Increased default timeout

src/autobigs/engine/analysis/bigsdb.py

@@ -15,7 +15,7 @@ from autobigs.engine.reading import read_fasta
 from autobigs.engine.structures.alignment import PairwiseAlignment
 from autobigs.engine.structures.genomics import NamedString
 from autobigs.engine.structures.mlst import Allele, NamedMLSTProfile, AlignmentStats, MLSTProfile
-from autobigs.engine.exceptions.database import BIGSdbResponseNotOkay, NoBIGSdbExactMatchesException, NoBIGSdbMatchesException, NoSuchBIGSdbDatabaseException
+from autobigs.engine.exceptions.database import NoBIGSdbExactMatchesException, NoBIGSdbMatchesException, NoSuchBIGSdbDatabaseException
 
 from Bio.Align import PairwiseAligner
 
@@ -43,12 +43,13 @@ class BIGSdbMLSTProfiler(AbstractAsyncContextManager):
 
 class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
 
-    def __init__(self, database_api: str, database_name: str, scheme_id: int, retry_requests: int = 5):
+    def __init__(self, database_api: str, database_name: str, scheme_id: int, retry_requests: int = 5, timeout: int = 1800):
+        self._timeout = timeout
         self._retry_limit = retry_requests
         self._database_name = database_name
         self._scheme_id = scheme_id
         self._base_url = f"{database_api}/db/{self._database_name}/schemes/{self._scheme_id}/"
-        self._http_client = ClientSession(self._base_url, timeout=ClientTimeout(300))
+        self._http_client = ClientSession(self._base_url, timeout=ClientTimeout(timeout))
 
     async def __aenter__(self):
         return self
@@ -99,10 +100,7 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
                                 )
                                 yield result_allele if isinstance(sequence_string, str) else (sequence_string.name, result_allele)
                         else:
-                            if response.status == 200:
-                                raise NoBIGSdbMatchesException(self._database_name, self._scheme_id, sequence_string.name if isinstance(sequence_string, NamedString) else None)
-                            else:
-                                raise BIGSdbResponseNotOkay(sequence_response)
+                            raise NoBIGSdbMatchesException(self._database_name, self._scheme_id, sequence_string.name if isinstance(sequence_string, NamedString) else None)
                 except (ConnectionError, ServerDisconnectedError, ClientOSError) as e: # Errors we will retry
                     last_error = e
                     success = False

src/autobigs/engine/exceptions/database.py

@@ -3,13 +3,11 @@ from typing import Union
 class BIGSDbDatabaseAPIException(Exception):
     pass
 
-class BIGSdbResponseNotOkay(BIGSDbDatabaseAPIException):
-    pass
 
 class NoBIGSdbMatchesException(BIGSDbDatabaseAPIException):
     def __init__(self, database_name: str, database_scheme_id: int, query_name: Union[None, str], *args):
         self._query_name = query_name
-        super().__init__(f"No matches found with scheme with ID {database_scheme_id} in the database \"{database_name}\".", *args)
+        super().__init__(f"No matches found with scheme with ID {database_scheme_id}  in the database \"{database_name}\".", *args)
     
     def get_causal_query_name(self) -> Union[str, None]:
         return self._query_name