Hi Dannon, I am also using postgres 9.1.9 (from Ubuntu precise repository)

$/usr/lib/postgresql/9.1/bin/postgres --version -> postgres (PostgreSQL) 9.1.9 hg summary -> parent: 10411:c42567f43aa7 tip

./scripts/cleanup_datasets/pgcleanup.py -d -o1 -s 'delete_datasets'

__load_config INFO 2013-09-26 10:02:10,368 Reading config from /opt/galaxy_testing/universe_wsgi.ini __connect_db INFO 2013-09-26 10:02:10,371 Connecting to database with URL: #############@#### Traceback (most recent call last): File "./scripts/cleanup_datasets/pgcleanup.py", line 774, in <module> cleanup = Cleanup() File "./scripts/cleanup_datasets/pgcleanup.py", line 55, in __init__ self.__connect_db() File "./scripts/cleanup_datasets/pgcleanup.py", line 115, in __connect_db self.conn = psycopg2.connect(**args) TypeError: 'username' is an invalid keyword argument for this function

and if I add *args['user'] = args['username']

**del args['username']* @ line 112 in pgcleanup.py

the script seems to work. ./scripts/cleanup_datasets/pgcleanup.py -d -o1 -s 'delete_datasets'

delete_datasets INFO 2013-09-26 10:04:10,430 Marking deleted all Datasets whose associations are all marked as deleted/purged that are older than the specified number of days. _create_event DEBUG 2013-09-26 10:04:10,457 SQL is: INSERT INTO cleanup_event (create_time, message) VALUES (NOW(), 'delete_datasets') RETURNING id;

_create_event INFO 2013-09-26 10:04:10,457 Executing SQL _create_event INFO 2013-09-26 10:04:10,458 Database status: INSERT 0 1 _update DEBUG 2013-09-26 10:04:10,458 SQL is: WITH deleted_dataset_ids AS ( UPDATE dataset SET deleted = true, update_time = NOW() WHERE NOT deleted AND NOT EXISTS (SELECT true FROM library_dataset_dataset_association WHERE (NOT deleted OR update_time

...

= (NOW() - interval '1 days')) AND dataset.id = dataset_id) AND NOT EXISTS (SELECT true FROM history_dataset_association WHERE (NOT purged OR update_time = (NOW() - interval '1 days')) AND dataset.id = dataset_id) RETURNING id), dataset_events AS (INSERT INTO cleanup_event_dataset_association (create_time, cleanup_event_id, dataset_id) SELECT NOW(), 2, id FROM deleted_dataset_ids) SELECT id FROM deleted_dataset_ids ORDER BY id;

_update INFO 2013-09-26 10:04:10,458 Executing SQL _update INFO 2013-09-26 10:04:10,461 Database status: SELECT 0 _flush INFO 2013-09-26 10:04:10,475 All changes committed _open_logfile DEBUG 2013-09-26 10:04:10,475 Opening log file: /opt/galaxy_testing/scripts/cleanup_datasets/delete_datasets.log _close_logfile DEBUG 2013-09-26 10:04:10,476 Closing log file: /opt/galaxy_testing/scripts/cleanup_datasets/delete_datasets.log _run INFO 2013-09-26 10:04:10,476 Finished delete_datasets

On 25 September 2013 17:45, Dannon Baker <dannon.baker@gmail.com> wrote:

Eric,

What version of posgresql are you using? The script has a comment that indicates you need 9.1+ (and I'm using 9.1.9), and it works out of the box for me.

-Dannon

On Fri, Sep 20, 2013 at 7:35 AM, Eric Kuyt <eric.kuijt@wur.nl<mailto: eric.kuijt@wur.nl>> wrote: Hi All,

I'm trying to do some cleanup in my test environment (galaxy-dist)

and pgcleanup.py ends with

Traceback (most recent call last): File "./scripts/cleanup_datasets/pgcleanup.py", line 773, in <module> cleanup = Cleanup() File "./scripts/cleanup_datasets/pgcleanup.py", line 55, in __init__ self.__connect_db() File "./scripts/cleanup_datasets/pgcleanup.py", line 114, in __connect_db self.conn = psycopg2.connect(**args) TypeError: 'username' is an invalid keyword argument for this function

Unless I add

args['user'] = args['username'] del args['username']

Is this a bug or a config error?

Eric

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