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Added client error as acceptable exception
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Harrison Deng 2025-03-13 18:13:38 +00:00
parent 1776f5aa51
commit 3cb10a4609
1 changed files with 5 additions and 5 deletions
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src/autobigs/engine/analysis/bigsdb.py
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@ -9,7 +9,7 @@ import shutil
import tempfile import tempfile
from typing import Any, AsyncGenerator, AsyncIterable, Coroutine, Iterable, Mapping, Sequence, Set, Union 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.reading import read_fasta
from autobigs.engine.structures.alignment import PairwiseAlignment 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) yield result_allele if isinstance(sequence_string, str) else (sequence_string.name, result_allele)
else: else:
raise NoBIGSdbMatchesException(self._database_name, self._scheme_id, sequence_string.name if isinstance(sequence_string, NamedString) else None) 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 last_error = e
success = False success = False
await asyncio.sleep(5) # In case the connection issue is due to rate issues 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: if not success and last_error is not None:
try: try:
raise last_error 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) 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]: 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: 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) 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 return result_mlst_profile
except (ConnectionError, ServerDisconnectedError) as e: except (ConnectionError, ServerDisconnectedError, ClientOSError) as e:
last_error = e last_error = e
success = False success = False
await asyncio.sleep(5) await asyncio.sleep(5)
@ -165,7 +165,7 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
try: try:
if last_error is not None: if last_error is not None:
raise last_error 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) 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.") raise ValueError("Last error was not recorded.")