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

Lincoln Stein lincoln.stein at gmail.com
Thu Jul 8 12:24:38 EDT 2010


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>


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