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I am experiencing a very strange behavior with org-babel code blocks. When I operate without the :session tag, I am free to use :dir to set my working directory. As you can see, the following code runs as expected:

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but if I now add a :session argument, babel ignores my :dir tag and instead returns my default working directory:

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What am I doing wrong?

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    Please do not include text as images: you can cut and paste it into the question instead and use code formatting.
    – NickD
    Apr 19 '20 at 18:16
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You are doing nothing wrong, but a :dir header arg will not affect an existing session. If you kill the existing session and then re-evaluate the source block, the current directory should be the one you specified in the header-arg property.

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  • Ah, you are right! Well I definitely don't want the code to just fail silently. But I can see how switching the working directory for an existing session might be problematic. Perhaps a prompt in the minibuffer would be best. Something like "Do you really want to change the working directory of an existing R session? [Y/n]"
    – Adam
    Apr 19 '20 at 22:58
  • It's not failing. It just doesn't see the :dir argument at all. When there is a session, the code block is executed by sending all the commands in the code block to the session: that's all. The header args are used to set up the session in the first place: after that, they are not used again.
    – NickD
    Apr 20 '20 at 1:20
  • I probably should have said "Some header args (like :session or :dir) are used to set up the session...". There are header args (like :results) that are used by org-babel to format the results that it retrieves from the session and those are used every time the code block is executed.
    – NickD
    Apr 20 '20 at 1:57
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After several days of hacking my way through eLisp, I may have a working solution. The following code automatically sets the working directory of whichever R process is frontmost to match the :dir value of whichever org-babel R block you are working from.

So suppose you manage all of your R projects from a single studies.org file, where each header represents a new project. Your org file may look something like this:

* Study 1
  :PROPERTIES:
  :header-args: :dir ~/org/studies/study_1
  :END:

  #+BEGIN_SRC R :session *R*
  getwd()
  #+END_SRC

* Study 2
* Study 3
  ...
* Study n

If you are working on a code in Study 1, you don't want your output saved to a project folder for Studies 2 or your data loaded from a csv from Study 3 (which is entirely possible under the default configuration).

The following code is intended to do something about this:

;; Get :dir
(defun org-header-arg (p)
  (setq args (org-babel-get-src-block-info))
  (assoc-default p (nth 2 args)))

;; Get language of source block
(defun get-src-language ()
  (setq args (org-babel-get-src-block-info))
  (nth 0 args))

;; Send message to R process
(defun send-msg-r (w)
  (ess-send-string 
   (get-process "R")
   (format "setwd(\"%s\")" w)))

;; If point is in an R code block then if R is running: setwd()
;; Else if R is not running, run R and setwd().  
(defun setwd-dir ()
  (if (string= (get-src-language) "R")
      (if (eq (get-process "R") nil)
      (progn 
        (setq w (org-header-arg :dir)) ;; Capture before R redirects
        (defadvice R (after set-working-dir-R activate) (send-msg-r w))
        (save-excursion (R)))
    (send-msg-r (org-header-arg :dir)))))

;; Advise org-edit-special
(defadvice org-edit-special (before set-working-dir activate)
  (setwd-dir))

;; Advise org-babel-execute-src-block
(defadvice org-babel-execute-src-block (before set-working-dir-b activate) 
  (setwd-dir))
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