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@@ -15,7 +15,7 @@ from autobigs.engine.reading import read_fasta
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from autobigs.engine.structures.alignment import PairwiseAlignment
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from autobigs.engine.structures.alignment import PairwiseAlignment
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from autobigs.engine.structures.genomics import NamedString
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from autobigs.engine.structures.genomics import NamedString
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from autobigs.engine.structures.mlst import Allele, NamedMLSTProfile, AlignmentStats, MLSTProfile
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from autobigs.engine.structures.mlst import Allele, NamedMLSTProfile, AlignmentStats, MLSTProfile
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from autobigs.engine.exceptions.database import NoBIGSdbExactMatchesException, NoBIGSdbMatchesException, NoSuchBIGSdbDatabaseException
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from autobigs.engine.exceptions.database import BIGSdbResponseNotOkay, NoBIGSdbExactMatchesException, NoBIGSdbMatchesException, NoSuchBIGSdbDatabaseException
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from Bio.Align import PairwiseAligner
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from Bio.Align import PairwiseAligner
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@@ -99,7 +99,10 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
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)
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)
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yield result_allele if isinstance(sequence_string, str) else (sequence_string.name, result_allele)
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yield result_allele if isinstance(sequence_string, str) else (sequence_string.name, result_allele)
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else:
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else:
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if response.status == 200:
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raise NoBIGSdbMatchesException(self._database_name, self._scheme_id, sequence_string.name if isinstance(sequence_string, NamedString) else None)
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raise NoBIGSdbMatchesException(self._database_name, self._scheme_id, sequence_string.name if isinstance(sequence_string, NamedString) else None)
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else:
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raise BIGSdbResponseNotOkay(sequence_response)
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except (ConnectionError, ServerDisconnectedError, ClientOSError) as e: # Errors we will retry
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except (ConnectionError, ServerDisconnectedError, ClientOSError) as e: # Errors we will retry
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last_error = e
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last_error = e
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success = False
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success = False
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