I am using postgres in production but want to validate my staging instance before pushing it into production. I do this with the functional tests. I guess I'll have to set up a postgres database for the staging instance as well.
On Mon, Jun 15, 2015 at 10:32 AM, John Chilton <jmchil...@gmail.com> wrote: > Not exactly - I feel like sqlite should be able to do the kinds of > things Galaxy does without this occurring - it should just be > inefficient. We are probably doing something across multiple threads > that we should not be - presumably related to job handling. After a > recent sqlalchemy upgrade - there is now a new error message in the > logs that should help track down the problem: > > sqlalchemy.pool.NullPool ERROR 2015-06-15 09:53:47,547 Exception > during reset or similar > Traceback (most recent call last): > File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 571, in > _finalize_fairy > fairy._reset(pool) > File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 705, in > _reset > pool._dialect.do_rollback(self) > File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", > line 412, in do_rollback > dbapi_connection.rollback() > ProgrammingError: SQLite objects created in a thread can only be used > in that same thread.The object was created in thread id > 140442561648384 and this is thread id 140442989479680 > > At any rate - we recommend using postgres in production for a reason - > these sqlite errors are pretty common. > > -John > > > On Fri, Jun 12, 2015 at 11:15 AM, Ryan G <ngsbioinformat...@gmail.com> > wrote: > > Is there a known cause for this? > > > > On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo <nsora...@tiscali.it> > > wrote: > >> > >> Hi Ryan, > >> there is no know fix for this, apart from moving to PostgreSQL. > >> > >> Cheers, > >> Nicola > >> > >> Il 12.06.2015 16:43 Ryan G ha scritto: > >> > >> Hi all - I'm running functional tests on a set of tools using > >> 'run_tests.sh -sid ...'. A few of the tests fail. When I go back and > run > >> the tool tests individually, they succeed. So I looked into why they > fail > >> when running them in batch, and it turns out to be a database lock. I'm > >> using the default sqllite database that run_tests.sh creates. Does this > >> need to be tuned somehow? > >> > >> > >> galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched > >> Error - : (OperationalError) database is locked u'SELECT api_keys.id AS > >> api_keys_id, api_keys.create_time AS api_keys_create_time, > api_keys.user_id > >> AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys > \nWHERE > >> api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) > >> URL: > >> > http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746714beb6212bc8 > >> File > >> > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py', > >> line 149 in __call__ > >> app_iter = self.application(environ, sr_checker) > >> File > >> > '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', > >> line 84 in __call__ > >> return self.application(environ, start_response) > >> File > >> > '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', > >> line 633 in __call__ > >> return self.application(environ, start_response) > >> File > >> > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', > >> line 132 in __call__ > >> return self.handle_request( environ, start_response ) > >> File > >> > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', > >> line 159 in handle_request > >> trans = self.transaction_factory( environ ) > >> File > >> > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', > >> line 71 in > >> self.set_transaction_factory( lambda e: self.transaction_chooser( e, > >> galaxy_app, session_cookie ) ) > >> File > >> > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', > >> line 102 in transaction_chooser > >> return GalaxyWebTransaction( environ, galaxy_app, self, > session_cookie ) > >> File > >> > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', > >> line 194 in __init__ > >> self.error_message = self._authenticate_api( session_cookie ) > >> File > >> > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', > >> line 283 in _authenticate_api > >> provided_key = self.sa_session.query( self.app.model.APIKeys ).filter( > >> self.app.model.APIKeys.table.c.key == api_key ).one() > >> File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2184 > in > >> one > >> File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2227 > in > >> __iter__ > >> File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2242 > in > >> _execute_and_instances > >> File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1449 > >> in execute > >> File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1584 > >> in _execute_clauseelement > >> File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1698 > >> in _execute_context > >> File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1691 > >> in _execute_context > >> File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py', line > 331 > >> in do_execute > >> OperationalError: (OperationalError) database is locked u'SELECT > >> api_keys.id AS api_keys_id, api_keys.create_time AS > api_keys_create_time, > >> api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key > \nFROM > >> api_keys \nWHERE api_keys."key" = ?' > (u'e4fe9bf787edb9ef746714beb6212bc8',) > >> > >> > >> > >> > >> > >> Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, > >> le video chiamate e persino le chiamate di gruppo. > >> E chiami gratis anche i numeri fissi e mobili nel mondo! > >> Scarica subito l’app Vai su https://www.indoona.com/ > >> > > > > > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. 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