[Bioperl-l] bioperl-db (Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver) LongTruncOk / LongReadLen

[Mark Johnson]

On Thu, Jan 29, 2009 at 4:22 PM, Hilmar Lapp <hlapp at gmx.net> wrote:
>
> On Jan 29, 2009, at 5:03 PM, Mark Johnson wrote:
>
>> # execute and fetch
>>   $sth->execute();
>>   $row = $sth->fetchall_arrayref();
>>   return (@$row ? $row->[0]->[0] : undef);
>>
>> ...which is in get_biosequence() in
>> Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver at around line 257?.
>> I don't see RaiseError being set anywhere, so shouldn't there be a
>> check here to throw an exception if the execute fails (such as if
>> LongTruncOk is 0 and a LOB is > LongReadLen?).
>
>
> RaiseError is one of the initialization parameters (in Bio::DB::BioDB->new()
> call) and is set when the database connection is opened.
>
> Not checking the return value in the above surely looks like a bug. Would
> you mind filing it in bugzilla?
>
>        -hilmar

Done.