[Genquire-dev] to Commit or not to Commit

[Mark Wilkinson]

David Block wrote:

> > Would anyone object to me pulling the "auto" out of "autocommit"?
> What the heck are you talking about?

well, in the current Genquire adaptor there is no user-control over the
decision to commit.  The $dbh->commit call is in an eval statement, and if
it fails, Genquire assumes that the database can not handle transactions and
sets "autocommit" to true.  If the call succeeds, then it sets "autocommit"
to false, and allows the statement to be executed at each _update_db
call...  but it makes no difference in the end since the $dbh->commit call
is hard-coded, so whether you want it or not the changes are commited
automatically under both circumstances.... which defeats the purpose of
having transactions in the first place, yeah? (or am I missing something?)

> You mean database updating not being live?  Which Commit are you
> worrying about here?

yes.


> Yes, that is a good idea.  Flat files are much more of a 'edit->publish'
> paradigm than a database which allows edits in-place.

but... a database that supported transactions would allow you to do an
editing session and then decide whether or not to keep it, right?


> I'm pretty sure it does - SeqIO->write_seq?  EMBL->GenBank->EMBL is one
> of the tests that is talked about on bioperl-l.

I had thought so, but I have never actually used it, so...


> Yes.  Good thing we have this list, eh?

what do you object to?

M


--
--------------------------------
"Speed is subsittute fo accurancy."
________________________________

Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK
Canada