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From: Isabelle P. <isa...@sb...> - 2008-12-15 18:40:43
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I rejoiced too soon....
There is a problem with the GO plugin, after the GO terms have been
loaded, I am getting:
Transitive closure (length 4000418): added 0 edges
DBD::Pg::st execute failed: ERROR: prepared statement "dbdpg_2" does
not exist
Isabelle
> -----Original Message-----
> From: Isabelle Phan
> Sent: Monday, December 15, 2008 10:29 AM
> To: 'Elisabetta Manduchi'; Jian Lu
> Cc: gus...@li...
> Subject: RE: [GUSDEV] how do I load GO terms
>
> > This command will no longer work with the new updates to the plugin
> > applied 2 days ago and reflected in the plugin John
> Brestelli sent to
> > Isabelle (also available in the gus svn trunk). The new
> > version takes in just one .obo file.
>
> Thanks Elisabetta.
>
> The new plugin works great. There is an minor issue with a
> very long GO synonym that required a change in the
> SRes.GOSynonym table. The problem might be specific for
> Postgres, where the SRes.GOSynonym.TEXT column type is set by
> default to varchar(255).
>
> This needs to be increased to accommodate the GO synonym to
> avoid this error:
>
> DBD::Pg::st execute failed: ERROR: value too long for type
> character varying(255)
>
> ERROR:
>
> SQL ERROR!! involving
>
> INSERT INTO SRes.GOSynonym (
> external_database_release_id, source_id, go_term_id,
> group_write, other_read, group_read, go_synonym_id,
> user_read, row_user_id, modification_date, other_write,
> row_alg_invocation_id, row_project_id, text, row_group_id,
> user_write )
> VALUES ( ?, null, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?,
> ?, ?, ? )
> Values: 170, 3222, 1, 1, 1, 4048, 1, 1, 0, 16, 1,
> UDP-D-xylose:glycoprotein (D-xylose to the 3,6-disubstituted
> mannose of
> N4-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3
)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]->
beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-a
> cetyl-beta-D-glucosaminyl}asparagine)
> 2-beta-D-xylosyltransferase activity, 1, 1 at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbH
andle.pm line 166
>
> Increasing the column size solves this issue, e.g. for Postgres:
>
> alter table GOSynonym alter column text type varchar(1000);
>
> Thanks,
>
> Isabelle
>
> --
> Isabelle Phan, DPhil
> Seattle Biomedical Research Institute
> +1(206)256 7113
>
>
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