I have a Flask server deployment which are access by only a few users in an infrequent manner, and I frequently bump into "MySQL server has gone away” when no one used it for a few days.
Initially I though it was a uwsgi problem (applying --lazy and --lazy-apps param to uwsgi), but sadly it didn't work.
Then I suspect it could be a SQLAlchemy problem or Flask-SQLAlchemy problem, which leads me to this article.
Flask-SQLAlchemy seems to use scoped session, so that is covered.
I found someone reported the same problem, where the patch seems to be applied on the package I downloaded (0.16).
Sadly, the patch is not applied to the version I had downloaded (the setup.py version number is not updated to 0.8); and the driver I happend to use is "mysql+mysqldb".
or I could set the settings manually through the Flask variable SQLALCHEMY_POOL_RECYCLE
I have not confirmed this solution works yet, have to observer for a few days ;)
Update 2012-02-26: Error "Can't reconnect until invalid transaction is rolled back" popup once in a while ("MySQL server has gone away" is observed as well), where refreshing the page doesn't make the problem go away (need restart).
Based on this, besides SQLALCHEMY_POOL_RECYCLE, the next culprit seems to be session is closed/remove before end of request (this is tricky).