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.ba...@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.ku...@wur.nl<mailto: > eric.ku...@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 > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > > -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.ku...@wur.nl Web: http://www.cvi.wur.nl
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/