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From: edgar@openmail.cc
To: emacs-orgmode@gnu.org
Subject: How to call nested bash and gnuplot with babel?
Date: Fri, 25 Aug 2017 03:26:58 +0000	[thread overview]
Message-ID: <8df2f105af6682485733fe21a879feb4@openmail.cc> (raw)

Hello, I am trying to run a "nested" babel code with bash and gnuplot.

* Configuration
I did the test like this
#+BEGIN_SRC bash
   emacs -Q
#+END_SRC

#+BEGIN_SRC emacs-lisp
   (require 'package)
   (package-initialize)

   (require 'org)
   ;; Org mode version 9.0.9

   (org-babel-do-load-languages ; babel, for executing
      'org-babel-load-languages   ; code in org-mode.
      '((shell . t)
        (python . t)
        (emacs-lisp . t)
        (org . t)
        (gnuplot . t)))
#+END_SRC

* Original code
#+NAME: bash-tjp-displ-stress
#+HEADER: :var file1="file1.csv"
#+HEADER: :var col1="3"
#+HEADER: :var file2="file2.csv"
#+HEADER: :var col2="7"
#+HEADER: :dir "Data"
#+BEGIN_SRC bash :results value :exports code
   paste "$file1" "$file2" | awk -F',' '/^[^#]/{print $'$col1' $'$col2'}'
#+END_SRC

#+NAME: gplt-tjp-febio-results
#+CAPTION: Gnuplot to plot
#+HEADER: :var data=bash-tjp-displ-stress
#+BEGIN_SRC gnuplot :results graphics :file /tmp/orig-out.png
   set xlabel 'var1'
   set ylabel 'var2'
   plot data u ($1 + 1):2 with lp notitle
#+END_SRC

** Alternative 1: ~:file~ after the function
  The result of this gives me the original output file
  #+CALL: gplt-tjp-febio-results() :file /tmp/test.png

  #+RESULTS:
  [[file:/tmp/orig-out.png]]

** Alternative 2: ~:file~ as a prefix to the function
  The result of this gives me the original output file
  #+CALL: gplt-tjp-febio-results[:file /tmp/test.png]()

  #+RESULTS:
  [[file:/tmp/orig-out.png]]

* Modified code
If I do this, I get the desired output file (add variable ~outfile~
and ~:results none~)

#+NAME: gplt-tjp-febio-results-new
#+CAPTION: Gnuplot to plot
#+HEADER: :var data=bash-tjp-displ-stress
#+HEADER: :var outfile="/tmp/test.png"
#+BEGIN_SRC gnuplot :results graphics
   set output outfile
   set xlabel 'var1'
   set ylabel 'var2'
   plot data u ($1 + 1):2 with lp notitle
#+END_SRC

#+CALL: gplt-tjp-febio-results-new[:results 
none](outfile="/tmp/new_out.png")

I type this manually:
[[/tmp/new_out.png]]

* What I expected
To call
#+BEGIN_EXAMPLE
   ,#+CALL: gplt-tjp-febio-results() :file /tmp/new_out.png
#+END_EXAMPLE

and get
#+BEGIN_EXAMPLE
   ,#+RESULTS:
   [[file:/tmp/orig-out.png]]
#+END_EXAMPLE

How do I achieve this?

* Thanks
Thank you! :D

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                 reply	other threads:[~2017-08-25 16:06 UTC|newest]

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