lisp/ob-ref.el

   1 ;;; ob-ref.el --- org-babel functions for referencing external data
   2
   3 ;; Copyright (C) 2009-2013 Free Software Foundation, Inc.
   4
   5 ;; Authors: Eric Schulte
   6 ;;       Dan Davison
   7 ;; Keywords: literate programming, reproducible research
   8 ;; Homepage: http://orgmode.org
   9
  10 ;; This file is part of GNU Emacs.
  11
  12 ;; GNU Emacs is free software: you can redistribute it and/or modify
  13 ;; it under the terms of the GNU General Public License as published by
  14 ;; the Free Software Foundation, either version 3 of the License, or
  15 ;; (at your option) any later version.
  16
  17 ;; GNU Emacs is distributed in the hope that it will be useful,
  18 ;; but WITHOUT ANY WARRANTY; without even the implied warranty of
  19 ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  20 ;; GNU General Public License for more details.
  21
  22 ;; You should have received a copy of the GNU General Public License
  23 ;; along with GNU Emacs.  If not, see <http://www.gnu.org/licenses/>.
  24
  25 ;;; Commentary:
  26
  27 ;; Functions for referencing data from the header arguments of a
  28 ;; org-babel block.  The syntax of such a reference should be
  29
  30 ;;   #+VAR: variable-name=file:resource-id
  31
  32 ;; - variable-name :: the name of the variable to which the value
  33 ;;                    will be assigned
  34
  35 ;; - file :: path to the file containing the resource, or omitted if
  36 ;;           resource is in the current file
  37
  38 ;; - resource-id :: the id or name of the resource
  39
  40 ;; So an example of a simple src block referencing table data in the
  41 ;; same file would be
  42
  43 ;;  #+NAME: sandbox
  44 ;;  | 1 |         2 | 3 |
  45 ;;  | 4 | org-babel | 6 |
  46 ;;
  47 ;;  #+begin_src emacs-lisp :var table=sandbox
  48 ;;    (message table)
  49 ;;  #+end_src
  50
  51 ;;; Code:
  52 (require 'ob-core)
  53 (eval-when-compile
  54   (require 'cl))
  55
  56 (declare-function org-remove-if-not "org" (predicate seq))
  57 (declare-function org-at-table-p "org" (&optional table-type))
  58 (declare-function org-count "org" (CL-ITEM CL-SEQ))
  59 (declare-function org-at-item-p "org-list" ())
  60 (declare-function org-narrow-to-subtree "org" ())
  61 (declare-function org-id-find-id-in-file "org-id" (id file &optional markerp))
  62 (declare-function org-id-find-id-file "org-id" (id))
  63 (declare-function org-show-context "org" (&optional key))
  64 (declare-function org-pop-to-buffer-same-window
  65                   "org-compat" (&optional buffer-or-name norecord label))
  66
  67 (defvar org-babel-ref-split-regexp
  68   "[ \f\t\n\r\v]*\\(.+?\\)[ \f\t\n\r\v]*=[ \f\t\n\r\v]*\\(.+\\)[ \f\t\n\r\v]*")
  69
  70 (defvar org-babel-update-intermediate nil
  71   "Update the in-buffer results of code blocks executed to resolve references.")
  72
  73 (defun org-babel-ref-parse (assignment)
  74   "Parse a variable ASSIGNMENT in a header argument.
  75 If the right hand side of the assignment has a literal value
  76 return that value, otherwise interpret as a reference to an
  77 external resource and find its value using
  78 `org-babel-ref-resolve'.  Return a list with two elements.  The
  79 first element of the list will be the name of the variable, and
  80 the second will be an emacs-lisp representation of the value of
  81 the variable."
  82   (when (string-match org-babel-ref-split-regexp assignment)
  83     (let ((var (match-string 1 assignment))
  84           (ref (match-string 2 assignment)))
  85       (cons (intern var)
  86             (let ((out (org-babel-read ref)))
  87               (if (equal out ref)
  88                   (if (string-match "^\".*\"$" ref)
  89                       (read ref)
  90                     (org-babel-ref-resolve ref))
  91                 out))))))
  92
  93 (defun org-babel-ref-goto-headline-id (id)
  94   (goto-char (point-min))
  95   (let ((rx (regexp-quote id)))
  96     (or (re-search-forward
  97          (concat "^[ \t]*:CUSTOM_ID:[ \t]+" rx "[ \t]*$") nil t)
  98         (let* ((file (org-id-find-id-file id))
  99                (m (when file (org-id-find-id-in-file id file 'marker))))
 100           (when (and file m)
 101             (message "file:%S" file)
 102             (org-pop-to-buffer-same-window (marker-buffer m))
 103             (goto-char m)
 104             (move-marker m nil)
 105             (org-show-context)
 106             t)))))
 107
 108 (defun org-babel-ref-headline-body ()
 109   (save-restriction
 110     (org-narrow-to-subtree)
 111     (buffer-substring
 112      (save-excursion (goto-char (point-min))
 113                      (forward-line 1)
 114                      (when (looking-at "[ \t]*:PROPERTIES:")
 115                        (re-search-forward ":END:" nil)
 116                        (forward-char))
 117                      (point))
 118      (point-max))))
 119
 120 (defvar org-babel-library-of-babel)
 121 (defun org-babel-ref-resolve (ref)
 122   "Resolve the reference REF and return its value."
 123   (save-window-excursion
 124     (save-excursion
 125       (let ((case-fold-search t)
 126             type args new-refere new-header-args new-referent result
 127             lob-info split-file split-ref index index-row index-col id)
 128         ;; if ref is indexed grab the indices -- beware nested indices
 129         (when (and (string-match "\\[\\([^\\[]+\\)\\]$" ref)
 130                    (let ((str (substring ref 0 (match-beginning 0))))
 131                      (= (org-count ?( str) (org-count ?) str))))
 132           (setq index (match-string 1 ref))
 133           (setq ref (substring ref 0 (match-beginning 0))))
 134         ;; assign any arguments to pass to source block
 135         (when (string-match
 136                "^\\(.+?\\)\\(\\[\\(.*\\)\\]\\|\\(\\)\\)\(\\(.*\\)\)$" ref)
 137           (setq new-refere      (match-string 1 ref))
 138           (setq new-header-args (match-string 3 ref))
 139           (setq new-referent    (match-string 5 ref))
 140           (when (> (length new-refere) 0)
 141             (when (> (length new-referent) 0)
 142               (setq args (mapcar (lambda (ref) (cons :var ref))
 143                                  (org-babel-ref-split-args new-referent))))
 144             (when (> (length new-header-args) 0)
 145               (setq args (append (org-babel-parse-header-arguments
 146                                   new-header-args) args)))
 147             (setq ref new-refere)))
 148         (when (string-match "^\\(.+\\):\\(.+\\)$" ref)
 149           (setq split-file (match-string 1 ref))
 150           (setq split-ref (match-string 2 ref))
 151           (find-file split-file) (setq ref split-ref))
 152         (save-restriction
 153           (widen)
 154           (goto-char (point-min))
 155           (if (let ((src-rx (org-babel-named-src-block-regexp-for-name ref))
 156                     (res-rx (org-babel-named-data-regexp-for-name ref)))
 157                 ;; goto ref in the current buffer
 158                 (or
 159                  ;; check for code blocks
 160                  (re-search-forward src-rx nil t)
 161                  ;; check for named data
 162                  (re-search-forward res-rx nil t)
 163                  ;; check for local or global headlines by id
 164                  (setq id (org-babel-ref-goto-headline-id ref))
 165                  ;; check the Library of Babel
 166                  (setq lob-info (cdr (assoc (intern ref)
 167                                             org-babel-library-of-babel)))))
 168               (unless (or lob-info id) (goto-char (match-beginning 0)))
 169             ;; ;; TODO: allow searching for names in other buffers
 170             ;; (setq id-loc (org-id-find ref 'marker)
 171             ;;       buffer (marker-buffer id-loc)
 172             ;;       loc (marker-position id-loc))
 173             ;; (move-marker id-loc nil)
 174             (error "Reference '%s' not found in this buffer" ref))
 175           (cond
 176            (lob-info (setq type 'lob))
 177            (id (setq type 'id))
 178            ((and (looking-at org-babel-src-name-regexp)
 179                  (save-excursion
 180                    (forward-line 1)
 181                    (or (looking-at org-babel-src-block-regexp)
 182                        (looking-at org-babel-multi-line-header-regexp))))
 183             (setq type 'source-block))
 184            (t (while (not (setq type (org-babel-ref-at-ref-p)))
 185                 (forward-line 1)
 186                 (beginning-of-line)
 187                 (if (or (= (point) (point-min)) (= (point) (point-max)))
 188                     (error "Reference not found")))))
 189           (let ((params (append args '((:results . "silent")))))
 190             (setq result
 191                   (case type
 192                     (results-line (org-babel-read-result))
 193                     (table        (org-babel-read-table))
 194                     (list         (org-babel-read-list))
 195                     (file         (org-babel-read-link))
 196                     (source-block (org-babel-execute-src-block
 197                                    nil nil (if org-babel-update-intermediate
 198                                                nil params)))
 199                     (lob          (org-babel-execute-src-block
 200                                    nil lob-info params))
 201                     (id           (org-babel-ref-headline-body)))))
 202           (if (symbolp result)
 203               (format "%S" result)
 204             (if (and index (listp result))
 205                 (org-babel-ref-index-list index result)
 206               result)))))))
 207
 208 (defun org-babel-ref-index-list (index lis)
 209   "Return the subset of LIS indexed by INDEX.
 210
 211 Indices are 0 based and negative indices count from the end of
 212 LIS, so 0 references the first element of LIS and -1 references
 213 the last.  If INDEX is separated by \",\"s then each \"portion\"
 214 is assumed to index into the next deepest nesting or dimension.
 215
 216 A valid \"portion\" can consist of either an integer index, two
 217 integers separated by a \":\" in which case the entire range is
 218 returned, or an empty string or \"*\" both of which are
 219 interpreted to mean the entire range and as such are equivalent
 220 to \"0:-1\"."
 221   (if (and (> (length index) 0) (string-match "^\\([^,]*\\),?" index))
 222       (let* ((ind-re "\\(\\([-[:digit:]]+\\):\\([-[:digit:]]+\\)\\|\*\\)")
 223              (lgth (length lis))
 224              (portion (match-string 1 index))
 225              (remainder (substring index (match-end 0)))
 226              (wrap (lambda (num) (if (< num 0) (+ lgth num) num)))
 227              (open (lambda (ls) (if (and (listp ls) (= (length ls) 1)) (car ls) ls))))
 228         (funcall
 229          open
 230          (mapcar
 231           (lambda (sub-lis)
 232             (if (listp sub-lis)
 233                 (org-babel-ref-index-list remainder sub-lis)
 234               sub-lis))
 235           (if (or (= 0 (length portion)) (string-match ind-re portion))
 236               (mapcar
 237                (lambda (n) (nth n lis))
 238                (apply 'org-number-sequence
 239                       (if (and (> (length portion) 0) (match-string 2 portion))
 240                           (list
 241                            (funcall wrap (string-to-number (match-string 2 portion)))
 242                            (funcall wrap (string-to-number (match-string 3 portion))))
 243                         (list (funcall wrap 0) (funcall wrap -1)))))
 244             (list (nth (funcall wrap (string-to-number portion)) lis))))))
 245     lis))
 246
 247 (defun org-babel-ref-split-args (arg-string)
 248   "Split ARG-STRING into top-level arguments of balanced parenthesis."
 249   (mapcar #'org-babel-trim (org-babel-balanced-split arg-string 44)))
 250
 251 (defvar org-bracket-link-regexp)
 252 (defun org-babel-ref-at-ref-p ()
 253   "Return the type of reference located at point.
 254 Return nil if none of the supported reference types are found.
 255 Supported reference types are tables and source blocks."
 256   (cond ((org-at-table-p) 'table)
 257         ((org-at-item-p) 'list)
 258         ((looking-at "^[ \t]*#\\+BEGIN_SRC") 'source-block)
 259         ((looking-at org-bracket-link-regexp) 'file)
 260         ((looking-at org-babel-result-regexp) 'results-line)))
 261
 262 (provide 'ob-ref)
 263
 264
 265
 266 ;;; ob-ref.el ends here