;;; ob-sh.el --- org-babel functions for shell evaluation
-;; Copyright (C) 2009-2011 Free Software Foundation, Inc.
+;; Copyright (C) 2009-2016 Free Software Foundation, Inc.
;; Author: Eric Schulte
;; Keywords: literate programming, reproducible research
;; Homepage: http://orgmode.org
-;; Version: 7.4
;; This file is part of GNU Emacs.
;;; Code:
(require 'ob)
-(require 'ob-comint)
-(require 'ob-eval)
(require 'shell)
(eval-when-compile (require 'cl))
-(declare-function org-babel-comint-in-buffer "ob-comint" (buffer &rest body))
(declare-function org-babel-comint-wait-for-output "ob-comint" (buffer))
(declare-function org-babel-comint-buffer-livep "ob-comint" (buffer))
-(declare-function org-babel-comint-with-output "ob-comint" (meta &rest body))
-(declare-function orgtbl-to-generic "org-table" (table params))
+(declare-function orgtbl-to-generic "org-table"
+ (table params &optional backend))
(defvar org-babel-default-header-args:sh '())
"Command used to invoke a shell.
This will be passed to `shell-command-on-region'")
+(defcustom org-babel-sh-var-quote-fmt
+ "$(cat <<'BABEL_TABLE'\n%s\nBABEL_TABLE\n)"
+ "Format string used to escape variables when passed to shell scripts."
+ :group 'org-babel
+ :type 'string)
+
(defun org-babel-execute:sh (body params)
"Execute a block of Shell commands with Babel.
This function is called by `org-babel-execute-src-block'."
(let* ((session (org-babel-sh-initiate-session
(cdr (assoc :session params))))
- (result-params (cdr (assoc :result-params params)))
+ (stdin (let ((stdin (cdr (assoc :stdin params))))
+ (when stdin (org-babel-sh-var-to-string
+ (org-babel-ref-resolve stdin)))))
(full-body (org-babel-expand-body:generic
body params (org-babel-variable-assignments:sh params))))
(org-babel-reassemble-table
- (org-babel-sh-evaluate session full-body result-params)
+ (org-babel-sh-evaluate session full-body params stdin)
(org-babel-pick-name
(cdr (assoc :colname-names params)) (cdr (assoc :colnames params)))
(org-babel-pick-name
;; helper functions
(defun org-babel-variable-assignments:sh (params)
- "Return list of shell statements assigning the block's variables"
+ "Return list of shell statements assigning the block's variables."
(let ((sep (cdr (assoc :separator params))))
(mapcar
(lambda (pair)
"Convert an elisp value to a shell variable.
Convert an elisp var into a string of shell commands specifying a
var of the same value."
- (if (listp var)
- (flet ((deep-string (el)
- (if (listp el)
- (mapcar #'deep-string el)
- (org-babel-sh-var-to-sh el sep))))
- (format "$(cat <<'BABEL_TABLE'\n%s\nBABEL_TABLE\n)"
- (orgtbl-to-generic
- (deep-string (if (listp (car var)) var (list var)))
- (list :sep (or sep "\t")))))
- (if (stringp var)
- (if (string-match "[\n\r]" var)
- (format "$(cat <<BABEL_STRING\n%s\nBABEL_STRING\n)" var)
- (format "%s" var))
- (format "%S" var))))
+ (format org-babel-sh-var-quote-fmt (org-babel-sh-var-to-string var sep)))
+
+(defun org-babel-sh-var-to-string (var &optional sep)
+ "Convert an elisp value to a string."
+ (let ((echo-var (lambda (v) (if (stringp v) v (format "%S" v)))))
+ (cond
+ ((and (listp var) (or (listp (car var)) (equal (car var) 'hline)))
+ (orgtbl-to-generic var (list :sep (or sep "\t") :fmt echo-var)))
+ ((listp var)
+ (mapconcat echo-var var "\n"))
+ (t (funcall echo-var var)))))
(defun org-babel-sh-table-or-results (results)
"Convert RESULTS to an appropriate elisp value.
(when (and session (not (string= session "none")))
(save-window-excursion
(or (org-babel-comint-buffer-livep session)
- (progn (shell session) (get-buffer (current-buffer)))))))
+ (progn
+ (shell session)
+ ;; Needed for Emacs 23 since the marker is initially
+ ;; undefined and the filter functions try to use it without
+ ;; checking.
+ (set-marker comint-last-output-start (point))
+ (get-buffer (current-buffer)))))))
(defvar org-babel-sh-eoe-indicator "echo 'org_babel_sh_eoe'"
"String to indicate that evaluation has completed.")
(defvar org-babel-sh-eoe-output "org_babel_sh_eoe"
"String to indicate that evaluation has completed.")
-(defun org-babel-sh-evaluate (session body &optional result-params)
+(defun org-babel-sh-evaluate (session body &optional params stdin)
"Pass BODY to the Shell process in BUFFER.
If RESULT-TYPE equals 'output then return a list of the outputs
of the statements in BODY, if RESULT-TYPE equals 'value then
return the value of the last statement in BODY."
- ((lambda (results)
- (when results
- (if (or (member "scalar" result-params)
- (member "output" result-params))
- results
- (let ((tmp-file (org-babel-temp-file "sh-")))
- (with-temp-file tmp-file (insert results))
- (org-babel-import-elisp-from-file tmp-file)))))
- (if (not session)
- (org-babel-eval org-babel-sh-command (org-babel-trim body))
- (mapconcat
- #'org-babel-sh-strip-weird-long-prompt
- (mapcar
- #'org-babel-trim
- (butlast
- (org-babel-comint-with-output
- (session org-babel-sh-eoe-output t body)
- (mapc
- (lambda (line)
- (insert line) (comint-send-input nil t) (sleep-for 0.25))
- (append
- (split-string (org-babel-trim body) "\n")
- (list org-babel-sh-eoe-indicator))))
- 2)) "\n"))))
+ (let ((results
+ (cond
+ (stdin ; external shell script w/STDIN
+ (let ((script-file (org-babel-temp-file "sh-script-"))
+ (stdin-file (org-babel-temp-file "sh-stdin-"))
+ (shebang (cdr (assoc :shebang params)))
+ (padline (not (string= "no" (cdr (assoc :padline params))))))
+ (with-temp-file script-file
+ (when shebang (insert (concat shebang "\n")))
+ (when padline (insert "\n"))
+ (insert body))
+ (set-file-modes script-file #o755)
+ (with-temp-file stdin-file (insert stdin))
+ (with-temp-buffer
+ (call-process-shell-command
+ (if shebang
+ script-file
+ (format "%s %s" org-babel-sh-command script-file))
+ stdin-file
+ (current-buffer))
+ (buffer-string))))
+ (session ; session evaluation
+ (mapconcat
+ #'org-babel-sh-strip-weird-long-prompt
+ (mapcar
+ #'org-babel-trim
+ (butlast
+ (org-babel-comint-with-output
+ (session org-babel-sh-eoe-output t body)
+ (mapc
+ (lambda (line)
+ (insert line)
+ (comint-send-input nil t)
+ (while (save-excursion
+ (goto-char comint-last-input-end)
+ (not (re-search-forward
+ comint-prompt-regexp nil t)))
+ (accept-process-output
+ (get-buffer-process (current-buffer)))))
+ (append
+ (split-string (org-babel-trim body) "\n")
+ (list org-babel-sh-eoe-indicator))))
+ 2)) "\n"))
+ ('otherwise ; external shell script
+ (if (and (cdr (assoc :shebang params))
+ (> (length (cdr (assoc :shebang params))) 0))
+ (let ((script-file (org-babel-temp-file "sh-script-"))
+ (shebang (cdr (assoc :shebang params)))
+ (padline (not (equal "no" (cdr (assoc :padline params))))))
+ (with-temp-file script-file
+ (when shebang (insert (concat shebang "\n")))
+ (when padline (insert "\n"))
+ (insert body))
+ (set-file-modes script-file #o755)
+ (org-babel-eval script-file ""))
+ (org-babel-eval org-babel-sh-command (org-babel-trim body)))))))
+ (when results
+ (let ((result-params (cdr (assoc :result-params params))))
+ (org-babel-result-cond result-params
+ results
+ (let ((tmp-file (org-babel-temp-file "sh-")))
+ (with-temp-file tmp-file (insert results))
+ (org-babel-import-elisp-from-file tmp-file)))))))
(defun org-babel-sh-strip-weird-long-prompt (string)
"Remove prompt cruft from a string of shell output."
(provide 'ob-sh)
+
;;; ob-sh.el ends here