[Biocorba-l] Re: Migrating to biocorba 2

[Jason Stajich]

I guess I'll be the first to comment then.

On Mon, 2 Apr 2001, Jason Stajich wrote:
> On Mon, 2 Apr 2001, Solbrig, Harold R. wrote:
>
> > Jason,
> >
> > I've taken a look at the interfaces and don't think that they will be too
> > much trouble - just a matter of time...  and it looks like I'll have some to
> > spare this week, so I should have something to report by Friday.  A few
> > issues, questions, etc...
> >
> > 1) Is there a UML model of the interface?  If not, I'd be glad to crank one
> > out, but I don't want to spend time on something that has already been done.
> >
There is not one yet, I'd be very happy to have you do one.  I can throw
it up on the webpage when you get finished.

> > 2) Do you anticipate that the Java use of this interface will be primarily
> > as a client, a service or both? If there already Corba enabled services out
> > there that handle databases, then perhaps the focus should be mostly on the
> > client aspects.

Well, I know that we have worked to make it solid for both client and
server code.  In bioperl we have a separate code base for the client code
to map biocorba objects into bioperl objects.  Perhaps this would be
useful in biojava-corba?  I think Matthew's implementation is to map
everything through the bridge so that the mapping (to/from biojava
objs) works on both client and server ends.  correct me if I am wrong.

> > 3) The BioEnv interface _from_file interface talks about file names.  Was it
> > the intent of the spec to allow URL's?  The reason that I'm asking is that,
> > as the documentation mentions, file names make little sense across the net.
> > Url's, however, have the potential of allowing one to make the BioEnv
> > factory aware of all sorts of new information sources.

Hmm, I don't think so - But I think we are open to good arguments here.  I
can certainly see how it would be useful, I think the initial intent here
was to just build a small system that met the basic needs of transforming
objects to/from biojava,bioperl, biojava.  Anything else is a separate IDL
which includes the biocorba IDL ala ensembl.idl.

> > 4) PrimarySeqDB - Would it make sense to have a method that lists all of the
> > version id's, perhaps with annotation, of a given accession?
My understanding is that sequence version databases are few and far
between.  I can imagine it being useful, not sure if any of the existing
bio* db code have implemented this (which drove the
biocorba design).

> > 5) GNOME root - Is this mechanism actually in place and behaving correctly?
> > How well has it worked?  Do all of the applications use it?
> >
Brad you want to take this - having done some more tests than me.  I never
refer to it directly.

> > Gnome policy questions:
> >
> > Who calls ref() when a method returns an object reference - the caller or
> > callee?
> > Does a sequence manage the references on its elements?
> > How are structures containing object references handled?
> > Is it necessary for applications that create objects directly to still do
> > reference counting?
> > What is the policy regarding circular references?
> >
> > 6) Are there strong feelings about using Java inheritence vs. delegation on
> > inherited interfaces?
> > 7) (Related to 6) Are there strong feelings about using the <class>_TIE
> > approach vs. the <class>POA?  While neither can be entirely transparent
> >

I haven't really spent a lot of time thinking about these so I don't really have an
answer for you.  I have only done the perl implementation so I think
some of these are specific to the language implementation.  I'd be
really happy for you to at least outline what *should* be happening, or to
investigate what is happening.  We suffer from a lack of developers here
so anything you can do would help.

> > I realize that I'm an newbie to this world and a lot of these issues may
> > have already been hashed out long ago.  If so, feel free to point me at the
> > FAQ so that I don't waste your own time.
> >
We are happy to have your CORBA expertise on board.

I would be really helpful if someone could compile a FAQ based on some of
these and other questions.  Perhaps we can start one in the wiki.
I'm having a hard time judging the interest level of the list subscribers
so I don't know where there is interest in going.


Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center
http://www.chg.duke.edu/