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

Hilmar Lapp hlapp at gmx.net
Thu Jan 29 22:22:22 UTC 2009

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 Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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