ubic.basecode.ontology.providers

Class AbstractOntologyMemoryBackedService

java.lang.Object

ubic.basecode.ontology.providers.AbstractOntologyService

ubic.basecode.ontology.providers.AbstractOntologyMemoryBackedService

Direct Known Subclasses:

CellLineOntologyService, CellTypeOntologyService, ChebiOntologyService, DiseaseOntologyService, ExperimentalFactorOntologyService, FMAOntologyService, HumanDevelopmentOntologyService, HumanPhenotypeOntologyService, MammalianPhenotypeOntologyService, MedicOntologyService, MouseDevelopmentOntologyService, NIFSTDOntologyService, ObiService, SequenceOntologyService, UberonOntologyService, UnitsOntologyService

public abstract class AbstractOntologyMemoryBackedService
extends AbstractOntologyService

This class has some stuff that's specific to in-memory ontologies. Unlike database backed ontologies we don't use a pool keeping only one instance of model in memory.

Author:

paul

Nested Class Summary

Nested classes/interfaces inherited from class ubic.basecode.ontology.providers.AbstractOntologyService

AbstractOntologyService.OntologyInitializationThread

Field Summary

Fields inherited from class ubic.basecode.ontology.providers.AbstractOntologyService

cacheReady, index, indexReady, individuals, initializationThread, isInitialized, log, model, modelReady, terms

Constructor Summary

Constructors

Constructor and Description
AbstractOntologyMemoryBackedService()

Method Summary

Modifier and Type	Method and Description
protected com.hp.hpl.jena.ontology.OntModel	loadModel() Delegates the call as to load the model into memory or leave it on disk.
void	loadTermsInNameSpace(InputStream is, boolean forceIndex) For testing!

Methods inherited from class ubic.basecode.ontology.providers.AbstractOntologyService

addTerms, closeIndex, findIndividuals, findResources, findTerm, findUsingAlternativeId, getAllURIs, getModel, getOntologyName, getOntologyUrl, getResource, getTerm, getTermIndividuals, index, isEnabled, isInitializationThreadAlive, isOntologyLoaded, loadTermsInNameSpace, startInitializationThread

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractOntologyMemoryBackedService

public AbstractOntologyMemoryBackedService()

Method Detail

loadTermsInNameSpace

public void loadTermsInNameSpace(InputStream is,
                                 boolean forceIndex)

For testing! Overrides normal way of loading the ontology. This does not index the ontology unless 'force' is true (if there is an existing index, it will be used)

Parameters:

is -

forceIndex - initialize the index. Otherwise it will only be initialized if it doesn't exist.

Throws:

IOException

loadModel

protected com.hp.hpl.jena.ontology.OntModel loadModel()

Description copied from class: AbstractOntologyService

Delegates the call as to load the model into memory or leave it on disk. Simply delegates to either OntologyLoader.loadMemoryModel( url ); OR OntologyLoader.loadPersistentModel( url, spec );

Specified by:

loadModel in class AbstractOntologyService

Returns: