Merge pull request #111 from dice-group/adding_static_funcs

Refactoring

.github/workflows/test.yml

@@ -25,6 +25,7 @@ jobs:
         run: |
           wget https://files.dice-research.org/projects/Ontolearn/KGs.zip
           unzip KGs.zip
+          pip install scikit-learn
           python -m pytest -p no:warnings -x
 
       - name: Coverage report

.gitignore

@@ -148,4 +148,4 @@ cython_debug/
 .vscode/
 
 # Project related files
-/KGs/
+KGs/

README.md

@@ -30,29 +30,6 @@ pytest -p no:warnings -x # Running  147 tests ~ 35 secs
 
 ## Examples
 
-### Sklearn to OWL Ontology
-
-<details><summary> Click me! </summary>
-
-```python
-from owlapy.owl_ontology_manager import SyncOntologyManager
-from owlapy.util_owl_static_funcs import csv_to_rdf_kg
-import pandas as pd
-from sklearn.datasets import load_iris
-data = load_iris()
-df = pd.DataFrame(data.data, columns=data.feature_names)
-df.to_csv("iris_dataset.csv", index=False)
-path_kg = "iris_kg.owl"
-# Construct an RDF Knowledge Graph from a CSV file
-csv_to_rdf_kg(path_csv="iris_dataset.csv", path_kg=path_kg, namespace="http://owlapy.com/iris")
-onto = SyncOntologyManager().load_ontology(path_kg)
-assert len(onto.get_abox_axioms()) == 750
-
-```
-
-</details>
-
-
 ### Exploring OWL Ontology
 
 <details><summary> Click me! </summary>
@@ -101,7 +78,8 @@ for axiom in onto.get_abox_axioms():
 
 </details>
 
-### Creating OWL Class Expressions
+### OWL Knowledge Engineering
+
 <details><summary> Click me! </summary>
 
 ```python
@@ -111,31 +89,27 @@ from owlapy import owl_expression_to_sparql, owl_expression_to_dl
 from owlapy.owl_ontology_manager import OntologyManager
 from owlapy.owl_axiom import OWLDeclarationAxiom, OWLClassAssertionAxiom
 from owlapy.owl_individual import OWLNamedIndividual, IRI
-
+from owlapy.static_funcs import create_ontology
 # Using owl classes to create a complex class expression
 male = OWLClass("http://example.com/society#male")
 hasChild = OWLObjectProperty("http://example.com/society#hasChild")
 hasChild_male = OWLObjectSomeValuesFrom(hasChild, male)
 teacher = OWLClass("http://example.com/society#teacher")
 teacher_that_hasChild_male = OWLObjectIntersectionOf([hasChild_male, teacher])
 
-# You can render and print owl class expressions in Description Logics syntax or convert it to SPARQL for example. 
+# You can render and print owl class expressions in Description Logics syntax or convert it to SPARQL for example.
 print(owl_expression_to_dl(teacher_that_hasChild_male)) # (∃ hasChild.male) ⊓ teacher
 print(owl_expression_to_sparql(teacher_that_hasChild_male)) #  SELECT DISTINCT ?x WHERE {  ?x <http://example.com/society#hasChild> ?s_1 . ?s_1 a <http://example.com/society#male> . ?x a <http://example.com/society#teacher> .  } }
 
-# Create an Ontology, add the axioms and save the Ontology.
-manager = OntologyManager()
-new_iri = IRI.create("file:/example_ontology.owl")
-ontology = manager.create_ontology(new_iri)
-
+# Create an ontology via ontology manager directly
+ontology = create_ontology("file:/example_ontology.owl",with_owlapi=False)
 john = OWLNamedIndividual("http://example.com/society#john")
 male_declaration_axiom = OWLDeclarationAxiom(male)
 hasChild_declaration_axiom = OWLDeclarationAxiom(hasChild)
 john_declaration_axiom = OWLDeclarationAxiom(john)
 john_a_male_assertion_axiom = OWLClassAssertionAxiom(john, male)
 ontology.add_axiom([male_declaration_axiom, hasChild_declaration_axiom, john_declaration_axiom, john_a_male_assertion_axiom])
-ontology.save()
-
+ontology.save(inplace=True)
 ```
 
 Every OWL object that can be used to classify individuals, is considered a class expression and 
@@ -201,5 +175,29 @@ stopJVM()
 
 Check also the [examples](https://github.com/dice-group/owlapy/tree/develop/examples) and [tests](https://github.com/dice-group/owlapy/tree/develop/tests) folders.
 
+
+### Sklearn to OWL Ontology
+
+<details><summary> Click me! </summary>
+
+```python
+from owlapy.owl_ontology_manager import SyncOntologyManager
+from owlapy.util_owl_static_funcs import csv_to_rdf_kg
+import pandas as pd
+from sklearn.datasets import load_iris
+data = load_iris()
+df = pd.DataFrame(data.data, columns=data.feature_names)
+df.to_csv("iris_dataset.csv", index=False)
+path_kg = "iris_kg.owl"
+# Construct an RDF Knowledge Graph from a CSV file
+csv_to_rdf_kg(path_csv="iris_dataset.csv", path_kg=path_kg, namespace="http://owlapy.com/iris")
+onto = SyncOntologyManager().load_ontology(path_kg)
+assert len(onto.get_abox_axioms()) == 750
+
+```
+
+</details>
+
+
 ## How to cite
 Currently, we are working on our manuscript describing our framework.

owlapy/class_expression/restriction.py

@@ -10,7 +10,7 @@
 from ..owl_individual import OWLIndividual
 from ..owl_datatype import OWLDatatype
 from ..owl_object import OWLObject
-from ..vocab import  OWLFacet
+from ..vocab import OWLFacet
 from datetime import datetime, date
 from pandas import Timedelta
 
@@ -53,7 +53,7 @@ class OWLHasValueRestriction(Generic[_T], OWLRestriction, HasFiller[_T], metacla
     """Represent a HasValue restriction in the OWL 2
 
     Args:
-        _T: The value type.
+        value: The value type _T.
     """
     __slots__ = ()
 
@@ -143,12 +143,14 @@ def get_filler(self) -> OWLClassExpression:
         return self._filler
 
 
-class OWLObjectCardinalityRestriction(OWLCardinalityRestriction[OWLClassExpression], OWLQuantifiedObjectRestriction):
+class OWLObjectCardinalityRestriction(OWLCardinalityRestriction[OWLClassExpression], OWLQuantifiedObjectRestriction,
+                                      metaclass=ABCMeta):
     """Represents Object Property Cardinality Restrictions in the OWL 2 specification."""
     __slots__ = ()
 
     _property: OWLObjectPropertyExpression
     # @TODO: CD: property shows the in-built function
+
     @abstractmethod
     def __init__(self, cardinality: int, property: OWLObjectPropertyExpression, filler: OWLClassExpression):
         super().__init__(cardinality, filler)
@@ -169,6 +171,7 @@ def __eq__(self, other):
                 and self._filler == other._filler
         else:
             return False
+
     def __hash__(self):
         return hash((self._property, self._cardinality, self._filler))
 
@@ -342,7 +345,6 @@ def __eq__(self, other):
         else:
             return False
 
-
     def __hash__(self):
         return hash(("OWLObjectHasSelf", self._property))
 
@@ -430,13 +432,16 @@ def as_object_union_of(self) -> OWLClassExpression:
         if len(self._values) == 1:
             return self
         return OWLObjectUnionOf(map(lambda _: OWLObjectOneOf(_), self.individuals()))
+
     def __hash__(self):
         return hash(("OWLObjectOneOf", self._values))
+
     def __eq__(self, other):
         if type(other) is type(self):
             return self._values == other._values
         else:
             return False
+
     def __repr__(self):
         return f'OWLObjectOneOf({self._values})'
 
@@ -466,6 +471,7 @@ def __init__(self, filler: OWLDataRange):
         assert isinstance(filler, OWLDataRange), "filler must be an OWLDataRange"
         self._filler = filler
     # @TODO:CD: define it as @property
+
     def get_filler(self) -> OWLDataRange:
         # documented in parent (HasFiller)
         return self._filler
@@ -479,13 +485,16 @@ class OWLDataCardinalityRestriction(OWLCardinalityRestriction[OWLDataRange],
 
     _property: OWLDataPropertyExpression
     # @TODO: CD: property shows the in-built function
+
     @abstractmethod
     def __init__(self, cardinality: int, property: OWLDataPropertyExpression, filler: OWLDataRange):
         assert isinstance(filler, OWLDataRange), "filler must be an OWLDataRange"
         super().__init__(cardinality, filler)
         self._property = property
+
     def __hash__(self):
         return hash(("OWLDataCardinalityRestriction",self._property, self._cardinality, self._filler))
+
     def __repr__(self):
         return f"{type(self).__name__}(" \
                f"property={repr(self.get_property())},{self.get_cardinality()},filler={repr(self.get_filler())})"
@@ -501,6 +510,7 @@ def get_property(self) -> OWLDataPropertyExpression:
         # documented in parent
         return self._property
 
+
 class OWLDataMinCardinality(OWLDataCardinalityRestriction):
     """A minimum cardinality expression DataMinCardinality( n DPE DR ) consists of a nonnegative integer n, a data
        property expression DPE, and a unary data range DR, and it contains all those individuals that are connected by
@@ -511,6 +521,7 @@ class OWLDataMinCardinality(OWLDataCardinalityRestriction):
 
     type_index: Final = 3015
     # @TODO: CD: property shows the in-built function
+
     def __init__(self, cardinality: int, property: OWLDataPropertyExpression, filler: OWLDataRange):
         """
         Args:
@@ -534,6 +545,7 @@ class OWLDataMaxCardinality(OWLDataCardinalityRestriction):
 
     type_index: Final = 3017
     # @TODO: CD: property shows the in-built function
+
     def __init__(self, cardinality: int, property: OWLDataPropertyExpression, filler: OWLDataRange):
         """
         Args:
@@ -557,6 +569,7 @@ class OWLDataExactCardinality(OWLDataCardinalityRestriction):
 
     type_index: Final = 3016
     # @TODO: CD: property shows the in-built function
+
     def __init__(self, cardinality: int, property: OWLDataPropertyExpression, filler: OWLDataRange):
         """
         Args:
@@ -593,6 +606,7 @@ class OWLDataSomeValuesFrom(OWLQuantifiedDataRestriction):
 
     _property: OWLDataPropertyExpression
     # @TODO: CD: property shows the in-built function
+
     def __init__(self, property: OWLDataPropertyExpression, filler: OWLDataRange):
         """Gets an OWLDataSomeValuesFrom restriction.
 
@@ -614,6 +628,7 @@ def __eq__(self, other):
             return self._filler == other._filler and self._property == other._property
         else:
             return False
+
     def __hash__(self):
         return hash(("OWLDataSomeValuesFrom",self._filler, self._property))
 
@@ -636,6 +651,7 @@ class OWLDataAllValuesFrom(OWLQuantifiedDataRestriction):
 
     _property: OWLDataPropertyExpression
     # @TODO:CD:property shows the in-built function
+
     def __init__(self, property: OWLDataPropertyExpression, filler: OWLDataRange):
         """Gets an OWLDataAllValuesFrom restriction.
 
@@ -657,6 +673,7 @@ def __eq__(self, other):
             return self._filler == other._filler and self._property == other._property
         else:
             return False
+
     def __hash__(self):
         return hash(("OWLDataAllValuesFrom",self._filler, self._property))
 
@@ -674,17 +691,20 @@ class OWLDataHasValue(OWLHasValueRestriction[OWLLiteral], OWLDataRestriction):
     __slots__ = '_property'
     # @TODO:CD:What is _v? even if it is inherited from somewhere, we should add it into docstring.
     # @TODO:CD: We should also name the class attributes in a more meaningful manner.
+    # AB re: _v is indeed inherited and represents the value of this DataHasValue CE. It's name is kept general
+    # because the value can have different types depending on the implementor of the base class.
 
     type_index: Final = 3014
 
     _property: OWLDataPropertyExpression
     # @TODO: CD: property shows the in-built function
+
     def __init__(self, property: OWLDataPropertyExpression, value: OWLLiteral):
         """Gets an OWLDataHasValue restriction.
 
         Args:
             property: The data property that the restriction acts along.
-            filler: The literal value.
+            value: The literal value.
 
         Returns:
             An OWLDataHasValue restriction along the specified property with the specified literal.
@@ -700,8 +720,9 @@ def __eq__(self, other):
             return self._v == other._v and self._property == other._property
         else:
             return False
+
     def __hash__(self):
-        return hash(("OWLDataHasValue",self._v, self._property))
+        return hash(("OWLDataHasValue", self._v, self._property))
 
     def as_some_values_from(self) -> OWLClassExpression:
         """A convenience method that obtains this restriction as an existential restriction with a nominal filler.
@@ -730,6 +751,7 @@ def __init__(self, values: Union[OWLLiteral, Iterable[OWLLiteral]]):
             for _ in values:
                 assert isinstance(_, OWLLiteral)
             self._values = tuple(values)
+
     def __repr__(self):
         return f'OWLDataOneOf({self._values})'
 
@@ -742,6 +764,7 @@ def __eq__(self, other):
         else:
             return False
     # TODO:CD: define it as @property as the name of the class method does not correspond to an action
+
     def values(self) -> Iterable[OWLLiteral]:
         """Gets the values that are in the oneOf.
 
@@ -770,7 +793,7 @@ class OWLDatatypeRestriction(OWLDataRange):
     _facet_restrictions: Sequence['OWLFacetRestriction']
 
     def __init__(self, type_: OWLDatatype, facet_restrictions: Union['OWLFacetRestriction',
-    Iterable['OWLFacetRestriction']]):
+                                                                     Iterable['OWLFacetRestriction']]):
         self._type = type_
         if isinstance(facet_restrictions, OWLFacetRestriction):
             facet_restrictions = facet_restrictions,
@@ -788,6 +811,7 @@ def __eq__(self, other):
                 and self._facet_restrictions == other._facet_restrictions
         else:
             return False
+
     def __hash__(self):
         return hash(("OWLDatatypeRestriction", self._type, self._facet_restrictions))
 
@@ -825,7 +849,7 @@ def __eq__(self, other):
             return False
 
     def __hash__(self):
-        return hash(("OWLFacetRestriction",self._facet, self._literal))
+        return hash(("OWLFacetRestriction", self._facet, self._literal))
 
     def __repr__(self):
         return f'OWLFacetRestriction({self._facet}, {repr(self._literal)})'

owlapy/owl_axiom.py

@@ -281,6 +281,9 @@ def __init__(self, class_expressions: List[OWLClassExpression],
                  annotations: Optional[Iterable['OWLAnnotation']] = None):
         super().__init__(class_expressions=class_expressions, annotations=annotations)
 
+    def __iter__(self):
+        yield from self._class_expressions
+
     def contains_named_equivalent_class(self) -> bool:
         return any(isinstance(ce, OWLClass) for ce in self._class_expressions)
 
@@ -1259,6 +1262,14 @@ def __init__(self, property_: _P, range_: _R, annotations: Optional[Iterable[OWL
         self._range = range_
         super().__init__(property_=property_, annotations=annotations)
 
+    @property
+    def prop(self):
+        return self._property
+
+    @property
+    def range(self):
+        return self._range
+
     def get_range(self) -> _R:
         return self._range
 
@@ -1290,6 +1301,10 @@ def __init__(self, property_: OWLObjectPropertyExpression, domain: OWLClassExpre
                  annotations: Optional[Iterable[OWLAnnotation]] = None):
         super().__init__(property_=property_, domain=domain, annotations=annotations)
 
+    @property
+    def prop(self):
+        return self._property
+
 
 class OWLDataPropertyDomainAxiom(OWLPropertyDomainAxiom[OWLDataPropertyExpression]):
     """ A data property domain axiom DataPropertyDomain( DPE CE ) states that the domain of the