Clojure Plotting to Org inline image in ob-clojure

ID: c63620be-3661-443f-9251-faa7d4e3666d

I did some hard search, found some links

• https://stackoverflow.com/questions/840190/changing-the-current-working-directory-in-java
• https://stackoverflow.com/questions/19008592/java-change-file-working-directory

Then I found JVM does not allow to change working directory because of security reason https://bugs.java.com/bugdatabase/view_bug.do?bug_id=4045688.

So, there is no reliable way to do this in pure Java. Setting the user.dir property via System.setProperty() or java -Duser.dir=... does seem to affect subsequent creations of Files, but not e.g. FileOutputStreams.

ID: 0720a1e8-a039-48e5-8d49-c174b9f4cf64

Because changing Clojure/JVM working directory is not available, so I find method on Emacs side, Org-mode other Babel lanaguages like R, Python have good image file result support. So I dive into source code, and try to add similar function to "ob-clojure". But I found some limites, then I created "ob-clojure-literate (GitHub repo)" (Now it is in Org-mode contrib lib).

ID: cc6d0973-7a2a-4dfd-aa09-511142b0692c

You can fake change Clojure REPL working directory by passing header argument variable into Clojure code. Like this:

#+begin_src clojure :results value :var dir=(concat (file-name-directory (buffer-file-name)) "data/images/")
(str dir "ob-clojure-literate.png")
#+end_src

#+RESULTS[<2018-05-17 01:12:55> 73be0ca9a40a4f1e4fdee8e535991955f77b034a]:
: "/home/stardiviner/Org/Wiki/Computer Technology/Programming/Emacs/data/Emacs Packages/Org mode/data/images/ob-clojure-literate.png"

Then you can use Clojure funciton to save graphics object to target file with correct absolute path:

#+HEADERS: :var cwd=(concat (file-name-directory (buffer-file-name)) "data/images/")
#+begin_src clojure :results graphics file link :dir "data/images" :file "ob-clojure-literate.png"
(use '(incanter core stats datasets charts io pdf))
(def hist (histogram (sample-normal 1000)))
(save hist (str cwd "ob-clojure-literate.png"))
#+end_src

(use '(incanter core stats datasets charts io pdf))
(def hist (histogram (sample-normal 1000)))
(save hist (str cwd "ob-clojure-literate.png"))

ID: ac0e66d2-e034-45d4-907c-d10a0d413ff2

#+begin_src clojure :results graphics file link :dir "data/images" :file "ob-clojure-incanter-move.png" :var dir=(concat (file-name-directory (buffer-file-name)) "data/images/")
(use '(incanter core stats datasets charts io pdf))
(import '(java.io File))

(def hist (histogram (sample-normal 1000)))
(save hist "ob-clojure-incanter-move.png")
(.renameTo (File. "ob-clojure-incanter-move.png") (File. (str dir "ob-clojure-incanter-move.png")))
#+end_src

(use '(incanter core stats datasets charts io pdf))
(import '(java.io File))

(def hist (histogram (sample-normal 1000)))
(save hist "ob-clojure-incanter-move.png")
(.renameTo (File. "ob-clojure-incanter-move.png") (File. (str dir "ob-clojure-incanter-move.png")))