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

Class FactorValueDaoImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractDao<FactorValue>

ubic.gemma.persistence.service.AbstractVoEnabledDao<FactorValue,FactorValueValueObject>

ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao<FactorValue,FactorValueValueObject>

ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl

All Implemented Interfaces:

BaseDao<FactorValue>, BaseVoEnabledDao<FactorValue,FactorValueValueObject>, FactorValueDao, FilteringDao<FactorValue>, FilteringVoEnabledDao<FactorValue,FactorValueValueObject>

@Repository
public class FactorValueDaoImpl
extends AbstractNoopFilteringVoEnabledDao<FactorValue,FactorValueValueObject>
implements FactorValueDao

Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.expression.experiment.FactorValue.

Field Summary

Fields inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao

REPORT_SLOW_QUERY_AFTER_MS

Fields inherited from class ubic.gemma.persistence.service.AbstractDao

log

Constructor Summary

Constructors

Constructor	Description
FactorValueDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
FactorValue	create(FactorValue factorValue)	Create an object.
protected FactorValueValueObject	doLoadValueObject(FactorValue entity)	Load a value object for a given entity.
FactorValue	find(FactorValue factorValue)	Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).
Collection<FactorValue>	findByValueStartingWith(String valuePrefix, int maxResults)	Locate based on string value of the value.
Map<FactorValue,Characteristic>	getExperimentalFactorCategories(Collection<FactorValue> factorValues)
Map<FactorValue,ExpressionExperiment>	getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)
Slice<FactorValue>	loadAll(int offset, int limit)	Load a slice of FactorValues.
Collection<Long>	loadAllIds()	Load all factor value IDs.
Slice<Long>	loadAllIds(int offset, int limit)	Load a slice of the factor values IDs.
Map<Long,Integer>	loadIdsWithNumberOfOldStyleCharacteristics(Set<Long> excludedIds)	Deprecated.
FactorValue	loadWithOldStyleCharacteristics(Long id, boolean readOnly)	Deprecated.
void	remove(FactorValue factorValue)	Remove a persistent instance
FactorValue	save(FactorValue entity)	Create or update an entity whether it is transient.
void	update(FactorValue entity)
void	updateIgnoreAcl(FactorValue fv)	Update a FactorValue without involving ACL advice.

Methods inherited from class ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, load, load, loadIds, loadValueObjects, loadValueObjects

Methods inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao

doLoadValueObjects, loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds, postProcessValueObjects

Methods inherited from class ubic.gemma.persistence.service.AbstractDao

countAll, create, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getEntityName, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, streamAll, streamAll, streamQuery, update

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

countAll, create, findOrCreate, getElementClass, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, streamAll, streamAll, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, load, load, loadIds

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

loadValueObjects, loadValueObjects

Constructor Details

FactorValueDaoImpl

@Autowired
public FactorValueDaoImpl(SessionFactory sessionFactory)

Method Details

create

public FactorValue create(FactorValue factorValue)

Description copied from interface: BaseDao

Create an object. If the entity type is immutable, this may also remove any existing entities identified by an appropriate 'find' method.

Specified by:

create in interface BaseDao<FactorValue>

Overrides:

create in class AbstractDao<FactorValue>

Parameters:

factorValue - the entity to create

Returns:

the persistent version of the entity

save

public FactorValue save(FactorValue entity)

Description copied from interface: BaseDao

Create or update an entity whether it is transient.

Unlike BaseDao.update(Identifiable), this method does not attach the given entity to the persistence context and the returned value must be used instead.

Specified by:

save in interface BaseDao<FactorValue>

Overrides:

save in class AbstractDao<FactorValue>

See Also:

• Session.persist(Object)
• Session.merge(Object)

update

public void update(FactorValue entity)

Specified by:

update in interface BaseDao<FactorValue>

Overrides:

update in class AbstractDao<FactorValue>

Parameters:

entity - Update the entity. Not supported if the entity is immutable.

loadAll

public Slice<FactorValue> loadAll(int offset,
 int limit)

Description copied from interface: FactorValueDao

Load a slice of FactorValues.

Results are filtered by ACL on the owning ExpressionExperiment.

Specified by:

loadAll in interface FactorValueDao

loadAllIds

public Collection<Long> loadAllIds()

Description copied from interface: FactorValueDao

Load all factor value IDs.

Results are filtered by ACL on the owning ExpressionExperiment.

Specified by:

loadAllIds in interface FactorValueDao

loadAllIds

public Slice<Long> loadAllIds(int offset,
 int limit)

Description copied from interface: FactorValueDao

Load a slice of the factor values IDs.

Results are filtered by ACL on the owning ExpressionExperiment.

Specified by:

loadAllIds in interface FactorValueDao

findByValueStartingWith

public Collection<FactorValue> findByValueStartingWith(String valuePrefix,
 int maxResults)

Description copied from interface: FactorValueDao

Locate based on string value of the value.

Results are filtered by ACL on the owning ExpressionExperiment.

Specified by:

findByValueStartingWith in interface FactorValueDao

Parameters:

valuePrefix - value prefix

maxResults - maximum number of results to return, or -1 for no limit

Returns:

collection of factor values

loadWithOldStyleCharacteristics

@Deprecated
public FactorValue loadWithOldStyleCharacteristics(Long id,
 boolean readOnly)

Deprecated.

Specified by:

loadWithOldStyleCharacteristics in interface FactorValueDao

loadIdsWithNumberOfOldStyleCharacteristics

@Deprecated
public Map<Long,Integer> loadIdsWithNumberOfOldStyleCharacteristics(Set<Long> excludedIds)

Deprecated.

Description copied from interface: FactorValueDao

Load all the factor values IDs with their number of old-style characteristics.

Specified by:

loadIdsWithNumberOfOldStyleCharacteristics in interface FactorValueDao

Parameters:

excludedIds - list of excluded IDs

getExperimentalFactorCategories

public Map<FactorValue,Characteristic> getExperimentalFactorCategories(Collection<FactorValue> factorValues)

Specified by:

getExperimentalFactorCategories in interface FactorValueDao

getExpressionExperimentsIgnoreAcls

public Map<FactorValue,ExpressionExperiment> getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)

Specified by:

getExpressionExperimentsIgnoreAcls in interface FactorValueDao

updateIgnoreAcl

public void updateIgnoreAcl(FactorValue fv)

Description copied from interface: FactorValueDao

Update a FactorValue without involving ACL advice.

Specified by:

updateIgnoreAcl in interface FactorValueDao

remove

public void remove(@Nullable
 FactorValue factorValue)

Description copied from interface: BaseDao

Remove a persistent instance

Specified by:

remove in interface BaseDao<FactorValue>

Overrides:

remove in class AbstractDao<FactorValue>

Parameters:

factorValue - the entity to be removed

find

public FactorValue find(FactorValue factorValue)

Description copied from interface: BaseDao

Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).

Specified by:

find in interface BaseDao<FactorValue>

Overrides:

find in class AbstractDao<FactorValue>

Parameters:

factorValue - the entity to look for.

Returns:

an entity that was found in the persistent storage, or null if no such entity was found.

doLoadValueObject

protected FactorValueValueObject doLoadValueObject(FactorValue entity)

Description copied from class: AbstractVoEnabledDao

Load a value object for a given entity.

This should be fast and efficient, and avoid any database query or post-processing. If you need to perform additional queries, implement AbstractVoEnabledDao.postProcessValueObjects(List) instead.

Specified by:

doLoadValueObject in class AbstractVoEnabledDao<FactorValue,FactorValueValueObject>