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 <ngsbioinformatics@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 <ngsbioinformatics@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 <jmchilton@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
Is there a known cause for this?
On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo <nsoranzo@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
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=e4fe9bf787edb9ef746...
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',
On Fri, Jun 12, 2015 at 11:15 AM, Ryan G <ngsbioinformatics@gmail.com> wrote: this 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',)
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