Hi,
Every morning when I come back to my lab and login to Galaxy I get the error below. I think it's the 'MySQL server has gone away' part that is the real cruel-pitand simply clicking refresh is enough to 'fix' the problem... This is not specifically a Galaxy problem. It's probably the result of caching connections and I have seen this before when I was using Perl modules to access MySQL databases. I guess this can be solved by fiddling with sqlalchemy settings maybe even in a Galaxy config file, but I'm a Python noob. If anyone has seen this before and knows how to properly fix it, please let me know.
Cheers,
Pi
URL: http://tadpole/galaxy/ File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/WebError-0.8a-py2.4.egg/weberror/evalexception/ middleware.py', line 364 in respond File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/Paste-1.5.1-py2.4.egg/paste/debug/prints.py', line 97 in __call__ File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/Paste-1.5.1-py2.4.egg/paste/wsgilib.py', line 539 in intercept_output File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/Beaker-0.5-py2.4.egg/beaker/session.py', line 103 in __call__ File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/Paste-1.5.1-py2.4.egg/paste/recursive.py', line 80 in __call__ File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/lib/galaxy/web/ framework/middleware/remoteuser.py', line 102 in __call__ return self.app( environ, start_response ) File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/Paste-1.5.1-py2.4.egg/paste/httpexceptions.py', line 632 in __call__ File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/lib/galaxy/web/ framework/base.py', line 100 in __call__ trans = self.transaction_factory( environ ) File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/lib/galaxy/web/ framework/__init__.py', line 109 in <lambda> self.set_transaction_factory( lambda e: UniverseWebTransaction( e, galaxy_app, self, session_cookie ) ) File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/lib/galaxy/web/ framework/__init__.py', line 149 in __init__ self.__ensure_valid_session( session_cookie ) File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/lib/galaxy/web/ framework/__init__.py', line 277 in __ensure_valid_session user_for_new_session = self.__get_or_create_remote_user( remote_user_email ) File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/lib/galaxy/web/ framework/__init__.py', line 361 in __get_or_create_remote_user user = self .app .model .User .filter( self.app.model.User.table.c.email==remote_user_email ).first() File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/orm/query.py', line 909 in first File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/orm/query.py', line 938 in __iter__ File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/orm/query.py', line 941 in _execute_and_instances File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/orm/session.py', line 628 in execute File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/engine/base.py', line 844 in execute File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/engine/base.py', line 895 in execute_clauseelement File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/engine/base.py', line 907 in _execute_compiled File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/engine/base.py', line 916 in __execute_raw File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/engine/base.py', line 960 in _cursor_execute File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/engine/base.py', line 942 in _handle_dbapi_exception OperationalError: (OperationalError) (2006, 'MySQL server has gone away') u'SELECT galaxy_user.id AS galaxy_user_id, galaxy_user.create_time AS galaxy_user_create_time, galaxy_user.update_time AS galaxy_user_update_time, galaxy_user.email AS galaxy_user_email, galaxy_user.password AS galaxy_user_password, galaxy_user.external AS galaxy_user_external, galaxy_user.deleted AS galaxy_user_deleted, galaxy_user.purged AS galaxy_user_purged \nFROM galaxy_user \nWHERE galaxy_user.email = %s ORDER BY galaxy_user.id \n LIMIT 0, 1' ['P.B.T.Neerincx@uu.nl']
------------------------------------------------------------- Biomolecular Mass Spectrometry and Proteomics Utrecht University
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Mail address: P.O. box 80.082 3508 TB Utrecht The Netherlands
phone: +31 (0)6-143 66 783 email: pieter.neerincx@gmail.com skype: pieter.online ------------------------------------------------------------