[BioRuby] Web interface

[GOTO Naohisa]

Hi,

On Tue, 20 Jan 2004 11:17:52 +0100
pjotr at pckassa.com wrote:

> Hi Everyone,
> 
> I am in the process of writing several programs where it would be nice
> to have a web front-end. Now, for submitting FASTA, the interface is
> usually pretty similar where you have a style sheet, header, footer
> and some input fields. This calls for some template solution. My idea
> is to use mod_ruby where the template looks like:
> 
> ~~~
> 
> require 'webtemplate'
> 
> page =
> WebTemplate.new(stylefn,headerfn,footerfn,templatefn,'nextpage.cgi')

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

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.

> The next step is to parse the results entered on the generated form
> and submit the query to the query engine - which has to be able to
> queue requests not to overload the machine. Results can be displayed
> or sent by E-mail.
> 
> The queue requests are simple batch invocations (not sure what
> infrastructure to use yet, gnuqueue http://www.gnuqueue.org/home.html
> is an option). That gives the advantage the programme can be run also
> from the command line by users who don't want the webinterface.

I tried GNU queue 1.30.1 last year, but it was still buggy.
Does someone know alternatives?

> A generic solution - and part of BioRuby - looks like a good idea to
> me. I can write it, but maybe there are some existing/better
> solutions to the same problem.
> 
> What do you think?

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.

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

Regards,
-- 
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp
Genome Information Research Center, Osaka University, Japan