removed optional arguments from abstract methods of OWLReasoner

owlapy/abstracts/abstract_owl_reasoner.py

@@ -1,7 +1,7 @@
 """OWL Reasoner"""
 from abc import ABCMeta, abstractmethod
 from typing import Iterable
-
+import logging
 
 from owlapy.class_expression import OWLClassExpression
 from owlapy.class_expression import OWLClass
@@ -12,6 +12,8 @@
 from owlapy.owl_individual import OWLNamedIndividual
 from owlapy.owl_literal import OWLLiteral
 
+logger = logging.getLogger(__name__)
+
 
 class OWLReasoner(metaclass=ABCMeta):
     """An OWLReasoner reasons over a set of axioms (the set of reasoner axioms) that is based on the imports closure of
@@ -79,13 +81,12 @@ def object_property_ranges(self, pe: OWLObjectProperty, direct: bool = False) ->
         pass
 
     @abstractmethod
-    def equivalent_classes(self, ce: OWLClassExpression, only_named: bool = True) -> Iterable[OWLClassExpression]:
+    def equivalent_classes(self, ce: OWLClassExpression) -> Iterable[OWLClassExpression]:
         """Gets the class expressions that are equivalent to the specified class expression with respect to the set of
         reasoner axioms.
 
         Args:
             ce: The class expression whose equivalent classes are to be retrieved.
-            only_named: Whether to only retrieve named equivalent classes or also complex class expressions.
 
         Returns:
             All class expressions C where the root ontology imports closure entails EquivalentClasses(ce C). If ce is
@@ -96,13 +97,12 @@ def equivalent_classes(self, ce: OWLClassExpression, only_named: bool = True) ->
         pass
 
     @abstractmethod
-    def disjoint_classes(self, ce: OWLClassExpression, only_named: bool = True) -> Iterable[OWLClassExpression]:
+    def disjoint_classes(self, ce: OWLClassExpression) -> Iterable[OWLClassExpression]:
         """Gets the class expressions that are disjoint with specified class expression with respect to the set of
         reasoner axioms.
 
         Args:
             ce: The class expression whose disjoint classes are to be retrieved.
-            only_named: Whether to only retrieve named disjoint classes or also complex class expressions.
 
         Returns:
             All class expressions D where the set of reasoner axioms entails EquivalentClasses(D ObjectComplementOf(ce))
@@ -167,15 +167,13 @@ def equivalent_data_properties(self, dp: OWLDataProperty) -> Iterable[OWLDataPro
         pass
 
     @abstractmethod
-    def data_property_values(self, e: OWLEntity, pe: OWLDataProperty, direct: bool = True) \
+    def data_property_values(self, e: OWLEntity, pe: OWLDataProperty) \
             -> Iterable['OWLLiteral']:
         """Gets the data property values for the specified entity and data property expression.
 
         Args:
             e: The owl entity (usually an individual) that is the subject of the data property values.
             pe: The data property expression whose values are to be retrieved for the specified entity.
-            direct: Specifies if the direct values should be retrieved (True), or if all values should be retrieved
-                (False), so that sub properties are taken into account.
 
         Note: Can be used to get values, for example, of 'label' property of owl entities such as classes and properties
         too (not only individuals).
@@ -187,15 +185,13 @@ def data_property_values(self, e: OWLEntity, pe: OWLDataProperty, direct: bool =
         pass
 
     @abstractmethod
-    def object_property_values(self, ind: OWLNamedIndividual, pe: OWLObjectPropertyExpression, direct: bool = True) \
+    def object_property_values(self, ind: OWLNamedIndividual, pe: OWLObjectPropertyExpression) \
             -> Iterable[OWLNamedIndividual]:
         """Gets the object property values for the specified individual and object property expression.
 
         Args:
             ind: The individual that is the subject of the object property values.
             pe: The object property expression whose values are to be retrieved for the specified individual.
-            direct: Specifies if the direct values should be retrieved (True), or if all values should be retrieved
-                (False), so that sub properties are taken into account.
 
         Returns:
             The named individuals such that for each individual j, the set of reasoner axioms entails
@@ -221,7 +217,7 @@ def instances(self, ce: OWLClassExpression, direct: bool = False) -> Iterable[OW
         pass
 
     @abstractmethod
-    def sub_classes(self, ce: OWLClassExpression, direct: bool = False, only_named: bool = True) \
+    def sub_classes(self, ce: OWLClassExpression, direct: bool = False) \
             -> Iterable[OWLClassExpression]:
         """Gets the set of named classes that are the strict (potentially direct) subclasses of the specified class
         expression with respect to the reasoner axioms.
@@ -230,7 +226,6 @@ def sub_classes(self, ce: OWLClassExpression, direct: bool = False, only_named:
             ce: The class expression whose strict (direct) subclasses are to be retrieved.
             direct: Specifies if the direct subclasses should be retrieved (True) or if the all subclasses
                 (descendant) classes should be retrieved (False).
-            only_named: Whether to only retrieve named sub-classes or also complex class expressions.
 
         Returns:
             If direct is True, each class C where reasoner axioms entails DirectSubClassOf(C, ce). If direct is False,
@@ -363,7 +358,7 @@ def get_root_ontology(self) -> OWLOntology:
         pass
 
     @abstractmethod
-    def super_classes(self, ce: OWLClassExpression, direct: bool = False, only_named: bool = True) \
+    def super_classes(self, ce: OWLClassExpression, direct: bool = False) \
             -> Iterable[OWLClassExpression]:
         """Gets the stream of named classes that are the strict (potentially direct) super classes of the specified
         class expression with respect to the imports closure of the root ontology.
@@ -372,14 +367,15 @@ class expression with respect to the imports closure of the root ontology.
             ce: The class expression whose strict (direct) super classes are to be retrieved.
             direct: Specifies if the direct super classes should be retrieved (True) or if the all super classes
                 (ancestors) classes should be retrieved (False).
-            only_named: Whether to only retrieve named super classes or also complex class expressions.
 
         Returns:
             If direct is True, each class C where the set of reasoner axioms entails DirectSubClassOf(ce, C).
             If direct is False, each class C where  set of reasoner axioms entails StrictSubClassOf(ce, C).
             If ce is equivalent to owl:Thing then nothing will be returned.
         """
         pass
+
+
 class OWLReasonerEx(OWLReasoner, metaclass=ABCMeta):
     """Extra convenience methods for OWL Reasoners"""
 
@@ -399,24 +395,21 @@ def data_property_ranges(self, pe: OWLDataProperty, direct: bool = False) -> Ite
             yield ax.get_range()
             if not direct:
                 logger.warning("indirect not implemented")
-                # TODO:
 
     # default
-    def all_data_property_values(self, pe: OWLDataProperty, direct: bool = True) -> Iterable[OWLLiteral]:
+    def all_data_property_values(self, pe: OWLDataProperty) -> Iterable[OWLLiteral]:
         """Gets all values for the given data property expression that appear in the knowledge base.
 
         Args:
             pe: The data property expression whose values are to be retrieved
-            direct: Specifies if only the direct values of the data property pe should be retrieved (True), or if
-                    the values of sub properties of pe should be taken into account (False).
 
         Returns:
             A set of OWLLiterals containing literals such that for each literal l in the set, the set of reasoner
             axioms entails DataPropertyAssertion(pe ind l) for any ind.
         """
         onto = self.get_root_ontology()
         for ind in onto.individuals_in_signature():
-            for lit in self.data_property_values(ind, pe, direct):
+            for lit in self.data_property_values(ind, pe):
                 yield lit
 
     # default
@@ -456,7 +449,7 @@ def ind_object_properties(self, ind: OWLNamedIndividual, direct: bool = True) ->
         onto = self.get_root_ontology()
         for op in onto.object_properties_in_signature():
             try:
-                next(iter(self.object_property_values(ind, op, direct)))
+                next(iter(self.object_property_values(ind, op)))
                 yield op
             except StopIteration:
-                pass
+                pass

owlapy/owl_reasoner.py

@@ -33,11 +33,6 @@
 
 _P = TypeVar('_P', bound=OWLPropertyExpression)
 
-# TODO:CD:The name of the classes defined with metaclass=ABCMeta should reflect that
-# TODO:CD: An instance cannot be created from those classes.
-# TODO:CD: We should move those Abstract Base Classes into a respective package, e.g.
-# TODO:CD: owlapy/abstract_owl_reasoner/abstract_owl_reasoner.py should contain OWLReasoner and OWLReasonerEx
-
 
 class OntologyReasoner(OWLReasonerEx):
     __slots__ = '_ontology', '_world'
@@ -1149,7 +1144,7 @@ def _retrieve_triples(self, pe: OWLPropertyExpression) -> Iterable:
         yield from relations
 
 
-class SyncReasoner:
+class SyncReasoner(OWLReasonerEx):
 
     def __init__(self, ontology: Union[SyncOntology, str], reasoner="HermiT"):
         """
@@ -1633,9 +1628,10 @@ def infer_axioms_and_save(self, output_path: str = None, output_format: str = No
 
     def generate_and_save_inferred_class_assertion_axioms(self, output="temp.ttl", output_format: str = None):
         """
-        Generates inferred class assertion axioms for the ontology managed by this instance's reasoner and saves them to a file.
-        This function uses the OWL API to generate inferred class assertion axioms based on the ontology and reasoner
-        associated with this instance. The inferred axioms are saved to the specified output file in the desired format.
+        Generates inferred class assertion axioms for the ontology managed by this instance's reasoner and saves them
+        to a file. This function uses the OWL API to generate inferred class assertion axioms based on the ontology
+        and reasoner associated with this instance. The inferred axioms are saved to the specified output file in
+        the desired format.
         Parameters:
         -----------
         output : str, optional