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Added pubMLST test case to bigsdb tests and updated to reflect codebase changes

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Harrison Deng 2025-02-12 15:53:14 +00:00
parent 175a51f968
commit 7fb3eab5b6
1 changed files with 2 additions and 2 deletions
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tests/autobigs/engine/analysis/test_bigsdb.py
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@ -9,7 +9,7 @@ from autobigs.engine.structures import mlst
from autobigs.engine.structures.genomics import NamedString from autobigs.engine.structures.genomics import NamedString
from autobigs.engine.structures.mlst import Allele, MLSTProfile from autobigs.engine.structures.mlst import Allele, MLSTProfile
from autobigs.engine.exceptions.database import NoBIGSdbExactMatchesException, NoBIGSdbMatchesException 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): async def generate_async_iterable(normal_iterable):
for dummy_sequence in 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", [ @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), (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: 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): 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):