diff options
Diffstat (limited to 'gn3/db')
| -rw-r--r-- | gn3/db/case_attributes.py | 65 | ||||
| -rw-r--r-- | gn3/db/sample_data.py | 4 |
2 files changed, 17 insertions, 52 deletions
diff --git a/gn3/db/case_attributes.py b/gn3/db/case_attributes.py index b16bbdd..48afc0c 100644 --- a/gn3/db/case_attributes.py +++ b/gn3/db/case_attributes.py @@ -4,7 +4,6 @@ from typing import Optional from dataclasses import dataclass from enum import Enum, auto -import os import json import pickle import lmdb @@ -52,13 +51,6 @@ def queue_edit(cursor, directory: Path, edit: CaseAttributeEdit) -> Optional[int 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 " @@ -67,10 +59,8 @@ def queue_edit(cursor, directory: Path, edit: CaseAttributeEdit) -> Optional[int "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 + directory.mkdir(parents=True, exist_ok=True) + env = lmdb.open(directory.as_posix(), map_size=8_000_000) # 1 MB with env.begin(write=True) as txn: review_ids = set() if reviews := txn.get(b"review"): @@ -143,16 +133,8 @@ def view_change(cursor, change_id: int) -> dict: Returns: dict: The deserialized JSON diff data as a dictionary if the - record exists and contains valid JSON; otherwise, an empty dictionary. - - Notes: - - The function assumes `change_id` is a valid integer - corresponding to a record in `caseattributes_audit`. - - The `json_diff_data` column is expected to contain a valid - JSON string or None. - - Uses parameterized queries to prevent SQL injection. - - The second column returned by `fetchone()` is - ignored (denoted by `_`). + record exists and contains valid JSON; otherwise, an + empty dictionary. Raises: json.JSONDecodeError: If the `json_diff_data` cannot be @@ -175,21 +157,18 @@ def view_change(cursor, change_id: int) -> dict: return {} -def get_changes(cursor, inbredset_id: int, directory: Path) -> dict: - """Retrieves case attribute changes for a given inbred set, - categorized by review status. +def get_changes(cursor, directory: Path) -> dict: + """Retrieves case attribute changes for given lmdb data in + directory categorized by review status. - Fetches change IDs from an LMDB database for the specified - `inbredset_id`, categorized as review, approved, or - rejected. Queries the `caseattributes_audit` table to retrieve - details for these changes using the internal + Fetches change IDs from an LMDB database, categorized as review, + approved, or rejected. Queries the `caseattributes_audit` table to + retrieve details for these changes using the internal `__fetch_case_attrs_changes__` function. Returns a dictionary with change details grouped by status. Args: - cursor: A MySQLdb cursor for executing SQL queries. - - inbredset_id (int): The ID of the inbred set to filter - changes. - directory (Path): The base directory path for the LMDB database. @@ -201,20 +180,6 @@ def get_changes(cursor, inbredset_id: int, directory: Path) -> dict: 'time_stamp'). Empty dictionaries are returned for categories with no changes. - Notes: - - Creates an LMDB environment in a subdirectory - `case-attributes/{inbredset_id}` if it doesn't exist, with a - map size of 8 MB. - - Uses LMDB to store sets of change IDs under keys 'review', - 'approved', and 'rejected'. - - The `__fetch_case_attrs_changes__` function is called for - each non-empty set of change IDs to retrieve details from - the `caseattributes_audit` table. - - If no change IDs exist for a category, an empty dictionary - is returned for that category. - - Assumes `inbredset_id` is a valid integer and the LMDB - database is properly formatted. - Raises: json.JSONDecodeError: If any `json_diff_data` in the audit table cannot be deserialized by @@ -223,11 +188,10 @@ def get_changes(cursor, inbredset_id: int, directory: Path) -> dict: cannot be deserialized. """ - directory = f"{directory}/case-attributes/{inbredset_id}" - if not os.path.exists(directory): - os.makedirs(directory) + directory.mkdir(parents=True, exist_ok=True) review_ids, approved_ids, rejected_ids = set(), set(), set() - env = lmdb.open(directory, map_size=8_000_000) # 1 MB + directory.mkdir(parents=True, exist_ok=True) + env = lmdb.open(directory.as_posix(), 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) @@ -313,7 +277,8 @@ def apply_change(cursor, change_type: EditStatus, change_id: int, directory: Pat """ review_ids, approved_ids, rejected_ids = set(), set(), set() - env = lmdb.open(directory, map_size=8_000_000) # 1 MB + directory.mkdir(parents=True, exist_ok=True) + env = lmdb.open(directory.as_posix(), 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) diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py index 446d18d..4e01a3a 100644 --- a/gn3/db/sample_data.py +++ b/gn3/db/sample_data.py @@ -59,7 +59,7 @@ def __extract_actions( return result def get_mrna_sample_data( - conn: Any, probeset_id: int, dataset_name: str, probeset_name: str = None + conn: Any, probeset_id: int, dataset_name: str, probeset_name: str = None # type: ignore ) -> Dict: """Fetch a mRNA Assay (ProbeSet in the DB) trait's sample data and return it as a dict""" with conn.cursor() as cursor: @@ -130,7 +130,7 @@ WHERE ps.Id = %s AND psf.Name= %s""", (probeset_id, dataset_name)) return "\n".join(trait_csv) def get_pheno_sample_data( - conn: Any, trait_name: int, phenotype_id: int, group_id: int = None + conn: Any, trait_name: int, phenotype_id: int, group_id: int = None # type: ignore ) -> Dict: """Fetch a phenotype (Publish in the DB) trait's sample data and return it as a dict""" with conn.cursor() as cursor: |