ydeng/autoBIGS.engine
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Fixed potential memory leak

Browse Source
This commit is contained in:
Harrison Deng 2025-01-27 22:02:52 +00:00
parent 6d0157581f
commit ba1f0aa318
1 changed files with 31 additions and 30 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

61
src/autobigs/engine/data/remote/databases/bigsdb.py
View File

@ -23,39 +23,40 @@ class BIGSdbMLSTProfiler(AbstractAsyncContextManager):
async def fetch_mlst_allele_variants(self, sequence_string: str, exact: bool) -> AsyncGenerator[Allele, Any]:
# See https://bigsdb.pasteur.fr/api/db/pubmlst_bordetella_seqdef/schemes
uri_path = "sequence"
response = await self._http_client.post(uri_path, json={
async with self._http_client.post(uri_path, json={
"sequence": sequence_string,
"partial_matches": not exact
})
sequence_response: dict = await response.json()
}) as response:
sequence_response: dict = await response.json()
if "exact_matches" in sequence_response:
# loci -> list of alleles with id and loci
exact_matches: dict[str, Sequence[dict[str, str]]] = sequence_response["exact_matches"]
for allele_loci, alleles in exact_matches.items():
for allele in alleles:
alelle_id = allele["allele_id"]
yield Allele(allele_loci=allele_loci, allele_variant=alelle_id, partial_match_profile=None)
elif "partial_matches" in sequence_response:
if exact:
raise NoBIGSdbExactMatchesException(self._database_name, self._schema_id)
partial_matches: dict[str, dict[str, Union[str, float, int]]] = sequence_response["partial_matches"]
for allele_loci, partial_match in partial_matches.items():
if len(partial_match) <= 0:
continue
partial_match_profile = PartialAllelicMatchProfile(
percent_identity=float(partial_match["identity"]),
mismatches=int(partial_match["mismatches"]),
bitscore=float(partial_match["bitscore"]),
gaps=int(partial_match["gaps"])
)
yield Allele(
allele_loci=allele_loci,
allele_variant=str(partial_match["allele"]),
partial_match_profile=partial_match_profile
)
else:
raise NoBIGSdbMatchesException(self._database_name, self._schema_id)
if "exact_matches" in sequence_response:
# loci -> list of alleles with id and loci
exact_matches: dict[str, Sequence[dict[str, str]]] = sequence_response["exact_matches"]
for allele_loci, alleles in exact_matches.items():
for allele in alleles:
alelle_id = allele["allele_id"]
yield Allele(allele_loci=allele_loci, allele_variant=alelle_id, partial_match_profile=None)
elif "partial_matches" in sequence_response:
if exact:
raise NoBIGSdbExactMatchesException(self._database_name, self._schema_id)
partial_matches: dict[str, dict[str, Union[str, float, int]]] = sequence_response["partial_matches"]
for allele_loci, partial_match in partial_matches.items():
if len(partial_match) <= 0:
continue
partial_match_profile = PartialAllelicMatchProfile(
percent_identity=float(partial_match["identity"]),
mismatches=int(partial_match["mismatches"]),
bitscore=float(partial_match["bitscore"]),
gaps=int(partial_match["gaps"])
)
yield Allele(
allele_loci=allele_loci,
allele_variant=str(partial_match["allele"]),
partial_match_profile=partial_match_profile
)
else:
raise NoBIGSdbMatchesException(self._database_name, self._schema_id)