"""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 class EditStatus(Enum): """Enumeration for the status of the edits.""" review = auto() # pylint: disable=[invalid-name] approved = auto() # pylint: disable=[invalid-name] rejected = auto() # pylint: disable=[invalid-name] def __str__(self): """Print out human-readable form.""" return self.name @dataclass class CaseAttributeEdit: """Represents an edit operation for case attributes in the database. Attributes: inbredset_id (int): The ID of the inbred set associated with the edit. user_id (str): The ID of the user performing the edit. changes (dict): A dictionary containing the changes to be applied to the case attributes. """ inbredset_id: int status: EditStatus user_id: str changes: dict def queue_edit(cursor, directory: Path, edit: CaseAttributeEdit) -> Optional[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, status, 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(edit.status), 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) _id = cursor.lastrowid review_ids.add(_id) txn.put(b"review", pickle.dumps(review_ids)) return _id def update_case_attribute(cursor, directory: Path, change_id: int, edit: CaseAttributeEdit) -> int: 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 modifications = {} if edit.changes.get("Modifications").get("Current"): modifications = edit.get("Modifications").get("Current") for strain, changes in modifications.items(): for case_attribute, value in changes.items(): value = str(value).strip() cursor.execute("SELECT Id AS StrainId, Name AS StrainName FROM Strain " "WHERE Name = %s", (strain,)) strain_id, _ = cursor.fetchone() cursor.execute("SELECT CaseAttributeId, Name AS CaseAttributeName " "FROM CaseAttribute WHERE InbredSetId = %s " "AND Name = %s", (inbredset_id, edit.inbredset_id,)) case_attr_id, _ = cursor.fetchone() cursor.execute( "INSERT INTO CaseAttributeXRefNew" "(InbredSetId, StrainId, CaseAttributeId, Value) " "VALUES (%s, %s, %s, %s) " "ON DUPLICATE KEY UPDATE Value=VALUES(value)", (edit.inbredset_id, strain_id, case_attr_id, value,)) cursor.execute( "UPDATE caseattributes_audit SET ", "status = %s WHERE id = %s", (str(edit.status), change_id,)) with env.begin(write=True) as txn: review_ids, approved_ids = set(), set() if reviews := txn.get(b"review"): review_ids = pickle.loads(reviews) review_ids.remove(change_id) if approvals := txn.get(b"review"): approved_ids = pickle.loads(approvals) approved_ids.add(change_id) txn.put(b"review", pickle.dumps(review_ids)) txn.put(b"approved", pickle.dumps(approved_ids))