OWL API: Traverse imported ontology - owl

Question

I'm trying to import an ontology to the primary ontology, and traverse over all classes:
manager = OWLManager.createOWLOntologyManager();
ontology = manager.loadOntologyFromOntologyDocument(new File("data/prim.owl"));
factory = manager.getOWLDataFactory();
OWLImportsDeclaration im = factory.getOWLImportsDeclaration(IRI.create("https://protege.stanford.edu/ontologies/pizza/pizza.owl"));
manager.applyChange(new AddImport(ontology,im));
reasoner = OpenlletReasonerFactory.getInstance().createReasoner(ontology);
I’m running this code to get all classes:
//*********************
Set<OWLClass> allCls = ontology.getClassesInSignature();
allCls.forEach(System.out::println);
Classes belonging to prim.owl are returned, but classes in the imported ontology (pizza.owl) are not returned.

Answer 1

The code in the question contains a mistake: it does not load the desired imported ontology (pizza) into the manager.
OWLImportsDeclaration im = factory.getOWLImportsDeclaration(IRI.create("https://protege.stanford.edu/ontologies/pizza/pizza.owl"));
manager.applyChange(new AddImport(ontology,im));
These lines just add the owl:imports declaration into the ontology header (_:x a owl:Ontology) for the pizza-iri.
To make the code work, you need to load the pizza-ontology separately:
OWLOntology pizza = manager.loadOntology(IRI.create("https://protege.stanford.edu/ontologies/pizza/pizza.owl"));
OWLImportsDeclaration im = factory.getOWLImportsDeclaration(pizza.getOntologyID().getOntologyIRI().orElseThrow(AssertionError::new));
manager.applyChange(new AddImport(ontology, im));
Now you can check that all imports and references are really present and correct, and, therefore, your ontology has a reference to the pizza ontology:
Assert.assertEquals(1, ontology.importsDeclarations().count());
Assert.assertEquals(1, ontology.imports().count());
Assert.assertEquals(2, manager.ontologies().count());
Then you can get all OWL-classes from both ontologies as a single collection or java-Stream:
ontology.classesInSignature(Imports.INCLUDED).forEach(System.err::println);
Also please note: the method Set<OWLClass> getClassesInSignature(boolean includeImportsClosure) is deprecated (in OWL-API v5).