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+;;; ob-ref.el --- org-babel functions for referencing external data
+
+;; Copyright (C) 2009-2012 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
+
+;; #+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 '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-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 (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
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