[Bioperl-l] bioperl-db: don't just add exceptions please

[Hilmar Lapp]

Juguang I reverted your change in BioSQL/BasePersistenceAdaptor.pm. You 
can't throw an exception there because it may arise from a valid 
condition that needs to be dealt with locally, which is actually stated 
if you read the code documentation a few lines downwards.

Generally speaking, bioperl-db right now can be quite noisy in the 
sense that you may see lots of error messages from DBI. Believe me, 
this is almost always if not always OK. All statements are checked for 
their return value after execution, and proper action is taken if 
required (barring any bugs ...). Please don't add throwing exceptions 
after every statement in case it fails. There is no need for this. In 
fact, if you do this, you introduce a bug, that you in this case didn't 
see on mysql, but which surfaces immediately under Oracle.

Also, note that some drivers upon certain errors not only return a 
value that evaluates to FALSE, they may also (or better, instead) throw 
an exception (i.e., die). The Oracle DBD driver is an example for this. 
This is why if the execution is encapsulated in an eval{}, you should 
*not* propagate the exception upwards if one occurs.

For those who find bioperl-db too noisy, there is an easy way to shut 
up DBI, which is where the noise comes from: edit 
Bio/DB/BioSQL/DBAdaptor.pm, search for AutoCommit in the code, and add 
a PrintError => 0 attribute. I'll do this for the release.

	-hilmar
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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