Move queue_edit to gn3.db.case_attributes.

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

2 files changed, 48 insertions, 39 deletions

diff --git a/gn3/case_attributes.py b/gn3/case_attributes.py
index dae6def..7646c92 100644
--- a/gn3/case_attributes.py
+++ b/gn3/case_attributes.py
@@ -15,7 +15,10 @@ from urllib.parse import urljoin
 
 import requests
 from MySQLdb.cursors import DictCursor
-from gn3.db.case_attributes import CaseAttributeEdit, EditStatus
+from gn3.db.case_attributes import (
+    CaseAttributeEdit,
+    EditStatus,
+    queue_edit)
 from authlib.integrations.flask_oauth2.errors import _HTTPException
 from flask import (
     jsonify,
@@ -98,44 +101,6 @@ def required_access(
         f"User does not have the privileges {access_levels}")
 
 
-def __queue_edits__(cursor, directory: Path, edit: CaseAttributeEdit) -> set:
-    """Queues a case attribute edit for review by inserting it into
-    the audit table and storing its review ID in an LMDB database.
-
-    Args:
-        cursor: A database cursor for executing SQL queries.
-        directory (Path): The base directory path for the LMDB database.
-        edit (CaseAttributeEdit): A dataclass containing the edit details, including
-            inbredset_id, user_id, and diff (the changes to be reviewed).
-
-    Returns:
-        set: A set of review IDs, including the newly added edit's ID, stored in the
-            LMDB database for the specified inbredset_id.
-
-    Notes:
-        - Inserts the edit into the `caseattributes_audit` table with status set to
-          `EditStatus.review`.
-        - Uses LMDB to store review IDs under the key b"review" for the given
-          inbredset_id.
-        - The LMDB map_size is set to 8 MB.
-        - The JSON diff data is serialized using a custom `CAJSONEncoder`.
-    """
-    cursor.execute(
-        "INSERT INTO "
-        "caseattributes_audit(status, editor, json_diff_data) "
-        "VALUES (%s, %s, %s) "
-        "ON DUPLICATE KEY UPDATE status=%s",
-        (str(EditStatus.review),
-         edit.user_id, json.dumps(edit.diff, cls=CAJSONEncoder), str(EditStatus.review),))
-    env = lmdb.open(f"{directory}/case-attributes/{edit.inbredset_id}",
-                    map_size=8_000_000)  # 1 MB
-    with env.begin() as txn:
-        review_ids = set()
-        if reviews := txn.get(b"review"):
-            review_ids = pickle.loads(reviews)
-        review_ids.add(cursor.lastrowid)
-        txn.put(b"review", pickle.dumps(review_ids))
-        return review_ids
 
 
 def __inbredset_group__(conn, inbredset_id):
diff --git a/gn3/db/case_attributes.py b/gn3/db/case_attributes.py
index a5fdc53..44fdf58 100644
--- a/gn3/db/case_attributes.py
+++ b/gn3/db/case_attributes.py
@@ -1,9 +1,13 @@
 """Module that contains functions for editing case-attribute data"""
+from pathlib import Path
 from typing import Any, Optional, Tuple
 from dataclasses import dataclass
 from enum import Enum, auto
 
+import os
 import json
+import pickle
+import lmdb
 import MySQLdb
 
 
@@ -35,6 +39,46 @@ class EditStatus(Enum):
         return self.name
 
 
+def queue_edit(cursor, directory: Path, edit: CaseAttributeEdit) -> int:
+    """Queues a case attribute edit for review by inserting it into
+    the audit table and storing its review ID in an LMDB database.
+
+    Args:
+        cursor: A database cursor for executing SQL queries.
+        directory (Path): The base directory path for the LMDB database.
+        edit (CaseAttributeEdit): A dataclass containing the edit details, including
+            inbredset_id, user_id, and changes.
+
+    Returns:
+        int: An id the particular case-attribute that was updated.
+
+    Notes:
+        - Inserts the edit into the `caseattributes_audit` table with status set to
+          `EditStatus.review`.
+        - Uses LMDB to store review IDs under the key b"review" for the given
+          inbredset_id.
+        - The LMDB map_size is set to 8 MB.
+    """
+    cursor.execute(
+        "INSERT INTO "
+        "caseattributes_audit(status, editor, json_diff_data) "
+        "VALUES (%s, %s, %s) "
+        "ON DUPLICATE KEY UPDATE status=%s",
+        (str(EditStatus.review),
+         edit.user_id, json.dumps(edit.changes), str(EditStatus.review),))
+    directory = f"{directory}/case-attributes/{edit.inbredset_id}"
+    if not os.path.exists(directory):
+        os.makedirs(directory)
+    env = lmdb.open(directory, map_size=8_000_000)  # 1 MB
+    with env.begin(write=True) as txn:
+        review_ids = set()
+        if reviews := txn.get(b"review"):
+            review_ids = pickle.loads(reviews)
+        review_ids.add(cursor.lastrowid)
+        txn.put(b"review", pickle.dumps(review_ids))
+        return review_ids
+
+
 def get_case_attributes(conn) -> Optional[Tuple]:
     """Get all the case attributes from the database."""
     with conn.cursor() as cursor: