org.molgenis.ontology.matching

Class OntologyServiceImpl

java.lang.Object

org.molgenis.ontology.matching.OntologyServiceImpl

All Implemented Interfaces:

OntologyService

public class OntologyServiceImpl
extends Object
implements OntologyService

Field Summary

Fields

Modifier and Type	Field and Description
static String	COMBINED_SCORE
static String	DEFAULT_MATCHING_IDENTIFIER
static String	DEFAULT_MATCHING_NAME_FIELD
static String	DEFAULT_MATCHING_SYNONYM_FIELD
static Character	DEFAULT_SEPARATOR
static String	SCORE
static String	SIGNIFICANT_VALUE

Constructor Summary

Constructors

Constructor and Description
OntologyServiceImpl(DataService dataService, SearchService searchService, InformationContentService informationContentService)

Method Summary

Modifier and Type	Method and Description
Iterable<OntologyTerm>	findOntologyTerms(String queryTerm, String ontologyIri)
Iterable<Ontology>	getAllOntologies()
Iterable<Entity>	getAllOntologyEntities()
Iterable<Entity>	getAllOntologyTermEntities(String ontologyIri)
Iterable<OntologyTerm>	getAllOntologyTerms(String ontologyIri)
Iterable<Entity>	getChildOntologyTermEntities(String ontologyIri, String ontologyTermIri)
Iterable<OntologyTerm>	getChildOntologyTerms(String ontologyIri, String ontologyTermIri)
Ontology	getOntology(String ontologyIri)
Entity	getOntologyEntity(String ontologyIri)
OntologyTerm	getOntologyTerm(String ontologyTermIri, String ontologyIri)
Entity	getOntologyTermEntity(String ontologyTermIri, String ontologyIri)
List<String>	getOntologyTermSynonyms(String ontologyTermIri, String ontologyIri)
Iterable<Entity>	getRootOntologyTermEntities(String ontologyIri)
Iterable<OntologyTerm>	getRootOntologyTerms(String ontologyIri)
String	removeIllegalCharWithEmptyString(String string)
String	removeIllegalCharWithSingleWhiteSpace(String string)
OntologyServiceResult	search(String ontologyUrl, String queryString)
OntologyServiceResult	searchEntity(String ontologyIri, Entity inputEntity)

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_FIELD

public static final String DEFAULT_MATCHING_SYNONYM_FIELD

See Also:

Constant Field Values

DEFAULT_MATCHING_IDENTIFIER

public static final String DEFAULT_MATCHING_IDENTIFIER

See Also:

Constant Field Values

SCORE

public static final String SCORE

See Also:

Constant Field Values

COMBINED_SCORE

public static final String COMBINED_SCORE

See Also:

Constant Field Values

Constructor Detail

OntologyServiceImpl

@Autowired
public OntologyServiceImpl(DataService dataService,
                                      SearchService searchService,
                                      InformationContentService informationContentService)

Method Detail

getAllOntologies

public Iterable<Ontology> getAllOntologies()

Specified by:

getAllOntologies in interface OntologyService

Returns:

a list of all available ontologies

getAllOntologyEntities

public Iterable<Entity> getAllOntologyEntities()

Specified by:

getAllOntologyEntities in interface OntologyService

Returns:

a list of untyped ontology entities

getOntology

public Ontology getOntology(String ontologyIri)

Specified by:

getOntology in interface OntologyService

Returns:

an ontology based on the ontologyIri

getOntologyEntity

public Entity getOntologyEntity(String ontologyIri)

Specified by:

getOntologyEntity in interface OntologyService

Returns:

an untyped ontology based on the ontologyIri

findOntologyTerms

public Iterable<OntologyTerm> findOntologyTerms(String queryTerm,
                                                String ontologyIri)

Specified by:

findOntologyTerms in interface OntologyService

Returns:

a list of ontology terms sorted based on the relevance

getOntologyTerm

public OntologyTerm getOntologyTerm(String ontologyTermIri,
                                    String ontologyIri)

Specified by:

getOntologyTerm in interface OntologyService

Returns:

an ontologyTerm based on specified ontologyTermIri in particular ontology

getOntologyTermEntity

public Entity getOntologyTermEntity(String ontologyTermIri,
                                    String ontologyIri)

Specified by:

getOntologyTermEntity in interface OntologyService

Returns:

an untyped ontologyTerm entity based on specified ontologyTermIri in particular ontology

getOntologyTermSynonyms

public List<String> getOntologyTermSynonyms(String ontologyTermIri,
                                            String ontologyIri)

Specified by:

getOntologyTermSynonyms in interface OntologyService

Returns:

a list of synonyms for ontology term provided

getAllOntologyTerms

public Iterable<OntologyTerm> getAllOntologyTerms(String ontologyIri)

Specified by:

getAllOntologyTerms in interface OntologyService

Returns:

a list of ontologyterms from specified ontology

getAllOntologyTermEntities

public Iterable<Entity> getAllOntologyTermEntities(String ontologyIri)

Specified by:

getAllOntologyTermEntities in interface OntologyService

Returns:

a list of untyped ontologyterm entities from specified ontology

getRootOntologyTerms

public Iterable<OntologyTerm> getRootOntologyTerms(String ontologyIri)

Specified by:

getRootOntologyTerms in interface OntologyService

Returns:

a list of root ontologyterms from specified ontology

getRootOntologyTermEntities

public Iterable<Entity> getRootOntologyTermEntities(String ontologyIri)

Specified by:

getRootOntologyTermEntities in interface OntologyService

Returns:

a list of untyped root ontologyterm entities from specified ontology

getChildOntologyTerms

public Iterable<OntologyTerm> getChildOntologyTerms(String ontologyIri,
                                                    String ontologyTermIri)

Specified by:

getChildOntologyTerms in interface OntologyService

Returns:

a list of child ontologyTerms from current ontologyTerm in specified ontology

getChildOntologyTermEntities

public Iterable<Entity> getChildOntologyTermEntities(String ontologyIri,
                                                     String ontologyTermIri)

Specified by:

getChildOntologyTermEntities in interface OntologyService

Returns:

a list of untyped child ontologyTerm entities from current ontologyTerm in specified ontology

searchEntity

public OntologyServiceResult searchEntity(String ontologyIri,
                                          Entity inputEntity)

Specified by:

searchEntity in interface OntologyService

inputEntity - input for storing the query information

Returns:

a list of relevant ontologyTerms based on the given input stored in an entity

search

public OntologyServiceResult search(String ontologyUrl,
                                    String queryString)

Specified by:

search in interface OntologyService

Returns:

a list of relevant ontologyTerms based on give queryString

removeIllegalCharWithSingleWhiteSpace

public String removeIllegalCharWithSingleWhiteSpace(String string)

removeIllegalCharWithEmptyString

public String removeIllegalCharWithEmptyString(String string)