Merge pull request #59 from dice-group/retrieval

Refactoring and Readme Update

README.md

@@ -30,8 +30,9 @@ pytest -p no:warnings -x # Running 103 tests takes ~ 30 mins
 
 ## Usage
 
-In this example we start with a simple atomic class expression and move to some more complex 
-ones and finally render and print the last of them in description logics syntax.
+
+### Creating OWL Class Expressions
+<details><summary> Click me! </summary>
 
 ```python
 from owlapy.class_expression import OWLClass, OWLObjectIntersectionOf, OWLObjectSomeValuesFrom
@@ -40,17 +41,13 @@ from owlapy import owl_expression_to_sparql, owl_expression_to_dl
 
 # Create the male class
 male = OWLClass("http://example.com/society#male")
-
 # Create an object property using the iri as a string for 'hasChild' property.
 hasChild = OWLObjectProperty("http://example.com/society#hasChild")
-
 # Create an existential restrictions
 hasChild_male = OWLObjectSomeValuesFrom(hasChild, male)
-
 # Let's make it more complex by intersecting with another class
 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 (and vice-versa)
 print(owl_expression_to_dl(teacher_that_hasChild_male))
 # (∃ hasChild.male) ⊓ teacher
@@ -68,7 +65,35 @@ class. In the above examples we have introduced 3 types of class expressions:
 Like we showed in this example, you can create all kinds of class expressions using the 
 OWL objects in [owlapy api](https://dice-group.github.io/owlapy/autoapi/owlapy/index.html).
 
-Many axioms can automatically inferred with a selected reasoner
+</details>
+
+### Logical Inference
+
+<details><summary> Click me! </summary>
+
+```python
+from owlapy.owl_ontology_manager import OntologyManager
+from owlapy.owlapi_adaptor import OWLAPIAdaptor
+
+ontology_path = "KGs/Family/family-benchmark_rich_background.owl"
+# Available OWL Reasoners: 'HermiT', 'Pellet', 'JFact', 'Openllet'
+owlapi_adaptor = OWLAPIAdaptor(path=ontology_path, name_reasoner="Pellet")
+onto = OntologyManager().load_ontology(ontology_path)
+# Iterate over defined owl Classes in the signature
+for i in onto.classes_in_signature():
+    # Performing type inference with Pellet
+    instances=owlapi_adaptor.instances(i,direct=False)
+    print(f"Class:{i}\t Num instances:{len(instances)}")
+owlapi_adaptor.stopJVM()
+```
+
+</details>
+
+### Ontology Enrichment
+
+<details><summary> Click me! </summary>
+
+An Ontology can be enriched by inferring many different axioms.
 ```python
 from owlapy.owlapi_adaptor import OWLAPIAdaptor
 
@@ -86,7 +111,10 @@ adaptor.infer_axioms_and_save(output_path="KGs/Family/inferred_family-benchmark_
 adaptor.stopJVM()
 ```
 
-Check also the [examples](https://github.com/dice-group/owlapy/tree/develop/examples) folder.
+</details>
+
+
+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.
 
 ## How to cite
 Currently, we are working on our manuscript describing our framework.

owlapy/owl_ontology_manager.py

@@ -27,7 +27,7 @@
 from owlapy.owl_ontology import OWLOntology, Ontology, ToOwlready2
 from owlapy.owl_property import OWLDataProperty, OWLObjectInverseOf, OWLObjectProperty, \
     OWLProperty
-
+from typing import Union
 
 class OWLOntologyChange(metaclass=ABCMeta):
     """Represents an ontology change."""
@@ -849,10 +849,18 @@ def __init__(self, world_store=None):
         else:
             self._world = owlready2.World(filename=world_store)
 
-    def create_ontology(self, iri: IRI) -> 'Ontology':
+    def create_ontology(self, iri:Union[str,IRI]=None) -> 'Ontology':
+        if isinstance(iri, str):
+            iri=IRI.create(iri)
+        else:
+            assert isinstance(iri, IRI), "iri either must be string or an instance of IRI Class"
         return Ontology(self, iri, load=False)
 
-    def load_ontology(self, iri: IRI) -> 'Ontology':
+    def load_ontology(self, iri: Union[str,IRI]=None) -> 'Ontology':
+        if isinstance(iri, str):
+            iri=IRI.create(iri)
+        else:
+            assert isinstance(iri, IRI), "iri either must be string or an instance of IRI Class"
         return Ontology(self, iri, load=True)
 
     def apply_change(self, change: OWLOntologyChange):
@@ -879,8 +887,7 @@ def save_ontology(self, ontology: OWLOntology, document_iri: IRI):
             filename = document_iri.as_str()[len('file:/'):]
             ont_x.save(file=filename)
         else:
-            # TODO XXX
-            raise NotImplementedError
+            raise NotImplementedError("Couldn't save because the namespace of document_iri does not start with **file:/**")
 
     def save_world(self):
         """Saves the actual state of the quadstore in the SQLite3 file.

owlapy/owl_reasoner.py

@@ -2,11 +2,10 @@
 import operator
 from abc import ABCMeta, abstractmethod
 from collections import defaultdict
-from enum import Enum, auto
 from functools import singledispatchmethod, reduce
 from itertools import chain, repeat
 from types import MappingProxyType, FunctionType
-from typing import DefaultDict, Iterable, Dict, Mapping, Set, Type, TypeVar, Optional, FrozenSet, List, cast
+from typing import DefaultDict, Iterable, Dict, Mapping, Set, Type, TypeVar, Optional, FrozenSet
 import logging
 
 import owlready2
@@ -18,11 +17,11 @@
     OWLDataAllValuesFrom
 from owlapy.class_expression import OWLClass
 from owlapy.iri import IRI
-from owlapy.owl_axiom import OWLAxiom, OWLSubClassOfAxiom
+from owlapy.owl_axiom import OWLSubClassOfAxiom
 from owlapy.owl_data_ranges import OWLDataRange, OWLDataComplementOf, OWLDataUnionOf, OWLDataIntersectionOf
 from owlapy.owl_datatype import OWLDatatype
 from owlapy.owl_object import OWLEntity
-from owlapy.owl_ontology import OWLOntology, Ontology, _parse_concept_to_owlapy, ToOwlready2
+from owlapy.owl_ontology import OWLOntology, Ontology, _parse_concept_to_owlapy
 from owlapy.owl_ontology_manager import OntologyManager
 from owlapy.owl_property import OWLObjectPropertyExpression, OWLDataProperty, OWLObjectProperty, OWLObjectInverseOf, \
     OWLPropertyExpression, OWLDataPropertyExpression
@@ -33,7 +32,12 @@
 
 logger = logging.getLogger(__name__)
 
+_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 OWLReasoner(metaclass=ABCMeta):
     """An OWLReasoner reasons over a set of axioms (the set of reasoner axioms) that is based on the imports closure of
     a particular ontology - the "root" ontology."""
@@ -401,20 +405,6 @@ class expression with respect to the imports closure of the root ontology.
             If ce is equivalent to owl:Thing then nothing will be returned.
         """
         pass
-
-
-# Deprecated
-# class BaseReasoner(Enum):
-#     """Enumeration class for base reasoner when calling sync_reasoner.
-#
-#     Attributes:
-#         PELLET: Pellet base reasoner.
-#         HERMIT: HermiT base reasoner.
-#     """
-#     PELLET = auto()
-#     HERMIT = auto()
-
-
 class OWLReasonerEx(OWLReasoner, metaclass=ABCMeta):
     """Extra convenience methods for OWL Reasoners"""
 
@@ -496,10 +486,9 @@ def ind_object_properties(self, ind: OWLNamedIndividual, direct: bool = True) ->
             except StopIteration:
                 pass
 
-
 class OntologyReasoner(OWLReasonerEx):
     __slots__ = '_ontology', '_world'
-
+    # TODO: CD: We will remove owlready2 from owlapy
     _ontology: Ontology
     _world: owlready2.World
 
@@ -1042,9 +1031,6 @@ def get_root_ontology(self) -> OWLOntology:
         return self._ontology
 
 
-_P = TypeVar('_P', bound=OWLPropertyExpression)
-
-
 class FastInstanceCheckerReasoner(OWLReasonerEx):
     """Tries to check instances fast (but maybe incomplete)."""
     __slots__ = '_ontology', '_base_reasoner', \

owlapy/owlapi_mapper.py

@@ -3,6 +3,7 @@
 
 import jpype.imports
 
+import owlapy.owl_ontology
 from owlapy import owl_expression_to_manchester, manchester_to_owl_expression
 from owlapy.class_expression import OWLClassExpression, OWLDataOneOf, OWLFacetRestriction, OWLDatatypeRestriction
 from owlapy.iri import IRI
@@ -90,7 +91,10 @@ def init(the_class):
 
 class OWLAPIMapper:
 
-    def __init__(self, ontology):
+    def __init__(self, ontology=None):
+        # TODO: CD: Please use class type of ontology
+        # TODO: CD: if ontology is None, then we should throw an exception with a useful information
+        # assert isinstance(ontology, OWLAPIMapper)
         self.ontology = ontology
         self.manager = ontology.getOWLOntologyManager()