Re: [Myexperiment-discuss] Re: [Taverna-hackers] Scufl 2 workflow language

[Jiten Bhagat]

Excellent, thanks Paul.

For the benefit of others - the Ruby Gems that Paul is referring to are
available for anyone to use, from here:

For Taverna 1:
http://github.com/mannie/taverna1-gem/

For Taverna 2 (t2flow)
http://github.com/mannie/taverna2-gem/

Cheers,
Jits


Paul Gordon wrote:
> The gems worked like a charm (so to speak), thanks. In case anyone is
> interested, here's a minimal CGI Ruby script to generate a T2Flow PNG
> diagram with no temp files:
>
> #!/usr/local/bin/ruby
> # Contents is the output for a T2Flow document (Taverna workflow)
> visualized
> # using myExperiment.org gems and 'dot'.  The workflow should be
> posted as a parameter called 'workflow'
> require 'cgi'
> require 'rubygems'
> require 't2flow/model.rb'
> require 't2flow/parser.rb'
> require 't2flow/dot.rb'
>
> # Create an instance of CGI
> cgi = CGI.new
> print "Content-type: image/png\n\n"
>
> # give dot the input (model) to render
> dot = IO.popen("/opt/csw/bin/dot -Tpng", "wb+")
> T2Flow::Dot.new.write_dot(dot, T2Flow::Parser.new.parse(cgi['workflow']))
>
> # terminate processing
> dot.close_write
> dot.each {|l| puts l}
> ___________________________________________________________
> Paul Gordon wrote:
>> Well, my situation os a follows.  I export a T2Flow workflow from
>> Seahawk, but it would be really nice to be able to preview the
>> workflow that would be generated (as there are few export options
>> available).  So the workflow is transient, and not necessarily
>> public.  A remote workflow image generator based on submission of a
>> T2Flow doc would be ideal, because then Seahawk would not need to
>> ensure dot is locally installed.  Looks like the easiest solution in
>> the absence of an existing idempotent generator in myExperiment is
>> for me to build a simple POST CGI in Ruby myself using the Gems
>> mentioned earlier.
>>
>> Thanks for the info,
>>
>> Paul
>>
>> Stian Soiland-Reyes wrote:
>>> On Mon, Jan 11, 2010 at 17:12, Paul Gordon <address@hidden> wrote:
>>>   
>>>> I don't suppose in the interim that there's a way to call the Ruby-based
>>>> T2Flow diagram generator of Biocatalogue remotely?
>>>>
>>>> Having a lightweight piece of code to generate the workflow diagrams
>>>> (either via a network client or a standalone JAR) is DEFINITELY
>>>> something I'd like!
>>>>     
>>>
>>> If you upload a workflow to myExperiment it should generate a picture for 
>>> you..
>>>
>>> I think that workflow upload also work via the myExperiment REST API -
>>> but I'm not sure if that would generate the preview for you in the
>>> same way that if you use it through the web page..
>>>
>>> CCed myExperiment discuss list. :)
>>>
>>>
>>>   
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