Re: [GUSDEV] how do I load GO terms

[John E. B. <jbr...@pc...>]

Argh... It must be the end of the week.  Sorry, I didn't see the bottom of 
your message.  (You already tried to insert into sres.externaldatabase)

constraint "pk_externaldatabase" is a primary key constraint.  We use 
sequences to select a unique number for the primary key of each table.
  -> The sequence for "Sres.ExternalDatabase" is "sres.externaldatabase_sq"

It seems there is a conflict between existing rows in 
Sres.ExternalDatabase and the values the plugin is trying to insert.
(Less likely but possible, your max allowed value from this sequence has exceeded the 
size of your primary key column).

Please run these 2 commands in sql:
select  sres.externaldatabase_sq.nextval from dual;
desc sres.externaldatabase;

1.Check that none of your existing rows in sres.externaldatabase have an 
"external_database_id" matching the sequence value.
2.Check the sequence value against the size of the "external_database_id" 
field in Sres.ExternalDatabase.

thanks
john

On Fri, 12 Dec 2008, Isabelle Phan wrote:

> Hello John
>
> Thanks for the new plugin. I unfortunately can't make it to work:
>
> $> ga GUS::Supported::Plugin::InsertGeneOntology
> --oboFile=gene_ontology.obo --extDbRlsName="GO ontology"
> --extDbRlsVer="4.513" --commit
> Couldn't find an external database release id for db 'GO ontology'
> version '4.513'.  Use the plugins InsertExternalDatabase and
> InsertExternalDatabaseRls to insert this information into the database
> at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/Plugin.pm
> line 818, <OBO> line 14.
>
>
> $> ga GUS::Supported::Plugin::InsertExternalDatabase --name 'GO
> ontology'  --commit
> DBD::Pg::st execute failed: ERROR:  duplicate key violates unique
> constraint "pk_externaldatabase"
>
> I don't understand: When I look into the table, I don't see that row:
>
> gus=> select * from externaldatabase where name like '%GO%';
> external_database_id |     name     |     modification_date      |
> user_read | user_write | group_read | group_write | other_read |
> other_write | row_user_id | row_group_id | row_project_id |
> row_alg_invocation_id
> ----------------------+--------------+----------------------------+-----
> ------+------------+------------+-------------+------------+------------
> -+-------------+--------------+----------------+-----------------------
>                 3002 | GO Component | 2008-12-10 16:57:17.446902 |
> 1 |          1 |          1 |           1 |          1 |           0 |
> 1 |            1 |              1 |                    10
>                 3005 | GOC          | 2008-12-10 16:57:17.446902 |
> 1 |          1 |          1 |           1 |          1 |           0 |
> 1 |            1 |              1 |                    10
>                 3024 | GOA          | 2008-12-10 16:57:17.446902 |
> 1 |          1 |          1 |           1 |          1 |           0 |
> 1 |            1 |              1 |                    10
>                 3001 | GO Function  | 2008-12-10 16:57:17.446902 |
> 1 |          1 |          1 |           1 |          1 |           0 |
> 1 |            1 |              1 |                    10
>                 3003 | GO Process   | 2008-12-10 16:57:17.446902 |
> 1 |          1 |          1 |           1 |          1 |           0 |
> 1 |            1 |              1 |                    10
> (5 rows)
>
> --
> Isabelle Phan, DPhil
> Seattle Biomedical Research Institute
> +1(206)256 7113
>
>
>> -----Original Message-----
>> From: John E. Brestelli [mailto:jbr...@pc...]
>> Sent: Thursday, December 11, 2008 3:11 PM
>> To: Isabelle Phan
>> Subject: RE: [GUSDEV] how do I load GO terms
>>
>> The files that plugin consumes have changed to the point it has
>> become outdated.
>>
>> I just replaced that plugin in the svn repository with one
>> which uses a
>> different input file
>> (http://www.geneontology.org/ontology/gene_ontology.obo)
>>
>> I've attached the new plugin.  Please replace the
>> InsertGeneOntology.pm in
>> your $PROJECT_HOME and rebuild.  (I think you could also
>> checkout the svn
>> to stay current)
>>
>> I need to be leaving now but can help more tomorrow if this
>> still isn't
>> working.
>>
>> john
>>
>>
>> On Thu, 11 Dec 2008, Isabelle Phan wrote:
>>
>>> 3.5
>>>
>>> Thanks
>>>
>>> Isabelle
>>>
>>>> -----Original Message-----
>>>> From: John E. Brestelli [mailto:jbr...@pc...]
>>>> Sent: Thursday, December 11, 2008 2:40 PM
>>>> To: Isabelle Phan
>>>> Subject: Re: [GUSDEV] how do I load GO terms
>>>>
>>>> Hi Isabelle - Which Version of GUS are you using?
>>>>
>>>> john
>>>>
>>>
>>
>