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)
  

d.total_size, d.id FROM history_dataset_association hda JOIN history h ON h.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

---

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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-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  <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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