"data_set package utilities" import datetime import os import json import hashlib from typing import List from flask import current_app as app from utility.configuration import get_setting from wqflask.database import parse_db_url, database_connection def geno_mrna_confidentiality(ob): with database_connection() as conn, conn.cursor() as cursor: cursor.execute( "SELECT confidentiality, " f"AuthorisedUsers FROM {ob.type}Freeze WHERE Name = %s", (ob.name,) ) result = cursor.fetchall() if len(result) > 0 and result[0]: return True def query_table_timestamp(dataset_type: str): """function to query the update timestamp of a given dataset_type""" # computation data and actions with database_connection() as conn, conn.cursor() as cursor: fetch_db_name = parse_db_url(get_setting(app, "SQL_URI")) cursor.execute( "SELECT UPDATE_TIME FROM " "information_schema.tables " f"WHERE TABLE_SCHEMA = '{fetch_db_name[3]}' " f"AND TABLE_NAME = '{dataset_type}Data'") date_time_obj = cursor.fetchone()[0] if not date_time_obj: date_time_obj = datetime.datetime.now() return date_time_obj.strftime("%Y-%m-%d %H:%M:%S") def generate_hash_file(dataset_name: str, dataset_type: str, dataset_timestamp: str, samplelist: str): """given the trait_name generate a unique name for this""" string_unicode = f"{dataset_name}{dataset_timestamp}{samplelist}".encode() md5hash = hashlib.md5(string_unicode) return md5hash.hexdigest() def cache_dataset_results(dataset_name: str, dataset_type: str, samplelist: List, query_results: List): """function to cache dataset query results to file input dataset_name and type query_results(already processed in default dict format) """ # data computations actions # store the file path on redis table_timestamp = query_table_timestamp(dataset_type) samplelist_as_str = ",".join(samplelist) file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp, samplelist_as_str) file_path = os.path.join(app.config["TMPDIR"], f"{file_name}.json") with open(file_path, "w") as file_handler: json.dump(query_results, file_handler) def fetch_cached_results(dataset_name: str, dataset_type: str, samplelist: List): """function to fetch the cached results""" table_timestamp = query_table_timestamp(dataset_type) samplelist_as_str = ",".join(samplelist) file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp, samplelist_as_str) file_path = os.path.join(app.config["TMPDIR"], f"{file_name}.json") try: with open(file_path, "r") as file_handler: return json.load(file_handler) except Exception: pass