[Pipet Devel] XML and Pise

[Catherine Letondal]

Brad Chapman writes:
> Hi Raynald;
>     Thanks for writing!
> 
> Raynald wrote:
> > However, it seems that the Piper XML is not yet completely defined. 
> I am
> > working in the Pasteur Institute and there is a software called Pise:
> > http://www-alt.pasteur.fr/~letondal/Pise/ written by Catherine 
> Letondal
> > (letondal at pasteur.fr).
> 
> I really like Pise a lot, and there was actually a bit of discussion 
> on the Loci list about it back when it was first GPLed. I've spent a 
> lot of time since then looking through the mounds of perl code that 
> make it up :-).
> 
> Raynald wrote:
> > In two words, this is an interface builder. It makes HTML pages and 
> CGI
> > scripts for unix programmes related with Biology. My point is it 
> uses XML to
> > describe the program to be interfaced. This program is under GPL and 
> well
> > documented. I think it would be great if Piper and Pise could share 
> the same
> > DTD...
> 
> As Jeff mentioned, we do have a semi-permanent DTD working for Piper 
> which is kind of a conglomeration between the old Loci XML format, and 
> the way that Overflow does things. This is not yet permanent, but has 
> been in place for a little while.
>     That being said, there is still room for some flexibility (since 
> I'm no stranger to rewriting code :-). A few months ago, I was really 
> ready to just use the Pise DTD for Loci, actually. However, as I've 
> got into Piper more and more I've realized that the Pise DTD isn't 
> really meant for the kind of system Piper is trying to be. The big 
> difference is that Pise is, as you mentioned, mostly concerned with 
> being an interface generator. 

That's right.

> By contrast, Piper (in my mind) is less 
> concerned with generating interfaces for specific programs, and a 
> little more concerned with creating an interface to make connecting 
> programs together more intutitive. 
>     The Piper DTD mainly focuses around three elements: Parameters, 
> Inputs and Outputs. The Pise DTD is mainly focused on the Parameter 
> part of this, which makes a lot of sense, since it is designed to 
> create specific GUIs. Pise does have a pipe element, which provides 
> some support for piping output from one program into another, but this 
> seems less developed then Piper is trying to be. This right here seems 
> to be the major sticking point, since Pise would have to add on quite 
> a few changes here to deal with this. You mentioned the possibility of 
> "some" modifications of the part of Pise, but I would imagine these 
> would be quite small, considering that Pise is already in use in quite 
> a few places. It seems like adding on whole another Input and Output 
> parts might not be favorable, but I don't know...

The pipe element in Pise is understood as an Input for InFile/Sequence 
parameters and as an Output for OutFile/Results parameters, so it would
be easy to add an information, maybe as an attribute of the pipe element?

I don't know Piper enough for now, but I think the main problem would
be for other kinds of parameters (Integer, List, ...) which are not connected
at all in Pise. There is a student project in Bielefeld to extend the
dataflow model of Pise this way.

>     There could probably be some reconciliation on the parameter 
> attribute on our part, but the thing I'm most worried about here is 
> that Jeff has been wanting to use BlueBox to do the generation of 
> user interfaces, so I don't know if the Pise model would fit with 
> this, since we haven't seen BlueBox yet. Did you have any ideas how 
> the Pise and Piper models could be combined, now that you've seen both 
> DTDs?
> 
> Jeff wrote:
> >> Also, Piper is meant to be general-purpose, not biology-related 
> (/Loci/ was
> >> originally supposed to be biology-related).  I see some Pise tags 
> like
> >> "Sequence", which we wouldn't want to use.
> 
> Well, this isn't a big concern to me, since we are not forced to use 
> all of the elements, and specific nodes that wanted to use biology 
> related terms could use them. I guess we would have a danger of 
> developing some huge monsterous DTD with lots of domain specific 
> information in it, which would be a bad thing.
> 
> Raynald:
> > What do you think of that ?
> 
> I think it is a really good idea, but am worried about the 
> technical difficulties of doing it because of the differences in the 
> goals of the two projects. Having read what I said, what do you think?
> 
> Brad
> 
> 
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--
Catherine Letondal -- Pasteur Institute Computing Center