13 Apr
2010
13 Apr
'10
1:27 a.m.
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 <http://genomics06.bio.tamu.edu:8080/#> |
Text<http://genomics06.bio.tamu.edu:8080/#>
| XML <http://genomics06.bio.tamu.edu:8080/#>
(full)<http://genomics06.bio.tamu.edu:8080/#>
⇝ 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
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>app_iter *=* self*.*application*
(*environ*,* detect_start_response*)*
Module paste.debug.prints:*98* in __call__
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>environ*,* self*.*app*)*
Module paste.wsgilib:*539* in intercept_output
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>app_iter *=* application*(*
environ*,* replacement_start_response*)*
Module paste.recursive:*80* in __call__
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>*return* self*.*application*(*
environ*,* start_response*)*
Module paste.httpexceptions:*632* in __call__
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>*return* self*.*application*(*
environ*,* start_response*)*
Module galaxy.web.framework.base:*99* in __call__
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>trans *=* self*.*
transaction_factory*(* environ *)*
Module galaxy.web.framework:*112* in <lambda>
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>self*.*set_transaction_factory*(
* *lambda* e*:* UniverseWebTransaction*(* e*,* galaxy_app*,* self*,*
session_cookie *)* *)*
Module galaxy.web.framework:*152* in __init__
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>self*.*__ensure_valid_session*(*
session_cookie *)*
Module galaxy.web.framework:*281* in __ensure_valid_session
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>self*.*app*.*model*.*
GalaxySession*.*table*.*c*.*is_valid*==*True *)* *)*
Module sqlalchemy.orm.query:*1300* in first
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>ret *=* list*(*self*[**0**:**1**
]**)*
Module sqlalchemy.orm.query:*1221* in __getitem__
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>*return* list*(*res*)*
Module sqlalchemy.orm.query:*1361* in __iter__
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>*return* self*.*
_execute_and_instances*(*context*)*
Module sqlalchemy.orm.query:*1364* in _execute_and_instances
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>result *=* self*.*session*.*
execute*(*querycontext*.*statement*,* params*=*self*.*_params*,* mapper*=*
self*.*_mapper_zero_or_none*(**)**)*
Module sqlalchemy.orm.session:*755* in execute
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>clause*,* params *or* *{**}**)*
Module sqlalchemy.engine.base:*824* in execute
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>*return* Connection*.*executors*
[*c*]**(*self*,* object*,* multiparams*,* params*)*
Module sqlalchemy.engine.base:*874* in _execute_clauseelement
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>*return* self*.*
__execute_context*(*context*)*
Module sqlalchemy.engine.base:*896* in __execute_context
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>self*.*_cursor_execute*(*context
*.*cursor*,* context*.*statement*,* context*.*parameters*[**0**]**,* context
*=*context*)*
Module sqlalchemy.engine.base:*950* in _cursor_execute
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>self*.*_handle_dbapi_exception*(
*e*,* statement*,* parameters*,* cursor*,* context*)*
Module sqlalchemy.engine.base:*931* in _handle_dbapi_exception
<http://genomics06.bio.tamu.edu:8080/#>
view <http://genomics06.bio.tamu.edu:8080/#>
>> <http://genomics06.bio.tamu.edu:8080/#>*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
13 Apr
13 Apr
3:08 p.m.
Roy;
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: [...]
*OperationalError: (OperationalError) (2006, 'MySQL server has gone away')
MySQL will close database connections after 8 hours, which results in this error. You want to look in your universe_wsgi.ini file for these lines and uncomment database_engine_option_pool_recycle: # If using MySQL, see: # http://rapd.wordpress.com/2008/03/02/sqlalchemy-sqlerror-operationalerror-20... # To handle this issue, try the following setting: #database_engine_option_pool_recycle = 7200 Brad
14 Apr
14 Apr
5:44 a.m.
Brad, Thanks, that took care if it. Rgds, Roy W. On Apr 13, 2010, at 8:08 AM, Brad Chapman <chapmanb@50mail.com> wrote:
Roy;
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: [...]
*OperationalError: (OperationalError) (2006, 'MySQL server has gone away')
MySQL will close database connections after 8 hours, which results in this error. You want to look in your universe_wsgi.ini file for these lines and uncomment database_engine_option_pool_recycle:
# If using MySQL, see: # http://rapd.wordpress.com/2008/03/02/sqlalchemy-sqlerror-operationalerror-20... # To handle this issue, try the following setting: #database_engine_option_pool_recycle = 7200
Brad
5699
Age (days ago)
5701
Last active (days ago)
2 comments
2 participants
participants (2)
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Brad Chapman -
Roy Weckiewicz