org.phenotips.vocabulary.script

Class OntologyScriptService

java.lang.Object

org.phenotips.vocabulary.script.OntologyScriptService

All Implemented Interfaces:

org.xwiki.script.service.ScriptService

Deprecated.

use $services.vocabularies instead

@Deprecated
 @Component
 @Named(value="ontologies")
 @Singleton
public class OntologyScriptService
extends Object
implements org.xwiki.script.service.ScriptService

Provides access to the available vocabularies and their terms to public scripts. This is a deprecated service still present for backwards compatibility reasons, please use $services.vocabulary instead.

Since:

1.2M4 (under a different package since 1.0M8)

Version:

$Id: f29a3f9f1985feee31fb9a506d2a5012e949f743 $

Constructor Summary

Constructors

Constructor and Description
OntologyScriptService() Deprecated.

Method Summary

Modifier and Type	Method and Description
Vocabulary	get(String vocabularyId) Deprecated. use $services.vocabularies.get instead
Vocabulary	getOntology(String vocabularyId) Deprecated. use $services.vocabularies.getVocabulary instead
VocabularyTerm	resolveTerm(String termId) Deprecated. use $services.vocabularies.resolveTerm instead

Methods inherited from class java.lang.Object

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

Constructor Detail

OntologyScriptService

public OntologyScriptService()

Deprecated.

Method Detail

resolveTerm

@Deprecated
public VocabularyTerm resolveTerm(String termId)

Deprecated. use $services.vocabularies.resolveTerm instead

Retrieve a term from its owner vocabulary. For this to work properly, the term identifier must contain a known vocabulary prefix.

Parameters:

termId - the term identifier, in the format <vocabulary prefix>:<term id>, for example HP:0002066

Returns:

the requested term, or null if the term doesn't exist in the vocabulary, or no matching vocabulary is available

getOntology

@Deprecated
public Vocabulary getOntology(String vocabularyId)

Deprecated. use $services.vocabularies.getVocabulary instead

Retrieve a vocabulary given its identifier.

Parameters:

vocabularyId - the vocabulary identifier, which is also used as a prefix in every term identifier from that vocabulary, or a known alias for it, for example MIM, hpo, HP or HPO

Returns:

the requested vocabulary, or null if it doesn't exist or isn't available in the platform

get

@Deprecated
public Vocabulary get(String vocabularyId)

Deprecated. use $services.vocabularies.get instead

Retrieve a vocabulary given its identifier. This is a shortcut for getOntology(String) which allows scripts to use the shorter $services.ontologies.hpo notation for accessing a vocabulary.

Parameters:

vocabularyId - the vocabulary identifier, which is also used as a prefix in every term identifier from that vocabulary, or a known alias for it, for example MIM, HP or HPO

Returns:

the requested vocabulary, or null if it doesn't exist or isn't available in the platform