[Bioperl-l] Bug in Bio::DB::SeqFeature::Store::DBI::mysql.pm (attached patch)

[Lincoln Stein]

My code is never very consistent, unfortunately. Thanks for the patch, but
it wasn't attached to the forwarded email. Could you try again?

Lincoln

On Thu, Jul 8, 2010 at 12:06 PM, Dan Bolser <dan.bolser at gmail.com> wrote:

> Editing subject to see if it gets through...
>
> On 8 July 2010 15:33, Dan Bolser <dan.bolser at gmail.com> wrote:
> > The bugtracker seems broken (or taking a painfully long time to log me
> > in). So here is my bug report before I forget:
> >
> >
> >
> > Title: Found a few bugs in bp_seqfeature_load.PLS when using -namespace
> >
> > Body:
> > The code had inconsistent use of the '_qualify' function, and one
> > instance of a hard-coded table name. These issues were not apparent
> > until "-namespace anything" was used.
> >
> > First I got the fatal error:
> >
> > DBD::mysql::st execute failed: Table 'dbolser.feature' doesn't exist
> > at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm
> > line 428, <GEN0> line 2.
> >
> >
> > which was due to a hard-coded table name. Then, after fixing, I got the
> error:
> >
> > Loading bulk data into database...DBD::mysql::db do failed: Table
> > 'dbolser.sheng_kai_sheng_kai_name' doesn't exist at
> > /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm
> > line 570, <GEN0> line 10000.
> >
> >
> > i.e. the prefix was being added to the table name twice.
> >
> >
> > I went through the code and tried to make all references to table
> > names consistent to ensure that bugs like this won't creep in again...
> > however, the code for this module isn't very consistent.
> >
> > (See patch attached).
> >
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-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>