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

Mark Johnson johnsonm at gmail.com
Thu Jan 29 17:03:34 EST 2009


    I notice that the DBI LongReadLen paramater is set to a particular
value in Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver, but
LongTruncOk is not set to 0.  The DBI docs seem to indicate that
LongTruncOk should default to false, but I just tracked down an issue
with long sequences not fetching out of our BioSQL instance with no
errors thrown.  I guess maybe that is due to this:

# 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?).


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