[BioSQL-l] Error in load_ncbi_taxonomy.pl

[Aaron J Mackey]

Of course as soon as I sent this I saw what I was doing wrong (not
wrapping large sets of inserts/updates in single transactions).  Things
should be significantly better now, please let me know if there are other
things I can do.

-Aaron

On Fri, 21 Mar 2003, Aaron J Mackey wrote:

>
> Well, I'm finding that postgres is just a bit slow compared to mysql; this
> whole process takes about 30 minutes on my mysql installation, now over 8
> hours on my postgres installation.  I'd love to have someone tell me what
> I'm doing wrong ... (perhaps I need to turn indexing off until I'm done
> with the bulk load?)
>
> -Aaron
>
> On Wed, 19 Mar 2003, Marc Colosimo wrote:
>
> > Thanks, I dropped the table and used the one from the cvs version and it
> > works. However, it is a bit slow in loading. This is a fast machine, but
> > it is a stock build of postgresql.
> >
> > marc
> >
> > On Tue, 18 Mar 2003, Aaron J Mackey
> > wrote:
> >
> > >
> > > Yeah, I just got bit by this today too; fixes are already checked in to
> > > CVS; you'll need to reinstantiate the database from the .sql (or at least
> > > the fktaxon foreign key constraint).
> > >
> > > -Aaron
> > >
> > > On Tue, 18 Mar 2003, Marc Colosimo wrote:
> > >
> > > > I tried using load_ncbi_taxonomy.pl (Rev 1.3 from 119 mins) and got this
> > > > error:
> > > >
> > > > [mcolosim]$ ./load_ncbi_taxonomy.pl -dbname bioseqdb -driver pg
> > > > DBD::Pg::st execute failed: ERROR:  fktaxon_taxon referential integrity
> > > > violation - key referenced from taxon not found in taxon at
> > > > ./load_ncbi_taxonomy.pl line 142.
> > > > DBD::Pg::st execute failed: ERROR:  fktaxon_taxon referential integrity
> > > > violation - key referenced from taxon not found in taxon at
> > > > ./load_ncbi_taxonomy.pl line 142.
> > > >
> > > >
> > > > _______________________________________________
> > > > BioSQL-l mailing list
> > > > BioSQL-l at open-bio.org
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> > > >
> > >
> > >
> >
>
>

-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey at virginia.edu