"""module contains performance tests for queries""" import time import sys from inspect import getmembers from inspect import isfunction from typing import Optional from functools import wraps from gn3.db_utils import database_connector def timer(func): """time function""" @wraps(func) def wrapper_time(*args, **kwargs): """time wrapper""" start_time = time.perf_counter() results = func(*args, **kwargs) end_time = time.perf_counter() run_time = end_time - start_time print(f"the time taken is {run_time:.3f} seconds") return results return wrapper_time def query_executor(query: str, dataset_name: Optional[str] = "dataset_name", fetch_all: bool = True): """function to execute a query""" conn, _ = database_connector() print(f"Performance test for {dataset_name}") with conn: cursor = conn.cursor() cursor.execute(query) if fetch_all: return cursor.fetchall() return cursor.fetchone() def fetch_probeset_query(dataset_name: str): """contains queries for datasets""" query = """SELECT * from ProbeSetData where StrainID in (4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 35, 36, 37, 39, 98, 99, 100, 103, 487, 105, 106, 110, 115,116, 117, 118, 119, 120, 919, 147, 121, 40, 41, 124, 125, 128, 135, 129, 130, 131, 132, 134, 138, 139, 140, 141, 142, 144, 145, 148, 149, 920, 922, 2, 3, 1, 1100) and id in (SELECT ProbeSetXRef.DataId FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze) WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and ProbeSetFreeze.Name = '{}' and ProbeSet.Id = ProbeSetXRef.ProbeSetId)""".format(dataset_name) return query @timer def perf_simple_query(): """initial simple query test""" query = """select * from ProbeSetData limit 1""" _results = query_executor(query) return {} @timer def perf_hc_m2_dataset(): """test the default dataset HC_M2_0606_P""" query = fetch_probeset_query("HC_M2_0606_P") _results = query_executor(query, "HC_M2_0606_P") return {} @timer def perf_umutaffyexon_dataset(): """largest dataset in gn""" query = fetch_probeset_query("UMUTAffyExon_0209_RMA") _results = query_executor(query, "UMUTAffyExon_0209_RMA") return {} def fetch_perf_functions(): """function to filter all functions strwith perf_""" name_func_dict = {name: func_obj for name, func_obj in getmembers(sys.modules[__name__], isfunction)if isfunction( func_obj) and func_obj.__module__ == __name__ and name.startswith('perf_')} return name_func_dict def fetch_cmd_args(): """function to fetch cmd args\ for example python file.py perf_hc_m2_dataset\ output [perf_hc_m2_dataset obj]""" cmd_args = sys.argv[1:] name_func_dict = fetch_perf_functions() if len(cmd_args) > 0: callables = [func_call for name, func_call in name_func_dict.items() if name in cmd_args] return callables return list(name_func_dict.values()) if __name__ == '__main__': func_list = fetch_cmd_args() for func_obj in func_list: func_obj()