Re: [Gusdev-gusdev] Problem using LoadTaxon plugin

[Deborah F. P. <pi...@pc...>]

Sorry, I forgot to ask if your Oracle error was as printed 
below, "SRES"."TAXO NNAME"."TAXON_ID")On Tue, 18 May 2004 or a space was 
inserted when you copied it. 





 Deborah F. Pinney wrote:

> There is a bug in LoadNRDB.pm that has not been fixed yet.  If you run the
> plugin without commit, the transaction closes after loading entries into
> sres.taxon and a new one is opened to load sres.taxonname. That means that
> all the inserts into taxon have been rolled back. Can you load with commit
> on? The bug will be fixed soon.
> 
>                                                        Debbie
> 
> 
> On Tue, 18 May 2004, 
> Madhura Sharangpani wrote:
> 
> > Hi All
> > 
> > I am trying to use the LoadTaxon plugin to load NCBI taxonomy files, I downloaded the taxdump files from ncbi.nih.gov, I also created bootstrap rows using xml file input and that worked fine, but when I was running the LoadTaxon plugin to load the NCBI taxonomy files using command:
> > 
> > ga GUS::Common::Plugin::LoadTaxon --nodes=nodes.dmp
> >  --names=names.dmp --gencode=gencode.dmp
> > 
> > I got following error:
> > 
> > Initially it went on for a while printing the tax_ids processed,
> > 
> > processed ncbi_tax_id : 40049
> > processed ncbi_tax_id : 192122
> > -------
> > so on
> > 
> > and then it stopped with following error
> > 
> > DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into ("SRES"."TAXO NNAME"."TAXON_ID") (DBD ERROR: OCIStmtExecute) at /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145, 
> > <NODES> line 217936. SQL ERROR!! involving INSERT INTO Res.TaxonName (  row_user_id, other_read,unique_name_variant,user_write, group_write, name_class, row_project_id, name, taxon_id,modification_date, ser_read, row_alg_invocation_id, group_read, other_write, row_group_id,   taxon_name_id  )  VALUES   (  ?, ?, '', ?, ?, ?, ?, ?, '', SYSDATE, ?, ?, ?, ?, ?, ? ) 
> > Values: 1, 1, 1, 1, scientific name, 1, Influenza C virus (C/Miyagi/9/96), 1, 91, 1, 0, 1, 1 
> > at/afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/ObjRelP/DbiDbHan dle.pm line 185 
> > 
> > Could someone explain what am I doing wrong?
> > 
> > Thanks!
> > 
> > 
> > Madhura
> > 
> > 
> 
> 
> 
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