Re: [GUSDEV] how do I load GO terms

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

Hi Isabelle - This plugin requires that a few rows already exist in in the 
Sres.ExternalDatabase and SRes.ExternalDatabaseRelease tables.
  -> These are used to track your dataset

Run these 2 plugins first.
ga GUS::Supported::Plugin::InsertExternalDatabase --name 'GO ontology' 
--commit
ga ga GUS::Supported::Plugin::InsertExternalDatabaseRls --databaseName 'GO 
ontology' --databaseVersion '4.513' --commit

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
>>>>
>>>
>>
>