Handle missing ontology file and improve OWL to OBO error handling

Add checks to handle the case where the ontology file is missing. Enhance error handling in the OWL to OBO conversion, ensuring appropriate notifications are sent when conversion fails.

app/helpers/obo_parser.py

@@ -90,6 +90,19 @@ def get_ontology_name(self):
         return ontology.name
 
     def parse(self, notifications: Notifications):
+
+        if self.ontology_file is None:
+            self.obo_file.ontologies = self.ontolgies
+            self.obo_file.terms = self.obo_file.terms
+            self.obo_file.relationships = self.obo_file.relationships
+
+            notifications.messages.append(Message(type="fail", message="Ontology could not be read"))
+
+
+
+            return self.obo_file.dict()
+
+
         # try to read ontology file
         try:
             graph = obonet.read_obo(self.ontology_file, ignore_obsolete=False)

app/tasks/ontology_tasks.py

@@ -36,12 +36,14 @@
 from resource import *
 
 from app.tasks.database_tasks import add_ontologies
-from app.helpers.notifications.models.notification_model import Notifications
+from app.helpers.notifications.models.notification_model import Notifications, Message
 
 from celery.backends.s3 import S3Backend
 from celery.backends.base import BaseKeyValueStoreBackend
 from app.helpers.storage_backend import StorageBackend
 
+from app.helpers.models.ontology.obo_file import *
+
 
 # def convert_owl_to_obo_in_memory(input_file: str):
 #     # Load the OWL file
@@ -69,20 +71,38 @@
 #
 #     return graph
 
-def convert_owl_to_obo(input_file: str) -> str:
-    # Load the OWL file
-    ontology = pronto.Ontology(input_file)
-    # Create a binary stream instead of a file
-    binary_stream = io.BytesIO()
-    # Save the ontology in OBO format
-    ontology.dump(binary_stream, format='obo')
-    # Get the OBO content from the binary stream
-    obo_content = binary_stream.getvalue().decode('utf-8')
-    # Close the stream
-    binary_stream.close()
-    return obo_content
+# def convert_owl_to_obo(input_file: str) -> str:
+#     # Load the OWL file
+#     ontology = pronto.Ontology(input_file)
+#     # Create a binary stream instead of a file
+#     binary_stream = io.BytesIO()
+#     # Save the ontology in OBO format
+#     ontology.dump(binary_stream, format='obo')
+#     # Get the OBO content from the binary stream
+#     obo_content = binary_stream.getvalue().decode('utf-8')
+#     # Close the stream
+#     binary_stream.close()
+#     print(f"Conversion and parsing successful: {input_file}")
+#     return obo_content
 
 
+def convert_owl_to_obo(input_file: str) -> str:
+    try:
+        # Load the OWL file
+        ontology = pronto.Ontology(input_file)
+        # Create a binary stream instead of a file
+        binary_stream = io.BytesIO()
+        # Save the ontology in OBO format
+        ontology.dump(binary_stream, format='obo')
+        # Get the OBO content from the binary stream
+        obo_content = binary_stream.getvalue().decode('utf-8')
+        # Close the stream
+        binary_stream.close()
+        print("returning obo conversion")
+        return obo_content
+    except Exception as e:
+        print("Failed to convert OWL to OBO: %s", e)
+        raise RuntimeError(f"Failed to convert OWL to OBO: {e}")
 
 @app.task
 def delete_ontology_task(payload):
@@ -113,20 +133,137 @@ def add_ontology_task(self, url, **notis):
 
     current_file = general_downloader.download_file()
 
+    # if url.endswith(".owl"):
+    #     print("owl file detected")
+    #     ontology_buffer = convert_owl_to_obo(current_file)
+    # else:
+    #     ontology_buffer = io.TextIOWrapper(current_file, newline=None)
+
+    # data = None
+    #
+    #
+    # try:
+    #     if url.endswith(".owl"):
+    #         print("owl file detected")
+    #         ontology_buffer = convert_owl_to_obo(url)
+    #     else:
+    #         ontology_buffer = io.TextIOWrapper(current_file, newline=None)
+    #
+    #     obo_parser = OBO_Parser(ontology_buffer)
+    #     data = obo_parser.parse(notifications)
+    # except Exception as e:
+    #     print("e", e)
+    #     notifications.messages.append(f"Error in Pronto conversion. Detailed message: {e}")
+    #     # raise self.retry(exc=e)
+
+    data = None
+
+    # if url.endswith(".owl"):
+    #     print("owl file detected")
+    #     try:
+    #         obo_converted = convert_owl_to_obo(current_file)
+    #
+    #         # ontology_buffer = io.TextIOWrapper(obo_converted, newline=None)
+    #
+    #         ontology_buffer = io.TextIOWrapper(io.BytesIO(obo_converted.encode('utf-8')), newline=None)
+    #
+    #         obo_parser = OBO_Parser(ontology_buffer)
+    #
+    #         data = obo_parser.parse(notifications)
+    #     except:
+    #         print("failed")
+    #         data = None
+    #         notifications.messages.append(Message(type="fail", message="Error in Pronto conversion"))
+    #
+    #         print(f"notificatoins {notifications}")
+    # else:
+    #     ontology_buffer = io.TextIOWrapper(current_file, newline=None)
+    #
+    #     # print("ontology buffer", ontology_buffer)
+    #     print("after ontology buffer", ontology_buffer)
+    #
+    #     obo_parser = OBO_Parser(ontology_buffer)
+    #     data = obo_parser.parse(notifications)
+    #
+    #
+    #     print("data is", data)
+    #
+    #     # print("data", data)
+    #
+    #     print("finished")
+
+
+    # if url.endswith(".owl"):
+    #     print("owl file detected")
+    #     try:
+    #         obo_converted = convert_owl_to_obo(current_file)
+    #
+    #         # ontology_buffer = io.TextIOWrapper(obo_converted, newline=None)
+    #
+    #         ontology_buffer = io.TextIOWrapper(io.BytesIO(obo_converted.encode('utf-8')), newline=None)
+    #
+    #         obo_parser = OBO_Parser(ontology_buffer)
+    #
+    #         data = obo_parser.parse(notifications)
+    #     except:
+    #         print("failed")
+    #         data = None
+    #         notifications.messages.append(Message(type="fail", message="Error in Pronto conversion"))
+    #
+    #         print(f"notificatoins {notifications}")
+    # else:
+    #     ontology_buffer = io.TextIOWrapper(current_file, newline=None)
+    #
+    #     # print("ontology buffer", ontology_buffer)
+    #     print("after ontology buffer", ontology_buffer)
+    #
+    #     obo_parser = OBO_Parser(ontology_buffer)
+    #     data = obo_parser.parse(notifications)
+    #
+    #
+    #     print("data is", data)
+    #
+    #     # print("data", data)
+    #
+    #     print("finished")
+
+
     if url.endswith(".owl"):
         print("owl file detected")
-        ontology_buffer = convert_owl_to_obo(current_file)
+        try:
+            obo_converted = convert_owl_to_obo(current_file)
+
+            ontology_buffer = io.TextIOWrapper(io.BytesIO(obo_converted.encode('utf-8')), newline=None)
+
+            # obo_parser = OBO_Parser(ontology_buffer)
+
+            # data = obo_parser.parse(notifications)
+        except:
+            print("failed")
+            # data = None
+            ontology_buffer = None
+            notifications.messages.append(Message(type="fail", message="Error in Pronto conversion"))
+
+            print(f"notificatoins {notifications}")
     else:
         ontology_buffer = io.TextIOWrapper(current_file, newline=None)
 
+
     obo_parser = OBO_Parser(ontology_buffer)
     data = obo_parser.parse(notifications)
 
+
+
+
     # stop if ontology could not be parsed
-    if data is None:
-        notifications_json = notifications.dict()
-        res = {"task_id": self.request.id, "notifications": notifications_json}
-        return res
+    # if data is None:
+    #     print("data is None")
+    #     notifications_json = notifications.dict()
+    #     res = {"task_id": self.request.id, "notifications": notifications_json}
+    #     return res
+
+    # if data is None:
+    #     data = {"terms":[], "relationships":[], "ontologies":[]}
 
     print("parsing finished")