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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
#+end_src
All the best,
Tom
--
Thomas S. Dye
http://www.tsdye.com