Question: 'Mysql Server Has Gone Away'
0
Pieter Neerincx • 360 wrote:
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
Visiting address:
H.R. Kruyt building room O607
Padualaan 8
3584 CH Utrecht
The Netherlands
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
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modified 9.3 years ago
by
James Casbon • 370
•
written
9.3 years ago by
Pieter Neerincx • 360
