Bioperl-guts: CORBA + Perl + exceptions

Jason Stajich
Tue, 25 Apr 2000 09:38:56 -0400 (EDT)

On Fri, 21 Apr 2000, Ewan Birney wrote:
> Oh dear guys - I also have been working on teh bioperl corba server
> as well - I thought I had a clean sheet and noone else was working on
> this, so I have alot of stuff to commit.
> doh! stupid - I should have posted to teh list first. Idiot ewan.
> Jason - do you want to commit first, and then I'll handle any conflicts my
> end? TEll me when you have committed.

I went ahead and merged to get your current changes.  

Most of my stuff has been barebones as I have been getting hung up on the
Exceptions - can't seem to throw org::Biocorba::Seqcore::XX exceptions and
have them caught by the client.

I had made a separate module that contains an explicit implementation of
exceptions but it is a little roundabout for a simple exception throw.  I
haven't submitted that code as I am not sure it is the correct way to go
with these.

I submitted a Makefile.PL and a Changes file.  I had made corrections to
PrimarySeq, but I see they were already fixed in your version.  I did
implement the inherited function [AnonymousSeq] 'type' for the PrimarySeq
object by just calling moltype on the seqtype, but I wasn't sure if you
had other designs for that since it isn't implemented. accession_number
and version aren't implemented either.  I think we'll need a stub here
even if nothing is returned so the server won't balk on a request. 

I have started on the SeqFeatureIterator but have been trying to decide
how we will be handling the collection of features - are they Bioperl
SeqFeatures or Biocorba SeqFeatures... Brad and I have been conversing on
this point - I think it obviously depends on how they will be obtained.

Didn't know if you had any more insight. The philosophy applies to a lot
of the modules and can have memory implications too.
> (I feel pretty stupid for not getting us all coordinated)...
So it doesn't happen any more, do you want to say which modules you think
you'll be working on.  I was starting on SeqFeatureIterator and was
planning on moving to the PrimarySeqDB .  But if you have started/finished
any of these let me know so I don't carry my code any further.

> Re: exceptions:
> bioperl-corba-server should catch bioperl exceptions and throw corba
> exceptions. 
> bioperl-corba-client (stubs on my disk) should catch corba exceptions and
> throw bioperl exceptions.

How soon before you check that stuff in?  

> future goal for bioperl - move all exceptions to the "standard" perl
> exception system. This is a 0.7 or a 0.8 goal, and not now for sure.
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <>. 
> -----------------------------------------------------------------

Jason Stajich
Duke University Medical Center
Center for Human Genetics
(919)684-1806 (office)
(919)684-2275 (fax)

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