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Fixed multiple string typing failure handling

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Harrison Deng
2025-01-10 16:00:27 +00:00
parent 0c0a2c9d4c
commit f20a656f45
3 changed files with 31 additions and 11 deletions
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4
src/automlst/engine/exceptions/database.py
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@@ -6,9 +6,9 @@ class BIGSDbDatabaseAPIException(Exception):
class NoBIGSdbMatchesException(BIGSDbDatabaseAPIException):
def __init__(self, database_name: str, database_schema_id: int, *args):
super().__init__(f"No exact match found with schema with ID {database_schema_id} in the database \"{database_name}\".", *args)
super().__init__(f"No matches found with schema with ID {database_schema_id} in the database \"{database_name}\".", *args)
class NoBIGSdbExactMatchesException(BIGSDbDatabaseAPIException):
class NoBIGSdbExactMatchesException(NoBIGSdbMatchesException):
def __init__(self, database_name: str, database_schema_id: int, *args):
super().__init__(f"No exact match found with schema with ID {database_schema_id} in the database \"{database_name}\".", *args)

6
src/automlst/engine/remote/databases/bigsdb.py
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@@ -82,7 +82,9 @@ class BIGSdbMLSTProfiler(AbstractAsyncContextManager):
for exact_match_loci, exact_match_alleles in schema_exact_matches.items():
for exact_match_allele in exact_match_alleles:
allele_map[exact_match_loci].append(Allele(exact_match_loci, exact_match_allele["allele_id"], None))
return MLSTProfile(allele_map, schema_fields_returned["ST"], schema_fields_returned["clonal_complex"])
if len(allele_map) == 0:
raise ValueError("Passed in no alleles.")
return MLSTProfile(dict(allele_map), schema_fields_returned["ST"], schema_fields_returned["clonal_complex"])
async def profile_string(self, string: str, exact: bool = False) -> MLSTProfile:
alleles = self.fetch_mlst_allele_variants(string, exact)
@@ -93,7 +95,7 @@ class BIGSdbMLSTProfiler(AbstractAsyncContextManager):
async for named_string in namedStrings:
try:
yield (named_string.name, await self.profile_string(named_string.sequence, exact))
except NoBIGSdbExactMatchesException as e:
except NoBIGSdbMatchesException as e:
if stop_on_fail:
raise e
yield (named_string.name, None)