blob: eaa71c2cce4133ad80a17c14158aba48cdfbc480 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
|
"""API endpoint for retrieving sample data from LMDB storage"""
import hashlib
from pathlib import Path
import lmdb
from flask import Blueprint, current_app, jsonify
lmdb_sample_data = Blueprint("lmdb_sample_data", __name__)
@lmdb_sample_data.route("/sample-data/<string:dataset>/<int:trait_id>", methods=["GET"])
def get_sample_data(dataset: str, trait_id: int):
"""Retrieve sample data from LMDB for a given dataset and trait.
Path Parameters:
dataset: The name of the dataset
trait_id: The ID of the trait
Returns:
JSON object mapping sample IDs to their values
"""
checksum = hashlib.md5(
f"{dataset}-{trait_id}".encode()
).hexdigest()
db_path = Path(current_app.config["LMDB_DATA_PATH"]) / checksum
if not db_path.exists():
return jsonify(error="No data found for given dataset and trait"), 404
try:
with lmdb.open(str(db_path), max_dbs=15, readonly=True) as env:
data = {}
with env.begin(write=False) as txn:
cursor = txn.cursor()
for key, value in cursor:
data[key.decode()] = float(value.decode())
return jsonify(data)
except lmdb.Error as err:
return jsonify(error=f"LMDB error: {str(err)}"), 500
|
