Merge remote-tracking branch 'origin/develop' into issues-solving

owlapy/owl_ontology_manager.py

@@ -113,6 +113,10 @@ def save_world(self):
 
 
 class SyncOntologyManager(AbstractOWLOntologyManager):
+    """
+    Create OWLManager in Python
+    https://owlcs.github.io/owlapi/apidocs_5/org/semanticweb/owlapi/apibinding/OWLManager.html
+    """
 
     # WARN: Do not move local imports to top of the module
     def __init__(self):

owlapy/owl_reasoner.py

@@ -1,8 +1,6 @@
 """OWL Reasoner"""
 import operator
 import logging
-import threading
-
 import owlready2
 
 from collections import defaultdict
@@ -29,26 +27,12 @@
     OWLPropertyExpression, OWLDataPropertyExpression
 from owlapy.owl_individual import OWLNamedIndividual
 from owlapy.owl_literal import OWLLiteral
-from owlapy.utils import LRUCache
+from owlapy.utils import LRUCache, run_with_timeout
 from owlapy.abstracts.abstract_owl_reasoner import AbstractOWLReasoner, AbstractOWLReasonerEx
-
 logger = logging.getLogger(__name__)
 
 _P = TypeVar('_P', bound=OWLPropertyExpression)
 
-
-def run_with_timeout(func, timeout, args=(), kwargs={}):
-    result = [None]
-    thread = threading.Thread(target=lambda: result.append(func(*args, **kwargs)))
-    thread.start()
-    thread.join(timeout)
-    if thread.is_alive():
-        print(f"{func.__self__.__class__.__name__}.instances timed out! Timeout limit is currently set to {timeout} "
-              f"seconds\nReturning empty results...")
-        return []
-    return result[-1]
-
-
 class OntologyReasoner(AbstractOWLReasonerEx):
     __slots__ = '_ontology', '_world'
     # TODO: CD: We will remove owlready2 from owlapy
@@ -1185,8 +1169,10 @@ def __init__(self, ontology: Union[SyncOntology, str], reasoner="HermiT"):
             self.manager = ontology.manager
             self.ontology = ontology
         elif isinstance(ontology, str):
+            # https://owlcs.github.io/owlapi/apidocs_5/org/semanticweb/owlapi/apibinding/OWLManager.html
             self.manager = SyncOntologyManager()
-            self.ontology = self.manager.load_ontology(ontology)
+            # OWLOntology
+            self.ontology = self.manager.load_ontology(iri=ontology)
 
         self._owlapi_manager = self.manager.get_owlapi_manager()
         self._owlapi_ontology = self.ontology.get_owlapi_ontology()
@@ -1654,11 +1640,12 @@ def infer_axioms_and_save(self, output_path: str = None, output_format: str = No
             if java_object := self.inference_types_mapping.get(i, None):
                 generators.add(java_object)
         iog = InferredOntologyGenerator(self._owlapi_reasoner, generators)
-        inferred_axioms_ontology = self._owlapi_manager.createOntology()
-        iog.fillOntology(self._owlapi_manager.getOWLDataFactory(), inferred_axioms_ontology)
-        inferred_ontology_file = File(output_path).getAbsoluteFile()
-        output_stream = FileOutputStream(inferred_ontology_file)
-        self._owlapi_manager.saveOntology(inferred_axioms_ontology, document_format, output_stream)
+        # CD: No need to create a new ontology
+        # inferred_axioms_ontology = self._owlapi_manager.createOntology()
+        iog.fillOntology(self._owlapi_manager.getOWLDataFactory(), self._owlapi_ontology)
+        self._owlapi_manager.saveOntology(self._owlapi_ontology,
+                                          document_format,
+                                          FileOutputStream(File(output_path).getAbsoluteFile()))
 
     def generate_and_save_inferred_class_assertion_axioms(self, output="temp.ttl", output_format: str = None):
         """

owlapy/scripts/run.py

@@ -11,7 +11,8 @@
                    "InferredSubDataPropertyAxiomGenerator",
                    "InferredSubObjectPropertyAxiomGenerator",
                    "InferredDataPropertyCharacteristicAxiomGenerator",
-                   "InferredObjectPropertyCharacteristicAxiomGenerator"]
+                   "InferredObjectPropertyCharacteristicAxiomGenerator"
+                   ]
 
 
 def get_default_arguments(description=None):
@@ -38,12 +39,13 @@ def get_default_arguments(description=None):
 def main():
 
     args = get_default_arguments()
-    sync_reasoner = SyncReasoner(args.path_ontology)
+    sync_reasoner = SyncReasoner(ontology=args.path_ontology)
     if "all" in args.inference_types:
         it = inference_types
     else:
         it = args.inference_types
-    sync_reasoner.infer_axioms_and_save(output_path=args.out_ontology, output_format=args.output_type,
+    sync_reasoner.infer_axioms_and_save(output_path=args.out_ontology,
+                                        output_format=args.output_type,
                                         inference_types=it)
     print("Finished inferring axioms \nOutput filename: '{}'".format(args.out_ontology))
 

owlapy/utils.py

@@ -20,6 +20,17 @@
 from .owl_object import OWLObject
 from .owl_datatype import OWLDatatype
 
+import concurrent.futures
+def run_with_timeout(func, timeout, args=(), **kwargs):
+    with concurrent.futures.ThreadPoolExecutor() as executor:
+        future = executor.submit(func, *args, **kwargs)
+        try:
+            result = future.result(timeout=timeout)
+            return result
+        except concurrent.futures.TimeoutError:
+            return set()
+
+
 def concept_reducer(concepts:Iterable, opt:Callable):
     """
     Reduces a set of concepts by applying a binary operation to each pair of concepts.

tests/test_reasoner_alc_father_ontology.py

@@ -1,5 +1,5 @@
 from owlapy.owl_reasoner import SyncReasoner
-from owlapy.class_expression import OWLClass, OWLObjectSomeValuesFrom
+from owlapy.class_expression import OWLClass, OWLObjectSomeValuesFrom, OWLObjectAllValuesFrom
 from owlapy.owl_individual import OWLNamedIndividual
 from owlapy.iri import IRI
 from owlapy.owl_property import OWLObjectProperty
@@ -13,32 +13,47 @@ def test_readme(self):
 
         # Thing
         thing = OWLClass(IRI('http://www.w3.org/2002/07/owl#', 'Thing'))
+        # Nothing
+        nothing = OWLClass(IRI('http://www.w3.org/2002/07/owl#', 'Nothing'))
+
         # Person OWL Class
         person = eval("OWLClass(IRI('http://example.com/father#', 'person'))")
         # Female OWL CLass
         female = eval("OWLClass(IRI('http://example.com/father#', 'female'))")
         # hasChild object property
         hasChild = OWLObjectProperty(IRI('http://example.com/father#', 'hasChild'))
 
-        # Things
+        # Sanity checking = Things
         assert hermit.instances(thing) == {OWLNamedIndividual(IRI('http://example.com/father#', 'anna')), OWLNamedIndividual(IRI('http://example.com/father#', 'martin')), OWLNamedIndividual(IRI('http://example.com/father#', 'heinz')), OWLNamedIndividual(IRI('http://example.com/father#', 'stefan')), OWLNamedIndividual(IRI('http://example.com/father#', 'michelle')), OWLNamedIndividual(IRI('http://example.com/father#', 'markus'))}
+        # De Morgen Rules : Thing \equiv \neg Bottom
+        assert hermit.instances(thing) == hermit.instances(nothing.get_object_complement_of())
 
-        # hasChild a thing.
+        # Sanity checking = \exist hasChild Thing.
         assert hermit.instances(OWLObjectSomeValuesFrom(property=hasChild, filler=thing)) == eval(
             "{OWLNamedIndividual(IRI('http://example.com/father#', 'markus')), OWLNamedIndividual(IRI('http://example.com/father#', 'martin')), OWLNamedIndividual(IRI('http://example.com/father#', 'stefan')), OWLNamedIndividual(IRI('http://example.com/father#', 'anna'))}")
-
-        # hasChild a person.
+        # Sanity checking \exist hasChild Person.
         assert hermit.instances(OWLObjectSomeValuesFrom(property=hasChild, filler=person)) == eval(
             "{OWLNamedIndividual(IRI('http://example.com/father#', 'markus')), OWLNamedIndividual(IRI('http://example.com/father#', 'martin')), OWLNamedIndividual(IRI('http://example.com/father#', 'stefan')), OWLNamedIndividual(IRI('http://example.com/father#', 'anna'))}")
+        # \exist hasChild a person = \exist hasChild a thing
+        assert hermit.instances(OWLObjectSomeValuesFrom(property=hasChild, filler=thing)) == hermit.instances(
+            OWLObjectSomeValuesFrom(property=hasChild, filler=person))
 
-        # hasChild a female.
+        # Sanity checking: \exist hasChild a female.
         assert hermit.instances(OWLObjectSomeValuesFrom(property=hasChild, filler=female)) == eval(
             "{OWLNamedIndividual(IRI('http://example.com/father#', 'markus'))}")
         # Question: hasChild something that hasChild a female.
-        # Answer: stefan
-        # (stefan haschild markus) and markus haschild anna
+        # Answer: stefan: (stefan haschild markus) and (markus haschild anna)
         assert hermit.instances(OWLObjectSomeValuesFrom(property=hasChild,
                                                         filler=OWLObjectSomeValuesFrom(property=hasChild,
                                                                                        filler=female))) == eval(
             "{OWLNamedIndividual(IRI('http://example.com/father#', 'stefan'))}")
-
+        # De morgen rule: \neg \exist r \neg T  = \forall  r T
+        c = thing
+        forall_r_c = OWLObjectAllValuesFrom(hasChild, c)
+        neg_exist_r_neg_c = OWLObjectSomeValuesFrom(hasChild, c.get_object_complement_of()).get_object_complement_of()
+        assert hermit.instances(neg_exist_r_neg_c) == hermit.instances(forall_r_c)
+        # De morgen rule: \neg \exist r \neg bottom  = \forall  r bottom
+        c = nothing
+        forall_r_c = OWLObjectAllValuesFrom(hasChild, c)
+        neg_exist_r_neg_c = OWLObjectSomeValuesFrom(hasChild, c.get_object_complement_of()).get_object_complement_of()
+        assert hermit.instances(neg_exist_r_neg_c) == hermit.instances(forall_r_c)