Merge pull request #128 from dice-group/develop

Merge with main

.github/workflows/docs.yml

@@ -6,6 +6,8 @@ on:
      - main
      - documentation # just for testing
   pull_request:
+    branches:
+      - main
 
 jobs:
   docs:

.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

@@ -1,7 +1,9 @@
 # OWLAPY
+[![Downloads](https://static.pepy.tech/badge/owlapy)](https://pepy.tech/project/owlapy)
+[![Downloads](https://img.shields.io/pypi/dm/owlapy)](https://pypi.org/project/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-1.3.3-blue)](https://pypi.org/project/owlapy/1.3.3/)
-[![Docs](https://img.shields.io/badge/documentation-1.3.3-yellow)](https://dice-group.github.io/owlapy/usage/main.html)
+[![Pypi](https://img.shields.io/badge/pypi-1.4.0-blue)](https://pypi.org/project/owlapy/1.4.0/)
+[![Docs](https://img.shields.io/badge/documentation-1.4.0-yellow)](https://dice-group.github.io/owlapy/usage/main.html)
 
 ![OWLAPY](docs/_static/images/owlapy_logo.png)
 
@@ -20,16 +22,40 @@ or
 ```bash
 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  142 tests ~ 30 secs
+pytest -p no:warnings -x # Running  147 tests ~ 35 secs
 ```
 
 ## Examples
 
+### OWL Reasoning from Command line
+
+<details><summary> Click me! </summary>
+
+```shell
+owlapy --path_ontology "KGs/Family/family-benchmark_rich_background.owl" --inference_types "all" --out_ontology "enriched_family.owl"
+```
+
+```--inference_types``` can be specified by selecting one from 
+
+``` 
+["InferredClassAssertionAxiomGenerator",
+"InferredSubClassAxiomGenerator",
+"InferredDisjointClassesAxiomGenerator",
+"InferredEquivalentClassAxiomGenerator",
+"InferredEquivalentDataPropertiesAxiomGenerator",
+"InferredEquivalentObjectPropertyAxiomGenerator",
+"InferredInverseObjectPropertiesAxiomGenerator",
+"InferredSubDataPropertyAxiomGenerator",
+"InferredSubObjectPropertyAxiomGenerator",
+"InferredDataPropertyCharacteristicAxiomGenerator",
+"InferredObjectPropertyCharacteristicAxiomGenerator"]
+```
+
+</details>
+
 ### Exploring OWL Ontology
 
 <details><summary> Click me! </summary>
@@ -78,7 +104,8 @@ for axiom in onto.get_abox_axioms():
 
 </details>
 
-### Creating OWL Class Expressions
+### OWL Knowledge Engineering
+
 <details><summary> Click me! </summary>
 
 ```python
@@ -88,31 +115,27 @@ 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 
@@ -178,5 +201,28 @@ 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.

docs/conf.py

@@ -13,7 +13,7 @@
 
 project = 'OWLAPY'
 author = 'Ontolearn Team'
-release = '1.3.3'
+release = '1.4.0'
 
 # -- 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 1.3.3
+**Version:** owlapy 1.4.0
 
 **GitHub repository:** [https://github.com/dice-group/owlapy](https://github.com/dice-group/owlapy)
 

examples/owlapy_serve.py

@@ -0,0 +1,64 @@
+# To start the FastAPI server with the 'family-benchmark_rich_background.owl' ontology,
+# run the following command in your terminal:
+# $ owlapy-serve --path_kb KGs/Family/family-benchmark_rich_background.owl --reasoner HermiT
+
+# Optionally, you provide custom host and port for the FastAPI server:
+# $ owlapy-serve --path_kb KGs/Family/family-benchmark_rich_background.owl --reasoner HermiT --host 0.0.0.0 --port 8000
+import requests
+
+# Base URL where your FastAPI server is running
+BASE_URL = 'http://localhost:8000'
+
+# 1. Get Classes in the Ontology
+print("1. Get Classes:")
+response = requests.get(f'{BASE_URL}/classes')
+print('Classes:', response.json())
+
+# 2. Get Object Properties in the Ontology
+print("\n2. Get Object Properties:")
+response = requests.get(f'{BASE_URL}/object_properties')
+print('Object Properties:', response.json())
+
+# 3. Get Data Properties in the Ontology
+print("\n3. Get Data Properties:")
+response = requests.get(f'{BASE_URL}/data_properties')
+print('Data Properties:', response.json())
+
+# 4. Get Individuals in the Ontology
+print("\n4. Get Individuals:")
+response = requests.get(f'{BASE_URL}/individuals')
+print('Individuals:', response.json())
+
+# 5. Get ABox Axioms (Assertions about individuals)
+print("\n5. Get ABox Axioms:")
+response = requests.get(f'{BASE_URL}/abox')
+print('ABox Axioms:', response.json())
+
+# 6. Get TBox Axioms (Class and property definitions)
+print("\n6. Get TBox Axioms:")
+response = requests.get(f'{BASE_URL}/tbox')
+print('TBox Axioms:', response.json())
+
+# 7. Get Instances of a Specific Class
+print("\n7. Get Instances of a Class:")
+class_iri_request = {
+    "class_iri": "http://www.example.org/family#Person"
+}
+response = requests.post(f'{BASE_URL}/instances', json=class_iri_request)
+print('Instances of Class:', response.json())
+
+# 8. Infer Axioms of a Specific Type
+print("\n8. Infer Subclass Axioms:")
+inference_request = {
+    "inference_type": "InferredSubClassAxiomGenerator"
+}
+response = requests.post(f'{BASE_URL}/infer_axioms', json=inference_request)
+print('Inferred Subclass Axioms:', response.json())
+
+# 9. Infer All Types of Axioms
+print("\n9. Infer All Axioms:")
+inference_request = {
+    "inference_type": "all"
+}
+response = requests.post(f'{BASE_URL}/infer_axioms', json=inference_request)
+print('All Inferred Axioms:', response.json())

owlapy/__init__.py

@@ -3,7 +3,7 @@
 from .converter import owl_expression_to_sparql, owl_expression_to_sparql_with_confusion_matrix
 from .owl_ontology_manager import OntologyManager
 
-__version__ = '1.3.3'
+__version__ = '1.4.0'
 
 __all__ = [
     'owl_expression_to_dl', 'owl_expression_to_manchester',

owlapy/abstracts/abstract_owl_ontology.py

@@ -174,6 +174,7 @@ def remove_axiom(self, axiom: Union[OWLAxiom, Iterable[OWLAxiom]]):
         """
         pass
 
+    @abstractmethod
     def save(self, document_iri: Optional[IRI] = None):
         """Saves this ontology, using its IRI to determine where/how the ontology should be
          saved.

owlapy/class_expression/class_expression.py

@@ -84,6 +84,15 @@ class OWLObjectComplementOf(OWLBooleanClassExpression, HasOperands[OWLClassExpre
 
     _operand: OWLClassExpression
 
+    def __new__(cls, op: OWLClassExpression):
+        """
+        Creates a new instance or returns the operand if op is already a complement.
+        """
+        if isinstance(op, OWLObjectComplementOf):
+            return op.get_operand()
+        else:
+            return super(OWLObjectComplementOf, cls).__new__(cls)
+
     def __init__(self, op: OWLClassExpression):
         """
         Args:

owlapy/class_expression/nary_boolean_expression.py

@@ -29,9 +29,9 @@ def __repr__(self):
 
     def __eq__(self, other):
         if type(other) is type(self):
-            return {i for i in self._operands} == { j for j in other.operands()}
-        else:
-            return False
+            return (set(self._operands) == set(other.operands())
+                    and len(list(self._operands)) == len(list(other.operands())))
+        return False
 
     def __hash__(self):
         return hash(self._operands)