Re: [Gusdev-gusdev] LoadGoOntology Plugin

[Dave B. <db...@pc...>]

Hey Arnaud,

I think you are correct about the incorrect type of the GO Id.  I'll have
a look and see if I can apply a fix.

Dave

On Tue, 18 Mar 2003, Arnaud Kerhornou wrote:

> Hi
>
> I'm testing the LoadGoOntology plugin to load the GO component ontology.
>
> The CBIL archive, CBIL_v1-2-0.tar.gz, has the following path,
> CBIL/Bio/lib/perl/GeneOntolgyParser where GeneOntologyParser is misspelled.
>
> I renamed the directory to be able to test the plugin but the run stops
> at some point :
>
> -------------------------->
>
> >ga GUS::GOPredict::Plugin::LoadGoOntology --verbose --flat_file=component.ontology --file_path=/nfs/pathsoft/databases/go_cvs/ontology --id_file=2.318
>
> sqlExec:
>     INSERT INTO SRes.GOTerm (  row_user_id, go_id, user_write, group_write, ancestor_go_term_id, row_project_id, name, external_database_release_id, is_obsolete, group_read, minimum_level, row_group_id, go_term_id, other_read, source_id, modification_date, user_read, row_alg_invocation_id, number_of_levels, maximum_level, definition, other_write )
>     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? )
>   bindValues (1, GO:0000325, 1, 1, GO:0005575, 1, vacuole (sensu Magnoliophyta), 228, 0, 1, 6, 1, 1, 1, GO:0000325, 1, 4, 1, 6, vacuole (sensu Magnoliophyta), 0)
> DBD::Oracle::st execute failed: ORA-01722: invalid number (DBD ERROR: OCIStmtExecute) at /nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 139.
>
> <--------------------------
>
> I think it's because of "ancestor_go_term_id" which expects a number and gets "GO:0005575" a GO term instead of the Primary Key for this GO ancestor term.
>
> Can someone have a look at it ?
>
> cheers
> Arnaud
>
>
>
>
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