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"""Module that contains functions for editing case-attribute data"""
from pathlib import Path
from typing import Optional
from dataclasses import dataclass
from enum import Enum, auto
import os
import json
import pickle
import lmdb
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 __fetch_case_attrs_changes__(cursor, change_ids: tuple) -> list:
placeholders = ','.join(['%s'] * len(change_ids))
cursor.execute(
"SELECT editor, json_diff_data, time_stamp "
f"FROM caseattributes_audit WHERE id IN ({placeholders})"
"ORDER BY time_stamp DESC",
change_ids
)
results = cursor.fetchall()
for el in results:
el["json_diff_data"] = json.loads(el["json_diff_data"])
return results
def view_change(cursor, change_id: int) -> dict:
cursor.execute(
"SELECT json_diff_data "
"FROM caseattributes_audit "
"WHERE id = %s",
(change_id,)
)
json_diff_data, _ = cursor.fetchone()
if json_diff_data:
json_diff_data = json.loads(json_diff_data)
return json_diff_data
return {}
def get_changes(cursor, inbredset_id: int, directory: Path) -> dict:
directory = f"{directory}/case-attributes/{inbredset_id}"
if not os.path.exists(directory):
os.makedirs(directory)
review_ids, approved_ids, rejected_ids = set(), set(), set()
env = lmdb.open(directory, map_size=8_000_000) # 1 MB
with env.begin(write=False) as txn:
if reviews := txn.get(b"review"):
review_ids = pickle.loads(reviews)
if approvals := txn.get(b"approved"):
approved_ids = pickle.loads(approvals)
if rejections := txn.get(b"rejected"):
rejected_ids = pickle.loads(rejections)
reviews, approvals, rejections = {}, {}, {}
if review_ids:
reviews = dict(zip(review_ids,
__fetch_case_attrs_changes__(cursor, tuple(review_ids))))
if approved_ids:
approvals = dict(zip(approved_ids,
__fetch_case_attrs_changes__(cursor, tuple(approved_ids))))
if rejected_ids:
rejections = dict(zip(rejected_ids,
__fetch_case_attrs_changes__(cursor, tuple(rejected_ids))))
return {
"reviews": reviews,
"approvals": approvals,
"rejections": rejections
}
def apply_change(cursor, change_type: EditStatus, change_id: int, directory: Path) -> bool:
review_ids, approved_ids, rejected_ids = set(), set(), set()
env = lmdb.open(directory, map_size=8_000_000) # 1 MB
with env.begin(write=True) as txn:
if reviews := txn.get(b"review"):
review_ids = pickle.loads(reviews)
if change_id not in review_ids:
return False
match change_type:
case EditStatus.rejected:
cursor.execute(
"UPDATE caseattributes_audit "
"SET status = %s "
"WHERE id = %s",
(str(change_type), change_id))
review_ids.discard(change_id)
rejected_ids.add(change_id)
txn.put(b"review", pickle.dumps(review_ids))
txn.put(b"rejected", pickle.dumps(rejected_ids))
return True
case EditStatus.approved:
cursor.execute(
"SELECT json_diff_data "
"FROM caseattributes_audit WHERE "
"id = %s",
(change_id,)
)
json_diff_data, _ = cursor.fetchone()
json_diff_data = json.loads(json_diff_data)
inbredset_id = json_diff_data.get("inbredset_id")
modifications = json_diff_data.get(
"Modifications", {}).get("Current", {})
strains = tuple(modifications.keys())
case_attrs = set()
for data in modifications.values():
case_attrs.update(data.keys())
# Bulk fetch strain ids
strain_id_map = {}
if strains:
cursor.execute(
"SELECT Name, Id FROM Strain WHERE Name IN "
f"({', '.join(['%s'] * len(strains))})",
strains
)
for name, strain_id in cursor.fetchall():
strain_id_map[name] = strain_id
# Bulk fetch case attr ids
caseattr_id_map = {}
if case_attrs:
cursor.execute(
"SELECT Name, CaseAttributeId FROM CaseAttribute "
"WHERE InbredSetId = %s AND Name IN "
f"({', '.join(['%s'] * len(case_attrs))})",
(inbredset_id, *case_attrs)
)
for name, caseattr_id in cursor.fetchall():
caseattr_id_map[name] = caseattr_id
# Bulk insert data
insert_data = []
for strain, data in modifications.items():
strain_id = strain_id_map.get(strain)
for case_attr, value in data.items():
insert_data.append({
"inbredset_id": inbredset_id,
"strain_id": strain_id,
"caseattr_id": caseattr_id_map.get(case_attr),
"value": value,
})
if insert_data:
cursor.executemany(
"INSERT INTO CaseAttributeXRefNew "
"(InbredSetId, StrainId, CaseAttributeId, Value) "
"VALUES (%(inbredset_id)s, %(strain_id)s, %(caseattr_id)s, %(value)s) "
"ON DUPLICATE KEY UPDATE Value = VALUES(Value)",
insert_data
)
# Update LMDB and audit table
cursor.execute(
"UPDATE caseattributes_audit "
"SET status = %s "
"WHERE id = %s",
(str(change_type), change_id))
if approvals := txn.get(b"approved"):
approved_ids = pickle.loads(approvals)
review_ids.discard(change_id)
approved_ids.add(change_id)
txn.put(b"review", pickle.dumps(review_ids))
txn.put(b"approvals", pickle.dumps(approved_ids))
return True
case _:
raise ValueError
|
