Package ubic.basecode.ontology.jena

Class AbstractOntologyService

java.lang.Object

ubic.basecode.ontology.jena.AbstractOntologyService

All Implemented Interfaces:

AutoCloseable, OntologyService

Direct Known Subclasses:

ClasspathOntologyService, TdbOntologyService, UrlOntologyService

public abstract class AbstractOntologyService
extends Object
implements OntologyService

Nested Class Summary

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

OntologyService.InferenceMode, OntologyService.LanguageLevel

Field Summary

Fields

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

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractOntologyService(String ontologyName, String ontologyUrl, boolean ontologyEnabled, @Nullable String cacheName)

Method Summary

Modifier and Type	Method	Description
void	cancelInitializationThread()	Cancel the initialization thread.
void	close()
Collection<OntologySearchResult<OntologyIndividual>>	findIndividuals(String search, int maxResults, boolean keepObsoletes)	Looks for any individuals that match the given search string.
Collection<OntologySearchResult<OntologyResource>>	findResources(String searchString, int maxResults, boolean keepObsoletes)	Looks for any resources (terms or individuals) that match the given search string
Collection<OntologySearchResult<OntologyTerm>>	findTerm(String search, int maxResults, boolean keepObsoletes)	Looks for any terms that match the given search string.
@Nullable OntologyTerm	findUsingAlternativeId(String alternativeId)	Find a term using an alternative ID.
Set<String>	getAdditionalPropertyUris()	Obtain the URIs used as additional properties when inferring parents and children.
Set<String>	getAllURIs()	Obtain all the resource URIs in this ontology.
protected @Nullable String	getCacheName()
Set<OntologyTerm>	getChildren(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)	Obtain all the children of a given set of terms.
@Nullable String	getDescription()	Obtain a description of this ontology if available.
Set<String>	getExcludedWordsFromStemming()	Obtain the words that should be excluded from stemming.
OntologyService.InferenceMode	getInferenceMode()	Obtain the inference mode used for this ontology.
OntologyService.LanguageLevel	getLanguageLevel()	Obtain the OWL language level supported by this ontology.
@Nullable String	getName()	Obtain the name of this ontology if available.
protected String	getOntologyName()
protected String	getOntologyUrl()
Set<OntologyTerm>	getParents(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)	Obtain all the parents of a given set of terms.
boolean	getProcessImports()	Check if this ontology will process imports.
@Nullable OntologyResource	getResource(String uri)	Looks through both Terms and Individuals for a OntologyResource that has a uri matching the uri given.
protected com.hp.hpl.jena.ontology.OntModelSpec	getSpec(OntologyService.LanguageLevel languageLevel, OntologyService.InferenceMode inferenceMode)
@Nullable 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.
protected boolean	isOntologyEnabled()
boolean	isOntologyLoaded()	Used for determining if the Ontology has finished loading into memory.
boolean	isSearchEnabled()	Check if this ontology has full-text search enabled.
protected abstract OntologyModel	loadModel(boolean processImports, OntologyService.LanguageLevel languageLevel, OntologyService.InferenceMode inferenceMode)	Delegates the call as to load the model into memory or leave it on disk.
protected abstract OntologyModel	loadModelFromStream(InputStream is, boolean processImports, OntologyService.LanguageLevel languageLevel, OntologyService.InferenceMode inferenceMode)	Load a model from a given input stream.
void	loadTermsInNameSpace(InputStream is, boolean forceIndex)	For testing!
void	setAdditionalPropertyUris(Set<String> additionalPropertyUris)	Set the URIs to be used as additional properties when inferring parents and children.
void	setExcludedWordsFromStemming(Set<String> excludedWordsFromStemming)	Set words that should be excluded from stemming when searching.
void	setInferenceMode(OntologyService.InferenceMode inferenceMode)	Set the inference mode used for this ontology.
void	setLanguageLevel(OntologyService.LanguageLevel languageLevel)	Set the OWL language level supported by this ontology.
void	setProcessImports(boolean processImports)	Allow of forbid this ontology to process imports.
void	setSearchEnabled(boolean searchEnabled)	Enable or disable search for this ontology.
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 Details

log

protected static org.slf4j.Logger log

Constructor Details

AbstractOntologyService

protected AbstractOntologyService(String ontologyName,
 String ontologyUrl,
 boolean ontologyEnabled,
 @Nullable String cacheName)

Method Details

getOntologyName

protected String getOntologyName()

getOntologyUrl

protected String getOntologyUrl()

isOntologyEnabled

protected boolean isOntologyEnabled()

getCacheName

protected @Nullable String getCacheName()

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

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.

getName

public @Nullable String getName()

Description copied from interface: OntologyService

Obtain the name of this ontology if available.

Specified by:

getName in interface OntologyService

getDescription

public @Nullable String getDescription()

Description copied from interface: OntologyService

Obtain a description of this ontology if available.

Specified by:

getDescription in interface OntologyService

getLanguageLevel

public OntologyService.LanguageLevel getLanguageLevel()

Description copied from interface: OntologyService

Obtain the OWL language level supported by this ontology.

The default is to use OntologyService.LanguageLevel.FULL.

Specified by:

getLanguageLevel in interface OntologyService

setLanguageLevel

public void setLanguageLevel(OntologyService.LanguageLevel languageLevel)

Description copied from interface: OntologyService

Set the OWL language level supported by this ontology.

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

Specified by:

setLanguageLevel in interface OntologyService

getInferenceMode

public OntologyService.InferenceMode getInferenceMode()

Description copied from interface: OntologyService

Obtain the inference mode used for this ontology.

The default is OntologyService.InferenceMode.TRANSITIVE.

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()

Description copied from interface: OntologyService

Check if this ontology will process imports.

If disabled, ontologies imported by this ontology will not be loaded.

Specified by:

getProcessImports in interface OntologyService

setProcessImports

public void setProcessImports(boolean processImports)

Description copied from interface: OntologyService

Allow of forbid this ontology to process imports.

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

Specified by:

setProcessImports in interface OntologyService

isSearchEnabled

public boolean isSearchEnabled()

Description copied from interface: OntologyService

Check if this ontology has full-text search enabled.

This is necessary for finding term using full-text queries. If enabled, an index will be generated in during initialization by OntologyService.initialize(boolean, boolean).

Search is enabled by default.

Specified by:

isSearchEnabled in interface OntologyService

See Also:

• OntologyService.findTerm(String, int, boolean)
• OntologyService.findIndividuals(String, int, boolean)
• OntologyService.findResources(String, int, boolean)

setSearchEnabled

public void setSearchEnabled(boolean searchEnabled)

Description copied from interface: OntologyService

Enable or disable search for this ontology.

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

Specified by:

setSearchEnabled in interface OntologyService

getExcludedWordsFromStemming

public Set<String> getExcludedWordsFromStemming()

Description copied from interface: OntologyService

Obtain the words that should be excluded from stemming.

By default, all words are subject to stemming. The exact implementation of stemming depends on the actual search implementation.

Specified by:

getExcludedWordsFromStemming in interface OntologyService

setExcludedWordsFromStemming

public void setExcludedWordsFromStemming(Set<String> excludedWordsFromStemming)

Description copied from interface: OntologyService

Set words that should be excluded from stemming when searching.

Specified by:

setExcludedWordsFromStemming in interface OntologyService

getAdditionalPropertyUris

public Set<String> getAdditionalPropertyUris()

Description copied from interface: OntologyService

Obtain the URIs used as additional properties when inferring parents and children.

The default is to use part of, proper part of and all of their sub-properties if inference is enabled.

Specified by:

getAdditionalPropertyUris in interface OntologyService

See Also:

• OntologyService.getParents(Collection, boolean, boolean, boolean)
• OntologyService.getChildren(Collection, boolean, boolean, boolean)

setAdditionalPropertyUris

public void setAdditionalPropertyUris(Set<String> additionalPropertyUris)

Description copied from interface: OntologyService

Set the URIs to be used as additional properties when inferring parents and children.

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

Specified by:

setAdditionalPropertyUris 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

findIndividuals

public Collection<OntologySearchResult<OntologyIndividual>> findIndividuals(String search,
 int maxResults,
 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<OntologySearchResult<OntologyResource>> findResources(String searchString,
 int maxResults,
 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<OntologySearchResult<OntologyTerm>> findTerm(String search,
 int maxResults,
 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 @Nullable 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 @Nullable 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 @Nullable 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

loadModel

protected abstract OntologyModel loadModel(boolean processImports,
 OntologyService.LanguageLevel languageLevel,
 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 is,
 boolean processImports,
 OntologyService.LanguageLevel languageLevel,
 OntologyService.InferenceMode inferenceMode)
                                              throws IOException

Load a model from a given input stream.

Throws:

IOException

getSpec

protected com.hp.hpl.jena.ontology.OntModelSpec getSpec(OntologyService.LanguageLevel languageLevel,
 OntologyService.InferenceMode inferenceMode)

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:

• (String)
• OntologyService.findTerm(String, int)
• OntologyService.findResources(String, int)

close

public void close()
           throws Exception

Specified by:

close in interface AutoCloseable

Throws:

Exception

toString

public String toString()

Overrides:

toString in class Object