Using Hermit with ONT-API and SPARQL Query

I am using the OWL-API to load and owl ontology with SWRL rules.

I loaded an ontology with the following code:

IRI iri = IRI.create(BASE_URL);
OntologyManager manager = OntManagers.createManager();
// Load an ontology
Ontology ontologyWithRules = manager.loadOntologyFromOntologyDocument(iri);

Then I instantiate a Hermit reasoner:

import org.semanticweb.HermiT.ReasonerFactory;

OWLReasonerFactory reasonerFactory = new ReasonerFactory();
OWLReasoner reasoner = reasonerFactory.createReasoner(ontologyWithRules);

Finally, I'd like to query this model:

try (
    QueryExecution qexec = QueryExecutionFactory.create(QueryFactory
        .create("SELECT ?s ?p ?o WHERE {  ?s ?p ?o }"), ontologyWithRules.asGraphModel())
) {
    ResultSet res = qexec.execSelect();
    while (res.hasNext()) {
        System.out.println(res.next());
    }
}

However the reasoner wasn't used. Is there a way to use the SPARQL query over the graph with the reasoner turned on?

Running inferences over the model was the missing step. Therefore, I needed to use the InferredOntologyGenerator class.

One line of code speaks more than a thousand words:

/** 
* Important imports:
* import org.semanticweb.HermiT.ReasonerFactory;
* import org.semanticweb.owlapi.util.InferredOntologyGenerator;
**/

IRI iri = IRI.create(BASE_URL);
OntologyManager manager = OntManagers.createManager();
// Load an ontology
Ontology ontologyWithRules = manager.loadOntologyFromOntologyDocument(iri);

// Instantiate a Hermit reasoner:
OWLReasonerFactory reasonerFactory = new ReasonerFactory();
OWLReasoner reasoner = reasonerFactory.createReasoner(ontologyWithRules);

OWLDataFactory df = manager.getOWLDataFactory();

// Create an inference generator over Hermit reasoner
InferredOntologyGenerator inference = new  InferredOntologyGenerator(reasoner);

// Infer
inference.fillOntology(df, ontologyWithRules);

// Query
try (
    QueryExecution qexec = QueryExecutionFactory.create(QueryFactory
        .create("SELECT ?s ?p ?o WHERE { ?s ?p ?o } "), ontologyWithRules.asGraphModel())
) {
    ResultSet res = qexec.execSelect();
    while (res.hasNext()) {
        System.out.println(res.next());
    }
}