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testing for existence of galaxy db fails for restrictive postgres setups #7941

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bernt-matthias opened this issue May 13, 2019 · 0 comments

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@bernt-matthias
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sqlalchemy-util tries to connect to a db called 'postgres' for testing the existence of the galaxy data base (it also does for creation and dropping the galaxy db). If there is no connect privilege for this DB we get:

Queue Worker on sqlalchemy+postgresql://********:********@postgres.intranet.ufz.de/galaxy-dev
Traceback (most recent call last):
  File "lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory
    app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs)
  File "lib/galaxy/app.py", line 89, in __init__
    self._configure_models(check_migrate_databases=self.config.check_migrate_databases, check_migrate_tools=check_migrate_tools, config_file=config_file)
  File "lib/galaxy/config.py", line 1165, in _configure_models
    create_or_verify_database(db_url, config_file, self.config.database_engine_options, app=self)
  File "lib/galaxy/model/migrate/check.py", line 33, in create_or_verify_database
    new_database = not database_exists(url)
  File "/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/site-packages/sqlalchemy_utils/functions/database.py", line 481, in database_exists
    return bool(get_scalar_result(engine, text))
....
  File "/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/site-packages/psycopg2/__init__.py", line 130, in connect
    conn = _connect(dsn, connection_factory=connection_factory, **kwasync)
OperationalError: (psycopg2.OperationalError) FATAL:  permission denied for database "postgres"
DETAIL:  User does not have CONNECT privilege.

For usegalaxy-eu the solution is this: usegalaxy-eu@59305ef

Maybe the following PR for sqlalchemy-utils brings a better solution kvesteri/sqlalchemy-utils#372

bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue May 24, 2019
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue May 24, 2019
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue May 24, 2019
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jun 18, 2019
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jun 18, 2019
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jun 18, 2019
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jul 29, 2019
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Aug 13, 2019
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Aug 13, 2019
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Sep 9, 2019
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Oct 9, 2019
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Nov 4, 2019
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Nov 6, 2019
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Nov 13, 2019
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Nov 14, 2019
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Nov 17, 2019
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jan 9, 2020
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jan 21, 2020
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jan 21, 2020
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jan 27, 2020
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jan 31, 2020
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Feb 1, 2020
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Feb 26, 2020
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue May 11, 2020
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jun 15, 2020
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jul 1, 2020
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jul 8, 2020
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Nov 30, 2020
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Dec 11, 2020
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Dec 23, 2020
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jan 21, 2021
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Mar 5, 2021
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Mar 5, 2021
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Mar 19, 2021
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Apr 9, 2021
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Apr 10, 2021
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Apr 23, 2021
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jun 28, 2021
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jul 6, 2021
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Feb 8, 2022
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Feb 19, 2022
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Mar 7, 2022
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jul 5, 2022
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jul 18, 2022
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Aug 9, 2022
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Aug 19, 2022
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Aug 30, 2022
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Aug 30, 2022
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Aug 30, 2022
- due to a bug in sqlalchemy: galaxyproject#7941
- similar to the patch used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Aug 30, 2022
- due to a bug in sqlalchemy: galaxyproject#7941
- similar to the patch used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Aug 30, 2022
- due to a bug in sqlalchemy: galaxyproject#7941
- similar to the patch used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Nov 10, 2022
- due to a bug in sqlalchemy: galaxyproject#7941
- similar to the patch used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Dec 7, 2022
- due to a bug in sqlalchemy: galaxyproject#7941
- same as used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Dec 9, 2022
- due to a bug in sqlalchemy: galaxyproject#7941
- similar to the patch used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jan 13, 2023
- due to a bug in sqlalchemy: galaxyproject#7941
- similar to the patch used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Feb 7, 2023
- due to a bug in sqlalchemy: galaxyproject#7941
- similar to the patch used on usegalaxy.eu: usegalaxy-eu@59305ef
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Mar 31, 2023
- due to a bug in sqlalchemy: galaxyproject#7941
- similar to the patch used on usegalaxy.eu: usegalaxy-eu@59305ef
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