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 <lpars...@princeton.edu>wrote: > Thanks for confirmation Björn. > > Pull request was submitted: > https://bitbucket.org/galaxy/galaxy-central/pull-request/97/fix-for-postgres-versions-9/diff > > 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-from-mysql > > 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) > d.total_size, d.id > FROM > history_dataset_association hda > JOIN history h ONh.id = > hda.history_id > JOIN dataset d ON > hda.dataset_id = d.id > @@ -62,7 +62,7 @@ > AND d.purged = false > AND d.id NOT IN > (SELECT dataset_id > > FROM library_dataset_dataset_association) > - GROUP BY 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 > > > ___________________________________________________________ > 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/ > > > > -- > Lance Parsons - Scientific Programmer > 134 Carl C. Icahn Laboratory > Lewis-Sigler Institute for Integrative Genomics > Princeton University > > > ___________________________________________________________ > 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/ >
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