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:
> Posting to galaxy-...@bx.psu.edu<mailto:galaxy-...@bx.psu.edu> to give the
> question better exposure to the development community.
> Please remove the galaxy-u...@bx.psu.edu<mailto:galaxy-u...@bx.psu.edu>
> mailing list from all replies - we want to avoid double posts.
>
>
> For discussion of
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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
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