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

Added a server disconnect error catch
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 16:27:59 +00:00
parent e088d1080b
commit 96d715fdcb
1 changed files with 15 additions and 9 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

18
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
from aiohttp import ClientSession, ClientTimeout, ServerDisconnectedError
from autobigs.engine.reading import read_fasta
from autobigs.engine.structures.alignment import PairwiseAlignment
@ -64,6 +64,7 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
success = False
last_error = None
while not success and attempts < self._retry_limit:
attempts += 1
request = self._http_client.post(uri_path, json={
"sequence": sequence_string if isinstance(sequence_string, str) else sequence_string.sequence,
"partial_matches": True
@ -99,7 +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 Exception as e:
except ConnectionError|ServerDisconnectedError 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
@ -108,7 +109,7 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
if not success and last_error is not None:
try:
raise last_error
except ConnectionResetError as e:
except ConnectionError|ServerDisconnectedError 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]:
@ -137,6 +138,7 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
success = False
last_error = None
while attempts < self._retry_limit and not success:
attempts += 1
try:
async with self._http_client.post(uri_path, json=request_json) as response:
response_json: dict = await response.json()
@ -154,15 +156,19 @@ 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 Exception as e:
except ConnectionError|ServerDisconnectedError as e:
last_error = e
success = False
await asyncio.sleep(5)
if not success and last_error is not None:
else:
success = True
try:
if last_error is not None:
raise last_error
except ConnectionResetError as e:
except ServerDisconnectedError|ConnectionError 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.")
async def profile_string(self, query_sequence_strings: Iterable[Union[NamedString, str]]) -> Union[NamedMLSTProfile, MLSTProfile]:
alleles = self.determine_mlst_allele_variants(query_sequence_strings)