[BioSQL-l] error using load_seqdatabase.pl

[Hilmar Lapp]

This looks clearly like a bug since the generated statement is incorrect.
What puzzles me is that I update RefSeq (which is in Genbank format) on a
daily basis on an Oracle instance and I'm not seeing this error. Also, I
thought there is a test for genbank. I need to check that there is.

Did you pre-load the NCBI taxon database? If no, consider doing so, as it
will likely spare you from some trouble down the road with species that
aren't parsed correctly by flat file parsers.

    -hilmar
 
On 9/24/03 2:49 AM, "Gerben Menschaert" <Gerben.Menschaert at devgen.com>
wrote:

> Hello,
> 
> I'm trying to load a genbank file into biosql:
> perl load_seqdatabase.pl --driver Oracle --dbuser biosql --dbpass biosql
> --dbname sfr01  --lookup --noupdate --safe  /data/lazy/gbinv1.seq
> 
> Every genbank entry load failes with the following error:
> 
> DBD::Oracle::db prepare failed: ORA-00918: column ambiguously defined (DBD
> ERROR: OCIStmtExecute/Describ
> e) [for statement ``SELECT taxon_name.tax_oid, NULL, NULL, taxon_name.tax_oid,
> taxon_name.name, NULL FRO
> M taxon, taxon_name WHERE taxon.oid = taxon_name.tax_oid AND name_class = ?
> AND tax_oid = ?'']) at /usr/
> local/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/Oracle/SpeciesAdaptorDriver.pm
> line 214, <GEN0> line 22212
> 9.
> This error is normal since the tax_oid in the where clause is indeed
> ambiguously defined (it missed the prefix "tax_name.").
> 
> I'm running biosql on Oracle, bioperl-1.2.2 is installed and I'm using the
> main branch of bioperl-db. I recently changed from bioperl-1.2.1 to 1.2.2.
> 
> Any ideas?
> 
> Gerben
> 
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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