[Gusdev-gusdev] GBParser error

[Jeetendra S. <so...@vb...>]

I am trying to upload a genbank flat file, and I am getting the error
listed below.
    When I looked at the source code of GbParser.pm, I figured out that
the plugin is getting the database name as 'taxon' from the db_xref
qualifier (e.g. db_xref='taxon:4932') and is trying to retrieve the
external_database_id and external_database_release_id for the 'taxon'
database. Now, even though I have an entry for 'Taxonomy' database in
my Sres.ExternalDatabase table, it is unable to match that since it is
looking for 'taxon' as the database name. Finally, it tries to insert
new entry for 'taxon' database in the Sres.ExternalDatabase and
Sres.ExternalDatabaseRelease tables, and the insert statement fails ..
don't know why ?

I would greatly appreciate if someone could help me on this.

Thanks,
Jeetendra.



allNonNullsSet: db_ref_na_feature_id not set... = ''
allNonNullsSet: external_database_id not set... = ''
GUS::Model::SRes::ExternalDatabase->retrieveFromDB($doNotRetrieveAtts=,)
Submitting GUS::Model::SRes::ExternalDatabase:
 Table: ExternalDatabase
        lowercase_name: [taxon]
        name: [taxon]

HasChangedAttributes='0'
Setting all foreign keys
GUS::Model::SRes::ExternalDatabase->Submit: All foreign keys are
set...proceeding
allNonNullsSet: external_database_id not set... = ''
Inserting:
Table: ExternalDatabase
        group_write: [1]
        other_read: [1]
        group_read: [1]
        lowercase_name: [taxon]
        name: [taxon]
        user_read: [1]
        row_user_id: [1]
        modification_date: [SYSDATE]
        other_write: [0]
        row_alg_invocation_id: [171]
        row_project_id: [1]
        row_group_id: [1]
        user_write: [1]
DBD::Oracle::st execute failed: ORA-00001: unique constraint
(SRES.PK_EXTERNALDATABASE) violated (DBD ERROR: OCIStmtExecute)$
    INSERT INTO SRes.ExternalDatabase (  group_write, other_read,
group_read, lowercase_name, name, user_read, row_user_id, $
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) " with
ParamValues: :p5='taxon', :p12='1', :p8='7', :p10='1$
Wed Aug 18 17:44:50 2004        Genbank entries inserted= 0;  updated= 0;
total #(inserted::updated::deleted)=16::::

Wed Aug 18 17:44:50 2004        FAILURES        Unable to process 2
entries. See gbparserFailures/
Wed Aug 18 17:44:50 2004        RESULT  Genbank entries inserted= 0; 
updated= 0;  failed= 2




-- 
Jeetendra Soneja
Research Associate
Virginia Bioinformatics Institute
1880 Pratt Dr., Building XV
Blacksburg, VA 24060, USA
Phone: (540)-231-2789
http://www.vbi.vt.edu