[Bioperl-l] bioperl-db (Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver) LongTruncOk / LongReadLen
johnsonm at gmail.com
Sun Feb 15 13:54:20 EST 2009
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
>> $row = $sth->fetchall_arrayref();
>> return (@$row ? $row->-> : 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?
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