From 7fb3eab5b6c4f02f36c9208c9000b5f33fb3c4d9 Mon Sep 17 00:00:00 2001 From: Harrison Deng Date: Wed, 12 Feb 2025 15:53:14 +0000 Subject: [PATCH] Added pubMLST test case to bigsdb tests and updated to reflect codebase changes --- tests/autobigs/engine/analysis/test_bigsdb.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/autobigs/engine/analysis/test_bigsdb.py b/tests/autobigs/engine/analysis/test_bigsdb.py index 1984ca7..d689d65 100644 --- a/tests/autobigs/engine/analysis/test_bigsdb.py +++ b/tests/autobigs/engine/analysis/test_bigsdb.py @@ -9,7 +9,7 @@ from autobigs.engine.structures import mlst from autobigs.engine.structures.genomics import NamedString from autobigs.engine.structures.mlst import Allele, MLSTProfile from autobigs.engine.exceptions.database import NoBIGSdbExactMatchesException, NoBIGSdbMatchesException -from autobigs.engine.analysis.bigsdb import BIGSdbIndex, BIGSdbMLSTProfiler, LocalBIGSdbMLSTProfiler, RemoteBIGSdbMLSTProfiler +from autobigs.engine.analysis.bigsdb import BIGSdbIndex, BIGSdbMLSTProfiler, RemoteBIGSdbMLSTProfiler async def generate_async_iterable(normal_iterable): for dummy_sequence in normal_iterable: @@ -76,7 +76,7 @@ hinfluenzae_fdaargos_fragmented_sequence = tuple(SeqIO.parse("tests/resources/to @pytest.mark.parametrize("local_db,database_api,database_name,schema_id,seq_path,feature_seqs_path,expected_profile,bad_profile", [ (False, "https://bigsdb.pasteur.fr/api", "pubmlst_bordetella_seqdef", 3, "tohama_I_bpertussis.fasta", "tohama_I_bpertussis_features.fasta", bpertussis_tohamaI_profile, bpertussis_tohamaI_bad_profile), - (True, "https://bigsdb.pasteur.fr/api", "pubmlst_bordetella_seqdef", 3, "tohama_I_bpertussis.fasta", "tohama_I_bpertussis_features.fasta", bpertussis_tohamaI_profile, bpertussis_tohamaI_bad_profile), + (False, "https://bigsdb.pasteur.fr/api", "pubmlst_hinfluenzae_seqdef", 1, "fdaargos_1560_hinfluenza.fasta", "fdaargos_1560_hinfluenza_features.fasta", hinfluenzae_fdaargos_profile, hinfluenzae_fdaargos_bad_profile), ]) class TestBIGSdbMLSTProfiler: async def test_profiling_results_in_exact_matches_when_exact(self, local_db, database_api, database_name, schema_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):