Derar all, I have recently moved from galaxy-central to galaxy-dist and all seems to work fine except that everytime I start a new session (ie: I go to my galaxy with my browser), I get the error below. I just need to reload the page and all is fine again. I would mention that while the whole 'dist' is original, the ./database/ directory is a mere copy (and updated) of the one I had in galaxy-central. Needless to say that the MySQL engine is never down :) Any help is most than welcome Thanks a million! Here's the error I get. URL: http://galaxy.cbs.dtu.dk/galaxy/ File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 111 in __call__ return self.app( environ, start_response ) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 134 in __call__ trans = self.transaction_factory( environ ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 187 in <lambda> self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 207 in transaction_chooser return GalaxyWebUITransaction( environ, galaxy_app, self, session_cookie ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 870 in __init__ self._ensure_valid_session( session_cookie ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 351 in _ensure_valid_session self.app.model.GalaxySession.table.c.is_valid==True ) ) \ File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py', line 1300 in first ret = list(self[0:1]) File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py', line 1221 in __getitem__ return list(res) File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py', line 1361 in __iter__ return self._execute_and_instances(context) File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.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 '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/session.py', line 755 in execute clause, params or {}) File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 824 in execute return Connection.executors[c](self, object, multiparams, params) File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 874 in _execute_clauseelement return self.__execute_context(context) File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 896 in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 950 in _cursor_execute self._handle_dbapi_exception(e, statement, parameters, cursor, context) File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.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, galaxy_session.disk_usage AS galaxy_session_disk_usage \nFROM galaxy_session \nWHERE galaxy_session.session_key = %s AND galaxy_session.is_valid = %s \n LIMIT 0, 1' ['ac609feb8dfe0f5669378398dde80af3', 1] -- Federico De Masi, PhD, Assistant Professor The Technical University of Denmark - DTU Center for Biological Sequence Analysis - CBS Kemitorvet 208/002 DK-2800 KGS. LYNGBY, DENMARK Telephone: (+45) 45 25 24 21 Fax: (+45) 45 93 15 85 http://rg.cbs.dtu.dk
On Apr 9, 2012, at 3:11 AM, Federico De Masi wrote:
Derar all,
I have recently moved from galaxy-central to galaxy-dist and all seems to work fine except that everytime I start a new session (ie: I go to my galaxy with my browser), I get the error below. I just need to reload the page and all is fine again. I would mention that while the whole 'dist' is original, the ./database/ directory is a mere copy (and updated) of the one I had in galaxy-central. Needless to say that the MySQL engine is never down :)
Any help is most than welcome
Thanks a million!
Here's the error I get.
… 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, galaxy_session.disk_usage AS galaxy_session_disk_usage \nFROM galaxy_session \nWHERE galaxy_session.session_key = %s AND galaxy_session.is_valid = %s \n LIMIT 0, 1' ['ac609feb8dfe0f5669378398dde80af3', 1]
Hi Federico, Try setting the following config option: # If using MySQL and the server logs the error "MySQL server has gone away", # you will want to set this to some positive value (7200 should work). #database_engine_option_pool_recycle = -1 --nate
-- Federico De Masi, PhD, Assistant Professor The Technical University of Denmark - DTU Center for Biological Sequence Analysis - CBS Kemitorvet 208/002 DK-2800 KGS. LYNGBY, DENMARK Telephone: (+45) 45 25 24 21 Fax: (+45) 45 93 15 85 http://rg.cbs.dtu.dk ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (2)
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Federico De Masi -
Nate Coraor