Class AbstractDao<T extends Identifiable>

java.lang.Object
ubic.gemma.persistence.service.AbstractDao<T>
All Implemented Interfaces:
BaseDao<T>
Direct Known Subclasses:
AbstractDesignElementDataVectorDao, AbstractVoEnabledDao, AnnotationAssociationDaoImpl, AnnotationRelationDaoImpl, AnnotationSetDaoImpl, AnnotationSetDispositionDaoImpl, AnnotationSetTriageDaoImpl, AuditEventDaoImpl, AuditTrailDaoImpl, BlatAssociationDaoImpl, ChromosomeDaoImpl, CompoundDaoImpl, ContactDaoImpl, CurationDecisionDaoImpl, DifferentialExpressionResultDaoImpl, ExperimentalDesignDaoImpl, ExpressionExperimentSubSetDaoImpl, ExternalDatabaseDaoImpl, Gene2GOAssociationDaoImpl, GeneAliasDaoImpl, GeneDiffExMetaAnalysisDaoImpl, GeneSetDaoImpl, GeneSetMemberDaoImpl, PersonDaoImpl, PipelineJobBatchDaoImpl, PipelineJobDaoImpl, PipelineJobEventDaoImpl, PrincipalComponentAnalysisDaoImpl, ProtocolDaoImpl, PublicationAssociationDaoImpl, ReferenceAssociationDaoImpl, SingleCellDimensionExperimentDaoImpl, StatementDaoImpl, TicketDaoImpl, UnitDaoImpl, UserDaoImpl, UserGroupDaoImpl
public abstract class AbstractDao<T extends Identifiable> extends Object implements BaseDao<T>
AbstractDao finds the generic type at runtime and provides default BaseDao implementations on top of SessionFactory.
Author:
Anton, Nicolas

  • Field Details

    • log

      protected final org.apache.commons.logging.Log log

  • Constructor Details

    • AbstractDao

      protected AbstractDao(Class<? extends T> elementClass, SessionFactory sessionFactory)

  • Method Details

    • getElementClass

      public Class<? extends T> getElementClass()
      Description copied from interface: BaseDao
      Obtain the element class of T.
      Specified by:
      getElementClass in interface BaseDao<T extends Identifiable>

    • getEntityName

      protected String getEntityName()

    • getIdentifierPropertyName

      protected String getIdentifierPropertyName()

    • create

      public Collection<T> create(Collection<T> entities)
      Description copied from interface: BaseDao
      Create all the given entities in the persistent storage.
      Specified by:
      create in interface BaseDao<T extends Identifiable>
      Parameters:
      entities - the entities to be crated.
      Returns:
      collection of entities representing the entities in the persistent storage that were created.

    • create

      @OverridingMethodsMustInvokeSuper public T create(T entity)
      Description copied from interface: BaseDao
      Create an entity in the persistent storage.
      Specified by:
      create in interface BaseDao<T extends Identifiable>
      Parameters:
      entity - the entity to create
      Returns:
      the persistent version of the entity
      See Also:

    • save

      public Collection<T> save(Collection<T> entities)
      Description copied from interface: BaseDao
      Create (if transient) or update all the given entities in the persistent storage.

      Unlike BaseDao.update(Collection), this method does not attach the given entities to the persistence context; the returned values must be used instead.

      Specified by:
      save in interface BaseDao<T extends Identifiable>
      See Also:

    • save

      @OverridingMethodsMustInvokeSuper public T save(T entity)
      Description copied from interface: BaseDao
      Create (if transient) or update an entity.

      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<T extends Identifiable>
      See Also:

    • load

      public Collection<T> load(Collection<Long> ids)
      Description copied from interface: BaseDao
      Loads entities with given ids form the persistent storage.
      Specified by:
      load in interface BaseDao<T extends Identifiable>
      Parameters:
      ids - the IDs of entities to be loaded. If some IDs are not found or null, they are skipped.
      Returns:
      collection of entities with given ids.
      See Also:

    • load

      public T load(Long id)
      Description copied from interface: BaseDao
      Loads the entity with given id from the persistent storage.
      Specified by:
      load in interface BaseDao<T extends Identifiable>
      Parameters:
      id - the id of entity to load.
      Returns:
      the entity with given ID, or null if such entity does not exist or if the passed ID was null
      See Also:

    • loadAll

      public Collection<T> loadAll()
      Description copied from interface: BaseDao
      Loads all entities of type T from the persistent storage.
      Specified by:
      loadAll in interface BaseDao<T extends Identifiable>
      Returns:
      a collection containing all entities that are currently accessible.

    • loadReference

      public Collection<T> loadReference(Collection<Long> ids)
      Description copied from interface: BaseDao
      Load references of entities of type T for all the given IDs.

      Entities already in the current session will be returned directly.

      Specified by:
      loadReference in interface BaseDao<T extends Identifiable>

    • loadReference

      @NonNull public T loadReference(Long id)
      Description copied from interface: BaseDao
      Load reference for an entity.

      If the entity is already in the session, it will be returned instead. Note that unlike BaseDao.load(Long), this method will not return null if the entity does not exist.

      You may freely access the Identifiable.getId() field without triggering proxy initialization.

      Specified by:
      loadReference in interface BaseDao<T extends Identifiable>
      See Also:

    • reload

      @NonNull public T reload(T entity)
      Description copied from interface: BaseDao
      Reload an entity from the persistent storage.

      This does nothing if the entity is already in the session.

      Specified by:
      reload in interface BaseDao<T extends Identifiable>

    • reload

      @NonNull public Collection<T> reload(Collection<T> entities)
      Description copied from interface: BaseDao
      Reload an entity from the persistent storage.

      This does nothing for entities already in the session.

      Specified by:
      reload in interface BaseDao<T extends Identifiable>

    • countAll

      public long countAll()
      Description copied from interface: BaseDao
      Counts all entities of T in the persistent storage.
      Specified by:
      countAll in interface BaseDao<T extends Identifiable>
      Returns:
      number that is the amount of entities currently accessible.

    • streamAll

      public Stream<T> streamAll()
      Description copied from interface: BaseDao
      Stream all entities of T from the persistent storage.

      Note that the stream will only be valid while the current database session is active. To create a stream that can outlive the current session, use BaseDao.streamAll(boolean) passing true.

      Specified by:
      streamAll in interface BaseDao<T extends Identifiable>

    • streamAll

      public Stream<T> streamAll(boolean createNewSession)
      Description copied from interface: BaseDao
      Stream all entities of type T from the persistent storage.

      If creating a new session, the caller is responsible for closing the stream to avoid resource leaks. It is recommended to use try-with-resource statement.

      Specified by:
      streamAll in interface BaseDao<T extends Identifiable>
      Parameters:
      createNewSession - whether to create a new session for the stream, it will be closed when the stream is closed

    • streamQuery

      protected <U> Stream<U> streamQuery(Function<Session, org.hibernate.query.Query<?>> queryCreator, Class<U> resultType, int fetchSize, boolean useCursorFetchIfSupported, boolean isStateless, boolean createNewSession)
      Produce a stream over a Query with a new session if desired.

    • remove

      public void remove(Collection<T> entities)
      Description copied from interface: BaseDao
      Remove all given persistent entities.
      Specified by:
      remove in interface BaseDao<T extends Identifiable>

    • remove

      @OverridingMethodsMustInvokeSuper public void remove(T entity)
      Description copied from interface: BaseDao
      Remove a persistent entity.
      Specified by:
      remove in interface BaseDao<T extends Identifiable>
      Parameters:
      entity - the entity to be removed

    • update

      public void update(Collection<T> entities)
      Description copied from interface: BaseDao
      Update the given entities.

      Not supported if the entity is immutable or loaded in read-only mode.

      Specified by:
      update in interface BaseDao<T extends Identifiable>

    • update

      @OverridingMethodsMustInvokeSuper public void update(T entity)
      Description copied from interface: BaseDao
      Update the given entity.

      Not supported if the entity is immutable or loaded in read-only mode.

      Specified by:
      update in interface BaseDao<T extends Identifiable>

    • find

      public T find(T entity)
      Description copied from interface: BaseDao
      Does a look-up for the given entity in the persistent storage, usually looking for a specific identifier if Identifiable.getId() is set or a business key.
      Specified by:
      find in interface BaseDao<T extends Identifiable>
      Parameters:
      entity - the entity to look for.
      Returns:
      an entity that was found in the persistent storage, or null if no such entity was found.

    • findOrCreate

      public T findOrCreate(T entity)
      Description copied from interface: BaseDao
      Calls the BaseDao.find(Identifiable) method, and if this method returns null, creates a new entity in the persistent storage pas per BaseDao.create(Identifiable).
      Specified by:
      findOrCreate in interface BaseDao<T extends Identifiable>
      Parameters:
      entity - the entity to look for and persist if not found.
      Returns:
      the given entity, guaranteed to be representing an entity present in the persistent storage.

    • getSessionFactory

      protected final SessionFactory getSessionFactory()

    • getBatchSize

      protected final int getBatchSize()

    • findOneByProperty

      @Nullable protected T findOneByProperty(String propertyName, Object propertyValue)

    • findIdByProperty

      @Nullable protected Long findIdByProperty(String propertyName, Object propertyValue)

    • findByProperty

      protected List<T> findByProperty(String propertyName, Object propertyValue)

    • findByPropertyIn

      protected List<T> findByPropertyIn(String propertyName, Collection<?> propertyValues)