Package ubic.gemma.core.ontology

Class OntologyServiceImpl

java.lang.Object

ubic.gemma.core.ontology.OntologyServiceImpl

All Implemented Interfaces:

InitializingBean, OntologyService

@Service
public class OntologyServiceImpl
extends Object
implements OntologyService, InitializingBean

Has a static method for finding out which ontologies are loaded into the system and a general purpose find method that delegates to the many ontology services. NOTE: Logging messages from this service are important for tracking changes to annotations.

Author:

pavlidis

Constructor Summary

Constructors

Constructor	Description
OntologyServiceImpl()

Method Summary

Modifier and Type	Method	Description
void	afterPropertiesSet()
Collection<CharacteristicValueObject>	findExperimentsCharacteristicTags(String searchQuery, int maxResults, boolean useNeuroCartaOntology, long timeout, TimeUnit timeUnit)	Using the ontology and values in the database, for a search searchQuery given by the client give an ordered list of possible choices
Map<OntologyTerm,Long>	findObsoleteTermUsage(long timeout, TimeUnit timeUnit)	Locates usages of obsolete terms in Characteristics, ignoring Gene Ontology annotations.
Collection<OntologySearchResult<OntologyTerm>>	findTerms(String search, int maxResults, long timeout, TimeUnit timeUnit)	Given a search string will look through the loaded ontologies for terms that match the search term.
Collection<CharacteristicValueObject>	findTermsInexact(String queryString, int maxResults, Taxon taxon, long timeout, TimeUnit timeUnit)	Given a search string will first look through the characteristic database for any entries that have a match.
Map<String,OntologyTerm>	fixOntologyTermLabels(boolean dryRun, long timeout, TimeUnit timeUnit)	Check all system uses of ontology terms for the correct label and fix any mismatches based on the ontology OWL files.
Set<OntologyTerm>	getCategoryTerms()	Obtain terms which are allowed for use in the category of a Characteristic.
Set<OntologyTerm>	getChildren(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, long timeout, TimeUnit timeUnit)	Obtain the children of a collection of terms.
String	getDefinition(String uri, long timeout, TimeUnit timeUnit)	Obtain a definition for the given URI.
Set<OntologyTerm>	getParents(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, long timeout, TimeUnit timeUnit)	Obtain the parents of a collection of terms.
Set<OntologyProperty>	getRelationTerms()	Obtain terms allowed for the predicate (relationship) in a Statement.
OntologyTerm	getTerm(String uri, long timeout, TimeUnit timeUnit)	Obtain a term for the given URI.
Set<OntologyTerm>	getTerms(Collection<String> uris, long timeout, TimeUnit timeUnit)	Return all the terms matching the given URIs.
void	reindexAllOntologies()	Recreate the search indices, for ontologies that are loaded.
void	reinitializeAndReindexAllOntologies()	Reinitialize (and reindex) all the ontologies "from scratch".

Methods inherited from class java.lang.Object

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

Constructor Detail

OntologyServiceImpl

public OntologyServiceImpl()

Method Detail

afterPropertiesSet

public void afterPropertiesSet()
                        throws Exception

Specified by:

afterPropertiesSet in interface InitializingBean

Throws:

Exception

findExperimentsCharacteristicTags

public Collection<CharacteristicValueObject> findExperimentsCharacteristicTags(String searchQuery,
                                                                               int maxResults,
                                                                               boolean useNeuroCartaOntology,
                                                                               long timeout,
                                                                               TimeUnit timeUnit)
                                                                        throws SearchException

Using the ontology and values in the database, for a search searchQuery given by the client give an ordered list of possible choices

Specified by:

findExperimentsCharacteristicTags in interface OntologyService

Parameters:

searchQuery - search query

useNeuroCartaOntology - use neurocarta ontology

Returns:

characteristic vos

Throws:

SearchTimeoutException - if the search times out

SearchException

findTerms

public Collection<OntologySearchResult<OntologyTerm>> findTerms(String search,
                                                                int maxResults,
                                                                long timeout,
                                                                TimeUnit timeUnit)
                                                         throws SearchException

Description copied from interface: OntologyService

Given a search string will look through the loaded ontologies for terms that match the search term. If the query looks like a URI, it just retrieves the term. For other queries, this a lucene backed search, is inexact and for general terms can return a lot of results.

Specified by:

findTerms in interface OntologyService

Parameters:

search - search query

Returns:

returns a collection of ontologyTerm's

Throws:

SearchTimeoutException - if the search times out

SearchException

findTermsInexact

public Collection<CharacteristicValueObject> findTermsInexact(String queryString,
                                                              int maxResults,
                                                              @Nullable
                                                              Taxon taxon,
                                                              long timeout,
                                                              TimeUnit timeUnit)
                                                       throws SearchException

Description copied from interface: OntologyService

Given a search string will first look through the characteristic database for any entries that have a match. If a ontologyTermURI is given it will add all the individuals from that URI that match the search term criteria to the returned list also.

Specified by:

findTermsInexact in interface OntologyService

Parameters:

queryString - query string

taxon - Only used if we're going to search for genes or taxon is otherwise relevant; if null, restriction is not used.

Returns:

characteristic vos

Throws:

SearchTimeoutException - if the search times out

SearchException

getParents

public Set<OntologyTerm> getParents(Collection<OntologyTerm> terms,
                                    boolean direct,
                                    boolean includeAdditionalProperties,
                                    long timeout,
                                    TimeUnit timeUnit)
                             throws TimeoutException

Description copied from interface: OntologyService

Obtain the parents of a collection of terms.

Specified by:

getParents in interface OntologyService

Throws:

TimeoutException - if the timeout is exceeded

See Also:

OntologyTerm.getParents(boolean, boolean)

getChildren

public Set<OntologyTerm> getChildren(Collection<OntologyTerm> terms,
                                     boolean direct,
                                     boolean includeAdditionalProperties,
                                     long timeout,
                                     TimeUnit timeUnit)
                              throws TimeoutException

Description copied from interface: OntologyService

Obtain the children of a collection of terms.

Specified by:

getChildren in interface OntologyService

Throws:

TimeoutException - if the timeout is exceeded

See Also:

OntologyTerm.getChildren(boolean, boolean)

getCategoryTerms

public Set<OntologyTerm> getCategoryTerms()

Description copied from interface: OntologyService

Obtain terms which are allowed for use in the category of a Characteristic.

Specified by:

getCategoryTerms in interface OntologyService

getRelationTerms

public Set<OntologyProperty> getRelationTerms()

Description copied from interface: OntologyService

Obtain terms allowed for the predicate (relationship) in a Statement.

Specified by:

getRelationTerms in interface OntologyService

getDefinition

public String getDefinition(String uri,
                            long timeout,
                            TimeUnit timeUnit)
                     throws TimeoutException

Description copied from interface: OntologyService

Obtain a definition for the given URI.

Specified by:

getDefinition in interface OntologyService

Throws:

TimeoutException

getTerm

public OntologyTerm getTerm(String uri,
                            long timeout,
                            TimeUnit timeUnit)
                     throws TimeoutException

Description copied from interface: OntologyService

Obtain a term for the given URI.

Specified by:

getTerm in interface OntologyService

Throws:

TimeoutException

getTerms

public Set<OntologyTerm> getTerms(Collection<String> uris,
                                  long timeout,
                                  TimeUnit timeUnit)
                           throws TimeoutException

Description copied from interface: OntologyService

Return all the terms matching the given URIs.

Specified by:

getTerms in interface OntologyService

Throws:

TimeoutException - if the timeout is exceeded

reindexAllOntologies

public void reindexAllOntologies()

Description copied from interface: OntologyService

Recreate the search indices, for ontologies that are loaded.

Specified by:

reindexAllOntologies in interface OntologyService

reinitializeAndReindexAllOntologies

public void reinitializeAndReindexAllOntologies()

Description copied from interface: OntologyService

Reinitialize (and reindex) all the ontologies "from scratch". This is necessary if indices are old etc. This should be admin-only.

Specified by:

reinitializeAndReindexAllOntologies in interface OntologyService

findObsoleteTermUsage

public Map<OntologyTerm,Long> findObsoleteTermUsage(long timeout,
                                                          TimeUnit timeUnit)
                                                   throws TimeoutException

Description copied from interface: OntologyService

Locates usages of obsolete terms in Characteristics, ignoring Gene Ontology annotations. Requires the ontologies are loaded into memory.

Will also find terms that are no longer in an ontology we use.

Specified by:

findObsoleteTermUsage in interface OntologyService

Returns:

map of value URI to a representative characteristic using the term. The latter will contain a count of how many occurrences there were.

Throws:

TimeoutException

fixOntologyTermLabels

public Map<String,OntologyTerm> fixOntologyTermLabels(boolean dryRun,
                                                            long timeout,
                                                            TimeUnit timeUnit)
                                                     throws TimeoutException

Description copied from interface: OntologyService

Check all system uses of ontology terms for the correct label and fix any mismatches based on the ontology OWL files. This should be run periodically along with findObsoleteTerms.

Specified by:

fixOntologyTermLabels in interface OntologyService

Parameters:

dryRun - if true, no changes will be made in the database and just print them out instead.

Returns:

Throws:

TimeoutException