Hi all

After updating to the last stable galaxy when I'm trying to upgrade the database I'm getting the following message:

/steno-internal/projects/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/url.py:105: SADeprecationWarning: The SQLAlchemy PostgreSQL dialect has been renamed from 'postgres' to 'postgresql'. The new URL format is postgresql[+driver]://<user>:<pass>@<host>/<dbname>

If I change the line in universe_wsgi.ini from

database_connection = postgres://galaxy:password@localhost:5432/galaxydb

to

database_connection = postgresql://galaxy:password@localhost:5432/galaxydb

I get the following when restarting galaxy.

migrate.versioning.repository DEBUG 2013-07-17 15:23:53,462 Config: {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 'version_table': 'migrate_version', 'repository_id': 'Galaxy'}} galaxy.model.migrate.check ERROR 2013-07-17 15:23:53,463 database_connection contains an unknown SQLAlchemy database dialect: postgresql Traceback (most recent call last): File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/app.py", line 52, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 50, in create_or_verify_database engine = create_engine( url, **engine_options ) File "/steno-internal/projects/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/__init__.py", line 338, in create_engine return strategy.create(*args, **kwargs) File "/steno-internal/projects/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/strategies.py", line 64, in create dbapi = dialect_cls.dbapi(**dbapi_args) File "/steno-internal/projects/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/postgresql/psycopg2.py", line 312, in dbapi psycopg = __import__('psycopg2') ImportError: No module named psycopg2 Removing PID file web0.pid

I tried to install psycopg2 with no success but I guess it must have already been there for postgres to work before the renaming.

Is there any (simple) solution to this that I'm missing?

Bests, Nikos

p.s.: sorry for the first incomplete message

2013/7/17 Nikos Sidiropoulos nikos.sidiro@gmail.com

Hi all

After updating to the last stable galaxy when I'm trying to upgrade the database I'm getting the following message:

/steno-internal/projects/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/url.py:105: SADeprecationWarning: The SQLAlchemy PostgreSQL dialect has been renamed from 'postgres' to 'postgresql'. The new URL format is postgresql[+driver]://<user>:<pass>@<host>/<dbname>

If I change the line in universe_wsgi.ini from

database_connection = postgresql://galaxy:password@localhost:5432/galaxydb

to