Package ubic.gemma.core.ontology

Class OntologyUtils

java.lang.Object

ubic.gemma.core.ontology.OntologyUtils

public class OntologyUtils
extends Object

Utilities for working with ontologies.

Author:

poirigui

Field Summary

Fields

Modifier and Type	Field	Description
static final String	BASE_PURL_URI	Base URI used by PURL ontologies.

Constructor Summary

Constructors

Constructor	Description
OntologyUtils()

Method Summary

Modifier and Type	Method	Description
static void	ensureInitialized(OntologyService service)	Ensure that a given ontology is initialized, force-loading it via OntologyService.initialize(boolean, boolean) if necessary.
static void	ensureInitialized(OntologyService service, OntologyService.InferenceMode mode, OntologyService.LanguageLevel level, Boolean searchEnabled, Boolean processImports)	Ensure that a given ontology is initialized, force-loading it via OntologyService.initialize(boolean, boolean), but first setting how we load it.
static void	ensureInitializedLite(OntologyService service)	Ensure that a given ontology is initialized, force-loading it via OntologyService.initialize(boolean, boolean), but setting the language level to LITE, Inferencing to NONE, processImports to false, and enable search to false, if the ontology isn't already loaded.

Methods inherited from class java.lang.Object

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

Field Details

BASE_PURL_URI

public static final String BASE_PURL_URI

Base URI used by PURL ontologies.

Read more about PURL here.

See Also:

• Constant Field Values

Constructor Details

OntologyUtils

public OntologyUtils()

Method Details

ensureInitialized

public static void ensureInitialized(OntologyService service)
                              throws InterruptedException

Ensure that a given ontology is initialized, force-loading it via OntologyService.initialize(boolean, boolean) if necessary.

If the ontology was started via OntologyService.startInitializationThread(boolean, boolean), this method will patiently wait until it completes.

Throws:

InterruptedException - in case the ontology initialization thread is started, we will wait which implies a possible interrupt

ensureInitializedLite

public static void ensureInitializedLite(OntologyService service)
                                  throws InterruptedException

Ensure that a given ontology is initialized, force-loading it via OntologyService.initialize(boolean, boolean), but setting the language level to LITE, Inferencing to NONE, processImports to false, and enable search to false, if the ontology isn't already loaded.

Throws:

InterruptedException

ensureInitialized

public static void ensureInitialized(OntologyService service,
 OntologyService.InferenceMode mode,
 OntologyService.LanguageLevel level,
 Boolean searchEnabled,
 Boolean processImports)
                              throws InterruptedException

Ensure that a given ontology is initialized, force-loading it via OntologyService.initialize(boolean, boolean), but first setting how we load it. However, those parameters are ignored if the ontology is already loaded or in progress.

Throws:

InterruptedException - in case the ontology initialization thread is started, we will wait which implies a possible interrupt