Re: [Gusdev-gusdev] Problem using LoadTaxon plugin

[Madhura S. <sma...@st...>]

The space was inserted when I copied it, the error is:
"SRES"."TAXONNAME"."TAXON_ID")
Let me try loading with commit on
Thanks!
Madhura

----- Original Message ----- 
From: "Deborah F. Pinney" <pi...@pc...>
To: "Madhura Sharangpani" <sma...@st...>
Cc: <gus...@li...>
Sent: Tuesday, May 18, 2004 11:46 AM
Subject: Re: [Gusdev-gusdev] Problem using LoadTaxon plugin


> 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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