Class BioMaterialServiceImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractVoEnabledService<BioMaterial, BioMaterialValueObject>

ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl

All Implemented Interfaces:

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

@Service
public class BioMaterialServiceImpl
extends AbstractVoEnabledService<BioMaterial, BioMaterialValueObject>
implements BioMaterialService

Author:

pavlidis, keshav

See Also:

• BioMaterialService

Field Summary

Fields inherited from class AbstractService

log

Constructor Summary

Constructors

Constructor	Description
BioMaterialServiceImpl(BioMaterialDao bioMaterialDao, FactorValueDao factorValueDao, BioAssayDao bioAssayDao, ExperimentalFactorDao experimentalFactorDao, CharacteristicService characteristicService, BioMaterialReadService bioMaterialReadService)

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)	Reason-carrying overload.
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)	Reason-carrying overload; see addAnnotation(ExpressionExperiment, BioMaterial, Characteristic, String).
void	removeCharacteristics(BioMaterial bm, Collection<Characteristic> characteristicsToRemove)	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 class AbstractVoEnabledService

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, 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 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

Constructor Details

BioMaterialServiceImpl

@Autowired
public BioMaterialServiceImpl(BioMaterialDao bioMaterialDao,
 FactorValueDao factorValueDao,
 BioAssayDao bioAssayDao,
 ExperimentalFactorDao experimentalFactorDao,
 CharacteristicService characteristicService,
 BioMaterialReadService bioMaterialReadService)

Method Details

copy

public BioMaterial copy(BioMaterial bioMaterial)

Description copied from interface: BioMaterialService

Copies a bioMaterial.

Specified by:

copy in interface BioMaterialService

Parameters:

bioMaterial - ba to copy

Returns:

the copy

findSubBioMaterials

public Collection<BioMaterial> findSubBioMaterials(BioMaterial bioMaterial,
 boolean direct)

Specified by:

findSubBioMaterials in interface BioMaterialService

See Also:

• BioMaterialDao.findSubBioMaterials(BioMaterial, boolean)

findSiblings

public Collection<BioMaterial> findSiblings(BioMaterial bioMaterial)

Description copied from interface: BioMaterialService

Find the siblings of a given biomaterial.

Specified by:

findSiblings in interface BioMaterialService

findByExperiment

public Collection<BioMaterial> findByExperiment(ExpressionExperiment experiment)

Specified by:

findByExperiment in interface BioMaterialService

findByFactor

public Collection<BioMaterial> findByFactor(ExperimentalFactor experimentalFactor)

Specified by:

findByFactor in interface BioMaterialService

loadAndThawOrFail

public <T extends Exception> BioMaterial loadAndThawOrFail(Long bmId,
 Function<String,T> exceptionSupplier,
 String message)
                                                    throws T

Specified by:

loadAndThawOrFail in interface BioMaterialService

Throws:

T

getExpressionExperiments

public Map<BioMaterial, Map<BioAssay, ExpressionExperiment>> getExpressionExperiments(BioMaterial bm)

Specified by:

getExpressionExperiments in interface BioMaterialService

thaw

public BioMaterial thaw(BioMaterial bioMaterial)

Specified by:

thaw in interface BioMaterialService

thaw

public Collection<BioMaterial> thaw(Collection<BioMaterial> bioMaterials)

Specified by:

thaw in interface BioMaterialService

updateBioMaterials

@Transactional
public Collection<BioMaterial> updateBioMaterials(Collection<BioMaterialValueObject> valueObjects)

Description copied from interface: BioMaterialService

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

Specified by:

updateBioMaterials in interface BioMaterialService

Parameters:

valueObjects - VOs

Returns:

the biomaterials that were modified.

associateBatchFactor

@Transactional
public <T> void associateBatchFactor(Map<BioMaterial, T> descriptors,
 Map<T, FactorValue> d2fv)

Description copied from interface: BioMaterialService

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

Specified by:

associateBatchFactor in interface BioMaterialService

Parameters:

d2fv - map of dates to factor values

addCharacteristic

@Transactional
public void addCharacteristic(BioMaterial bm,
 Characteristic vc)

Description copied from interface: BioMaterialService

Will persist the give vocab characteristic to the given biomaterial

Specified by:

addCharacteristic in interface BioMaterialService

See Also:

• ExpressionExperimentService.addCharacteristic(ExpressionExperiment, Characteristic)

removeCharacteristics

@Transactional
public void removeCharacteristics(BioMaterial bm,
 Collection<Characteristic> characteristicsToRemove)

Description copied from interface: BioMaterialService

Remove the given characteristic from the given biomaterial

Specified by:

removeCharacteristics in interface BioMaterialService

updateAnnotations

@Transactional
@AuditedConditional(value=ManualAnnotationEvent.class,
                    when="#result > 0",
                    messageSpel="'Replaced sample annotations via API (' + #result + ' change(s)) on biomaterial ' + #bm.id")
public int updateAnnotations(ExpressionExperiment owner,
 BioMaterial bm,
 Collection<Characteristic> desired)

Description copied from interface: BioMaterialService

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)).

Specified by:

updateAnnotations in interface BioMaterialService

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

@Transactional
@Audited(value=TagAddedEvent.class,
         messageSpel="'Added tag ' + #vc.category + ' = ' + #vc.value + ' to biomaterial ' + #bm.id")
public Characteristic addAnnotation(ExpressionExperiment owner,
 BioMaterial bm,
 Characteristic vc)

Description copied from interface: BioMaterialService

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.

Specified by:

addAnnotation in interface BioMaterialService

Parameters:

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

Returns:

the persisted characteristic

addAnnotation

@Transactional
@Audited(value=TagAddedEvent.class,
         messageSpel="'Added tag ' + #vc.category + ' = ' + #vc.value + ' to biomaterial ' + #bm.id + (#reason != null ? ' \u2014 ' + #reason : '')")
public Characteristic addAnnotation(ExpressionExperiment owner,
 BioMaterial bm,
 Characteristic vc,
 @Nullable
 String reason)

Reason-carrying overload. A separate method rather than a parameter on the one above so every existing caller keeps its signature; the two differ only in the audit note the aspect writes. Both delegate to the same private body through a plain this call, which is not re-advised, so one call still writes one event.

Specified by:

addAnnotation in interface BioMaterialService

removeAnnotation

@Transactional
@AuditedConditional(value=TagRemovedEvent.class,
                    when="#result != null",
                    messageSpel="'Removed tag ' + #result.category + ' = ' + #result.value + ' from biomaterial ' + #bm.id")
@Nullable
public Characteristic removeAnnotation(ExpressionExperiment owner,
 BioMaterial bm,
 Long annotationId)

Description copied from interface: BioMaterialService

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.

Specified by:

removeAnnotation in interface BioMaterialService

Parameters:

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

removeAnnotation

@Transactional
@AuditedConditional(value=TagRemovedEvent.class,
                    when="#result != null",
                    messageSpel="'Removed tag ' + #result.category + ' = ' + #result.value + ' from biomaterial ' + #bm.id + (#reason != null ? ' \u2014 ' + #reason : '')")
@Nullable
public Characteristic removeAnnotation(ExpressionExperiment owner,
 BioMaterial bm,
 Long annotationId,
 @Nullable
 String reason)

Reason-carrying overload; see addAnnotation(ExpressionExperiment, BioMaterial, Characteristic, String).

Specified by:

removeAnnotation in interface BioMaterialService