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 [1] 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
[2]
> 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 [3] 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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