Merge pull request #111 from openvar/develop_v3

Added check for connection within cursor decorator

VariantValidator/modules/utils.py

@@ -5,6 +5,7 @@
 import logging
 import re
 import copy
+import mysql.connector
 
 logger = logging.getLogger(__name__)
 
@@ -15,6 +16,12 @@ def handleCursor(func):
     """
     @functools.wraps(func)
     def wrapper(self, *args, **kwargs):
+        try:
+            self.conn.ping(reconnect=True, attempts=3, delay=5)
+        except mysql.connector.Error:
+            logger.warning("MySQL connection lost. Reconnecting.")
+            self.init_db()
+
         self.cursor = self.conn.cursor(buffered=True)
         out = func(self, *args, **kwargs)
         if self.cursor:

VariantValidator/modules/vvDBInit.py

@@ -8,13 +8,13 @@ class Mixin:
     """
     def __init__(self, db_config):
         self.conn = None
+        self.pool = None
         # self.cursor will be none UNLESS you're wrapping a function in @handleCursor, which automatically opens and
         # closes connections for you.
         self.cursor = None
         self.dbConfig = db_config
 
-        self.pool = mysql.connector.pooling.MySQLConnectionPool(pool_size=10, connect_timeout=1209600, **self.dbConfig)
-        self.conn = self.pool.get_connection()
+        self.init_db()
 
     def __del__(self):
         if self.conn.is_connected():
@@ -26,6 +26,10 @@ def __del__(self):
         if self.pool:
             self.pool = None
 
+    def init_db(self):
+        self.pool = mysql.connector.pooling.MySQLConnectionPool(pool_size=10, connect_timeout=1209600, **self.dbConfig)
+        self.conn = self.pool.get_connection()
+
 # <LICENSE>
 # Copyright (C) 2019 VariantValidator Contributors
 #