Package ubic.gemma.persistence.service.expression.experiment

Interface FactorValueService

All Superinterfaces:

BaseImmutableService<FactorValue>, BaseReadOnlyService<FactorValue>, BaseService<FactorValue>, BaseVoEnabledService<FactorValue,FactorValueValueObject>, FilteringService<FactorValue>, FilteringVoEnabledService<FactorValue,FactorValueValueObject>

All Known Implementing Classes:

FactorValueServiceImpl

public interface FactorValueService
extends BaseService<FactorValue>, FilteringVoEnabledService<FactorValue,FactorValueValueObject>

Author:

kelsey

Method Summary

Modifier and Type	Method	Description
void	clearNeedsAttentionFlag(FactorValue factorValue, String note)	Clear a needs attention flag on a given factor value.
Statement	createStatement(FactorValue factorValue, Statement statement)	Create a given statement and add it to the given factor value.
Collection<FactorValue>	findByValue(String valuePrefix)	Deprecated.
FactorValue	findOrCreate(FactorValue factorValue)	Does a search for the entity in the persistent storage, and if not found, creates it.
FactorValue	load(Long id)	Loads object with given ID.
Map<Long,Integer>	loadIdsWithNumberOfOldStyleCharacteristics(Set<Long> excludedIds)	Deprecated. do not use, this is only for migrating old-style characteristics to statements and will be removed
FactorValue	loadWithExperimentalFactor(Long id)
FactorValue	loadWithExperimentalFactorOrFail(Long id)	Load a FactorValue with an initialized experimental factor or fail.
FactorValue	loadWithOldStyleCharacteristics(Long id, boolean readOnly)	Deprecated. do not use this, it is only meant for the purpose of migrating old-style characteristics to statements
void	markAsNeedsAttention(FactorValue factorValue, String note)	Mark a given factor value as needs attention.
void	remove(FactorValue factorValue)	Removes the given entity from the persistent storage.
void	removeStatement(FactorValue fv, Statement c)	Remove a statement from a factor value.
Statement	saveStatement(FactorValue fv, Statement statement)	Create a given statement as per createStatement(FactorValue, Statement) if it is transient, otherwise update an existing statement.
Statement	saveStatementIgnoreAcl(FactorValue fv, Statement statement)	Deprecated. do not use this, it is meant for FactorValue migration only
void	update(Collection<FactorValue> factorValues)	Updates all entities in the given collection in the persistent storage.
void	update(FactorValue factorValue)	Updates the given entity in the persistent storage.

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

create, create, remove, remove

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

countAll, find, findOrFail, getElementClass, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail

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

save, save

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getIdentifierPropertyName, getSort, load, load, loadIds

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

loadValueObjects, loadValueObjects

Method Detail

findByValue

@Deprecated
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<FactorValue> findByValue(String valuePrefix)

Deprecated.

findOrCreate

@Secured({"GROUP_USER","AFTER_ACL_READ"})
FactorValue findOrCreate(FactorValue factorValue)

Description copied from interface: BaseImmutableService

Does a search for the entity in the persistent storage, and if not found, creates it.

Specified by:

findOrCreate in interface BaseImmutableService<FactorValue>

Parameters:

factorValue - the entity to look for, and create if not found.

Returns:

the entity retrieved from the persistent storage, either found or created.

load

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
FactorValue load(Long id)

Description copied from interface: BaseReadOnlyService

Loads object with given ID.

Specified by:

load in interface BaseReadOnlyService<FactorValue>

Parameters:

id - the ID of entity to be loaded.

Returns:

the entity with matching ID, or null if the entity does not exist or if the passed ID was null

loadWithExperimentalFactor

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
FactorValue loadWithExperimentalFactor(Long id)

loadWithExperimentalFactorOrFail

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
FactorValue loadWithExperimentalFactorOrFail(Long id)

Load a FactorValue with an initialized experimental factor or fail.

loadWithOldStyleCharacteristics

@Nullable
@Deprecated
@Secured("GROUP_ADMIN")
FactorValue loadWithOldStyleCharacteristics(Long id,
                                            boolean readOnly)

Deprecated.

do not use this, it is only meant for the purpose of migrating old-style characteristics to statements

Load a FactorValue along with its old-style characteristics.

loadIdsWithNumberOfOldStyleCharacteristics

@Deprecated
@Secured("GROUP_ADMIN")
Map<Long,Integer> loadIdsWithNumberOfOldStyleCharacteristics(Set<Long> excludedIds)

Deprecated.

do not use, this is only for migrating old-style characteristics to statements and will be removed

See Also:

FactorValueDao.loadIdsWithNumberOfOldStyleCharacteristics(Set)

remove

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void remove(FactorValue factorValue)

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<FactorValue>

Parameters:

factorValue - the entity to be removed.

createStatement

@CheckReturnValue
@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
Statement createStatement(FactorValue factorValue,
                          Statement statement)

Create a given statement and add it to the given factor value.

Parameters:

factorValue - the factor value to add the statement to

statement - the statement to be created and added to the factor value

Returns:

the created statement

Throws:

IllegalArgumentException - if the statement already exists

saveStatement

@CheckReturnValue
@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
Statement saveStatement(FactorValue fv,
                        Statement statement)

Create a given statement as per createStatement(FactorValue, Statement) if it is transient, otherwise update an existing statement.

saveStatementIgnoreAcl

@Deprecated
@CheckReturnValue
@Secured("GROUP_ADMIN")
Statement saveStatementIgnoreAcl(FactorValue fv,
                                 Statement statement)

Deprecated.

do not use this, it is meant for FactorValue migration only

Save a statement ignoring ACLs.

This requires the GROUP_ADMIN authority.

removeStatement

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeStatement(FactorValue fv,
                     Statement c)

Remove a statement from a factor value.

update

@Secured({"GROUP_USER","ACL_SECURABLE_COLLECTION_EDIT"})
void update(Collection<FactorValue> factorValues)

Description copied from interface: BaseService

Updates all entities in the given collection in the persistent storage.

Specified by:

update in interface BaseService<FactorValue>

Parameters:

factorValues - the entities to be updated.

update

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void update(FactorValue factorValue)

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<FactorValue>

Parameters:

factorValue - the entity to be updated.

markAsNeedsAttention

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void markAsNeedsAttention(FactorValue factorValue,
                          String note)

Mark a given factor value as needs attention.

Parameters:

factorValue - a factor value to mark as needs attention

note - note to use for the FactorValueNeedsAttentionEvent

Throws:

IllegalArgumentException - if the factor value already needs attention

clearNeedsAttentionFlag

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void clearNeedsAttentionFlag(FactorValue factorValue,
                             String note)

Clear a needs attention flag on a given factor value.

Parameters:

factorValue - a factor value whose needs flag will be cleared

note - a note to use for the DoesNotNeedAttentionEvent if the dataset does not need attention for any other reason.

Throws:

IllegalArgumentException - if the factor value does not need attention