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
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>>>>> >   http://galaxyproject.org/search/mailinglists/
>>>>>
>>>>
>>>>
>>> ___________________________________________________________
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>>
>>
>
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