Package ubic.gemma.core.ontology.providers

Class OntologyServiceFactory<T extends OntologyService>

java.lang.Object

org.springframework.beans.factory.config.AbstractFactoryBean<T>

ubic.gemma.core.ontology.providers.OntologyServiceFactory<T>

Type Parameters:

T - the type of ontology service this factory produces

All Implemented Interfaces:

org.springframework.beans.factory.Aware, org.springframework.beans.factory.BeanClassLoaderAware, org.springframework.beans.factory.BeanFactoryAware, org.springframework.beans.factory.DisposableBean, org.springframework.beans.factory.FactoryBean<T>, org.springframework.beans.factory.InitializingBean

public class OntologyServiceFactory<T extends OntologyService>
extends org.springframework.beans.factory.config.AbstractFactoryBean<T>

Factory bean for baseCode's OntologyService.

Field Summary

Fields inherited from class org.springframework.beans.factory.config.AbstractFactoryBean

logger

Constructor Summary

Constructors

Constructor	Description
OntologyServiceFactory(Class<T> ontologyServiceClass)	Create a factory for an ontology service class.
OntologyServiceFactory(T ontologyService)	Create a factory for a pre-existing ontology service.

Method Summary

Modifier and Type	Method	Description
protected T	createInstance()
protected void	destroyInstance(T instance)
Class<?>	getObjectType()
boolean	isSingleton()
void	setAdditionalPropertyUris(Set<String> additionalPropertyUris)	Set the URIs used for inferring additional properties.
void	setAllowedUriPrefixes(String[] allowedUriPrefixes)	Set the URI prefixes that can be returned from the ontology.
void	setAutoLoad(boolean autoLoad)	Enable loading of ontologies on startup.
void	setEnableSearch(boolean enableSearch)	Enable full-text search for the ontology.
void	setExcludedWordsFromStemming(Set<String> excludedWordsFromStemming)	Set the list of words that should be excluded from stemming.
void	setForceIndexing(boolean forceIndexing)	Force indexing for full-text search.
void	setForceLoad(boolean forceLoad)	Force loading, regardless of the load.{name}Ontology property value.
void	setInferenceMode(OntologyService.InferenceMode inferenceMode)	Set the inference mode for the ontology.
void	setLanguageLevel(OntologyService.LanguageLevel languageLevel)	Set the supported OWL language level for the ontology.
void	setLoadInBackground(boolean loadInBackground)	Initialize the service using a background thread.
void	setProcessImports(boolean processImports)	Enable import processing for the ontology.
void	setTaskExecutor(org.springframework.core.task.TaskExecutor taskExecutor)	Set the task executor used for initializing ontology service in background.

Methods inherited from class org.springframework.beans.factory.config.AbstractFactoryBean

afterPropertiesSet, destroy, getBeanFactory, getBeanTypeConverter, getEarlySingletonInterfaces, getObject, setBeanClassLoader, setBeanFactory, setSingleton

Methods inherited from class java.lang.Object

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

Constructor Details

OntologyServiceFactory

public OntologyServiceFactory(Class<T> ontologyServiceClass)

Create a factory for an ontology service class.

The class must have a no-arg constructor.

OntologyServiceFactory

public OntologyServiceFactory(T ontologyService)

Create a factory for a pre-existing ontology service.

Method Details

setAutoLoad

public void setAutoLoad(boolean autoLoad)

Enable loading of ontologies on startup.

setForceLoad

public void setForceLoad(boolean forceLoad)

Force loading, regardless of the load.{name}Ontology property value.

setForceIndexing

public void setForceIndexing(boolean forceIndexing)

Force indexing for full-text search.

setLoadInBackground

public void setLoadInBackground(boolean loadInBackground)

Initialize the service using a background thread.

If an executor is supplied via setTaskExecutor(TaskExecutor), it will be used for initializing the ontology, otherwise one thread per ontology will be created via OntologyService.startInitializationThread(boolean, boolean).

If false, the ontology will be initialized in the foreground. This will dramatically impact the startup time of Gemma.

See Also:

• OntologyService.startInitializationThread(boolean, boolean)
• OntologyService.initialize(boolean, boolean)

setTaskExecutor

public void setTaskExecutor(org.springframework.core.task.TaskExecutor taskExecutor)

Set the task executor used for initializing ontology service in background.

setLanguageLevel

public void setLanguageLevel(OntologyService.LanguageLevel languageLevel)

Set the supported OWL language level for the ontology.

See Also:

• OntologyService.setLanguageLevel(OntologyService.LanguageLevel)

setInferenceMode

public void setInferenceMode(OntologyService.InferenceMode inferenceMode)

Set the inference mode for the ontology.

See Also:

• OntologyService.setInferenceMode(OntologyService.InferenceMode)

setEnableSearch

public void setEnableSearch(boolean enableSearch)

Enable full-text search for the ontology.

See Also:

• OntologyService.setSearchEnabled(boolean)

setExcludedWordsFromStemming

public void setExcludedWordsFromStemming(@Nullable
 Set<String> excludedWordsFromStemming)

Set the list of words that should be excluded from stemming.

See Also:

• OntologyService.setExcludedWordsFromStemming(Set)

setProcessImports

public void setProcessImports(boolean processImports)

Enable import processing for the ontology.

See Also:

• OntologyService.setProcessImports(boolean)

setAdditionalPropertyUris

public void setAdditionalPropertyUris(@Nullable
 Set<String> additionalPropertyUris)

Set the URIs used for inferring additional properties.

If null, baseCode's defaults will be used. You may use an empty set to disable additional properties inference.

See Also:

• OntologyService.setAdditionalPropertyUris(Set)

setAllowedUriPrefixes

public void setAllowedUriPrefixes(@Nullable
 String[] allowedUriPrefixes)

Set the URI prefixes that can be returned from the ontology.

See Also:

• OntologyService.setAllowedUriPrefixes(String...)

getObjectType

public Class<?> getObjectType()

Specified by:

getObjectType in interface org.springframework.beans.factory.FactoryBean<T extends OntologyService>

Specified by:

getObjectType in class org.springframework.beans.factory.config.AbstractFactoryBean<T extends OntologyService>

isSingleton

public boolean isSingleton()

Specified by:

isSingleton in interface org.springframework.beans.factory.FactoryBean<T extends OntologyService>

Overrides:

isSingleton in class org.springframework.beans.factory.config.AbstractFactoryBean<T extends OntologyService>

createInstance

protected T createInstance()
                    throws Exception

Specified by:

createInstance in class org.springframework.beans.factory.config.AbstractFactoryBean<T extends OntologyService>

Throws:

Exception

destroyInstance

protected void destroyInstance(T instance)
                        throws Exception

Overrides:

destroyInstance in class org.springframework.beans.factory.config.AbstractFactoryBean<T extends OntologyService>

Throws:

Exception