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Improve performance of AnyVar.put_object() by eliminating unnecessary digest computation #73

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merged 4 commits into from
Jan 16, 2024
Merged

Improve performance of AnyVar.put_object() by eliminating unnecessary digest computation #73

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26a3b7f
Return digest from vrs_enref instead of recomputing
ehclark Jan 5, 2024
ff96f1b
Removed unused import
ehclark Jan 5, 2024
5882f31
Bump ga4gh.vrs dependency version to 2.0.0a2
ehclark Jan 8, 2024
deac73b
Change unused var name to "_"
ehclark Jan 16, 2024
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2 changes: 1 addition & 1 deletion setup.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ install_requires =
fastapi >= 0.95.0
python-multipart
uvicorn
ga4gh.vrs[extras] ~= 2.0.0a1
ga4gh.vrs[extras] ~= 2.0.0a2
psycopg[binary]
snowflake-connector-python ~= 3.4.1

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5 changes: 2 additions & 3 deletions src/anyvar/anyvar.py
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Expand Up @@ -9,7 +9,6 @@
from typing import Optional
from urllib.parse import urlparse

from ga4gh.core import ga4gh_identify
from ga4gh.vrs import vrs_deref, vrs_enref

from anyvar.storage import DEFAULT_STORAGE_URI, _Storage
Expand Down Expand Up @@ -83,10 +82,10 @@ def put_object(self, variation_object: VrsObject) -> Optional[str]:
:return: Object digest if successful, None otherwise
"""
try:
v = vrs_enref(variation_object, self.object_store)
id, v = vrs_enref(variation_object, self.object_store, True)
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except ValueError:
return None
return ga4gh_identify(v)
return id

def get_object(self, object_id: str, deref: bool = False) -> Optional[VrsObject]:
"""Retrieve registered variation.
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