lisp/ob-ref.el

   1 ;;; ob-ref.el --- org-babel functions for referencing external data
   2
   3 ;; Copyright (C) 2009-2011  Free Software Foundation, Inc.
   4
   5 ;; Author: 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 ;;  #+TBLNAME: 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)
  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-show-context "org" (&optional key))
  63 (declare-function org-pop-to-buffer-same-window
  64                   "org-compat" (&optional buffer-or-name norecord label))
  65
  66 (defvar org-babel-ref-split-regexp
  67   "[ \f\t\n\r\v]*\\(.+?\\)[ \f\t\n\r\v]*=[ \f\t\n\r\v]*\\(.+\\)[ \f\t\n\r\v]*")
  68
  69 (defvar org-babel-update-intermediate nil
  70   "Update the in-buffer results of code blocks executed to resolve references.")
  71
  72 (defun org-babel-ref-parse (assignment)
  73   "Parse a variable ASSIGNMENT in a header argument.
  74 If the right hand side of the assignment has a literal value
  75 return that value, otherwise interpret as a reference to an
  76 external resource and find its value using
  77 `org-babel-ref-resolve'.  Return a list with two elements.  The
  78 first element of the list will be the name of the variable, and
  79 the second will be an emacs-lisp representation of the value of
  80 the variable."
  81   (when (string-match org-babel-ref-split-regexp assignment)
  82     (let ((var (match-string 1 assignment))
  83           (ref (match-string 2 assignment)))
  84       (cons (intern var)
  85             (let ((out (org-babel-read ref)))
  86               (if (equal out ref)
  87                   (if (string-match "^\".*\"$" ref)
  88                       (read ref)
  89                     (org-babel-ref-resolve ref))
  90                 out))))))
  91
  92 (defun org-babel-ref-goto-headline-id (id)
  93   (goto-char (point-min))
  94   (let ((rx (regexp-quote id)))
  95     (or (re-search-forward
  96          (concat "^[ \t]*:CUSTOM_ID:[ \t]+" rx "[ \t]*$") nil t)
  97         (let* ((file (org-id-find-id-file id))
  98                (m (when file (org-id-find-id-in-file id file 'marker))))
  99           (when (and file m)
 100             (message "file:%S" file)
 101             (org-pop-to-buffer-same-window (marker-buffer m))
 102             (goto-char m)
 103             (move-marker m nil)
 104             (org-show-context)
 105             t)))))
 106
 107 (defun org-babel-ref-headline-body ()
 108   (save-restriction
 109     (org-narrow-to-subtree)
 110     (buffer-substring
 111      (save-excursion (goto-char (point-min))
 112                      (forward-line 1)
 113                      (when (looking-at "[ \t]*:PROPERTIES:")
 114                        (re-search-forward ":END:" nil)
 115                        (forward-char))
 116                      (point))
 117      (point-max))))
 118
 119 (defvar org-babel-library-of-babel)
 120 (defun org-babel-ref-resolve (ref)
 121   "Resolve the reference REF and return its value."
 122   (save-window-excursion
 123   (save-excursion
 124     (let ((case-fold-search t)
 125           type args new-refere new-header-args new-referent result
 126           lob-info split-file split-ref index index-row index-col id)
 127       ;; if ref is indexed grab the indices -- beware nested indices
 128       (when (and (string-match "\\[\\([^\\[]+\\)\\]$" ref)
 129                  (let ((str (substring ref 0 (match-beginning 0))))
 130                    (= (org-count ?( str) (org-count ?) str))))
 131         (setq index (match-string 1 ref))
 132         (setq ref (substring ref 0 (match-beginning 0))))
 133       ;; assign any arguments to pass to source block
 134       (when (string-match
 135              "^\\(.+?\\)\\(\\[\\(.*\\)\\]\\|\\(\\)\\)\(\\(.*\\)\)$" ref)
 136         (setq new-refere      (match-string 1 ref))
 137         (setq new-header-args (match-string 3 ref))
 138         (setq new-referent    (match-string 5 ref))
 139         (when (> (length new-refere) 0)
 140           (when (> (length new-referent) 0)
 141             (setq args (mapcar (lambda (ref) (cons :var ref))
 142                                (org-babel-ref-split-args new-referent))))
 143           (when (> (length new-header-args) 0)
 144             (setq args (append (org-babel-parse-header-arguments
 145                                 new-header-args) args)))
 146           (setq ref new-refere)))
 147       (when (string-match "^\\(.+\\):\\(.+\\)$" ref)
 148         (setq split-file (match-string 1 ref))
 149         (setq split-ref (match-string 2 ref))
 150         (find-file split-file) (setq ref split-ref))
 151       (save-restriction
 152         (widen)
 153         (goto-char (point-min))
 154         (if (let ((src-rx (org-babel-named-src-block-regexp-for-name ref))
 155                   (res-rx (org-babel-named-data-regexp-for-name ref)))
 156               ;; goto ref in the current buffer
 157               (or
 158                ;; check for code blocks
 159                (re-search-forward src-rx nil t)
 160                ;; check for named data
 161                (re-search-forward res-rx nil t)
 162                ;; check for local or global headlines by id
 163                (setq id (org-babel-ref-goto-headline-id ref))
 164                ;; check the Library of Babel
 165                (setq lob-info (cdr (assoc (intern ref)
 166                                           org-babel-library-of-babel)))))
 167             (unless (or lob-info id) (goto-char (match-beginning 0)))
 168           ;; ;; TODO: allow searching for names in other buffers
 169           ;; (setq id-loc (org-id-find ref 'marker)
 170           ;;       buffer (marker-buffer id-loc)
 171           ;;       loc (marker-position id-loc))
 172           ;; (move-marker id-loc nil)
 173           (error "reference '%s' not found in this buffer" ref))
 174         (cond
 175          (lob-info (setq type 'lob))
 176          (id (setq type 'id))
 177          ((and (looking-at org-babel-src-name-regexp)
 178                (save-excursion
 179                  (forward-line 1)
 180                  (or (looking-at org-babel-src-block-regexp)
 181                      (looking-at org-babel-multi-line-header-regexp))))
 182           (setq type 'source-block))
 183          (t (while (not (setq type (org-babel-ref-at-ref-p)))
 184               (forward-line 1)
 185               (beginning-of-line)
 186               (if (or (= (point) (point-min)) (= (point) (point-max)))
 187                   (error "reference not found")))))
 188         (let ((params (append args '((:results . "silent")))))
 189           (setq result
 190                 (case type
 191                   (results-line (org-babel-read-result))
 192                   (table        (org-babel-read-table))
 193                   (list         (org-babel-read-list))
 194                   (file         (org-babel-read-link))
 195                   (source-block (org-babel-execute-src-block
 196                                  nil nil (if org-babel-update-intermediate
 197                                              nil params)))
 198                   (lob          (org-babel-execute-src-block
 199                                  nil lob-info params))
 200                   (id           (org-babel-ref-headline-body)))))
 201         (if (symbolp result)
 202             (format "%S" result)
 203           (if (and index (listp result))
 204               (org-babel-ref-index-list index result)
 205             result)))))))
 206
 207 (defun org-babel-ref-index-list (index lis)
 208   "Return the subset of LIS indexed by INDEX.
 209
 210 Indices are 0 based and negative indices count from the end of
 211 LIS, so 0 references the first element of LIS and -1 references
 212 the last.  If INDEX is separated by \",\"s then each \"portion\"
 213 is assumed to index into the next deepest nesting or dimension.
 214
 215 A valid \"portion\" can consist of either an integer index, two
 216 integers separated by a \":\" in which case the entire range is
 217 returned, or an empty string or \"*\" both of which are
 218 interpreted to mean the entire range and as such are equivalent
 219 to \"0:-1\"."
 220   (if (and (> (length index) 0) (string-match "^\\([^,]*\\),?" index))
 221       (let ((ind-re "\\(\\([-[:digit:]]+\\):\\([-[:digit:]]+\\)\\|\*\\)")
 222             (length (length lis))
 223             (portion (match-string 1 index))
 224             (remainder (substring index (match-end 0))))
 225         (flet ((wrap (num) (if (< num 0) (+ length num) num))
 226                (open (ls) (if (and (listp ls) (= (length ls) 1)) (car ls) ls)))
 227           (open
 228            (mapcar
 229             (lambda (sub-lis)
 230               (if (listp sub-lis)
 231                   (org-babel-ref-index-list remainder sub-lis)
 232                 sub-lis))
 233             (if (or (= 0 (length portion)) (string-match ind-re portion))
 234                 (mapcar
 235                  (lambda (n) (nth n lis))
 236                  (apply 'org-number-sequence
 237                         (if (and (> (length portion) 0) (match-string 2 portion))
 238                             (list
 239                              (wrap (string-to-number (match-string 2 portion)))
 240                              (wrap (string-to-number (match-string 3 portion))))
 241                           (list (wrap 0) (wrap -1)))))
 242               (list (nth (wrap (string-to-number portion)) lis)))))))
 243     lis))
 244
 245 (defun org-babel-ref-split-args (arg-string)
 246   "Split ARG-STRING into top-level arguments of balanced parenthesis."
 247   (let ((index 0) (depth 0) (buffer "") holder return)
 248     ;; crawl along string, splitting at any ","s which are on the top level
 249     (while (< index (length arg-string))
 250       (setq holder (substring arg-string index (+ 1 index)))
 251       (setq buffer (concat buffer holder))
 252       (setq index (+ 1 index))
 253       (cond
 254        ((string= holder ",")
 255         (when (= depth 0)
 256           (setq return (cons (substring buffer 0 -1) return))
 257           (setq buffer "")))
 258        ((or (string= holder "(") (string= holder "[")) (setq depth (+ depth 1)))
 259        ((or (string= holder ")") (string= holder "]")) (setq depth (- depth 1)))))
 260     (mapcar #'org-babel-trim (reverse (cons buffer return)))))
 261
 262 (defvar org-bracket-link-regexp)
 263 (defun org-babel-ref-at-ref-p ()
 264   "Return the type of reference located at point.
 265 Return nil if none of the supported reference types are found.
 266 Supported reference types are tables and source blocks."
 267   (cond ((org-at-table-p) 'table)
 268         ((org-at-item-p) 'list)
 269         ((looking-at "^[ \t]*#\\+BEGIN_SRC") 'source-block)
 270         ((looking-at org-bracket-link-regexp) 'file)
 271         ((looking-at org-babel-result-regexp) 'results-line)))
 272
 273 (provide 'ob-ref)
 274
 275
 276
 277 ;;; ob-ref.el ends here