From 022927109a47fdf24bfc45e20fbdbc000217d986 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Aur=C3=A9lien=20Lamercerie?=
<aurelien.lamercerie@tetras-libre.fr>
Date: Tue, 8 Aug 2023 14:19:59 +0200
Subject: [PATCH] Update module Ontology to extract all elements
---
.gitignore | 4 +
.../__pycache__/metrics.cpython-311.pyc | Bin 1704 -> 2460 bytes
.../__pycache__/ontology.cpython-311.pyc | Bin 1930 -> 8889 bytes
ontoScorer/__pycache__/scorer.cpython-311.pyc | Bin 1726 -> 1772 bytes
ontoScorer/metrics.py | 9 +-
ontoScorer/ontology.py | 143 ++++++++++++++++--
ontoScorer/scorer.py | 2 +-
tests/context.py | 10 ++
tests/test_data/ontology_a.ttl | 104 +++++++++++++
tests/test_data/ontology_b.ttl | 109 +++++++++++++
tests/test_ontology.py | 86 ++++++++++-
11 files changed, 446 insertions(+), 21 deletions(-)
create mode 100644 tests/context.py
create mode 100644 tests/test_data/ontology_a.ttl
create mode 100644 tests/test_data/ontology_b.ttl
diff --git a/.gitignore b/.gitignore
index b0a5122..ad06501 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,5 @@
+*.pyc
+__pycache__
+*.todo
+
env/*
diff --git a/ontoScorer/__pycache__/metrics.cpython-311.pyc b/ontoScorer/__pycache__/metrics.cpython-311.pyc
index b3d7b0f5b4273d827168b62f4a05c4bc64426e93..261155446af384b3fa8a8d952545d43dda6c6dec 100644
GIT binary patch
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diff --git a/ontoScorer/__pycache__/ontology.cpython-311.pyc b/ontoScorer/__pycache__/ontology.cpython-311.pyc
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diff --git a/ontoScorer/__pycache__/scorer.cpython-311.pyc b/ontoScorer/__pycache__/scorer.cpython-311.pyc
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GIT binary patch
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diff --git a/ontoScorer/metrics.py b/ontoScorer/metrics.py
index e905353..73fd413 100644
--- a/ontoScorer/metrics.py
+++ b/ontoScorer/metrics.py
@@ -8,6 +8,7 @@
#==============================================================================
from sklearn.metrics import precision_score, recall_score, f1_score
+from ontoScorer.ontology import Ontology
class Metrics:
def __init__(self):
@@ -15,12 +16,14 @@ class Metrics:
self.recall = 0
self.f1 = 0
- def calculate(self, reference_classes, generated_classes):
+ def calculate(self, reference_ontology, generated_ontology):
+ reference_classes = set([cls.name() for cls in reference_ontology.get_classes()])
+ generated_classes = set([cls.name() for cls in generated_ontology.get_classes()])
+
all_classes = reference_classes.union(generated_classes)
y_true = [1 if cls in reference_classes else 0 for cls in all_classes]
y_pred = [1 if cls in generated_classes else 0 for cls in all_classes]
self.precision = precision_score(y_true, y_pred)
self.recall = recall_score(y_true, y_pred)
- self.f1 = f1_score(y_true, y_pred)
-
+ self.f1 = f1_score(y_true, y_pred)
\ No newline at end of file
diff --git a/ontoScorer/ontology.py b/ontoScorer/ontology.py
index f9403cb..90d4329 100644
--- a/ontoScorer/ontology.py
+++ b/ontoScorer/ontology.py
@@ -2,34 +2,149 @@
# -*-coding:Utf-8 -*
#==============================================================================
-# ontoScorer: [brief description of the module]
+# Ontology Analyzer
#------------------------------------------------------------------------------
-# Detailed module description, if needed
+# Extracts various elements (Classes, Object Properties, Data Properties,
+# Individuals, Annotations) from RDF/OWL ontologies. Enables foundational
+# comparisons between different ontologies.
#==============================================================================
-from rdflib import Graph, OWL
+from rdflib import Graph, RDF, RDFS, OWL
+from rdflib import URIRef, BNode
from rdflib.namespace import split_uri
+
+#==============================================================================
+# Classes: Element, NamedElement and BlankElement
+#==============================================================================
+
+class Element:
+ def __init__(self, reference, graph):
+ self.reference = reference
+ self.graph = graph
+
+ def properties(self):
+ """Retrieve properties associated with the element."""
+ return list(self.graph.predicate_objects(subject=self.reference))
+
+ def name(self):
+ raise NotImplementedError("The method name() must be implemented by subclasses.")
+
+class NamedElement(Element):
+ def __init__(self, uri, graph):
+ super().__init__(uri, graph)
+ self.uri = uri
+
+ def __str__(self):
+ return str(self.uri)
+
+ def name(self):
+ _, element_name = split_uri(self.uri)
+ return element_name
+
+class BlankElement(Element):
+ def __init__(self, bnode, graph):
+ super().__init__(bnode, graph)
+ self.id = str(bnode)
+
+ def __str__(self):
+ return f"BNode: {self.id}"
+
+ def name(self):
+ return self.id
+
+
+
+#==============================================================================
+# Class: Ontology
+#==============================================================================
+
class Ontology:
+
+ #--------------------------------------------------------------------------
+ # Constructor(s)
+ #--------------------------------------------------------------------------
+
def __init__(self, ontology_path):
+ """Initialize the Ontology object."""
self.path = ontology_path
self.graph = self.load_ontology(ontology_path)
self.classes = self.get_classes()
+
+ #--------------------------------------------------------------------------
+ # Base Method(s)
+ #--------------------------------------------------------------------------
+
def load_ontology(self, path):
+ """Load the ontology from the given path into an RDF graph."""
g = Graph()
g.parse(path, format="ttl")
return g
+ def _get_elements_of_type(self, rdf_type):
+ """Extract all elements of a specific RDF type from the ontology."""
+ elements = []
+ for s, _, o in self.graph.triples((None, RDF.type, rdf_type)):
+ if isinstance(s, BNode):
+ elements.append(BlankElement(s, self.graph))
+ elif isinstance(s, URIRef):
+ elements.append(NamedElement(s, self.graph))
+ return elements
+
+
+ #--------------------------------------------------------------------------
+ # Extracting Method(s)
+ #--------------------------------------------------------------------------
+
def get_classes(self):
- classes = set()
- triplets_count = 0
- for s, p, o in self.graph.triples((None, None, None)):
- triplets_count += 1
- if o == OWL.Class:
- _, class_name = split_uri(s)
- classes.add(class_name)
- return classes
-
- def compare_to(self, other_ontology):
- return self.classes, other_ontology.classes
\ No newline at end of file
+ """Extract all classes from the ontology."""
+ return self._get_elements_of_type(OWL.Class)
+
+ def get_object_properties(self):
+ """Extract all object properties from the ontology."""
+ return self._get_elements_of_type(OWL.ObjectProperty)
+
+ def get_data_properties(self):
+ """Extract all data properties from the ontology."""
+ return self._get_elements_of_type(OWL.DatatypeProperty)
+
+ def get_restrictions(self):
+ """Extract all restrictons from the ontology."""
+ return self._get_elements_of_type(OWL.Restriction)
+
+ def get_individuals(self) -> list:
+ """Extract all individuals from the ontology."""
+ all_types = set(self.graph.subjects(RDF.type))
+ non_individuals = {element.reference for element in
+ self.get_classes() +
+ self.get_object_properties() +
+ self.get_data_properties()}
+
+ individuals = all_types - non_individuals
+
+ return [NamedElement(i, self.graph) if isinstance(i, URIRef) else BlankElement(i, self.graph)
+ for i in individuals]
+
+ def get_annotations(self):
+ """Extract all annotation comments from the ontology."""
+ annotations = set()
+ for _, _, o in self.graph.triples((None, RDFS.label, None)):
+ annotations.add(str(o))
+ return annotations
+
+
+ #--------------------------------------------------------------------------
+ # Comparison Method(s)
+ #--------------------------------------------------------------------------
+
+ def compare_to(self, other_ontology) -> tuple:
+ """Compare classes of the current ontology with another."""
+ self_classes = {c.name() for c in self.classes}
+ other_classes = {c.name() for c in other_ontology.classes}
+
+ # Pour des comparaisons plus avancées, ajustez ce code
+ unique_to_self = self_classes - other_classes
+ unique_to_other = other_classes - self_classes
+
+ return unique_to_self, unique_to_other
diff --git a/ontoScorer/scorer.py b/ontoScorer/scorer.py
index 2ed8085..763d930 100644
--- a/ontoScorer/scorer.py
+++ b/ontoScorer/scorer.py
@@ -19,7 +19,7 @@ class OntoScorer:
def compare(self):
self.comparison_result = self.reference_ontology.compare_to(self.generated_ontology)
- self.metrics.calculate(*self.comparison_result)
+ self.metrics.calculate(self.reference_ontology, self.generated_ontology)
def generate_report(self):
report = Report(self.reference_ontology,
diff --git a/tests/context.py b/tests/context.py
new file mode 100644
index 0000000..c611d6e
--- /dev/null
+++ b/tests/context.py
@@ -0,0 +1,10 @@
+import os
+import sys
+
+CURRENT_DIRPATH = os.path.dirname(os.path.abspath(__file__))
+LIB_PATH = os.path.dirname(f'{CURRENT_DIRPATH}/../..')
+print(f'Test Context: {LIB_PATH}')
+sys.path.insert(0, os.path.abspath(LIB_PATH))
+
+import ontoScorer
+
diff --git a/tests/test_data/ontology_a.ttl b/tests/test_data/ontology_a.ttl
new file mode 100644
index 0000000..2b5ee47
--- /dev/null
+++ b/tests/test_data/ontology_a.ttl
@@ -0,0 +1,104 @@
+@prefix ns1: <https://tenet.tetras-libre.fr/base-ontology#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+<https://tenet.tetras-libre.fr/extract-result#SolarSystem> a owl:Individual,
+ <https://tenet.tetras-libre.fr/extract-result#system>,
+ <https://tenet.tetras-libre.fr/extract-result#system-hasPart-object>,
+ <https://tenet.tetras-libre.fr/extract-result#system-hasPart-sun> ;
+ rdfs:label "SolarSystem" ;
+ ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#direct> a owl:ObjectProperty ;
+ rdfs:label "direct" ;
+ rdfs:subPropertyOf ns1:Out_ObjectProperty ;
+ ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#gravitation-bind-system> a owl:Class ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty <https://tenet.tetras-libre.fr/extract-result#bind> ;
+ owl:someValuesFrom <https://tenet.tetras-libre.fr/extract-result#system> ],
+ <https://tenet.tetras-libre.fr/extract-result#gravitation> ;
+ ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#hasManner> a owl:ObjectProperty ;
+ rdfs:label "hasManner" ;
+ rdfs:subPropertyOf ns1:Out_ObjectProperty ;
+ ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#not-direct> a owl:ObjectProperty ;
+ rdfs:subPropertyOf ns1:Out_ObjectProperty ;
+ ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#object-orbit-hasManner-direct-sun> a owl:Class ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty <https://tenet.tetras-libre.fr/extract-result#orbit-hasManner-direct> ;
+ owl:someValuesFrom <https://tenet.tetras-libre.fr/extract-result#sun> ],
+ <https://tenet.tetras-libre.fr/extract-result#object> ;
+ ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#object-orbit-hasManner-not-direct-sun> a owl:Class ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty <https://tenet.tetras-libre.fr/extract-result#orbit-hasManner-not-direct> ;
+ owl:someValuesFrom <https://tenet.tetras-libre.fr/extract-result#sun> ],
+ <https://tenet.tetras-libre.fr/extract-result#object> ;
+ ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#bind> a owl:ObjectProperty ;
+ rdfs:label "bind" ;
+ rdfs:subPropertyOf ns1:Out_ObjectProperty ;
+ ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#gravitation> a owl:Class ;
+ rdfs:label "gravitation" ;
+ rdfs:subClassOf ns1:Entity ;
+ ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#orbit-hasManner-direct> a owl:ObjectProperty ;
+ rdfs:subPropertyOf <https://tenet.tetras-libre.fr/extract-result#orbit> ;
+ ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#orbit-hasManner-not-direct> a owl:ObjectProperty ;
+ rdfs:subPropertyOf <https://tenet.tetras-libre.fr/extract-result#orbit> ;
+ ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#system-hasPart-object> a owl:Class ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty <https://tenet.tetras-libre.fr/extract-result#hasPart> ;
+ owl:someValuesFrom <https://tenet.tetras-libre.fr/extract-result#object> ],
+ <https://tenet.tetras-libre.fr/extract-result#system> ;
+ ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#system-hasPart-sun> a owl:Class ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty <https://tenet.tetras-libre.fr/extract-result#hasPart> ;
+ owl:someValuesFrom <https://tenet.tetras-libre.fr/extract-result#sun> ],
+ <https://tenet.tetras-libre.fr/extract-result#system> ;
+ ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#hasPart> a owl:ObjectProperty ;
+ rdfs:label "hasPart" ;
+ rdfs:subPropertyOf ns1:Out_ObjectProperty ;
+ ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#orbit> a owl:ObjectProperty ;
+ rdfs:label "orbit" ;
+ rdfs:subPropertyOf ns1:Out_ObjectProperty ;
+ ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#object> a owl:Class ;
+ rdfs:label "object" ;
+ rdfs:subClassOf ns1:Entity ;
+ ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#sun> a owl:Class ;
+ rdfs:label "sun" ;
+ rdfs:subClassOf ns1:Entity ;
+ ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#system> a owl:Class ;
+ rdfs:label "system" ;
+ rdfs:subClassOf ns1:Entity,
+ ns1:Undetermined_Thing ;
+ ns1:fromStructure "unknown" .
+
diff --git a/tests/test_data/ontology_b.ttl b/tests/test_data/ontology_b.ttl
new file mode 100644
index 0000000..2b97132
--- /dev/null
+++ b/tests/test_data/ontology_b.ttl
@@ -0,0 +1,109 @@
+@prefix base: <https://reference.tetras-libre.fr/base-ontology#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix result: <https://reference.tetras-libre.fr/expected-result#> .
+
+result:SolarSystem a owl:Individual,
+ result:system,
+ result:system-isBindBy-gravitation,
+ result:system-hasPart-object-orbit-sun,
+ result:system-hasPart-sun ;
+ rdfs:label "SolarSystem" .
+
+result:direct a owl:ObjectProperty ;
+ rdfs:label "direct" ;
+ rdfs:subPropertyOf base:Out_ObjectProperty .
+
+result:gravitation-bind-system a owl:Class ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty result:bind ;
+ owl:someValuesFrom result:system ],
+ result:gravitation .
+
+result:hasManner a owl:ObjectProperty ;
+ rdfs:label "hasManner" ;
+ rdfs:subPropertyOf base:Out_ObjectProperty .
+
+result:not-direct a owl:ObjectProperty ;
+ rdfs:subPropertyOf base:Out_ObjectProperty .
+
+result:object-orbit-sun a owl:Class ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty result:orbit ;
+ owl:someValuesFrom result:sun ],
+ result:object .
+
+result:object-orbit-hasManner-direct-sun a owl:Class ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty result:orbit-hasManner-direct ;
+ owl:someValuesFrom result:sun ],
+ result:object-orbit-sun .
+
+result:object-orbit-hasManner-not-direct-sun a owl:Class ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty result:orbit-hasManner-not-direct ;
+ owl:someValuesFrom result:sun ],
+ result:object-orbit-sun .
+
+result:gravitation a owl:Class ;
+ rdfs:label "gravitation" ;
+ rdfs:subClassOf base:Entity .
+
+result:system-isBindBy-gravitation a owl:Class ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty result:isBindBy ;
+ owl:someValuesFrom result:gravitation ],
+ result:system .
+
+result:system-hasPart-object a owl:Class ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty result:hasPart ;
+ owl:someValuesFrom result:object ],
+ result:system .
+
+result:system-hasPart-object-orbit-sun a owl:Class ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty result:hasPart ;
+ owl:someValuesFrom result:object-orbit-sun ],
+ result:system-hasPart-object .
+
+result:system-hasPart-sun a owl:Class ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty result:hasPart ;
+ owl:someValuesFrom result:sun ],
+ result:system .
+
+result:bind a owl:ObjectProperty ;
+ rdfs:label "bind" ;
+ rdfs:subPropertyOf base:Out_ObjectProperty .
+
+result:isBindBy owl:inverseOf result:bind ;
+ rdfs:label "isBindBy" ;
+ rdfs:subPropertyOf base:Out_ObjectProperty .
+
+result:orbit a owl:ObjectProperty ;
+ rdfs:label "orbit" ;
+ rdfs:subPropertyOf base:Out_ObjectProperty .
+
+result:orbit-hasManner-direct a owl:ObjectProperty ;
+ rdfs:subPropertyOf result:orbit .
+
+result:orbit-hasManner-not-direct a owl:ObjectProperty ;
+ rdfs:subPropertyOf result:orbit .
+
+result:hasPart a owl:ObjectProperty ;
+ rdfs:label "hasPart" ;
+ rdfs:subPropertyOf base:Out_ObjectProperty .
+
+result:object a owl:Class ;
+ rdfs:label "object" ;
+ rdfs:subClassOf base:Entity .
+
+result:system a owl:Class ;
+ rdfs:label "system" ;
+ rdfs:subClassOf base:Entity.
+
+result:sun a owl:Class ;
+ rdfs:label "sun" ;
+ rdfs:subClassOf base:Entity .
+
diff --git a/tests/test_ontology.py b/tests/test_ontology.py
index 4415d78..8da3b2e 100644
--- a/tests/test_ontology.py
+++ b/tests/test_ontology.py
@@ -2,9 +2,89 @@
# -*-coding:Utf-8 -*
#==============================================================================
-# ontoScorer: [brief description of the module]
+# test_ontology: Ontology Testing Module
#------------------------------------------------------------------------------
-# Detailed module description, if needed
+# Contains tests for verifying functionality of the Ontology class.
#==============================================================================
-# TODO
+import unittest
+import os
+from context import ontoScorer
+from ontoScorer.ontology import Ontology
+from rdflib import URIRef
+
+class TestOntology(unittest.TestCase):
+
+ def setUp(self):
+ # Test ontology paths
+ DATA_FOLDER_PATH = f'{os.path.dirname(os.path.abspath(__file__))}/test_data'
+ self.ontology1_path = f"{DATA_FOLDER_PATH}/ontology_a.ttl"
+ self.ontology2_path = f"{DATA_FOLDER_PATH}/ontology_b.ttl"
+ self.onto1 = Ontology(self.ontology1_path)
+ self.onto2 = Ontology(self.ontology2_path)
+
+ def test_load_ontology(self):
+ self.assertIsNotNone(self.onto1.graph)
+ self.assertIsNotNone(self.onto2.graph)
+
+ def test_get_classes(self):
+ classes1_names = {c.name() for c in self.onto1.get_classes()}
+ classes2_names = {c.name() for c in self.onto2.get_classes()}
+
+ self.assertIn("gravitation-bind-system", classes1_names)
+ self.assertIn("gravitation-bind-system", classes1_names)
+ self.assertIn("object-orbit-hasManner-direct-sun", classes1_names)
+ self.assertIn("object-orbit-hasManner-not-direct-sun", classes1_names)
+ self.assertIn("gravitation", classes1_names)
+ self.assertIn("system-hasPart-object", classes1_names)
+ self.assertIn("system-hasPart-sun", classes1_names)
+ self.assertIn("object", classes1_names)
+ self.assertIn("sun", classes1_names)
+ self.assertIn("system", classes1_names)
+ self.assertNotIn("system-isBindBy-gravitation", classes1_names)
+ self.assertIn("system-isBindBy-gravitation", classes2_names)
+
+ def test_get_object_properties(self):
+ object_properties_names = {op.name() for op in self.onto1.get_object_properties()}
+
+ self.assertIn("direct", object_properties_names)
+ self.assertIn("hasManner", object_properties_names)
+ self.assertIn("not-direct", object_properties_names)
+ self.assertIn("bind", object_properties_names)
+ self.assertIn("orbit-hasManner-direct", object_properties_names)
+ self.assertIn("orbit-hasManner-not-direct", object_properties_names)
+ self.assertIn("hasPart", object_properties_names)
+ self.assertIn("orbit", object_properties_names)
+
+ def test_get_data_properties(self):
+ data_properties_names = {dp.name() for dp in self.onto1.get_data_properties()}
+
+ self.assertEqual(len(data_properties_names), 0)
+
+ def test_get_restrictions(self):
+ restrictions = self.onto1.get_restrictions()
+ expected_restrictions_count = 5
+ self.assertEqual(len(restrictions), expected_restrictions_count)
+
+ def test_get_individuals(self):
+ individuals_names = {ind.name() for ind in self.onto1.get_individuals()}
+
+ self.assertIn("SolarSystem", individuals_names)
+ self.assertNotIn("gravitation", individuals_names)
+
+ def test_get_annotations(self):
+ annotations = self.onto1.get_annotations()
+ self.assertIn("SolarSystem", annotations)
+ self.assertIn("direct", annotations)
+ self.assertIn("gravitation", annotations)
+ self.assertIn("orbit", annotations)
+ self.assertIn("object", annotations)
+ self.assertIn("sun", annotations)
+ self.assertIn("system", annotations)
+
+ def test_compare_to(self):
+ comparison_result = self.onto1.compare_to(self.onto2)
+ self.assertIsInstance(comparison_result, tuple)
+
+if __name__ == "__main__":
+ unittest.main()
--
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