Merge pull request #105 from dice-group/refactoring_SyncReasoner

Refactoring sync reasoner

README.md

@@ -30,6 +30,54 @@ pytest -p no:warnings -x # Running  142 tests ~ 30 secs
 
 ## Examples
 
+### Exploring OWL Ontology
+
+<details><summary> Click me! </summary>
+
+```python
+from owlapy.owl_ontology_manager import SyncOntologyManager
+
+ontology_path = "KGs/Family/father.owl"
+onto = SyncOntologyManager().load_ontology(ontology_path)
+
+print({owl_class.reminder for owl_class in onto.classes_in_signature()}) 
+# {'Thing', 'female', 'male', 'person'}
+
+print({individual.reminder for individual in onto.individuals_in_signature()}) 
+# {'michelle', 'stefan', 'martin', 'anna', 'heinz', 'markus'}
+
+print({object_property.reminder for object_property in onto.object_properties_in_signature()})
+# {'hasChild'}
+
+for owl_subclass_of_axiom in onto.get_tbox_axioms():
+    print(owl_subclass_of_axiom)
+
+# OWLEquivalentClassesAxiom([OWLClass(IRI('http://example.com/father#', 'male')), OWLObjectComplementOf(OWLClass(IRI('http://example.com/father#', 'female')))],[])
+# OWLSubClassOfAxiom(sub_class=OWLClass(IRI('http://example.com/father#', 'female')),super_class=OWLClass(IRI('http://example.com/father#', 'person')),annotations=[])
+# OWLSubClassOfAxiom(sub_class=OWLClass(IRI('http://example.com/father#', 'male')),super_class=OWLClass(IRI('http://example.com/father#', 'person')),annotations=[])
+# OWLSubClassOfAxiom(sub_class=OWLClass(IRI('http://example.com/father#', 'person')),super_class=OWLClass(IRI('http://www.w3.org/2002/07/owl#', 'Thing')),annotations=[])
+# OWLObjectPropertyRangeAxiom(OWLObjectProperty(IRI('http://example.com/father#', 'hasChild')),OWLClass(IRI('http://example.com/father#', 'person')),[])
+# OWLObjectPropertyDomainAxiom(OWLObjectProperty(IRI('http://example.com/father#', 'hasChild')),OWLClass(IRI('http://example.com/father#', 'person')),[])
+
+
+for axiom in onto.get_abox_axioms():
+    print(axiom)
+
+# OWLClassAssertionAxiom(individual=OWLNamedIndividual(IRI('http://example.com/father#', 'anna')),class_expression=OWLClass(IRI('http://example.com/father#', 'female')),annotations=[])
+# OWLClassAssertionAxiom(individual=OWLNamedIndividual(IRI('http://example.com/father#', 'michelle')),class_expression=OWLClass(IRI('http://example.com/father#', 'female')),annotations=[])
+# OWLClassAssertionAxiom(individual=OWLNamedIndividual(IRI('http://example.com/father#', 'martin')),class_expression=OWLClass(IRI('http://example.com/father#', 'male')),annotations=[])
+# OWLClassAssertionAxiom(individual=OWLNamedIndividual(IRI('http://example.com/father#', 'markus')),class_expression=OWLClass(IRI('http://example.com/father#', 'male')),annotations=[])
+# OWLClassAssertionAxiom(individual=OWLNamedIndividual(IRI('http://example.com/father#', 'heinz')),class_expression=OWLClass(IRI('http://example.com/father#', 'male')),annotations=[])
+# OWLClassAssertionAxiom(individual=OWLNamedIndividual(IRI('http://example.com/father#', 'stefan')),class_expression=OWLClass(IRI('http://example.com/father#', 'male')),annotations=[])
+# OWLObjectPropertyAssertionAxiom(subject=OWLNamedIndividual(IRI('http://example.com/father#', 'markus')),property_=OWLObjectProperty(IRI('http://example.com/father#', 'hasChild')),object_=OWLNamedIndividual(IRI('http://example.com/father#', 'anna')),annotations=[])
+# OWLObjectPropertyAssertionAxiom(subject=OWLNamedIndividual(IRI('http://example.com/father#', 'martin')),property_=OWLObjectProperty(IRI('http://example.com/father#', 'hasChild')),object_=OWLNamedIndividual(IRI('http://example.com/father#', 'heinz')),annotations=[])
+# OWLObjectPropertyAssertionAxiom(subject=OWLNamedIndividual(IRI('http://example.com/father#', 'stefan')),property_=OWLObjectProperty(IRI('http://example.com/father#', 'hasChild')),object_=OWLNamedIndividual(IRI('http://example.com/father#', 'markus')),annotations=[])
+# OWLObjectPropertyAssertionAxiom(subject=OWLNamedIndividual(IRI('http://example.com/father#', 'anna')),property_=OWLObjectProperty(IRI('http://example.com/father#', 'hasChild')),object_=OWLNamedIndividual(IRI('http://example.com/father#', 'heinz')),annotations=[])
+
+```
+
+</details>
+
 ### Creating OWL Class Expressions
 <details><summary> Click me! </summary>
 

owlapy/owl_axiom.py

@@ -523,6 +523,13 @@ def __init__(self, sub_class: OWLClassExpression, super_class: OWLClassExpressio
         self._super_class = super_class
         super().__init__(annotations=annotations)
 
+    @property
+    def sub_class(self) -> OWLClassExpression:
+        return self._sub_class
+    @property
+    def super_class(self) -> OWLClassExpression:
+        return self._super_class
+
     def get_sub_class(self) -> OWLClassExpression:
         return self._sub_class
 
@@ -533,7 +540,8 @@ def __eq__(self, other):
         if type(other) is type(self):
             return self._super_class == other._super_class and self._sub_class == other._sub_class \
                 and self._annotations == other._annotations
-        return NotImplemented
+        else:
+            return False
 
     def __hash__(self):
         return hash((self._super_class, self._sub_class, *self._annotations))

owlapy/owl_individual.py

@@ -35,11 +35,12 @@ def __init__(self, iri: Union[IRI, str]):
             self._iri = iri
         else:
             self._iri = IRI.create(iri)
-
     @property
     def iri(self) -> IRI:
         return self._iri
-
     @property
     def str(self):
         return self._iri.as_str()
+    @property
+    def reminder(self):
+        return self._iri.reminder

owlapy/owl_ontology.py

@@ -126,7 +126,6 @@ def __eq__(self, other):
 
 def _check_expression(expr: OWLObject, ontology: AbstractOWLOntology, world: owlready2.namespace.World):
     """
-    @TODO:CD: Documentation
     Creates all entities (individuals, classes, properties) that appear in the given (complex) class expression
     and do not exist in the given ontology yet
 
@@ -1035,7 +1034,6 @@ def _get_imports_enum(self, include_imports_closure: bool):
         else:
             imports = Imports.EXCLUDED
         return imports
-
     def get_signature(self, include_imports_closure: bool = True):
         """Gets the entities that are in the signature of this ontology.
 
@@ -1045,6 +1043,7 @@ def get_signature(self, include_imports_closure: bool = True):
         Returns:
             Entities in signature.
         """
+        # @TODO: CD: Is this class method redundant given that we have the individuals_in_signature ?
         return self.mapper.map_(self.owlapi_ontology.getSignature(self._get_imports_enum(include_imports_closure)))
 
     def get_abox_axioms(self, include_imports_closure: bool = True) -> Iterable[OWLAxiom]:
@@ -1056,7 +1055,6 @@ def get_abox_axioms(self, include_imports_closure: bool = True) -> Iterable[OWLA
         Returns:
             ABox axioms.
         """
-
         return self.mapper.map_(self.owlapi_ontology.getABoxAxioms(self._get_imports_enum(include_imports_closure)))
 
     def get_tbox_axioms(self, include_imports_closure: bool = True) -> Iterable[OWLAxiom]:
@@ -1100,7 +1098,14 @@ def __hash__(self):
         return int(self.owlapi_ontology.getOntologyID().hashCode())
 
     def __repr__(self):
-        return f'SyncOntology({self.manager}, {self.path}, {self.new})'
+        return (f'SyncOntology:'
+                f'\t|Tbox|={len(self.get_tbox_axioms())}'
+                f'\t|Abox|={len(self.get_abox_axioms())}'
+                f'\t|Individuals|={len(self.individuals_in_signature())}'
+                f'\t|Classes|={len(self.classes_in_signature())}'
+                f'\t|Object Properties|={len(self.object_properties_in_signature())}'
+                f'\t|Data Properties|={len(self.data_properties_in_signature())}'
+                f'\n{self.manager}\tPath:{self.path}\tNew:{self.new}')
 
 
 OWLREADY2_FACET_KEYS = MappingProxyType({

owlapy/owl_ontology_manager.py

@@ -103,8 +103,7 @@ def apply_change(self, change: AbstractOWLOntologyChange):
             ont_x.imported_ontologies.append(
                 self._world.get_ontology(change.get_import_declaration().str))
         else:
-            # TODO XXX
-            raise NotImplementedError
+            raise NotImplementedError("Change is not yet implemented.")
 
     def save_world(self):
         """Saves the actual state of the quadstore in the SQLite3 file.
@@ -139,4 +138,4 @@ def get_owlapi_manager(self):
         return self.owlapi_manager
 
     def apply_change(self, change: AbstractOWLOntologyChange):
-        raise NotImplementedError()
+        raise NotImplementedError("A change cannot be applied at the moment.")

owlapy/owl_property.py

@@ -113,6 +113,10 @@ class OWLObjectProperty(OWLObjectPropertyExpression, OWLProperty):
 
     _iri: IRI
 
+    @property
+    def reminder(self):
+        return self._iri.reminder
+
     def get_named_property(self) -> 'OWLObjectProperty':
         # documented in parent
         return self

owlapy/owl_reasoner.py

@@ -1013,53 +1013,9 @@ def __init__(self, ontology: Union[SyncOntology, str], reasoner="HermiT"):
 
         self._owlapi_manager = self.manager.get_owlapi_manager()
         self._owlapi_ontology = self.ontology.get_owlapi_ontology()
-        # super().__init__(self.ontology)
         self.mapper = self.ontology.mapper
-        from org.semanticweb.owlapi.util import (InferredClassAssertionAxiomGenerator, InferredSubClassAxiomGenerator,
-                                                 InferredEquivalentClassAxiomGenerator,
-                                                 InferredDisjointClassesAxiomGenerator,
-                                                 InferredEquivalentDataPropertiesAxiomGenerator,
-                                                 InferredEquivalentObjectPropertyAxiomGenerator,
-                                                 InferredInverseObjectPropertiesAxiomGenerator,
-                                                 InferredSubDataPropertyAxiomGenerator,
-                                                 InferredSubObjectPropertyAxiomGenerator,
-                                                 InferredDataPropertyCharacteristicAxiomGenerator,
-                                                 InferredObjectPropertyCharacteristicAxiomGenerator)
-
-        self.inference_types_mapping = {"InferredClassAssertionAxiomGenerator": InferredClassAssertionAxiomGenerator(),
-                                        "InferredSubClassAxiomGenerator": InferredSubClassAxiomGenerator(),
-                                        "InferredDisjointClassesAxiomGenerator": InferredDisjointClassesAxiomGenerator(),
-                                        "InferredEquivalentClassAxiomGenerator": InferredEquivalentClassAxiomGenerator(),
-                                        "InferredInverseObjectPropertiesAxiomGenerator": InferredInverseObjectPropertiesAxiomGenerator(),
-                                        "InferredEquivalentDataPropertiesAxiomGenerator": InferredEquivalentDataPropertiesAxiomGenerator(),
-                                        "InferredEquivalentObjectPropertyAxiomGenerator": InferredEquivalentObjectPropertyAxiomGenerator(),
-                                        "InferredSubDataPropertyAxiomGenerator": InferredSubDataPropertyAxiomGenerator(),
-                                        "InferredSubObjectPropertyAxiomGenerator": InferredSubObjectPropertyAxiomGenerator(),
-                                        "InferredDataPropertyCharacteristicAxiomGenerator": InferredDataPropertyCharacteristicAxiomGenerator(),
-                                        "InferredObjectPropertyCharacteristicAxiomGenerator": InferredObjectPropertyCharacteristicAxiomGenerator(),
-                                        }
-
-        # () Create a reasoner using the ontology
-        if reasoner == "HermiT":
-            from org.semanticweb.HermiT import ReasonerFactory
-            self._owlapi_reasoner = ReasonerFactory().createReasoner(self._owlapi_ontology)
-            assert self._owlapi_reasoner.getReasonerName() == "HermiT"
-        elif reasoner == "JFact":
-            from uk.ac.manchester.cs.jfact import JFactFactory
-            self._owlapi_reasoner = JFactFactory().createReasoner(self._owlapi_ontology)
-        elif reasoner == "Pellet":
-            from openllet.owlapi import PelletReasonerFactory
-            self._owlapi_reasoner = PelletReasonerFactory().createReasoner(self._owlapi_ontology)
-        elif reasoner == "Openllet":
-            from openllet.owlapi import OpenlletReasonerFactory
-            self._owlapi_reasoner = OpenlletReasonerFactory().getInstance().createReasoner(self._owlapi_ontology)
-        elif reasoner == "Structural":
-            from org.semanticweb.owlapi.reasoner.structural import StructuralReasonerFactory
-            self._owlapi_reasoner = StructuralReasonerFactory().createReasoner(self._owlapi_ontology)
-        else:
-            raise NotImplementedError("Not implemented")
-
-        self.reasoner = reasoner
+        self.inference_types_mapping = import_and_include_axioms_generators()
+        self._owlapi_reasoner = initialize_reasoner(reasoner,self._owlapi_ontology)
 
     def _instances(self, ce: OWLClassExpression, direct=False) -> Set[OWLNamedIndividual]:
         """
@@ -1378,11 +1334,11 @@ def disjoint_data_properties(self, p: OWLDataProperty):
         yield from [self.mapper.map_(pe) for pe in
                     self._owlapi_reasoner.getDisjointDataProperties(self.mapper.map_(p)).getFlattened()]
 
-    def types(self, i: OWLNamedIndividual, direct: bool = False):
+    def types(self, individual: OWLNamedIndividual, direct: bool = False):
         """Gets the named classes which are (potentially direct) types of the specified named individual.
 
         Args:
-            i: The individual whose types are to be retrieved.
+            individual: The individual whose types are to be retrieved.
             direct: Specifies if the direct types should be retrieved (True), or if all types should be retrieved
                 (False).
 
@@ -1392,7 +1348,7 @@ def types(self, i: OWLNamedIndividual, direct: bool = False):
             entails ClassAssertion(C, ind).
         """
         yield from [self.mapper.map_(ind) for ind in
-                    self._owlapi_reasoner.getTypes(self.mapper.map_(i), direct).getFlattened()]
+                    self._owlapi_reasoner.getTypes(self.mapper.map_(individual), direct).getFlattened()]
 
     def has_consistent_ontology(self) -> bool:
         """
@@ -1544,3 +1500,48 @@ def unsatisfiable_classes(self):
 
     def get_root_ontology(self) -> AbstractOWLOntology:
         return self.ontology
+
+def initialize_reasoner(reasoner:str, owlapi_ontology):
+    # () Create a reasoner using the ontology
+    if reasoner == "HermiT":
+        from org.semanticweb.HermiT import ReasonerFactory
+        owlapi_reasoner = ReasonerFactory().createReasoner(owlapi_ontology)
+        assert owlapi_reasoner.getReasonerName() == "HermiT"
+    elif reasoner == "JFact":
+        from uk.ac.manchester.cs.jfact import JFactFactory
+        owlapi_reasoner = JFactFactory().createReasoner(owlapi_ontology)
+    elif reasoner == "Pellet":
+        from openllet.owlapi import PelletReasonerFactory
+        owlapi_reasoner = PelletReasonerFactory().createReasoner(owlapi_ontology)
+    elif reasoner == "Openllet":
+        from openllet.owlapi import OpenlletReasonerFactory
+        owlapi_reasoner = OpenlletReasonerFactory().getInstance().createReasoner(owlapi_ontology)
+    elif reasoner == "Structural":
+        from org.semanticweb.owlapi.reasoner.structural import StructuralReasonerFactory
+        owlapi_reasoner = StructuralReasonerFactory().createReasoner(owlapi_ontology)
+    else:
+        raise NotImplementedError("Not implemented")
+    return owlapi_reasoner
+def import_and_include_axioms_generators():
+    from org.semanticweb.owlapi.util import (InferredClassAssertionAxiomGenerator, InferredSubClassAxiomGenerator,
+                                             InferredEquivalentClassAxiomGenerator,
+                                             InferredDisjointClassesAxiomGenerator,
+                                             InferredEquivalentDataPropertiesAxiomGenerator,
+                                             InferredEquivalentObjectPropertyAxiomGenerator,
+                                             InferredInverseObjectPropertiesAxiomGenerator,
+                                             InferredSubDataPropertyAxiomGenerator,
+                                             InferredSubObjectPropertyAxiomGenerator,
+                                             InferredDataPropertyCharacteristicAxiomGenerator,
+                                             InferredObjectPropertyCharacteristicAxiomGenerator)
+
+    return {"InferredClassAssertionAxiomGenerator": InferredClassAssertionAxiomGenerator(),
+                                    "InferredSubClassAxiomGenerator": InferredSubClassAxiomGenerator(),
+                                    "InferredDisjointClassesAxiomGenerator": InferredDisjointClassesAxiomGenerator(),
+                                    "InferredEquivalentClassAxiomGenerator": InferredEquivalentClassAxiomGenerator(),
+                                    "InferredInverseObjectPropertiesAxiomGenerator": InferredInverseObjectPropertiesAxiomGenerator(),
+                                    "InferredEquivalentDataPropertiesAxiomGenerator": InferredEquivalentDataPropertiesAxiomGenerator(),
+                                    "InferredEquivalentObjectPropertyAxiomGenerator": InferredEquivalentObjectPropertyAxiomGenerator(),
+                                    "InferredSubDataPropertyAxiomGenerator": InferredSubDataPropertyAxiomGenerator(),
+                                    "InferredSubObjectPropertyAxiomGenerator": InferredSubObjectPropertyAxiomGenerator(),
+                                    "InferredDataPropertyCharacteristicAxiomGenerator": InferredDataPropertyCharacteristicAxiomGenerator(),
+                                    "InferredObjectPropertyCharacteristicAxiomGenerator": InferredObjectPropertyCharacteristicAxiomGenerator()}

tests/test_sync_ontology.py

@@ -80,6 +80,13 @@ class TestSyncReasoner(unittest.TestCase):
     manager = SyncOntologyManager()
     onto = manager.load_ontology(ontology_path)
 
+    def test_interface_father_dataset(self):
+        ontology_path = "KGs/Family/father.owl"
+        onto = SyncOntologyManager().load_ontology(ontology_path)
+        assert {owl_class.reminder for owl_class in onto.classes_in_signature()}=={'male', 'female', 'Thing', 'person'}
+        assert {individual.reminder for individual in onto.individuals_in_signature()}=={'markus', 'anna', 'martin', 'stefan', 'heinz', 'michelle'}
+        assert {object_property.reminder for object_property in onto.object_properties_in_signature()}=={'hasChild'}
+
     # NOTE AB: The name of "assertCountEqual" may be misleading,but it's essentially an order-insensitive "assertEqual".
 
     def test_classes_in_signature(self):