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

Class SortaServiceImpl

java.lang.Object

org.molgenis.ontology.sorta.service.impl.SortaServiceImpl

All Implemented Interfaces:

SortaService

public class SortaServiceImpl
extends Object
implements SortaService

Field Summary

Fields

Modifier and Type	Field	Description
static String	DEFAULT_MATCHING_IDENTIFIER
static String	DEFAULT_MATCHING_NAME_FIELD
static String	DEFAULT_MATCHING_SYNONYM_PREFIX_FIELD
static Character	DEFAULT_SEPARATOR
static String	SIGNIFICANT_VALUE

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
Iterable<org.molgenis.data.Entity>	findOntologyTermEntities(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.
Iterable<org.molgenis.data.Entity>	getAllOntologyEntities()	Get all ontology entities in generic type
org.molgenis.data.Entity	getOntologyEntity(String ontologyIri)	Get a specified ontology entity in generic type based on the given ontologyIri
org.molgenis.data.Entity	getOntologyTermEntity(String ontologyTermIri, 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 String SIGNIFICANT_VALUE

See Also:

Constant Field Values

DEFAULT_SEPARATOR

public static final Character DEFAULT_SEPARATOR

DEFAULT_MATCHING_NAME_FIELD

public static final String DEFAULT_MATCHING_NAME_FIELD

See Also:

Constant Field Values

DEFAULT_MATCHING_SYNONYM_PREFIX_FIELD

public static final String DEFAULT_MATCHING_SYNONYM_PREFIX_FIELD

See Also:

Constant Field Values

DEFAULT_MATCHING_IDENTIFIER

public static final 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 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(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(String ontologyTermIri,
                                                      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 Iterable<org.molgenis.data.Entity> findOntologyTermEntities(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