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/# | Texthttp://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.*