ubic.basecode.ontology.providers

Class AbstractOntologyService

java.lang.Object

ubic.basecode.ontology.providers.AbstractOntologyService

Direct Known Subclasses:

AbstractOntologyMemoryBackedService, GenericOntologyService

public abstract class AbstractOntologyService
extends Object

Author:

kelsey

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	AbstractOntologyService.OntologyInitializationThread

Field Summary

Fields

Modifier and Type	Field and Description
protected AtomicBoolean	cacheReady
protected SearchIndex	index
protected AtomicBoolean	indexReady
protected Map<String,OntologyIndividual>	individuals
protected AbstractOntologyService.OntologyInitializationThread	initializationThread
protected AtomicBoolean	isInitialized
protected static org.slf4j.Logger	log
protected com.hp.hpl.jena.ontology.OntModel	model
protected AtomicBoolean	modelReady
protected Map<String,OntologyTerm>	terms

Constructor Summary

Constructors

Constructor and Description
AbstractOntologyService()

Method Summary

Modifier and Type	Method and Description
protected void	addTerms(Collection<OntologyResource> newTerms)
void	closeIndex() Do not do this except before re-indexing.
Collection<OntologyIndividual>	findIndividuals(String search) Looks for any OntologyIndividuals that match the given search string.
Collection<OntologyResource>	findResources(String searchString) Looks for any OntologyIndividuals or ontologyTerms that match the given search string
Collection<OntologyTerm>	findTerm(String search) Looks for any ontologyTerms that match the given search string.
OntologyTerm	findUsingAlternativeId(String alternativeId)
Set<String>	getAllURIs()
protected com.hp.hpl.jena.ontology.OntModel	getModel()
protected abstract String	getOntologyName() The simple name of the ontology.
protected abstract String	getOntologyUrl() Defines the location of the ontology eg: http://mged.sourceforge.net/ontologies/MGEDOntology.owl
OntologyResource	getResource(String uri) Looks through both Terms and Individuals for a OntologyResource that has a uri matching the uri given.
OntologyTerm	getTerm(String uri) Looks for a OntologyTerm that has the match in URI given
Collection<OntologyIndividual>	getTermIndividuals(String uri)
void	index(boolean force) Create the search index.
boolean	isEnabled()
boolean	isInitializationThreadAlive()
boolean	isOntologyLoaded() Used for determining if the Ontology has finished loading into memory.
protected abstract com.hp.hpl.jena.ontology.OntModel	loadModel() Delegates the call as to load the model into memory or leave it on disk.
protected void	loadTermsInNameSpace(String url, com.hp.hpl.jena.ontology.OntModel m)
void	startInitializationThread(boolean forceLoad, boolean forceIndexing)

Methods inherited from class java.lang.Object

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

Field Detail

log

protected static org.slf4j.Logger log

cacheReady

protected AtomicBoolean cacheReady

index

protected SearchIndex index

indexReady

protected AtomicBoolean indexReady

individuals

protected Map<String,OntologyIndividual> individuals

initializationThread

protected AbstractOntologyService.OntologyInitializationThread initializationThread

isInitialized

protected AtomicBoolean isInitialized

model

protected com.hp.hpl.jena.ontology.OntModel model

modelReady

protected AtomicBoolean modelReady

terms

protected Map<String,OntologyTerm> terms

Constructor Detail

AbstractOntologyService

public AbstractOntologyService()

Method Detail

closeIndex

public void closeIndex()

Do not do this except before re-indexing.

findIndividuals

public Collection<OntologyIndividual> findIndividuals(String search)
                                               throws OntologySearchException

Looks for any OntologyIndividuals that match the given search string.

Parameters:

search -

Returns:

Throws:

OntologySearchException

findResources

public Collection<OntologyResource> findResources(String searchString)
                                           throws OntologySearchException

Looks for any OntologyIndividuals or ontologyTerms that match the given search string

Parameters:

search -

Returns:

results, or an empty collection if the results are empty OR the ontology is not available to be searched.

Throws:

OntologySearchException

findTerm

public Collection<OntologyTerm> findTerm(String search)
                                  throws OntologySearchException

Looks for any ontologyTerms that match the given search string. Obsolete terms are filtered out.

Parameters:

search -

Returns:

Throws:

OntologySearchException

findUsingAlternativeId

public OntologyTerm findUsingAlternativeId(String alternativeId)

getAllURIs

public Set<String> getAllURIs()

getResource

public OntologyResource getResource(String uri)

Looks through both Terms and Individuals for a OntologyResource that has a uri matching the uri given. If no OntologyTerm is found only then will ontologyIndividuals be searched. returns null if nothing is found.

Parameters:

uri -

Returns:

getTerm

public OntologyTerm getTerm(String uri)

Looks for a OntologyTerm that has the match in URI given

Parameters:

uri -

Returns:

getTermIndividuals

public Collection<OntologyIndividual> getTermIndividuals(String uri)

Parameters:

uri -

Returns:

index

public void index(boolean force)

Create the search index.

Parameters:

force -

isEnabled

public boolean isEnabled()

Returns:

isInitializationThreadAlive

public boolean isInitializationThreadAlive()

isOntologyLoaded

public boolean isOntologyLoaded()

Used for determining if the Ontology has finished loading into memory. Although calls like getParents, getChildren will still work (its much faster once the ontologies have been preloaded into memory.)

startInitializationThread

public void startInitializationThread(boolean forceLoad,
                                      boolean forceIndexing)

Parameters:

forceLoad -

forceIndexing - If forceLoad is also true, indexing will be performed. If you know the index is up to date, there's no need to do it again. Normally indexing is only done if there is no index, or if the ontology has changed since last loaded.

addTerms

protected void addTerms(Collection<OntologyResource> newTerms)

Parameters:

newTerms -

getModel

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

getOntologyName

protected abstract String getOntologyName()

The simple name of the ontology. Used for indexing purposes. (ie this will determine the name of the underlying index for searching the ontology)

Returns:

getOntologyUrl

protected abstract String getOntologyUrl()

Defines the location of the ontology eg: http://mged.sourceforge.net/ontologies/MGEDOntology.owl

Returns:

loadModel

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

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 );

Parameters:

url -

Returns:

Throws:

IOException

loadTermsInNameSpace

protected void loadTermsInNameSpace(String url,
                                    com.hp.hpl.jena.ontology.OntModel m)

Parameters:

url -

m -

Throws:

IOException