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| | ;;; ob-sh.el --- org-babel functions for shell evaluation
;; Copyright (C) 2009-2013 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))
(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))
(defvar org-babel-default-header-args:sh '())
(defvar org-babel-sh-command "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))))
(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 params stdin)
(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:sh (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:sh 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:sh (session body params)
"Load BODY into SESSION."
(save-window-excursion
(let ((buffer (org-babel-prep-session:sh 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 (params)
"Return list of shell statements assigning the block's variables."
(let ((sep (cdr (assoc :separator params))))
(mapcar
(lambda (pair)
(format "%s=%s"
(car pair)
(org-babel-sh-var-to-sh (cdr pair) sep)))
(mapcar #'cdr (org-babel-get-header params :var)))))
(defun org-babel-sh-var-to-sh (var &optional sep)
"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."
(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.
If the results look like a table, then convert them into an
Emacs-lisp table, otherwise return the results as a string."
(org-babel-script-escape results))
(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) (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)
"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
(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."
(while (string-match "^% +[\r\n$]+ *" string)
(setq string (substring string (match-end 0))))
string)
(provide 'ob-sh)
;;; ob-sh.el ends here
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