;;; ob-ref.el --- Babel Functions for Referencing External Data -*- lexical-binding: t; -*- ;; Copyright (C) 2009-2018 Free Software Foundation, Inc. ;; Authors: Eric Schulte ;; Dan Davison ;; Keywords: literate programming, reproducible research ;; Homepage: https://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 <https://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) (require 'cl-lib) (declare-function org-babel-lob-get-info "ob-lob" (&optional datum)) (declare-function org-element-at-point "org-element" ()) (declare-function org-element-property "org-element" (property element)) (declare-function org-element-type "org-element" (element)) (declare-function org-end-of-meta-data "org" (&optional full)) (declare-function org-find-property "org" (property &optional value)) (declare-function org-id-find-id-file "org-id" (id)) (declare-function org-id-find-id-in-file "org-id" (id file &optional markerp)) (declare-function org-in-commented-heading-p "org" (&optional no-inheritance)) (declare-function org-narrow-to-subtree "org" ()) (declare-function org-show-context "org" (&optional key)) (declare-function org-trim "org" (s &optional keep-lead)) (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 it as a reference to an external resource and find its value using `org-babel-ref-resolve'. Return a list with two elements: the name of the variable, and an Emacs Lisp representation of the value of the variable." (when (string-match "\\(.+?\\)=" assignment) (let ((var (org-trim (match-string 1 assignment))) (ref (org-trim (substring assignment (match-end 0))))) (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 (and (string-prefix-p "\"" ref) (string-suffix-p "\"" ref)) (read ref) (org-babel-ref-resolve ref)) out)))))) (defun org-babel-ref-goto-headline-id (id) (or (let ((h (org-find-property "CUSTOM_ID" id))) (when h (goto-char h))) (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) (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)) (org-end-of-meta-data) (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 (with-current-buffer (or org-babel-exp-reference-buffer (current-buffer)) (save-excursion (let ((case-fold-search t) args new-refere new-header-args new-referent split-file split-ref index) ;; if ref is indexed grab the indices -- beware nested indices (when (and (string-match "\\[\\([^\\[]+\\)\\]$" ref) (let ((str (substring ref 0 (match-beginning 0)))) (= (cl-count ?\( str) (cl-count ?\) 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)) (org-with-wide-buffer (goto-char (point-min)) (let* ((params (append args '((:results . "silent")))) (regexp (org-babel-named-data-regexp-for-name ref)) (result (catch :found ;; Check for code blocks or named data. (while (re-search-forward regexp nil t) ;; Ignore COMMENTed headings and orphaned ;; affiliated keywords. (unless (org-in-commented-heading-p) (let ((e (org-element-at-point))) (when (equal (org-element-property :name e) ref) (goto-char (org-element-property :post-affiliated e)) (pcase (org-element-type e) (`babel-call (throw :found (org-babel-execute-src-block nil (org-babel-lob-get-info e) params))) (`src-block (throw :found (org-babel-execute-src-block nil nil (and (not org-babel-update-intermediate) params)))) ((and (let v (org-babel-read-element e)) (guard v)) (throw :found v)) (_ (error "Reference not found"))))))) ;; Check for local or global headlines by ID. (when (org-babel-ref-goto-headline-id ref) (throw :found (org-babel-ref-headline-body))) ;; Check the Library of Babel. (let ((info (cdr (assq (intern ref) org-babel-library-of-babel)))) (when info (throw :found (org-babel-execute-src-block nil info params)))) (error "Reference `%s' not found in this buffer" ref)))) (cond ((symbolp result) (format "%S" result)) ((and index (listp result)) (org-babel-ref-index-list index result)) (t 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-trim (org-babel-balanced-split arg-string 44))) (provide 'ob-ref) ;;; ob-ref.el ends here