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"""module contains performance tests for queries"""
import time
import sys
from inspect import getmembers
from inspect import isfunction
from functools import wraps
from gn3.db_utils import database_connection
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,
sql_uri: str,
fetch_all: bool = True):
"""function to execute a query"""
with database_connection(sql_uri) as conn:
with conn.cursor() as 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 = f"""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 = '{dataset_name}'
and ProbeSet.Id = ProbeSetXRef.ProbeSetId)"""
return query
@timer
def perf_hc_m2_dataset(sql_uri: str):
"""test the default dataset HC_M2_0606_P"""
dataset_name = "HC_M2_0606_P"
print(f"Performance test for {dataset_name}")
query_executor(fetch_probeset_query(dataset_name=dataset_name), sql_uri)
@timer
def perf_umutaffyexon_dataset(sql_uri):
"""largest dataset in gn"""
dataset_name = "UMUTAffyExon_0209_RMA"
print(f"Performance test for {dataset_name}")
query_executor(fetch_probeset_query(dataset_name=dataset_name), sql_uri)
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"""
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__':
# Figure out how to pass the database uri here... Maybe use click.
func_list = fetch_cmd_args()
for func_obj in func_list:
func_obj()
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