fix nb total abstract information

llm_semantic_annotator/core.py

@@ -57,6 +57,9 @@ def main_populate_ncbi_taxon_tag_embeddings(config_all):
 def main_populate_abstract_embeddings(config_all):
     get_abstract_manager(config_all).manage_abstracts()
 
+def get_doi_file(config_all):
+    return config_all['retention_dir']+"/total_doi.txt"
+
 def main_compute_tag_chunk_similarities(config_all):
     """Fonction principale pour calculer la similarité entre tous les tags et chunks."""
     tags_pth_files = get_owl_tag_manager(config_all).get_files_tags_embeddings()
@@ -92,7 +95,7 @@ def main_compute_tag_chunk_similarities(config_all):
     ### -----------------------  
     keep_tag_embeddings = {}
     results_complete_similarities = {}
-        
+    total_doi = 0
     for abstracts_pth_file in abstracts_pth_files:
         json_f = str(os.path.splitext(abstracts_pth_file)[0])+"_scores.json"
         if os.path.exists(json_f) :
@@ -101,6 +104,7 @@ def main_compute_tag_chunk_similarities(config_all):
         chunk_embeddings = mem.load_filepth(abstracts_pth_file)
 
         for doi,res in mem.compare_tags_with_chunks(tag_embeddings, chunk_embeddings).items():
+            total_doi+=1
             if doi not in results_complete_similarities:
                 results_complete_similarities[doi] = res
                 for tag in res.keys():
@@ -119,6 +123,9 @@ def main_compute_tag_chunk_similarities(config_all):
 
         with open(json_f, "w") as fichier:
             json.dump(results_complete_similarities, fichier)
+
+        with open(get_doi_file(config_all), "w") as fichier:
+            fichier.write(str(total_doi))
 
 def get_scores_files(retention_dir):
     scores_files = []
@@ -170,14 +177,14 @@ def get_results_complete_similarities_and_tags_embedding(config_all):
     return results_complete_similarities,tag_embeddings
 
 def main_display_summary(config_all):
-
+    doi_file = get_doi_file(config_all)
     results_complete_similarities,tag_embeddings = get_results_complete_similarities_and_tags_embedding(config_all)    
     retention_dir = config_all['retention_dir']
 
     if len(results_complete_similarities)>0:
         display_best_similarity_abstract_tag(results_complete_similarities,tag_embeddings,retention_dir)
         display_ontologies_summary(results_complete_similarities,tag_embeddings,retention_dir)
-        display_ontologies_distribution(results_complete_similarities,tag_embeddings)
+        display_ontologies_distribution(results_complete_similarities,tag_embeddings,doi_file)
     else:
         print("No results found")
 

llm_semantic_annotator/misc/scientific_abstract_rdf_annotator.py

@@ -46,7 +46,7 @@ def create_rdf_graph(results_complete_similarities,
     abstracts_processed = len(results_complete_similarities)
 
     for doi, complete_similarities in results_complete_similarities.items():
-        doi_uri = URIRef(urllib.parse.quote(f"https://doi.org/{doi}"))
+        doi_uri = URIRef("https://doi.org/"+urllib.parse.quote(doi))
         for tag, similarity in complete_similarities.items():
             tag_uri = URIRef(tag)
             annotation_node = BNode()

llm_semantic_annotator/misc/stats.py

@@ -4,9 +4,13 @@
 from rich.panel import Panel
 from rich.text import Text
 
-def display_ontologies_distribution(data, keep_tag_embeddings):
+def display_ontologies_distribution(data, keep_tag_embeddings,total_doi_file):
     console = Console()
 
+    nb_doi = 0
+    with open(total_doi_file, 'r') as file:
+        nb_doi = int(file.read()) 
+
     # Extract key prefixes
     ontologies = []
     labels = []
@@ -21,14 +25,13 @@ def display_ontologies_distribution(data, keep_tag_embeddings):
     distributionLabels = Counter(labels)
 
     # General statistics
-    nb_abstracts = len(data)
-    nb_annotated = sum(1 for item in data.values() if len(item) > 0)
+    nb_annotated = len(data)
     total_labels = sum(distributionOntologies.values())
 
     # Display general statistics
     console.print(Panel(
         f"[bold cyan]General Statistics[/bold cyan]\n"
-        f"Total number of abstracts: [green]{nb_abstracts}[/green]\n"
+        f"Total number of abstracts: [green]{nb_doi}[/green]\n"
         f"Number of annotated abstracts: [green]{nb_annotated}[/green]\n"
         f"Total number of labels used: [green]{total_labels}[/green]",
         title="Summary",