fix integration test connection mock

Author: nmdefries

integrations/acquisition/rvdss/test_scenarios.py

@@ -2,7 +2,6 @@
 # standard library
 import unittest
 from unittest.mock import MagicMock, patch
-import mock
 from copy import copy
 
 # first party
@@ -11,12 +10,10 @@
 import delphi.operations.secrets as secrets
 from delphi_utils import get_structured_logger
 
-
 # third party
 import mysql.connector
 import pandas as pd
 from pathlib import Path
-import pdb
 
 # py3tester coverage target (equivalent to `import *`)
 # __test_target__ = 'delphi.epidata.acquisition.covid_hosp.facility.update'
@@ -25,7 +22,7 @@
 
 class AcquisitionTests(unittest.TestCase):
   logger = get_structured_logger()
-  
+
   def setUp(self):
     """Perform per-test setup."""
 
@@ -54,76 +51,51 @@ def setUp(self):
     epidata_cnx.commit()
     epidata_cur.close()
     #epidata_cnx.close()
-    
+
     # make connection and cursor available to test cases
     self.cnx = epidata_cnx
-    #self.cur = epidata_cnx.cursor()
-    
+    self.cur = epidata_cnx.cursor()
+
   def tearDown(self):
     """Perform per-test teardown."""
-    #self.cur.close()
+    self.cur.close()
     self.cnx.close()
 
-  @mock.patch("mysql.connector.connect")
-  def test_rvdss_repiratory_detections(self,mock_sql):
+  @patch("mysql.connector.connect")
+  def test_rvdss_repiratory_detections(self, mock_sql):
+    connection_mock = MagicMock()
+
     TEST_DIR = Path(__file__).parent.parent.parent.parent
-    detection_data = pd.read_csv(str(TEST_DIR) + "/testdata/acquisition/rvdss/RVD_CurrentWeekTable_Formatted.csv")    
+    detection_data = pd.read_csv(str(TEST_DIR) + "/testdata/acquisition/rvdss/RVD_CurrentWeekTable_Formatted.csv")
     detection_data['time_type'] = "week"
-    detection_subset = detection_data[(detection_data['geo_value'].isin(['nl', 'nb'])) & (detection_data['time_value'].isin([202408-31, 20240907])) ]
+    detection_subset = detection_data[(detection_data['geo_value'].isin(['nl', 'nb'])) & (detection_data['time_value'].isin([20240831, 20240907])) ]
 
-    connection_mock = MagicMock()
     # make sure the data does not yet exist
     with self.subTest(name='no data yet'):
       response = Epidata.rvdss(geo_type='province',
                                time_values= [202435, 202436],
                                geo_value = ['nl','nb'])
       self.assertEqual(response['result'], -2, response)
 
-
     # acquire sample data into local database
-    with self.subTest(name='first acquisition'):        
-        #mock_sql.cursor.return_value = self.cnx.cursor()
+    with self.subTest(name='first acquisition'):
+        # When the MagicMock connection's `cursor()` method is called, return
+        # a real cursor made from the current open connection `cnx`.
         connection_mock.cursor.return_value = self.cnx.cursor()
+        # Commit via the current open connection `cnx`, from which the cursor
+        # is derived
+        connection_mock.commit = self.cnx.commit
         mock_sql.return_value = connection_mock
-        
-        rvdss_cols_subset = [col for col in detection_subset.columns if col in rvdss_cols]
-        pdb.set_trace()
-        update(detection_subset,self.logger)
-        
-        response = Epidata.rvdss(geo_type='province',
-                                 time_values= [202435, 202436],
-                                 geo_value = ['nl','nb'])
-        
-        self.assertEqual(response['result'], 1)
-        
-    with self.subTest(name='first acquisition2'):       
-        #mock_sql.cursor.return_value = self.cnx.cursor()
-        connection_mock.cursor.return_value = self.cnx.cursor()
-        mock_sql.return_value = connection_mock
-        
-        rvdss_cols_subset = [col for col in detection_subset.columns if col in rvdss_cols]
-        update(detection_subset,self.logger)
-        
-        response = Epidata.rvdss(geo_type='province',
-                                 time_values= [202435, 202436],
-                                 geo_value = ['nl','nb'])
-        
-        self.assertEqual(response['result'], 1)
-        
-    with self.subTest(name='first acquisition3'):
-        #mock_sql.cursor.return_value = self.cnx.cursor()
-        connection_mock.cursor.return_value = self.cnx.cursor()
-        mock_sql.return_value = connection_mock
-        
-        rvdss_cols_subset = [col for col in detection_subset.columns if col in rvdss_cols]
-        update(detection_subset,self.logger)
-        
+
+        update(detection_subset, self.logger)
+
         response = Epidata.rvdss(geo_type='province',
                                  time_values= [202435, 202436],
                                  geo_value = ['nl','nb'])
-        
+
         self.assertEqual(response['result'], 1)
 
+
     # # make sure the data now exists
     # with self.subTest(name='initial data checks'):
     #   expected_spotchecks = {
@@ -164,5 +136,3 @@ def test_rvdss_repiratory_detections(self,mock_sql):
     #       '450822', Epidata.range(20200101, 20210101))
     #   self.assertEqual(response['result'], 1)
     #   self.assertEqual(len(response['epidata']), 2)
-    pass
-

src/acquisition/rvdss/database.py

@@ -76,36 +76,36 @@ def get_num_rows(cursor):
         pass
     return num
 
-def update(data,logger):
+def update(data, logger):
     # connect to the database
     u, p = secrets.db.epi
     cnx = mysql.connector.connect(user=u, password=p, database="epidata")
     cur = cnx.cursor()
 
     rvdss_cols_subset = [col for col in data.columns if col in rvdss_cols]
     data = data.to_dict(orient = "records")
-    
+
     field_names = ", ".join(f"`{name}`" for name in rvdss_cols_subset)
     field_values = ", ".join(f"%({name})s" for name in rvdss_cols_subset)
-        
+
     #check rvdss for new and/or revised data
     sql = f"""
     INSERT INTO rvdss ({field_names})
     VALUES ({field_values})
     """
-        
+
     # keep track of how many rows were added
     rows_before = get_num_rows(cur)
     total_rows = 0
-        
-    #insert data 
+
+    #insert data
     cur.executemany(sql, data)
-    cnx.commit()
-        
+
     # keep track of how many rows were added
     rows_after = get_num_rows(cur)
     logger.info(f"Inserted {int(rows_after - rows_before)}/{int(total_rows)} row(s) into table rvdss")
-    
+
     # cleanup
+    cnx.commit()
     cur.close()
     cnx.close()