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@@ -1022,6 +1022,14 @@ block but are passed literally to the \"example-block\"."
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(nb-add (buffer-substring index (point-max)))))
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new-body))
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+(defun org-babel-error-notify (exit-code stderr)
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+ (message (format "Shell command exited with code %d" exit-code))
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+ (let ((buf (get-buffer-create "*Org-Babel Error Output*")))
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+ (with-current-buffer buf
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+ (goto-char (point-max))
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+ (save-excursion (insert stderr)))
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+ (display-buffer buf)))
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+
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(defun org-babel-clean-text-properties (text)
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"Strip all properties from text return."
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(set-text-properties 0 (length text) nil text) text)
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@@ -1055,22 +1063,23 @@ This is taken almost directly from `org-read-prop'."
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"Read the results located at FILE-NAME into an elisp table. If
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the table is trivial, then return it as a scalar."
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(let (result)
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- (with-temp-buffer
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- (condition-case nil
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- (progn
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- (org-table-import file-name nil)
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- (delete-file file-name)
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- (setq result (mapcar (lambda (row)
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- (mapcar #'org-babel-string-read row))
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- (org-table-to-lisp))))
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- (error nil)))
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- (if (null (cdr result)) ;; if result is trivial vector, then scalarize it
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- (if (consp (car result))
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- (if (null (cdr (car result)))
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- (caar result)
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- result)
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- (car result))
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- result)))
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+ (save-window-excursion
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+ (with-temp-buffer
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+ (condition-case nil
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+ (progn
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+ (org-table-import file-name nil)
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+ (delete-file file-name)
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+ (setq result (mapcar (lambda (row)
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+ (mapcar #'org-babel-string-read row))
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+ (org-table-to-lisp))))
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+ (error nil)))
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+ (if (null (cdr result)) ;; if result is trivial vector, then scalarize it
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+ (if (consp (car result))
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+ (if (null (cdr (car result)))
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+ (caar result)
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+ result)
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+ (car result))
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+ result))))
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(defun org-babel-string-read (cell)
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"Strip nested \"s from around strings in exported R values."
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@@ -1120,5 +1129,189 @@ Fixes a bug in `tramp-handle-call-process-region'."
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(concat "/" user (when user "@") host ":" file))
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file))
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+(defun org-babel-shell-command-on-region (start end command
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+ &optional output-buffer replace
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+ error-buffer display-error-buffer)
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+ "Execute string COMMAND in inferior shell with region as input.
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+
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+Fixes bugs in the emacs 23.1.1 version of `shell-command-on-region'
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+
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+Normally display output (if any) in temp buffer `*Shell Command Output*';
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+Prefix arg means replace the region with it. Return the exit code of
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+COMMAND.
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+
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+To specify a coding system for converting non-ASCII characters
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+in the input and output to the shell command, use \\[universal-coding-system-argument]
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+before this command. By default, the input (from the current buffer)
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+is encoded in the same coding system that will be used to save the file,
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+`buffer-file-coding-system'. If the output is going to replace the region,
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+then it is decoded from that same coding system.
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+
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+The noninteractive arguments are START, END, COMMAND,
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+OUTPUT-BUFFER, REPLACE, ERROR-BUFFER, and DISPLAY-ERROR-BUFFER.
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+Noninteractive callers can specify coding systems by binding
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+`coding-system-for-read' and `coding-system-for-write'.
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+
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+If the command generates output, the output may be displayed
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+in the echo area or in a buffer.
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+If the output is short enough to display in the echo area
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+\(determined by the variable `max-mini-window-height' if
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+`resize-mini-windows' is non-nil), it is shown there. Otherwise
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+it is displayed in the buffer `*Shell Command Output*'. The output
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+is available in that buffer in both cases.
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+
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+If there is output and an error, a message about the error
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+appears at the end of the output.
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+
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+If there is no output, or if output is inserted in the current buffer,
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+then `*Shell Command Output*' is deleted.
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+
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+If the optional fourth argument OUTPUT-BUFFER is non-nil,
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+that says to put the output in some other buffer.
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+If OUTPUT-BUFFER is a buffer or buffer name, put the output there.
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+If OUTPUT-BUFFER is not a buffer and not nil,
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+insert output in the current buffer.
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+In either case, the output is inserted after point (leaving mark after it).
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+
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+If REPLACE, the optional fifth argument, is non-nil, that means insert
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+the output in place of text from START to END, putting point and mark
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+around it.
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+
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+If optional sixth argument ERROR-BUFFER is non-nil, it is a buffer
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+or buffer name to which to direct the command's standard error output.
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+If it is nil, error output is mingled with regular output.
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+If DISPLAY-ERROR-BUFFER is non-nil, display the error buffer if there
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+were any errors. (This is always t, interactively.)
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+In an interactive call, the variable `shell-command-default-error-buffer'
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+specifies the value of ERROR-BUFFER."
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+ (interactive (let (string)
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+ (unless (mark)
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+ (error "The mark is not set now, so there is no region"))
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+ ;; Do this before calling region-beginning
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+ ;; and region-end, in case subprocess output
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+ ;; relocates them while we are in the minibuffer.
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+ (setq string (read-shell-command "Shell command on region: "))
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+ ;; call-interactively recognizes region-beginning and
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+ ;; region-end specially, leaving them in the history.
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+ (list (region-beginning) (region-end)
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+ string
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+ current-prefix-arg
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+ current-prefix-arg
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+ shell-command-default-error-buffer
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+ t)))
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+ (let ((error-file
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+ (if error-buffer
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+ (make-temp-file
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+ (expand-file-name "scor"
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+ (or small-temporary-file-directory
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+ temporary-file-directory)))
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+ nil))
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+ exit-status)
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+ (if (or replace
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+ (and output-buffer
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+ (not (or (bufferp output-buffer) (stringp output-buffer)))))
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+ ;; Replace specified region with output from command.
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+ (let ((swap (and replace (< start end))))
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+ ;; Don't muck with mark unless REPLACE says we should.
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+ (goto-char start)
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+ (and replace (push-mark (point) 'nomsg))
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+ (setq exit-status
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+ (call-process-region start end shell-file-name t
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+ (if error-file
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+ (list output-buffer error-file)
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+ t)
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+ nil shell-command-switch command))
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+ ;; It is rude to delete a buffer which the command is not using.
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+ ;; (let ((shell-buffer (get-buffer "*Shell Command Output*")))
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+ ;; (and shell-buffer (not (eq shell-buffer (current-buffer)))
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+ ;; (kill-buffer shell-buffer)))
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+ ;; Don't muck with mark unless REPLACE says we should.
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+ (and replace swap (exchange-point-and-mark)))
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+ ;; No prefix argument: put the output in a temp buffer,
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+ ;; replacing its entire contents.
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+ (let ((buffer (get-buffer-create
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+ (or output-buffer "*Shell Command Output*"))))
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+ (unwind-protect
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+ (if (eq buffer (current-buffer))
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+ ;; If the input is the same buffer as the output,
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+ ;; delete everything but the specified region,
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+ ;; then replace that region with the output.
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+ (progn (setq buffer-read-only nil)
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+ (delete-region (max start end) (point-max))
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+ (delete-region (point-min) (min start end))
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+ (setq exit-status
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+ (call-process-region (point-min) (point-max)
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+ shell-file-name t
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+ (if error-file
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+ (list t error-file)
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+ t)
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+ nil shell-command-switch
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+ command)))
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+ ;; Clear the output buffer, then run the command with
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+ ;; output there.
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+ (let ((directory default-directory))
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+ (save-excursion
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+ (set-buffer buffer)
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+ (setq buffer-read-only nil)
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+ (if (not output-buffer)
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+ (setq default-directory directory))
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+ (erase-buffer)))
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+ (setq exit-status
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+ (call-process-region start end shell-file-name nil
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+ (if error-file
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+ (list buffer error-file)
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+ buffer)
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+ nil shell-command-switch command)))
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+ ;; Report the output.
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+ (with-current-buffer buffer
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+ (setq mode-line-process
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+ (cond ((null exit-status)
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+ " - Error")
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+ ((stringp exit-status)
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+ (format " - Signal [%s]" exit-status))
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+ ((not (equal 0 exit-status))
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+ (format " - Exit [%d]" exit-status)))))
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+ (if (with-current-buffer buffer (> (point-max) (point-min)))
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+ ;; There's some output, display it
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+ (display-message-or-buffer buffer)
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+ ;; No output; error?
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+ (let ((output
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+ (if (and error-file
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+ (< 0 (nth 7 (file-attributes error-file))))
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+ "some error output"
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+ "no output")))
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+ (cond ((null exit-status)
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+ (message "(Shell command failed with error)"))
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+ ((equal 0 exit-status)
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+ (message "(Shell command succeeded with %s)"
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+ output))
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+ ((stringp exit-status)
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+ (message "(Shell command killed by signal %s)"
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+ exit-status))
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+ (t
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+ (message "(Shell command failed with code %d and %s)"
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+ exit-status output))))
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+ ;; Don't kill: there might be useful info in the undo-log.
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+ ;; (kill-buffer buffer)
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+ ))))
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+
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+ (when (and error-file (file-exists-p error-file))
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+ (if (< 0 (nth 7 (file-attributes error-file)))
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+ (with-current-buffer (get-buffer-create error-buffer)
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+ (let ((pos-from-end (- (point-max) (point))))
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+ (or (bobp)
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+ (insert "\f\n"))
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+ ;; Do no formatting while reading error file,
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+ ;; because that can run a shell command, and we
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+ ;; don't want that to cause an infinite recursion.
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+ (format-insert-file error-file nil)
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+ ;; Put point after the inserted errors.
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+ (goto-char (- (point-max) pos-from-end)))
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+ (and display-error-buffer
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+ (display-buffer (current-buffer)))))
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+ (delete-file error-file))
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+ exit-status))
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+
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+
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(provide 'org-babel)
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;;; org-babel.el ends here
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Carsten Dominik