1326 lines
56 KiB
EmacsLisp
1326 lines
56 KiB
EmacsLisp
;;; org-babel.el --- facilitating communication between programming languages and people
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;; Copyright (C) 2009 Eric Schulte, Dan Davison
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;; Author: Eric Schulte, Dan Davison
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;; Keywords: literate programming, reproducible research
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;; Homepage: http://orgmode.org
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;; Version: 0.01
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;;; License:
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;; This program 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
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;; the Free Software Foundation; either version 3, or (at your option)
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;; any later version.
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;;
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;; This program is distributed in the hope that it will be useful,
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU General Public License for more details.
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;;
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;; You should have received a copy of the GNU General Public License
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;; along with GNU Emacs; see the file COPYING. If not, write to the
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;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
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;; Boston, MA 02110-1301, USA.
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;;; Commentary:
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;; See org-babel.org in the parent directory for more information
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;;; Code:
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(require 'org)
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(defun org-babel-execute-src-block-maybe ()
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"Detect if this is context for a org-babel src-block and if so
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then run `org-babel-execute-src-block'."
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(interactive)
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(let ((info (org-babel-get-src-block-info)))
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(if info (progn (org-babel-execute-src-block current-prefix-arg info) t) nil)))
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(add-hook 'org-ctrl-c-ctrl-c-hook 'org-babel-execute-src-block-maybe)
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(defadvice org-edit-special (around org-babel-prep-session-for-edit activate)
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"Prepare the current source block's session according to it's
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header arguments before editing in an org-src buffer. This
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function is called when `org-edit-special' is called with a
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prefix argument from inside of a source-code block."
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(when current-prefix-arg
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(let* ((info (org-babel-get-src-block-info))
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(lang (first info))
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(params (third info))
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(session (cdr (assoc :session params))))
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(when (and info session) ;; if we are in a source-code block which has a session
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(funcall (intern (concat "org-babel-prep-session:" lang)) session params))))
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ad-do-it)
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(defadvice org-open-at-point (around org-babel-open-at-point activate)
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"If `point' is on a source code block, then open that block's
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results with `org-babel-open-src-block-results', otherwise defer
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to `org-open-at-point'."
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(interactive "P")
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(or (call-interactively #'org-babel-open-src-block-result) ad-do-it))
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(defun org-babel-load-in-session-maybe ()
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"Detect if this is context for a org-babel src-block and if so
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then run `org-babel-load-in-session'."
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(interactive)
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(let ((info (org-babel-get-src-block-info)))
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(if info (progn (org-babel-load-in-session current-prefix-arg info) t) nil)))
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(add-hook 'org-metaup-hook 'org-babel-load-in-session-maybe)
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(defun org-babel-pop-to-session-maybe ()
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"Detect if this is context for a org-babel src-block and if so
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then run `org-babel-pop-to-session'."
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(interactive)
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(let ((info (org-babel-get-src-block-info)))
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(if info (progn (org-babel-pop-to-session current-prefix-arg info) t) nil)))
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(add-hook 'org-metadown-hook 'org-babel-pop-to-session-maybe)
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(defconst org-babel-header-arg-names
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'(cache cmdline colnames dir exports file noweb results session tangle var)
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"Common header arguments used by org-babel. Note that
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individual languages may define their own language specific
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header arguments as well.")
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(defvar org-babel-default-header-args
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'((:session . "none") (:results . "replace") (:exports . "code") (:cache . "no") (:noweb . "no"))
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"Default arguments to use when evaluating a source block.")
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(defvar org-babel-default-inline-header-args
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'((:session . "none") (:results . "silent") (:exports . "results"))
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"Default arguments to use when evaluating an inline source block.")
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(defvar org-babel-src-block-regexp nil
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"Regexp used to test when inside of a org-babel src-block")
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(defvar org-babel-inline-src-block-regexp nil
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"Regexp used to test when on an inline org-babel src-block")
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(defvar org-babel-result-regexp
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"^[ \t]*#\\+res\\(ults\\|name\\)\\(\\[\\([[:alnum:]]+\\)\\]\\)?\\:"
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"Regular expression used to match result lines. If the
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results are associated with a hash key then the hash will be
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saved in the second match data.")
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(defvar org-babel-source-name-regexp
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"^[ \t]*#\\+\\(srcname\\|source\\|function\\):[ \t]*"
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"Regular expression used to match a source name line.")
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(defvar org-babel-min-lines-for-block-output 10
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"If number of lines of output is equal to or exceeds this
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value, the output is placed in a #+begin_example...#+end_example
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block. Otherwise the output is marked as literal by inserting
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colons at the starts of the lines. This variable only takes
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effect if the :results output option is in effect.")
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(defvar org-babel-noweb-error-langs nil
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"List of language for which errors should be raised when the
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source code block satisfying a noweb reference in this language
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can not be resolved.")
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(defvar org-babel-hash-show 4
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"Number of initial characters to show of a hidden results hash.")
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(defvar org-babel-after-execute-hook nil
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"Hook for functions to be called after `org-babel-execute-src-block'")
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(defun org-babel-named-src-block-regexp-for-name (name)
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"Regexp used to match named src block."
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(concat org-babel-source-name-regexp (regexp-quote name) "[ \t\n]*"
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(substring org-babel-src-block-regexp 1)))
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(defun org-babel-set-interpreters (var value)
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(set-default var value)
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(setq org-babel-src-block-regexp
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(concat "^[ \t]*#\\+begin_src[ \t]+\\(" ;; (1) lang
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(mapconcat 'regexp-quote value "\\|")
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"\\)[ \t]*"
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"\\([^\":\n]*\"[^\"\n*]*\"[^\":\n]*\\|[^\":\n]*\\)" ;; (2) switches
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"\\([^\n]*\\)\n" ;; (3) header arguments
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"\\([^\000]+?\\)#\\+end_src")) ;; (4) body
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(setq org-babel-inline-src-block-regexp
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(concat "[ \f\t\n\r\v]\\(src_" ;; (1) replacement target
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"\\(" ;; (2) lang
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(mapconcat 'regexp-quote value "\\|")
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"\\)"
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"\\(\\|\\[\\(.*\\)\\]\\)" ;; (3,4) (unused, headers)
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"{\\([^\f\n\r\v]+\\)}" ;; (5) body
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"\\)")))
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(defun org-babel-add-interpreter (interpreter)
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"Add INTERPRETER to `org-babel-interpreters' and update
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`org-babel-src-block-regexp' appropriately."
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(unless (member interpreter org-babel-interpreters)
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(setq org-babel-interpreters (cons interpreter org-babel-interpreters))
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(org-babel-set-interpreters 'org-babel-interpreters org-babel-interpreters)))
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(defcustom org-babel-interpreters '()
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"Interpreters allows for evaluation tags.
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This is a list of program names (as strings) that can evaluate code and
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insert the output into an Org-mode buffer. Valid choices are
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R Evaluate R code
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emacs-lisp Evaluate Emacs Lisp code and display the result
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sh Pass command to the shell and display the result
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perl The perl interpreter
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python The python interpreter
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ruby The ruby interpreter
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The source block regexp `org-babel-src-block-regexp' is updated
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when a new interpreter is added to this list through the
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customize interface. To add interpreters to this variable from
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lisp code use the `org-babel-add-interpreter' function."
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:group 'org-babel
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:set 'org-babel-set-interpreters
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:type '(set :greedy t
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(const "R")
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(const "emacs-lisp")
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(const "sh")
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(const "perl")
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(const "python")
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(const "ruby")))
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;;; functions
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(defun org-babel-execute-src-block (&optional arg info params)
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"Execute the current source code block, and insert the results
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into the buffer. Source code execution and the collection and
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formatting of results can be controlled through a variety of
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header arguments.
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Optionally supply a value for INFO in the form returned by
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`org-babel-get-src-block-info'.
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Optionally supply a value for PARAMS which will be merged with
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the header arguments specified at the front of the source code
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block."
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(interactive)
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;; (message "supplied params=%S" params) ;; debugging
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(let* ((info (or info (org-babel-get-src-block-info)))
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(lang (first info))
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(params (setf (third info)
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(sort (org-babel-merge-params (third info) params)
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(lambda (el1 el2) (string< (symbol-name (car el1))
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(symbol-name (car el2)))))))
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(new-hash (if (and (cdr (assoc :cache params))
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(string= "yes" (cdr (assoc :cache params)))) (org-babel-sha1-hash info)))
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(old-hash (org-babel-result-hash info))
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(body (setf (second info)
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(if (and (cdr (assoc :noweb params))
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(string= "yes" (cdr (assoc :noweb params))))
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(org-babel-expand-noweb-references info) (second info))))
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(result-params (split-string (or (cdr (assoc :results params)) "")))
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(result-type (cond ((member "output" result-params) 'output)
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((member "value" result-params) 'value)
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(t 'value)))
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(cmd (intern (concat "org-babel-execute:" lang)))
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(dir (cdr (assoc :dir params)))
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(default-directory
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(or (and dir (file-name-as-directory dir)) default-directory))
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(call-process-region-original
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(if (boundp 'call-process-region-original) call-process-region-original
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(symbol-function 'call-process-region)))
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result)
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;; (message "params=%S" params) ;; debugging
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(flet ((call-process-region (&rest args)
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(apply 'org-babel-tramp-handle-call-process-region args)))
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(unless (member lang org-babel-interpreters)
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(error "Language is not in `org-babel-interpreters': %s" lang))
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(if (and (not arg) new-hash (equal new-hash old-hash))
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(save-excursion ;; return cached result
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(goto-char (org-babel-where-is-src-block-result nil info))
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(move-end-of-line 1) (forward-char 1)
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(setq result (org-babel-read-result))
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(message (replace-regexp-in-string "%" "%%" (format "%S" result))) result)
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(setq result (funcall cmd body params))
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(if (eq result-type 'value)
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(setq result (if (and (or (member "vector" result-params)
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(member "table" result-params))
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(not (listp result)))
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(list (list result))
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result)))
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(org-babel-insert-result result result-params info new-hash)
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(run-hooks 'org-babel-after-execute-hook)
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result))))
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(defun org-babel-load-in-session (&optional arg info)
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"Load the body of the current source-code block. Evaluate the
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header arguments for the source block before entering the
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session. After loading the body this pops open the session."
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(interactive)
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(let* ((info (or info (org-babel-get-src-block-info)))
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(lang (first info))
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(body (second info))
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(params (third info))
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(session (cdr (assoc :session params))))
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(unless (member lang org-babel-interpreters)
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(error "Language is not in `org-babel-interpreters': %s" lang))
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;; if called with a prefix argument, then process header arguments
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(pop-to-buffer (funcall (intern (concat "org-babel-load-session:" lang)) session body params))
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(move-end-of-line 1)))
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(defun org-babel-switch-to-session (&optional arg info)
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"Switch to the session of the current source-code block.
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If called with a prefix argument then evaluate the header arguments
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for the source block before entering the session. Copy the body
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of the source block to the kill ring."
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(interactive)
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(let* ((info (or info (org-babel-get-src-block-info)))
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(lang (first info))
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(body (second info))
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(params (third info))
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(session (cdr (assoc :session params)))
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(dir (cdr (assoc :dir params)))
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(default-directory
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(or (and dir (file-name-as-directory dir)) default-directory)))
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(unless (member lang org-babel-interpreters)
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(error "Language is not in `org-babel-interpreters': %s" lang))
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;; copy body to the kill ring
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(with-temp-buffer (insert (org-babel-trim body)) (copy-region-as-kill (point-min) (point-max)))
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;; if called with a prefix argument, then process header arguments
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(if arg (funcall (intern (concat "org-babel-prep-session:" lang)) session params))
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;; just to the session using pop-to-buffer
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(pop-to-buffer (funcall (intern (format "org-babel-%s-initiate-session" lang)) session params))
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(move-end-of-line 1)))
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(defalias 'org-babel-pop-to-session 'org-babel-switch-to-session)
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(defun org-babel-open-src-block-result (&optional re-run)
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"If `point' is on a src block then open the results of the
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source code block, otherwise return nil. With optional prefix
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argument RE-RUN the source-code block is evaluated even if
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results already exist."
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(interactive "P")
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(when (org-babel-get-src-block-info)
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(save-excursion
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;; go to the results, if there aren't any then run the block
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(goto-char (or (and (not re-run) (org-babel-where-is-src-block-result))
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(progn (org-babel-execute-src-block)
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(org-babel-where-is-src-block-result))))
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(move-end-of-line 1) (forward-char 1)
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;; open the results
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(if (looking-at org-bracket-link-regexp)
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;; file results
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(org-open-at-point)
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(let ((results (org-babel-read-result)))
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(flet ((echo-res (result)
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(if (stringp result) result (format "%S" result))))
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(pop-to-buffer (get-buffer-create "org-babel-results"))
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(delete-region (point-min) (point-max))
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(if (listp results)
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;; table result
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(insert (orgtbl-to-generic results '(:sep "\t" :fmt echo-res)))
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;; scalar result
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(insert (echo-res results))))))
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t)))
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(defun org-babel-execute-buffer (&optional arg)
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"Call `org-babel-execute-src-block' on every source block in
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the current buffer."
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(interactive "P")
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(save-excursion
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(goto-char (point-min))
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(while (re-search-forward org-babel-src-block-regexp nil t)
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(let ((pos-end (match-end 0)))
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(goto-char (match-beginning 0))
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(org-babel-execute-src-block arg)
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(goto-char pos-end)))))
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(defun org-babel-execute-subtree (&optional arg)
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"Call `org-babel-execute-src-block' on every source block in
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the current subtree."
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(interactive "P")
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(save-excursion
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(org-narrow-to-subtree)
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(org-babel-execute-buffer)
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(widen)))
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(defun org-babel-get-src-block-info (&optional header-vars-only)
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"Get information of the current source block.
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Returns a list
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(language body header-arguments-alist switches name function-args).
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Unless HEADER-VARS-ONLY is non-nil, any variable
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references provided in 'function call style' (i.e. in a
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parenthesised argument list following the src block name) are
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added to the header-arguments-alist."
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(let ((case-fold-search t) head info args)
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(if (setq head (org-babel-where-is-src-block-head))
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(save-excursion
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(goto-char head)
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(setq info (org-babel-parse-src-block-match))
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(forward-line -1)
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(when (looking-at (concat org-babel-source-name-regexp
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"\\([^ ()\f\t\n\r\v]+\\)\\(\(\\(.*\\)\)\\|\\)"))
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(setq info (append info (list (org-babel-clean-text-properties (match-string 2)))))
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;; Note that e.g. "name()" and "name( )" result in ((:var . "")).
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;; We maintain that behaviour, and the resulting non-nil sixth
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;; element is relied upon in org-babel-exp-code to detect a functional-style
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;; block in those cases. However, "name" without any
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;; parentheses would result in the same thing, so we
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;; explicitly avoid that.
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(if (setq args (match-string 4))
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(setq info (append info (list (mapcar (lambda (ref) (cons :var ref))
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(org-babel-ref-split-args args))))))
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(unless header-vars-only
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(setf (third info)
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(org-babel-merge-params (sixth info) (third info)))))
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info)
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(if (save-excursion ;; inline source block
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(re-search-backward "[ \f\t\n\r\v]" nil t)
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(looking-at org-babel-inline-src-block-regexp))
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(org-babel-parse-inline-src-block-match)
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nil)))) ;; indicate that no source block was found
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(defun org-babel-sha1-hash (&optional info)
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(interactive)
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(let* ((info (or info (org-babel-get-src-block-info)))
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(hash (sha1 (format "%s-%s" (mapconcat (lambda (arg) (format "%S" arg))
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(third info) ":")
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(second info)))))
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(when (interactive-p) (message hash))
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hash))
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(defun org-babel-result-hash (&optional info)
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(org-babel-where-is-src-block-result nil info)
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(org-babel-clean-text-properties (match-string 3)))
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(defun org-babel-hide-hash ()
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"Hide the hash in the current results line. Only the initial
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`org-babel-hash-show' characters of the hash will remain
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visible."
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(org-add-to-invisibility-spec '(org-babel-hide-hash . t))
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(save-excursion
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(when (and (re-search-forward org-babel-result-regexp nil t)
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(match-string 3))
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(let* ((start (match-beginning 3))
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(hide-start (+ org-babel-hash-show start))
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(end (match-end 3))
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(hash (match-string 3))
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ov1 ov2)
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(setq ov1 (org-make-overlay start hide-start))
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(setq ov2 (org-make-overlay hide-start end))
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(org-overlay-put ov2 'invisible 'org-babel-hide-hash)
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(org-overlay-put ov1 'babel-hash hash)))))
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(defun org-babel-hide-all-hashes ()
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"Hide the hash in the current buffer. Only the initial
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`org-babel-hash-show' characters of each hash will remain
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visible. This function should be called as part of the
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`org-mode-hook'."
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(save-excursion
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(while (re-search-forward org-babel-result-regexp nil t)
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(goto-char (match-beginning 0))
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(org-babel-hide-hash)
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(goto-char (match-end 0)))))
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(add-hook 'org-mode-hook 'org-babel-hide-all-hashes)
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(defun org-babel-hash-at-point (&optional point)
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"Return the value of the hash at `point'. The hash is also
|
|
added as the last element of the kill ring. This can be called
|
|
with C-c C-c."
|
|
(interactive)
|
|
(let ((hash (car (delq nil (mapcar
|
|
(lambda (ol) (org-overlay-get ol 'babel-hash))
|
|
(org-overlays-at (or point (point))))))))
|
|
(when hash (kill-new hash) (message hash))))
|
|
(add-hook 'org-ctrl-c-ctrl-c-hook 'org-babel-hash-at-point)
|
|
|
|
(defun org-babel-result-hide-spec ()
|
|
(org-add-to-invisibility-spec '(org-babel-hide-result . t)))
|
|
(add-hook 'org-mode-hook 'org-babel-result-hide-spec)
|
|
|
|
(defvar org-babel-hide-result-overlays nil
|
|
"Overlays hiding results.")
|
|
|
|
(defun org-babel-result-hide-all ()
|
|
"Fold all results in the current buffer."
|
|
(interactive)
|
|
(org-babel-show-result-all)
|
|
(save-excursion
|
|
(while (re-search-forward org-babel-result-regexp nil t)
|
|
(save-excursion (goto-char (match-beginning 0))
|
|
(org-babel-hide-result-toggle-maybe)))))
|
|
|
|
(defun org-babel-show-result-all ()
|
|
"Unfold all results in the current buffer."
|
|
(mapc 'org-delete-overlay org-babel-hide-result-overlays)
|
|
(setq org-babel-hide-result-overlays nil))
|
|
|
|
(defun org-babel-hide-result-toggle-maybe ()
|
|
"Toggle visibility of result at point."
|
|
(interactive)
|
|
(let ((case-fold-search t))
|
|
(if (save-excursion
|
|
(beginning-of-line 1)
|
|
(looking-at org-babel-result-regexp))
|
|
(progn (org-babel-hide-result-toggle)
|
|
t) ;; to signal that we took action
|
|
nil))) ;; to signal that we did not
|
|
|
|
(defun org-babel-hide-result-toggle (&optional force)
|
|
"Toggle the visibility of the current result."
|
|
(interactive)
|
|
(save-excursion
|
|
(beginning-of-line)
|
|
(if (re-search-forward org-babel-result-regexp nil t)
|
|
(let ((start (progn (beginning-of-line 2) (- (point) 1)))
|
|
(end (progn (goto-char (- (org-babel-result-end) 1)) (point)))
|
|
ov)
|
|
(if (memq t (mapcar (lambda (overlay)
|
|
(eq (org-overlay-get overlay 'invisible)
|
|
'org-babel-hide-result))
|
|
(org-overlays-at start)))
|
|
(if (or (not force) (eq force 'off))
|
|
(mapc (lambda (ov)
|
|
(when (member ov org-babel-hide-result-overlays)
|
|
(setq org-babel-hide-result-overlays
|
|
(delq ov org-babel-hide-result-overlays)))
|
|
(when (eq (org-overlay-get ov 'invisible)
|
|
'org-babel-hide-result)
|
|
(org-delete-overlay ov)))
|
|
(org-overlays-at start)))
|
|
(setq ov (org-make-overlay start end))
|
|
(org-overlay-put ov 'invisible 'org-babel-hide-result)
|
|
;; make the block accessible to isearch
|
|
(org-overlay-put
|
|
ov 'isearch-open-invisible
|
|
(lambda (ov)
|
|
(when (member ov org-babel-hide-result-overlays)
|
|
(setq org-babel-hide-result-overlays
|
|
(delq ov org-babel-hide-result-overlays)))
|
|
(when (eq (org-overlay-get ov 'invisible)
|
|
'org-babel-hide-result)
|
|
(org-delete-overlay ov))))
|
|
(push ov org-babel-hide-result-overlays)))
|
|
(error "Not looking at a result line"))))
|
|
|
|
;; org-tab-after-check-for-cycling-hook
|
|
(add-hook 'org-tab-first-hook 'org-babel-hide-result-toggle-maybe)
|
|
;; Remove overlays when changing major mode
|
|
(add-hook 'org-mode-hook
|
|
(lambda () (org-add-hook 'change-major-mode-hook
|
|
'org-babel-show-result-all 'append 'local)))
|
|
|
|
(defmacro org-babel-map-source-blocks (file &rest body)
|
|
"Evaluate BODY forms on each source-block in FILE."
|
|
(declare (indent 1))
|
|
`(let ((visited-p (get-buffer (file-name-nondirectory ,file))))
|
|
(save-window-excursion
|
|
(find-file ,file) (goto-char (point-min))
|
|
(while (re-search-forward org-babel-src-block-regexp nil t)
|
|
(goto-char (match-beginning 0))
|
|
(save-match-data ,@body)
|
|
(goto-char (match-end 0))))
|
|
(unless visited-p (kill-buffer (file-name-nondirectory file)))))
|
|
|
|
(defun org-babel-params-from-properties ()
|
|
"Return an association list of any source block params which
|
|
may be specified in the properties of the current outline entry."
|
|
(save-match-data
|
|
(delq nil
|
|
(mapcar
|
|
(lambda (header-arg)
|
|
(let ((val (or (condition-case nil
|
|
(org-entry-get (point) header-arg t)
|
|
(error nil))
|
|
(cdr (assoc header-arg org-file-properties)))))
|
|
(when val
|
|
;; (message "prop %s=%s" header-arg val) ;; debugging
|
|
(cons (intern (concat ":" header-arg)) val))))
|
|
(mapcar 'symbol-name org-babel-header-arg-names)))))
|
|
|
|
(defun org-babel-parse-src-block-match ()
|
|
(let* ((lang (org-babel-clean-text-properties (match-string 1)))
|
|
(lang-headers (intern (concat "org-babel-default-header-args:" lang)))
|
|
(switches (match-string 2))
|
|
(body (org-babel-clean-text-properties (match-string 4)))
|
|
(preserve-indentation (or org-src-preserve-indentation
|
|
(string-match "-i\\>" switches))))
|
|
(list lang
|
|
;; get src block body removing properties, protective commas, and indentation
|
|
(with-temp-buffer
|
|
(save-match-data
|
|
(insert (org-babel-strip-protective-commas body))
|
|
(unless preserve-indentation (org-do-remove-indentation))
|
|
(buffer-string)))
|
|
(org-babel-merge-params
|
|
org-babel-default-header-args
|
|
(org-babel-params-from-properties)
|
|
(if (boundp lang-headers) (eval lang-headers) nil)
|
|
(org-babel-parse-header-arguments (org-babel-clean-text-properties (or (match-string 3) ""))))
|
|
switches)))
|
|
|
|
(defun org-babel-parse-inline-src-block-match ()
|
|
(let* ((lang (org-babel-clean-text-properties (match-string 2)))
|
|
(lang-headers (intern (concat "org-babel-default-header-args:" lang))))
|
|
(list lang
|
|
(org-babel-strip-protective-commas (org-babel-clean-text-properties (match-string 5)))
|
|
(org-babel-merge-params
|
|
org-babel-default-inline-header-args
|
|
(org-babel-params-from-properties)
|
|
(if (boundp lang-headers) (eval lang-headers) nil)
|
|
(org-babel-parse-header-arguments (org-babel-clean-text-properties (or (match-string 4) "")))))))
|
|
|
|
(defun org-babel-parse-header-arguments (arg-string)
|
|
"Parse a string of header arguments returning an alist."
|
|
(if (> (length arg-string) 0)
|
|
(delq nil
|
|
(mapcar
|
|
(lambda (arg)
|
|
(if (string-match "\\([^ \f\t\n\r\v]+\\)[ \f\t\n\r\v]+\\([^ \f\t\n\r\v]+.*\\)" arg)
|
|
(cons (intern (concat ":" (match-string 1 arg)))
|
|
(let ((raw (org-babel-chomp (match-string 2 arg))))
|
|
(if (org-babel-number-p raw) raw (eval (org-babel-read raw)))))
|
|
(cons (intern (concat ":" arg)) nil)))
|
|
(split-string (concat " " arg-string) "[ \f\t\n\r\v]+:" t)))))
|
|
|
|
(defun org-babel-process-params (params)
|
|
"Parse params and resolve references.
|
|
|
|
Return a list (session vars result-params result-type)."
|
|
(let* ((session (cdr (assoc :session params)))
|
|
(vars (org-babel-ref-variables params))
|
|
(result-params (split-string (or (cdr (assoc :results params)) "")))
|
|
(result-type (cond ((member "output" result-params) 'output)
|
|
((member "value" result-params) 'value)
|
|
(t 'value))))
|
|
(list session vars result-params result-type)))
|
|
|
|
(defun org-babel-where-is-src-block-head ()
|
|
"Return the point at the beginning of the current source
|
|
block. Specifically at the beginning of the #+BEGIN_SRC line.
|
|
If the point is not on a source block then return nil."
|
|
(let ((initial (point)) top bottom)
|
|
(or
|
|
(save-excursion ;; on a source name line
|
|
(beginning-of-line 1)
|
|
(and (looking-at org-babel-source-name-regexp) (forward-line 1)
|
|
(looking-at org-babel-src-block-regexp)
|
|
(point)))
|
|
(save-excursion ;; on a #+begin_src line
|
|
(beginning-of-line 1)
|
|
(and (looking-at org-babel-src-block-regexp)
|
|
(point)))
|
|
(save-excursion ;; inside a src block
|
|
(and
|
|
(re-search-backward "#\\+begin_src" nil t) (setq top (point))
|
|
(re-search-forward "#\\+end_src" nil t) (setq bottom (point))
|
|
(< top initial) (< initial bottom)
|
|
(goto-char top) (move-beginning-of-line 1)
|
|
(looking-at org-babel-src-block-regexp)
|
|
(point))))))
|
|
|
|
(defun org-babel-goto-named-source-block (&optional name)
|
|
"Go to a named source-code block."
|
|
(interactive "ssource-block name: ")
|
|
(let ((point (org-babel-find-named-block name)))
|
|
(if point
|
|
;; taken from `org-open-at-point'
|
|
(progn (goto-char point) (org-show-context))
|
|
(message "source-code block '%s' not found in this buffer" name))))
|
|
|
|
(defun org-babel-find-named-block (name)
|
|
"Find a named source-code block.
|
|
Return the location of the source block identified by source
|
|
NAME, or nil if no such block exists. Set match data according to
|
|
org-babel-named-src-block-regexp."
|
|
(save-excursion
|
|
(let ((case-fold-search t)
|
|
(regexp (org-babel-named-src-block-regexp-for-name name)) msg)
|
|
(goto-char (point-min))
|
|
(when (or (re-search-forward regexp nil t)
|
|
(re-search-backward regexp nil t))
|
|
(match-beginning 0)))))
|
|
|
|
(defun org-babel-find-named-result (name)
|
|
"Return the location of the result named NAME in the current
|
|
buffer or nil if no such result exists."
|
|
(save-excursion
|
|
(goto-char (point-min))
|
|
(when (re-search-forward
|
|
(concat org-babel-result-regexp "[ \t]" (regexp-quote name) "[ \t\n\f\v\r]") nil t)
|
|
(move-beginning-of-line 0) (point))))
|
|
|
|
(defun org-babel-where-is-src-block-result (&optional insert info hash)
|
|
"Return the point at the beginning of the result of the current
|
|
source block. Specifically at the beginning of the results line.
|
|
If no result exists for this block then create a results line
|
|
following the source block."
|
|
(save-excursion
|
|
(let* ((on-lob-line (progn (beginning-of-line 1)
|
|
(looking-at org-babel-lob-one-liner-regexp)))
|
|
(name (if on-lob-line (first (org-babel-lob-get-info))
|
|
(fifth (or info (org-babel-get-src-block-info)))))
|
|
(head (unless on-lob-line (org-babel-where-is-src-block-head))) end)
|
|
(when head (goto-char head))
|
|
(or (and name (org-babel-find-named-result name))
|
|
(and (or on-lob-line (re-search-forward "#\\+end_src" nil t))
|
|
(progn (move-end-of-line 1)
|
|
(if (eobp) (insert "\n") (forward-char 1))
|
|
(setq end (point))
|
|
(or (and (not name)
|
|
(progn ;; unnamed results line already exists
|
|
(re-search-forward "[^ \f\t\n\r\v]" nil t)
|
|
(move-beginning-of-line 1)
|
|
(looking-at (concat org-babel-result-regexp "\n"))))
|
|
;; or (with optional insert) back up and make one ourselves
|
|
(when insert
|
|
(goto-char end)
|
|
(if (looking-at "[\n\r]") (forward-char 1) (insert "\n"))
|
|
(insert (concat "#+results" (if hash (concat "["hash"]"))
|
|
":"(if name (concat " " name)) "\n"))
|
|
(move-beginning-of-line 0)
|
|
(if hash (org-babel-hide-hash)) t)))
|
|
(point))))))
|
|
|
|
(defun org-babel-read-result ()
|
|
"Read the result at `point' into emacs-lisp."
|
|
(let ((case-fold-search t) result-string)
|
|
(cond
|
|
((org-at-table-p) (org-babel-read-table))
|
|
((looking-at org-bracket-link-regexp) (org-babel-read-link))
|
|
((looking-at org-block-regexp) (org-babel-trim (match-string 4)))
|
|
((looking-at ": ")
|
|
(setq result-string
|
|
(org-babel-trim
|
|
(mapconcat (lambda (line) (if (and (> (length line) 1)
|
|
(string= ": " (substring line 0 2)))
|
|
(substring line 2)
|
|
line))
|
|
(split-string
|
|
(buffer-substring (point) (org-babel-result-end)) "[\r\n]+")
|
|
"\n")))
|
|
(or (org-babel-number-p result-string) result-string))
|
|
((looking-at org-babel-result-regexp)
|
|
(save-excursion (forward-line 1) (org-babel-read-result))))))
|
|
|
|
(defun org-babel-read-table ()
|
|
"Read the table at `point' into emacs-lisp."
|
|
(mapcar (lambda (row)
|
|
(if (and (symbolp row) (equal row 'hline)) row
|
|
(mapcar #'org-babel-read row)))
|
|
(org-table-to-lisp)))
|
|
|
|
(defun org-babel-read-link ()
|
|
"Read the link at `point' into emacs-lisp. If the path of the
|
|
link is a file path it is expanded using `expand-file-name'."
|
|
(let* ((case-fold-search t)
|
|
(raw (and (looking-at org-bracket-link-regexp)
|
|
(org-babel-clean-text-properties (match-string 1))))
|
|
(type (and (string-match org-link-types-re raw)
|
|
(match-string 1 raw))))
|
|
(cond
|
|
((not type) (expand-file-name raw))
|
|
((string= type "file")
|
|
(and (string-match "file\\(.*\\):\\(.+\\)" raw)
|
|
(expand-file-name (match-string 2 raw))))
|
|
(t raw))))
|
|
|
|
(defun org-babel-insert-result (result &optional result-params info hash)
|
|
"Insert RESULT into the current buffer after the end of the
|
|
current source block. With optional argument RESULT-PARAMS
|
|
controls insertion of results in the org-mode file.
|
|
RESULT-PARAMS can take the following values...
|
|
|
|
replace - (default option) insert results after the source block
|
|
replacing any previously inserted results
|
|
|
|
silent -- no results are inserted
|
|
|
|
file ---- the results are interpreted as a file path, and are
|
|
inserted into the buffer using the Org-mode file syntax
|
|
|
|
raw ----- results are added directly to the org-mode file. This
|
|
is a good option if you code block will output org-mode
|
|
formatted text.
|
|
|
|
org ----- this is the same as the 'raw' option
|
|
|
|
html ---- results are added inside of a #+BEGIN_HTML block. This
|
|
is a good option if you code block will output html
|
|
formatted text.
|
|
|
|
latex --- results are added inside of a #+BEGIN_LATEX block.
|
|
This is a good option if you code block will output
|
|
latex formatted text.
|
|
|
|
code ---- the results are extracted in the syntax of the source
|
|
code of the language being evaluated and are added
|
|
inside of a #+BEGIN_SRC block with the source-code
|
|
language set appropriately."
|
|
(if (stringp result)
|
|
(progn
|
|
(setq result (org-babel-clean-text-properties result))
|
|
(when (member "file" result-params)
|
|
(setq result (org-babel-result-to-file result))))
|
|
(unless (listp result) (setq result (format "%S" result))))
|
|
(if (and result-params (member "replace" result-params)
|
|
(not (member "silent" result-params)))
|
|
(org-babel-remove-result info))
|
|
(if (= (length result) 0)
|
|
(if (member "value" result-params)
|
|
(message "No result returned by source block")
|
|
(message "Source block produced no output"))
|
|
(if (and result-params (member "silent" result-params))
|
|
(progn (message (replace-regexp-in-string "%" "%%" (format "%S" result)))
|
|
result)
|
|
(when (and (stringp result) ;; ensure results end in a newline
|
|
(not (or (string-equal (substring result -1) "\n")
|
|
(string-equal (substring result -1) "\r"))))
|
|
(setq result (concat result "\n")))
|
|
(save-excursion
|
|
(let ((existing-result (org-babel-where-is-src-block-result t info hash))
|
|
(results-switches (cdr (assoc :results_switches (third info)))))
|
|
(when existing-result (goto-char existing-result) (forward-line 1))
|
|
(setq results-switches
|
|
(if results-switches (concat " " results-switches) ""))
|
|
(cond
|
|
;; assume the result is a table if it's not a string
|
|
((not (stringp result))
|
|
(insert (concat (orgtbl-to-orgtbl
|
|
(if (and (listp (car result))
|
|
(listp (cdr (car result))))
|
|
result (list result))
|
|
'(:fmt (lambda (cell) (format "%s" cell)))) "\n"))
|
|
(forward-line -1) (org-cycle))
|
|
((member "file" result-params)
|
|
(insert result))
|
|
((member "html" result-params)
|
|
(insert (format "#+BEGIN_HTML%s\n%s#+END_HTML\n" results-switches result)))
|
|
((member "latex" result-params)
|
|
(insert (format "#+BEGIN_LaTeX%s\n%s#+END_LaTeX\n" results-switches result)))
|
|
((member "code" result-params)
|
|
(insert (format "#+BEGIN_SRC %s%s\n%s#+END_SRC\n" lang results-switches result)))
|
|
((or (member "raw" result-params) (member "org" result-params))
|
|
(save-excursion (insert result)) (if (org-at-table-p) (org-cycle)))
|
|
(t
|
|
(org-babel-examplize-region
|
|
(point) (progn (insert result) (point)) results-switches)))))
|
|
(message "finished"))))
|
|
|
|
(defun org-babel-result-to-org-string (result)
|
|
"Return RESULT as a string in org-mode format. This function
|
|
relies on `org-babel-insert-result'."
|
|
(with-temp-buffer (org-babel-insert-result result) (buffer-string)))
|
|
|
|
(defun org-babel-remove-result (&optional info)
|
|
"Remove the result of the current source block."
|
|
(interactive)
|
|
(let ((location (org-babel-where-is-src-block-result nil info)) start)
|
|
(when location
|
|
(save-excursion
|
|
(goto-char location) (setq start (point)) (forward-line 1)
|
|
(delete-region start (org-babel-result-end))))))
|
|
|
|
(defun org-babel-result-end ()
|
|
"Return the point at the end of the current set of results"
|
|
(save-excursion
|
|
(if (org-at-table-p)
|
|
(progn (goto-char (org-table-end)) (point))
|
|
(let ((case-fold-search t))
|
|
(cond
|
|
((looking-at "#\\+begin_latex")
|
|
(search-forward "#+end_latex" nil t)
|
|
(forward-line 1))
|
|
((looking-at "#\\+begin_html")
|
|
(search-forward "#+end_html" nil t)
|
|
(forward-line 1))
|
|
((looking-at "#\\+begin_example")
|
|
(search-forward "#+end_example" nil t)
|
|
(forward-line 1))
|
|
((looking-at "#\\+begin_src")
|
|
(search-forward "#+end_src" nil t)
|
|
(forward-line 1))
|
|
(t (progn (while (looking-at "\\(: \\|\\[\\[\\)")
|
|
(forward-line 1))))))
|
|
(point))))
|
|
|
|
(defun org-babel-result-to-file (result)
|
|
"Convert RESULT into an `org-mode' link. If the
|
|
`default-directory' is different from the containing file's
|
|
directory then expand relative links."
|
|
(format
|
|
"[[file:%s]]"
|
|
(if (and default-directory
|
|
buffer-file-name
|
|
(not (string= (expand-file-name default-directory)
|
|
(expand-file-name (file-name-directory buffer-file-name)))))
|
|
(expand-file-name result default-directory)
|
|
result)))
|
|
|
|
(defun org-babel-examplize-region (beg end &optional results-switches)
|
|
"Comment out region using the ': ' org example quote."
|
|
(interactive "*r")
|
|
(let ((size (abs (- (line-number-at-pos end)
|
|
(line-number-at-pos beg)))))
|
|
(save-excursion
|
|
(cond ((= size 0)
|
|
(error "This should be impossible: a newline was appended to result if missing"))
|
|
((< size org-babel-min-lines-for-block-output)
|
|
(goto-char beg)
|
|
(dotimes (n size)
|
|
(move-beginning-of-line 1) (insert ": ") (forward-line 1)))
|
|
(t
|
|
(goto-char beg)
|
|
(insert (if results-switches
|
|
(format "#+begin_example%s\n" results-switches)
|
|
"#+begin_example\n"))
|
|
(forward-char (- end beg))
|
|
(insert "#+end_example\n"))))))
|
|
|
|
(defun org-babel-merge-params (&rest plists)
|
|
"Combine all parameter association lists in PLISTS. Later
|
|
elements of PLISTS override the values of previous element. This
|
|
takes into account some special considerations for certain
|
|
parameters when merging lists."
|
|
(let ((results-exclusive-groups
|
|
'(("file" "vector" "table" "scalar" "raw" "org" "html" "latex" "code" "pp")
|
|
("replace" "silent")
|
|
("output" "value")))
|
|
(exports-exclusive-groups
|
|
'(("code" "results" "both" "none")))
|
|
params results exports tangle noweb cache vars var ref shebang comments)
|
|
(flet ((e-merge (exclusive-groups &rest result-params)
|
|
;; maintain exclusivity of mutually exclusive parameters
|
|
(let (output)
|
|
(mapc (lambda (new-params)
|
|
(mapc (lambda (new-param)
|
|
(mapc (lambda (exclusive-group)
|
|
(when (member new-param exclusive-group)
|
|
(mapcar (lambda (excluded-param)
|
|
(setq output (delete excluded-param output)))
|
|
exclusive-group)))
|
|
exclusive-groups)
|
|
(setq output (org-uniquify (cons new-param output))))
|
|
new-params))
|
|
result-params)
|
|
output)))
|
|
(mapc (lambda (plist)
|
|
(mapc (lambda (pair)
|
|
(case (car pair)
|
|
(:var
|
|
;; we want only one specification per variable
|
|
(when (string-match "^\\([^= \f\t\n\r\v]+\\)[ \t]*=[ \t]*\\([^\f\n\r\v]+\\)$" (cdr pair))
|
|
;; TODO: When is this not true?
|
|
(setq var (intern (match-string 1 (cdr pair)))
|
|
ref (match-string 2 (cdr pair))
|
|
vars (cons (cons var ref) (assq-delete-all var vars)))))
|
|
(:results
|
|
(setq results
|
|
(e-merge results-exclusive-groups results (split-string (cdr pair)))))
|
|
(:file
|
|
(when (cdr pair)
|
|
(setq results (e-merge results-exclusive-groups results '("file")))
|
|
(unless (or (member "both" exports)
|
|
(member "none" exports)
|
|
(member "code" exports))
|
|
(setq exports (e-merge exports-exclusive-groups exports '("results"))))
|
|
(setq params (cons pair (assq-delete-all (car pair) params)))))
|
|
(:exports
|
|
(setq exports (e-merge exports-exclusive-groups
|
|
exports (split-string (cdr pair)))))
|
|
(:tangle ;; take the latest -- always overwrite
|
|
(setq tangle (or (list (cdr pair)) tangle)))
|
|
(:noweb
|
|
(setq noweb (e-merge '(("yes" "no"))
|
|
noweb (split-string (or (cdr pair) "")))))
|
|
(:cache
|
|
(setq cache (e-merge '(("yes" "no"))
|
|
cache (split-string (or (cdr pair) "")))))
|
|
(:shebang ;; take the latest -- always overwrite
|
|
(setq shebang (or (list (cdr pair)) shebang)))
|
|
(:comments
|
|
(setq comments (e-merge '(("yes" "no"))
|
|
comments (split-string (or (cdr pair) "")))))
|
|
(t ;; replace: this covers e.g. :session
|
|
(setq params (cons pair (assq-delete-all (car pair) params))))))
|
|
plist))
|
|
plists))
|
|
(setq vars (mapcar (lambda (pair) (format "%s=%s" (car pair) (cdr pair))) vars))
|
|
(while vars (setq params (cons (cons :var (pop vars)) params)))
|
|
(cons (cons :comments (mapconcat 'identity comments " "))
|
|
(cons (cons :shebang (mapconcat 'identity shebang " "))
|
|
(cons (cons :cache (mapconcat 'identity cache " "))
|
|
(cons (cons :noweb (mapconcat 'identity noweb " "))
|
|
(cons (cons :tangle (mapconcat 'identity tangle " "))
|
|
(cons (cons :exports (mapconcat 'identity exports " "))
|
|
(cons (cons :results (mapconcat 'identity results " "))
|
|
params)))))))))
|
|
|
|
(defun org-babel-expand-noweb-references (&optional info parent-buffer)
|
|
"This function expands Noweb style references in the body of
|
|
the current source-code block. For example the following
|
|
reference would be replaced with the body of the source-code
|
|
block named 'example-block'.
|
|
|
|
<<example-block>>
|
|
|
|
Note that any text preceding the <<foo>> construct on a line will
|
|
be interposed between the lines of the replacement text. So for
|
|
example if <<foo>> is placed behind a comment, then the entire
|
|
replacement text will also be commented.
|
|
|
|
This function must be called from inside of the buffer containing
|
|
the source-code block which holds BODY.
|
|
|
|
In addition the following syntax can be used to insert the
|
|
results of evaluating the source-code block named 'example-block'.
|
|
|
|
<<example-block()>>
|
|
|
|
Any optional arguments can be passed to example-block by placing
|
|
the arguments inside the parenthesis following the convention
|
|
defined by `org-babel-lob'. For example
|
|
|
|
<<example-block(a=9)>>
|
|
|
|
would set the value of argument \"a\" equal to \"9\". Note that
|
|
these arguments are not evaluated in the current source-code
|
|
block but are passed literally to the \"example-block\"."
|
|
(let* ((parent-buffer (or parent-buffer (current-buffer)))
|
|
(info (or info (org-babel-get-src-block-info)))
|
|
(lang (first info))
|
|
(body (second info))
|
|
(new-body "") index source-name evaluate prefix)
|
|
(flet ((nb-add (text)
|
|
(setq new-body (concat new-body text))))
|
|
(with-temp-buffer
|
|
(insert body) (goto-char (point-min))
|
|
(funcall (intern (concat (or (and (cdr (assoc lang org-src-lang-modes))
|
|
(symbol-name
|
|
(cdr (assoc lang org-src-lang-modes))))
|
|
lang) "-mode")))
|
|
(setq index (point))
|
|
(while (and (re-search-forward "<<\\(.+?\\)>>" nil t))
|
|
(save-match-data (setf source-name (match-string 1)))
|
|
(save-match-data (setq evaluate (string-match "\(.*\)" source-name)))
|
|
(save-match-data
|
|
(setq prefix (buffer-substring (match-beginning 0)
|
|
(save-excursion
|
|
(move-beginning-of-line 1) (point)))))
|
|
;; add interval to new-body (removing noweb reference)
|
|
(goto-char (match-beginning 0))
|
|
(nb-add (buffer-substring index (point)))
|
|
(goto-char (match-end 0))
|
|
(setq index (point))
|
|
(nb-add (save-excursion
|
|
(set-buffer parent-buffer)
|
|
(mapconcat ;; interpose `prefix' between every line
|
|
#'identity
|
|
(split-string
|
|
(if evaluate
|
|
(let ((raw (org-babel-ref-resolve-reference
|
|
source-name nil)))
|
|
(if (stringp raw) raw (format "%S" raw)))
|
|
(let ((point (org-babel-find-named-block source-name)))
|
|
(if point
|
|
(save-excursion
|
|
(goto-char point)
|
|
(org-babel-trim (org-babel-expand-noweb-references
|
|
(org-babel-get-src-block-info))))
|
|
;; optionally raise an error if named
|
|
;; source-block doesn't exist
|
|
(if (member lang org-babel-noweb-error-langs)
|
|
(error
|
|
"<<%s>> could not be resolved (see `org-babel-noweb-error-langs')"
|
|
source-name)
|
|
"")))) "[\n\r]") (concat "\n" prefix)))))
|
|
(nb-add (buffer-substring index (point-max)))))
|
|
new-body))
|
|
|
|
(defun org-babel-error-notify (exit-code stderr)
|
|
(message (format "Shell command exited with code %d" exit-code))
|
|
(let ((buf (get-buffer-create "*Org-Babel Error Output*")))
|
|
(with-current-buffer buf
|
|
(goto-char (point-max))
|
|
(save-excursion (insert stderr)))
|
|
(display-buffer buf)))
|
|
|
|
(defun org-babel-clean-text-properties (text)
|
|
"Strip all properties from text return."
|
|
(set-text-properties 0 (length text) nil text) text)
|
|
|
|
(defun org-babel-strip-protective-commas (body)
|
|
"Strip protective commas from bodies of source blocks."
|
|
(replace-regexp-in-string "^,#" "#" body))
|
|
|
|
(defun org-babel-read (cell)
|
|
"Convert the string value of CELL to a number if appropriate.
|
|
Otherwise if cell looks like lisp (meaning it starts with a
|
|
\"(\" or a \"'\") then read it as lisp, otherwise return it
|
|
unmodified as a string.
|
|
|
|
This is taken almost directly from `org-read-prop'."
|
|
(if (and (stringp cell) (not (equal cell "")))
|
|
(or (org-babel-number-p cell)
|
|
(if (or (equal "(" (substring cell 0 1))
|
|
(equal "'" (substring cell 0 1)))
|
|
(read cell)
|
|
(progn (set-text-properties 0 (length cell) nil cell) cell)))
|
|
cell))
|
|
|
|
(defun org-babel-number-p (string)
|
|
"Return t if STRING represents a number"
|
|
(if (and (string-match "^-?[[:digit:]]*\\.?[[:digit:]]*$" string)
|
|
(= (match-end 0) (length string)))
|
|
(string-to-number string)))
|
|
|
|
(defun org-babel-import-elisp-from-file (file-name)
|
|
"Read the results located at FILE-NAME into an elisp table. If
|
|
the table is trivial, then return it as a scalar."
|
|
(let (result)
|
|
(save-window-excursion
|
|
(with-temp-buffer
|
|
(condition-case nil
|
|
(progn
|
|
(org-table-import file-name nil)
|
|
(delete-file file-name)
|
|
(setq result (mapcar (lambda (row)
|
|
(mapcar #'org-babel-string-read row))
|
|
(org-table-to-lisp))))
|
|
(error nil)))
|
|
(if (null (cdr result)) ;; if result is trivial vector, then scalarize it
|
|
(if (consp (car result))
|
|
(if (null (cdr (car result)))
|
|
(caar result)
|
|
result)
|
|
(car result))
|
|
result))))
|
|
|
|
(defun org-babel-string-read (cell)
|
|
"Strip nested \"s from around strings in exported R values."
|
|
(org-babel-read (or (and (stringp cell)
|
|
(string-match "\\\"\\(.+\\)\\\"" cell)
|
|
(match-string 1 cell))
|
|
cell)))
|
|
|
|
(defun org-babel-reverse-string (string)
|
|
(apply 'string (reverse (string-to-list string))))
|
|
|
|
(defun org-babel-chomp (string &optional regexp)
|
|
"Remove any trailing space or carriage returns characters from
|
|
STRING. Default regexp used is \"[ \f\t\n\r\v]\" but can be
|
|
overwritten by specifying a regexp as a second argument."
|
|
(let ((regexp (or regexp "[ \f\t\n\r\v]")))
|
|
(while (and (> (length string) 0) (string-match regexp (substring string -1)))
|
|
(setq string (substring string 0 -1)))
|
|
string))
|
|
|
|
(defun org-babel-trim (string &optional regexp)
|
|
"Like `org-babel-chomp' only it runs on both the front and back of the string"
|
|
(org-babel-chomp (org-babel-reverse-string
|
|
(org-babel-chomp (org-babel-reverse-string string) regexp)) regexp))
|
|
|
|
(defun org-babel-tramp-handle-call-process-region
|
|
(start end program &optional delete buffer display &rest args)
|
|
"Use tramp to handle call-process-region.
|
|
Fixes a bug in `tramp-handle-call-process-region'."
|
|
(if (and (featurep 'tramp) (file-remote-p default-directory))
|
|
(let ((tmpfile (tramp-compat-make-temp-file "")))
|
|
(write-region start end tmpfile)
|
|
(when delete (delete-region start end))
|
|
(unwind-protect
|
|
;; (apply 'call-process program tmpfile buffer display args) ;; bug in tramp
|
|
(apply 'process-file program tmpfile buffer display args)
|
|
(delete-file tmpfile)))
|
|
;; call-process-region-original is the original emacs definition. It
|
|
;; is in scope from the let binding in org-babel-execute-src-block
|
|
(apply call-process-region-original start end program delete buffer display args)))
|
|
|
|
(defun org-babel-maybe-remote-file (file)
|
|
(if (file-remote-p default-directory)
|
|
(let* ((vec (tramp-dissect-file-name default-directory))
|
|
(user (tramp-file-name-user vec))
|
|
(host (tramp-file-name-host vec)))
|
|
(concat "/" user (when user "@") host ":" file))
|
|
file))
|
|
|
|
(defun org-babel-shell-command-on-region (start end command
|
|
&optional output-buffer replace
|
|
error-buffer display-error-buffer)
|
|
"Execute string COMMAND in 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 ((error-file
|
|
(if error-buffer
|
|
(make-temp-file
|
|
(expand-file-name "scor"
|
|
(or small-temporary-file-directory
|
|
temporary-file-directory)))
|
|
nil))
|
|
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))
|
|
(setq exit-status
|
|
(call-process-region start end shell-file-name t
|
|
(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))
|
|
(setq exit-status
|
|
(call-process-region (point-min) (point-max)
|
|
shell-file-name t
|
|
(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))
|
|
(save-excursion
|
|
(set-buffer buffer)
|
|
(setq buffer-read-only nil)
|
|
(if (not output-buffer)
|
|
(setq default-directory directory))
|
|
(erase-buffer)))
|
|
(setq exit-status
|
|
(call-process-region start end 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 error-file (file-exists-p error-file))
|
|
(if (< 0 (nth 7 (file-attributes error-file)))
|
|
(with-current-buffer (get-buffer-create error-buffer)
|
|
(let ((pos-from-end (- (point-max) (point))))
|
|
(or (bobp)
|
|
(insert "\f\n"))
|
|
;; Do no formatting while reading error file,
|
|
;; because that can run a shell command, and we
|
|
;; don't want that to cause an infinite recursion.
|
|
(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)))))
|
|
(delete-file error-file))
|
|
exit-status))
|
|
|
|
|
|
(provide 'org-babel)
|
|
;;; org-babel.el ends here
|