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Fixed exception syntax
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Harrison Deng 2025-03-13 16:49:37 +00:00
parent 96d715fdcb
commit 1776f5aa51
1 changed files with 4 additions and 4 deletions
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8
src/autobigs/engine/analysis/bigsdb.py
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@ -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) 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) 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) 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 ServerDisconnectedError|ConnectionError as e: except (ConnectionError, ServerDisconnectedError) 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.")