSubBioAssays

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<BioAssay> findSubBioAssays(BioAssay bioAssay,
 boolean direct)

See Also:

• BioMaterialService.findSubBioMaterials(BioMaterial, boolean)

findSiblings

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<BioAssay> findSiblings(BioAssay bioAssay)

getBioAssaySets

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<BioAssaySet> getBioAssaySets(BioAssay bioAssay)

Obtain all the BioAssaySet that contain the given BioAssay.

removeBioMaterialAssociation

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeBioMaterialAssociation(BioAssay bioAssay,
 BioMaterial bioMaterial)

Removes the association between a specific bioMaterial and a bioAssay.

Parameters:

bioAssay - bio assay

bioMaterial - bio material

thaw

@CheckReturnValue
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
BioAssay thaw(BioAssay bioAssay)

thaw

@CheckReturnValue
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
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)