Lost connection to MySQL server during query with Sanic and Asyncmy (MySQL) - asynchronous

Question

I'm facing an issue I'm having a hard time to identify.
I made a Database context system to wrap requests inside with that creates a connection to Mysql. Here's the full code :
custom/database/database.py
# -*- coding:utf-8 -*-
from sqlalchemy import exc, event
from sqlalchemy.ext.asyncio import create_async_engine, AsyncSession as SQLAlchemyAsyncSession
from sqlalchemy.orm import sessionmaker, Session
from sqlalchemy.pool import Pool, QueuePool # NullPool
from sqlalchemy.exc import OperationalError
from contextvars import ContextVar
from sanic import Sanic
class EngineNotInitialisedError(Exception):
pass
class DBSessionContext:
def __init__(self, read_session: Session, write_session: Session, commit_on_exit: bool = True) -> None:
self.read_session = read_session
self.write_session = write_session
self.commit_on_exit = commit_on_exit
self.token = None
self._read = None
self._write = None
def _disable_flush(self, *args, **kwargs):
raise NotImplementedError('Unable to flush a read-only session.')
async def close(self, exc_type=None, exc_value=None, traceback=None):
if self._write:
if exc_value and getattr(exc_value, 'status_code', 500) > 300:
await self._write.rollback()
else:
await self._write.commit()
try:
await self._write.close()
except OperationalError as e:
if e.orig.args[0] != 2013: # Lost connection to MySQL server during query
raise e
if self._read:
try:
await self._read.close()
except OperationalError as e:
if e.orig.args[0] != 2013: # Lost connection to MySQL server during query
raise e
def set_token(self, token):
self.token = token
#property
def read(self) -> Session:
if not self._read:
self._read = self.read_session()
self._read.flush = self._disable_flush
return self._read
#property
def write(self) -> Session:
if not self._write:
self._write = self.write_session()
return self._write
class AsyncSession(SQLAlchemyAsyncSession):
async def execute(self, statement, **parameters):
return await super().execute(statement, parameters)
async def first(self, statement, **parameters):
executed = await self.execute(statement, **parameters)
return executed.first()
async def all(self, statement, **parameters):
executed = await self.execute(statement, **parameters)
return executed.all()
class DBSession:
def __init__(self):
self.app = None
self.read_engine = None
self.read_session = None
self.write_engine = None
self.write_session = None
self._session = None
self.context = ContextVar("context", default=None)
self.commit_on_exit = True
def init_app(self, app: Sanic) -> None:
self.app = app
self.commit_on_exit = self.app.config.get('DATABASE_COMMIT_ON_EXIT', cast=bool, default=True)
engine_args = {
'echo': self.app.config.get('DATABASE_ECHO', cast=bool, default=False),
'echo_pool': self.app.config.get('DATABASE_ECHO_POOL', cast=bool, default=False),
'poolclass': QueuePool, # will be used to create a connection pool instance using the connection parameters given in the URL
# if pool_class is not NullPool:
# if True will enable the connection pool “pre-ping” feature that tests connections for liveness upon each checkout
'pool_pre_ping': self.app.config.get('DATABASE_POOL_PRE_PING', cast=bool, default=True),
# the number of connections to allow in connection pool “overflow”
'max_overflow': self.app.config.get('DATABASE_MAX_OVERFLOW', cast=int, default=10),
# the number of connections to keep open inside the connection pool
'pool_size': self.app.config.get('DATABASE_POOL_SIZE', cast=int, default=100),
# this setting causes the pool to recycle connections after the given number of seconds has passed
'pool_recycle': self.app.config.get('DATABASE_POOL_RECYCLE', cast=int, default=3600),
# number of seconds to wait before giving up on getting a connection from the pool
'pool_timeout': self.app.config.get('DATABASE_POOL_TIMEOUT', cast=int, default=5),
}
self.read_engine = create_async_engine(
self.app.config.get('DATABASE_READ_URL'),
connect_args={
'connect_timeout': self.app.config.get('DATABASE_CONNECT_TIMEOUT', cast=int, default=3)
},
**engine_args
)
# #see https://writeonly.wordpress.com/2009/07/16/simple-read-only-sqlalchemy-sessions/
self.read_session = sessionmaker(
bind=self.read_engine,
expire_on_commit=False,
class_=AsyncSession,
autoflush=False,
autocommit=False
)
self.write_engine = create_async_engine(
self.app.config.get('DATABASE_WRITE_URL'),
connect_args={
'connect_timeout': self.app.config.get('DATABASE_CONNECT_TIMEOUT', cast=int, default=3)
},
**engine_args
)
self.write_session = sessionmaker(
bind=self.write_engine,
expire_on_commit=False,
class_=AsyncSession,
autoflush=True
)
async def __aenter__(self):
session_ctx = DBSessionContext(self.read_session, self.write_session, self.commit_on_exit)
session_ctx.set_token(self.context.set(session_ctx))
return session_ctx
async def __aexit__(self, exc_type, exc_value, traceback):
session_ctx = self.context.get()
await session_ctx.close(exc_type, exc_value, traceback)
self.context.reset(session_ctx.token)
#property
def read(self) -> Session:
return self.context.get().read
#property
def write(self) -> Session:
return self.context.get().write
#event.listens_for(Pool, "checkout")
def check_connection(dbapi_con, con_record, con_proxy):
'''Listener for Pool checkout events that pings every connection before using.
Implements pessimistic disconnect handling strategy. See also:
http://docs.sqlalchemy.org/en/rel_0_8/core/pooling.html#disconnect-handling-pessimistic'''
cursor = dbapi_con.cursor()
try:
cursor.execute("SELECT 1")
except exc.OperationalError as ex:
if ex.args[0] in (2006, # MySQL server has gone away
2013, # Lost connection to MySQL server during query
2055): # Lost connection to MySQL server at '%s', system error: %d
raise exc.DisconnectionError() # caught by pool, which will retry with a new connection
else:
raise
cursor.close()
db = DBSession()
Using it is quite simple, I do the following. In the router, I made a wrapper that calls the handler with the db initiated:
custom/route.py
class Route:
async def __call__(self, request: Request, **kwargs):
async with db:
response = await self.handler(*args)
# process the response, such as chaning a str to a text response, etc
return response
Unfortunately, I noticed that I have a lot of
(2013, 'Lost connection to MySQL server during query')
And I don't know how or why this happens. This happens to relatively small queries (that contains "LIMIT 1" with indexed columns that should be fast)
Here's the full stack trace:
[2022-05-19 09:35:25 +0000] [92185] [ERROR] Exception occurred while handling uri: 'https://api.pdfshift.io/redacted'
Traceback (most recent call last):
File "asyncmy/connection.pyx", line 610, in asyncmy.connection.Connection._read_bytes
data = await self._reader.readexactly(num_bytes)
File "/usr/lib/python3.9/asyncio/streams.py", line 721, in readexactly
raise exceptions.IncompleteReadError(incomplete, n)
asyncio.exceptions.IncompleteReadError: 0 bytes read on a total of 4 expected bytes
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1802, in _execute_context
self.dialect.do_execute(
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/engine/default.py", line 732, in do_execute
cursor.execute(statement, parameters)
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/dialects/mysql/asyncmy.py", line 92, in execute
return self.await_(self._execute_async(operation, parameters))
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/util/_concurrency_py3k.py", line 76, in await_only
return current.driver.switch(awaitable)
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/util/_concurrency_py3k.py", line 129, in greenlet_spawn
value = await result
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/dialects/mysql/asyncmy.py", line 104, in _execute_async
result = await self._cursor.execute(operation, parameters)
File "asyncmy/cursors.pyx", line 180, in execute
result = await self._query(query)
File "asyncmy/cursors.pyx", line 365, in _query
await conn.query(q)
File "asyncmy/connection.pyx", line 455, in query
await self._read_query_result(unbuffered=unbuffered)
File "asyncmy/connection.pyx", line 636, in _read_query_result
await result.read()
File "asyncmy/connection.pyx", line 1023, in read
first_packet = await self.connection.read_packet()
File "asyncmy/connection.pyx", line 578, in read_packet
packet_header = await self._read_bytes(4)
File "asyncmy/connection.pyx", line 618, in _read_bytes
raise errors.OperationalError(CR_SERVER_LOST, msg) from e
asyncmy.errors.OperationalError: (2013, 'Lost connection to MySQL server during query')
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "handle_request", line 83, in handle_request
)
File "/var/www/project/www/custom/route.py", line 162, in __call__
response = await response
File "/var/www/project/www/apps/webhooks/views.py", line 104, in stripe
await account.reset_usage()
File "/var/www/project/www/apps/accounts/models.py", line 133, in reset_usage
while await db.read.first(query, uuid=self.uuid):
File "/var/www/project/www/custom/database/database.py", line 73, in first
executed = await self.execute(statement, **parameters)
File "/var/www/project/www/custom/database/database.py", line 70, in execute
return await super().execute(statement, parameters)
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/ext/asyncio/session.py", line 211, in execute
return await greenlet_spawn(
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/util/_concurrency_py3k.py", line 134, in greenlet_spawn
result = context.throw(*sys.exc_info())
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/orm/session.py", line 1692, in execute
result = conn._execute_20(statement, params or {}, execution_options)
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1614, in _execute_20
return meth(self, args_10style, kwargs_10style, execution_options)
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/sql/elements.py", line 325, in _execute_on_connection
return connection._execute_clauseelement(
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1481, in _execute_clauseelement
ret = self._execute_context(
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1845, in _execute_context
self._handle_dbapi_exception(
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 2026, in _handle_dbapi_exception
util.raise_(
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
raise exception
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1802, in _execute_context
self.dialect.do_execute(
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/engine/default.py", line 732, in do_execute
cursor.execute(statement, parameters)
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/dialects/mysql/asyncmy.py", line 92, in execute
return self.await_(self._execute_async(operation, parameters))
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/util/_concurrency_py3k.py", line 76, in await_only
return current.driver.switch(awaitable)
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/util/_concurrency_py3k.py", line 129, in greenlet_spawn
value = await result
File "/var/www/project/env/lib/python3.9/site-packages/sqlalchemy/dialects/mysql/asyncmy.py", line 104, in _execute_async
result = await self._cursor.execute(operation, parameters)
File "asyncmy/cursors.pyx", line 180, in execute
result = await self._query(query)
File "asyncmy/cursors.pyx", line 365, in _query
await conn.query(q)
File "asyncmy/connection.pyx", line 455, in query
await self._read_query_result(unbuffered=unbuffered)
File "asyncmy/connection.pyx", line 636, in _read_query_result
await result.read()
File "asyncmy/connection.pyx", line 1023, in read
first_packet = await self.connection.read_packet()
File "asyncmy/connection.pyx", line 578, in read_packet
packet_header = await self._read_bytes(4)
File "asyncmy/connection.pyx", line 618, in _read_bytes
raise errors.OperationalError(CR_SERVER_LOST, msg) from e
sqlalchemy.exc.OperationalError: (asyncmy.errors.OperationalError) (2013, 'Lost connection to MySQL server during query')
[SQL: SELECT id FROM conversions WHERE [redacted] LIMIT 1]
[parameters: ('redacted',)]
(Background on this error at: https://sqlalche.me/e/14/e3q8)
When connecting to the database, here's the parameter I provide:
DATABASE_POOL_PRE_PING = True
DATABASE_MAX_OVERFLOW = 10
DATABASE_POOL_SIZE = 100
DATABASE_POOL_RECYCLE = 3600
DATABASE_POOL_TIMEOUT = 5
DATABASE_CONNECT_TIMEOUT = 3
(If you need details from the MySQL server side, let me know which command to run and I'll add the output here).
My assumption is that somehow, the connection is not properly closed when exiting the async with db part, so when another requests comes in, the same connection is used, but ultimately, MySQL kills it, causing the above error Lost connection to MySQL server during query
Further details :
The error is the same, but the queries changes, showing that the error is not from a specific part of the code, but related to the connection
I was able to catch this issue when sending a webhook event from Stripe. The error returned by Stripe is "Expired". Which seems to indicate that before being stopped, the connection hangs (probably waiting on the SQL query to finish)
This doesn't happen everytime : I was able to run some webhooks successfully, and other not, for the same event (Stripe), so again, it doesn't seems to be an error with the code related to handling the request (but maybe on how the DB is managed)
Thank you for your help !