org-mode/lisp/ob-sh.el

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;;; ob-sh.el --- org-babel functions for shell evaluation
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;; Copyright (C) 2009, 2010 Free Software Foundation, Inc.
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;; Author: Eric Schulte
;; Keywords: literate programming, reproducible research
;; Homepage: http://orgmode.org
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;; Version: 7.4
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;; This file is part of GNU Emacs.
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;; GNU Emacs is free software: you can redistribute it and/or modify
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;; 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,
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;; 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.
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;; You should have received a copy of the GNU General Public License
;; along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>.
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;;; Commentary:
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;; Org-Babel support for evaluating shell source code.
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;;; Code:
(require 'ob)
(require 'ob-comint)
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(require 'ob-eval)
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(require 'shell)
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(eval-when-compile (require 'cl))
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(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))
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(defvar org-babel-default-header-args:sh '())
(defvar org-babel-sh-command "sh"
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"Command used to invoke a shell.
This will be passed to `shell-command-on-region'")
(defun org-babel-execute:sh (body params)
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"Execute a block of Shell commands with Babel.
This function is called by `org-babel-execute-src-block'."
babel:removing calls to ob-process-params, and updating use of results * lisp/ob-C.el (org-babel-C-execute): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-R.el (org-babel-execute:R): removing call to org-babel-process-params which should no longer be called from within a language file (org-babel-R-variable-assignments): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-asymptote.el (org-babel-execute:asymptote): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-clojure.el (org-babel-execute:clojure): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-dot.el (org-babel-execute:dot): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-emacs-lisp.el (org-babel-expand-body:emacs-lisp): removing call to org-babel-process-params which should no longer be called from within a language file (org-babel-execute:emacs-lisp): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-haskell.el (org-babel-execute:haskell): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-js.el (org-babel-execute:js): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-lisp.el (org-babel-execute:lisp): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-ocaml.el (org-babel-execute:ocaml): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-octave.el (org-babel-execute:octave): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-perl.el (org-babel-execute:perl): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-python.el (org-babel-execute:python): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-ruby.el (org-babel-execute:ruby): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-scheme.el (org-babel-execute:scheme): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-screen.el (org-babel-execute:screen): removing call to org-babel-process-params which should no longer be called from within a language file (org-babel-prep-session:screen): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-sh.el (org-babel-execute:sh): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-sql.el (org-babel-execute:sql): removing call to org-babel-process-params which should no longer be called from within a language file * ob-haskell.el (org-babel-execute:haskell): Remove reference to processed params * ob-clojure.el (org-babel-execute:clojure): Remove reference to processed params * ob-R.el (org-babel-execute:R): Remove reference to processed params
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(let* ((session (org-babel-sh-initiate-session
(cdr (assoc :session params))))
(result-params (cdr (assoc :result-params params)))
(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-pick-name
babel:removing calls to ob-process-params, and updating use of results * lisp/ob-C.el (org-babel-C-execute): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-R.el (org-babel-execute:R): removing call to org-babel-process-params which should no longer be called from within a language file (org-babel-R-variable-assignments): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-asymptote.el (org-babel-execute:asymptote): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-clojure.el (org-babel-execute:clojure): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-dot.el (org-babel-execute:dot): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-emacs-lisp.el (org-babel-expand-body:emacs-lisp): removing call to org-babel-process-params which should no longer be called from within a language file (org-babel-execute:emacs-lisp): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-haskell.el (org-babel-execute:haskell): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-js.el (org-babel-execute:js): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-lisp.el (org-babel-execute:lisp): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-ocaml.el (org-babel-execute:ocaml): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-octave.el (org-babel-execute:octave): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-perl.el (org-babel-execute:perl): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-python.el (org-babel-execute:python): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-ruby.el (org-babel-execute:ruby): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-scheme.el (org-babel-execute:scheme): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-screen.el (org-babel-execute:screen): removing call to org-babel-process-params which should no longer be called from within a language file (org-babel-prep-session:screen): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-sh.el (org-babel-execute:sh): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-sql.el (org-babel-execute:sql): removing call to org-babel-process-params which should no longer be called from within a language file * ob-haskell.el (org-babel-execute:haskell): Remove reference to processed params * ob-clojure.el (org-babel-execute:clojure): Remove reference to processed params * ob-R.el (org-babel-execute:R): Remove reference to processed params
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(cdr (assoc :colname-names params)) (cdr (assoc :colnames params)))
(org-babel-pick-name
babel:removing calls to ob-process-params, and updating use of results * lisp/ob-C.el (org-babel-C-execute): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-R.el (org-babel-execute:R): removing call to org-babel-process-params which should no longer be called from within a language file (org-babel-R-variable-assignments): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-asymptote.el (org-babel-execute:asymptote): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-clojure.el (org-babel-execute:clojure): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-dot.el (org-babel-execute:dot): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-emacs-lisp.el (org-babel-expand-body:emacs-lisp): removing call to org-babel-process-params which should no longer be called from within a language file (org-babel-execute:emacs-lisp): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-haskell.el (org-babel-execute:haskell): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-js.el (org-babel-execute:js): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-lisp.el (org-babel-execute:lisp): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-ocaml.el (org-babel-execute:ocaml): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-octave.el (org-babel-execute:octave): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-perl.el (org-babel-execute:perl): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-python.el (org-babel-execute:python): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-ruby.el (org-babel-execute:ruby): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-scheme.el (org-babel-execute:scheme): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-screen.el (org-babel-execute:screen): removing call to org-babel-process-params which should no longer be called from within a language file (org-babel-prep-session:screen): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-sh.el (org-babel-execute:sh): removing call to org-babel-process-params which should no longer be called from within a language file * lisp/ob-sql.el (org-babel-execute:sql): removing call to org-babel-process-params which should no longer be called from within a language file * ob-haskell.el (org-babel-execute:haskell): Remove reference to processed params * ob-clojure.el (org-babel-execute:clojure): Remove reference to processed params * ob-R.el (org-babel-execute:R): Remove reference to processed params
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(cdr (assoc :rowname-names params)) (cdr (assoc :rownames params))))))
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(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)))
removing obsoleted optional third argument from org-babel-expand-body:LANG * lisp/ob-C.el (org-babel-expand-body:c++): removing obsoleted optional third argument (org-babel-expand-body:c++): removing obsoleted optional third argument (org-babel-C-expand): removing obsoleted optional third argument * lisp/ob-R.el: (org-babel-expand-body:R): removing obsoleted optional third argument (org-babel-execute:R): removing obsoleted optional third argument (org-babel-R-variable-assignments): removing obsoleted optional third argument * lisp/ob-asymptote.el: (org-babel-expand-body:asymptote): removing obsoleted optional third argument (org-babel-execute:asymptote): removing obsoleted optional third argument * lisp/ob-clojure.el: (org-babel-expand-body:clojure): removing obsoleted optional third argument (org-babel-execute:clojure): removing obsoleted optional third argument * lisp/ob-css.el: (org-babel-expand-body:css): removing obsoleted optional third argument * lisp/ob-ditaa.el: (org-babel-expand-body:ditaa): removing obsoleted optional third argument * lisp/ob-dot.el: (org-babel-expand-body:dot): removing obsoleted optional third argument (org-babel-execute:dot): removing obsoleted optional third argument * lisp/ob-emacs-lisp.el: (org-babel-expand-body:emacs-lisp): removing obsoleted optional third argument (org-babel-execute:emacs-lisp): removing obsoleted optional third argument * lisp/ob-gnuplot.el: (org-babel-expand-body:gnuplot): removing obsoleted optional third argument * lisp/ob-haskell.el: (org-babel-expand-body:haskell): removing obsoleted optional third argument (org-babel-execute:haskell): removing obsoleted optional third argument (org-babel-load-session:haskell): removing obsoleted optional third (org-babel-prep-session:haskell): removing obsoleted optional third * lisp/ob-js.el: (org-babel-expand-body:js): removing obsoleted optional third argument (org-babel-execute:js): removing obsoleted optional third argument * lisp/ob-latex.el: (org-babel-expand-body:latex): removing obsoleted optional third argument * lisp/ob-lisp.el: (org-babel-expand-body:lisp): removing obsoleted optional third argument (org-babel-execute:lisp): removing obsoleted optional third argument * lisp/ob-mscgen.el: (org-babel-expand-body:mscgen): removing obsoleted optional third argument * lisp/ob-ocaml.el: (org-babel-expand-body:ocaml): removing obsoleted optional third argument (org-babel-execute:ocaml): removing obsoleted optional third argument * lisp/ob-octave.el: (org-babel-expand-body:matlab): removing obsoleted optional third argument (org-babel-expand-body:octave): removing obsoleted optional third argument (org-babel-execute:octave): removing obsoleted optional third argument (org-babel-octave-variable-assignments): removing obsoleted optional third * lisp/ob-org.el: (org-babel-expand-body:org): removing obsoleted optional third argument * lisp/ob-perl.el: (org-babel-expand-body:perl): removing obsoleted optional third argument (org-babel-execute:perl): removing obsoleted optional third argument * lisp/ob-plantuml.el: (org-babel-expand-body:plantuml): removing obsoleted optional third argument * lisp/ob-python.el: (org-babel-expand-body:python): removing obsoleted optional third argument (org-babel-execute:python): removing obsoleted optional third argument (org-babel-python-variable-assignments): removing obsoleted optional third * lisp/ob-ruby.el: (org-babel-expand-body:ruby): removing obsoleted optional third argument (org-babel-execute:ruby): removing obsoleted optional third argument * lisp/ob-sass.el: (org-babel-expand-body:sass): removing obsoleted optional third argument * lisp/ob-scheme.el: (org-babel-expand-body:scheme): removing obsoleted optional third argument (org-babel-execute:scheme): removing obsoleted optional third argument * lisp/ob-screen.el: (org-babel-expand-body:screen): removing obsoleted optional third argument * lisp/ob-sh.el: (org-babel-expand-body:sh): removing obsoleted optional third argument (org-babel-execute:sh): removing obsoleted optional third argument (org-babel-sh-variable-assignments): removing obsoleted optional third * lisp/ob-sql.el: (org-babel-expand-body:sql): removing obsoleted optional third argument * lisp/ob-sqlite.el: (org-babel-expand-body:sqlite): removing obsoleted optional third argument (org-babel-execute:sqlite): removing obsoleted optional third argument * lisp/ob.el: (org-babel-expand-body:generic): removing obsoleted optional third argument
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(mapcar #'cdr (org-babel-get-header params :var)))))
(defun org-babel-sh-var-to-sh (var &optional sep)
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"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."
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(if (listp var)
(flet ((deep-string (el)
(if (listp el)
(mapcar #'deep-string el)
(org-babel-sh-var-to-sh el sep))))
(format "$(cat <<'BABEL_TABLE'\n%s\nBABEL_TABLE\n)"
(orgtbl-to-generic
(deep-string (if (listp (car var)) var (list var)))
(list :sep (or sep "\t")))))
(if (stringp var)
(if (string-match "[ \t\n\r]" var)
(format "$(cat <<BABEL_STRING\n%s\nBABEL_STRING\n)" var)
(format "%s" var))
(format "%S" var))))
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(defun org-babel-sh-table-or-results (results)
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"Convert RESULTS to an appropriate elisp value.
If the results look like a table, then convert them into an
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Emacs-lisp table, otherwise return the results as a string."
(org-babel-script-escape results))
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(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'"
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"String to indicate that evaluation has completed.")
(defvar org-babel-sh-eoe-output "org_babel_sh_eoe"
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"String to indicate that evaluation has completed.")
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(defun org-babel-sh-evaluate (session body &optional result-params)
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"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."
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((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)))))
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(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"))))
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(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)
;; arch-tag: 416dd531-c230-4b0a-a5bf-8d948f990f2d
;;; ob-sh.el ends here