Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into main

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()