lisp/ob-ref.el

   1 ;;; ob-ref.el --- org-babel functions for referencing external data
   2
   3 ;; Copyright (C) 2009-2014 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 (save-excursion
  87                          (when org-babel-current-src-block-location
  88                            (goto-char org-babel-current-src-block-location))
  89                          (org-babel-read ref))))
  90               (if (equal out ref)
  91                   (if (string-match "^\".*\"$" ref)
  92                       (read ref)
  93                     (org-babel-ref-resolve ref))
  94                 out))))))
  95
  96 (defun org-babel-ref-goto-headline-id (id)
  97   (goto-char (point-min))
  98   (let ((rx (regexp-quote id)))
  99     (or (re-search-forward
 100          (concat "^[ \t]*:CUSTOM_ID:[ \t]+" rx "[ \t]*$") nil t)
 101         (let* ((file (org-id-find-id-file id))
 102                (m (when file (org-id-find-id-in-file id file 'marker))))
 103           (when (and file m)
 104             (message "file:%S" file)
 105             (org-pop-to-buffer-same-window (marker-buffer m))
 106             (goto-char m)
 107             (move-marker m nil)
 108             (org-show-context)
 109             t)))))
 110
 111 (defun org-babel-ref-headline-body ()
 112   (save-restriction
 113     (org-narrow-to-subtree)
 114     (buffer-substring
 115      (save-excursion (goto-char (point-min))
 116                      (forward-line 1)
 117                      (when (looking-at "[ \t]*:PROPERTIES:")
 118                        (re-search-forward ":END:" nil)
 119                        (forward-char))
 120                      (point))
 121      (point-max))))
 122
 123 (defvar org-babel-library-of-babel)
 124 (defun org-babel-ref-resolve (ref)
 125   "Resolve the reference REF and return its value."
 126   (save-window-excursion
 127     (save-excursion
 128       (let ((case-fold-search t)
 129             type args new-refere new-header-args new-referent result
 130             lob-info split-file split-ref index index-row index-col id)
 131         ;; if ref is indexed grab the indices -- beware nested indices
 132         (when (and (string-match "\\[\\([^\\[]+\\)\\]$" ref)
 133                    (let ((str (substring ref 0 (match-beginning 0))))
 134                      (= (org-count ?( str) (org-count ?) str))))
 135           (setq index (match-string 1 ref))
 136           (setq ref (substring ref 0 (match-beginning 0))))
 137         ;; assign any arguments to pass to source block
 138         (when (string-match
 139                "^\\(.+?\\)\\(\\[\\(.*\\)\\]\\|\\(\\)\\)\(\\(.*\\)\)$" ref)
 140           (setq new-refere      (match-string 1 ref))
 141           (setq new-header-args (match-string 3 ref))
 142           (setq new-referent    (match-string 5 ref))
 143           (when (> (length new-refere) 0)
 144             (when (> (length new-referent) 0)
 145               (setq args (mapcar (lambda (ref) (cons :var ref))
 146                                  (org-babel-ref-split-args new-referent))))
 147             (when (> (length new-header-args) 0)
 148               (setq args (append (org-babel-parse-header-arguments
 149                                   new-header-args) args)))
 150             (setq ref new-refere)))
 151         (when (string-match "^\\(.+\\):\\(.+\\)$" ref)
 152           (setq split-file (match-string 1 ref))
 153           (setq split-ref (match-string 2 ref))
 154           (find-file split-file) (setq ref split-ref))
 155         (save-restriction
 156           (widen)
 157           (goto-char (point-min))
 158           (if (let ((src-rx (org-babel-named-src-block-regexp-for-name ref))
 159                     (res-rx (org-babel-named-data-regexp-for-name ref)))
 160                 ;; goto ref in the current buffer
 161                 (or
 162                  ;; check for code blocks
 163                  (re-search-forward src-rx nil t)
 164                  ;; check for named data
 165                  (re-search-forward res-rx nil t)
 166                  ;; check for local or global headlines by id
 167                  (setq id (org-babel-ref-goto-headline-id ref))
 168                  ;; check the Library of Babel
 169                  (setq lob-info (cdr (assoc (intern ref)
 170                                             org-babel-library-of-babel)))))
 171               (unless (or lob-info id) (goto-char (match-beginning 0)))
 172             ;; ;; TODO: allow searching for names in other buffers
 173             ;; (setq id-loc (org-id-find ref 'marker)
 174             ;;       buffer (marker-buffer id-loc)
 175             ;;       loc (marker-position id-loc))
 176             ;; (move-marker id-loc nil)
 177             (error "Reference '%s' not found in this buffer" ref))
 178           (cond
 179            (lob-info (setq type 'lob))
 180            (id (setq type 'id))
 181            ((and (looking-at org-babel-src-name-regexp)
 182                  (save-excursion
 183                    (forward-line 1)
 184                    (or (looking-at org-babel-src-block-regexp)
 185                        (looking-at org-babel-multi-line-header-regexp))))
 186             (setq type 'source-block))
 187            (t (while (not (setq type (org-babel-ref-at-ref-p)))
 188                 (forward-line 1)
 189                 (beginning-of-line)
 190                 (if (or (= (point) (point-min)) (= (point) (point-max)))
 191                     (error "Reference not found")))))
 192           (let ((params (append args '((:results . "silent")))))
 193             (setq result
 194                   (case type
 195                     (results-line (org-babel-read-result))
 196                     (table        (org-babel-read-table))
 197                     (list         (org-babel-read-list))
 198                     (file         (org-babel-read-link))
 199                     (source-block (org-babel-execute-src-block
 200                                    nil nil (if org-babel-update-intermediate
 201                                                nil params)))
 202                     (lob          (org-babel-execute-src-block
 203                                    nil lob-info params))
 204                     (id           (org-babel-ref-headline-body)))))
 205           (if (symbolp result)
 206               (format "%S" result)
 207             (if (and index (listp result))
 208                 (org-babel-ref-index-list index result)
 209               result)))))))
 210
 211 (defun org-babel-ref-index-list (index lis)
 212   "Return the subset of LIS indexed by INDEX.
 213
 214 Indices are 0 based and negative indices count from the end of
 215 LIS, so 0 references the first element of LIS and -1 references
 216 the last.  If INDEX is separated by \",\"s then each \"portion\"
 217 is assumed to index into the next deepest nesting or dimension.
 218
 219 A valid \"portion\" can consist of either an integer index, two
 220 integers separated by a \":\" in which case the entire range is
 221 returned, or an empty string or \"*\" both of which are
 222 interpreted to mean the entire range and as such are equivalent
 223 to \"0:-1\"."
 224   (if (and (> (length index) 0) (string-match "^\\([^,]*\\),?" index))
 225       (let* ((ind-re "\\(\\([-[:digit:]]+\\):\\([-[:digit:]]+\\)\\|\*\\)")
 226              (lgth (length lis))
 227              (portion (match-string 1 index))
 228              (remainder (substring index (match-end 0)))
 229              (wrap (lambda (num) (if (< num 0) (+ lgth num) num)))
 230              (open (lambda (ls) (if (and (listp ls) (= (length ls) 1)) (car ls) ls))))
 231         (funcall
 232          open
 233          (mapcar
 234           (lambda (sub-lis)
 235             (if (listp sub-lis)
 236                 (org-babel-ref-index-list remainder sub-lis)
 237               sub-lis))
 238           (if (or (= 0 (length portion)) (string-match ind-re portion))
 239               (mapcar
 240                (lambda (n) (nth n lis))
 241                (apply 'org-number-sequence
 242                       (if (and (> (length portion) 0) (match-string 2 portion))
 243                           (list
 244                            (funcall wrap (string-to-number (match-string 2 portion)))
 245                            (funcall wrap (string-to-number (match-string 3 portion))))
 246                         (list (funcall wrap 0) (funcall wrap -1)))))
 247             (list (nth (funcall wrap (string-to-number portion)) lis))))))
 248     lis))
 249
 250 (defun org-babel-ref-split-args (arg-string)
 251   "Split ARG-STRING into top-level arguments of balanced parenthesis."
 252   (mapcar #'org-babel-trim (org-babel-balanced-split arg-string 44)))
 253
 254 (defvar org-bracket-link-regexp)
 255 (defun org-babel-ref-at-ref-p ()
 256   "Return the type of reference located at point.
 257 Return nil if none of the supported reference types are found.
 258 Supported reference types are tables and source blocks."
 259   (cond ((org-at-table-p) 'table)
 260         ((org-at-item-p) 'list)
 261         ((looking-at "^[ \t]*#\\+BEGIN_SRC") 'source-block)
 262         ((looking-at org-bracket-link-regexp) 'file)
 263         ((looking-at org-babel-result-regexp) 'results-line)))
 264
 265 (provide 'ob-ref)
 266
 267
 268
 269 ;;; ob-ref.el ends here