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1 | ;;; ob-ref.el --- org-babel functions for referencing external data |
2 | ||
ba318903 | 3 | ;; Copyright (C) 2009-2014 Free Software Foundation, Inc. |
86fbb8ca | 4 | |
dfd98937 BG |
5 | ;; Authors: Eric Schulte |
6 | ;; Dan Davison | |
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7 | ;; Keywords: literate programming, reproducible research |
8 | ;; Homepage: http://orgmode.org | |
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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 | ||
271672fa | 43 | ;; #+NAME: sandbox |
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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: | |
271672fa | 52 | (require 'ob-core) |
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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)) | |
3ab2c837 BG |
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)) | |
bdebdb64 | 62 | (declare-function org-id-find-id-file "org-id" (id)) |
3ab2c837 | 63 | (declare-function org-show-context "org" (&optional key)) |
14e1337f | 64 | (declare-function org-pop-to-buffer-same-window |
e66ba1df | 65 | "org-compat" (&optional buffer-or-name norecord label)) |
86fbb8ca | 66 | |
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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 | ||
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70 | (defvar org-babel-update-intermediate nil |
71 | "Update the in-buffer results of code blocks executed to resolve references.") | |
72 | ||
afe98dfa | 73 | (defun org-babel-ref-parse (assignment) |
86fbb8ca CD |
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 | |
a98edce9 | 77 | external resource and find its value using |
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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) | |
271672fa BG |
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)))) | |
acedf35c | 90 | (if (equal out ref) |
3ab2c837 | 91 | (if (string-match "^\".*\"$" ref) |
acedf35c CD |
92 | (read ref) |
93 | (org-babel-ref-resolve ref)) | |
94 | out)))))) | |
86fbb8ca | 95 | |
3ab2c837 BG |
96 | (defun org-babel-ref-goto-headline-id (id) |
97 | (goto-char (point-min)) | |
98 | (let ((rx (regexp-quote id))) | |
99 | (or (re-search-forward | |
100 | (concat "^[ \t]*:CUSTOM_ID:[ \t]+" rx "[ \t]*$") 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) | |
e66ba1df | 105 | (org-pop-to-buffer-same-window (marker-buffer m)) |
3ab2c837 BG |
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 | ||
86fbb8ca | 123 | (defvar org-babel-library-of-babel) |
afe98dfa | 124 | (defun org-babel-ref-resolve (ref) |
86fbb8ca | 125 | "Resolve the reference REF and return its value." |
3ab2c837 | 126 | (save-window-excursion |
8223b1d2 BG |
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))))))) | |
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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)) | |
8223b1d2 BG |
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)))))) | |
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248 | lis)) |
249 | ||
250 | (defun org-babel-ref-split-args (arg-string) | |
251 | "Split ARG-STRING into top-level arguments of balanced parenthesis." | |
e66ba1df | 252 | (mapcar #'org-babel-trim (org-babel-balanced-split arg-string 44))) |
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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) | |
3ab2c837 | 260 | ((org-at-item-p) 'list) |
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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 | ||
5b409b39 | 267 | |
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268 | |
269 | ;;; ob-ref.el ends here |