Package org.molgenis.ontology.sorta.service.impl

Class SortaServiceImpl

  • All Implemented Interfaces:
    SortaService
    public class SortaServiceImpl
extends java.lang.Object
implements SortaService

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.lang.Iterable<org.molgenis.data.Entity> findOntologyTermEntities​(java.lang.String ontologyIri, org.molgenis.data.Entity inputEntity)
      Find a list of relevant ontologyterm typed entities using lexical matching (elasticsearch + ngram) in generic type based on given ontologyIri and a set of query inputs (name, synonym, ontology database id, e.g.
      java.lang.Iterable<org.molgenis.data.Entity> getAllOntologyEntities()
      Get all ontology entities in generic type
      org.molgenis.data.Entity getOntologyEntity​(java.lang.String ontologyIri)
      Get a specified ontology entity in generic type based on the given ontologyIri
      org.molgenis.data.Entity getOntologyTermEntity​(java.lang.String ontologyTermIri, java.lang.String ontologyIri)
      Get a specified ontologyterm in generic type based on the given ontologyIri and ontologyTermIri

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • SIGNIFICANT_VALUE

        public static final java.lang.String SIGNIFICANT_VALUE
        See Also:
        Constant Field Values

      • DEFAULT_SEPARATOR

        public static final java.lang.Character DEFAULT_SEPARATOR

      • DEFAULT_MATCHING_NAME_FIELD

        public static final java.lang.String DEFAULT_MATCHING_NAME_FIELD
        See Also:
        Constant Field Values

      • DEFAULT_MATCHING_SYNONYM_PREFIX_FIELD

        public static final java.lang.String DEFAULT_MATCHING_SYNONYM_PREFIX_FIELD
        See Also:
        Constant Field Values

      • DEFAULT_MATCHING_IDENTIFIER

        public static final java.lang.String DEFAULT_MATCHING_IDENTIFIER
        See Also:
        Constant Field Values

    • Constructor Detail

      • SortaServiceImpl

        public SortaServiceImpl​(org.molgenis.data.DataService dataService,
                        InformationContentService informationContentService,
                        OntologyTermHitMetaData ontologyTermHitMetaData,
                        org.molgenis.ontology.core.meta.OntologyTermSynonymFactory ontologyTermSynonymFactory)

    • Method Detail

      • getAllOntologyEntities

        public java.lang.Iterable<org.molgenis.data.Entity> getAllOntologyEntities()
        Description copied from interface: SortaService
        Get all ontology entities in generic type
        Specified by:
        getAllOntologyEntities in interface SortaService
        Returns:
        list of untyped ontology entities

      • getOntologyEntity

        public org.molgenis.data.Entity getOntologyEntity​(java.lang.String ontologyIri)
        Description copied from interface: SortaService
        Get a specified ontology entity in generic type based on the given ontologyIri
        Specified by:
        getOntologyEntity in interface SortaService
        Returns:
        specified ontology entity in generic type

      • getOntologyTermEntity

        public org.molgenis.data.Entity getOntologyTermEntity​(java.lang.String ontologyTermIri,
                                                      java.lang.String ontologyIri)
        Description copied from interface: SortaService
        Get a specified ontologyterm in generic type based on the given ontologyIri and ontologyTermIri
        Specified by:
        getOntologyTermEntity in interface SortaService
        Returns:
        specifieid ontologyterm entity in a generic type

      • findOntologyTermEntities

        public java.lang.Iterable<org.molgenis.data.Entity> findOntologyTermEntities​(java.lang.String ontologyIri,
                                                                             org.molgenis.data.Entity inputEntity)
        Description copied from interface: SortaService
        Find a list of relevant ontologyterm typed entities using lexical matching (elasticsearch + ngram) in generic type based on given ontologyIri and a set of query inputs (name, synonym, ontology database id, e.g. hpo, omim)
        Specified by:
        findOntologyTermEntities in interface SortaService
        Returns:
        a list of ontologyterm entities in generic type