Merge remote-tracking branch 'origin/develop' into issues-solving

examples/ontology_reasoning_retrieval_agreements_and_runtimes.py

@@ -1,58 +1,28 @@
 """ A script to show that OWL Reasoners return the same retrieval results in different runtimes """
 import time
 
-from owlapy.class_expression import OWLClass, OWLObjectSomeValuesFrom, OWLObjectAllValuesFrom
+from owlapy.class_expression import (OWLClass, OWLObjectSomeValuesFrom, OWLObjectAllValuesFrom,
+                                     OWLObjectIntersectionOf, OWLObjectUnionOf)
 from owlapy.owl_ontology_manager import OntologyManager
 from owlapy.owl_reasoner import SyncReasoner
-from owlapy.utils import concept_reducer_properties
-
+from owlapy.utils import concept_reducer_properties, concept_reducer
+from owlapy import owl_expression_to_dl
 import matplotlib.pyplot as plt
 import seaborn as sns
 import numpy as np
 from tqdm import tqdm
 
-ontology_path = "../KGs/Family/family-benchmark_rich_background.owl"
-
-owl_reasoners = dict()
-owl_reasoners["HermiT"] = SyncReasoner(ontology=ontology_path, reasoner="HermiT")
-owl_reasoners["Pellet"] = SyncReasoner(ontology=ontology_path, reasoner="Pellet")
-owl_reasoners["JFact"] = SyncReasoner(ontology=ontology_path, reasoner="JFact")
-owl_reasoners["Openllet"] = SyncReasoner(ontology=ontology_path, reasoner="Openllet")
-onto = OntologyManager().load_ontology(ontology_path)
-c: OWLClass
-###################################################################
-# GENERATE ALCQ CONCEPTS TO EVALUATE RETRIEVAL PERFORMANCES
-# (3) R: Extract object properties.
-object_properties = {i for i in onto.object_properties_in_signature()}
-# (4) R⁻: Inverse of object properties.
-object_properties_inverse = {i.get_inverse_property() for i in object_properties}
-# (5) R*: R UNION R⁻.
-object_properties_and_inverse = object_properties.union(object_properties_inverse)
-# (6) NC: Named owl concepts.
-nc = {i for i in onto.classes_in_signature()}
-# (7) NC⁻: Complement of NC.
-nnc = {i.get_object_complement_of() for i in nc}
-# (8) \exist r. C s.t. C \in NC and r \in R* .
-exist_nc = concept_reducer_properties(
-    concepts=nc,
-    properties=object_properties_and_inverse,
-    cls=OWLObjectSomeValuesFrom)
-# (9) \forall r. C s.t. C \in NC and r \in R* .
-forall_nc = concept_reducer_properties(
-    concepts=nc,
-    properties=object_properties_and_inverse,
-    cls=OWLObjectAllValuesFrom,
-)
-
-
-def eval_reasoners(iter_owl_exp, mapping):
+def eval_reasoners(iter_owl_exp, mapping,info:str=""):
     results = dict()
     runtime_results = dict()
-    for c in tqdm(iter_owl_exp):
+    for c in (tqdm_bar:=tqdm(iter_owl_exp)):
         for name_i, reasoner_i in mapping.items():
             start_time_i = time.time()
             result_reasoner_i = {i.str for i in reasoner_i.instances(c)}
             runtime_results.setdefault(name_i, []).append(time.time() - start_time_i)
+
+            tqdm_bar.set_description_str(f"{owl_expression_to_dl(c)}\t")
+
             for name_j, reasoner_j in mapping.items():
                 if name_i == name_j:
                     continue  # Skip self-comparison
@@ -108,21 +78,57 @@ def plot_similarity_btw_reasoners(results):
     plt.ylabel('Reasoner')
     plt.show()
 
+ontology_path = "../KGs/Family/father.owl"
 
-# EVAL Named Concepts
-print("Evaluation over named concepts...")
-similarity_results, average_runtime_owl_reasoners = eval_reasoners(nc, owl_reasoners)
+owl_reasoners = dict()
+owl_reasoners["HermiT"] = SyncReasoner(ontology=ontology_path, reasoner="HermiT")
+owl_reasoners["Pellet"] = SyncReasoner(ontology=ontology_path, reasoner="Pellet")
+owl_reasoners["JFact"] = SyncReasoner(ontology=ontology_path, reasoner="JFact")
+owl_reasoners["Openllet"] = SyncReasoner(ontology=ontology_path, reasoner="Openllet")
+onto = OntologyManager().load_ontology(ontology_path)
+c: OWLClass
+# () C: OWL Class.
+c = {i for i in onto.classes_in_signature()}
+similarity_results, average_runtime_owl_reasoners = eval_reasoners(c, owl_reasoners)
 plot_similarity_btw_reasoners(similarity_results)
-plot_runtimes(average_runtime_owl_reasoners, title="Avg Runtime of Reasoners on Named Concepts")
+plot_runtimes(average_runtime_owl_reasoners, title="Avg Runtime of Reasoners on Classes")
 
-# EVAL Negated Concepts
-print("Evaluation over negated named concepts...")
-similarity_results, average_runtime_owl_reasoners = eval_reasoners(nnc, owl_reasoners)
+# () Negated OWL CLasses.
+nc = {i.get_object_complement_of() for i in c}
+similarity_results, average_runtime_owl_reasoners = eval_reasoners(nc, owl_reasoners)
 plot_similarity_btw_reasoners(similarity_results)
-plot_runtimes(average_runtime_owl_reasoners, title="Avg Runtime of Reasoners on Negated Named Concepts")
+plot_runtimes(average_runtime_owl_reasoners, title="Avg Runtime of Reasoners on Negated Classes")
+# () Intersection of OWL Classes
+intersections_classes = concept_reducer(c, opt=OWLObjectIntersectionOf)
+similarity_results, average_runtime_owl_reasoners = eval_reasoners(intersections_classes, owl_reasoners)
+plot_similarity_btw_reasoners(similarity_results)
+plot_runtimes(average_runtime_owl_reasoners, title="Avg Runtime of Reasoners on Intersection of Classes")
+# () Union  of OWL Classes
+unions_classes = concept_reducer(c, opt=OWLObjectUnionOf)
+similarity_results, average_runtime_owl_reasoners = eval_reasoners(unions_classes, owl_reasoners)
+plot_similarity_btw_reasoners(similarity_results)
+plot_runtimes(average_runtime_owl_reasoners, title="Avg Runtime of Reasoners on Union of Classes")
+# () Object Property Restrictions - Existential Quantification
+object_properties = {i for i in onto.object_properties_in_signature()}
+exist_c = concept_reducer_properties(concepts=c, properties=object_properties, cls=OWLObjectSomeValuesFrom)
+similarity_results, average_runtime_owl_reasoners = eval_reasoners(exist_c, owl_reasoners)
+plot_similarity_btw_reasoners(similarity_results)
+plot_runtimes(average_runtime_owl_reasoners, title="Avg Runtime of Reasoners on Existential Quantifiers")
+# () Object Property Restrictions - Universal Quantification
+forall_c = concept_reducer_properties(concepts=c, properties=object_properties, cls=OWLObjectAllValuesFrom)
+similarity_results, average_runtime_owl_reasoners = eval_reasoners(forall_c, owl_reasoners)
+plot_similarity_btw_reasoners(similarity_results)
+plot_runtimes(average_runtime_owl_reasoners, title="Avg Runtime of Reasoners on Universal Quantifiers")
 
-# EVAL Exist R. NC
-print("Evaluation over existential object property restrictions... takes some time")
-similarity_results, average_runtime_owl_reasoners = eval_reasoners(exist_nc, owl_reasoners)
+# () Object Property Restrictions - Existential Quantification
+inverse_object_properties = {i.get_inverse_property() for i in onto.object_properties_in_signature()}
+exist_inverse_c = concept_reducer_properties(concepts=c, properties=inverse_object_properties, cls=OWLObjectSomeValuesFrom)
+similarity_results, average_runtime_owl_reasoners = eval_reasoners(exist_inverse_c, owl_reasoners)
+plot_similarity_btw_reasoners(similarity_results)
+plot_runtimes(average_runtime_owl_reasoners, title="Avg Runtime of Reasoners on Existential Quantifiers with inverse properties")
+# () Object Property Restrictions - Universal Quantification
+forall_inverse_c = concept_reducer_properties(concepts=c, properties=inverse_object_properties, cls=OWLObjectAllValuesFrom)
+similarity_results, average_runtime_owl_reasoners = eval_reasoners(forall_inverse_c, owl_reasoners)
 plot_similarity_btw_reasoners(similarity_results)
-plot_runtimes(average_runtime_owl_reasoners, title="Avg Runtime of Reasoners on OWLObjectSomeValuesFrom")
+plot_runtimes(average_runtime_owl_reasoners, title="Avg Runtime of Reasoners on Universal Quantifiers with inverse properties")
+

owlapy/class_expression/owl_class.py

@@ -62,10 +62,4 @@ def get_nnf(self) -> 'OWLClass':
         # documented in parent
         return self
 
-    def __str__(self):
-        return f"OWLClass({self.reminder})"
-
-    def __repr__(self):
-        return f"OWLClass({self._iri})"
-
 

owlapy/owl_reasoner.py

@@ -1216,7 +1216,10 @@ def __init__(self, ontology: Union[SyncOntology, str], reasoner="HermiT"):
         else:
             raise NotImplementedError("Not implemented")
 
-    def instances(self, ce: OWLClassExpression, direct=False) -> List[OWLNamedIndividual]:
+
+        self.reasoner=reasoner
+
+    def instances(self, ce: OWLClassExpression, direct=False) -> Set[OWLNamedIndividual]:
         """
         Get the instances for a given class expression using HermiT.
 
@@ -1225,11 +1228,13 @@ def instances(self, ce: OWLClassExpression, direct=False) -> List[OWLNamedIndivi
             direct (bool): Whether to get direct instances or not. Defaults to False.
 
         Returns:
-            list: A list of individuals classified by the given class expression.
+            set: A set of individuals classified by the given class expression.
         """
-        inds = self._owlapi_reasoner.getInstances(self.mapper.map_(ce), direct).getFlattened()
-        assert str(type(inds)) == "<java class 'java.util.LinkedHashSet'>"
-        return [self.mapper.map_(ind) for ind in inds]
+        mapped_ce=self.mapper.map_(ce)
+        instances = self._owlapi_reasoner.getInstances(mapped_ce, direct)
+        flattended_instances = instances.getFlattened()
+        assert str(type(flattended_instances)) == "<java class 'java.util.LinkedHashSet'>"
+        return {self.mapper.map_(ind) for ind in flattended_instances}
 
     def equivalent_classes(self, ce: OWLClassExpression) -> List[OWLClassExpression]:
         """

tests/test_reasoner_alc_father_ontology.py

@@ -0,0 +1,44 @@
+from owlapy.owl_reasoner import SyncReasoner
+from owlapy.class_expression import OWLClass, OWLObjectSomeValuesFrom
+from owlapy.owl_individual import OWLNamedIndividual
+from owlapy.iri import IRI
+from owlapy.owl_property import OWLObjectProperty
+
+
+class TestHermitFather:
+    def test_readme(self):
+
+        ontology_path = "KGs/Family/father.owl"
+        hermit = SyncReasoner(ontology=ontology_path, reasoner="HermiT")
+
+        # Thing
+        thing = OWLClass(IRI('http://www.w3.org/2002/07/owl#', 'Thing'))
+        # Person OWL Class
+        person = eval("OWLClass(IRI('http://example.com/father#', 'person'))")
+        # Female OWL CLass
+        female = eval("OWLClass(IRI('http://example.com/father#', 'female'))")
+        # hasChild object property
+        hasChild = OWLObjectProperty(IRI('http://example.com/father#', 'hasChild'))
+
+        # Things
+        assert hermit.instances(thing) == {OWLNamedIndividual(IRI('http://example.com/father#', 'anna')), OWLNamedIndividual(IRI('http://example.com/father#', 'martin')), OWLNamedIndividual(IRI('http://example.com/father#', 'heinz')), OWLNamedIndividual(IRI('http://example.com/father#', 'stefan')), OWLNamedIndividual(IRI('http://example.com/father#', 'michelle')), OWLNamedIndividual(IRI('http://example.com/father#', 'markus'))}
+
+        # hasChild a thing.
+        assert hermit.instances(OWLObjectSomeValuesFrom(property=hasChild, filler=thing)) == eval(
+            "{OWLNamedIndividual(IRI('http://example.com/father#', 'markus')), OWLNamedIndividual(IRI('http://example.com/father#', 'martin')), OWLNamedIndividual(IRI('http://example.com/father#', 'stefan')), OWLNamedIndividual(IRI('http://example.com/father#', 'anna'))}")
+
+        # hasChild a person.
+        assert hermit.instances(OWLObjectSomeValuesFrom(property=hasChild, filler=person)) == eval(
+            "{OWLNamedIndividual(IRI('http://example.com/father#', 'markus')), OWLNamedIndividual(IRI('http://example.com/father#', 'martin')), OWLNamedIndividual(IRI('http://example.com/father#', 'stefan')), OWLNamedIndividual(IRI('http://example.com/father#', 'anna'))}")
+
+        # hasChild a female.
+        assert hermit.instances(OWLObjectSomeValuesFrom(property=hasChild, filler=female)) == eval(
+            "{OWLNamedIndividual(IRI('http://example.com/father#', 'markus'))}")
+        # Question: hasChild something that hasChild a female.
+        # Answer: stefan
+        # (stefan haschild markus) and markus haschild anna
+        assert hermit.instances(OWLObjectSomeValuesFrom(property=hasChild,
+                                                        filler=OWLObjectSomeValuesFrom(property=hasChild,
+                                                                                       filler=female))) == eval(
+            "{OWLNamedIndividual(IRI('http://example.com/father#', 'stefan'))}")
+