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

Lincoln Stein lincoln.stein at gmail.com
Thu Jul 8 12:28:14 EDT 2010

Never mind. I found the patch in the earlier message.

Thanks again for tracking down the issues.


On Thu, Jul 8, 2010 at 10:33 AM, 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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