;;; ob-ref.el --- Babel Functions for Referencing External Data -*- lexical-binding: t; -*-
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;; Copyright (C) 2009-2018 Free Software Foundation, Inc.
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;; Authors: Eric Schulte
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;; Dan Davison
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;; Keywords: literate programming, reproducible research
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;; Homepage: https://orgmode.org
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;; This file is part of GNU Emacs.
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;; GNU Emacs is free software: you can redistribute it and/or modify
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;; it under the terms of the GNU General Public License as published by
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;; the Free Software Foundation, either version 3 of the License, or
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;; (at your option) any later version.
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;; GNU Emacs is distributed in the hope that it will be useful,
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU General Public License for more details.
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;; You should have received a copy of the GNU General Public License
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;; along with GNU Emacs. If not, see <https://www.gnu.org/licenses/>.
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;;; Commentary:
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;; Functions for referencing data from the header arguments of a
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;; org-babel block. The syntax of such a reference should be
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;; #+VAR: variable-name=file:resource-id
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;; - variable-name :: the name of the variable to which the value
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;; will be assigned
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;; - file :: path to the file containing the resource, or omitted if
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;; resource is in the current file
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;; - resource-id :: the id or name of the resource
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;; So an example of a simple src block referencing table data in the
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;; same file would be
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;; #+NAME: sandbox
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;; | 1 | 2 | 3 |
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;; | 4 | org-babel | 6 |
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;;
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;; #+begin_src emacs-lisp :var table=sandbox
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;; (message table)
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;; #+end_src
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;;; Code:
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(require 'ob-core)
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(require 'cl-lib)
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(declare-function org-babel-lob-get-info "ob-lob" (&optional datum))
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(declare-function org-element-at-point "org-element" ())
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(declare-function org-element-property "org-element" (property element))
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(declare-function org-element-type "org-element" (element))
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(declare-function org-end-of-meta-data "org" (&optional full))
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(declare-function org-find-property "org" (property &optional value))
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(declare-function org-id-find-id-file "org-id" (id))
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(declare-function org-id-find-id-in-file "org-id" (id file &optional markerp))
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(declare-function org-in-commented-heading-p "org" (&optional no-inheritance))
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(declare-function org-narrow-to-subtree "org" ())
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(declare-function org-show-context "org" (&optional key))
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(declare-function org-trim "org" (s &optional keep-lead))
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(defvar org-babel-update-intermediate nil
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"Update the in-buffer results of code blocks executed to resolve references.")
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(defun org-babel-ref-parse (assignment)
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"Parse a variable ASSIGNMENT in a header argument.
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If the right hand side of the assignment has a literal value
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return that value, otherwise interpret it as a reference to an
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external resource and find its value using `org-babel-ref-resolve'.
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Return a list with two elements: the name of the variable, and an
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Emacs Lisp representation of the value of the variable."
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(when (string-match "\\(.+?\\)=" assignment)
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(let ((var (org-trim (match-string 1 assignment)))
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(ref (org-trim (substring assignment (match-end 0)))))
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(cons (intern var)
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(let ((out (save-excursion
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(when org-babel-current-src-block-location
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(goto-char (if (markerp org-babel-current-src-block-location)
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(marker-position org-babel-current-src-block-location)
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org-babel-current-src-block-location)))
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(org-babel-read ref))))
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(if (equal out ref)
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(if (and (string-prefix-p "\"" ref)
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(string-suffix-p "\"" ref))
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(read ref)
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(org-babel-ref-resolve ref))
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out))))))
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(defun org-babel-ref-goto-headline-id (id)
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(or (let ((h (org-find-property "CUSTOM_ID" id)))
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(when h (goto-char h)))
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(let* ((file (org-id-find-id-file id))
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(m (when file (org-id-find-id-in-file id file 'marker))))
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(when (and file m)
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(message "file:%S" file)
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(pop-to-buffer-same-window (marker-buffer m))
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(goto-char m)
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(move-marker m nil)
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(org-show-context)
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t))))
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(defun org-babel-ref-headline-body ()
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(save-restriction
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(org-narrow-to-subtree)
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(buffer-substring
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(save-excursion (goto-char (point-min))
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(org-end-of-meta-data)
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(point))
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(point-max))))
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(defvar org-babel-library-of-babel)
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(defun org-babel-ref-resolve (ref)
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"Resolve the reference REF and return its value."
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(save-window-excursion
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(with-current-buffer (or org-babel-exp-reference-buffer (current-buffer))
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(save-excursion
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(let ((case-fold-search t)
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args new-refere new-header-args new-referent split-file split-ref
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index)
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;; if ref is indexed grab the indices -- beware nested indices
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(when (and (string-match "\\[\\([^\\[]+\\)\\]$" ref)
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(let ((str (substring ref 0 (match-beginning 0))))
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(= (cl-count ?\( str) (cl-count ?\) str))))
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(setq index (match-string 1 ref))
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(setq ref (substring ref 0 (match-beginning 0))))
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;; assign any arguments to pass to source block
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(when (string-match
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"^\\(.+?\\)\\(\\[\\(.*\\)\\]\\|\\(\\)\\)(\\(.*\\))$" ref)
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(setq new-refere (match-string 1 ref))
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(setq new-header-args (match-string 3 ref))
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(setq new-referent (match-string 5 ref))
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(when (> (length new-refere) 0)
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(when (> (length new-referent) 0)
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(setq args (mapcar (lambda (ref) (cons :var ref))
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(org-babel-ref-split-args new-referent))))
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(when (> (length new-header-args) 0)
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(setq args (append (org-babel-parse-header-arguments
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new-header-args) args)))
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(setq ref new-refere)))
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(when (string-match "^\\(.+\\):\\(.+\\)$" ref)
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(setq split-file (match-string 1 ref))
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(setq split-ref (match-string 2 ref))
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(find-file split-file)
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(setq ref split-ref))
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(org-with-wide-buffer
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(goto-char (point-min))
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(let* ((params (append args '((:results . "silent"))))
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(regexp (org-babel-named-data-regexp-for-name ref))
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(result
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(catch :found
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;; Check for code blocks or named data.
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(while (re-search-forward regexp nil t)
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;; Ignore COMMENTed headings and orphaned
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;; affiliated keywords.
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(unless (org-in-commented-heading-p)
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(let ((e (org-element-at-point)))
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(when (equal (org-element-property :name e) ref)
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(goto-char
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(org-element-property :post-affiliated e))
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(pcase (org-element-type e)
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(`babel-call
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(throw :found
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(org-babel-execute-src-block
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nil (org-babel-lob-get-info e) params)))
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(`src-block
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(throw :found
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(org-babel-execute-src-block
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nil nil
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(and
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(not org-babel-update-intermediate)
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params))))
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((and (let v (org-babel-read-element e))
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(guard v))
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(throw :found v))
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(_ (error "Reference not found")))))))
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;; Check for local or global headlines by ID.
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(when (org-babel-ref-goto-headline-id ref)
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(throw :found (org-babel-ref-headline-body)))
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;; Check the Library of Babel.
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(let ((info (cdr (assq (intern ref)
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org-babel-library-of-babel))))
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(when info
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(throw :found
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(org-babel-execute-src-block nil info params))))
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(error "Reference `%s' not found in this buffer" ref))))
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(cond
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((symbolp result) (format "%S" result))
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((and index (listp result))
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(org-babel-ref-index-list index result))
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(t result)))))))))
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(defun org-babel-ref-index-list (index lis)
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"Return the subset of LIS indexed by INDEX.
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Indices are 0 based and negative indices count from the end of
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LIS, so 0 references the first element of LIS and -1 references
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the last. If INDEX is separated by \",\"s then each \"portion\"
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is assumed to index into the next deepest nesting or dimension.
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A valid \"portion\" can consist of either an integer index, two
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integers separated by a \":\" in which case the entire range is
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returned, or an empty string or \"*\" both of which are
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interpreted to mean the entire range and as such are equivalent
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to \"0:-1\"."
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(if (and (> (length index) 0) (string-match "^\\([^,]*\\),?" index))
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(let* ((ind-re "\\(\\([-[:digit:]]+\\):\\([-[:digit:]]+\\)\\|\\*\\)")
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(lgth (length lis))
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(portion (match-string 1 index))
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(remainder (substring index (match-end 0)))
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(wrap (lambda (num) (if (< num 0) (+ lgth num) num)))
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(open (lambda (ls) (if (and (listp ls) (= (length ls) 1)) (car ls) ls))))
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(funcall
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open
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(mapcar
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(lambda (sub-lis)
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(if (listp sub-lis)
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(org-babel-ref-index-list remainder sub-lis)
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sub-lis))
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(if (or (= 0 (length portion)) (string-match ind-re portion))
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(mapcar
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(lambda (n) (nth n lis))
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(apply 'org-number-sequence
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(if (and (> (length portion) 0) (match-string 2 portion))
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(list
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(funcall wrap (string-to-number (match-string 2 portion)))
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(funcall wrap (string-to-number (match-string 3 portion))))
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(list (funcall wrap 0) (funcall wrap -1)))))
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(list (nth (funcall wrap (string-to-number portion)) lis))))))
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lis))
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(defun org-babel-ref-split-args (arg-string)
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"Split ARG-STRING into top-level arguments of balanced parenthesis."
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(mapcar #'org-trim (org-babel-balanced-split arg-string 44)))
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(provide 'ob-ref)
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;;; ob-ref.el ends here
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