;;; ob-shell.el --- org-babel functions for shell evaluation
;; Copyright (C) 2009-2016 Free Software Foundation, Inc.
;; Author: Eric Schulte
;; Keywords: literate programming, reproducible research
;; Homepage: http://orgmode.org
;; This file is part of GNU Emacs.
;; GNU Emacs is free software: you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation, either version 3 of the License, or
;; (at your option) any later version.
;; GNU Emacs is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;; GNU General Public License for more details.
;; You should have received a copy of the GNU General Public License
;; along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>.
;;; Commentary:
;; Org-Babel support for evaluating shell source code.
;;; Code:
(require 'ob)
(require 'shell)
(eval-when-compile (require 'cl))
(declare-function org-babel-comint-in-buffer "ob-comint" (buffer &rest body)
t)
(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)
t)
(declare-function orgtbl-to-generic "org-table" (table params))
(defvar org-babel-default-header-args:shell '())
(defcustom org-babel-shell-names
'("sh" "bash" "csh" "ash" "dash" "ksh" "mksh" "posh")
"List of names of shell supported by babel shell code blocks."
:group 'org-babel
:type 'string
:initialize
(lambda (symbol value)
(set-default symbol (second value))
(mapc
(lambda (name)
(eval `(defun ,(intern (concat "org-babel-execute:" name)) (body params)
,(format "Execute a block of %s commands with Babel." name)
(let ((shell-file-name ,name))
(org-babel-execute:shell body params)))))
(second value))))
(defun org-babel-execute:shell (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))))
(stdin (let ((stdin (cdr (assoc :stdin params))))
(when stdin (org-babel-sh-var-to-string
(org-babel-ref-resolve stdin)))))
(cmdline (cdr (assoc :cmdline params)))
(full-body (org-babel-expand-body:generic
body params (org-babel-variable-assignments:shell params))))
(org-babel-reassemble-table
(org-babel-sh-evaluate session full-body params stdin cmdline)
(org-babel-pick-name
(cdr (assoc :colname-names params)) (cdr (assoc :colnames params)))
(org-babel-pick-name
(cdr (assoc :rowname-names params)) (cdr (assoc :rownames params))))))
(defun org-babel-prep-session:shell (session params)
"Prepare SESSION according to the header arguments specified in PARAMS."
(let* ((session (org-babel-sh-initiate-session session))
(var-lines (org-babel-variable-assignments:shell params)))
(org-babel-comint-in-buffer session
(mapc (lambda (var)
(insert var) (comint-send-input nil t)
(org-babel-comint-wait-for-output session)) var-lines))
session))
(defun org-babel-load-session:shell (session body params)
"Load BODY into SESSION."
(save-window-excursion
(let ((buffer (org-babel-prep-session:shell session params)))
(with-current-buffer buffer
(goto-char (process-mark (get-buffer-process (current-buffer))))
(insert (org-babel-chomp body)))
buffer)))
;; helper functions
(defun org-babel-variable-assignments:sh-generic
(varname values &optional sep hline)
"Returns a list of statements declaring the values as a generic variable."
(format "%s=%s" varname (org-babel-sh-var-to-sh values sep hline)))
(defun org-babel-variable-assignments:bash_array
(varname values &optional sep hline)
"Returns a list of statements declaring the values as a bash array."
(format "unset %s\ndeclare -a %s=( %s )"
varname varname
(mapconcat
(lambda (value) (org-babel-sh-var-to-sh value sep hline))
values
" ")))
(defun org-babel-variable-assignments:bash_assoc
(varname values &optional sep hline)
"Returns a list of statements declaring the values as bash associative array."
(format "unset %s\ndeclare -A %s\n%s"
varname varname
(mapconcat
(lambda (items)
(format "%s[%s]=%s"
varname
(org-babel-sh-var-to-sh (car items) sep hline)
(org-babel-sh-var-to-sh (cdr items) sep hline)))
values
"\n")))
(defun org-babel-variable-assignments:bash (varname values &optional sep hline)
"Represents the parameters as useful Bash shell variables."
(if (listp values)
(if (and (listp (car values)) (= 1 (length (car values))))
(org-babel-variable-assignments:bash_array varname values sep hline)
(org-babel-variable-assignments:bash_assoc varname values sep hline))
(org-babel-variable-assignments:sh-generic varname values sep hline)))
(defun org-babel-variable-assignments:shell (params)
"Return list of shell statements assigning the block's variables."
(let ((sep (cdr (assoc :separator params)))
(hline (when (string= "yes" (cdr (assoc :hlines params)))
(or (cdr (assoc :hline-string params))
"hline"))))
(mapcar
(lambda (pair)
(if (string-match "bash$" shell-file-name)
(org-babel-variable-assignments:bash
(car pair) (cdr pair) sep hline)
(org-babel-variable-assignments:sh-generic
(car pair) (cdr pair) sep hline)))
(mapcar #'cdr (org-babel-get-header params :var)))))
(defun org-babel-sh-var-to-sh (var &optional sep hline)
"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."
(concat "'" (replace-regexp-in-string
"'" "'\"'\"'"
(org-babel-sh-var-to-string var sep hline))
"'"))
(defun org-babel-sh-var-to-string (var &optional sep hline)
"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
:hline hline)))
((listp var)
(mapconcat echo-var var "\n"))
(t (funcall echo-var var)))))
(defun org-babel-sh-initiate-session (&optional session params)
"Initiate a session named SESSION according to PARAMS."
(when (and session (not (string= session "none")))
(save-window-excursion
(or (org-babel-comint-buffer-livep session)
(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 params stdin cmdline)
"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."
(let ((results
(cond
((or stdin cmdline) ; 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 (or stdin "")))
(with-temp-buffer
(call-process-shell-command
(concat (if shebang script-file
(format "%s %s" shell-file-name script-file))
(and cmdline (concat " " cmdline)))
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 shell-file-name (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."
(while (string-match "^% +[\r\n$]+ *" string)
(setq string (substring string (match-end 0))))
string)
(provide 'ob-shell)
;;; ob-shell.el ends here