[Gusdev-gusdev] LoadGoOntology Plugin

[Arnaud K. <ax...@sa...>]

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 :

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>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.

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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