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|
;;; ob-ref.el --- Babel Functions for Referencing External Data -*- lexical-binding: t; -*-
;; Copyright (C) 2009-2021 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 source 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 'org-macs)
(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))
(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
|
