Package ubic.gemma.persistence.service.expression.bioAssay

Interface BioAssayService

All Superinterfaces:
BaseImmutableService<BioAssay>, BaseReadOnlyService<BioAssay>, BaseService<BioAssay>, BaseVoEnabledService<BioAssay,BioAssayValueObject>, FilteringService<BioAssay>, FilteringVoEnabledService<BioAssay,BioAssayValueObject>
All Known Implementing Classes:
BioAssayServiceImpl
@Service public interface BioAssayService extends BaseService<BioAssay>, FilteringVoEnabledService<BioAssay,BioAssayValueObject>
Author:
kelsey

  • Method Details

    • addBioMaterialAssociation

      @PreAuthorize("hasPermission(#bioAssay, \'write\') or hasPermission(#bioAssay, \'administration\')") void addBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial)
      Associates a bioMaterial with a specified bioAssay.
      Parameters:
      bioAssay - bio assay
      bioMaterial - bio material

    • findBioAssayDimensions

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) Collection<BioAssayDimension> findBioAssayDimensions(BioAssay bioAssay)
      Locate all BioAssayDimensions in which the selected BioAssay occurs
      Parameters:
      bioAssay - bio assay
      Returns:
      bio assay dimensions

    • findByShortName

      @Nullable @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"}) BioAssay findByShortName(String shortName)

    • findByAccession

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"}) Collection<BioAssay> findByAccession(String accession)
      Parameters:
      accession - eg GSM12345.
      Returns:
      BioAssays that match based on the plain accession (unconstrained by ExternalDatabase).

    • findSubBioAssays

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"}) Collection<BioAssay> findSubBioAssays(BioAssay bioAssay, boolean direct)
      See Also:

    • findSiblings

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"}) Collection<BioAssay> findSiblings(BioAssay bioAssay)

    • findOrCreate

      @Secured({"GROUP_USER","AFTER_ACL_READ"}) BioAssay findOrCreate(BioAssay bioAssay)
      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<BioAssay>
      Parameters:
      bioAssay - the entity to look for, and create if not found.
      Returns:
      the entity retrieved from the persistent storage, either found or created.

    • create

      @Secured("GROUP_USER") BioAssay create(BioAssay bioAssay)
      Description copied from interface: BaseImmutableService
      Creates the given entity in the persistent storage.
      Specified by:
      create in interface BaseImmutableService<BioAssay>
      Parameters:
      bioAssay - the entity to be created.
      Returns:
      object referencing the persistent instance of the given entity.

    • load

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"}) Collection<BioAssay> load(Collection<Long> ids)
      Description copied from interface: BaseReadOnlyService
      Loads objects with given ids.
      Specified by:
      load in interface BaseReadOnlyService<BioAssay>
      Parameters:
      ids - the ids of objects to be loaded.
      Returns:
      collection containing object with given IDs.

    • load

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"}) BioAssay load(Long id)
      Description copied from interface: BaseReadOnlyService
      Loads object with given ID.
      Specified by:
      load in interface BaseReadOnlyService<BioAssay>
      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

    • loadAll

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"}) Collection<BioAssay> loadAll()
      Description copied from interface: BaseReadOnlyService
      Loads all the entities of specific type.
      Specified by:
      loadAll in interface BaseReadOnlyService<BioAssay>
      Returns:
      collection of all entities currently available in the persistent storage.

    • remove

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

    • update

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

    • getBioAssaySets

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"}) Collection<BioAssaySet> getBioAssaySets(BioAssay bioAssay)
      Obtain all the BioAssaySet that contain the given BioAssay.

    • removeBioMaterialAssociation

      @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) void removeBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial)
      Removes the association between a specific bioMaterial and a bioAssay.
      Parameters:
      bioAssay - bio assay
      bioMaterial - bio material

    • thaw

      @CheckReturnValue @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) BioAssay thaw(BioAssay bioAssay)

    • thaw

      @CheckReturnValue @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"}) Collection<BioAssay> thaw(Collection<BioAssay> bioAssays)

    • loadValueObjects

      List<BioAssayValueObject> loadValueObjects(Collection<BioAssay> entities, @Nullable Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
      See Also: