Expose more Java-side methods for SyncOntology

[htmai-880]

The issue

So I realized that a lot of methods for SyncOntology could be helpful but are currently unavailable on Python-side, and I currently find myself implementing by hand in very roundabout ways.

For example, the only way to verify that an ontology contains an axiom on Python-side is to go through all the axioms and check if the axiom is in it. Likewise, if we want to check if an OWLClass/OWLObjectProperty/etc is in an ontology, we have to go through all the classes/object properties/etc of the SyncOntology then verify.

So my thought is that there are a couple of useful Java-side methods that we could basically expose as class methods on Python-side.
Some examples of useful methods:

• getAxioms
• containsAxiom
• containsClassInSignature, containsObjectPropertyInSignature, containsDataPropertyInSignature, containsAnnotationPropertyInSignature, containsIndividualInSignature
• isDeclared
• getPunnedIRIs (useful for reasoning tasks)

What are your thoughts?

[Demirrr]

Agreed. We decided to add those useful Java-side methods per request. I will ensure that the mentioned methods will be available soon

[Demirrr]

@htmai-880 ab1a08e fixes this issue. Please validate it and do not hesitate to reopen the issue if something is missing!

[htmai-880]

Thanks a lot!

[htmai-880]

I found an issue with get_punned_iris. I tried to run with the following code:

from owlapy.owl_ontology import SyncOntology
from owlapy.iri import IRI
from owlapy.owl_individual import OWLNamedIndividual
from owlapy.class_expression import OWLClass
from owlapy.owl_axiom import *

alice_ind = OWLNamedIndividual(IRI.create("http://example.org/ontology#Alice"))
person = OWLClass(IRI.create("http://example.org/ontology#Person"))

alice_class = OWLClass(IRI.create("http://example.org/ontology#Alice"))

alice_axiom = OWLClassAssertionAxiom(alice_ind, person)
subclass_axiom = OWLSubClassOfAxiom(alice_class, person)

ontology = SyncOntology("http://example.org/ontology", load=False)
ontology.add_axiom(alice_axiom)
ontology.add_axiom(subclass_axiom)

print("Axioms in the ontology:", ontology.get_axioms())
print("Punned IRIs in the ontology:", ontology.get_punned_iris())

I get the following output:

Axioms in the ontology: [OWLSubClassOfAxiom(sub_class=OWLClass(IRI('http://example.org/ontology#', 'Alice')),super_class=OWLClass(IRI('http://example.org/ontology#', 'Person')),annotations=[]), OWLClassAssertionAxiom(individual=OWLNamedIndividual(IRI('http://example.org/ontology#', 'Alice')),class_expression=OWLClass(IRI('http://example.org/ontology#', 'Person')),annotations=[])]
Traceback (most recent call last):
  File "/home/XXX/.local/share/uv/python/cpython-3.11.15-linux-x86_64-gnu/lib/python3.11/functools.py", line 832, in dispatch
    impl = dispatch_cache[cls]
           ~~~~~~~~~~~~~~^^^^^
  File "/home/XXX/.local/share/uv/python/cpython-3.11.15-linux-x86_64-gnu/lib/python3.11/weakref.py", line 415, in __getitem__
    return self.data[ref(key)]
           ~~~~~~~~~^^^^^^^^^^
KeyError: <weakref at 0x7afeec5f28e0; to '_jpype._JClass' at 0x56ace5d84de0 (java.util.HashSet)>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/XXX/.local/share/uv/python/cpython-3.11.15-linux-x86_64-gnu/lib/python3.11/functools.py", line 835, in dispatch
    impl = registry[cls]
           ~~~~~~~~^^^^^
KeyError: <java class 'java.util.HashSet'>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/XXX/Documents/XXX-2/test_punning.py", line 20, in <module>
    print("Punned IRIs in the ontology:", ontology.get_punned_iris())
                                          ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/XXX/Documents/XXX-2/XXX-2-env/lib/python3.11/site-packages/owlapy/owl_ontology.py", line 1528, in get_punned_iris
    return self.mapper.map_(self.owlapi_ontology.getPunnedIRIs(self._get_imports_enum(include_imports_closure)))
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/XXX/.local/share/uv/python/cpython-3.11.15-linux-x86_64-gnu/lib/python3.11/functools.py", line 945, in _method
    method = self.dispatcher.dispatch(args[0].__class__)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/XXX/.local/share/uv/python/cpython-3.11.15-linux-x86_64-gnu/lib/python3.11/functools.py", line 837, in dispatch
    impl = _find_impl(cls, registry)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/XXX/.local/share/uv/python/cpython-3.11.15-linux-x86_64-gnu/lib/python3.11/functools.py", line 784, in _find_impl
    mro = _compose_mro(cls, registry.keys())
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/XXX/.local/share/uv/python/cpython-3.11.15-linux-x86_64-gnu/lib/python3.11/functools.py", line 772, in _compose_mro
    return _c3_mro(cls, abcs=mro)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/XXX/.local/share/uv/python/cpython-3.11.15-linux-x86_64-gnu/lib/python3.11/functools.py", line 726, in _c3_mro
    return _c3_merge(
           ^^^^^^^^^^
  File "/home/XXX/.local/share/uv/python/cpython-3.11.15-linux-x86_64-gnu/lib/python3.11/functools.py", line 680, in _c3_merge
    raise RuntimeError("Inconsistent hierarchy")
RuntimeError: Inconsistent hierarchy

I think this is due to the fact that the OWLAPI mapper doesn't have support to map java.util.HashSet.

[Demirrr]

I will see what we can. Thank you for the report 😊

[Demirrr]

Fix for the `get_punned_iris()` / `java.util.HashSet` mapping issue is up: #280

Root cause: `getPunnedIRIs()` returns a concrete `java.util.HashSet` when non-empty, and `OWLAPIMapper.map_()` had no exact registration for it, causing `functools.singledispatch` to fail MRO resolution over JPype's Java proxies (`RuntimeError: Inconsistent hierarchy`) -- the same issue `LinkedHashSet` was patched for previously. Registered `HashSet` the same way.