;;; ob-ref.el --- org-babel functions for referencing external data
-;; Copyright (C) 2009-2011 Free Software Foundation, Inc.
+;; Copyright (C) 2009-2016 Free Software Foundation, Inc.
-;; Author: Eric Schulte, Dan Davison
+;; Authors: Eric Schulte
+;; Dan Davison
;; Keywords: literate programming, reproducible research
;; Homepage: http://orgmode.org
-;; Version: 7.4
;; This file is part of GNU Emacs.
;; So an example of a simple src block referencing table data in the
;; same file would be
-;; #+TBLNAME: sandbox
+;; #+NAME: sandbox
;; | 1 | 2 | 3 |
;; | 4 | org-babel | 6 |
;;
;; #+end_src
;;; Code:
-(require 'ob)
+(require 'ob-core)
(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" ())
+(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 it's value using
+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
(let ((var (match-string 1 assignment))
(ref (match-string 2 assignment)))
(cons (intern var)
- (let ((out (org-babel-read ref)))
+ (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 "^\".+\"$" ref)
+ (if (string-match "^\".*\"$" 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]*$") nil t)
+ (let* ((file (org-id-find-id-file id))
+ (m (when file (org-id-find-id-in-file id file 'marker))))
+ (when (and file m)
+ (message "file:%S" file)
+ (org-pop-to-buffer-same-window (marker-buffer m))
+ (goto-char m)
+ (move-marker m nil)
+ (org-show-context)
+ t)))))
+
+(defun org-babel-ref-headline-body ()
+ (save-restriction
+ (org-narrow-to-subtree)
+ (buffer-substring
+ (save-excursion (goto-char (point-min))
+ (forward-line 1)
+ (when (looking-at "[ \t]*:PROPERTIES:")
+ (re-search-forward ":END:" nil)
+ (forward-char))
+ (point))
+ (point-max))))
+
(defvar org-babel-library-of-babel)
(defun org-babel-ref-resolve (ref)
"Resolve the reference REF and return its value."
- (save-excursion
- (let ((case-fold-search t)
- type args new-refere new-header-args new-referent result
- lob-info split-file split-ref index index-row index-col)
- ;; if ref is indexed grab the indices -- beware nested indices
- (when (and (string-match "\\[\\([^\\[]+\\)\\]$" 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]*$")))
- ;; goto ref in the current buffer
- (or (and (not args)
- (or (re-search-forward result_regexp nil t)
- (re-search-backward result_regexp nil t)))
- (re-search-forward regexp nil t)
- (re-search-backward regexp nil t)
- ;; check the Library of Babel
- (setq lob-info (cdr (assoc (intern ref)
- org-babel-library-of-babel)))))
- (unless lob-info (goto-char (match-beginning 0)))
- ;; ;; TODO: allow searching for names in other buffers
- ;; (setq id-loc (org-id-find ref 'marker)
- ;; buffer (marker-buffer id-loc)
- ;; loc (marker-position id-loc))
- ;; (move-marker id-loc nil)
- (error "reference '%s' not found in this buffer" ref))
- (if lob-info
- (setq type 'lob)
- (while (not (setq type (org-babel-ref-at-ref-p)))
- (forward-line 1)
- (beginning-of-line)
- (if (or (= (point) (point-min)) (= (point) (point-max)))
- (error "reference not found"))))
- (let ((params (append args '((:results . "silent")))))
- (setq result
- (case type
- (results-line (org-babel-read-result))
- (table (org-babel-read-table))
- (list (org-babel-read-list))
- (file (org-babel-read-link))
- (source-block (org-babel-execute-src-block nil nil params))
- (lob (org-babel-execute-src-block nil lob-info params)))))
- (if (symbolp result)
- (format "%S" result)
- (if (and index (listp result))
- (org-babel-ref-index-list index result)
- result))))))
+ (save-window-excursion
+ (save-excursion
+ (let ((case-fold-search t)
+ type args new-refere new-header-args new-referent result
+ lob-info split-file split-ref index index-row index-col id)
+ ;; if ref is indexed grab the indices -- beware nested indices
+ (when (and (string-match "\\[\\([^\\[]+\\)\\]$" 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.
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)))))))
+ (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."
- (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)))))
+ (mapcar #'org-babel-trim (org-babel-balanced-split arg-string 44)))
(defvar org-bracket-link-regexp)
(defun org-babel-ref-at-ref-p ()
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)
+ ((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