Hi,
I'm trying to update ob-awk.el to allow for code to be executed on remote
machines. This doesn't seem to work at present:
#+begin_src awk :dir /ssh:gpsc:data/rubus
END { print "I ran!"}
#+end_src
: awk: fatal: cannot open source file `/ssh:gpsc:/home/tys000/awk-oQ0Av9' for
reading: No such file : or directory
: [ Babel evaluation exited with code 2 ]
Digging through the code, particularly ~org-babel-execute:awk~ in the file
~ob-awk.el~, I think the issue is the code chunk is stored as a temporary file
on the remote machine, and then we try to run awk on the remote machine with
the path to the code file *relative to my local machine*. i.e.,
awk -f /ssh:gpsc:/home/tys000/awk-qSxjHH
I don't think Awk can process paths in this format in any case.
I've come up with a solution. Instead of saving the code to a temporary file,
we could just pass the code chunk as a string to awk. In the body of
~org-babel-execute:awk~ the awk command is constructed like this:
...
(list org-babel-awk-command
"-f" code-file cmd-line)
...
Where code-file is the path (a string) to the temporary file with the code in
it.
If I replace this with:
....
(list org-babel-awk-command
;;"-f" code-file
cmd-line (shell-quote-argument full-body)
...
The command we ask to run on the remote machine is:
awk END\ \{\ print\ \"I\ ran\!\"\}
My toy Awk program works as expected:
#+begin_src awk :dir /ssh:gpsc:data/rubus
END { print "I ran!"}
#+end_src
#+RESULTS:
: I ran!
After some limited testing, this seems to work. Does that sound like a good
approach?
If anyone wants to try this out I'd appreciate tests. The full function is
below.
- tyler
(defun org-babel-execute:awk (body params)
"Execute a block of Awk code BODY with org-babel.
PARAMS is a plist of src block parameters .
This function is called by `org-babel-execute-src-block'."
(let* ((result-params (cdr (assq :result-params params)))
(cmd-line (cdr (assq :cmd-line params)))
(in-file (cdr (assq :in-file params)))
(full-body (org-babel-expand-body:awk body params))
(code-file (let ((file (org-babel-temp-file "awk-")))
(with-temp-file file (insert full-body)) file))
(stdin (let ((stdin (cdr (assq :stdin params))))
(when stdin
(let ((tmp (org-babel-temp-file "awk-stdin-"))
(res (org-babel-ref-resolve stdin)))
(with-temp-file tmp
(insert (org-babel-awk-var-to-awk res)))
tmp))))
(cmd (mapconcat #'identity
(append
(list org-babel-awk-command
;;"-f" code-file
cmd-line (shell-quote-argument full-body))
(mapcar (lambda (pair)
(format "-v %s='%s'"
(car pair)
(org-babel-awk-var-to-awk
(cdr pair))))
(org-babel--get-vars params))
(list in-file))
" ")))
(org-babel-reassemble-table
(let ((results
(cond
(stdin (with-temp-buffer
(call-process-shell-command cmd stdin (current-buffer))
(buffer-string)))
(t (org-babel-eval cmd "")))))
(when results
(org-babel-result-cond result-params
results
(let ((tmp (org-babel-temp-file "awk-results-")))
(with-temp-file tmp (insert results))
(org-babel-import-elisp-from-file tmp)))))
(org-babel-pick-name
(cdr (assq :colname-names params)) (cdr (assq :colnames params)))
(org-babel-pick-name
(cdr (assq :rowname-names params)) (cdr (assq :rownames params))))))
--
plantarum.ca
