[BioRuby] Web interface

[pjotr at pckassa.com]

On Tue, Jan 20, 2004 at 10:33:33PM +0900, GOTO Naohisa wrote:
> I'd rather like to do with single template file, by using Amrita or
> HTML/Template or something like these.
> http://raa.ruby-lang.org/list.rhtml?name=html-template

Hmmm. This one is too simple mindend and I don't see the advantage
over eruby - really.

> http://www.brain-tokyo.jp/research/amrita/index.html

Amrita is more interesting. I'll consider that.

> Though, whatever approach we choose, template's template may be needed :-)
> > Where templatefn looks like:
> > 
> > TextField,query,'Query'
> > AminoAcids,field1
> > SubmitFile,field2
> > SelectField,field3,'Choose',{0,'Type1',0,'Type2',1,'Type3'}
> > etc.
> 
> Is there much computer-friendly and natural format?
> I think YAML is a good candidate, because Ruby already have YAML's parser.

I like that! Thanks for the pointer.

> There are some web application frameworks written in Ruby and/or
> usable with Ruby. 
> 
> I think some kinds of biological CGI frameworks or templates
> may be needed.
> 
> I wish, a code writing with the framework can run as both CGI and
> GUI and command-line applications with very few efforts.

That is a bit of a holy grail ;-). And in fact my experience with J2EE
has taught me that, while 3-tier systems can scale well they tend to
increase complexity. Which can be unacceptable.

My 'solution' for new project is to keep it simple, and keep the
interface as small as possible. A command line version should always
be there and that allows for a CGI script to call the command line
version - similarly for a GUI front-end (kinda minimal MVC pattern).

If a command line is too simple (or too slow, because there are
penalties) for what you want the choice of a frame work comes up.

Note that most Unix tools are based on a similar 'phylosophy'.

> There are some web application frameworks written in Ruby and/or
> usable with Ruby. Using one of them might save time and effort.

Had a look at Arrow
http://dev.rubycrafters.com/arrow-manual/tutorial.html but that looks
immature. Also I am a bit confused because (unlike EJBs) it seems to
sit tight with the webserver.

OK, what I'll do is provide something minimal shared across my
two/three projects. Once that is done I'll post it.

Pj.