Deprecating "Ontology Manager"

README.md

@@ -61,10 +61,10 @@ owlapy --path_ontology "KGs/Family/family-benchmark_rich_background.owl" --infer
 <details><summary> Click me! </summary>
 
 ```python
-from owlapy.owl_ontology_manager import SyncOntologyManager
+from owlapy.owl_ontology import SyncOntology
 
 ontology_path = "KGs/Family/father.owl"
-onto = SyncOntologyManager().load_ontology(ontology_path)
+onto = SyncOntology(ontology_path)
 
 print({owl_class.reminder for owl_class in onto.classes_in_signature()}) 
 # {'Thing', 'female', 'male', 'person'}
@@ -112,10 +112,9 @@ for axiom in onto.get_abox_axioms():
 from owlapy.class_expression import OWLClass, OWLObjectIntersectionOf, OWLObjectSomeValuesFrom
 from owlapy.owl_property import OWLObjectProperty
 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
+from owlapy.owl_individual import OWLNamedIndividual
+from owlapy.util_owl_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")
@@ -155,14 +154,14 @@ OWL objects in [owlapy api](https://dice-group.github.io/owlapy/autoapi/owlapy/i
 <details><summary> Click me! </summary>
 
 ```python
-from owlapy.owl_ontology_manager import OntologyManager
 from owlapy.owl_reasoner import SyncReasoner
 from owlapy.static_funcs import stopJVM
+from owlapy.owl_ontology import Ontology
 
 ontology_path = "KGs/Family/family-benchmark_rich_background.owl"
 # Available OWL Reasoners: 'HermiT', 'Pellet', 'JFact', 'Openllet'
 sync_reasoner = SyncReasoner(ontology = ontology_path, reasoner="Pellet")
-onto = OntologyManager().load_ontology(ontology_path)
+onto = Ontology(ontology_path)
 # Iterate over defined owl Classes in the signature
 for i in onto.classes_in_signature():
     # Performing type inference with Pellet
@@ -206,7 +205,7 @@ Check also the [examples](https://github.com/dice-group/owlapy/tree/develop/exam
 <details><summary> Click me! </summary>
 
 ```python
-from owlapy.owl_ontology_manager import SyncOntologyManager
+from owlapy.owl_ontology import SyncOntology
 from owlapy.util_owl_static_funcs import csv_to_rdf_kg
 import pandas as pd
 from sklearn.datasets import load_iris
@@ -216,7 +215,7 @@ 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)
+onto = SyncOntology(path_kg)
 assert len(onto.get_abox_axioms()) == 750
 
 ```

examples/ontology_reasoning_retrieval_agreements.py

@@ -1,10 +1,10 @@
 from owlapy.owl_reasoner import SyncReasoner
-from owlapy import OntologyManager
+from owlapy.owl_ontology import Ontology
 from owlapy.class_expression import OWLClassExpression
 from typing import Dict
 ontology_path = "../KGs/Family/family-benchmark_rich_background.owl"
 # () Load ontology
-onto = OntologyManager().load_ontology(ontology_path)
+onto = Ontology(ontology_path, load=True)
 
 # () Initialize Reasoners
 reasoners = dict()
@@ -13,6 +13,7 @@
 reasoners["JFact"] = SyncReasoner(ontology=ontology_path, reasoner="JFact")
 reasoners["Openllet"] = SyncReasoner(ontology=ontology_path, reasoner="Openllet")
 
+
 def compute_agreements(owl_reasoners:Dict[str,SyncReasoner], expression: OWLClassExpression, verbose=False):
     if verbose:
         print(f"Computing agreements between Reasoners on {expression}...",end="\t")
@@ -27,6 +28,7 @@ def compute_agreements(owl_reasoners:Dict[str,SyncReasoner], expression: OWLClas
         print(f"Successful:{flag}")
     return flag
 
+
 # () Iterate over named classes
 for c in onto.classes_in_signature():
     # reasoners must agree

owlapy/abstracts/__init__.py

@@ -1,4 +1,4 @@
-from .abstract_owl_ontology_manager import AbstractOWLOntologyManager, AbstractOWLOntologyChange, AbstractOWLOntology
 from .abstract_owl_reasoner import AbstractOWLReasoner
+from .abstract_owl_ontology import AbstractOWLOntology
 
-__all__ = ['AbstractOWLOntologyManager', 'AbstractOWLOntologyChange', 'AbstractOWLOntology', 'AbstractOWLReasoner']
+__all__ = ['AbstractOWLOntology', 'AbstractOWLReasoner']

owlapy/abstracts/abstract_owl_ontology.py

@@ -9,7 +9,6 @@
 from owlapy.owl_object import OWLObject
 from owlapy.owl_property import OWLDataProperty, OWLObjectProperty
 
-_M = TypeVar('_M', bound='OWLOntologyManager')  # noqa: F821
 _OI = TypeVar('_OI', bound='OWLOntologyID')  # noqa: F821
 
 
@@ -20,8 +19,6 @@ class AbstractOWLOntology(OWLObject, metaclass=ABCMeta):
     An ontology can have an ontology IRI which can be used to identify the ontology. If it has an ontology IRI then
     it may also have an ontology version IRI. Since OWL 2, an ontology need not have an ontology IRI. (See the OWL 2
     Structural Specification).
-
-    An ontology cannot be modified directly. Changes must be applied via its OWLOntologyManager.
     """
     __slots__ = ()
     type_index: Final = 1

owlapy/owl_ontology.py

@@ -1005,7 +1005,11 @@ def __init__(self, path: Union[IRI, str], load: bool = True):
             if isinstance(path, IRI):
                 self.owlapi_ontology = self.owlapi_manager.createOntology(Stream.empty(), owlapi_IRI.create(path.str))
             else:
-                raise NotImplementedError("Cant initialize a new ontology using path. Use IRI instead")
+                try:
+                    self.owlapi_ontology = self.owlapi_manager.createOntology(Stream.empty(),
+                                                                              owlapi_IRI.create(path))
+                except Exception as e:
+                    raise NotImplementedError("Cant initialize a new ontology using path. Use IRI instead")
         else:  # means we are loading an existing ontology
             self.owlapi_ontology = self.owlapi_manager.loadOntologyFromOntologyDocument(File(file_path))
         self.mapper = OWLAPIMapper()

owlapy/owl_reasoner.py

@@ -1040,8 +1040,7 @@ def __init__(self, ontology: Union[SyncOntology, str], reasoner="HermiT"):
         if isinstance(ontology, SyncOntology):
             self.ontology = ontology
         elif isinstance(ontology, str):
-            manager = OWLManager.createOWLOntologyManager()
-            self.ontology = manager.load_ontology(ontology)
+            self.ontology = SyncOntology(ontology)
 
         self._owlapi_manager = self.ontology.owlapi_manager
         self._owlapi_ontology = self.ontology.get_owlapi_ontology()

owlapy/static_funcs.py

@@ -6,9 +6,9 @@
 import jpype
 import jpype.imports
 import pkg_resources
-from owlapy.owl_ontology import SyncOntology, Ontology
 
-# NOTE: Static functions closely related with owl classes should be placed in utils.py not here
+# NOTE: Static functions closely related with owl classes should be placed in utils.py
+# or util_owl_static_funcs.py not here
 
 
 def move(*args):
@@ -58,11 +58,3 @@ def stopJVM() -> None:
     if jpype.isJVMStarted():
         jpype.detachThreadFromJVM()
         jpype.shutdownJVM()
-
-
-def create_ontology(iri, with_owlapi=False):
-    """ A convenient function"""
-    if with_owlapi:
-        return SyncOntology(iri, load=False)
-    else:
-        return Ontology(iri, load=False)

owlapy/util_owl_static_funcs.py

@@ -1,5 +1,4 @@
 from .owl_ontology import Ontology, SyncOntology
-from .owl_ontology_manager import OntologyManager
 from .class_expression import OWLClassExpression, OWLClass
 from .owl_individual import OWLNamedIndividual
 from .iri import IRI
@@ -11,10 +10,11 @@
 from tqdm import tqdm
 import pandas as pd
 
+
 def save_owl_class_expressions(expressions: OWLClassExpression | List[OWLClassExpression],
                                path: str = 'predictions',
                                rdf_format: str = 'rdfxml',
-                               namespace:str=None) -> None:
+                               namespace: str = None) -> None:
     """
     Saves a set of OWL class expressions to an ontology file in RDF/XML format.
 
@@ -49,20 +49,20 @@ def save_owl_class_expressions(expressions: OWLClassExpression | List[OWLClassEx
     if isinstance(expressions, OWLClassExpression):
         expressions = [expressions]
 
-    namespace= 'https://dice-research.org/predictions#' if namespace is None else namespace
+    namespace = 'https://dice-research.org/predictions#' if namespace is None else namespace
     assert "#" == namespace[-1], "namespace must end with #"
     # Initialize an Ontology Manager.
-    manager = OntologyManager()
     # Create an ontology given an ontology manager.
-    ontology:Ontology = manager.create_ontology(namespace)
+    ontology: Ontology = Ontology(namespace, load=False)
     # () Iterate over concepts
     for th, i in enumerate(expressions):
         cls_a = OWLClass(IRI.create(namespace, str(th)))
         equivalent_classes_axiom = OWLEquivalentClassesAxiom([cls_a, i])
         ontology.add_axiom(equivalent_classes_axiom)
     ontology.save(path=path, inplace=False, rdf_format=rdf_format)
 
-def csv_to_rdf_kg(path_csv:str=None,path_kg:str=None,namespace:str=None):
+
+def csv_to_rdf_kg(path_csv: str = None, path_kg: str = None, namespace: str = None):
     """
     Transfroms a CSV file to an RDF Knowledge Graph in RDF/XML format.
 
@@ -87,24 +87,21 @@ def csv_to_rdf_kg(path_csv:str=None,path_kg:str=None,namespace:str=None):
         >>> print("Dataset saved as iris_dataset.csv")
         >>> csv_to_rdf_kg("iris_dataset.csv")
     """
-    from owlapy.owl_ontology_manager import SyncOntologyManager
     assert path_csv is not None, "path cannot be None"
     assert os.path.exists(path_csv), f"path **{path_csv}**does not exist."
     assert path_kg is not None, f"path_kg cannot be None.Currently {path_kg}"
     assert namespace is not None, "namespace cannot be None"
-    assert namespace[:7]=="http://", "First characters of namespace must be 'http://'"
+    assert namespace[:7] == "http://", "First characters of namespace must be 'http://'"
 
-    # Initialize an Ontology Manager.
-    manager = SyncOntologyManager()
     # Create an ontology given an ontology manager.
-    ontology:SyncOntology = manager.create_ontology(namespace)
+    ontology: SyncOntology = SyncOntology(namespace, load=False)
 
     # Read the CSV file
     df = pd.read_csv(path_csv)
 
     # () Iterate over rows
-    for index, row in (tqdm_bar := tqdm(df.iterrows()) ):
-        individual=OWLNamedIndividual(f"{namespace}#{str(index)}".replace(" ","_"))
+    for index, row in (tqdm_bar := tqdm(df.iterrows())):
+        individual = OWLNamedIndividual(f"{namespace}#{str(index)}".replace(" ", "_"))
         tqdm_bar.set_description_str(f"Creating RDF Graph from Row:{index}")
         # column_name is considered as a predicate
         # value is considered as a data property
@@ -126,6 +123,7 @@ def csv_to_rdf_kg(path_csv:str=None,path_kg:str=None,namespace:str=None):
                                           f"has not been decided")
     ontology.save(path=path_kg)
 
+
 def rdf_kg_to_csv(path_kg: str = None, path_csv: str = None):
     """
     Constructs a CSV file from an RDF Knowledge Graph (RDF/XML) 
@@ -145,16 +143,14 @@ def rdf_kg_to_csv(path_kg: str = None, path_csv: str = None):
     """
     import os
     import pandas as pd
-    from owlapy.owl_ontology_manager import SyncOntologyManager
 
     # Validate arguments
     assert path_kg is not None, "path_kg cannot be None"
     assert path_csv is not None, "path_csv cannot be None"
     assert os.path.exists(path_kg), f"RDF Knowledge Graph file {path_kg} does not exist."
 
     # Load the ontology
-    manager = SyncOntologyManager()
-    ontology = manager.load_ontology(path_kg)
+    ontology = SyncOntology(path_kg, load=True)
     # Extract individuals and data property assertions
     rows = {}
     columns_list = []
@@ -206,3 +202,11 @@ def rdf_kg_to_csv(path_kg: str = None, path_csv: str = None):
     df = pd.DataFrame(data_list, columns=columns)
     df.to_csv(path_csv, index=False, na_rep="")
     print(f"CSV reconstructed and saved to {path_csv}")
+
+
+def create_ontology(iri, with_owlapi=False):
+    """ A convenient function"""
+    if with_owlapi:
+        return SyncOntology(iri, load=False)
+    else:
+        return Ontology(iri, load=False)

tests/test_ontology.py

@@ -1,5 +1,4 @@
 import unittest
-from owlapy.owl_ontology_manager import RDFLibOntologyManager
 from owlapy.owl_ontology import SyncOntology, Ontology
 from owlapy.owl_ontology import RDFLibOntology
 
@@ -11,7 +10,7 @@ def test_counting(self):
         o_owlready: Ontology
         o_owlready = Ontology(ontology_iri="KGs/Family/father.owl")
         o_rdf: RDFLibOntology
-        o_rdf = RDFLibOntologyManager().load_ontology(path="KGs/Family/father.owl")
+        o_rdf = RDFLibOntology(path="KGs/Family/father.owl")
 
         assert len({i for i in o_sync.get_tbox_axioms()})==len({i for i in o_rdf.get_tbox_axioms()})
         assert len({i for i in o_sync.get_abox_axioms()})==len({i for i in o_rdf.get_abox_axioms()})