[Pipet Devel] Another XML proposal - Part deux.

[J.W. Bizzaro]

Justin Bradford wrote:
> 
> > As loci are loaded into the workspace, they can register the ability
> > to handle a particular DTD or set of DTDs.
> 
> Possibly even more than that -- for instance, a loci to handle a specific
> relationship between sets of DTDs (I don't have a good example, though).

Okay.  But again, the Workspace continually updates a database with this
information.

> 
> > We also need not pass around the entire XML object each time, for
> > example only a url for a reference need be included in the results
> > from an analysis, not the entire paper.
> 
> Yes. It was my intention for the workflow system to just give a locus what
> it needs (probably by creating a second Paos object). It should present it
> with the necessary data and control information, rather than sending the
> whole object with potentially extraneous data and control info.
> The locus updates the object with status information (recorded to the
> master Paos object, which the gui can get info from). And then transmits
> the generated data back via Paos. That's consolidated into the master
> object and fed to the gui client.

This reminds me of the Notebook, which we have talked very little about.  It
will give the user a written log, in HTML, of the analyses, but where large
amounts of data have been developed, the HTML gives only a link to the file
(archived XML).  At a later point, the user can view the log using the Notebook,
click on a link, and the archived XML will be brought back to life and sent to
the appropriate view.

Damn this project is complex, but fun! ;-)

> Or something along these lines. This example is missing a lot of things.
> I'm not sure how python handles hashes either. This is actually perl/c-ish
> here.

Python doesn't use symbols to type variables.

> 
> (note: Ok, now I'm going to ramble some...)
> 
> Although, perhaps we don't even need to bother trying to express the
> internal Loci data stuff as XML. Will we ever need to write it out to XML?
> Possibly only the actual biological data needs XML expression, just to
> facilitate interaction between Loci derived data and non-Loci tools.
> Theoretically, we don't need XML for anything, since structures in Paos
> could hold all of the biological data, too. It just seems like a good way
> to describe things for stuff that isn't entirely internal to Loci. But on
> similar grounds, we will need to define the internal Loci info interface
> adequately for tools to make use of it, and perhaps an XML representation
> of that would make it more clear.

Ahh.  The old PAOS vs. XML argument.  It's a good argument.  I think we could go
100% PAOS or 100% XML, and both ways would work.  But I think the combination of
the two can give us some advantages.  The way I see it, and I guess you do too:

    PAOS -> for active communication about the internals of Loci
    XML  -> for archiving and translating bio data

Actually, I'll say it again:  I want PAOS to have built-in XML parsing to make
this more uniform.


Cheers,
Jeff
-- 
J.W. Bizzaro                  mailto:bizzaro at bc.edu
Boston College Chemistry      http://www.uml.edu/Dept/Chem/Bizzaro/

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