ubic.basecode.ontology.providers

Class AbstractOntologyService

java.lang.Object

ubic.basecode.ontology.providers.AbstractOntologyService

All Implemented Interfaces:

OntologyService

Direct Known Subclasses:

AbstractOntologyMemoryBackedService, GenericOntologyService

public abstract class AbstractOntologyService
extends Object
implements OntologyService

Author:

kelsey

Field Summary

Fields

Modifier and Type	Field and Description
protected static org.slf4j.Logger	log

Constructor Summary

Constructors

Constructor and Description
AbstractOntologyService()

Method Summary

Modifier and Type	Method and Description
void	cancelInitializationThread() Cancel the initialization thread.
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 abstract String	getOntologyName() The simple getOntologyName() of the ontology.
protected abstract String	getOntologyUrl() Defines the location of the ontology eg: MGED
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.
protected abstract 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!
void	startInitializationThread(boolean forceLoad, boolean forceIndexing) Start the initialization thread.
void	waitForInitializationThread() Wait for the initialization thread to finish.

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

Constructor Detail

AbstractOntologyService

public AbstractOntologyService()

Method Detail

initialize

public void initialize(boolean forceLoad,
                       boolean forceIndexing)

Description copied from interface: OntologyService

Initialize this ontology service.

Specified by:

initialize in interface OntologyService

closeIndex

public void closeIndex()

Do not do this except before re-indexing.

findIndividuals

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

Description copied from interface: OntologyService

Looks for any OntologyIndividuals that match the given search string.

Specified by:

findIndividuals in interface OntologyService

Throws:

OntologySearchException

findResources

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

Description copied from interface: OntologyService

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

Specified by:

findResources in interface OntologyService

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

Description copied from interface: OntologyService

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

Specified by:

findTerm in interface OntologyService

Throws:

OntologySearchException

findUsingAlternativeId

public OntologyTerm findUsingAlternativeId(String alternativeId)

Specified by:

findUsingAlternativeId in interface OntologyService

getAllURIs

public Set<String> getAllURIs()

Specified by:

getAllURIs in interface OntologyService

getResource

public OntologyResource getResource(String uri)

Description copied from interface: OntologyService

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.

Specified by:

getResource in interface OntologyService

getTerm

public OntologyTerm getTerm(String uri)

Description copied from interface: OntologyService

Looks for a OntologyTerm that has the match in URI given

Specified by:

getTerm in interface OntologyService

getTermIndividuals

public Collection<OntologyIndividual> getTermIndividuals(String uri)

Specified by:

getTermIndividuals in interface OntologyService

isEnabled

public boolean isEnabled()

Specified by:

isEnabled in interface OntologyService

isOntologyLoaded

public boolean isOntologyLoaded()

Description copied from interface: OntologyService

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.)

Specified by:

isOntologyLoaded in interface OntologyService

startInitializationThread

public void startInitializationThread(boolean forceLoad,
                                      boolean forceIndexing)

Description copied from interface: OntologyService

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.

Specified by:

startInitializationThread in interface OntologyService

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

public boolean isInitializationThreadAlive()

Specified by:

isInitializationThreadAlive in interface OntologyService

isInitializationThreadCancelled

public boolean isInitializationThreadCancelled()

Specified by:

isInitializationThreadCancelled in interface OntologyService

cancelInitializationThread

public void cancelInitializationThread()

Cancel the initialization thread.

Specified by:

cancelInitializationThread in interface OntologyService

waitForInitializationThread

public void waitForInitializationThread()
                                 throws InterruptedException

Description copied from interface: OntologyService

Wait for the initialization thread to finish.

Specified by:

waitForInitializationThread in interface OntologyService

Throws:

InterruptedException

getOntologyName

protected abstract String getOntologyName()

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

getOntologyUrl

protected abstract String getOntologyUrl()

Defines the location of the ontology eg: MGED

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 );

index

public void index(boolean force)

Description copied from interface: OntologyService

Index the ontology for performing full-text searches.

Specified by:

index in interface OntologyService

See Also:

OntologyService.findIndividuals(String), OntologyService.findTerm(String), OntologyService.findResources(String)

loadTermsInNameSpace

public void loadTermsInNameSpace(InputStream is,
                                 boolean forceIndex)

Description copied from interface: OntologyService

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)

Specified by:

loadTermsInNameSpace in interface OntologyService

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.