Package ubic.gemma.persistence.service

Class AbstractQueryFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>

java.lang.Object

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

ubic.gemma.persistence.service.AbstractVoEnabledDao<O,VO>

ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao<O,VO>

ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao<O,VO>

All Implemented Interfaces:

org.springframework.beans.factory.InitializingBean, BaseDao<O>, BaseVoEnabledDao<O,VO>, CachedFilteringDao<O>, CachedFilteringVoEnabledDao<O,VO>, FilteringDao<O>, FilteringVoEnabledDao<O,VO>

Direct Known Subclasses:

AbstractCuratableDao, CompositeSequenceDaoImpl, GeneDaoImpl, TaxonDaoImpl

public abstract class AbstractQueryFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>
extends AbstractFilteringVoEnabledDao<O,VO>
implements CachedFilteringVoEnabledDao<O,VO>

Partial implementation of FilteringVoEnabledDao based on the Hibernate Query API.

Author:

poirigui

See Also:

• for utilities to generate HQL clauses from a Filters
• for utilities to generate ACL clauses to filter VOs by ACL at the database-level
• as an alternative

Nested Class Summary

Nested classes/interfaces inherited from class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao

AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer, AbstractFilteringVoEnabledDao.FilterablePropertyMeta

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

Modifier	Constructor	Description
protected	AbstractQueryFilteringVoEnabledDao(String objectAlias, Class<O> elementClass, SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
long	count(Filters filters)	Count VOs matching the given filters.
long	countWithCache(Filters filters)
protected TypedResultTransformer<O>	getEntityTransformer()	Obtain an entity transformer for the results of getFilteringQuery(Filters, Sort).
protected Query	getFilteringCountQuery(Filters filters)	Produce a query that will be used to retrieve the size of getFilteringQuery(Filters, Sort).
protected Query	getFilteringIdQuery(Filters filters, Sort sort)	Produce a query that will be used to retrieve IDs of getFilteringQuery(Filters, Sort).
protected abstract Query	getFilteringQuery(Filters filters, Sort sort)	Produce a query for retrieving value objects after applying a set of filters and a given ordering.
protected TypedResultTransformer<VO>	getValueObjectTransformer()	Obtain a value object transformer for the results of getFilteringQuery(Filters, Sort).
protected abstract void	initializeCachedFilteringResult(O cachedEntity)	Initialize a result from getFilteringQuery(Filters, Sort) retrieved from the Hibernate StandardQueryCache.
List<O>	load(Filters filters, Sort sort)	Load entities matching the given filters.
Slice<O>	load(Filters filters, Sort sort, int offset, int limit)	Load a slice of entities matching the given filters.
List<Long>	loadIds(Filters filters, Sort sort)	Load IDs of entities matching the given filters.
List<Long>	loadIdsWithCache(Filters filters, Sort sort)
List<VO>	loadValueObjects(Filters filters, Sort sort)	Load VOs with minimal ordering and filtering.
Slice<VO>	loadValueObjects(Filters filters, Sort sort, int offset, int limit)	Load VOs with ordering, filtering and offset/limit.
List<VO>	loadValueObjectsWithCache(Filters filters, Sort sort)
Slice<VO>	loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
List<O>	loadWithCache(Filters filters, Sort sort)
Slice<O>	loadWithCache(Filters filters, Sort sort, int offset, int limit)

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

afterPropertiesSet, configureFilterableProperties, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyMeta, getFilterablePropertyMeta, getFilterablePropertyType, getSort

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

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

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

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

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyType, getSort

Constructor Details

AbstractQueryFilteringVoEnabledDao

protected AbstractQueryFilteringVoEnabledDao(String objectAlias,
 Class<O> elementClass,
 SessionFactory sessionFactory)

Method Details

getFilteringQuery

protected abstract Query getFilteringQuery(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Produce a query for retrieving value objects after applying a set of filters and a given ordering.

Note that if your implementation does not produce a List of AbstractQueryFilteringVoEnabledDao when Query.list() is invoked, you must override getValueObjectTransformer().

The make the cached query (i.e. loadWithCache(Filters, Sort) behave the same, you also have to explicitly initialize any lazy relations in AbstractVoEnabledDao.doLoadValueObject(Identifiable) because the VO constructor will not initialize them.

Returns:

a Query that produce a list of AbstractQueryFilteringVoEnabledDao

initializeCachedFilteringResult

protected abstract void initializeCachedFilteringResult(O cachedEntity)

Initialize a result from getFilteringQuery(Filters, Sort) retrieved from the Hibernate StandardQueryCache.

Lazy-loaded relations that are fetched in getFilteringQuery(Filters, Sort) must be initialized manually in this method to ensure that the entity has all the expected fields if they are retrieved from the second-level cache.

getFilteringIdQuery

protected Query getFilteringIdQuery(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Produce a query that will be used to retrieve IDs of getFilteringQuery(Filters, Sort).

getFilteringCountQuery

protected Query getFilteringCountQuery(@Nullable
 Filters filters)

Produce a query that will be used to retrieve the size of getFilteringQuery(Filters, Sort).

Returns:

a Query which must return a single Long value

getEntityTransformer

protected TypedResultTransformer<O> getEntityTransformer()

Obtain an entity transformer for the results of getFilteringQuery(Filters, Sort).

The default entity transformer simply returns the first element of the tuple and omit null values.

getValueObjectTransformer

protected TypedResultTransformer<VO> getValueObjectTransformer()

Obtain a value object transformer for the results of getFilteringQuery(Filters, Sort).

By default, it will process the first element of the tuple with AbstractVoEnabledDao.doLoadValueObjects(Collection) and then post-process the resulting VOs with AbstractVoEnabledDao.postProcessValueObjects(List).

loadIds

public List<Long> loadIds(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Description copied from interface: FilteringDao

Load IDs of entities matching the given filters.

Specified by:

loadIds in interface FilteringDao<O extends Identifiable>

loadIdsWithCache

public List<Long> loadIdsWithCache(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Specified by:

loadIdsWithCache in interface CachedFilteringDao<O extends Identifiable>

See Also:

• FilteringDao.loadIds(Filters, Sort)

load

public List<O> load(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Description copied from interface: FilteringDao

Load entities matching the given filters.

Specified by:

load in interface FilteringDao<O extends Identifiable>

loadWithCache

public Slice<O> loadWithCache(@Nullable
 Filters filters,
 @Nullable
 Sort sort,
 int offset,
 int limit)

Specified by:

loadWithCache in interface CachedFilteringDao<O extends Identifiable>

See Also:

• FilteringDao.load(Filters, Sort, int, int)

load

public Slice<O> load(@Nullable
 Filters filters,
 @Nullable
 Sort sort,
 int offset,
 int limit)

Description copied from interface: FilteringDao

Load a slice of entities matching the given filters.

Specified by:

load in interface FilteringDao<O extends Identifiable>

loadWithCache

public List<O> loadWithCache(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Specified by:

loadWithCache in interface CachedFilteringDao<O extends Identifiable>

See Also:

• FilteringDao.load(Filters, Sort)

loadValueObjects

public Slice<VO> loadValueObjects(@Nullable
 Filters filters,
 @Nullable
 Sort sort,
 int offset,
 int limit)

Description copied from interface: FilteringVoEnabledDao

Load VOs with ordering, filtering and offset/limit.

Consider using FilteringDao.getFilter(String, Filter.Operator, String) and FilteringDao.getSort(String, Sort.Direction, Sort.NullMode) to produce the filters and sort safely from user input.

Specified by:

loadValueObjects in interface FilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>

Parameters:

filters - filters applied on the search. The properties mentioned in the Filter must exist and be visible to Hibernate. You can use nested properties such as "curationDetails.lastUpdated".

sort - an object property and direction to order by. This property must exist and be visible to Hibernate. You can use nested properties such as "curationDetails.lastUpdated".

offset - an offset from which entities are retrieved when sorted according to the sort argument, or 0 to ignore

limit - a limit on the number of returned results, or -1 to ignore

Returns:

a slice of the relevant data

See Also:

• FilteringDao.load(Filters, Sort, int, int)

loadValueObjectsWithCache

public Slice<VO> loadValueObjectsWithCache(@Nullable
 Filters filters,
 @Nullable
 Sort sort,
 int offset,
 int limit)

Specified by:

loadValueObjectsWithCache in interface CachedFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>

loadValueObjects

public List<VO> loadValueObjects(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Description copied from interface: FilteringVoEnabledDao

Load VOs with minimal ordering and filtering.

Use this as an alternative to FilteringVoEnabledDao.loadValueObjects(Filters, Sort, int, int) if you do not intend to provide pagination capabilities.

Specified by:

loadValueObjects in interface FilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>

See Also:

• FilteringDao.load(Filters, Sort)
• FilteringVoEnabledDao.loadValueObjects(Filters, Sort, int, int)

loadValueObjectsWithCache

public List<VO> loadValueObjectsWithCache(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Specified by:

loadValueObjectsWithCache in interface CachedFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>

count

public long count(@Nullable
 Filters filters)

Description copied from interface: FilteringDao

Count VOs matching the given filters.

Specified by:

count in interface FilteringDao<O extends Identifiable>

countWithCache

public long countWithCache(@Nullable
 Filters filters)

Specified by:

countWithCache in interface CachedFilteringDao<O extends Identifiable>

See Also:

• FilteringDao.count(Filters)