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

Interface FactorValueService

All Superinterfaces:
BaseImmutableService<FactorValue>, BaseReadOnlyService<FactorValue>, BaseService<FactorValue>, BaseVoEnabledService<FactorValue,FactorValueValueObject>, FilteringService<FactorValue>, FilteringVoEnabledService<FactorValue,FactorValueValueObject>
All Known Implementing Classes:
FactorValueServiceImpl
public interface FactorValueService extends BaseService<FactorValue>, FilteringVoEnabledService<FactorValue,FactorValueValueObject>
Author:
kelsey

  • Method Details

    • findByValue

      @Deprecated @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"}) Collection<FactorValue> findByValue(String valuePrefix, int maxResults)
      Deprecated.

    • findOrCreate

      @Secured({"GROUP_USER","AFTER_ACL_READ"}) FactorValue findOrCreate(FactorValue factorValue)
      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<FactorValue>
      Parameters:
      factorValue - 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_READ"}) FactorValue load(Long id)
      Description copied from interface: BaseReadOnlyService
      Loads object with given ID.
      Specified by:
      load in interface BaseReadOnlyService<FactorValue>
      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

    • loadWithExperimentalFactor

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"}) FactorValue loadWithExperimentalFactor(Long id)

    • loadWithExperimentalFactorOrFail

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"}) FactorValue loadWithExperimentalFactorOrFail(Long id)
      Load a FactorValue with an initialized experimental factor or fail.

    • loadWithOldStyleCharacteristics

      @Nullable @Deprecated @Secured("GROUP_ADMIN") FactorValue loadWithOldStyleCharacteristics(Long id, boolean readOnly)
      Deprecated.
      do not use this, it is only meant for the purpose of migrating old-style characteristics to statements
      Load a FactorValue along with its old-style characteristics.

    • loadIdsWithNumberOfOldStyleCharacteristics

      @Deprecated @Secured("GROUP_ADMIN") Map<Long,Integer> loadIdsWithNumberOfOldStyleCharacteristics(Set<Long> excludedIds)
      Deprecated.
      do not use, this is only for migrating old-style characteristics to statements and will be removed
      See Also:

    • remove

      @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) void remove(FactorValue factorValue)
      Description copied from interface: BaseImmutableService
      Removes the given entity from the persistent storage.
      Specified by:
      remove in interface BaseImmutableService<FactorValue>
      Parameters:
      factorValue - the entity to be removed.

    • createStatement

      @CheckReturnValue @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) Statement createStatement(FactorValue factorValue, Statement statement)
      Create a given statement and add it to the given factor value.
      Parameters:
      factorValue - the factor value to add the statement to
      statement - the statement to be created and added to the factor value
      Returns:
      the created statement
      Throws:
      IllegalArgumentException - if the statement already exists

    • saveStatement

      @CheckReturnValue @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) Statement saveStatement(FactorValue fv, Statement statement)
      Create a given statement as per createStatement(FactorValue, Statement) if it is transient, otherwise update an existing statement.

    • saveStatementIgnoreAcl

      @Deprecated @CheckReturnValue @Secured("GROUP_ADMIN") Statement saveStatementIgnoreAcl(FactorValue fv, Statement statement)
      Deprecated.
      do not use this, it is meant for FactorValue migration only
      Save a statement ignoring ACLs.

      This requires the GROUP_ADMIN authority.

    • removeStatement

      @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) void removeStatement(FactorValue fv, Statement c)
      Remove a statement from a factor value.

    • update

      @Secured({"GROUP_USER","ACL_SECURABLE_COLLECTION_EDIT"}) void update(Collection<FactorValue> factorValues)
      Description copied from interface: BaseService
      Updates all entities in the given collection in the persistent storage.
      Specified by:
      update in interface BaseService<FactorValue>
      Parameters:
      factorValues - the entities to be updated.

    • update

      @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) void update(FactorValue factorValue)
      Description copied from interface: BaseService
      Updates the given entity in the persistent storage.
      Specified by:
      update in interface BaseService<FactorValue>
      Parameters:
      factorValue - the entity to be updated.

    • markAsNeedsAttention

      @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) void markAsNeedsAttention(FactorValue factorValue, String note)
      Mark a given factor value as needs attention.
      Parameters:
      factorValue - a factor value to mark as needs attention
      note - note to use for the FactorValueNeedsAttentionEvent
      Throws:
      IllegalArgumentException - if the factor value already needs attention

    • clearNeedsAttentionFlag

      @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) void clearNeedsAttentionFlag(FactorValue factorValue, String note)
      Clear a needs attention flag on a given factor value.
      Parameters:
      factorValue - a factor value whose needs flag will be cleared
      note - a note to use for the DoesNotNeedAttentionEvent if the dataset does not need attention for any other reason.
      Throws:
      IllegalArgumentException - if the factor value does not need attention