Re: Apollo on Chado

[Scott Cain]

Hi Barry,

Sorry for the confusion--most people don't use Apollo with those
triggers any more and instead use the adapter that comes with Apollo
that doesn't need database triggers.  It's the one that is used with
the Apollo tutorial on the gmod website:

  http://gmod.org/wiki/Apollo_Tutorial

I've updated the README in the Chado distribution so that doesn't
happen to anyone else, though I'll still distribute the triggers with
Chado (though not have them installed by default) in case anybody
still wants to use them.

Scott


On Tue, Sep 20, 2011 at 12:10 AM, Barry Moore <[hidden email]> wrote:

> Hey Scott,
> Sorry, this should go to the list - I'll sign up, but just wanted to get
> this sorted out for now
>
> Modifying a Chado instance to run Apollo against.  Using the README.Apollo
> in Chado 1.11.  I think this is a question for you.
> I modified chado-1.11/modules/sequence/apollo-bridge/apollo.inserts and
> commented out the first couple sections on Rice specific analysis types and
> DBxrefs
> Any comments on the following two errors:
> postgres@lettuce:~$ psql lettuce <
> /usr/local/chado-1.11/modules/sequence/apollo-bridge/apollo.inserts
> INSERT 0 1
> CREATE SEQUENCE
> INSERT 0 1
> INSERT 0 1
> INSERT 0 1
> ERROR:  null value in column "cv_id" violates not-null constraint
> NOTICE:  CREATE TABLE will create implicit sequence
> "feature_namegenerator_feature_namegenerator_id_seq" for serial column
> "feature_namegenerator.feature_namegenerator_id"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "feature_namegenerator_pkey" for table "feature_namegenerator"
> CREATE TABLE
> INSERT 0 0
> INSERT 0 0
> ERROR:  aggregates not allowed in WHERE clause
> LINE 2: ...rator_id from feature_namegenerator where count = max(count)...
>                                                              ^
> NOTICE:  ALTER TABLE / ADD UNIQUE will create implicit index
> "feature_namegenerator_c1" for table "feature_namegenerator"
> ALTER TABLE
>
> B
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> [phone]
>
>
>
>

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research