ubic.basecode.ontology.jena

Class AbstractOntologyService

java.lang.Object

ubic.basecode.ontology.jena.AbstractOntologyService

All Implemented Interfaces:

OntologyService

Direct Known Subclasses:

AbstractOntologyMemoryBackedService

public abstract class AbstractOntologyService
extends Object
implements OntologyService

Base class for Jena-based ontology services.

Author:

kelsey

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.basecode.ontology.providers.OntologyService

OntologyService.InferenceMode

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, boolean keepObsoletes) Looks for any individuals that match the given search string.
Collection<OntologyResource>	findResources(String searchString, boolean keepObsoletes) Looks for any resources (terms or individuals) that match the given search string
Collection<OntologyTerm>	findTerm(String search, boolean keepObsoletes) Looks for any terms that match the given search string.
OntologyTerm	findUsingAlternativeId(String alternativeId) Find a term using an alternative ID.
Set<String>	getAllURIs() Obtain all the resource URIs in this ontology.
protected String	getCacheName() A name for caching this ontology, or null to disable caching.
Set<OntologyTerm>	getChildren(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes) Obtain all the children of a given set of terms.
OntologyService.InferenceMode	getInferenceMode() Obtain the inference mode used for this ontology.
protected abstract String	getOntologyName() The simple getOntologyName() of the ontology.
protected abstract String	getOntologyUrl() Defines the location of the ontology eg: MGED
Set<OntologyTerm>	getParents(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes) Obtain all the parents of a given set of terms.
boolean	getProcessImports()
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) Obtain all the individuals for a given term URI.
void	index(boolean force) Index the ontology for performing full-text searches.
void	initialize(boolean forceLoad, boolean forceIndexing) Initialize this ontology service.
void	initialize(InputStream stream, boolean forceIndexing) Initialize this ontology service from a stream.
boolean	isEnabled() Check if this ontology is enabled.
boolean	isInitializationThreadAlive() Check if the initialization thread is alive.
boolean	isInitializationThreadCancelled() Check if the initialization thread is cancelled.
boolean	isOntologyLoaded() Used for determining if the Ontology has finished loading into memory.
boolean	isSearchEnabled()
protected abstract OntologyModel	loadModel(boolean processImports, OntologyService.InferenceMode inferenceMode) Delegates the call as to load the model into memory or leave it on disk.
protected abstract OntologyModel	loadModelFromStream(InputStream stream, boolean processImports, OntologyService.InferenceMode inferenceMode) Load a model from a given input stream.
void	loadTermsInNameSpace(InputStream is, boolean forceIndex) For testing! Overrides normal way of loading the ontology.
void	setInferenceMode(OntologyService.InferenceMode inferenceMode) Set the inference mode used for this ontology.
void	setProcessImports(boolean processImports)
void	setSearchEnabled(boolean searchEnabled)
void	startInitializationThread(boolean forceLoad, boolean forceIndexing) Start the initialization thread.
String	toString()
void	waitForInitializationThread() Wait for the initialization thread to finish.

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.basecode.ontology.providers.OntologyService

findIndividuals, findResources, findTerm, getChildren, getParents

Field Detail

log

protected static org.slf4j.Logger log

Constructor Detail

AbstractOntologyService

public AbstractOntologyService()

Method Detail

getInferenceMode

public OntologyService.InferenceMode getInferenceMode()

Description copied from interface: OntologyService

Obtain the inference mode used for this ontology.

Specified by:

getInferenceMode in interface OntologyService

setInferenceMode

public void setInferenceMode(OntologyService.InferenceMode inferenceMode)

Description copied from interface: OntologyService

Set the inference mode used for this ontology.

Changes are applicable only if the service is re-initialized.

Specified by:

setInferenceMode in interface OntologyService

getProcessImports

public boolean getProcessImports()

Specified by:

getProcessImports in interface OntologyService

setProcessImports

public void setProcessImports(boolean processImports)

Specified by:

setProcessImports in interface OntologyService

isSearchEnabled

public boolean isSearchEnabled()

Specified by:

isSearchEnabled in interface OntologyService

setSearchEnabled

public void setSearchEnabled(boolean searchEnabled)

Specified by:

setSearchEnabled in interface OntologyService

initialize

public void initialize(boolean forceLoad,
                       boolean forceIndexing)

Description copied from interface: OntologyService

Initialize this ontology service.

Specified by:

initialize 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.

initialize

public void initialize(InputStream stream,
                       boolean forceIndexing)

Description copied from interface: OntologyService

Initialize this ontology service from a stream.

Note that when this method of initialization is used, the ontology cache is not created on-disk.

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,
                                                      boolean keepObsoletes)
                                               throws OntologySearchException

Description copied from interface: OntologyService

Looks for any individuals that match the given search string.

Specified by:

findIndividuals in interface OntologyService

Parameters:

search - search query

keepObsoletes - retain obsolete terms

Throws:

OntologySearchException

findResources

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

Description copied from interface: OntologyService

Looks for any resources (terms or individuals) that match the given search string

Specified by:

findResources in interface OntologyService

Parameters:

searchString - search query

keepObsoletes - retain obsolete terms

Throws:

OntologySearchException

findTerm

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

Description copied from interface: OntologyService

Looks for any terms that match the given search string.

Specified by:

findTerm in interface OntologyService

Parameters:

search - search query

keepObsoletes - retain obsolete terms

Throws:

OntologySearchException

findUsingAlternativeId

public OntologyTerm findUsingAlternativeId(String alternativeId)

Description copied from interface: OntologyService

Find a term using an alternative ID.

Specified by:

findUsingAlternativeId in interface OntologyService

getAllURIs

public Set<String> getAllURIs()

Description copied from interface: OntologyService

Obtain all the resource URIs in this ontology.

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)

Description copied from interface: OntologyService

Obtain all the individuals for a given term URI.

Specified by:

getTermIndividuals in interface OntologyService

getParents

public Set<OntologyTerm> getParents(Collection<OntologyTerm> terms,
                                    boolean direct,
                                    boolean includeAdditionalProperties,
                                    boolean keepObsoletes)

Description copied from interface: OntologyService

Obtain all the parents of a given set of terms.

Specified by:

getParents in interface OntologyService

Parameters:

terms - set of terms whose parents are retrieved

direct - only retain direct parents

includeAdditionalProperties - also include parents matched via additional properties

keepObsoletes - retain obsolete terms

Returns:

a set of parent terms

getChildren

public Set<OntologyTerm> getChildren(Collection<OntologyTerm> terms,
                                     boolean direct,
                                     boolean includeAdditionalProperties,
                                     boolean keepObsoletes)

Description copied from interface: OntologyService

Obtain all the children of a given set of terms.

Specified by:

getChildren in interface OntologyService

Parameters:

terms - set of terms whose children are retrieved

direct - only retain direct children

includeAdditionalProperties - also include children matched via additional properties

keepObsoletes - retain obsolete terms

Returns:

a set of child terms

isEnabled

public boolean isEnabled()

Description copied from interface: OntologyService

Check if this ontology is enabled.

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()

Description copied from interface: OntologyService

Check if the initialization thread is alive.

Specified by:

isInitializationThreadAlive in interface OntologyService

isInitializationThreadCancelled

public boolean isInitializationThreadCancelled()

Description copied from interface: OntologyService

Check if the initialization thread is cancelled.

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 OntologyModel loadModel(boolean processImports,
                                           OntologyService.InferenceMode inferenceMode)
                                    throws IOException

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 );

Throws:

IOException

loadModelFromStream

protected abstract OntologyModel loadModelFromStream(InputStream stream,
                                                     boolean processImports,
                                                     OntologyService.InferenceMode inferenceMode)
                                              throws IOException

Load a model from a given input stream.

Throws:

IOException

getCacheName

@Nullable
protected String getCacheName()

A name for caching this ontology, or null to disable caching.

Note that if null is returned, the ontology will not have full-text search capabilities.

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

Parameters:

force - if true, perform indexing even if an index already exists

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.

toString

public String toString()

Overrides:

toString in class Object