Examples with InferredOntologyGenerator org.semanticweb.owlapi.util.InferredOntologyGenerator used on opensource projects

Example 1 with InferredOntologyGenerator

use of org.semanticweb.owlapi.util.InferredOntologyGenerator in project goci by EBISPOT.

the class DefaultGWASOWLPublisher method saveGWASDataInferredView.

public void saveGWASDataInferredView(OWLReasoner reasoner, File outputFile) throws OWLConversionException {
    try {
        // create new ontology to hold inferred axioms
        OWLOntology inferredOntology = getConverter().createConversionOntology();
        getLog().info("Saving inferred view...");
        List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
        // we require all inferred stuff except for disjoints...
        gens.add(new InferredClassAssertionAxiomGenerator());
        gens.add(new InferredDataPropertyCharacteristicAxiomGenerator());
        gens.add(new InferredEquivalentClassAxiomGenerator());
        gens.add(new InferredEquivalentDataPropertiesAxiomGenerator());
        gens.add(new InferredEquivalentObjectPropertyAxiomGenerator());
        gens.add(new InferredInverseObjectPropertiesAxiomGenerator());
        gens.add(new InferredObjectPropertyCharacteristicAxiomGenerator());
        gens.add(new InferredPropertyAssertionGenerator());
        gens.add(new InferredSubClassAxiomGenerator());
        gens.add(new InferredSubDataPropertyAxiomGenerator());
        gens.add(new InferredSubObjectPropertyAxiomGenerator());
        // now create the target ontology and save
        OWLOntologyManager inferredManager = inferredOntology.getOWLOntologyManager();
        InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
        iog.fillOntology(inferredManager, inferredOntology);
        inferredManager.saveOntology(inferredOntology, IRI.create(outputFile));
        getLog().info("Inferred view saved ok");
    } catch (OWLOntologyStorageException e) {
        throw new OWLConversionException("Failed to save GWAS data (inferred view)", e);
    }
}

Example 2 with InferredOntologyGenerator

use of org.semanticweb.owlapi.util.InferredOntologyGenerator in project stanbol by apache.

the class AbstractOWLApiReasoningService method run.

/**
     * Generic method for running the reasoner
     * 
     * @param input
     * @param generators
     * @return
     */
@Override
public Set<OWLAxiom> run(OWLOntology input, List<InferredAxiomGenerator<? extends OWLAxiom>> generators) throws ReasoningServiceException, InconsistentInputException {
    log.debug("run(OWLOntology input, List<InferredAxiomGenerator<? extends OWLAxiom>> generators)");
    try {
        // Get the manager
        OWLOntologyManager manager = createOWLOntologyManager();
        // Get the reasoner
        OWLReasoner reasoner = getReasoner(input);
        log.info("Running {} reasoner on {} ", reasoner.getClass(), input.getOntologyID());
        // To generate inferred axioms
        InferredOntologyGenerator inferred = new InferredOntologyGenerator(reasoner, generators);
        // We fill an anonymous ontology with the result, the return the
        // axiom set
        Set<OWLAxiom> axioms = new HashSet<OWLAxiom>();
        try {
            OWLOntology output = manager.createOntology();
            log.debug("Created output ontology: {}", output);
            try {
                inferred.fillOntology(manager, output);
            } catch (InconsistentOntologyException i) {
                throw i;
            } catch (Throwable t) {
                log.error("Some problem occurred:\n {}", t.getStackTrace());
                throw new ReasoningServiceException();
            }
            log.debug("Filled ontology: {}", output);
            log.debug("Temporary ID is {}", output.getOntologyID());
            axioms = manager.getOntology(output.getOntologyID()).getAxioms();
            // IMPORTANT We remove the ontology from the manager
            manager.removeOntology(output);
        } catch (OWLOntologyCreationException e) {
            log.error("An exception have been thrown when instantiating the ontology");
            throw new ReasoningServiceException();
        }
        return axioms;
    } catch (InconsistentOntologyException inconsistent) {
        /**
             * TODO Add report. Why it is inconsistent?
             */
        throw new InconsistentInputException();
    } catch (Exception exception) {
        log.error("An exception have been thrown while executing method run()", exception);
        throw new ReasoningServiceException();
    }
}