Thanks. Let me know how I can help. On Wed, Jun 17, 2015 at 12:08 PM, Dannon Baker <dannon.ba...@gmail.com> wrote:
> Thanks, I'll take a look. Non-tool-based functional tests should *not* > fail out of the box, and we'll fix them :) > > On Wed, Jun 17, 2015 at 12:04 PM Ryan G <ngsbioinformat...@gmail.com> > wrote: > >> All the functional.test_admin_features >> Most of the functional.test_data_security >> functional.test_history_functions >> >> I'm attaching a PDF printout of the run_functional_tests.html >> >> >> >> On Wed, Jun 17, 2015 at 12:01 PM, Dannon Baker <dannon.ba...@gmail.com> >> wrote: >> >>> Which tests are failing, specifically? Many tests will fail without the >>> underlying tools installed. >>> >>> On Wed, Jun 17, 2015 at 12:01 PM Ryan G <ngsbioinformat...@gmail.com> >>> wrote: >>> >>>> I've migrated my staging instance to use postgres and ran the >>>> functional tests. I see lots failing. I know this is known and perhaps >>>> expected, but it still bothers me. I would expect to see all the tests >>>> pass on a clean instance. If the tests aren't passing, to me, that >>>> indicates a problem somewhere. What's the point in having the tests if >>>> they always fail? >>>> >>>> >>>> >>>> On Tue, Jun 16, 2015 at 1:12 PM, Ryan G <ngsbioinformat...@gmail.com> >>>> wrote: >>>> >>>>> 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. To manage your subscriptions to this >>>>>> > and other Galaxy lists, please use the interface at: >>>>>> > https://lists.galaxyproject.org/ >>>>>> > >>>>>> > To search Galaxy mailing lists use the unified search at: >>>>>> > http://galaxyproject.org/search/mailinglists/ >>>>>> >>>>> >>>>> >>>> ___________________________________________________________ >>>> 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: >>>> https://lists.galaxyproject.org/ >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >>> >>> >>
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