OWLAnonymousIndividual not implemented

[htmai-880]

The issue

Anonymous individuals are not implemented in OWLAPY. For example, attempting to load the following ontology (e.g., ontology_with_anonymous_individual.ttl):

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix ex: <http://example.org/> .

# Ontology declarations
<http://example.org/ontology> a owl:Ontology ;
    rdfs:label "Example Ontology with Anonymous Individual" .

# Class definitions
ex:Person a owl:Class ;
    rdfs:label "Person" .

ex:knows a owl:ObjectProperty ;
    rdfs:label "knows" ;
    rdfs:domain ex:Person ;
    rdfs:range ex:Person .

# Name

ex:Alice a ex:Person ;
    rdfs:label "Alice" ;
    ex:knows [ a ex:Person ] .

Using:

from owlapy.owl_ontology import SyncOntology
ontology = SyncOntology("ontology_with_anonymous_individual.ttl")
abox_axioms = ontology.get_abox_axioms()

Results in:

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 0x713b5ac1f4c0; to '_jpype._JClass' at 0x6067a4bbad50 (uk.ac.manchester.cs.owl.owlapi.OWLAnonymousIndividualImpl)>

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 'uk.ac.manchester.cs.owl.owlapi.OWLAnonymousIndividualImpl'>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/XXX/Documents/owlapy-fix/owlapy-fixed/owlapy/owl_ontology.py", line 1346, in get_abox_axioms
    return self.mapper.map_(self.owlapi_ontology.getABoxAxioms(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 946, in _method
    return method.__get__(obj, cls)(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/XXX/Documents/owlapy-fix/owlapy-fixed/owlapy/owlapi_mapper.py", line 644, in _
    python_list.append(self.map_(obj))
                       ^^^^^^^^^^^^^^
  File "/home/XXX/.local/share/uv/python/cpython-3.11.15-linux-x86_64-gnu/lib/python3.11/functools.py", line 946, in _method
    return method.__get__(obj, cls)(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/XXX/Documents/owlapy-fix/owlapy-fixed/owlapy/owlapi_mapper.py", line 432, in _
    return OWLClassAssertionAxiom(self.map_(e.getIndividual()), self.map_(e.getClassExpression()),
                                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  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 725, in _c3_mro
    other_c3_mros = [_c3_mro(base, abcs=abcs) for base in other_bases]
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/XXX/.local/share/uv/python/cpython-3.11.15-linux-x86_64-gnu/lib/python3.11/functools.py", line 725, in <listcomp>
    other_c3_mros = [_c3_mro(base, abcs=abcs) for base in other_bases]
                     ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/XXX/.local/share/uv/python/cpython-3.11.15-linux-x86_64-gnu/lib/python3.11/functools.py", line 725, in _c3_mro
    other_c3_mros = [_c3_mro(base, abcs=abcs) for base in other_bases]
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/XXX/.local/share/uv/python/cpython-3.11.15-linux-x86_64-gnu/lib/python3.11/functools.py", line 725, in <listcomp>
    other_c3_mros = [_c3_mro(base, abcs=abcs) for base in other_bases]
                     ^^^^^^^^^^^^^^^^^^^^^^^^
  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")

Such a feature could be helpful for purposes such as class membership inference, in case not all individuals are known in advance, but some anonymous placeholders can be inserted.

[Demirrr]

Thank you @htmai-880. Agreed. Would you like to take over the task or shall I do it ?

[htmai-880]

I would prefer if you could take a look at it, as I don't have a good idea of how to manage anonymous individual IDs. See:

• https://github.com/owlcs/owlapi/blob/d7e997a53b470e32700de89cc610d9daf01ea769/impl/src/main/java/uk/ac/manchester/cs/owl/owlapi/OWLAnonymousIndividualImpl.java#L26
• https://github.com/owlcs/owlapi/blob/owlapi-parent-5.1.9/api/src/main/java/org/semanticweb/owlapi/model/NodeID.java

It would be better if you can coordinate on your end how to map these to Python constructs, if that's okay for you.

[Demirrr]

Sure. It might take little more time than usual as @alkidbaci is not actively working on the project :(

[alkidbaci]

Not actively but surely not forgetful :)

After a quick look on this issue, I would suggest the following:

• Implement a new class OWLAnonymousIndividual which inherit from the existing one: OWLIndividual (@ owl_individual.py module)
• Fortunately we already have people who have thought of the structure (from owlapi) so implementation can be done similarly to OWLAnonymousIndividualImpl.java, the class that @htmai-880 shared.
• The NodeID would also be necessary, since we still need to identify these individuals in some way
• Should also add mapping for these classes to OWLAPIMapper so that they can be mapped correctly, for example during axiom retrieval.

I believe doing that should solve the issue.

I don't have an active copilot subscription but would give these instructions to copilot together with the links that @htmai-880 shared and let it do its magic.