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
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