making error catching more broad for all bagel methods

parsers/LitCoin/src/bagel/bagel.py

@@ -41,9 +41,8 @@ def get_orion_bagel_results(text, term, abstract_id):
     update_by_id(terms, nr_results, "NameRes")
     update_by_id(terms, sb_results, "SAPBert")
     augment_results(terms, nameres, taxon_id_to_name)
+    # make the call to the LLM asking it to classify the synonyms
     gpt_class_desc_response = ask_classes_and_descriptions(text, term, terms, abstract_id, session)
-    # gpt_label_response = ask_labels(abstract, term, terms)
-    # gpt_class_response = ask_classes(abstract, term, terms)
     return gpt_class_desc_response
 
 

parsers/LitCoin/src/loadLitCoin.py

@@ -300,10 +300,10 @@ def bagelize_entity(self, entity_name, abstract_id, abstract_text):
                                                        entity=entity_name,
                                                        abstract_id=abstract_id)
                 self.bagel_results_lookup[abstract_id]["terms"][entity_name] = bagel_results
-            except requests.exceptions.HTTPError as e:
+            except Exception as e:
                 error_message = f'Failed Bagelization: {type(e)}:{e}'
                 self.logger.error(error_message)
-                if e.response.status_code == 429:
+                if isinstance(e, requests.exceptions.HTTPError) and e.response.status_code == 429:
                     raise e
                 self.parsing_metadata['bagelization_errors'] += 1
                 bagel_results = {'error': error_message}