;;; ob-eval.el --- org-babel functions for external code evaluation
-;; Copyright (C) 2009-2013 Free Software Foundation, Inc.
+;; Copyright (C) 2009-2015 Free Software Foundation, Inc.
;; Author: Eric Schulte
;; Keywords: literate programming, reproducible research, comint
;; shell commands.
;;; Code:
+(require 'org-macs)
(eval-when-compile (require 'cl))
(defvar org-babel-error-buffer-name "*Org-Babel Error Output*")
+(declare-function org-babel-temp-file "ob-core" (prefix &optional suffix))
(defun org-babel-eval-error-notify (exit-code stderr)
"Open a buffer to display STDERR and a message with the value of EXIT-CODE."
(with-temp-buffer
(insert body)
(setq exit-code
- (org-babel-shell-command-on-region
- (point-min) (point-max) cmd t 'replace err-buff))
+ (org-babel--shell-command-on-region
+ (point-min) (point-max) cmd err-buff))
(if (or (not (numberp exit-code)) (> exit-code 0))
(progn
(with-current-buffer err-buff
(with-temp-buffer (insert-file-contents file)
(buffer-string)))
-(defun org-babel-shell-command-on-region (start end command
- &optional output-buffer replace
- error-buffer display-error-buffer)
+(defun org-babel--shell-command-on-region (start end command error-buffer)
"Execute COMMAND in an inferior shell with region as input.
-Fixes bugs in the emacs 23.1.1 version of `shell-command-on-region'
-
-Normally display output (if any) in temp buffer `*Shell Command Output*';
-Prefix arg means replace the region with it. Return the exit code of
-COMMAND.
-
-To specify a coding system for converting non-ASCII characters in
-the input and output to the shell command, use
-\\[universal-coding-system-argument] before this command. By
-default, the input (from the current buffer) is encoded in the
-same coding system that will be used to save the file,
-`buffer-file-coding-system'. If the output is going to replace
-the region, then it is decoded from that same coding system.
-
-The noninteractive arguments are START, END, COMMAND,
-OUTPUT-BUFFER, REPLACE, ERROR-BUFFER, and DISPLAY-ERROR-BUFFER.
-Noninteractive callers can specify coding systems by binding
-`coding-system-for-read' and `coding-system-for-write'.
-
-If the command generates output, the output may be displayed
-in the echo area or in a buffer.
-If the output is short enough to display in the echo area
-\(determined by the variable `max-mini-window-height' if
-`resize-mini-windows' is non-nil), it is shown there. Otherwise
-it is displayed in the buffer `*Shell Command Output*'. The output
-is available in that buffer in both cases.
-
-If there is output and an error, a message about the error
-appears at the end of the output.
-
-If there is no output, or if output is inserted in the current buffer,
-then `*Shell Command Output*' is deleted.
-
-If the optional fourth argument OUTPUT-BUFFER is non-nil,
-that says to put the output in some other buffer.
-If OUTPUT-BUFFER is a buffer or buffer name, put the output there.
-If OUTPUT-BUFFER is not a buffer and not nil,
-insert output in the current buffer.
-In either case, the output is inserted after point (leaving mark after it).
-
-If REPLACE, the optional fifth argument, is non-nil, that means insert
-the output in place of text from START to END, putting point and mark
-around it.
-
-If optional sixth argument ERROR-BUFFER is non-nil, it is a buffer
-or buffer name to which to direct the command's standard error output.
-If it is nil, error output is mingled with regular output.
-If DISPLAY-ERROR-BUFFER is non-nil, display the error buffer if there
-were any errors. (This is always t, interactively.)
-In an interactive call, the variable `shell-command-default-error-buffer'
-specifies the value of ERROR-BUFFER."
- (interactive (let (string)
- (unless (mark)
- (error "The mark is not set now, so there is no region"))
- ;; Do this before calling region-beginning
- ;; and region-end, in case subprocess output
- ;; relocates them while we are in the minibuffer.
- (setq string (read-shell-command "Shell command on region: "))
- ;; call-interactively recognizes region-beginning and
- ;; region-end specially, leaving them in the history.
- (list (region-beginning) (region-end)
- string
- current-prefix-arg
- current-prefix-arg
- shell-command-default-error-buffer
- t)))
- (let ((input-file (org-babel-temp-file "input-"))
- (error-file (if error-buffer (org-babel-temp-file "scor-") nil))
+Stripped down version of shell-command-on-region for internal use
+in Babel only. This lets us work around errors in the original
+function in various versions of Emacs.
+"
+ (let ((input-file (org-babel-temp-file "ob-input-"))
+ (error-file (if error-buffer (org-babel-temp-file "ob-error-") nil))
+ ;; Unfortunately, `executable-find' does not support file name
+ ;; handlers. Therefore, we could use it in the local case
+ ;; only.
(shell-file-name
- (if (file-executable-p
- (concat (file-remote-p default-directory) shell-file-name))
- shell-file-name
- "/bin/sh"))
+ (cond ((and (not (file-remote-p default-directory))
+ (executable-find shell-file-name))
+ shell-file-name)
+ ((file-executable-p
+ (concat (file-remote-p default-directory) shell-file-name))
+ shell-file-name)
+ ("/bin/sh")))
exit-status)
- (if (or replace
- (and output-buffer
- (not (or (bufferp output-buffer) (stringp output-buffer)))))
- ;; Replace specified region with output from command.
- (let ((swap (and replace (< start end))))
- ;; Don't muck with mark unless REPLACE says we should.
- (goto-char start)
- (and replace (push-mark (point) 'nomsg))
- (write-region start end input-file)
- (delete-region start end)
- (setq exit-status
- (process-file shell-file-name input-file
- (if error-file
- (list output-buffer error-file)
- t)
- nil shell-command-switch command))
- ;; It is rude to delete a buffer which the command is not using.
- ;; (let ((shell-buffer (get-buffer "*Shell Command Output*")))
- ;; (and shell-buffer (not (eq shell-buffer (current-buffer)))
- ;; (kill-buffer shell-buffer)))
- ;; Don't muck with mark unless REPLACE says we should.
- (and replace swap (exchange-point-and-mark)))
- ;; No prefix argument: put the output in a temp buffer,
- ;; replacing its entire contents.
- (let ((buffer (get-buffer-create
- (or output-buffer "*Shell Command Output*"))))
- (unwind-protect
- (if (eq buffer (current-buffer))
- ;; If the input is the same buffer as the output,
- ;; delete everything but the specified region,
- ;; then replace that region with the output.
- (progn (setq buffer-read-only nil)
- (delete-region (max start end) (point-max))
- (delete-region (point-min) (min start end))
- (write-region (point-min) (point-max) input-file)
- (delete-region (point-min) (point-max))
- (setq exit-status
- (process-file shell-file-name input-file
- (if error-file
- (list t error-file)
- t)
- nil shell-command-switch command)))
- ;; Clear the output buffer, then run the command with
- ;; output there.
- (let ((directory default-directory))
- (with-current-buffer buffer
- (setq buffer-read-only nil)
- (if (not output-buffer)
- (setq default-directory directory))
- (erase-buffer)))
- (setq exit-status
- (process-file shell-file-name nil
- (if error-file
- (list buffer error-file)
- buffer)
- nil shell-command-switch command)))
- ;; Report the output.
- (with-current-buffer buffer
- (setq mode-line-process
- (cond ((null exit-status)
- " - Error")
- ((stringp exit-status)
- (format " - Signal [%s]" exit-status))
- ((not (equal 0 exit-status))
- (format " - Exit [%d]" exit-status)))))
- (if (with-current-buffer buffer (> (point-max) (point-min)))
- ;; There's some output, display it
- (display-message-or-buffer buffer)
- ;; No output; error?
- (let ((output
- (if (and error-file
- (< 0 (nth 7 (file-attributes error-file))))
- "some error output"
- "no output")))
- (cond ((null exit-status)
- (message "(Shell command failed with error)"))
- ((equal 0 exit-status)
- (message "(Shell command succeeded with %s)"
- output))
- ((stringp exit-status)
- (message "(Shell command killed by signal %s)"
- exit-status))
- (t
- (message "(Shell command failed with code %d and %s)"
- exit-status output))))
- ;; Don't kill: there might be useful info in the undo-log.
- ;; (kill-buffer buffer)
- ))))
-
- (when (and input-file (file-exists-p input-file))
+ ;; There is an error in `process-file' when `error-file' exists.
+ ;; This is fixed in Emacs trunk as of 2012-12-21; let's use this
+ ;; workaround for now.
+ (unless (file-remote-p default-directory)
+ (delete-file error-file))
+ ;; we always call this with 'replace, remove conditional
+ ;; Replace specified region with output from command.
+ (let ((swap (< start end)))
+ (goto-char start)
+ (push-mark (point) 'nomsg)
+ (write-region start end input-file)
+ (delete-region start end)
+ (setq exit-status
+ (process-file shell-file-name input-file
+ (if error-file
+ (list t error-file)
+ t)
+ nil shell-command-switch command))
+ (when swap (exchange-point-and-mark)))
+
+ (when (and input-file (file-exists-p input-file)
+ ;; bind org-babel--debug-input around the call to keep
+ ;; the temporary input files available for inspection
+ (not (when (boundp 'org-babel--debug-input)
+ org-babel--debug-input)))
(delete-file input-file))
(when (and error-file (file-exists-p error-file))
(format-insert-file error-file nil)
;; Put point after the inserted errors.
(goto-char (- (point-max) pos-from-end)))
- (and display-error-buffer
- (display-buffer (current-buffer)))))
+ (current-buffer)))
(delete-file error-file))
exit-status))