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)
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 bioAssay)

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

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")
@PostAuthorize("returnObject == null or hasPermission(returnObject, 'READ') or hasPermission(returnObject, 'ADMINISTRATION')")
BioAssay findByShortName(String shortName)

findByAccession

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
@PostFilter("hasPermission(filterObject, 'READ') or hasPermission(filterObject, 'ADMINISTRATION')")
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")
@PostFilter("hasPermission(filterObject, 'READ') or hasPermission(filterObject, 'ADMINISTRATION')")
Collection<BioAssay> findSubBioAssays(BioAssay bioAssay,
 boolean direct)

See Also:

• BioMaterialService.findSubBioMaterials(BioMaterial, boolean)

findSiblings

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
@PostFilter("hasPermission(filterObject, 'READ') or hasPermission(filterObject, 'ADMINISTRATION')")
Collection<BioAssay> findSiblings(BioAssay bioAssay)

getBioAssaySets

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
@PostFilter("hasPermission(filterObject, 'READ') or hasPermission(filterObject, 'ADMINISTRATION')")
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")
@PostFilter("hasPermission(filterObject, 'READ') or hasPermission(filterObject, 'ADMINISTRATION')")
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

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
CursorPage<BioAssayValueObject> loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment ee,
 @Nullable
 Cursor cursor,
 int limit)

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.

See Also:

• BioAssayDao.loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment, Cursor, int)

loadValueObjectsByCursorForSubSet

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
CursorPage<BioAssayValueObject> loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet subset,
 @Nullable
 Cursor cursor,
 int limit)

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).

See Also:

• BioAssayDao.loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet, Cursor, int)