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 Hibernate Query.

Author:

poirigui

Nested Class Summary

Nested classes/interfaces inherited from class AbstractFilteringVoEnabledDao

AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer, AbstractFilteringVoEnabledDao.FilterablePropertyMeta

Nested classes/interfaces inherited from interface FilteringDao

FilteringDao.ConjunctSpec

Field Summary

Fields inherited from class AbstractVoEnabledDao

REPORT_SLOW_QUERY_AFTER_MS

Fields inherited from class 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()
protected org.hibernate.query.Query<?>	getFilteringCountQuery(Filters filters)
protected org.hibernate.query.Query<?>	getFilteringIdQuery(Filters filters, Sort sort)
protected abstract org.hibernate.query.Query<?>	getFilteringQuery(Filters filters, Sort sort)	Produce a query for retrieving filtered entities or VOs after applying filters and ordering.
protected String	getQueryCacheRegion()	Name of the Hibernate L2 query-cache region to use for filtered-VO queries from this DAO, or null to use Hibernate's default StandardQueryCache region.
protected TypedResultTransformer<VO>	getValueObjectTransformer()
protected abstract void	initializeCachedFilteringResult(O cachedEntity)	Initialize a result from getFilteringQuery(Filters, Sort) retrieved from cache.
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.
CursorPage<VO>	loadValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Load VOs by keyset (cursor) pagination.
CursorPage<VO>	loadValueObjectsByCursorWithCache(Filters filters, Sort sort, Cursor cursor, int limit)	Cursor-paged sister of loadValueObjectsWithCache(Filters, Sort, int, int).
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 AbstractFilteringVoEnabledDao

afterPropertiesSet, configureFilterableProperties, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyMeta, getFilterablePropertyObjectAliases, getFilterablePropertyType, getObjectAlias, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, resolveFilterablePropertyMeta, resolveFilterablePropertyMeta

Methods inherited from class AbstractVoEnabledDao

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

Methods inherited from class AbstractDao

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

Methods inherited from class Object

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

Methods inherited from interface BaseDao

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

Methods inherited from interface BaseVoEnabledDao

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface FilteringDao

getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery

Constructor Details

AbstractQueryFilteringVoEnabledDao

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

Method Details

getFilteringQuery

protected abstract org.hibernate.query.Query<?> getFilteringQuery(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Produce a query for retrieving filtered entities or VOs after applying filters and ordering.

The query is expected to return a List of O. Implementations that return tuples should also override getValueObjectTransformer().

initializeCachedFilteringResult

protected abstract void initializeCachedFilteringResult(O cachedEntity)

Initialize a result from getFilteringQuery(Filters, Sort) retrieved from cache. Lazy-loaded relations fetched by the filtering query must be initialized here so that VOs populated from the second-level cache have the expected fields.

getFilteringIdQuery

protected org.hibernate.query.Query<?> getFilteringIdQuery(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

getFilteringCountQuery

protected org.hibernate.query.Query<?> getFilteringCountQuery(@Nullable
 Filters filters)

getQueryCacheRegion

@Nullable
protected String getQueryCacheRegion()

Name of the Hibernate L2 query-cache region to use for filtered-VO queries from this DAO, or null to use Hibernate's default StandardQueryCache region.

Subclasses with a hot filter path (e.g. ExpressionExperimentDaoImpl) override this to shard their cache entries into a dedicated, separately-bounded region declared in EhcacheConfig. Shared sharding here is safe because each subclass's getFilteringQuery(Filters, Sort) already produces type-specific HQL — there is no risk of two DAO types colliding on the same cache key.

Default: null (fall back to StandardQueryCache). See HIBERNATE_L2_CACHE_AUDIT.md recommendation #4 for context.

getEntityTransformer

protected TypedResultTransformer<O> getEntityTransformer()

getValueObjectTransformer

protected TypedResultTransformer<VO> getValueObjectTransformer()

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>>

loadValueObjectsByCursor

public CursorPage<VO> loadValueObjectsByCursor(@Nullable
 Filters filters,
 Sort sort,
 @Nullable
 Cursor cursor,
 int limit)

Description copied from interface: FilteringVoEnabledDao

Load VOs by keyset (cursor) pagination.

Cursor pagination avoids the O(N) scan-and-discard cost of FilteringVoEnabledDao.loadValueObjects(Filters, Sort, int, int) on deep pages and is drift-resistant under concurrent inserts (a row inserted into the middle of the sorted order between two page requests will not produce duplicates or skips at the page boundary).

Sort requirements. The resolved Sort must be deterministic, i.e. it must end with a unique key (typically the identifier property). Initial support is limited to a single sort component on the identifier property (+id / -id); compound sorts are intentionally rejected until the index audit (recce §5.1) has been completed for the sorting columns of interest.

When cursor is null, the page returned is the first page in the sort order, with a non-null CursorPage.getNextCursor() if more rows exist.

Specified by:

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

Parameters:

filters - filters applied on the search; same shape as FilteringVoEnabledDao.loadValueObjects(Filters, Sort, int, int)

sort - deterministic sort (must end in a unique key); must not be null for cursor mode

cursor - the cursor token decoded from a previous response, or null to fetch the first page

limit - page size; the implementation fetches one additional row internally to detect whether a next page exists, but the returned page contains at most limit rows

Returns:

a CursorPage with the rows, the nextCursor (or null at the end of the collection), prevCursor (when known), and a totalElements of null (cursor mode does not count by default)

loadValueObjectsByCursorWithCache

public CursorPage<VO> loadValueObjectsByCursorWithCache(@Nullable
 Filters filters,
 Sort sort,
 @Nullable
 Cursor cursor,
 int limit)

Cursor-paged sister of loadValueObjectsWithCache(Filters, Sort, int, int).

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)