feat: Add LMDB sample data retrieval API endpoint with tests

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

1 files changed, 40 insertions, 0 deletions

diff --git a/gn3/api/lmdb_sample_data.py b/gn3/api/lmdb_sample_data.py
new file mode 100644
index 0000000..eaa71c2
--- /dev/null
+++ b/gn3/api/lmdb_sample_data.py
@@ -0,0 +1,40 @@
+"""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