Re: [O] babel work flow

[Eric Schulte]

address@hidden (Thomas S. Dye) writes:

> "Sebastien Vauban" <address@hidden> writes:
>
>> Hi Thomas,
>>
>> Thomas S. Dye wrote:
>>> I want to use one of the dot utilities, tred, in a way that preserves my
>>> ability to distribute the Org-mode file as reproducible research, i.e.,
>>> intermediate results should end up in the Org-mode file or be passed
>>> along in a chain.
>>>
>>> Right now I have a python routine that reads a couple of Org-mode tables
>>> and outputs a valid dot graph.  I'm saving this to a file, dot-temp.gv,
>>> and then running some shell commands, like this:
>>>
>>> #+begin_src sh
>>>   tred dot-temp.gv > test.gv
>>>   dot -o test.pdf -Tpdf test.gv
>>>   open test.pdf
>>> #+end_src
>>>
>>> The graph is just what I want, but I can't see how to automate the
>>> process in Org-mode.  In particular, the tred step trips me up.  Do I
>>> have to make babel, tred-aware?
>>
>> Sorry if I misunderstand, but could you be more explicit (for me) on what the
>> problem is?  Why is it a problem for you to have that sh block inside your
>> Org. It is executed automagically upon exporting, no?  If yes, why is that 
>> not
>> good enough?
>>
>> Best regards,
>>   Seb
>
> Aloha Seb,
>
> Yes, babel is working fine and the sh block does its job.
>
> The problem is that I like to see intermediate results in the Org-mode
> file and the sh block works instead with files that reside outside Org-mode.
>
> In this particular case, I'd prefer to have dot-temp.gv in a results
> block in the Org-mode file, and then pass this results block into a
> source code block where tred can manipulate it, and which returns its
> results to the Org-mode file.
>
> That way, the skeptical inquirer need only consult the Org-mode file to
> be convinced that tred removed the transitive relations from the
> digraph.  It would be an easy matter to compare the two results blocks.
>
> All the best,
> Tom

Hi Tom,

Maybe rather than saving the output of your python block to an external
file you could save it into the Org-mode file, into a results block
named e.g., "dot-temp", and then you could do the following in your sh
code block...

#+begin_src sh :var body=dot-temp
  echo $dot-temp > dot-temp.gv 
  tred dot-temp.gv > test.gv
  dot -o test.pdf -Tpdf test.gv
  rm dot-temp.gv
  open test.pdf
#+end_src

Hope this helps -- Eric

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/