Merge pull request #1211 from cmu-delphi/EPID-65-fluview-fluview-clinical-data-stale

Added host to database connection

Author: dmytrotsko

src/acquisition/fluview/fluview_notify.py

@@ -46,7 +46,7 @@
 
     # connect
     u, p = secrets.db.epi
-    cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+    cnx = mysql.connector.connect(user=u, password=p, database="epidata", host=secrets.db.host)
     cur = cnx.cursor()
 
     # get the last known issue from the automation table `variables`

src/acquisition/fluview/fluview_update.py

@@ -311,7 +311,7 @@ def update_from_file_clinical(issue, date, filename, test_mode=False):
 
     # database connection
     u, p = secrets.db.epi
-    cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+    cnx = mysql.connector.connect(user=u, password=p, database="epidata", host=secrets.db.host)
     rows1 = get_rows(cnx, CL_TABLE)
     print(f"rows before: {int(rows1)}")
     insert = cnx.cursor()
@@ -364,7 +364,7 @@ def update_from_file_clinical(issue, date, filename, test_mode=False):
         rows2 = rows1
     else:
         cnx.commit()
-        rows2 = get_rows(cnx)
+        rows2 = get_rows(cnx, CL_TABLE)
     print(f"rows after: {int(rows2)} (added {int(rows2 - rows1)})")
     cnx.close()
 
@@ -376,7 +376,7 @@ def update_from_file_public(issue, date, filename, test_mode=False):
 
     # database connection
     u, p = secrets.db.epi
-    cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+    cnx = mysql.connector.connect(user=u, password=p, database="epidata", host=secrets.db.host)
     rows1 = get_rows(cnx, PHL_TABLE)
     print(f"rows before: {int(rows1)}")
     insert = cnx.cursor()
@@ -433,7 +433,7 @@ def update_from_file_public(issue, date, filename, test_mode=False):
         rows2 = rows1
     else:
         cnx.commit()
-        rows2 = get_rows(cnx)
+        rows2 = get_rows(cnx, PHL_TABLE)
     print(f"rows after: {int(rows2)} (added {int(rows2 - rows1)})")
     cnx.close()
 
@@ -445,7 +445,7 @@ def update_from_file(issue, date, filename, test_mode=False):
 
     # database connection
     u, p = secrets.db.epi
-    cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+    cnx = mysql.connector.connect(user=u, password=p, database="epidata", host=secrets.db.host)
     rows1 = get_rows(cnx)
     print(f"rows before: {int(rows1)}")
     insert = cnx.cursor()

src/acquisition/fluview/impute_missing_values.py

@@ -135,7 +135,7 @@ class Sql:
     def connect(self):
         """Connect to the database."""
         u, p = secrets.db.epi
-        self.cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+        self.cnx = mysql.connector.connect(user=u, password=p, database="epidata", host=secrets.db.host)
         self.cur = self.cnx.cursor()
 
     def close(self, commit):