Package ubic.gemma.persistence.service.genome.taxon

Interface TaxonService

All Superinterfaces:
BaseImmutableService<Taxon>, BaseReadOnlyService<Taxon>, BaseVoEnabledService<Taxon,TaxonValueObject>, FilteringService<Taxon>, FilteringVoEnabledService<Taxon,TaxonValueObject>
All Known Implementing Classes:
TaxonServiceImpl
public interface TaxonService extends BaseImmutableService<Taxon>, FilteringVoEnabledService<Taxon,TaxonValueObject>
Author:
kelsey

  • Method Details

    • findByCommonName

      Taxon findByCommonName(String commonName)

    • findByScientificName

      Taxon findByScientificName(String scientificName)

    • findByNcbiId

      Taxon findByNcbiId(Integer ncbiId)

    • findOrCreate

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

    • remove

      @Secured("GROUP_USER") void remove(Collection<Taxon> entities)
      Description copied from interface: BaseImmutableService
      Removes all the given entities from persistent storage.
      Specified by:
      remove in interface BaseImmutableService<Taxon>
      Parameters:
      entities - the entities to be removed.

    • remove

      @Secured("GROUP_ADMIN") void remove(Long id)
      Description copied from interface: BaseImmutableService
      Removes the entity with given ID from the persistent storage.
      Specified by:
      remove in interface BaseImmutableService<Taxon>
      Parameters:
      id - the ID of entity to be removed.

    • remove

      @Secured("GROUP_USER") void remove(Taxon taxon)
      Description copied from interface: BaseImmutableService
      Removes the given entity from the persistent storage.
      Specified by:
      remove in interface BaseImmutableService<Taxon>
      Parameters:
      taxon - the entity to be removed.

    • loadAllTaxaWithGenes

      Collection<Taxon> loadAllTaxaWithGenes()
      Returns:
      Taxon that have genes loaded into Gemma and that should be used

    • getTaxaWithGenes

      Collection<TaxonValueObject> getTaxaWithGenes()
      Returns:
      Taxon that have genes loaded into Gemma and that should be used

    • getTaxaWithDatasets

      Collection<TaxonValueObject> getTaxaWithDatasets()
      Returns:
      collection of taxa that have expression experiments available.

    • getTaxaWithArrays

      Collection<TaxonValueObject> getTaxaWithArrays()
      Returns:
      List of taxa with array designs in gemma

    • updateGenesUsable

      void updateGenesUsable(Taxon taxon, boolean isGenesUsable)