id	summary	reporter	owner	description	type	status	priority	milestone	component	resolution	keywords	cc	parents
5411	Error running alembic migrations: database locked	ayleph		"I've got a test instance using the sqlite backend. I recently updated to current master and tried to run `dbupdate`. I received the error below.

{{{
(mediagoblin-dev) ~/mediagoblin-dev $ bin/gmg dbupdate
/path/to/mediagoblin/mediagoblin/media_types/video/transcoders.py:37: PyGIWarning: GstPbutils was imported without specifying a version first. Use gi.require_version('GstPbutils', '1.0') before import to ensure that the right version gets loaded.
  from gi.repository import GstPbutils
/path/to/mediagoblin/lib/python2.7/site-packages/SQLAlchemy-0.8.7-py2.7-linux-x86_64.egg/sqlalchemy/engine/default.py:459: SAWarning: Unicode type received non-unicode bind param value.
INFO  [alembic.migration] Context impl SQLiteImpl.
INFO  [alembic.migration] Will assume non-transactional DDL.
INFO  [alembic.migration] Running upgrade 101510e3a713 -> 8429e33fdf7, Remove the Graveyard objects from CommentNotification objects
Traceback (most recent call last):
  File ""bin/gmg"", line 9, in <module>
    load_entry_point('mediagoblin', 'console_scripts', 'gmg')()
  File ""/path/to/mediagoblin/mediagoblin/gmg_commands/__init__.py"", line 142, in main_cli
    args.func(args)
  File ""/path/to/mediagoblin/mediagoblin/gmg_commands/dbupdate.py"", line 162, in dbupdate
    run_dbupdate(app_config, global_config)
  File ""/path/to/mediagoblin/mediagoblin/gmg_commands/dbupdate.py"", line 134, in run_dbupdate
    run_alembic_migrations(db, app_config, global_config)
  File ""/path/to/mediagoblin/mediagoblin/gmg_commands/dbupdate.py"", line 116, in run_alembic_migrations
    manager.init_or_migrate()
  File ""/path/to/mediagoblin/mediagoblin/db/migration_tools.py"", line 84, in init_or_migrate
    self.upgrade(version)
  File ""/path/to/mediagoblin/mediagoblin/db/migration_tools.py"", line 60, in upgrade
    return command.upgrade(self.alembic_cfg, version or 'head')
  File ""/path/to/mediagoblin/lib/python2.7/site-packages/alembic-0.6.6-py2.7.egg/alembic/command.py"", line 125, in upgrade
    script.run_env()
  File ""/path/to/mediagoblin/lib/python2.7/site-packages/alembic-0.6.6-py2.7.egg/alembic/script.py"", line 203, in run_env
    util.load_python_file(self.dir, 'env.py')
  File ""/path/to/mediagoblin/lib/python2.7/site-packages/alembic-0.6.6-py2.7.egg/alembic/util.py"", line 215, in load_python_file
    module = load_module_py(module_id, path)
  File ""/path/to/mediagoblin/lib/python2.7/site-packages/alembic-0.6.6-py2.7.egg/alembic/compat.py"", line 58, in load_module_py
    mod = imp.load_source(module_id, path, fp)
  File ""/path/to/mediagoblin/mediagoblin/db/migrations/env.py"", line 62, in <module>
    run_migrations_online()
  File ""/path/to/mediagoblin/mediagoblin/db/migrations/env.py"", line 57, in run_migrations_online
    context.run_migrations()
  File ""<string>"", line 7, in run_migrations
  File ""/path/to/mediagoblin/lib/python2.7/site-packages/alembic-0.6.6-py2.7.egg/alembic/environment.py"", line 689, in run_migrations
    self.get_context().run_migrations(**kw)
  File ""/path/to/mediagoblin/lib/python2.7/site-packages/alembic-0.6.6-py2.7.egg/alembic/migration.py"", line 263, in run_migrations
    change(**kw)
  File ""/path/to/mediagoblin/mediagoblin/db/migrations/versions/8429e33fdf7_remove_the_graveyard_objects_from_.py"", line 45, in upgrade
    notification_table.c.object_id == gmr.id
  File ""build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py"", line 1614, in execute
  File ""build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py"", line 662, in execute
  File ""build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py"", line 761, in _execute_clauseelement
  File ""build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py"", line 908, in _execute_context
  File ""build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py"", line 491, in _commit_impl
  File ""build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py"", line 1024, in _handle_dbapi_exception
  File ""build/bdist.linux-x86_64/egg/sqlalchemy/util/compat.py"", line 196, in raise_from_cause
  File ""build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py"", line 488, in _commit_impl
  File ""build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py"", line 297, in do_commit
sqlalchemy.exc.OperationalError: (OperationalError) database is locked None None
}}}"	defect	closed	major	0.9.0	programming	fixed	sqlalchemy,alembic,migration,database,locked	tsyesika