[Pipet Devel] toolkit and data access/storage

J.W. Bizzaro bizzaro at bc.edu
Thu Jan 21 20:44:48 EST 1999

Carlos Maltzahn wrote:
> I'm not sure how Paos should communicate with the actual tools (in the
> case people agree to use it as "gatekeeper").

Actually, I was not calling Paos "Gatekeeper".  Let's see if I have the Paos
model right:  Some clients are local to the user, and the server is remote and
acts as hub for remote clients to communicate with local clients.  Correct?

If I am correct, the Gatekeeper would be a remote client to Paos.  It converts
queries into command-lines (via Ajax by EMBOSS?) for execution by the analysis
algorithms, waits for response, gets ASCI text response, formats it into XML
(according to a template), and sends it back to the client.

on the server side, we are catering to
fork-request-once-response-once-terminate programs made by who-knows and
whenever with whatever language.  In other words, we still need a CGI-like
system.  But this is only one type of Loci client.  Other clients can make
better use of Paos.

> I personally don't like CGI
> because of it's unflexible fork-request-once-response-once-terminate
> assumption. I suspect these tools are running for a longer time period and
> we would like to be able to find out about their state.
Yes!  This is something I realized would not work with standard CGI.  These
analysis algorithms (server side only) will be longer lived than standard CGI
scripts.  Some may take hours or days to complete.  I would like to return the
state or maybe the time elapsed to the client so that the user knows something
is happening and the whole thing didn't just die.

> On the other
> hand it's probably not a good idea to run them natively in Paos
> because of their size, no? What are people's thoughts about this?

Because biological analysis algorithms tend to be command-line,
run-once-and-terminate, I think we will just have to treat them like rather
big CGI programs.  That's not to say that other tools, libraries, etc.,
written for Loci, will not communicate directly using Paos and XML...They can
and will.

J.W. Bizzaro                  Phone: 617-552-3905
Boston College                mailto:bizzaro at bc.edu
Department of Chemistry       http://www.uml.edu/Dept/Chem/Bizzaro/

More information about the Pipet-Devel mailing list