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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