Merge pull request #86 from dice-group/develop

New release: owlapy 1.3.1

README.md

@@ -1,7 +1,7 @@
 # OWLAPY
 [![Coverage](https://img.shields.io/badge/coverage-78%25-green)](https://dice-group.github.io/owlapy/usage/further_resources.html#coverage-report)
-[![Pypi](https://img.shields.io/badge/pypi-1.3.0-blue)](https://pypi.org/project/owlapy/1.3.0/)
-[![Docs](https://img.shields.io/badge/documentation-1.3.0-yellow)](https://dice-group.github.io/owlapy/usage/main.html)
+[![Pypi](https://img.shields.io/badge/pypi-1.3.1-blue)](https://pypi.org/project/owlapy/1.3.1/)
+[![Docs](https://img.shields.io/badge/documentation-1.3.1-yellow)](https://dice-group.github.io/owlapy/usage/main.html)
 
 ![OWLAPY](docs/_static/images/owlapy_logo.png)
 
@@ -25,11 +25,10 @@ pip3 install owlapy
 ```shell
 # To download RDF knowledge graphs
 wget https://files.dice-research.org/projects/Ontolearn/KGs.zip -O ./KGs.zip && unzip KGs.zip
-pytest -p no:warnings -x # Running  102 tests takes ~ 1 min
+pytest -p no:warnings -x # Running  142 tests ~ 30 secs
 ```
 
-## Usage
-
+## Examples
 
 ### Creating OWL Class Expressions
 <details><summary> Click me! </summary>
@@ -91,7 +90,7 @@ from owlapy.static_funcs import stopJVM
 
 ontology_path = "KGs/Family/family-benchmark_rich_background.owl"
 # Available OWL Reasoners: 'HermiT', 'Pellet', 'JFact', 'Openllet'
-reasoner = SyncReasoner(ontology = ontology_path, reasoner="Pellet")
+sync_reasoner = SyncReasoner(ontology = ontology_path, reasoner="Pellet")
 onto = OntologyManager().load_ontology(ontology_path)
 # Iterate over defined owl Classes in the signature
 for i in onto.classes_in_signature():

docs/conf.py

@@ -13,7 +13,7 @@
 
 project = 'OWLAPY'
 author = 'Ontolearn Team'
-release = '1.3.0'
+release = '1.3.1'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

docs/usage/main.md

@@ -1,6 +1,6 @@
 # About owlapy
 
-**Version:** owlapy 1.3.0
+**Version:** owlapy 1.3.1
 
 **GitHub repository:** [https://github.com/dice-group/owlapy](https://github.com/dice-group/owlapy)
 

examples/ontology_engineering.py

@@ -0,0 +1,51 @@
+from owlapy.class_expression import OWLClass
+from owlapy.owl_axiom import OWLDeclarationAxiom, OWLClassAssertionAxiom
+from owlapy.owl_individual import OWLNamedIndividual
+from owlapy.owl_ontology_manager import OntologyManager
+from owlapy.iri import IRI
+from owlapy.static_funcs import download_external_files
+# (1) Download the datasets if KGs does not exist.
+download_external_files("https://files.dice-research.org/projects/Ontolearn/KGs.zip")
+# (2) Load the father ontology using a new ontology manager.
+onto = OntologyManager().load_ontology(path='file://../KGs/Family/father.owl')
+# (3) Iterate over defined OWL classes, object properties.
+print("OWL Classes:")
+for c in onto.classes_in_signature():
+    print(c)
+print("\nOWL Properties:")
+for p in onto.properties_in_signature():
+    print(p)
+print("\nOWL Individuals:")
+for i in onto.individuals_in_signature():
+    print(i)
+print("\nOWL Class Axioms:")
+for a in onto.general_class_axioms():
+    print(a)
+"""
+@TODO: Will be implemented.
+for a in onto.tbox_axioms():
+    print(a)
+for a in onto.abox_axioms_between_individuals():
+    print(a)
+for a in onto.abox_axioms_between_individuals_and_classes():
+    print(a)
+"""
+# (4) Create a new class (father)
+father = OWLClass(IRI.create('http://example.com/father#child'))
+# (5) Add a declaration axiom for this class,
+onto.add_axiom(axiom=OWLDeclarationAxiom(father))
+# (6) Check whether the newly defined class is in the signature.
+assert father in [ c for c in onto.classes_in_signature()]
+# (7) Iterate over owl individuals
+print("\nOWL Individuals:")
+for i in onto.individuals_in_signature():
+    print(i)
+# (8) Create an owl individual and used it in an axiom.
+cdemir = OWLNamedIndividual('http://example.com/father#cdemir')
+onto.add_axiom(OWLClassAssertionAxiom(cdemir, father))
+# (9) Check whether cdemir is in the signature.
+assert cdemir in [ c for c in onto.individuals_in_signature()]
+# (10) Save the modified ontology locally.
+onto.save(path="babo.owl",rdf_format = "rdfxml")
+
+

examples/ontology_reasoning_retrieval.py

@@ -0,0 +1,39 @@
+"""
+
+KB = { (A subclass B), (B subclass C), (x type A) }
+
+KB = { (A subclass B), (B subclass C), (x type A), (x type B), (x type C) }
+
+Missing types are inferred due to subclass hierarchy.
+"""
+from owlapy.class_expression import OWLClass
+from owlapy.owl_axiom import OWLDeclarationAxiom, OWLClassAssertionAxiom, OWLSubClassOfAxiom
+from owlapy.owl_ontology_manager import OntologyManager
+from owlapy.owl_individual import OWLNamedIndividual
+from owlapy.iri import IRI
+from owlapy.owl_reasoner import SyncReasoner
+# () Define a base IRI.
+base_iri = IRI(namespace="https://github.com/dice-group/owlapy#")
+# () Create an empty ontology.
+onto = OntologyManager().create_ontology(iri=base_iri)
+# () Define classes and individuals.
+A = OWLClass(iri=base_iri.get_namespace() + "A")
+B = OWLClass(iri=base_iri.get_namespace() + "B")
+C = OWLClass(iri=base_iri.get_namespace() + "C")
+x = OWLNamedIndividual(iri=base_iri.get_namespace() + "x")
+# () Add axioms.
+onto.add_axiom([OWLDeclarationAxiom(A),
+                OWLDeclarationAxiom(B),
+                OWLDeclarationAxiom(C),
+                OWLDeclarationAxiom(x),
+                OWLSubClassOfAxiom(A,B),
+                OWLSubClassOfAxiom(B,C),
+                OWLClassAssertionAxiom(x,A)])
+# () Save axioms [ (A subclass B), (B subclass C), (x type A) ].
+onto.save("new_ontology.owl")
+# () Initialize reasoner.
+reasoner = SyncReasoner(ontology="new_ontology.owl", reasoner="Pellet")
+# () Infer instances.
+for i in reasoner.ontology.classes_in_signature():
+    print(f"Retrieve {i}:",end=" ")
+    print(" ".join( [_.str for _ in reasoner.instances(i)]))

examples/ontology_reasoning_retrieval_agreements.py

@@ -0,0 +1,33 @@
+from owlapy.owl_reasoner import SyncReasoner
+from owlapy import OntologyManager
+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)
+
+# () Initialize Reasoners
+reasoners = dict()
+reasoners["HermiT"] = SyncReasoner(ontology=ontology_path, reasoner="HermiT")
+reasoners["Pellet"] = SyncReasoner(ontology=ontology_path, reasoner="Pellet")
+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")
+    retrieval_result = None
+    flag = False
+    for __, reasoner in owl_reasoners.items():
+        if retrieval_result:
+            flag = retrieval_result == {_.str for _ in reasoner.instances(expression)}
+        else:
+            retrieval_result = {_.str for _ in reasoner.instances(expression)}
+    if verbose:
+        print(f"Successful:{flag}")
+    return flag
+
+# () Iterate over named classes
+for c in onto.classes_in_signature():
+    # reasoners must agree
+    assert compute_agreements(reasoners, c, True)