ubic.basecode.ontology.providers

Interface OntologyService

All Known Implementing Classes:

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

public interface OntologyService

Method Summary

Modifier and Type	Method and Description
void	cancelInitializationThread()
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()
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) Index the ontology for performing full-text searches.
void	initialize(boolean forceLoad, boolean forceIndexing) Initialize this ontology service.
boolean	isEnabled()
boolean	isInitializationThreadAlive()
boolean	isInitializationThreadCancelled()
boolean	isOntologyLoaded() Used for determining if the Ontology has finished loading into memory.
void	loadTermsInNameSpace(InputStream is, boolean forceIndex) For testing!
void	startInitializationThread(boolean forceLoad, boolean forceIndexing) Start the initialization thread.
void	waitForInitializationThread() Wait for the initialization thread to finish.

Method Detail

initialize

void initialize(boolean forceLoad,
                boolean forceIndexing)

Initialize this ontology service.

findIndividuals

Collection<OntologyIndividual> findIndividuals(String search)
                                        throws OntologySearchException

Looks for any OntologyIndividuals that match the given search string.

Throws:

OntologySearchException

findResources

Collection<OntologyResource> findResources(String searchString)
                                    throws OntologySearchException

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

Returns:

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

Throws:

OntologySearchException

findTerm

Collection<OntologyTerm> findTerm(String search)
                           throws OntologySearchException

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

Throws:

OntologySearchException

findUsingAlternativeId

OntologyTerm findUsingAlternativeId(String alternativeId)

getAllURIs

Set<String> getAllURIs()

getResource

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.

getTerm

OntologyTerm getTerm(String uri)

Looks for a OntologyTerm that has the match in URI given

getTermIndividuals

Collection<OntologyIndividual> getTermIndividuals(String uri)

isEnabled

boolean isEnabled()

isOntologyLoaded

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

void startInitializationThread(boolean forceLoad,
                               boolean forceIndexing)

Start the initialization thread.

If the initialization thread is already running, this method does nothing. If the initialization thread previously completed, the ontology will be reinitialized.

Parameters:

forceLoad - Force loading of ontology, even if it is already loaded

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.

isInitializationThreadAlive

boolean isInitializationThreadAlive()

isInitializationThreadCancelled

boolean isInitializationThreadCancelled()

cancelInitializationThread

void cancelInitializationThread()

waitForInitializationThread

void waitForInitializationThread()
                          throws InterruptedException

Wait for the initialization thread to finish.

Throws:

InterruptedException

index

void index(boolean force)

Index the ontology for performing full-text searches.

See Also:

findIndividuals(String), findTerm(String), findResources(String)

loadTermsInNameSpace

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 - input stream from which the ontology model is loaded

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