Interface TaxonService

    • Method Detail

      • findByCommonName

        Taxon findByCommonName​(String commonName)
      • findByScientificName

        Taxon findByScientificName​(String scientificName)
      • 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_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.
      • update

        @Secured("GROUP_USER")
        void update​(Collection<Taxon> entities)
        Description copied from interface: BaseService
        Updates all entities in the given collection in the persistent storage.
        Specified by:
        update in interface BaseService<Taxon>
        Parameters:
        entities - the entities to be updated.
      • update

        @Secured("GROUP_USER")
        void update​(Taxon taxon)
        Description copied from interface: BaseService
        Updates the given entity in the persistent storage.
        Specified by:
        update in interface BaseService<Taxon>
        Parameters:
        taxon - the entity to be updated.
      • 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.