diff options
| -rw-r--r-- | gn3/case_attributes.py | 43 | ||||
| -rw-r--r-- | gn3/db/case_attributes.py | 44 |
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: |