This occurs both on etch and lenny Linux 64 bit nodes. The python
version is 2.4
I would be helpful for any suggestions. Can move to postgresql, but
rather stay with mysql.
Marina Gourtovaia
URL: http://sf-2-1-02.internal.sanger.ac.uk:9700/
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/exceptions/errormiddleware.py',
line 143 in __call__
app_iter = self.application(environ, start_response)
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/debug/prints.py',
line 97 in __call__
status, headers, body = wsgilib.intercept_output(
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/wsgilib.py',
line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
line 119 in __call__
trans = self.transaction_factory( environ )
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 161 in<lambda>
self.set_transaction_factory( lambda e: self.transaction_chooser(
e, galaxy_app, session_cookie ) )
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 181 in transaction_chooser
return GalaxyWebUITransaction( environ, galaxy_app, self,
session_cookie )
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 791 in __init__
self._ensure_valid_session( session_cookie )
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 318 in _ensure_valid_session
self.app.model.GalaxySession.table.c.is_valid==True ) ) \
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/query.py',
line 1300 in first
ret = list(self[0:1])
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/query.py',
line 1221 in __getitem__
return list(res)
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/query.py',
line 1361 in __iter__
return self._execute_and_instances(context)
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/query.py',
line 1364 in _execute_and_instances
result = self.session.execute(querycontext.statement,
params=self._params, mapper=self._mapper_zero_or_none())
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py',
line 754 in execute
return self.__connection(engine, close_with_result=True).execute(
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py',
line 824 in execute
return Connection.executors[c](self, object, multiparams, params)
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py',
line 874 in _execute_clauseelement
return self.__execute_context(context)
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py',
line 896 in __execute_context
self._cursor_execute(context.cursor, context.statement,
context.parameters[0], context=context)
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py',
line 950 in _cursor_execute
self._handle_dbapi_exception(e, statement, parameters, cursor, context)
File
'/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py',
line 931 in _handle_dbapi_exception
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' ['6683a26145119b72ce04fc6d4c6d7a0f', 1]
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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