[Pipet Devel] Peep

[deanne at density.biop.umich.edu]

> I'd like it to work as much like the Unix shell/CLI as possible.  So, hitting
> return on a blank line should give you another prompt.

I think I can do that just by redefining what "" does on input. 

> Interesting.  I was thinking about a non-interactive, all-in-one command
> like...
> 
>   nodeset number=1 type=1 ip=121.0.0.0
> 
> But command-lines like this are hard to remember.  How about we combine the
> two: If the user enters an incomplete command, Peep asks for the extra values?

Pretty easy to do. I was thinking of that too...I'm an inpatient user, and
I hate prompts...I love command line stuff. But I figured it would also
order the process a bit more if that ability was there. I'll write that
in.

> 
> Okay, maybe this is just a test/example, but node numbering should be
> automatic...probably handled by the UI (not the DL).

*nods*...the UI probably should hand it off. The numbering part is easy
enough. I'll just assign a list of loci. Editing a large stack of loci
after they're built won't be too hard in python, looks like, since
dictionary data types are mutable and searchable. Did I mention I really
love python? :)

> 
> > Enter new node type: type2
> > Enter the remote IP or name for this node: 121.00.00.01
> 
> These two are really for specifying a BRAND NEW node, and I'm not sure how
> much or if that will be needed.  Piper should know what is on the local
> filesystem and any remote systems you're connected to.  The user should be
> able to type a "list" command to see all basic nodes available and all
> pre-prepared networks.

Yup. This was just a test case, to figure out how stuff works. I can have
a command in peep to add to the network list, too, as part of the UI. As a
user, I'd like to see that functionality in peep so I don't have to leave
peep to define new loci. 

Is there a central datafile (I guess this is for Brad) with loci lists and
local network lists?

> I think the only time the user will need to enter an IP is to link with a
> Piper on another, known system.

*nods* THat could be a submenu entry, then.


> 
> Yeah, this is what I was thinking about.  It's something like the ls command,
> aint it?

Yup. Peep will probably be pulling this stuff from the ls subroutine. I
was just playing with learning how to select out dictionary entries. :) 

> 
> If the UI would simply assign a number (dynamically -- if a locus is removed,
> everything is renumbered) to each locus:pipe in the network, it'd be a lot
> easier on the user.  So, if...
> 
>     piper://bioinformatics.org:1000/unix/commands/ls = 1
>     piper://bioinformatics.org:1000/unix/commands/ls = 2
> 
> and
> 
>     out1pipe = C
>     in1pipe = A    (attached to different loci, actually)
> 
> the user can type...
> 
>     connect 1:C 2:A
> 
> Simple.

Yup, but that sounds even longer than I personally would like as a
user. How about a configuration file somewhere that has those definitions
in it, maybe indexed by locus nickname, and the user can select from 
a list they get with "config list" or something, like...

<peep> job1 target testing.file

<peep> config list

Nickname    Process Type
----------------------------------------------------
bioinf_ls  piper:// bioinformatics.org:1000/unix/commands/ls
density_ls piper://density.biop.umich.edu:1000/unix/commands/ls
bioinfo_ps piper://bioinformatics.org:1000/unix/commands/ps  
density_gcg piper://density.biop.umich.edu:1000/usr/local/gcg <options>
bioinf_psc  piper://bioinformatics.org:1000/usr/local/psc <options>
density_rpl piper://density.biop.umich.edu:1000/usr/local/perl/r.pl <file>

<peep> job initiate testing testing.file
	
	Intializing job named "testing" with input data "testing.file"

<peep> testing  loci1 density_gcg  -> bioinf_psc -align_center
<peep> testing  loci2 -> density_rpl
<peep> testing  loci3 -> density_ls (etc)

<peep> loci map testing

Job: Testing
Locus:A    
Input Pipe: density.biop.umich.edu:1000/usr/local/gcg
Output Pipe: bioinformatics.org:1000/unix/commands/psc -align center

Locus:B
(etc)