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

Dan Bolser dan.bolser at gmail.com
Thu Jul 8 12:06:59 EDT 2010


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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