[Pipet Devel] embedding queries in XML

[J.W. Bizzaro]

Carlos Maltzahn wrote:

> This sounds like a workflow system to me. Except the agents are now tools
> instead of office workers.

Yes!  I ignored the concept of the workflow system because it related to office
workers, but I guess we can treat the loci as workers.  Great!  Now where did I
see a workflow system recently?  Zope does this, right?

> I assume that an XML object is an intermediate result in the execution of
> some composition of analysis tools, correct? 

The XML is generated from whatever biological data the user starts with.  They
will get some piece of info (a sequence or a structure) and will want to do
something with it.  As soon as Loci knows what the data is, it is put into XML,
and it stays in XML indefinitely.

> So I see Paos as control and monitoring infrastructure for shells which
> receive and send XML objects from/to other shells and start and feed tools
> according to these XML objects. I think you call these shells analysis
> loci (correct?).

If by shells you mean analysis tools, in whatever language, wrapped in Python so
that they become transparent, then yes.

> But you could use the same shells as visualization loci.

Well...They're shells in the sense that GTK/GNOME GUI are wrapped in Python. 
But they will be pure Python.

> For me a visualization loci is just another glyph in a GCL construct. To
> the user the only difference to an analysis loci is the fact that it
> usually runs fairly local to the user and calls a tool that shows up as
> a Gnome application that visualizes data.
> 
> Let me know whether this sounds right.

Yes!  I think you see it the way I do.  Only visualization loci are always
local/client, while analysis loci can be remote/Internet-server (as I have been
describing them) _or_ local/client.  The mechanism for local or remote analysis
loci (gatekeeper and porta) should work nearly the same.  My reasoning for
having both is that local analysis will give better control and faster feedback,
while remote analysis will expand the Loci installation to the extent of what is
on the Internet.

BTW, Carlos, don't worry about rushing to get the documentation done.  We
understand that your thesis is your personal life and much more important ;-)


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