[Pipet Devel] hierarchy (was: icons)

[Brad Chapman]

Jeff wrote:
* the revised options *
> I'll reword the Option list:
> 
>     Exactly what does the BL connect to directly (that the user can 
see)?
> 
>         A.  Only BL and PL nets
> 
>         A1. Option A, but BL nets are transparent
> 
>         B.  Option A, plus a couple nodes such as documents and
>             containers
> 
>         C.  Anything

>From the few comments I got back,

Jeff, I don't know if I am the only dumb one, but I haven't been 
commenting on this thread because I really don't understand what is 
going on :-). I understand what PL networks are because these are the 
networks that Overflow uses right now. The way I have been working 
with things is to make an Overflow network map directly onto the 
Loci "workspace" and dealing with things like this. 
    What I don't understand is:

1. What exactly is a BL network?

2. How does a BL network differ from a PL network? Does it have to do 
with network location? 

2a. If it has to do with network location, I am really confused about 
what is going on, because I thought the dl would be mostly responsible 
for remote communication. In the documentation for the definition 
layer (http://bioinformatics.org/piper/documentation/dl_info.pdf) I 
wrote up with diagrams about how I thought remote communication would 
work, and this doesn't involve the bl communicating remotely. I 
thought this was how we were working, but maybe not. Do people not 
like this? Is this thinking incorrect? Please let me know so I can not 
only change it, but modify my thinking as well.

3. Shouldn't the whole entire implementation system of Piper be 
invisibile to the user? I thought this was the point of separating out 
the build time and run time layers. Why should the user have to worry 
about whether they are adding a bl or pl network or whatever?

4. What is the point of the PL and BL, exactly, in other people's 
minds? I thought that the PL handled application wrapping and basic 
piping between internal nodes, and that the BL would handle 
"organizing the workflow diagram" into a fast model, and implementing 
cool genetic algorithms to think of ways to make connected nodes run 
faster. Am I totally off? Maybe someone could clarify what is going on 
here if I am :-)

5. Shouldn't dealing with the filesystem (like loading documents) or 
dealing with databases be done by the "build time system" and thus be 
handled by the definition layer? It seems like the run time system 
only cares about having data and manipulating it, and not having to 
deal with stuff like connecting to different databases, etc.

6. What are people's immmediate development goals for Piper? What I 
have been working towards is adding all of the functionality from 
Overflow into Piper, using the Piper framework. So when the system is 
done, we would have something with mostly Overflow functionality, but 
with the added advantage of one user interface, dealing with remote 
connections, having genetic algorithsm to improve running speed in the 
BL, etc. Does this BL/PL network stuff that you are talking about 
affect how I should be coding right now? If so, what should I be 
doing differently?

Okay, I guess all of that is enough to show that I am thoroughly 
confused about what is going with this whole discussion :-). I 
apologize for being so dense about all of this...

Brad