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|
;;; ob-ref.el --- org-babel functions for referencing external data
;; Copyright (C) 2009-2016 Free Software Foundation, Inc.
;; Authors: Eric Schulte
;; Dan Davison
;; Keywords: literate programming, reproducible research
;; Homepage: http://orgmode.org
;; 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
;; #+NAME: sandbox
;; | 1 | 2 | 3 |
;; | 4 | org-babel | 6 |
;;
;; #+begin_src emacs-lisp :var table=sandbox
;; (message table)
;; #+end_src
;;; Code:
(require 'ob-core)
(eval-when-compile
(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-at-item-p "org-list" ())
(declare-function org-narrow-to-subtree "org" ())
(declare-function org-id-find-id-in-file "org-id" (id file &optional markerp))
(declare-function org-id-find-id-file "org-id" (id))
(declare-function org-show-context "org" (&optional key))
(declare-function org-pop-to-buffer-same-window
"org-compat" (&optional buffer-or-name norecord label))
(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]*")
(defvar org-babel-update-intermediate nil
"Update the in-buffer results of code blocks executed to resolve references.")
(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 its 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 (save-excursion
(when org-babel-current-src-block-location
(goto-char (if (markerp org-babel-current-src-block-location)
(marker-position org-babel-current-src-block-location)
org-babel-current-src-block-location)))
(org-babel-read ref))))
(if (equal out ref)
(if (string-match "^\".*\"$" ref)
(read ref)
(org-babel-ref-resolve ref))
out))))))
(defun org-babel-ref-goto-headline-id (id)
(goto-char (point-min))
(let ((rx (regexp-quote id)))
(or (re-search-forward
(concat "^[ \t]*:CUSTOM_ID:[ \t]+" rx "[ \t]*$") nil t)
(let* ((file (org-id-find-id-file id))
(m (when file (org-id-find-id-in-file id file 'marker))))
(when (and file m)
(message "file:%S" file)
(org-pop-to-buffer-same-window (marker-buffer m))
(goto-char m)
(move-marker m nil)
(org-show-context)
t)))))
(defun org-babel-ref-headline-body ()
(save-restriction
(org-narrow-to-subtree)
(buffer-substring
(save-excursion (goto-char (point-min))
(forward-line 1)
(when (looking-at "[ \t]*:PROPERTIES:")
(re-search-forward ":END:" nil)
(forward-char))
(point))
(point-max))))
(defvar org-babel-library-of-babel)
(defun org-babel-ref-resolve (ref)
"Resolve the reference REF and return its value."
(save-window-excursion
(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 id)
;; 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 ((src-rx (org-babel-named-src-block-regexp-for-name ref))
(res-rx (org-babel-named-data-regexp-for-name ref)))
;; goto ref in the current buffer
(or
;; check for code blocks
(re-search-forward src-rx nil t)
;; check for named data
(re-search-forward res-rx nil t)
;; check for local or global headlines by id
(setq id (org-babel-ref-goto-headline-id ref))
;; check the Library of Babel
(setq lob-info (cdr (assoc (intern ref)
org-babel-library-of-babel)))))
(unless (or lob-info id) (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))
(cond
(lob-info (setq type 'lob))
(id (setq type 'id))
((and (looking-at org-babel-src-name-regexp)
(save-excursion
(forward-line 1)
(or (looking-at org-babel-src-block-regexp)
(looking-at org-babel-multi-line-header-regexp))))
(setq type 'source-block))
(t (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 (if org-babel-update-intermediate
nil params)))
(lob (org-babel-execute-src-block
nil lob-info params))
(id (org-babel-ref-headline-body)))))
(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:]]+\\)\\|\\*\\)")
(lgth (length lis))
(portion (match-string 1 index))
(remainder (substring index (match-end 0)))
(wrap (lambda (num) (if (< num 0) (+ lgth num) num)))
(open (lambda (ls) (if (and (listp ls) (= (length ls) 1)) (car ls) ls))))
(funcall
open
(mapcar
(lambda (sub-lis)
(if (listp sub-lis)
(org-babel-ref-index-list remainder sub-lis)
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
(funcall wrap (string-to-number (match-string 2 portion)))
(funcall wrap (string-to-number (match-string 3 portion))))
(list (funcall wrap 0) (funcall wrap -1)))))
(list (nth (funcall 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."
(mapcar #'org-babel-trim (org-babel-balanced-split arg-string 44)))
(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-at-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
|
