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Author SHA1 Message Date
29fcf8c176 Added check for HTTP 200 status
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autoBIGS.engine/pipeline/head This commit looks good
2025-04-09 16:57:48 +00:00
8264242fa5 Fixed typo (extra space) 2025-04-08 18:53:50 +00:00
2 changed files with 8 additions and 3 deletions

View File

@ -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 NoBIGSdbExactMatchesException, NoBIGSdbMatchesException, NoSuchBIGSdbDatabaseException
from autobigs.engine.exceptions.database import BIGSdbResponseNotOkay, NoBIGSdbExactMatchesException, NoBIGSdbMatchesException, NoSuchBIGSdbDatabaseException
from Bio.Align import PairwiseAligner
@ -99,7 +99,10 @@ 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)
except (ConnectionError, ServerDisconnectedError, ClientOSError) as e: # Errors we will retry
last_error = e
success = False

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@ -3,6 +3,8 @@ 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):