Interface BioMaterialService

All Superinterfaces:

BaseImmutableService<BioMaterial>, BaseReadOnlyService<BioMaterial>, BaseService<BioMaterial>, BaseVoEnabledService<BioMaterial, BioMaterialValueObject>, SecurableBaseImmutableService<BioMaterial>, SecurableBaseReadOnlyService<BioMaterial>, SecurableBaseService<BioMaterial>, SecurableBaseVoEnabledService<BioMaterial, BioMaterialValueObject>

All Known Implementing Classes:

BioMaterialServiceImpl

public interface BioMaterialService
extends SecurableBaseService<BioMaterial>, SecurableBaseVoEnabledService<BioMaterial, BioMaterialValueObject>

Author:

kelsey

Method Summary

Modifier and Type	Method	Description
Characteristic	addAnnotation(ExpressionExperiment owner, BioMaterial bm, Characteristic vc)	Per-tag add of a characteristic to a biomaterial, the sample-level counterpart of ExpressionExperimentService.addAnnotation(ExpressionExperiment, Characteristic).
Characteristic	addAnnotation(ExpressionExperiment owner, BioMaterial bm, Characteristic vc, String reason)	As addAnnotation(ExpressionExperiment, BioMaterial, Characteristic), with a caller-supplied reason appended to the audit note after the server's own description.
void	addCharacteristic(BioMaterial bm, Characteristic vc)	Will persist the give vocab characteristic to the given biomaterial
<T> void	associateBatchFactor(Map<BioMaterial, T> descriptors, Map<T, FactorValue> d2fv)	Associate dates with bioassays and any new factors with the biomaterials.
BioMaterial	copy(BioMaterial bioMaterial)	Copies a bioMaterial.
Collection<BioMaterial>	findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	findByFactor(ExperimentalFactor experimentalFactor)
Collection<BioMaterial>	findSiblings(BioMaterial bioMaterial)	Find the siblings of a given biomaterial.
Collection<BioMaterial>	findSubBioMaterials(BioMaterial bioMaterial, boolean direct)
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	getExpressionExperiments(BioMaterial bm)
<T extends Exception> BioMaterial	loadAndThawOrFail(Long bmId, Function<String,T> exceptionSupplier, String message)
Characteristic	removeAnnotation(ExpressionExperiment owner, BioMaterial bm, Long annotationId)	Per-tag remove of a characteristic from a biomaterial by id, the sample-level counterpart of ExpressionExperimentService.removeAnnotation(ExpressionExperiment, Long).
Characteristic	removeAnnotation(ExpressionExperiment owner, BioMaterial bm, Long annotationId, String reason)	As removeAnnotation(ExpressionExperiment, BioMaterial, Long), with a caller-supplied reason appended to the audit note.
void	removeCharacteristics(BioMaterial bm, Collection<Characteristic> vc)	Remove the given characteristic from the given biomaterial
Collection<BioMaterial>	thaw(Collection<BioMaterial> bioMaterials)
BioMaterial	thaw(BioMaterial bioMaterial)
int	updateAnnotations(ExpressionExperiment owner, BioMaterial bm, Collection<Characteristic> desired)	Idempotent set-replace for a biomaterial's direct characteristic set, the sample-level counterpart of ExpressionExperimentService.updateAnnotations(ExpressionExperiment, Collection).
Collection<BioMaterial>	updateBioMaterials(Collection<BioMaterialValueObject> valueObjects)	Update the biomaterials that are described by the given valueObjects.

Methods inherited from interface BaseReadOnlyService

countAll, getElementClass, loadOrFail, loadOrFail

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

Method Details

copy

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
BioMaterial copy(BioMaterial bioMaterial)

Copies a bioMaterial.

Parameters:

bioMaterial - ba to copy

Returns:

the copy

findSubBioMaterials

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<BioMaterial> findSubBioMaterials(BioMaterial bioMaterial,
 boolean direct)

See Also:

• BioMaterialDao.findSubBioMaterials(BioMaterial, boolean)

findSiblings

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<BioMaterial> findSiblings(BioMaterial bioMaterial)

Find the siblings of a given biomaterial.

findByExperiment

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<BioMaterial> findByExperiment(ExpressionExperiment experiment)

findByFactor

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<BioMaterial> findByFactor(ExperimentalFactor experimentalFactor)

loadAndThawOrFail

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
@PostAuthorize("returnObject == null or hasPermission(returnObject, 'READ') or hasPermission(returnObject, 'ADMINISTRATION')")
<T extends Exception> BioMaterial loadAndThawOrFail(Long bmId,
 Function<String,T> exceptionSupplier,
 String message)
                                             throws T

Throws:

T

getExpressionExperiments

@Nullable
@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
@PostFilter("hasPermission(filterObject.key, 'READ') or hasPermission(filterObject.key, 'ADMINISTRATION')")
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>> getExpressionExperiments(BioMaterial bm)

thaw

@CheckReturnValue
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
BioMaterial thaw(BioMaterial bioMaterial)

thaw

@CheckReturnValue
@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
@PostFilter("hasPermission(filterObject, 'READ') or hasPermission(filterObject, 'ADMINISTRATION')")
Collection<BioMaterial> thaw(Collection<BioMaterial> bioMaterials)

updateBioMaterials

@Secured("GROUP_ADMIN")
Collection<BioMaterial> updateBioMaterials(Collection<BioMaterialValueObject> valueObjects)

Update the biomaterials that are described by the given valueObjects. This is used to update experimental designs in particular.

Parameters:

valueObjects - VOs

Returns:

the biomaterials that were modified.

associateBatchFactor

@Secured("GROUP_ADMIN")
<T> void associateBatchFactor(Map<BioMaterial, T> descriptors,
 Map<T, FactorValue> d2fv)

Associate dates with bioassays and any new factors with the biomaterials. Note we can have missing values.

Parameters:

d2fv - map of dates to factor values

addCharacteristic

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void addCharacteristic(BioMaterial bm,
 Characteristic vc)

Will persist the give vocab characteristic to the given biomaterial

See Also:

• ExpressionExperimentService.addCharacteristic(ExpressionExperiment, Characteristic)

removeCharacteristics

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeCharacteristics(BioMaterial bm,
 Collection<Characteristic> vc)

Remove the given characteristic from the given biomaterial

Throws:

IllegalArgumentException - if the characteristic does not belong to the biomaterial

updateAnnotations

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
int updateAnnotations(ExpressionExperiment owner,
 BioMaterial bm,
 Collection<Characteristic> desired)

Idempotent set-replace for a biomaterial's direct characteristic set, the sample-level counterpart of ExpressionExperimentService.updateAnnotations(ExpressionExperiment, Collection).

The owner experiment is the audit + ACL target: the ManualAnnotationEvent is recorded on the experiment (not the sample) and ACL_SECURABLE_EDIT is checked against it, so all tag edits — experiment- or sample-level — surface on the experiment's history and share one permission gate. The diff is statement-aware (see CharacteristicUtils.sameTag(Characteristic, Characteristic)).

Parameters:

owner - the experiment that owns bm (audit + ACL target)

bm - the biomaterial whose characteristics are replaced

desired - the full desired characteristic set (empty clears)

Returns:

the number of changes (adds + removes); zero means the set was already as desired

addAnnotation

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
Characteristic addAnnotation(ExpressionExperiment owner,
 BioMaterial bm,
 Characteristic vc)

Per-tag add of a characteristic to a biomaterial, the sample-level counterpart of ExpressionExperimentService.addAnnotation(ExpressionExperiment, Characteristic). Records a TagAddedEvent on owner and rejects a duplicate (by statement-aware sameTag) with IllegalArgumentException.

Parameters:

owner - the experiment that owns bm (audit + ACL target)

Returns:

the persisted characteristic

addAnnotation

Characteristic addAnnotation(ExpressionExperiment owner,
 BioMaterial bm,
 Characteristic vc,
 @Nullable
 String reason)

As addAnnotation(ExpressionExperiment, BioMaterial, Characteristic), with a caller-supplied reason appended to the audit note after the server's own description.

removeAnnotation

@Nullable
@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
Characteristic removeAnnotation(ExpressionExperiment owner,
 BioMaterial bm,
 Long annotationId)

Per-tag remove of a characteristic from a biomaterial by id, the sample-level counterpart of ExpressionExperimentService.removeAnnotation(ExpressionExperiment, Long). Records a TagRemovedEvent on owner; returns null when the id is not in bm's characteristic set so the caller can surface a 404.

Parameters:

owner - the experiment that owns bm (audit + ACL target)

removeAnnotation

Characteristic removeAnnotation(ExpressionExperiment owner,
 BioMaterial bm,
 Long annotationId,
 @Nullable
 String reason)

As removeAnnotation(ExpressionExperiment, BioMaterial, Long), with a caller-supplied reason appended to the audit note. A deletion has no surviving annotation to carry evidence, so this is the only place its reason can be recorded.