I've managed to resolve this issue. I'm not sure how I ended up with this issue, but in case anyone else get's hit by it, here's what I've learned: -At version 0.6, SQLAlchemy changed the format for connecting to postgresql: [postgresql] The "postgres" dialect is now named "postgresql" -I somehow managed to get multiple eggs pointing to different versions of SQLAlchemy: [galaxy@login002 galaxy-dist]$ ls eggs/SQLAlchemy-0. SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/ SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/ SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg -During my early stages of rolling out Galaxy, I managed to use the 0.7.9 version of SQLAlchemy which forced me to change my database_connection syntax: [galaxy@login002 galaxy-dist]$ ./run.sh --daemon -this updates some of the "eggs" -it doesn't start; check the logs: [galaxy@login002 galaxy-dist]$ tail paster.log ... ile__', None ), self.config.database_engine_options, app=self ) File "/home/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 107, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest, config_arg ) ) Exception: Your database has version '114' but this code expects version '115'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'. Removing PID file paster.pid [galaxy@login002 galaxy-dist]$ sh manage_db.sh upgrade /home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.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> -at that point I changed my database_connection from: database_connection = postgres:// to: database_connection = postgresql:// and everything appeared to be happy. Everything that is except for the cleanup script. -I've now changed everything to: database_connection = postgres:// and everything appears to be happy. I really don't understand how this came out. I was using postgresql:// for quite a while without issues, so it would seem that I could *not* have been using 0.5.6 of SQLAlchemy unless this was modified by the Galaxy community. Cheers, Malcolm On Thursday 26 September 2013 17:16:16 Jennifer Jackson wrote:
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On 9/26/13 7:29 AM, Malcolm Tobias wrote:
All,
My understanding is that the cleanup_datasets.py under scripts/cleanup_datasets should be compatible with 'older' versions of postgresql. I'm running 8.1 under CentOS 5. When I attempt to run the scripts, it fails to clean any data sets. From the logs, I'm noticing messages like:
database_connection contains an unknown SQLAlchemy database dialect: postgresql
In my universe_wsgi.ini I've defined the database_connection as:
database_connection = postgresql://galaxy:********@localhost:5432/galaxydb
and am confident it's working as Galaxy works fine, other than this problem with deleting older datasets.
The pgcleanup.py script isn't an option, as it requires postgresql >=9.1. I noticed yet another version of cleanup_datasets.py under cron which looks like it might be compatible with postgres, but am leary of trying it as I'm not sure what it means by "1: database directory to clean". I'm not sure what directory to point this to, nor am I confident that just deleting data from the directory is the safest thing.
Any suggestions on how to proceed?
Thanks!
Malcolm
--
Malcolm Tobias
314.362.1594
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-- Jennifer Hillman-Jackson http://galaxyproject.org
-- Malcolm Tobias 314.362.1594