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+;;; org-bibtex-extras --- extras for working with org-bibtex entries
+
+;; Copyright (C) 2008-2012 Free Software Foundation, Inc.
+
+;; Author: Eric Schulte <eric dot schulte at gmx dot com>
+;; Keywords: outlines, hypermedia, bibtex, d3
+;; Homepage: http://orgmode.org
+;; Version: 0.01
+
+;; This file is not yet 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, 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:
+
+;; Warning: This should certainly be considered EXPERIMENTAL and still
+;; in development, feedback is welcome, but don't expect it
+;; to work.
+
+;; This file add some extra functionality to your bibtex entries which
+;; are stored as Org-mode headlines using org-bibtex.el. Most
+;; features expect that you keep all of your reading notes in a single
+;; file, set the `obe-bibtex-file' variable to the path to this file.
+;;
+;; - d3 view :: d3 is a Javascript library which supports interactive
+;; display of graphs. To view your citations as a d3
+;; graph, execute the following which will create a .json
+;; export of your references file, then grab a copy of
+;; d3, edit examples/force/force.js to replace
+;;
+;; var source`"miserables.json";
+;;
+;; with
+;;
+;; var source`"your-references.json";
+;;
+;; then view examples/force/force.html in your browser.
+;;
+;; - HTML export :: Customize the `obe-html-link-base' variable so
+;; that it points to an html export of your
+;; references, then add the following to your html
+;; export hook, and citations will be resolved during
+;; html export.
+;;
+;; (add-hook 'org-export-first-hook
+;; (lambda ()
+;; (when (equal org-export-current-backend 'html)
+;; (obe-html-export-citations))))
+
+;;; Code:
+(require 'org-bibtex)
+
+(defcustom obe-bibtex-file nil "File holding bibtex entries.")
+
+(defcustom obe-html-link-base nil
+ "Base of citation links.
+For example, to point to your `obe-bibtex-file' use the following.
+
+ (setq obe-html-link-base (format \"file:%s\" obe-bibtex-file))
+")
+
+(defvar obe-citations nil)
+(defun obe-citations ()
+ "Return all citations from `obe-bibtex-file'."
+ (or obe-citations
+ (save-window-excursion
+ (find-file obe-bibtex-file)
+ (goto-char (point-min))
+ (while (re-search-forward " :CUSTOM_ID: \\(.+\\)$" nil t)
+ (push (org-babel-clean-text-properties (match-string 1))
+ obe-citations))
+ obe-citations)))
+
+(defun obe-goto-citation (&optional citation)
+ "Visit a citation given its ID."
+ (interactive)
+ (let ((citation (or citation
+ (org-icompleting-read "Citation: "
+ (obe-citations)))))
+ (find-file obe-bibtex-file)
+ (goto-char (point-min))
+ (when (re-search-forward (format " :CUSTOM_ID: %s" citation) nil t)
+ (outline-previous-visible-heading 1)
+ t)))
+
+(defun obe-html-export-citations ()
+ "Convert all \\cite{...} citations in the current file into HTML links."
+ (save-excursion
+ (goto-char (point-min))
+ (while (re-search-forward "\\\\cite{\\([^\000}]+\\)}" nil t)
+ (replace-match
+ (save-match-data
+ (mapconcat (lambda (c) (format "[[%s#%s][%s]]" obe-html-link-base c c))
+ (mapcar #'org-babel-trim
+ (split-string (match-string 1) ",")) ", "))))))
+
+(defun obe-get-meta-data (citation)
+ "Collect meta-data for CITATION."
+ (save-excursion
+ (when (obe-goto-citation citation)
+ (let ((pt (point)))
+ `((:authors . ,(split-string (org-entry-get pt "AUTHOR") " and " t))
+ (:title . ,(org-babel-clean-text-properties (org-get-heading 1 1)))
+ (:journal . ,(org-entry-get pt "JOURNAL")))))))
+
+(defun obe-meta-to-json (meta &optional fields)
+ "Turn a list of META data from citations into a string of json."
+ (let ((counter 1) nodes links)
+ (flet ((id (it) (position it nodes :test #'string= :key #'car))
+ (col (k) (mapcar (lambda (r) (cdr (assoc k r))) meta))
+ (add (lst)
+ (dolist (el lst) (push (cons el counter) nodes))
+ (incf counter)))
+ ;; build the nodes of the graph
+ (add (col :title))
+ (add (remove-if (lambda (author) (string-match "others" author))
+ (remove-duplicates (apply #'append (col :authors))
+ :test #'string=)))
+ (dolist (field fields)
+ (add (remove-duplicates (col field) :test #'string=)))
+ ;; build the links in the graph
+ (dolist (citation meta)
+ (let ((dest (id (cdr (assoc :title citation)))))
+ (dolist (author (mapcar #'id (cdr (assoc :authors citation))))
+ (when author (push (cons author dest) links)))
+ (let ((jid (id (cdr (assoc :journal citation)))))
+ (when jid (push (cons jid dest) links)))
+ (let ((cid (id (cdr (assoc :category citation)))))
+ (when cid (push (cons cid dest) links)))))
+ ;; build the json string
+ (format "{\"nodes\":[%s],\"links\":[%s]}"
+ (mapconcat
+ (lambda (pair)
+ (format "{\"name\":%S,\"group\":%d}"
+ (car pair) (cdr pair)))
+ nodes ",")
+ (mapconcat
+ (lambda (link)
+ (format "{\"source\":%d,\"target\":%d,\"value\":1}"
+ (car link) (cdr link)))
+ (meta-to-links meta nodes) ",")))))
+
+(provide 'org-bibtex-extras)
+;;; org-bibtex-extras ends here