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Re: [O] babel work flow

From: Thomas S. Dye
Subject: Re: [O] babel work flow
Date: Fri, 15 Jul 2011 06:58:39 -1000

Eric Schulte <address@hidden> writes:

> 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

Aloha Eric,

With a few modifications I got exactly what I wanted.  Thanks!

This takes a valid dot digraph in a results block, runs it through tred
so transitive relations are removed, creates a pdf file, and then writes
the dot source produced by tred back to the Org-mode file.

 #+begin_src sh :var body=dot-digraph :results output raw
    echo $body > dot-temp.gv
    tred dot-temp.gv > dot-temp-tred.gv
    dot -o test.pdf -Tpdf dot-temp-tred.gv
    cat dot-temp-tred.gv
    rm dot-temp-tred.gv

All the best,

Thomas S. Dye

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