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

Interface ExperimentalFactorService

All Superinterfaces:

BaseImmutableService<ExperimentalFactor>, BaseReadOnlyService<ExperimentalFactor>, BaseService<ExperimentalFactor>, BaseVoEnabledService<ExperimentalFactor,ExperimentalFactorValueObject>

All Known Implementing Classes:

ExperimentalFactorServiceImpl

public interface ExperimentalFactorService
extends BaseService<ExperimentalFactor>, BaseVoEnabledService<ExperimentalFactor,ExperimentalFactorValueObject>

Author:

paul

Field Summary

Fields

Modifier and Type	Field	Description
static String	BATCH_FACTOR_CATEGORY_NAME
static String	BATCH_FACTOR_CATEGORY_URI
static String	BATCH_FACTOR_NAME
static String	BATCH_FACTOR_NAME_PREFIX
static String	FACTOR_VALUE_RNAME_PREFIX

Method Summary

Modifier and Type	Method	Description
ExperimentalFactor	find(ExperimentalFactor experimentalFactor)	Does a search for the entity in the persistent storage
ExperimentalFactor	findOrCreate(ExperimentalFactor experimentalFactor)	Does a search for the entity in the persistent storage, and if not found, creates it.
ExperimentalFactor	load(Long id)	Loads object with given ID.
Collection<ExperimentalFactor>	load(Collection<Long> ids)	Loads objects with given ids.
Collection<ExperimentalFactor>	loadAll()	Loads all the entities of specific type.
void	remove(Long id)	Removes the entity with given ID from the persistent storage.
void	remove(Collection<ExperimentalFactor> entities)	Removes all the given entities from persistent storage.
void	remove(ExperimentalFactor experimentalFactor)	Delete the factor, its associated factor values and all differential expression analyses in which it is used.
ExperimentalFactor	thaw(ExperimentalFactor ef)
void	update(Collection<ExperimentalFactor> entities)	Updates all entities in the given collection in the persistent storage.
void	update(ExperimentalFactor experimentalFactor)	Updates the given entity in the persistent storage.

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

create, create

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

countAll, findOrFail, getElementClass, 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

Field Detail

BATCH_FACTOR_NAME_PREFIX

static final String BATCH_FACTOR_NAME_PREFIX

See Also:

Constant Field Values

BATCH_FACTOR_CATEGORY_URI

static final String BATCH_FACTOR_CATEGORY_URI

See Also:

Constant Field Values

BATCH_FACTOR_CATEGORY_NAME

static final String BATCH_FACTOR_CATEGORY_NAME

See Also:

Constant Field Values

BATCH_FACTOR_NAME

static final String BATCH_FACTOR_NAME

See Also:

Constant Field Values

FACTOR_VALUE_RNAME_PREFIX

static final String FACTOR_VALUE_RNAME_PREFIX

See Also:

Constant Field Values

Method Detail

remove

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void remove(ExperimentalFactor experimentalFactor)

Delete the factor, its associated factor values and all differential expression analyses in which it is used.

Specified by:

remove in interface BaseImmutableService<ExperimentalFactor>

Parameters:

experimentalFactor - the factor to be deleted

remove

@Secured({"GROUP_USER","ACL_SECURABLE_COLLECTION_EDIT"})
void remove(Collection<ExperimentalFactor> entities)

Description copied from interface: BaseImmutableService

Removes all the given entities from persistent storage.

Specified by:

remove in interface BaseImmutableService<ExperimentalFactor>

Parameters:

entities - the entities to be removed.

remove

@Secured("GROUP_ADMIN")
void remove(Long id)

Description copied from interface: BaseImmutableService

Removes the entity with given ID from the persistent storage.

Specified by:

remove in interface BaseImmutableService<ExperimentalFactor>

Parameters:

id - the ID of entity to be removed.

find

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
ExperimentalFactor find(ExperimentalFactor experimentalFactor)

Description copied from interface: BaseReadOnlyService

Does a search for the entity in the persistent storage

Specified by:

find in interface BaseReadOnlyService<ExperimentalFactor>

Parameters:

experimentalFactor - the entity to be searched for

Returns:

the version of entity retrieved from the persistent storage, if found, otherwise null.

findOrCreate

@Secured({"GROUP_USER","AFTER_ACL_READ"})
ExperimentalFactor findOrCreate(ExperimentalFactor experimentalFactor)

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<ExperimentalFactor>

Parameters:

experimentalFactor - 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_COLLECTION_READ"})
Collection<ExperimentalFactor> load(Collection<Long> ids)

Description copied from interface: BaseReadOnlyService

Loads objects with given ids.

Specified by:

load in interface BaseReadOnlyService<ExperimentalFactor>

Parameters:

ids - the ids of objects to be loaded.

Returns:

collection containing object with given IDs.

load

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

Description copied from interface: BaseReadOnlyService

Loads object with given ID.

Specified by:

load in interface BaseReadOnlyService<ExperimentalFactor>

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

loadAll

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExperimentalFactor> loadAll()

Description copied from interface: BaseReadOnlyService

Loads all the entities of specific type.

Specified by:

loadAll in interface BaseReadOnlyService<ExperimentalFactor>

Returns:

collection of all entities currently available in the persistent storage.

update

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void update(ExperimentalFactor experimentalFactor)

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<ExperimentalFactor>

Parameters:

experimentalFactor - the entity to be updated.

update

@Secured({"GROUP_USER","ACL_SECURABLE_COLLECTION_EDIT"})
void update(Collection<ExperimentalFactor> entities)

Description copied from interface: BaseService

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

Specified by:

update in interface BaseService<ExperimentalFactor>

Parameters:

entities - the entities to be updated.

thaw

ExperimentalFactor thaw(ExperimentalFactor ef)