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authorzsloan2021-06-16 19:40:57 +0000
committerzsloan2021-06-16 19:40:57 +0000
commitc553b52e140de1d7e5ed49f07bae2f4a120266f8 (patch)
tree49dbdd7b8b607a882275c8ef8ab9c298d3c0bb1e /tests
parent1c32cb1df09475ef70dbe2d7310ba33026baea22 (diff)
parent9d6af6049fa73c6aae4d224245d319e87bccbd6a (diff)
downloadgenenetwork3-c553b52e140de1d7e5ed49f07bae2f4a120266f8.tar.gz
Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into main
Diffstat (limited to 'tests')
-rw-r--r--tests/performance/__init__.py0
-rw-r--r--tests/performance/perf_query.py109
2 files changed, 109 insertions, 0 deletions
diff --git a/tests/performance/__init__.py b/tests/performance/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/tests/performance/__init__.py
diff --git a/tests/performance/perf_query.py b/tests/performance/perf_query.py
new file mode 100644
index 0000000..12cb944
--- /dev/null
+++ b/tests/performance/perf_query.py
@@ -0,0 +1,109 @@
+"""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_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,
+ fetch_all: bool = True):
+ """function to execute a query"""
+ conn, _ = database_connector()
+
+ 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_hc_m2_dataset():
+ """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))
+
+
+@timer
+def perf_umutaffyexon_dataset():
+ """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))
+
+
+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__':
+ func_list = fetch_cmd_args()
+ for func_obj in func_list:
+ func_obj()