Add skipping mechanism for list of studies

emgapi/management/commands/populate_metagenomics_exchange.py

@@ -131,6 +131,9 @@ def process_to_index_and_update_records(self, analyses_to_index_and_update):
                         mgya=annotation_job.accession,
                         sequence_accession=sequence_accession,
                     )
+                    if not response:
+                        logging.warning(f"Error occurred {annotation_job}")
+                        continue
                     if response.ok:
                         logging.info(f"Successfully added {annotation_job}")
                         registry_id, metadata_match = self.mgx_api.check_analysis(

emgapi/metagenomics_exchange.py

@@ -18,7 +18,7 @@
 
 import requests
 from django.conf import settings
-from requests.exceptions import HTTPError
+from requests.exceptions import HTTPError, JSONDecodeError
 
 
 class MetagenomicsExchangeAPI:
@@ -108,14 +108,20 @@ def add_analysis(self, mgya: str, sequence_accession: str):
         data = self.generate_metadata(mgya, sequence_accession)
         try:
             response = self.post_request(endpoint="datasets", data=data)
+            response.raise_for_status()  # Ensure we raise for HTTP errors
+            return response
         except HTTPError as http_error:
             try:
                 response_json = http_error.response.json()
                 logging.error(f"API response content: {response_json}")
-            except:
-                pass
-            raise http_error
-        return response
+            except JSONDecodeError:  # Catch JSON decoding errors
+                logging.error(f"Failed to decode JSON from response: {http_error.response.text}")
+            except Exception as e:
+                logging.error(f"Unexpected error: {e}")
+
+            # Log the HTTP status code and the error message
+            logging.error(f"HTTPError occurred: {http_error}")
+            return None
 
     def check_analysis(self, mgya: str, sequence_accession: str, metadata=None):
         """Check if a sequence exists in the M. Exchange