[Pipet Devel] Universal Description, Discovery, and Integration

[jarl van katwijk]

Brad Chapman wrote:

> I wrote some documentation (now out of date, of course) about how this
> works, which can be found at:
>
> http://www.bioinformatics.org/piper/documentation/piper_plugin.pdf

You could have spared yourself a lengthy email and just gave me this link Brad
:)

This is what I understand of Alexandre's and Brad's e-mail about Narval's and
Piper's
pattern to describe 'applications': both methods are more or less the same in
the
aspect of both focussing on the application as a unix user in a shell would do.
The
name, input and output are well handled. I will wait for this to become more
detailed
once we can do some testing, and as Jeff said: we should not touch the
stdin\out.

But at the same time I see some critical issues missing, which are noticed by
Brad and
documented by some ?'s. The first is 'environment description'. By this I mean
things
like path (-relocation), dependencies and local issues (like hardware dependent
stuff).
The 2nd is about errors. I think Piper needs some basic form of exception
handling,
this can be just a simple retry of node execution. Maybe the PL already has
something
like this build in. (JeanMarc?). The 3th is event handling. Many applications
only make
sense to execute when there an special situation.

Anybody has thoughts about these three points I feel missing?

bye,
jarl