Added test to check CSV name is not repeated

tests/autobigs/engine/analysis/test_bigsdb.py

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

tests/autobigs/engine/test_writing.py

@@ -31,9 +31,21 @@ async def test_column_order_is_same_as_expected_file(dummy_alphabet_mlst_profile
         with open(output_path) as csv_handle:
             csv_reader = reader(csv_handle)
             lines = list(csv_reader)
-            target_columns = lines[4:]
+            target_columns = lines[0][3:]
             assert target_columns == sorted(target_columns)
 
+async def test_csv_writing_sample_name_not_repeated_when_single_sequence(dummy_alphabet_mlst_profile):
+    dummy_profiles = [dummy_alphabet_mlst_profile]
+    with tempfile.TemporaryDirectory() as temp_dir:
+        output_path = path.join(temp_dir, "out.csv")
+        await write_mlst_profiles_as_csv(iterable_to_asynciterable(dummy_profiles), output_path)
+        with open(output_path) as csv_handle:
+            csv_reader = reader(csv_handle)
+            lines = list(csv_reader)
+            sample_name = lines[1][0]
+            assert sample_name == "name"
+
+
 async def test_alleles_to_text_map_mapping_is_correct(dummy_alphabet_mlst_profile: NamedMLSTProfile):
     mapping = alleles_to_text_map(dummy_alphabet_mlst_profile.mlst_profile.alleles) # type: ignore
     expected_mapping = {
@@ -45,3 +57,4 @@ async def test_alleles_to_text_map_mapping_is_correct(dummy_alphabet_mlst_profil
     for allele_name, allele_ids in mapping.items():
         assert allele_name in expected_mapping
         assert allele_ids == expected_mapping[allele_name]
+