ydeng/autoBIGS.engine
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Added client error as acceptable exception
All checks were successful
autoBIGS.engine/pipeline/head This commit looks good
Details

Browse Source
This commit is contained in:
Harrison Deng 2025-03-13 18:13:38 +00:00
parent 1776f5aa51
commit 3cb10a4609
1 changed files with 5 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
src/autobigs/engine/analysis/bigsdb.py
View File

@ -9,7 +9,7 @@ import shutil
import tempfile
from typing import Any, AsyncGenerator, AsyncIterable, Coroutine, Iterable, Mapping, Sequence, Set, Union
from aiohttp import ClientSession, ClientTimeout, ServerDisconnectedError
from aiohttp import ClientOSError, ClientSession, ClientTimeout, ServerDisconnectedError
from autobigs.engine.reading import read_fasta
from autobigs.engine.structures.alignment import PairwiseAlignment
@ -100,7 +100,7 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
yield result_allele if isinstance(sequence_string, str) else (sequence_string.name, result_allele)
else:
raise NoBIGSdbMatchesException(self._database_name, self._scheme_id, sequence_string.name if isinstance(sequence_string, NamedString) else None)
except (ConnectionError, ServerDisconnectedError) as e: # Errors we will retry
except (ConnectionError, ServerDisconnectedError, ClientOSError) as e: # Errors we will retry
last_error = e
success = False
await asyncio.sleep(5) # In case the connection issue is due to rate issues
@ -109,7 +109,7 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
if not success and last_error is not None:
try:
raise last_error
except (ConnectionError, ServerDisconnectedError) as e: # Non-fatal errors
except (ConnectionError, ServerDisconnectedError, ClientOSError) as e: # Non-fatal errors
yield Allele("error", "error", None)
async def determine_mlst_st(self, alleles: Union[AsyncIterable[Union[Allele, tuple[str, Allele]]], Iterable[Union[Allele, tuple[str, Allele]]]]) -> Union[MLSTProfile, NamedMLSTProfile]:
@ -156,7 +156,7 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
if len(names_list) > 0:
result_mlst_profile = NamedMLSTProfile(str(tuple(names_list)) if len(set(names_list)) > 1 else names_list[0], result_mlst_profile)
return result_mlst_profile
except (ConnectionError, ServerDisconnectedError) as e:
except (ConnectionError, ServerDisconnectedError, ClientOSError) as e:
last_error = e
success = False
await asyncio.sleep(5)
@ -165,7 +165,7 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
try:
if last_error is not None:
raise last_error
except (ConnectionError, ServerDisconnectedError) as e:
except (ConnectionError, ServerDisconnectedError, ClientOSError) as e:
result_mlst_profile = NamedMLSTProfile((str(tuple(names_list)) if len(set(names_list)) > 1 else names_list[0]) + ":Error", None)
raise ValueError("Last error was not recorded.")