Added test to check CSV name is not repeated
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@@ -7,7 +7,7 @@ import pytest
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from autobigs.engine.analysis import bigsdb
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from autobigs.engine.structures import mlst
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from autobigs.engine.structures.genomics import NamedString
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from autobigs.engine.structures.mlst import Allele, MLSTProfile
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from autobigs.engine.structures.mlst import Allele, MLSTProfile, NamedMLSTProfile
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from autobigs.engine.exceptions.database import NoBIGSdbExactMatchesException, NoBIGSdbMatchesException
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from autobigs.engine.analysis.bigsdb import BIGSdbIndex, BIGSdbMLSTProfiler, RemoteBIGSdbMLSTProfiler
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@@ -131,11 +131,21 @@ class TestBIGSdbMLSTProfiler:
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async with bigsdb.get_BIGSdb_MLST_profiler(local_db, database_api, database_name, scheme_id) as dummy_profiler:
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async for named_profile in dummy_profiler.profile_multiple_strings(generate_async_iterable(dummy_sequences)):
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name, profile = named_profile.name, named_profile.mlst_profile
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assert profile is not None
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assert isinstance(profile, MLSTProfile)
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assert profile.clonal_complex == expected_profile.clonal_complex
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assert profile.sequence_type == expected_profile.sequence_type
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async def test_bigsdb_profile_named_string_no_repeat_name(self, local_db, database_api, database_name, scheme_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):
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sequence = get_first_sequence_from_fasta(seq_path)
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async with bigsdb.get_BIGSdb_MLST_profiler(local_db, database_api, database_name, scheme_id) as dummy_profiler:
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named_profile = await dummy_profiler.profile_string([NamedString("BX470248.1", sequence)])
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assert isinstance(named_profile, NamedMLSTProfile)
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name, profile = named_profile.name, named_profile.mlst_profile
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assert isinstance(profile, MLSTProfile)
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assert profile.clonal_complex == expected_profile.clonal_complex
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assert profile.sequence_type == expected_profile.sequence_type
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assert name == "BX470248.1"
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async def test_bigsdb_profile_multiple_strings_exactmatch_fail_second_no_stop(self, local_db, database_api, database_name, scheme_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):
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valid_seq = get_first_sequence_from_fasta(seq_path)
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dummy_sequences = [[NamedString("seq1", valid_seq)], [NamedString("should_fail", gene_scrambler(valid_seq, 0.3))], [NamedString("seq3", valid_seq)]]
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