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?
Cheers,
Holger
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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