Unable to create DB (gearbox setup-db) from scratch (default branch)

[Long Vu]

Hi,

Running code from this PR
https://bitbucket.org/conservancy/kallithea/pull-requests/314

To reproduce:
docker run --name reprobug -d -p 8085:5000 tlvu/kallithea-evolve:2017-04-11
docker logs reprobug

Then clean up:
docker stop reprobug
docker rm -v reprobug

I might have the wrong way of invoking gearbox setup-db.  Please let
me know what's the correct way.


root at a53ac866b92e:/kallithea/config# /bin/bash -x /kallithea/run.sh
+ KALLITHEA_ADMIN_USER=admin
+ KALLITHEA_ADMIN_PASS=secret
+ KALLITHEA_ADMIN_MAIL=admin at example.com
+ cd /kallithea/config
+ '[' '!' -e kallithea.ini ']'
+ echo 'Creating configuration file...'
Creating configuration file...
+ gearbox make-config kallithea.ini
Wrote new config file in /kallithea/config/kallithea.ini
+ '[' -n '' ']'
+ echo 'Creating database...'
Creating database...
+ gearbox setup-db -c kallithea.ini --user=admin --password=secret
--email=admin at example.com --repos=/kallithea/repos --force-yes
2017-04-12 17:01:27.872 INFO  [kallithea.model.base] initializing db
for sqlite:////kallithea/config/kallithea.db?timeout=60
2017-04-12 17:01:27.875 INFO  [kallithea.lib.auth] getting information
about all available permissions
2017-04-12 17:01:27.986 ERROR [gearbox] (sqlite3.OperationalError) no
such table: permissions [SQL: u'SELECT permissions.permission_id AS
permissions_permission_id, permissions.permission_name AS
permissions_per
mission_name \nFROM permissions']
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/gearbox/main.py", line
167, in _run_subcommand
    return cmd.run(parsed_args)
  File "/kallithea/kallithea/kallithea/lib/paster_commands/common.py",
line 65, in run
    self._bootstrap_config(args.config_file)
  File "/kallithea/kallithea/kallithea/lib/paster_commands/common.py",
line 90, in _bootstrap_config
    make_app(conf.global_conf, **conf.local_conf)
  File "/kallithea/kallithea/kallithea/config/middleware.py", line 46,
in make_app
    app = make_base_app(global_conf, full_stack=full_stack, **app_conf)
  File "/usr/local/lib/python2.7/dist-packages/tg/configuration/app_config.py",
line 1240, in make_base_app
    tg.hooks.notify('configure_new_app', args=(app,))
  File "/usr/local/lib/python2.7/dist-packages/tg/configuration/hooks.py",
line 109, in notify
    self._call_handler(hook_name, trap_exceptions, func, args, kwargs)
  File "/usr/local/lib/python2.7/dist-packages/tg/configuration/hooks.py",
line 33, in _call_handler
    return func(*args, **kwargs)
  File "/kallithea/kallithea/kallithea/config/app_cfg.py", line 142,
in setup_configuration
    set_available_permissions(config)
  File "/kallithea/kallithea/kallithea/lib/auth.py", line 728, in
set_available_permissions
    all_perms = sa.query(Permission).all()
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/query.py",
line 2613, in all
    return list(self)
  File "/kallithea/kallithea/kallithea/lib/caching_query.py", line 81,
in __iter__
    return Query.__iter__(self)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/query.py",
line 2761, in __iter__
    return self._execute_and_instances(context)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/query.py",
line 2776, in _execute_and_instances
    result = conn.execute(querycontext.statement, self._params)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py",
line 914, in execute
    return meth(self, multiparams, params)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/sql/elements.py",
line 323, in _execute_on_connection
    return connection._execute_clauseelement(self, multiparams, params)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py",
line 1010, in _execute_clauseelement
    compiled_sql, distilled_params
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py",
line 1146, in _execute_context
    context)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py",
line 1341, in _handle_dbapi_exception
    exc_info
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/util/compat.py",
line 203, in raise_from_cause
    reraise(type(exception), exception, tb=exc_tb, cause=cause)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py",
line 1139, in _execute_context
    context)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/default.py",
line 450, in do_execute
    cursor.execute(statement, parameters)
OperationalError: (sqlite3.OperationalError) no such table:
permissions [SQL: u'SELECT permissions.permission_id AS
permissions_permission_id, permissions.permission_name AS
permissions_permission_name \nFROM pe
rmissions']


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