Package ubic.basecode.ontology.providers

Interface OntologyService

    • Method Detail

      • getProcessImports

        boolean getProcessImports()
        Check if this ontology will process imports.

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

      • setProcessImports

        void setProcessImports​(boolean processImports)
        Allow of forbid this ontology to process imports.

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

      • setLanguageLevel

        void setLanguageLevel​(OntologyService.LanguageLevel languageLevel)
        Set the OWL language level supported by this ontology.

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

      • setInferenceMode

        void setInferenceMode​(OntologyService.InferenceMode inferenceMode)
        Set the inference mode used for this ontology.

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

      • setSearchEnabled

        void setSearchEnabled​(boolean searchEnabled)
        Enable or disable search for this ontology.

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

      • setAdditionalPropertyUris

        void setAdditionalPropertyUris​(Set<String> additionalPropertyUris)
        Set the URIs to be used as additional properties when inferring parents and children.

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

      • initialize

        void initialize​(boolean forceLoad,
                boolean forceIndexing)
        Initialize this ontology service.
        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

        void initialize​(InputStream stream,
                boolean forceIndexing)
        Initialize this ontology service from a stream.

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

      • getAllURIs

        Set<String> getAllURIs()
        Obtain all the resource URIs in this ontology.

      • getResource

        @Nullable
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.

      • getParents

        Set<OntologyTerm> getParents​(Collection<OntologyTerm> terms,
                             boolean direct,
                             boolean includeAdditionalProperties,
                             boolean keepObsoletes)
        Obtain all the parents of a given set of terms.
        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

        Set<OntologyTerm> getChildren​(Collection<OntologyTerm> terms,
                              boolean direct,
                              boolean includeAdditionalProperties,
                              boolean keepObsoletes)
        Obtain all the children of a given set of terms.
        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

        boolean isEnabled()
        Check if this ontology is enabled.

      • 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()
        Check if the initialization thread is alive.

      • isInitializationThreadCancelled

        boolean isInitializationThreadCancelled()
        Check if the initialization thread is cancelled.

      • cancelInitializationThread

        void cancelInitializationThread()
        Cancel a running initialization thread.

      • loadTermsInNameSpace

        @Deprecated
void loadTermsInNameSpace​(InputStream is,
                          boolean forceIndex)
        Deprecated.
        use initialize(InputStream, boolean) instead and possibly cancelInitializationThread() prior to get any running initialization thread out of the way
        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.