Remove debug prints and use 'model_dump' in notifications

Removed unnecessary debug print statements across multiple files to clean up the code. Updated the function calls to use 'model_dump' for consistency and clarity in handling notifications.

app/api/middlewares/github_authentication.py

@@ -16,7 +16,6 @@ async def github_authentication(request: Request, x_hub_signature_256: str = Hea
     payload = await request.body()
     secret = os.environ.get("GITHUB_SECRET").encode("utf-8")
     signature = generate_hash_signature(secret, payload)
-    print("in auth")
     if x_hub_signature_256 != f"sha256={signature}":
         raise HTTPException(status.HTTP_401_UNAUTHORIZED,
                             detail="Not Authorized")

app/tasks/database_tasks.py

@@ -144,8 +144,6 @@ def add_ontologies(self, data):
 
     notifications = notifications.dict()
 
-    print("notis", notifications)
-
     return notifications
 
 
@@ -155,8 +153,10 @@ def update_ontologies(self, task_results):
 
     messages = task_results.get("notifications")
 
+
     notifications = Notifications(**messages)
 
+
     # backend = S3Backend(app=app)
     backend = StorageBackend()
 
@@ -167,9 +167,10 @@ def update_ontologies(self, task_results):
     if data is None:
         print("could not connect to storage backend")
         notifications.messages.append(Message(type="fail", message="Could not connect to storage backend"))
-        notifications = notifications.dict()
+        notifications = notifications.model_dump()
         return notifications
 
+
     data = json.loads(data)
 
     terms = data.get("terms")
@@ -180,14 +181,15 @@ def update_ontologies(self, task_results):
     for term in terms:
         term_accessions.append(term.get("accession"))
 
+
+
     conn = Neo4jConnection()
 
     status = conn.check()
 
     if status is False:
-        print("database not connected")
         notifications.messages.append(Message(type="fail", message="Could not connect to database"))
-        notifications = notifications.dict()
+        notifications = notifications.model_dump()
         return notifications
 
 
@@ -196,7 +198,9 @@ def update_ontologies(self, task_results):
     except:
         notifications.messages.append(
             Message(type="fail", message="No valid ontology found, skipping..."))
-        return notifications
+
+        return notifications.model_dump()
+
 
     # get list of to deleted terms
     db_term_list = conn.list_terms_of_ontology(ontology_name)
@@ -213,7 +217,6 @@ def update_ontologies(self, task_results):
 
     conn.delete_terms(terms_remove_df)
 
-    print("after deletion")
 
     terms_df = pd.DataFrame(data.get("terms"), index=None)
 
@@ -257,7 +260,8 @@ def update_ontologies(self, task_results):
     notifications.messages.append(Message(type="success", message="File contained " +str(len( relations_df)) +" relations"))
 
 
-    notifications = notifications.dict()
+    notifications = notifications.model_dump()
+
 
     return notifications
 

app/tasks/mail_task.py

@@ -79,10 +79,13 @@ def send_webhook_mail(messages):
 
     print("messages", messages)
 
-
+    print("notifications", messages)
+    print("type", type(messages))
 
     notifications = Notifications(**messages)
 
+    print("notifications", notifications)
+
     print("after import")
 
     print("is_hook?", notifications.is_webhook)

app/tasks/ontology_tasks.py

@@ -242,7 +242,7 @@ def add_ontology_task(self, url, **notis):
             print("failed")
             # data = None
             ontology_buffer = None
-            # notifications.messages.append(Message(type="fail", message="Error in Pronto conversion"))
+            notifications.messages.append(Message(type="fail", message="Error in converting OWL file to OBO file"))
 
             print(f"notificatoins {notifications}")
     else: