No problem, glad it was helpful. Dannon Baker wrote:
Thanks for the bug fix, (and for the reminder that it was still sitting in the inbox, sorry about that). I've verified the fix as well and pulled it into -central.
-Dannon
On Thu, Jun 6, 2013 at 10:13 AM, Lance Parsons <lparsons@princeton.edu <mailto:lparsons@princeton.edu>> wrote:
Thanks for confirmation Björn.
Pull request was submitted: https://bitbucket.org/galaxy/galaxy-central/pull-request/97/fix-for-postgres...
Trello card also created: https://trello.com/c/Z0EynAV2
Björn Grüning wrote:
Hi Lance,
I can confirm both the regression and the fix. A pull request would be great I think. I can also do it if you want.
Thanks, Björn
The recent updates to set_user_disk_usage.py for Postgres users have an issue with Postgres 8.x. The SQL in the pgcalc method (line 51) leads to the following error:
sqlalchemy.exc.ProgrammingError: (ProgrammingError) column "d.total_size" must appear in the GROUP BY clause or be used in an aggregate function LINE 4: FROM ( SELECT d.total_siz... ^
The problem is that version of Postgres before 9.x were a bit more restrictive in the use of GROUP BY. This can be fixed using DISTINCT ON instead. See this StackOverflow post for more info: http://stackoverflow.com/questions/1769361/postgresql-group-by-different-fro...
I've included a patch below. Let me know if a pull request would be preferred.
--- a/scripts/set_user_disk_usage.py +++ b/scripts/set_user_disk_usage.py @@ -52,7 +52,7 @@ sql = """ UPDATE galaxy_user SET disk_usage = (SELECT COALESCE(SUM(total_size), 0) - FROM ( SELECT d.total_size + FROM ( SELECT DISTINCT ON (d.id <http://d.id>) d.total_size,d.id <http://d.id> FROM history_dataset_association hda JOIN history h ON h.id <http://h.id> = hda.history_id JOIN dataset d ON hda.dataset_id =d.id <http://d.id> @@ -62,7 +62,7 @@ AND d.purged = false ANDd.id <http://d.id> NOT IN (SELECT dataset_id
FROM library_dataset_dataset_association) - GROUP BYd.id <http://d.id>) sizes) + ) sizes) WHERE id = :id RETURNING disk_usage; """ -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University
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-- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University
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-- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University