On Jan 20, 2012, at 9:04 AM, Holger Klein wrote:
> Dear all,
>
> due to some work on the user management of our servers we had to rename
> the user galaxy runs as. Up to now we used ident as postgres
> authentication method, meaning that here postgres expects unix username
> "galaxy" to have permissions of "galaxy" postgres user.
>
> The entry in universe_wsgi.ini is simply:
> database_connection = postgres:///galaxy?host=/var/run/postgresql
>
> After the renaming, the new user "galaxynew" didn't get access at all at
> first. Now I tried two things:
> - adding a user "galaxynew" to postgres with permissions for database galaxy
> and
> - dumping the contents of database "galaxy" into a file and re-reading
> this into database "galaxynew", which is owned by the user "galaxynew"
> and of course changing the config file line to
> database_connection = postgres:///galaxynew?host=/var/run/postgresql
>
> In both cases I end up with an error during startup of galaxy:
> [...]
> WARNING 2012-01-20 14:46:55,556 Error closing cursor: current
> transaction is aborted, commands ignored until end of transaction block
> [...]
> ProgrammingError: (ProgrammingError) permission denied for relation
> migrate_version
> 'SELECT migrate_version.repository_id, migrate_version.repository_path,
> migrate_version.version \nFROM migrate_version \nWHERE
> migrate_version.repository_id = %(repository_id_1)s' {'repository_id_1':
> 'Galaxy'}
>
> (complete traceback below).
>
> Does anyone have a hint on how I could fix this?
Hi Holger,
I'd use \dp in psql to check the table and sequence permissions. Most likely
the restore set permissions on all the db objects back to the 'galaxy' postgres
role even though the database itself is owned by galaxynew.
--nate
>
> Cheers,
> Holger
>
>
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>
> sqlalchemy.pool.QueuePool.0x...8d10 WARNING 2012-01-20 14:46:55,556
> Error closing cursor: current transaction is aborted, commands ignored
> until end of transaction block
>
> Traceback (most recent call last):
> File
> "/local/data/home/galaxy/galaxy-dist-2011-11-23/lib/galaxy/web/buildapp.py",
> line 82, in app_factory
> app = UniverseApplication( global_conf = global_conf, **kwargs )
> File
> "/local/data/home/galaxy/galaxy-dist-2011-11-23/lib/galaxy/app.py", line
> 39, in __init__
> create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
> ).get( '__file__', None ), self.config.database_engine_options )
> File
> "/local/data/home/galaxy/galaxy-dist-2011-11-23/lib/galaxy/model/migrate/check.py",
> line 99, in create_or_verify_database
> db_schema = schema.ControlledSchema( engine, migrate_repository )
> File
> "/local/data/home/galaxy/galaxy-dist-2011-11-23/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
> line 24, in __init__
> self._load()
> File
> "/local/data/home/galaxy/galaxy-dist-2011-11-23/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
> line 41, in _load
> self.table.c.repository_id == str(self.repository.id)))
> File
> "/local/data/home/galaxy/galaxy-dist-2011-11-23/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 1202, in execute
> return connection.execute(statement, *multiparams, **params)
> File
> "/local/data/home/galaxy/galaxy-dist-2011-11-23/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 824, in execute
> return Connection.executors[c](self, object, multiparams, params)
> File
> "/local/data/home/galaxy/galaxy-dist-2011-11-23/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 874, in _execute_clauseelement
> return self.__execute_context(context)
> File
> "/local/data/home/galaxy/galaxy-dist-2011-11-23/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 896, in __execute_context
> self._cursor_execute(context.cursor, context.statement,
> context.parameters[0], context=context)
> File
> "/local/data/home/galaxy/galaxy-dist-2011-11-23/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 950, in _cursor_execute
> self._handle_dbapi_exception(e, statement, parameters, cursor, context)
> File
> "/local/data/home/galaxy/galaxy-dist-2011-11-23/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 931, in _handle_dbapi_exception
> raise exc.DBAPIError.instance(statement, parameters, e,
> connection_invalidated=is_disconnect)
> ProgrammingError: (ProgrammingError) permission denied for relation
> migrate_version
> 'SELECT migrate_version.repository_id, migrate_version.repository_path,
> migrate_version.version \nFROM migrate_version \nWHERE
> migrate_version.repository_id = %(repository_id_1)s' {'repository_id_1':
> 'Galaxy'}
>
>
>
> --
> Dr. Holger Klein
> Core Facility Bioinformatics
> Institute of Molecular Biology gGmbH (IMB)
> http://www.imb-mainz.de/
> Tel: +49(6131) 39 21511
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