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',)

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