1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
|
;;; ob-ref.el --- org-babel functions for referencing external data
;; Copyright (C) 2009-2011 Free Software Foundation, Inc.
;; Author: Eric Schulte, Dan Davison
;; Keywords: literate programming, reproducible research
;; Homepage: http://orgmode.org
;; Version: 7.4
;; This file is part of GNU Emacs.
;; GNU Emacs is free software: you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation, either version 3 of the License, or
;; (at your option) any later version.
;; GNU Emacs is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;; GNU General Public License for more details.
;; You should have received a copy of the GNU General Public License
;; along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>.
;;; Commentary:
;; Functions for referencing data from the header arguments of a
;; org-babel block. The syntax of such a reference should be
;; #+VAR: variable-name=file:resource-id
;; - variable-name :: the name of the variable to which the value
;; will be assigned
;; - file :: path to the file containing the resource, or omitted if
;; resource is in the current file
;; - resource-id :: the id or name of the resource
;; So an example of a simple src block referencing table data in the
;; same file would be
;; #+TBLNAME: sandbox
;; | 1 | 2 | 3 |
;; | 4 | org-babel | 6 |
;;
;; #+begin_src emacs-lisp :var table=sandbox
;; (message table)
;; #+end_src
;;; Code:
(require 'ob)
(eval-when-compile
(require 'org-list)
(require 'cl))
(declare-function org-remove-if-not "org" (predicate seq))
(declare-function org-at-table-p "org" (&optional table-type))
(declare-function org-count "org" (CL-ITEM CL-SEQ))
(declare-function org-in-item-p "org-list" ())
(defvar org-babel-ref-split-regexp
"[ \f\t\n\r\v]*\\(.+?\\)[ \f\t\n\r\v]*=[ \f\t\n\r\v]*\\(.+\\)[ \f\t\n\r\v]*")
(defun org-babel-ref-parse (assignment)
"Parse a variable ASSIGNMENT in a header argument.
If the right hand side of the assignment has a literal value
return that value, otherwise interpret as a reference to an
external resource and find it's value using
`org-babel-ref-resolve'. Return a list with two elements. The
first element of the list will be the name of the variable, and
the second will be an emacs-lisp representation of the value of
the variable."
(when (string-match org-babel-ref-split-regexp assignment)
(let ((var (match-string 1 assignment))
(ref (match-string 2 assignment)))
(cons (intern var)
(let ((out (org-babel-read ref)))
(if (equal out ref)
(if (string-match "^\".+\"$" ref)
(read ref)
(org-babel-ref-resolve ref))
out))))))
(defvar org-babel-library-of-babel)
(defun org-babel-ref-resolve (ref)
"Resolve the reference REF and return its value."
(save-excursion
(let ((case-fold-search t)
type args new-refere new-header-args new-referent result
lob-info split-file split-ref index index-row index-col)
;; if ref is indexed grab the indices -- beware nested indices
(when (and (string-match "\\[\\([^\\[]+\\)\\]$" ref)
(let ((str (substring ref 0 (match-beginning 0))))
(= (org-count ?( str) (org-count ?) str))))
(setq index (match-string 1 ref))
(setq ref (substring ref 0 (match-beginning 0))))
;; assign any arguments to pass to source block
(when (string-match
"^\\(.+?\\)\\(\\[\\(.*\\)\\]\\|\\(\\)\\)\(\\(.*\\)\)$" ref)
(setq new-refere (match-string 1 ref))
(setq new-header-args (match-string 3 ref))
(setq new-referent (match-string 5 ref))
(when (> (length new-refere) 0)
(when (> (length new-referent) 0)
(setq args (mapcar (lambda (ref) (cons :var ref))
(org-babel-ref-split-args new-referent))))
(when (> (length new-header-args) 0)
(setq args (append (org-babel-parse-header-arguments new-header-args)
args)))
(setq ref new-refere)))
(when (string-match "^\\(.+\\):\\(.+\\)$" ref)
(setq split-file (match-string 1 ref))
(setq split-ref (match-string 2 ref))
(find-file split-file) (setq ref split-ref))
(save-restriction
(widen)
(goto-char (point-min))
(if (let ((result_regexp (concat "^[ \t]*#\\+\\(TBLNAME\\|RESNAME"
"\\|RESULTS\\):[ \t]*"
(regexp-quote ref) "[ \t]*$"))
(regexp (concat org-babel-src-name-regexp
(regexp-quote ref) "\\(\(.*\)\\)?" "[ \t]*$")))
;; goto ref in the current buffer
(or (and (not args)
(or (re-search-forward result_regexp nil t)
(re-search-backward result_regexp nil t)))
(re-search-forward regexp nil t)
(re-search-backward regexp nil t)
;; check the Library of Babel
(setq lob-info (cdr (assoc (intern ref)
org-babel-library-of-babel)))))
(unless lob-info (goto-char (match-beginning 0)))
;; ;; TODO: allow searching for names in other buffers
;; (setq id-loc (org-id-find ref 'marker)
;; buffer (marker-buffer id-loc)
;; loc (marker-position id-loc))
;; (move-marker id-loc nil)
(error "reference '%s' not found in this buffer" ref))
(if lob-info
(setq type 'lob)
(while (not (setq type (org-babel-ref-at-ref-p)))
(forward-line 1)
(beginning-of-line)
(if (or (= (point) (point-min)) (= (point) (point-max)))
(error "reference not found"))))
(let ((params (append args '((:results . "silent")))))
(setq result
(case type
('results-line (org-babel-read-result))
('table (org-babel-read-table))
('list (org-babel-read-list))
('file (org-babel-read-link))
('source-block (org-babel-execute-src-block nil nil params))
('lob (org-babel-execute-src-block nil lob-info params)))))
(if (symbolp result)
(format "%S" result)
(if (and index (listp result))
(org-babel-ref-index-list index result)
result))))))
(defun org-babel-ref-index-list (index lis)
"Return the subset of LIS indexed by INDEX.
Indices are 0 based and negative indices count from the end of
LIS, so 0 references the first element of LIS and -1 references
the last. If INDEX is separated by \",\"s then each \"portion\"
is assumed to index into the next deepest nesting or dimension.
A valid \"portion\" can consist of either an integer index, two
integers separated by a \":\" in which case the entire range is
returned, or an empty string or \"*\" both of which are
interpreted to mean the entire range and as such are equivalent
to \"0:-1\"."
(if (and (> (length index) 0) (string-match "^\\([^,]*\\),?" index))
(let ((ind-re "\\(\\([-[:digit:]]+\\):\\([-[:digit:]]+\\)\\|\*\\)")
(length (length lis))
(portion (match-string 1 index))
(remainder (substring index (match-end 0))))
(flet ((wrap (num) (if (< num 0) (+ length num) num))
(open (ls) (if (and (listp ls) (= (length ls) 1)) (car ls) ls)))
(open
(mapcar
(lambda (sub-lis) (org-babel-ref-index-list remainder sub-lis))
(if (or (= 0 (length portion)) (string-match ind-re portion))
(mapcar
(lambda (n) (nth n lis))
(apply 'org-number-sequence
(if (and (> (length portion) 0) (match-string 2 portion))
(list
(wrap (string-to-number (match-string 2 portion)))
(wrap (string-to-number (match-string 3 portion))))
(list (wrap 0) (wrap -1)))))
(list (nth (wrap (string-to-number portion)) lis)))))))
lis))
(defun org-babel-ref-split-args (arg-string)
"Split ARG-STRING into top-level arguments of balanced parenthesis."
(let ((index 0) (depth 0) (buffer "") holder return)
;; crawl along string, splitting at any ","s which are on the top level
(while (< index (length arg-string))
(setq holder (substring arg-string index (+ 1 index)))
(setq buffer (concat buffer holder))
(setq index (+ 1 index))
(cond
((string= holder ",")
(when (= depth 0)
(setq return (reverse (cons (substring buffer 0 -1) return)))
(setq buffer "")))
((or (string= holder "(") (string= holder "[")) (setq depth (+ depth 1)))
((or (string= holder ")") (string= holder "]")) (setq depth (- depth 1)))))
(mapcar #'org-babel-trim (reverse (cons buffer return)))))
(defvar org-bracket-link-regexp)
(defun org-babel-ref-at-ref-p ()
"Return the type of reference located at point.
Return nil if none of the supported reference types are found.
Supported reference types are tables and source blocks."
(cond ((org-at-table-p) 'table)
((org-in-item-p) 'list)
((looking-at "^[ \t]*#\\+BEGIN_SRC") 'source-block)
((looking-at org-bracket-link-regexp) 'file)
((looking-at org-babel-result-regexp) 'results-line)))
(provide 'ob-ref)
;;; ob-ref.el ends here
|
