Update main script

main.py

 #!/usr/bin/python3.10
 # -*-coding:Utf-8 -*
 
-#==============================================================================
-# ontoScorer: [brief description of the module]
-#------------------------------------------------------------------------------
-# Detailed module description, if needed
-#==============================================================================
+"""
+ontoScorer: [brief description of the module]
+------------------------------------------------------------------------------
+Detailed module description, if needed
+"""
 
 from ontoScorer.scorer import OntoScorer
 
 def main():
-    # Define the path to the data folder
+    # Paths to data
     DATA_FOLDER_PATH = "data"
-
-    # Define paths to the ontology files
     REFERENCE_ONTOLOGY_PATH = f"{DATA_FOLDER_PATH}/reference_ontology.ttl"
     GENERATED_ONTOLOGY_PATH = f"{DATA_FOLDER_PATH}/generated_ontology.ttl"
     
-    # Initialize the scorer
-    scorer = OntoScorer(REFERENCE_ONTOLOGY_PATH, GENERATED_ONTOLOGY_PATH)
+    # Equivalent Prefix (used to harmonize the ontologies)
+    EQUIVALENT_PREFIX = [
+        ("base", "https://reference.tetras-libre.fr/base-ontology#", "https://tenet.tetras-libre.fr/base-ontology#"),
+        ("result", "https://reference.tetras-libre.fr/expected-result#", "https://tenet.tetras-libre.fr/extract-result#")
+    ]    
 
-    # Compare the ontologies
+    # Scorer Process Run
+    scorer = OntoScorer(REFERENCE_ONTOLOGY_PATH, GENERATED_ONTOLOGY_PATH, EQUIVALENT_PREFIX)
     scorer.compute_metrics()
-
-    # Generate a report
     scorer.generate_report()
 
 if __name__ == "__main__":

ontoScorer/scorer.py

 #!/usr/bin/python3.10
-# -*-coding:Utf-8 -*
+# -*-coding:Utf-8 -*-
 
-#==============================================================================
-# ontoScorer: [brief description of the module]
-#------------------------------------------------------------------------------
-# Detailed module description, if needed
-#==============================================================================
+"""
+ontoScorer: Module for comparing a reference ontology with a generated one.
+------------------------------------------------------------------------------
+This module provides functionality to compute various metrics comparing
+a manually crafted reference ontology and a generated ontology. It also
+facilitates the creation of detailed comparison reports.
+"""
 
 from ontology import Ontology
 from report import Report
 from metrics import Metrics
 
 class OntoScorer:
-    def __init__(self, reference_ontology_path, generated_ontology_path):
-        self.reference_ontology = Ontology(reference_ontology_path)
-        self.generated_ontology = Ontology(generated_ontology_path)
+    """
+    The OntoScorer class is used to compare a reference ontology with a generated one.
+
+    Attributes:
+    - reference_ontology (Ontology): The manually crafted reference ontology.
+    - generated_ontology (Ontology): The automatically generated ontology.
+    - metrics (Metrics): An instance of the Metrics class to compute scores for comparison.
+
+    Methods:
+    - compute_metrics(): Computes various metrics comparing reference and generated ontologies.
+    - generate_report(): Produces a detailed report based on computed metrics.
+    """
+
+    def __init__(self, reference_ontology_path, generated_ontology_path, equivalent_prefix):
+        """
+        Initializes the OntoScorer with paths to reference and generated ontologies.
+        
+        Args:
+        - reference_ontology_path (str): Path to the reference ontology file.
+        - generated_ontology_path (str): Path to the generated ontology file.
+        - equivalent_prefix (str): Prefix to handle equivalent terms or concepts.
+        """
+        self.reference_ontology = Ontology(reference_ontology_path, equivalent_prefix)
+        self.generated_ontology = Ontology(generated_ontology_path, equivalent_prefix)
         self.metrics = Metrics()
 
     def compute_metrics(self):
         self.metrics.compute_entity_scores(self.reference_ontology, self.generated_ontology)
+        self.metrics.compute_taxonomic_relation_scores(self.reference_ontology, self.generated_ontology)
+        self.metrics.compute_non_taxonomic_relation_scores(self.reference_ontology, self.generated_ontology)
+        self.metrics.compute_axiom_scores(self.reference_ontology, self.generated_ontology)
+
 
     def generate_report(self):
-        report = Report(self.reference_ontology,
-                        self.generated_ontology,
-                        self.metrics)
+        report = Report(self.reference_ontology, self.generated_ontology, self.metrics)
         print(report.generate())
 
 
-    # def generate_report(self, report_path):
-    #     report = Report(self.comparison_result, self.metrics)
-    #     report.generate(report_path)