Hello,

I have a galaxy installation on OSX with a MySQL backend and galaxy running as a daemon. After extended periods of non-use, I get the following error when trying to access my galaxy installation via the web browser:

Error Traceback:

View as:   Interactive  |  Text  |  XML (full)
⇝ OperationalError: (OperationalError) (2006, 'MySQL server has gone away') u'SELECT galaxy_session.id AS galaxy_session_id, galaxy_session.create_time AS galaxy_session_create_time, galaxy_session.update_time AS galaxy_session_update_time, galaxy_session.user_id AS galaxy_session_user_id, galaxy_session.remote_host AS galaxy_session_remote_host, galaxy_session.remote_addr AS galaxy_session_remote_addr, galaxy_session.referer AS galaxy_session_referer, galaxy_session.current_history_id AS galaxy_session_current_history_id, galaxy_session.session_key AS galaxy_session_session_key, galaxy_session.is_valid AS galaxy_session_is_valid, galaxy_session.prev_session_id AS galaxy_session_prev_session_id \nFROM galaxy_session \nWHERE galaxy_session.session_key = %s AND galaxy_session.is_valid = %s \n LIMIT 0, 1' ['8f166da7c3aa375a667392ff4c5fb20b', 1]
URL: http://genomics06.bio.tamu.edu:8080/
Module weberror.evalexception.middleware:364 in respond          view
>>  app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__          view
>>  environ, self.app)
Module paste.wsgilib:539 in intercept_output          view
>>  app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__          view
>>  return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__          view
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:99 in __call__          view
>>  trans = self.transaction_factory( environ )
Module galaxy.web.framework:112 in <lambda>          view
>>  self.set_transaction_factory( lambda e: UniverseWebTransaction( e, galaxy_app, self, session_cookie ) )
Module galaxy.web.framework:152 in __init__          view
>>  self.__ensure_valid_session( session_cookie )
Module galaxy.web.framework:281 in __ensure_valid_session          view
>>  self.app.model.GalaxySession.table.c.is_valid==True ) )
Module sqlalchemy.orm.query:1300 in first          view
>>  ret = list(self[0:1])
Module sqlalchemy.orm.query:1221 in __getitem__          view
>>  return list(res)
Module sqlalchemy.orm.query:1361 in __iter__          view
>>  return self._execute_and_instances(context)
Module sqlalchemy.orm.query:1364 in _execute_and_instances          view
>>  result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none())
Module sqlalchemy.orm.session:755 in execute          view
>>  clause, params or {})
Module sqlalchemy.engine.base:824 in execute          view
>>  return Connection.executors[c](self, object, multiparams, params)
Module sqlalchemy.engine.base:874 in _execute_clauseelement          view
>>  return self.__execute_context(context)
Module sqlalchemy.engine.base:896 in __execute_context          view
>>  self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context)
Module sqlalchemy.engine.base:950 in _cursor_execute          view
>>  self._handle_dbapi_exception(e, statement, parameters, cursor, context)
Module sqlalchemy.engine.base:931 in _handle_dbapi_exception          view
>>  raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect)
OperationalError: (OperationalError) (2006, 'MySQL server has gone away') u'SELECT galaxy_session.id AS galaxy_session_id, galaxy_session.create_time AS galaxy_session_create_time, galaxy_session.update_time AS galaxy_session_update_time, galaxy_session.user_id AS galaxy_session_user_id, galaxy_session.remote_host AS galaxy_session_remote_host, galaxy_session.remote_addr AS galaxy_session_remote_addr, galaxy_session.referer AS galaxy_session_referer, galaxy_session.current_history_id AS galaxy_session_current_history_id, galaxy_session.session_key AS galaxy_session_session_key, galaxy_session.is_valid AS galaxy_session_is_valid, galaxy_session.prev_session_id AS galaxy_session_prev_session_id \nFROM galaxy_session \nWHERE galaxy_session.session_key = %s AND galaxy_session.is_valid = %s \n LIMIT 0, 1' ['8f166da7c3aa375a667392ff4c5fb20b', 1]

The error only appears once, though, and galaxy works fine if I attempt to access it again.


Any ideas as to why it is doing this?



Rgds,


Roy W.

--
Roy Weckiewicz
Texas A&M University