1 # -*- org-edit-src-content-indentation: 0; -*-
2 #+TITLE: Org-ref - The best reference handling for org-mode
8 This document is an experiment at creating a literate program to provide similar features as reftex for org-mode referencing. These features include:
10 1. using completion to create links
11 2. storing links to places,
12 3. Clickable links that do useful things
13 4. Exportable links to LaTeX
14 5. Utility functions for dealing with bibtex files and org-files
16 Some additional features include
17 1. Get minibuffer messages for the cite/ref/label link under point
19 With helm integration (default) you can:
21 1. C-c ] to insert a citation link
23 - Enter to insert or append citation(s)
24 - C-u Enter to insert an alternative cite link
25 - C-u C-u Enter to replace the citation at point
26 2. C-u C-c ] to insert a ref link with helm completion
27 3. C-u C-u C-c ] to insert a label with completion
28 4. M-x org-ref to get a helm completion buffer with link checks, utilities and export options
31 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
32 ;;; org-ref.el --- cite and cross-reference in org-mode
34 ;; Copyright(C) 2014 John Kitchin
36 ;; Author: John Kitchin <jkitchin@andrew.cmu.edu>
37 ;; URL: https://github.com/jkitchin/org-ref
39 ;; Keywords: org-mode, cite, ref, label
40 ;; Package-Requires: ((dash) (helm) (helm-bibtex))
42 ;; This file is not currently part of GNU Emacs.
44 ;; This program is free software; you can redistribute it and/or
45 ;; modify it under the terms of the GNU General Public License as
46 ;; published by the Free Software Foundation; either version 2, or (at
47 ;; your option) any later version.
49 ;; This program is distributed in the hope that it will be useful, but
50 ;; WITHOUT ANY WARRANTY; without even the implied warranty of
51 ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
52 ;; General Public License for more details.
54 ;; You should have received a copy of the GNU General Public License
55 ;; along with this program ; see the file COPYING. If not, write to
56 ;; the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
57 ;; Boston, MA 02111-1307, USA.
61 ;; Lisp code to setup bibliography cite, ref and label org-mode links.
62 ;; also sets up reftex and helm for org-mode citations. The links are
63 ;; clickable and do things that are useful. You should really read
64 ;; org-ref.org for details.
71 The only external require is reftex-cite
73 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
74 (require 'reftex-cite)
77 (require 'helm-config)
78 (require 'helm-bibtex)
83 There are some variables needed later to tell this library where you store your pdf files, where your notes file is, and your default bibliography. This variable is similar to the reftex-default-bibliography. I do not remember why I made it separate.
85 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
87 "customization group for org-ref")
89 (defcustom org-ref-bibliography-notes
91 "filename to where you will put all your notes about an entry in
92 the default bibliography."
96 (defcustom org-ref-default-bibliography
98 "list of bibtex files to search for. You should use full-paths for each file."
99 :type '(repeat :tag "List of bibtex files" file)
102 (defcustom org-ref-pdf-directory
104 "directory where pdfs are stored by key. put a trailing / in"
108 (defcustom org-ref-default-citation-link
110 "The default type of citation link to use"
114 (defcustom org-ref-insert-cite-key
116 "Keyboard shortcut to insert a citation."
120 (defcustom org-ref-bibliography-entry-format
121 '(("article" . "%a, %t, <i>%j</i>, <b>%v(%n)</b>, %p (%y). <a href=\"%U\">link</a>. <a href=\"http://dx.doi.org/%D\">doi</a>.")
123 ("book" . "%a, %t, %u (%y).")
125 ("proceedings" . "%e, %t in %S, %u (%y).")
127 ("inproceedings" . "%a, %t, %p, in %b, edited by %e, %u (%y)"))
129 "string to format an entry. Just the reference, no numbering at the beginning, etc... see the `org-ref-reftex-format-citation' docstring for the escape codes."
133 (defcustom org-ref-open-notes-function
139 ;;(org-tree-to-indirect-buffer)
140 (outline-previous-visible-heading 1)
141 (recenter-top-bottom 0))
142 "User-defined way to open a notes entry. This is excecuted after the entry is found, with the cursor at the beginning of the headline. The default setting fully expands the notes, and moves the headline to the top of the buffer"
147 (defcustom org-ref-open-pdf-function
148 'org-ref-open-pdf-at-point
149 "User-defined function to open a pdf from a link. The function must get the key at point, and derive a path to the pdf file, then open it. The default function is `org-ref-open-pdf-at-point'."
154 (defcustom org-ref-insert-cite-function
155 'org-ref-helm-insert-cite-link
156 "Function to call to insert citation links. The default is `org-ref-helm-insert-cite-link' which uses `helm-bibtex'. org-ref modifies helm-bibtex a little bit to give org-mode citations, and to reorder default actions. You may use `org-ref-insert-cite-link' if you like the reftex interface."
161 (defcustom org-ref-cite-onclick-function
162 'org-ref-cite-click-helm
163 "Function that runs when you click on a cite link. The function must take no arguments. You may also use `org-ref-cite-onclick-minibuffer-menu' if you do not like helm. If you like `hydra', consider using `org-ref-cite-hydra'."
168 (defcustom org-ref-show-citation-on-enter t
169 "If non-nil add a hook function to show the citation summary in
170 the minibuffer just by putting the cursor in a link"
175 This next variable determines the citation types that are available in org-ref. Links for each one are automatically generated, and completion functions are automatically generated. Users may add to this list in their own init files.
177 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
178 (defcustom org-ref-cite-types
179 '("cite" "nocite" ;; the default latex cite commands
180 ;; natbib cite commands, http://ctan.unixbrain.com/macros/latex/contrib/natbib/natnotes.pdf
181 "citet" "citet*" "citep" "citep*"
182 "citealt" "citealt*" "citealp" "citealp*"
184 "citeauthor" "citeauthor*"
185 "citeyear" "citeyear*"
186 "Citet" "Citep" "Citealt" "Citealp" "Citeauthor"
188 ;; http://ctan.mirrorcatalogs.com/macros/latex/contrib/biblatex/doc/biblatex.pdf
190 "parencite" "Parencite"
191 "footcite" "footcitetext"
192 "textcite" "Textcite"
193 "smartcite" "Smartcite"
194 "cite*" "parencite*" "supercite"
195 "autocite" "Autocite" "autocite*" "Autocite*"
197 "citetitle" "citetitle*"
198 "citedate" "citedate*"
200 "fullcite" "footfullcite"
201 ;; "volcite" "Volcite" cannot support the syntax
202 "notecite" "Notecite"
203 "pnotecite" "Pnotecite"
205 ;; multicites. Very limited support for these.
206 "cites" "Cites" "parencites" "Parencites"
207 "footcites" "footcitetexts"
208 "smartcites" "Smartcites" "textcites" "Textcites"
209 "supercites" "autocites" "Autocites"
210 ;; for the bibentry package
213 "List of citation types known in org-ref"
214 :type '(repeat :tag "List of citation types" string)
218 We need a hook variable to store user-defined bibtex entry cleaning functions
219 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
220 (defcustom org-ref-clean-bibtex-entry-hook nil
221 "Hook that is run in org-ref-clean-bibtex-entry. The functions should take no arguments, and operate on the bibtex entry at point."
227 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
228 (defvar org-ref-bibliography-files
230 "variable to hold bibliography files to be searched")
233 ** org-mode / reftex setup
235 We setup reftex here. We use a custom insert cite link function defined here: [[*org-ref-insert-cite-link][org-ref-insert-cite-link]]. We setup reftex to use our org citation format.
237 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
239 (defun org-mode-reftex-setup ()
240 (and (buffer-file-name)
241 (file-exists-p (buffer-file-name))
242 (global-auto-revert-mode t)
243 ;; I do not remember why I put this next line in. It doesn't
244 ;; work for org-files. Nothing very bad happens, but it gives
245 ;; an annoying error. Commenting it out for now.
248 (make-local-variable 'reftex-cite-format)
249 (setq reftex-cite-format 'org))
251 ;; define key for inserting citations
252 (define-key org-mode-map
253 (kbd org-ref-insert-cite-key)
254 org-ref-insert-cite-function)
256 (add-hook 'org-mode-hook 'org-mode-reftex-setup)
258 (eval-after-load 'reftex-vars
260 (add-to-list 'reftex-cite-format-builtin
261 '(org "Org-mode citation"
262 ((?\C-m . "cite:%l") ; default
263 (?d . ",%l") ; for appending
269 (?h . "citeauthor:%l")
270 (?H . "citeauthor*:%l")
277 You may want to add new formats to the reftex-cite-format-builtin variable. Here is an example of adding two new formats. Note that this does not create the links.
279 #+BEGIN_SRC emacs-lisp :tangle no
281 (setf (nth 2 (assoc 'org reftex-cite-format-builtin))
282 (append (nth 2 (assoc 'org reftex-cite-format-builtin)) '((?W . "textcite:%l")
283 (?z . "newcite:%l"))))
286 You can define a new citation link like this:
287 #+BEGIN_SRC emacs-lisp :tangle no
288 (org-ref-define-citation-link "citez" ?z)
291 ** Messages for link at cursor
292 Here we setup code that shows you a context message for the element under the cursor when emacs is idle.
293 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
294 (defvar org-ref-message-timer nil
295 "Variable to store the link message timer in.")
298 (defun org-ref-show-link-messages ()
299 "Turn on link messages. You will see a message in the
300 minibuffer when on a cite, ref or label link."
302 (or org-ref-message-timer
303 (setq org-ref-message-timer
304 (run-with-idle-timer 0.5 t 'org-ref-link-message))))
307 (defun org-ref-cancel-link-messages ()
308 "Stop showing messages in minibuffer when on a link."
310 (cancel-timer org-ref-message-timer)
311 (setq org-ref-message-timer nil))
314 (when org-ref-show-citation-on-enter
315 (org-ref-show-link-messages))
317 ;; this approach caused the selected region to not be highlighted any more.
318 ; (add-hook 'post-command-hook 'org-ref-link-message))
319 ; (remove-hook 'post-command-hook 'org-ref-link-message))
322 ** Messages for context under mouse pointer
323 Sometimes, when reading a document, I actually use the mouse more than the cursor. This code enables the mouse cursor to trigger a message in the minibuffer about what is under the cursor. I run this on a timer.
325 The basic idea here is to get the mouse position, and if we can determine there is a character that (point) can move to, we move (point) and run the org-ref-link-message function. Since this runs on a timer, we store the last mouse position, and only run the function when the mouse has moved to avoid getting messages every time the timer runs.
327 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
328 (defvar org-ref-last-mouse-pos nil
329 "Stores last mouse position for use in `org-ref-mouse-message'.")
331 (defun org-ref-can-move-p ()
332 "See if a character is under the mouse. If so return the position for `goto-char'."
333 (let* ((line (cddr org-ref-last-mouse-pos))
334 (col (cadr org-ref-last-mouse-pos)))
336 (goto-char (window-start))
339 (> (- (line-end-position) (line-beginning-position)) col)
340 (progn (forward-char col) (point))
344 (defun org-ref-mouse-message ()
345 "Display message for link under mouse cursor"
347 (when (not (equal (mouse-position) org-ref-last-mouse-pos))
348 (setq org-ref-last-mouse-pos (mouse-position))
349 (let ((p (org-ref-can-move-p)))
353 (org-ref-link-message))))))
356 (defvar org-ref-message-timer-mouse nil
357 "Store mouse timer.")
360 (defvar org-ref-mouse-message-interval 0.5
361 "How often to run the mouse message timer in seconds")
364 (defun org-ref-mouse-messages-on ()
365 "Turn on mouse messages."
367 (or org-ref-message-timer-mouse
368 (setq org-ref-message-timer-mouse
369 (run-at-time "0.5 sec"
370 org-ref-mouse-message-interval
371 'org-ref-mouse-message))))
374 (defun org-ref-mouse-messages-off ()
375 "Turn off mouse messages"
377 (cancel-timer org-ref-message-timer-mouse)
378 (setq org-ref-message-timer-mouse nil)
379 (message "Mouse messages are off"))
383 : org-ref-mouse-messages-off
386 Here we make the org-ref links a different color.
394 cite:sokalski-2012-optim-ta,zhang-2011-spatial-tio2,li-2012-heter-ceram,li-2013-photoc
396 cite*:sokalski-2012-optim-ta,zhang-2011-spatial-tio2,li-2012-heter-ceram,li-2013-photoc
398 citenum:sokalski-2012-optim-ta,zhang-2011-spatial-tio2,li-2012-heter-ceram,li-2013-photoc
404 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
405 (defcustom org-ref-colorize-links
407 "When non-nil, change colors of links"
411 (defcustom org-ref-cite-color
413 "Color of cite like links"
417 (defcustom org-ref-ref-color
419 "Color of ref like links"
423 (defcustom org-ref-label-color
425 "Color of label links"
429 (defvar org-ref-cite-re nil
430 "regexp for cite links")
433 (setq org-ref-cite-re
434 (concat "\\(" (mapconcat
436 (replace-regexp-in-string "\*" "\\\\*" x)
438 org-ref-cite-types "\\|") "\\)"
439 ":\\([a-zA-Z0-9-_:]*,?\\)*"))
442 (setq org-ref-label-re
443 "label:\\([a-zA-Z0-9-_:]*,?\\)*")
447 "ref:\\([a-zA-Z0-9-_:]*,?\\)*")
450 (defface org-ref-cite-face
451 `((t (:inherit org-link :foreground ,org-ref-cite-color)))
452 "Color for cite-like links in org-ref.")
455 (defface org-ref-label-face
456 `((t (:inherit org-link :foreground ,org-ref-label-color)))
457 "Color for ref links in org-ref.")
460 (defface org-ref-ref-face
461 `((t (:inherit org-link :foreground ,org-ref-ref-color)))
462 "Face for ref links in org-ref.")
465 (defun org-ref-colorize-links ()
466 "Colorize org-ref links."
468 (highlight-regexp org-ref-cite-re 'org-ref-cite-face)
469 (highlight-regexp org-ref-label-re 'org-ref-label-face)
470 (highlight-regexp org-ref-ref-re 'org-ref-ref-face))
473 (when org-ref-colorize-links
474 (add-hook 'org-mode-hook 'org-ref-colorize-links))
481 Most of this library is the creation of functional links to help with references and citations.
483 We need several general utilities for this module. They are organized here. We frequently need to remove white space from the front and back of a string. Here we do that for a string.
485 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
486 (defun org-ref-strip-string (string)
487 "strip leading and trailing whitespace from the string"
488 (replace-regexp-in-string
489 (concat search-whitespace-regexp "$" ) ""
490 (replace-regexp-in-string
491 (concat "^" search-whitespace-regexp ) "" string)))
494 It is helpful to make the previous function operate on a list of strings here.
496 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
497 (defun org-ref-split-and-strip-string (string)
498 "split key-string and strip keys. Assumes the key-string is comma delimited"
499 (mapcar 'org-ref-strip-string (split-string string ",")))
502 ** bibliography and bibliographystyle
503 *** An html bibliography
505 Reftex is no longer being developed. I want a url and doi option for formatting, so I am modifying this [[file:emacs-24.3/lisp/textmodes/reftex-cite.el::(defun%20reftex-format-citation%20(entry%20format)][function]] from reftex-cite to provide that. We need to modify the reftex-get-bib-field code a bit to remove enclosing braces and quotes so we can make nice looking links.
507 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
508 (defun org-ref-reftex-get-bib-field (field entry &optional format)
509 "similar to reftex-get-bib-field, but removes enclosing braces and quotes"
511 (setq result (reftex-get-bib-field field entry format))
512 (when (and (not (string= result "")) (string= "{" (substring result 0 1)))
513 (setq result (substring result 1 -1)))
514 (when (and (not (string= result "")) (string= "\"" (substring result 0 1)))
515 (setq result (substring result 1 -1)))
518 (defun org-ref-reftex-format-citation (entry format)
519 "return a formatted string for the bibtex entry (from bibtex-parse-entry) according
520 to the format argument. The format is a string with these percent escapes.
522 In the format, the following percent escapes will be expanded.
524 %l The BibTeX label of the citation.
525 %a List of author names, see also `reftex-cite-punctuation'.
526 %2a Like %a, but abbreviate more than 2 authors like Jones et al.
527 %A First author name only.
528 %e Works like %a, but on list of editor names. (%2e and %E work a well)
530 It is also possible to access all other BibTeX database fields:
531 %b booktitle %c chapter %d edition %h howpublished
532 %i institution %j journal %k key %m month
533 %n number %o organization %p pages %P first page
534 %r address %s school %u publisher %t title
536 %B booktitle, abbreviated %T title, abbreviated
541 Usually, only %l is needed. The other stuff is mainly for the echo area
542 display, and for (setq reftex-comment-citations t).
544 %< as a special operator kills punctuation and space around it after the
545 string has been formatted.
547 A pair of square brackets indicates an optional argument, and RefTeX
548 will prompt for the values of these arguments.
550 Beware that all this only works with BibTeX database files. When
551 citations are made from the \bibitems in an explicit thebibliography
552 environment, only %l is available."
553 ;; Format a citation from the info in the BibTeX ENTRY
555 (unless (stringp format) (setq format "\\cite{%l}"))
557 (if (and reftex-comment-citations
558 (string-match "%l" reftex-cite-comment-format))
559 (error "reftex-cite-comment-format contains invalid %%l"))
562 "\\(\\`\\|[^%]\\)\\(\\(%\\([0-9]*\\)\\([a-zA-Z]\\)\\)[.,;: ]*\\)"
564 (let ((n (string-to-number (match-string 4 format)))
565 (l (string-to-char (match-string 5 format)))
571 (org-ref-reftex-get-bib-field "&key" entry)
572 (if reftex-comment-citations
573 reftex-cite-comment-format
575 ((= l ?a) (reftex-format-names
576 (reftex-get-bib-names "author" entry)
578 ((= l ?A) (car (reftex-get-bib-names "author" entry)))
579 ((= l ?b) (org-ref-reftex-get-bib-field "booktitle" entry "in: %s"))
580 ((= l ?B) (reftex-abbreviate-title
581 (org-ref-reftex-get-bib-field "booktitle" entry "in: %s")))
582 ((= l ?c) (org-ref-reftex-get-bib-field "chapter" entry))
583 ((= l ?d) (org-ref-reftex-get-bib-field "edition" entry))
584 ((= l ?D) (org-ref-reftex-get-bib-field "doi" entry))
585 ((= l ?e) (reftex-format-names
586 (reftex-get-bib-names "editor" entry)
588 ((= l ?E) (car (reftex-get-bib-names "editor" entry)))
589 ((= l ?h) (org-ref-reftex-get-bib-field "howpublished" entry))
590 ((= l ?i) (org-ref-reftex-get-bib-field "institution" entry))
591 ((= l ?j) (org-ref-reftex-get-bib-field "journal" entry))
592 ((= l ?k) (org-ref-reftex-get-bib-field "key" entry))
593 ((= l ?m) (org-ref-reftex-get-bib-field "month" entry))
594 ((= l ?n) (org-ref-reftex-get-bib-field "number" entry))
595 ((= l ?o) (org-ref-reftex-get-bib-field "organization" entry))
596 ((= l ?p) (org-ref-reftex-get-bib-field "pages" entry))
597 ((= l ?P) (car (split-string
598 (org-ref-reftex-get-bib-field "pages" entry)
600 ((= l ?s) (org-ref-reftex-get-bib-field "school" entry))
601 ((= l ?S) (org-ref-reftex-get-bib-field "series" entry))
602 ((= l ?u) (org-ref-reftex-get-bib-field "publisher" entry))
603 ((= l ?U) (org-ref-reftex-get-bib-field "url" entry))
604 ((= l ?r) (org-ref-reftex-get-bib-field "address" entry))
605 ;; strip enclosing brackets from title if they are there
606 ((= l ?t) (org-ref-reftex-get-bib-field "title" entry))
607 ((= l ?T) (reftex-abbreviate-title
608 (org-ref-reftex-get-bib-field "title" entry)))
609 ((= l ?v) (org-ref-reftex-get-bib-field "volume" entry))
610 ((= l ?y) (org-ref-reftex-get-bib-field "year" entry)))))
613 (setq b (match-beginning 2) e (match-end 2))
614 (setq b (match-beginning 3) e (match-end 3)))
615 (setq format (concat (substring format 0 b) rpl (substring format e)))))
616 (while (string-match "%%" format)
617 (setq format (replace-match "%" t t format)))
618 (while (string-match "[ ,.;:]*%<" format)
619 (setq format (replace-match "" t t format)))
620 ;; also replace carriage returns, tabs, and multiple whitespaces
621 (setq format (replace-regexp-in-string "\n\\|\t\\|\s+" " " format))
624 (defun org-ref-get-bibtex-entry-citation (key)
625 "returns a string for the bibliography entry corresponding to key, and formatted according to the type in `org-ref-bibliography-entry-format'"
627 (let ((org-ref-bibliography-files (org-ref-find-bibliography))
628 (file) (entry) (bibtex-entry) (entry-type) (format))
630 (setq file (catch 'result
631 (loop for file in org-ref-bibliography-files do
632 (if (org-ref-key-in-file-p key (file-truename file))
634 (message "%s not found in %s" key (file-truename file))))))
637 (insert-file-contents file)
638 (bibtex-search-entry key nil 0)
639 (setq bibtex-entry (bibtex-parse-entry))
640 (setq entry-type (downcase (cdr (assoc "=type=" bibtex-entry))))
641 (setq format (cdr (assoc entry-type org-ref-bibliography-entry-format)))
643 (setq entry (org-ref-reftex-format-citation bibtex-entry format))
645 (bibtex-narrow-to-entry)
646 (setq entry (buffer-string)))))
651 : org-ref-reftex-format-citation
653 Here is how to use the function. You call it with point in an entry in a bibtex file.
655 #+BEGIN_SRC emacs-lisp :tangle no
656 (let((org-ref-bibliography-entry-format "%a, %t, <i>%j</i>, <b>%v(%n)</b>, %p (%y). <a href=\"%U\">link</a>. <a href=\"http://dx.doi.org/%D\">doi</a>."))
657 (org-ref-get-bibtex-entry-citation "armiento-2014-high"))
660 : Armiento, Kozinsky, Hautier, , Fornari \& Ceder, High-throughput screening of perovskite alloys for piezoelectric performance and thermodynamic stability, <i>Phys. Rev. B</i>, <b>89()</b>, 134103 (2014). <a href="http://link.aps.org/doi/10.1103/PhysRevB.89.134103">link</a>. <a href="http://dx.doi.org/10.1103/PhysRevB.89.134103">doi</a>.
662 I am not sure why full author names are not used.
664 This code provides some functions to generate a simple sorted bibliography in html. First we get all the keys in the buffer.
666 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
667 (defun org-ref-get-bibtex-keys ()
668 "Return a list of unique keys in the buffer."
670 (org-element-map (org-element-parse-buffer) 'link
672 (let ((plist (nth 1 link)))
673 (when (-contains? org-ref-cite-types (plist-get plist ':type))
676 (org-ref-split-and-strip-string (plist-get plist ':path)))
677 (when (not (-contains? keys key))
678 (setq keys (append keys (list key))))))))
679 ;; set with-affiliated to get keys in captions
681 ;; Sort keys alphabetically
682 (setq keys (cl-sort keys 'string-lessp :key 'downcase))
686 This function gets the html for one entry.
688 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
689 (defun org-ref-get-bibtex-entry-html (key)
690 "returns an html string for the bibliography entry corresponding to key"
692 (format "<li><a id=\"%s\">[%s] %s</a></li>" key key (org-ref-get-bibtex-entry-citation key)))
695 Now, we map over the whole list of keys, and the whole bibliography, formatted as an unordered list.
697 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
698 (defun org-ref-get-html-bibliography ()
699 "Create an html bibliography when there are keys"
700 (let ((keys (org-ref-get-bibtex-keys)))
702 (concat "<h1>Bibliography</h1>
704 (mapconcat (lambda (x) (org-ref-get-bibtex-entry-html x)) keys "\n")
708 I do not have plans to make a numbered bibliography with numbered citations anytime soon. This will require changing the way the citation links are exported, and keeping track of the numbers.
710 *** An org bibliography
711 You can export an org-file to an org-file or org-buffer (org-org-epxort-as-org). In this case, it would be useful convert the cite links to links to custom_ids, and the bibliography link to a first-level heading Bibliography with org-bibtex like headings for each entry. This code should enable this. Right now, it does not appear to work for org export though.
713 First, we get the string for a single entry.
714 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
715 (defun org-ref-get-bibtex-entry-org (key)
716 "returns an org string for the bibliography entry corresponding to key"
717 (let ((org-ref-bibliography-files (org-ref-find-bibliography))
718 (file) (entry) (bibtex-entry) (entry-type) (format))
720 (setq file (catch 'result
721 (loop for file in org-ref-bibliography-files do
722 (if (org-ref-key-in-file-p key (file-truename file))
724 (message "%s not found in %s" key (file-truename file))))))
727 (insert-file-contents file)
728 (bibtex-search-entry key nil 0)
729 (setq entry (bibtex-parse-entry))
734 " (org-ref-reftex-get-bib-field "author" entry)
735 (org-ref-reftex-get-bib-field "title" entry)
736 (concat " :CUSTOM_ID: " (org-ref-reftex-get-bib-field "=key=" entry) "\n"
737 (mapconcat (lambda (element) (format " :%s: %s"
738 (upcase (car element))
744 Now, we loop over the keys, and combine all the entries into a bibliography.
745 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
746 (defun org-ref-get-org-bibliography ()
747 "Create an org bibliography when there are keys"
748 (let ((keys (org-ref-get-bibtex-keys)))
750 (concat "* Bibliography
752 (mapconcat (lambda (x) (org-ref-get-bibtex-entry-org x)) keys "\n")
756 *** An ascii bibliography
758 This function gets the html for one entry.
760 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
761 (defun org-ref-get-bibtex-entry-ascii (key)
762 "returns an ascii string for the bibliography entry corresponding to key"
764 (format "[%s] %s" key (org-ref-get-bibtex-entry-citation key)))
767 Now, we map over the whole list of keys, and the whole bibliography, formatted as an unordered list.
769 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
770 (defun org-ref-get-ascii-bibliography ()
771 "Create an html bibliography when there are keys"
772 (let ((keys (org-ref-get-bibtex-keys)))
778 (mapconcat (lambda (x) (org-ref-get-bibtex-entry-ascii x)) keys "\n")
784 We use a link for the bibliography so that we can click on it to open the bibliography file. The link may have more than one bibliography file in it, separated by commas. Clicking opens the file under the cursor. The bibliographies should be full filenames with the bib extension. Clicking on this link makes reftex-default-bibliography local and sets it to the list of files in the link. We need this to use reftex's searching capability.
786 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
787 (org-add-link-type "bibliography"
788 ;; this code is run on clicking. The bibliography
789 ;; may contain multiple files. this code finds the
790 ;; one you clicked on and opens it.
791 (lambda (link-string)
792 ;; get link-string boundaries
793 ;; we have to go to the beginning of the line, and then search forward
796 ;; object is the link you clicked on
797 (object (org-element-context))
798 (link-string-beginning)
802 (goto-char (org-element-property :begin object))
803 (search-forward link-string nil nil 1)
804 (setq link-string-beginning (match-beginning 0))
805 (setq link-string-end (match-end 0)))
807 ;; We set the reftex-default-bibliography
808 ;; here. it should be a local variable only in
809 ;; the current buffer. We need this for using
810 ;; reftex to do citations.
811 (set (make-local-variable 'reftex-default-bibliography)
812 (split-string (org-element-property :path object) ","))
814 ;; now if we have comma separated bibliographies
815 ;; we find the one clicked on. we want to
816 ;; search forward to next comma from point
818 (if (search-forward "," link-string-end 1 1)
819 (setq key-end (- (match-end 0) 1)) ; we found a match
820 (setq key-end (point)))) ; no comma found so take the point
821 ;; and backward to previous comma from point
823 (if (search-backward "," link-string-beginning 1 1)
824 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
825 (setq key-beginning (point)))) ; no match found
826 ;; save the key we clicked on.
827 (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
828 (find-file bibfile))) ; open file on click
831 (lambda (keyword desc format)
833 ((eq format 'org) (org-ref-get-org-bibliography))
834 ((eq format 'ascii) (org-ref-get-ascii-bibliography))
835 ((eq format 'html) (org-ref-get-html-bibliography))
837 ;; write out the latex bibliography command
838 (format "\\bibliography{%s}" (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity
839 (mapcar 'expand-file-name
840 (split-string keyword ","))
845 Believe it or not, sometimes it makes sense /not/ to include the bibliography in a document (e.g. when you are required to submit references as a separate file). To generate the references, in another file, you must make a little tex file with these contents, and then compile it.
848 \input{project-description.bbl}
851 Here, we make a =nobibliography= link that acts like the bibliography, enables creation of the bbl file, but does not put an actual bibliography in the file.
853 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
854 (org-add-link-type "nobibliography"
855 ;; this code is run on clicking. The bibliography
856 ;; may contain multiple files. this code finds the
857 ;; one you clicked on and opens it.
858 (lambda (link-string)
859 ;; get link-string boundaries
860 ;; we have to go to the beginning of the line, and then search forward
863 ;; object is the link you clicked on
864 (object (org-element-context))
866 (link-string-beginning)
870 (goto-char (org-element-property :begin object))
871 (search-forward link-string nil nil 1)
872 (setq link-string-beginning (match-beginning 0))
873 (setq link-string-end (match-end 0)))
875 ;; We set the reftex-default-bibliography
876 ;; here. it should be a local variable only in
877 ;; the current buffer. We need this for using
878 ;; reftex to do citations.
879 (set (make-local-variable 'reftex-default-bibliography)
880 (split-string (org-element-property :path object) ","))
882 ;; now if we have comma separated bibliographies
883 ;; we find the one clicked on. we want to
884 ;; search forward to next comma from point
886 (if (search-forward "," link-string-end 1 1)
887 (setq key-end (- (match-end 0) 1)) ; we found a match
888 (setq key-end (point)))) ; no comma found so take the point
889 ;; and backward to previous comma from point
891 (if (search-backward "," link-string-beginning 1 1)
892 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
893 (setq key-beginning (point)))) ; no match found
894 ;; save the key we clicked on.
895 (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
896 (find-file bibfile))) ; open file on click
899 (lambda (keyword desc format)
901 ((eq format 'org) (org-ref-get-org-bibliography))
902 ((eq format 'ascii) (org-ref-get-ascii-bibliography))
903 ((eq format 'html) (org-ref-get-html-bibliography))
905 ;; write out the latex bibliography command
907 ; (format "{\\setbox0\\vbox{\\bibliography{%s}}}"
908 ; (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity
909 ; (mapcar 'expand-file-name
910 ; (split-string keyword ","))
913 (format "\\nobibliography{%s}"
914 (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity
915 (mapcar 'expand-file-name
916 (split-string keyword ","))
922 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
923 (org-add-link-type "printbibliography"
924 (lambda (arg) (message "Nothing implemented for clicking here."))
925 (lambda (keyword desc format)
927 ((eq format 'org) (org-ref-get-org-bibliography))
928 ((eq format 'html) (org-ref-get-html-bibliography))
930 ;; write out the biblatex bibliography command
931 "\\printbibliography"))
935 We also create a bibliographystyle link. There is nothing to do on clicking here, and we create it for consistency. This sets the style for latex export, so use something appropriate there, e.g. unsrt, plain, plainnat, ...
937 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
938 (org-add-link-type "bibliographystyle"
939 (lambda (arg) (message "Nothing implemented for clicking here."))
940 (lambda (keyword desc format)
943 ;; write out the latex bibliography command
944 (format "\\bibliographystyle{%s}" keyword)))))
947 *** Completion for bibliography link
950 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
951 (defun org-bibliography-complete-link (&optional arg)
952 (format "bibliography:%s" (read-file-name "enter file: " nil nil t)))
954 (defun org-ref-insert-bibliography-link ()
955 "insert a bibliography with completion"
957 (insert (org-bibliography-complete-link)))
961 This is apparently used for biblatex.
962 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
963 (org-add-link-type "addbibresource"
964 ;; this code is run on clicking. The addbibresource
965 ;; may contain multiple files. this code finds the
966 ;; one you clicked on and opens it.
967 (lambda (link-string)
968 ;; get link-string boundaries
969 ;; we have to go to the beginning of the line, and then search forward
972 ;; object is the link you clicked on
973 (object (org-element-context))
975 (link-string-beginning)
979 (goto-char (org-element-property :begin object))
980 (search-forward link-string nil nil 1)
981 (setq link-string-beginning (match-beginning 0))
982 (setq link-string-end (match-end 0)))
984 ;; We set the reftex-default-addbibresource
985 ;; here. it should be a local variable only in
986 ;; the current buffer. We need this for using
987 ;; reftex to do citations.
988 (set (make-local-variable 'reftex-default-addbibresource)
989 (split-string (org-element-property :path object) ","))
991 ;; now if we have comma separated bibliographies
992 ;; we find the one clicked on. we want to
993 ;; search forward to next comma from point
995 (if (search-forward "," link-string-end 1 1)
996 (setq key-end (- (match-end 0) 1)) ; we found a match
997 (setq key-end (point)))) ; no comma found so take the point
998 ;; and backward to previous comma from point
1000 (if (search-backward "," link-string-beginning 1 1)
1001 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
1002 (setq key-beginning (point)))) ; no match found
1003 ;; save the key we clicked on.
1004 (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
1005 (find-file bibfile))) ; open file on click
1008 (lambda (keyword desc format)
1010 ((eq format 'html) (format "")); no output for html
1012 ;; write out the latex addbibresource command
1013 (format "\\addbibresource{%s}" keyword)))))
1018 In long documents, a list of figures is not uncommon. Here we create a clickable link that generates a temporary buffer containing a list of figures in the document, and their captions. We make a function that can be called interactively, and define a link type that is rendered in LaTeX to create the list of figures.
1020 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1021 (defun org-ref-list-of-figures (&optional arg)
1022 "Generate buffer with list of figures in them"
1024 (save-excursion (widen)
1025 (let* ((c-b (buffer-name))
1028 (org-element-map (org-element-parse-buffer) 'link
1030 "create a link for to the figure"
1032 (and (string= (org-element-property :type link) "file")
1034 "[^.]*\\.\\(png\\|jpg\\|eps\\|pdf\\)$"
1035 (org-element-property :path link)))
1038 (let* ((start (org-element-property :begin link))
1039 (parent (car (cdr (org-element-property :parent link))))
1040 (caption (caaar (plist-get parent :caption)))
1041 (name (plist-get parent :name)))
1044 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][figure %s: %s]] %s\n"
1045 c-b start counter (or name "") caption)
1047 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][figure %s: %s]]\n"
1048 c-b start counter (or name "")))))))))
1049 (switch-to-buffer "*List of Figures*")
1050 (setq buffer-read-only nil)
1053 (insert (mapconcat 'identity list-of-figures ""))
1054 (setq buffer-read-only t)
1055 (use-local-map (copy-keymap org-mode-map))
1056 (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))))
1060 'org-ref-list-of-figures ; on click
1061 (lambda (keyword desc format)
1064 (format "\\listoffigures")))))
1069 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1070 (defun org-ref-list-of-tables (&optional arg)
1071 "Generate a buffer with a list of tables"
1075 (let* ((c-b (buffer-name))
1078 (org-element-map (org-element-parse-buffer 'element) 'table
1080 "create a link for to the table"
1082 (let ((start (org-element-property :begin table))
1083 (name (org-element-property :name table))
1084 (caption (caaar (org-element-property :caption table))))
1087 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][table %s: %s]] %s\n"
1088 c-b start counter (or name "") caption)
1090 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][table %s: %s]]\n"
1091 c-b start counter (or name ""))))))))
1092 (switch-to-buffer "*List of Tables*")
1093 (setq buffer-read-only nil)
1096 (insert (mapconcat 'identity list-of-tables ""))
1097 (setq buffer-read-only t)
1098 (use-local-map (copy-keymap org-mode-map))
1099 (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))))
1103 'org-ref-list-of-tables
1104 (lambda (keyword desc format)
1107 (format "\\listoftables")))))
1111 The label link provides a way to create labels in org-mode. We make it clickable because we want to make sure labels are unique. This code will tell you how many instances of a label are found. We search for label links, LaTeX labels, and org-mode format for labels, tblnames too.
1113 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1114 (defun org-ref-count-labels (label)
1115 "Counts number of matches for label in the document"
1116 (+ (count-matches (format "label:%s\\b[^-:]" label) (point-min) (point-max))
1117 ;; for tblname, it is not enough to get word boundary
1118 ;; tab-little and tab-little-2 match then.
1119 (count-matches (format "^#\\+tblname:\\s-*%s\\b[^-:]" label) (point-min) (point-max))
1120 (count-matches (format "\\label{%s}" label) (point-min) (point-max))
1121 ;; this is the org-format #+label:
1122 (count-matches (format "^#\\+label:\\s-*%s\\b[^-:]" label) (point-min) (point-max))
1123 (let ((custom-id-count 0))
1126 (when (string= label (org-entry-get (point) "CUSTOM_ID"))
1127 (setq custom-id-count (+ 1 custom-id-count)))))
1133 "on clicking count the number of label tags used in the buffer. A number greater than one means multiple labels!"
1134 (let ((count (org-ref-count-labels label)))
1135 (message (format "%s occurence%s"
1141 (org-ref-count-labels label))))
1142 (lambda (keyword desc format)
1144 ((eq format 'html) (format "(<label>%s</label>)" path))
1146 (format "\\label{%s}" keyword)))))
1149 We want to store links on labels, so you can put the cursor on the label, press C-c l, and later use C-c C-l to insert a link to the label. We also want to store links to tables with a table name, and for sections with CUSTOM_ID.
1151 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1152 (defun org-label-store-link ()
1153 "store a link to a label. The output will be a ref to that label"
1154 ;; First we have to make sure we are on a label link.
1155 (let* ((object (org-element-context)))
1156 (when (and (equal (org-element-type object) 'link)
1157 (equal (org-element-property :type object) "label"))
1158 (org-store-link-props
1160 :link (concat "ref:" (org-element-property :path object))))
1162 ;; Store link on table
1163 (when (equal (org-element-type object) 'table)
1164 (org-store-link-props
1166 :link (concat "ref:" (org-element-property :name object))))
1168 ;; it turns out this does not work. you can already store a link to a heading with a CUSTOM_ID
1169 ;; store link on heading with custom_id
1170 ; (when (and (equal (org-element-type object) 'headline)
1171 ; (org-entry-get (point) "CUSTOM_ID"))
1172 ; (org-store-link-props
1174 ; :link (concat "ref:" (org-entry-get (point) "CUSTOM_ID"))))
1176 ;; and to #+label: lines
1177 (when (and (equal (org-element-type object) 'paragraph)
1178 (org-element-property :name object))
1179 (org-store-link-props
1181 :link (concat "ref:" (org-element-property :name object))))
1184 (add-hook 'org-store-link-functions 'org-label-store-link)
1188 The ref link allows you make links to labels. Clicking on the link takes you to the label, and provides a mark to go back to.
1190 At the moment, ref links are not usable for section links. You need [[#CUSTOM_ID]] type links.
1192 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1196 "on clicking goto the label. Navigate back with C-c &"
1197 (org-mark-ring-push)
1198 ;; next search from beginning of the buffer
1200 ;; it is possible you would not find the label if narrowing is in effect
1207 (goto-char (point-min))
1208 (re-search-forward (format "label:%s\\b" label) nil t))
1212 (goto-char (point-min))
1213 (re-search-forward (format "\\label{%s}" label) nil t))
1215 ;; #+label: name org-definition
1217 (goto-char (point-min))
1218 (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
1222 (goto-char (point-min))
1223 (re-search-forward (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t))
1225 ;; Commented out because these ref links do not actually translate correctly in LaTeX.
1226 ;; you need [[#label]] links.
1229 ; (goto-char (point-min))
1230 ; (re-search-forward (format ":CUSTOM_ID:\s-*\\(%s\\)" label) nil t))
1232 ;; we did not find anything, so go back to where we came
1233 (org-mark-ring-goto)
1234 (error "%s not found" label))
1236 (message "go back with (org-mark-ring-goto) `C-c &`"))
1238 (lambda (keyword desc format)
1240 ((eq format 'html) (format "(<ref>%s</ref>)" path))
1242 (format "\\ref{%s}" keyword)))))
1245 It would be nice to use completion to enter a ref link, where a list of labels is provided. The following code searches the buffer for org and latex labels, custom_ids, and table names as potential items to make a ref link to.
1247 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1248 (defun org-ref-get-org-labels ()
1249 "Return a list of #+LABEL: labels."
1251 (goto-char (point-min))
1252 (let ((matches '()))
1253 (while (re-search-forward "^#\\+label:\\s-+\\(.*\\)\\b" (point-max) t)
1254 (add-to-list 'matches (match-string-no-properties 1) t))
1258 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1259 (defun org-ref-get-custom-ids ()
1260 "Return a list of custom_id properties in the buffer."
1261 (let ((results '()) custom_id)
1264 (let ((custom_id (org-entry-get (point) "CUSTOM_ID")))
1265 (when (not (null custom_id))
1266 (setq results (append results (list custom_id)))))))
1270 Here we get a list of the labels defined as raw latex labels, e.g. \label{eqtre}.
1271 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1272 (defun org-ref-get-latex-labels ()
1274 (goto-char (point-min))
1275 (let ((matches '()))
1276 (while (re-search-forward "\\\\label{\\([a-zA-z0-9:-]*\\)}" (point-max) t)
1277 (add-to-list 'matches (match-string-no-properties 1) t))
1281 Finally, we get the table names.
1283 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1284 (defun org-ref-get-tblnames ()
1285 "Return list of table names in the buffer."
1286 (org-element-map (org-element-parse-buffer 'element) 'table
1288 (org-element-property :name table))))
1291 Now, we can put all the labels together which will give us a list of candidates.
1293 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1294 (defun org-ref-get-labels ()
1295 "Returns a list of labels in the buffer that you can make a ref link to.
1296 This is used to auto-complete ref links and in helm menus."
1300 (goto-char (point-min))
1301 (let ((matches '()))
1302 ;; these are the label:stuff kinds
1303 (while (re-search-forward "[^#+]label:\\([a-zA-z0-9:-]*\\)" (point-max) t)
1304 (add-to-list 'matches (match-string-no-properties 1) t))
1306 (org-ref-get-org-labels)
1307 (org-ref-get-latex-labels)
1308 (org-ref-get-tblnames)
1309 (org-ref-get-custom-ids))))))
1312 Let us make a helm function to insert a label link. This will help you enter unique labels by showing matching labels until they are all gone and you are left with a unique one. If you are on a link, it means you want to replace it.
1313 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1314 (defun org-ref-helm-insert-label-link ()
1315 "Insert a label link. helm just shows you what labels already exist.
1316 If you are on a label link, replace it."
1318 (let* ((labels (org-ref-get-labels))
1319 (cb (current-buffer)))
1320 (helm :sources `(((name . "Existing labels")
1321 (candidates . ,labels)
1322 ;; default action is to open to the label
1323 (action . (lambda (label)
1324 ;; unfortunately I do not have markers here
1325 (org-open-link-from-string (format "ref:%s" label))))
1326 ;; if you select a label, replace current one
1327 (action . (lambda (label)
1328 (switch-to-buffer ,cb)
1330 ;; no prefix or on a link
1331 ((equal helm-current-prefix-arg nil)
1332 (let* ((object (org-element-context))
1333 (last-char (save-excursion
1334 (goto-char (org-element-property :end object))
1336 (if (looking-at " ")
1339 (when (-contains? '("label")
1340 (org-element-property :type object))
1341 ;; we are on a link, so replace it.
1344 (org-element-property :begin object)
1345 (org-element-property :end object))
1347 (replace-regexp-in-string
1348 (org-element-property :path object)
1350 (org-element-property :raw-link object))
1352 ;; no prefix options defined
1354 ;; no matching selection creates a new label
1355 ((name . "Create new label")
1357 ;; default action creates a new label, or replaces old one
1358 (action . (lambda (label)
1359 (switch-to-buffer ,cb)
1360 (let* ((object (org-element-context))
1361 (last-char (save-excursion
1362 (goto-char (org-element-property :end object))
1364 (if (looking-at " ")
1367 (if (-contains? '("label")
1368 (org-element-property :type object))
1369 ;; we are on a link, so replace it.
1372 (org-element-property :begin object)
1373 (org-element-property :end object))
1375 (replace-regexp-in-string
1376 (org-element-property :path object)
1378 (org-element-property :raw-link object))
1385 helm-pattern))))))))))))
1388 Now we create a completion function. This works from the org-machinery, e.g. if you type C-c C-l to insert a link, and use completion by pressing tab.
1390 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1391 (defun org-ref-complete-link (&optional arg)
1392 "Completion function for ref links"
1394 (setq label (completing-read "label: " (org-ref-get-labels)))
1395 (format "ref:%s" label)))
1398 Alternatively, you may want to just call a function that inserts a link with completion:
1400 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1401 (defun org-ref-insert-ref-link ()
1403 (insert (org-ref-complete-link)))
1406 Another alternative ref insertion is to use helm.
1408 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1409 (defun org-ref-helm-insert-ref-link ()
1410 "Helm menu to insert ref links to labels in the document.
1411 If you are on link, replace with newly selected label.
1412 Use C-u to insert a different kind of ref link.
1413 Use C-u C-u to insert a [[#custom-id]] link
1416 (let* ((labels (org-ref-get-labels))
1417 (bs (buffer-string))
1418 (contexts (with-temp-buffer
1420 (mapcar 'org-ref-get-label-context labels)))
1421 (cb (current-buffer)))
1423 (helm :input (thing-at-point 'word)
1424 :sources `(((name . "Available labels to ref")
1425 (candidates . ,(loop for label in labels
1426 for context in contexts
1427 ;; we do some kludgy adding spaces
1428 ;; and bars to make it "easier" to
1430 collect (cons (concat
1435 (split-string context "\n")
1438 ;; default action to replace or insert ref link.
1439 (action . (lambda (label)
1440 (switch-to-buffer ,cb)
1443 ;; no prefix or on a link
1444 ((equal helm-current-prefix-arg nil)
1445 (let* ((object (org-element-context))
1446 (last-char (save-excursion
1447 (goto-char (org-element-property :end object))
1449 (if (looking-at " ")
1452 (if (-contains? '("ref" "eqref" "pageref" "nameref")
1453 (org-element-property :type object))
1454 ;; we are on a link, so replace it.
1457 (org-element-property :begin object)
1458 (org-element-property :end object))
1460 (replace-regexp-in-string
1461 (org-element-property :path object)
1463 (org-element-property :raw-link object))
1465 ;; insert a new link
1470 ;; one prefix, alternate ref link
1471 ((equal helm-current-prefix-arg '(4))
1474 (helm :sources '((name . "Ref link types")
1475 (candidates . ("ref" "eqref" "pageref" "nameref"))
1476 (action . (lambda (x) x))))
1478 ;; two prefixes, insert section custom-id link
1479 ((equal helm-current-prefix-arg '(16))
1481 (format "[[#%s]]" label)))
1487 : org-ref-helm-insert-ref-link
1491 This refers to the page of a label in LaTeX.
1493 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1497 "on clicking goto the label. Navigate back with C-c &"
1498 (org-mark-ring-push)
1499 ;; next search from beginning of the buffer
1505 (goto-char (point-min))
1506 (re-search-forward (format "label:%s\\b" label) nil t))
1510 (goto-char (point-min))
1511 (re-search-forward (format "\\label{%s}" label) nil t))
1513 ;; #+label: name org-definition
1515 (goto-char (point-min))
1516 (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
1520 (goto-char (point-min))
1521 (re-search-forward (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t))
1523 ;; Commented out because these ref links do not actually translate correctly in LaTeX.
1524 ;; you need [[#label]] links.
1527 ; (goto-char (point-min))
1528 ; (re-search-forward (format ":CUSTOM_ID:\s-*\\(%s\\)" label) nil t))
1530 ;; we did not find anything, so go back to where we came
1531 (org-mark-ring-goto)
1532 (error "%s not found" label))
1533 (message "go back with (org-mark-ring-goto) `C-c &`"))
1535 (lambda (keyword desc format)
1537 ((eq format 'html) (format "(<pageref>%s</pageref>)" path))
1539 (format "\\pageref{%s}" keyword)))))
1542 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1543 (defun org-pageref-complete-link (&optional arg)
1544 "Completion function for ref links"
1546 (setq label (completing-read "label: " (org-ref-get-labels)))
1547 (format "ref:%s" label)))
1550 Alternatively, you may want to just call a function that inserts a link with completion:
1552 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1553 (defun org-pageref-insert-ref-link ()
1555 (insert (org-pageref-complete-link)))
1560 The nameref link allows you make links to the text of a section with a label. Clicking on the link takes you to the label, and provides a mark to go back to. This only works if you put a raw latex label in the headline.
1562 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1566 "on clicking goto the label. Navigate back with C-c &"
1567 (org-mark-ring-push)
1568 ;; next search from beginning of the buffer
1574 (goto-char (point-min))
1575 (re-search-forward (format "\\label{%s}" label) nil t))
1577 ;; we did not find anything, so go back to where we came
1578 (org-mark-ring-goto)
1579 (error "%s not found" label))
1580 (message "go back with (org-mark-ring-goto) `C-c &`"))
1582 (lambda (keyword desc format)
1584 ((eq format 'html) (format "(<nameref>%s</nameref>)" path))
1586 (format "\\nameref{%s}" keyword)))))
1590 This is just the LaTeX ref for equations. On export, the reference is enclosed in parentheses.
1592 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1596 "on clicking goto the label. Navigate back with C-c &"
1597 (org-mark-ring-push)
1598 ;; next search from beginning of the buffer
1600 (goto-char (point-min))
1603 ;; search forward for the first match
1605 (re-search-forward (format "label:%s" label) nil t)
1607 (re-search-forward (format "\\label{%s}" label) nil t)
1608 ;; #+label: name org-definition
1609 (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
1610 (org-mark-ring-goto)
1611 (error "%s not found" label))
1612 (message "go back with (org-mark-ring-goto) `C-c &`"))
1614 (lambda (keyword desc format)
1616 ((eq format 'html) (format "(<eqref>%s</eqref>)" path))
1618 (format "\\eqref{%s}" keyword)))))
1622 This is the main reason this library exists. We want the following behavior. A cite link should be able to contain multiple bibtex keys. You should be able to click on the link, and get a brief citation of the entry for that key, and a menu of options to open the bibtex file, open a pdf if you have it, open your notes on the entry, or open a url if it exists. You should be able to insert new references onto an existing cite link, or create new ones easily. The following code implements these features.
1624 *** Implementing the click actions of cite
1626 **** Getting the key we clicked on
1627 The first thing we need is to get the bibtex key we clicked on.
1629 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1630 (defun org-ref-get-bibtex-key-under-cursor ()
1631 "returns key under the bibtex cursor. We search forward from
1632 point to get a comma, or the end of the link, and then backwards
1633 to get a comma, or the beginning of the link. that delimits the
1634 keyword we clicked on. We also strip the text properties."
1635 (let* ((object (org-element-context))
1636 (link-string (org-element-property :path object)))
1637 ;; you may click on the part before the citations. here we make
1638 ;; sure to move to the beginning so you get the first citation.
1640 (goto-char (org-element-property :begin object))
1641 (search-forward link-string (org-element-property :end object))
1642 (goto-char (match-beginning 0))
1643 ;; check if we clicked before the path and move as needed.
1644 (unless (< cp (point))
1647 (if (not (org-element-property :contents-begin object))
1648 ;; this means no description in the link
1650 ;; we need the link path start and end
1652 (goto-char (org-element-property :begin object))
1653 (search-forward link-string nil nil 1)
1654 (setq link-string-beginning (match-beginning 0))
1655 (setq link-string-end (match-end 0)))
1657 ;; The key is the text between commas, or the link boundaries
1659 (if (search-forward "," link-string-end t 1)
1660 (setq key-end (- (match-end 0) 1)) ; we found a match
1661 (setq key-end link-string-end))) ; no comma found so take the end
1662 ;; and backward to previous comma from point which defines the start character
1664 (if (search-backward "," link-string-beginning 1 1)
1665 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
1666 (setq key-beginning link-string-beginning))) ; no match found
1667 ;; save the key we clicked on.
1668 (setq bibtex-key (org-ref-strip-string (buffer-substring key-beginning key-end)))
1669 (set-text-properties 0 (length bibtex-key) nil bibtex-key)
1671 ;; link with description. assume only one key
1675 We also need to find which bibliography file that key is in. For that, we need to know which bibliography files are referred to in the file. If none are specified with a bibliography link, we use the default bibliography. This function searches for a bibliography link, and then the LaTeX bibliography link. We also consider the addbibresource link which is used with biblatex.
1677 **** Getting the bibliographies
1678 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1679 (defun org-ref-find-bibliography ()
1680 "find the bibliography in the buffer.
1681 This function sets and returns cite-bibliography-files, which is a list of files
1682 either from bibliography:f1.bib,f2.bib
1683 \bibliography{f1,f2}
1684 internal bibliographies
1686 falling back to what the user has set in org-ref-default-bibliography
1690 (goto-char (point-min))
1691 ;; look for a bibliography link
1692 (when (re-search-forward "\\<bibliography:\\([^\]\|\n]+\\)" nil t)
1693 (setq org-ref-bibliography-files
1694 (mapcar 'org-ref-strip-string (split-string (match-string 1) ",")))
1695 (throw 'result org-ref-bibliography-files))
1698 ;; we did not find a bibliography link. now look for \bibliography
1699 (goto-char (point-min))
1700 (when (re-search-forward "\\\\bibliography{\\([^}]+\\)}" nil t)
1701 ;; split, and add .bib to each file
1702 (setq org-ref-bibliography-files
1703 (mapcar (lambda (x) (concat x ".bib"))
1704 (mapcar 'org-ref-strip-string
1705 (split-string (match-string 1) ","))))
1706 (throw 'result org-ref-bibliography-files))
1708 ;; no bibliography found. maybe we need a biblatex addbibresource
1709 (goto-char (point-min))
1710 ;; look for a bibliography link
1711 (when (re-search-forward "addbibresource:\\([^\]\|\n]+\\)" nil t)
1712 (setq org-ref-bibliography-files
1713 (mapcar 'org-ref-strip-string (split-string (match-string 1) ",")))
1714 (throw 'result org-ref-bibliography-files))
1716 ;; we did not find anything. use defaults
1717 (setq org-ref-bibliography-files org-ref-default-bibliography)))
1719 ;; set reftex-default-bibliography so we can search
1720 (set (make-local-variable 'reftex-default-bibliography) org-ref-bibliography-files)
1721 org-ref-bibliography-files)
1724 **** Finding the bibliography file a key is in
1725 Now, we can see if an entry is in a file.
1727 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1728 (defun org-ref-key-in-file-p (key filename)
1729 "determine if the key is in the file"
1730 (save-current-buffer
1731 (let ((bibtex-files (list filename)))
1732 ;; This is something I am trying because when the bibtex file is open, and
1733 ;; you have added to it, the only way I find to get the update to update
1734 ;; is to close it and reopen it. or to save it and revert it.
1735 (when (get-file-buffer filename)
1736 (set-buffer (get-file-buffer filename))
1738 (revert-buffer t t))
1739 (bibtex-search-entry key t))))
1742 Finally, we want to know which file the key is in.
1744 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1745 (defun org-ref-get-bibtex-key-and-file (&optional key)
1746 "returns the bibtex key and file that it is in. If no key is provided, get one under point"
1747 (let ((org-ref-bibliography-files (org-ref-find-bibliography))
1750 (setq key (org-ref-get-bibtex-key-under-cursor)))
1751 (setq file (catch 'result
1752 (loop for file in org-ref-bibliography-files do
1753 (if (org-ref-key-in-file-p key (file-truename file))
1754 (throw 'result file)))))
1758 **** convenience functions to act on citation at point
1760 :ID: af0b2a82-a7c9-4c08-9dac-09f93abc4a92
1762 We need some convenience functions to open act on the citation at point. These will get the pdf, open the url, or open the notes.
1764 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1765 (defun org-ref-open-pdf-at-point ()
1766 "open the pdf for bibtex key under point if it exists"
1768 (let* ((results (org-ref-get-bibtex-key-and-file))
1770 (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key)))
1771 (if (file-exists-p pdf-file)
1772 (org-open-file pdf-file)
1773 (message "no pdf found for %s" key))))
1776 (defun org-ref-open-url-at-point ()
1777 "open the url for bibtex key under point."
1779 (let* ((results (org-ref-get-bibtex-key-and-file))
1781 (bibfile (cdr results)))
1784 (insert-file-contents bibfile)
1785 (bibtex-search-entry key)
1786 ;; I like this better than bibtex-url which does not always find
1789 (let ((url (bibtex-autokey-get-field "url")))
1791 (browse-url (s-trim url))
1794 (let ((doi (bibtex-autokey-get-field "doi")))
1796 (if (string-match "^http" doi)
1798 (browse-url (format "http://dx.doi.org/%s" (s-trim doi))))
1799 (throw 'done nil))))))))
1802 (defun org-ref-open-notes-at-point ()
1803 "open the notes for bibtex key under point."
1805 (let* ((results (org-ref-get-bibtex-key-and-file))
1807 (bibfile (cdr results)))
1810 (insert-file-contents bibfile)
1811 (bibtex-search-entry key)
1812 (org-ref-open-bibtex-notes)))))
1815 (defun org-ref-citation-at-point ()
1816 "give message of current citation at point"
1818 (let* ((cb (current-buffer))
1819 (results (org-ref-get-bibtex-key-and-file))
1821 (bibfile (cdr results)))
1822 (message "%s" (progn
1824 (insert-file-contents bibfile)
1825 (bibtex-search-entry key)
1826 (org-ref-bib-citation))))))
1829 (defun org-ref-open-citation-at-point ()
1830 "open bibtex file to key at point"
1832 (let* ((cb (current-buffer))
1833 (results (org-ref-get-bibtex-key-and-file))
1835 (bibfile (cdr results)))
1837 (bibtex-search-entry key)))
1840 **** the actual minibuffer menu
1841 Now, we create the menu. This is a rewrite of the cite action. This makes the function extendable by users.
1843 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1844 (defvar org-ref-cite-menu-funcs '()
1845 "Functions to run on cite click menu. Each entry is a list of (key menu-name function).
1846 The function must take no arguments and work on the key at point. Do not modify this variable, it is set to empty in the menu click function, and functions are conditionally added to it.")
1849 (defvar org-ref-user-cite-menu-funcs
1850 '(("C" "rossref" org-ref-crossref-at-point)
1851 ("y" "Copy entry to file" org-ref-copy-entry-at-point-to-file)
1852 ("s" "Copy summary" org-ref-copy-entry-as-summary))
1853 "user-defined functions to run on bibtex key at point.")
1856 (defun org-ref-copy-entry-as-summary ()
1857 "Copy the bibtex entry for the citation at point as a summary."
1859 (save-window-excursion
1860 (org-ref-open-citation-at-point)
1861 (kill-new (org-ref-bib-citation))))
1864 (defun org-ref-copy-entry-at-point-to-file ()
1865 "Copy the bibtex entry for the citation at point to NEW-FILE.
1866 Prompt for NEW-FILE includes bib files in org-ref-default-bibliography, and bib files in current working directory. You can also specify a new file."
1868 (let ((new-file (ido-completing-read
1870 (append org-ref-default-bibliography
1871 (f-entries "." (lambda (f) (f-ext? f "bib"))))))
1872 (key (org-ref-get-bibtex-key-under-cursor)))
1873 (save-window-excursion
1874 (org-ref-open-citation-at-point)
1875 (bibtex-copy-entry-as-kill))
1877 (let ((bibtex-files (list (file-truename new-file))))
1878 (if (assoc key (bibtex-global-key-alist))
1879 (message "That key already exists in %s" new-file)
1881 (save-window-excursion
1882 (find-file new-file)
1883 (goto-char (point-max))
1884 ;; make sure we are at the beginning of a line.
1885 (unless (looking-at "^") (insert "\n\n"))
1890 (defun org-ref-get-doi-at-point ()
1891 "Get doi for key at point."
1892 (let* ((results (org-ref-get-bibtex-key-and-file))
1894 (bibfile (cdr results))
1898 (insert-file-contents bibfile)
1899 (bibtex-search-entry key)
1900 (setq doi (bibtex-autokey-get-field "doi"))
1901 ;; in case doi is a url, remove the url part.
1902 (replace-regexp-in-string "^http://dx.doi.org/" "" doi)))))
1905 ;; functions that operate on key at point for click menu
1906 (defun org-ref-wos-at-point ()
1907 "open the doi in wos for bibtex key under point."
1909 (doi-utils-wos (org-ref-get-doi-at-point)))
1912 (defun org-ref-wos-citing-at-point ()
1913 "open the doi in wos citing articles for bibtex key under point."
1915 (doi-utils-wos-citing (org-ref-get-doi-at-point)))
1918 (defun org-ref-wos-related-at-point ()
1919 "open the doi in wos related articles for bibtex key under point."
1921 (doi-utils-wos-related (org-ref-get-doi-at-point)))
1924 (defun org-ref-google-scholar-at-point ()
1925 "open the doi in google scholar for bibtex key under point."
1927 (doi-utils-google-scholar (org-ref-get-doi-at-point)))
1930 (defun org-ref-pubmed-at-point ()
1931 "open the doi in pubmed for bibtex key under point."
1933 (doi-utils-pubmed (org-ref-get-doi-at-point)))
1936 (defun org-ref-crossref-at-point ()
1937 "open the doi in crossref for bibtex key under point."
1939 (doi-utils-crossref (org-ref-get-doi-at-point)))
1942 (defun org-ref-cite-onclick-minibuffer-menu (&optional link-string)
1943 "action when a cite link is clicked on.
1944 Provides a menu of context sensitive actions. If the bibtex entry has a pdf, you get an option to open it. If there is a doi, you get a lot of options."
1946 (let* ((results (org-ref-get-bibtex-key-and-file))
1948 (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key))
1949 (bibfile (cdr results))
1950 (url (save-excursion
1952 (insert-file-contents bibfile)
1953 (bibtex-search-entry key)
1954 (bibtex-autokey-get-field "url"))))
1955 (doi (save-excursion
1957 (insert-file-contents bibfile)
1958 (bibtex-search-entry key)
1959 ;; I like this better than bibtex-url which does not always find
1961 (bibtex-autokey-get-field "doi")))))
1963 (when (string= "" doi) (setq doi nil))
1964 (when (string= "" url) (setq url nil))
1965 (setq org-ref-cite-menu-funcs '())
1971 'org-ref-cite-menu-funcs
1972 '("o" "pen" org-ref-open-citation-at-point)))
1975 (when (file-exists-p pdf-file)
1977 'org-ref-cite-menu-funcs
1978 `("p" "df" ,org-ref-open-pdf-function) t))
1982 'org-ref-cite-menu-funcs
1983 '("n" "otes" org-ref-open-notes-at-point) t)
1988 'org-ref-cite-menu-funcs
1989 '("u" "rl" org-ref-open-url-at-point) t))
1994 'org-ref-cite-menu-funcs
1995 '("w" "os" org-ref-wos-at-point) t)
1998 'org-ref-cite-menu-funcs
1999 '("c" "iting" org-ref-wos-citing-at-point) t)
2002 'org-ref-cite-menu-funcs
2003 '("r" "elated" org-ref-wos-related-at-point) t)
2006 'org-ref-cite-menu-funcs
2007 '("g" "oogle scholar" org-ref-google-scholar-at-point) t)
2010 'org-ref-cite-menu-funcs
2011 '("P" "ubmed" org-ref-pubmed-at-point) t))
2013 ;; add user functions
2014 (dolist (tup org-ref-user-cite-menu-funcs)
2016 'org-ref-cite-menu-funcs
2021 'org-ref-cite-menu-funcs
2022 '("q" "uit" (lambda ())) t)
2024 ;; now we make a menu
2025 ;; construct menu string as a message
2028 (let* ((results (org-ref-get-bibtex-key-and-file))
2030 (bibfile (cdr results)))
2033 (insert-file-contents bibfile)
2034 (bibtex-search-entry key)
2035 (org-ref-bib-citation))))
2039 (concat "[" (elt tup 0) "]"
2041 org-ref-cite-menu-funcs "")))
2043 (let* ((input (read-char-exclusive))
2045 (char-to-string input) org-ref-cite-menu-funcs)))
2046 ;; now run the function (2nd element in choice)
2055 : org-ref-cite-onclick-minibuffer-menu
2057 *** A function to format a cite link
2059 Next, we define a formatting function for the cite link. This is done so that the cite link definition is very short, and easy to change. You just need to specify the functions in the definition. This function is deprecated. The formatting is defined later automatically.
2061 #+BEGIN_SRC emacs-lisp :tangle no
2062 ;(defun org-ref-cite-link-format (keyword desc format)
2064 ; ((eq format 'html) (mapconcat (lambda (key) (format "<a name=\"#%s\">%s</a>" key key) (org-ref-split-and-strip-string keyword) ",")))
2065 ; ((eq format 'latex)
2066 ; (concat "\\cite" (when desc (format "[%s]" desc)) "{"
2067 ; (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
2071 *** The actual cite link
2072 Finally, we define the cite link. This is deprecated; the links are autogenerated later. This is here for memory.
2074 #+BEGIN_SRC emacs-lisp :tangle no
2077 ; 'org-ref-cite-onclick-minibuffer-menu
2078 ; 'org-ref-cite-link-format)
2081 *** Automatic definition of the cite links
2082 There are many different kinds of citations in LaTeX, but they are all variants of a basic syntax of \citetype[optional text]{label1,label2}. Here we use lisp to generate the link definitions. We define a function that creates the code to create the link, and then we evaluate it. We also create the completion function for the new link, and add it to the list of known links.
2084 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2085 (defmacro org-ref-make-completion-function (type)
2086 `(defun ,(intern (format "org-%s-complete-link" type)) (&optional arg)
2092 (let ((bibtex-files (org-ref-find-bibliography)))
2093 (bibtex-global-key-alist))))))
2096 We will want to generate formatting functions for each citation type. The reason for doing this is so we can on the fly change the formatting later.
2098 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2099 (defmacro org-ref-make-format-function (type)
2100 `(defun ,(intern (format "org-ref-format-%s" type)) (keyword desc format)
2105 (format "[[#%s][%s]]" key key))
2106 (org-ref-split-and-strip-string keyword) ","))
2113 (org-ref-split-and-strip-string keyword) ",") "]"))
2118 (format "<a href=\"#%s\">%s</a>" key key))
2119 (org-ref-split-and-strip-string keyword) ","))
2122 (if (string= (substring type -1) "s")
2123 ;; biblatex format for multicite commands, which all end in s. These are formated as \cites{key1}{key2}...
2124 (concat "\\" ,type (mapconcat (lambda (key) (format "{%s}" key))
2125 (org-ref-split-and-strip-string keyword) ""))
2127 (concat "\\" ,type (when desc (org-ref-format-citation-description desc)) "{"
2128 (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
2130 ;; for markdown we generate pandoc citations
2133 (desc ;; pre and or post text
2134 (let* ((text (split-string desc "::"))
2138 (format "[@%s," keyword)
2139 (when pre (format " %s" pre))
2140 (when post (format ", %s" post))
2145 (lambda (key) (concat "@" key))
2146 (org-ref-split-and-strip-string keyword)
2152 We create the links by mapping the function onto the list of defined link types.
2154 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2155 (defun org-ref-format-citation-description (desc)
2156 "Return formatted citation description. If the cite link has a
2157 description, it is optional text for the citation command. You
2158 can specify pre and post text by separating these with ::, for
2159 example [[cite:key][pre text::post text]]."
2161 ((string-match "::" desc)
2162 (format "[%s][%s]" (car (setq results (split-string desc "::"))) (cadr results)))
2163 (t (format "[%s]" desc))))
2165 (defun org-ref-define-citation-link (type &optional key)
2166 "Add a citation link of TYPE for org-ref.
2167 With optional KEY, set the reftex binding. For example:
2168 (org-ref-define-citation-link \"citez\" ?z) will create a new citez link, with reftex key of z,
2169 and the completion function."
2170 (interactive "sCitation Type: \ncKey: ")
2172 ;; create the formatting function
2173 (eval `(org-ref-make-format-function ,type))
2178 org-ref-cite-onclick-function
2179 (quote ,(intern (format "org-ref-format-%s" type)))))
2181 ;; create the completion function
2182 (eval `(org-ref-make-completion-function ,type))
2184 ;; store new type so it works with adding citations, which checks
2185 ;; for existence in this list
2186 (add-to-list 'org-ref-cite-types type)
2188 ;; and finally if a key is specified, we modify the reftex menu
2190 (setf (nth 2 (assoc 'org reftex-cite-format-builtin))
2191 (append (nth 2 (assoc 'org reftex-cite-format-builtin))
2192 `((,key . ,(concat type ":%l")))))))
2194 ;; create all the link types and their completion functions
2195 (mapcar 'org-ref-define-citation-link org-ref-cite-types)
2200 *** org-ref-insert-cite-link
2201 We need a convenient method to insert links. In reftex you use the keystroke C-c ], which gives you a minibuffer to search the bibtex files from. This function is bound to that same keystroke here [[*org-mode%20/%20reftex%20setup][org-mode / reftex setup]]. This function will append to a cite link if you call it while on a link.
2203 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2204 (defun org-ref-insert-cite-link (alternative-cite)
2205 "Insert a default citation link using reftex. If you are on a link, it
2206 appends to the end of the link, otherwise, a new link is
2207 inserted. Use a prefix arg to get a menu of citation types."
2209 (org-ref-find-bibliography)
2210 (let* ((object (org-element-context))
2211 (link-string-beginning (org-element-property :begin object))
2212 (link-string-end (org-element-property :end object))
2213 (path (org-element-property :path object)))
2215 (if (not alternative-cite)
2218 ;; case where we are in a link
2219 ((and (equal (org-element-type object) 'link)
2220 (-contains? org-ref-cite-types (org-element-property :type object)))
2221 (goto-char link-string-end)
2222 ;; sometimes there are spaces at the end of the link
2223 ;; this code moves point pack until no spaces are there
2224 (while (looking-back " ") (backward-char))
2225 (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
2227 ;; We are next to a link, and we want to append
2230 (and (equal (org-element-type (org-element-context)) 'link)
2231 (-contains? org-ref-cite-types (org-element-property :type (org-element-context)))))
2232 (while (looking-back " ") (backward-char))
2233 (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
2235 ;; insert fresh link
2238 (concat org-ref-default-citation-link
2240 (mapconcat 'identity (reftex-citation t) ",")))))
2242 ;; you pressed a C-u so we run this code
2243 (reftex-citation))))
2245 cite:zhou-2004-first-lda-u,paier-2006-errat,boes-2015-estim-bulk
2249 : org-ref-insert-cite-link
2251 *** Completion in cite links
2252 If you know the specific bibtex key, you may like to use completion directly. You use this with the org-mode machinery and tab completion. Here is the prototypical completion function. These are now all created when the links are created.
2254 #+BEGIN_SRC emacs-lisp :tangle no
2255 (defun org-cite-complete-link (&optional arg)
2256 "Completion function for cite links"
2258 org-ref-default-citation-link
2261 (let ((bibtex-files (org-ref-find-bibliography)))
2262 (bibtex-global-key-alist)))))
2265 Alternatively, you may shortcut the org-machinery with this command. You will be prompted for a citation type, and then offered key completion.
2267 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2268 (defun org-ref-insert-cite-with-completion (type)
2269 "Insert a cite link with completion"
2270 (interactive (list (ido-completing-read "Type: " org-ref-cite-types)))
2271 (insert (funcall (intern (format "org-%s-complete-link" type)))))
2274 ** Storing links to a bibtex entry
2275 org-mode already defines a store link function for bibtex entries. It does not store the link I want though, it only stores a brief citation of the entry. I want a citation link. Here is a function to do that.
2277 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2278 (defun org-ref-store-bibtex-entry-link ()
2279 "Save a citation link to the current bibtex entry. Saves in the default link type."
2281 (let ((link (concat org-ref-default-citation-link
2284 (bibtex-beginning-of-entry)
2285 (reftex-get-bib-field "=key=" (bibtex-parse-entry))))))
2286 (message "saved %s" link)
2287 (push (list link) org-stored-links)
2288 (car org-stored-links)))
2292 org-ref minimally supports index entries. To make an index in a file, you should put in the LaTeX header these lines
2295 #+LATEX_HEADER: \usepackage{makeidx}
2296 #+LATEX_HEADER: \makeindex
2299 Finally, put \makeindex at the end of the document where you want the index to appear. You will need to run the makeindex program at an appropriate point in your LaTeX to pdf, or use ox-manuscript, which will do it for you.
2302 Use index links to create entries (see http://en.wikibooks.org/wiki/LaTeX/Indexing). Clicking on an index link runs occur on the buffer for the entry. The link exports to LaTeX. Some links may need to be enclosed in double brackets if they have spaces in them.
2307 [[index:hello!Sam@\textsl{Sam}]]
2308 [[index:Lin@\textbf{Lin}]]
2309 [[index:Joe|textit]]
2310 [[index:Lin@\textbf{Lin}]]
2311 [[index:Peter|see {hello}]]
2312 [[index:Jen|seealso{Jenny}]]
2314 index:encodings!input!cp850
2316 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2322 (lambda (path desc format)
2325 (format "\\index{%s}" path)))))
2327 ;; this will generate a temporary index of entries in the file.
2331 (let ((*index-links* '())
2332 (*initial-letters* '()))
2335 (org-element-map (org-element-parse-buffer) 'link
2337 (let ((type (nth 0 link))
2338 (plist (nth 1 link)))
2340 (when (equal (plist-get plist ':type) "index")
2343 (cons (plist-get plist :path)
2345 "[[elisp:(progn (switch-to-buffer \"%s\") (goto-char %s))][%s]]"
2347 (plist-get plist :begin) ;; position of link
2348 ;; grab a description
2350 (goto-char (plist-get plist :begin))
2351 (if (thing-at-point 'sentence)
2353 (replace-regexp-in-string
2354 "\n" "" (thing-at-point 'sentence))
2355 ;; or call it a link
2359 (setq *index-links* (cl-sort *index-links* 'string-lessp :key 'car))
2361 ;; now first letters
2362 (dolist (link *index-links*)
2363 (add-to-list '*initial-letters* (substring (car link) 0 1) t))
2365 ;; now create the index
2366 (switch-to-buffer (get-buffer-create "*index*"))
2369 (insert "#+TITLE: Index\n\n")
2370 (dolist (letter *initial-letters*)
2371 (insert (format "* %s\n" (upcase letter)))
2372 ;; now process the links
2375 (string= letter (substring (car (car *index-links*)) 0 1)))
2376 (let ((link (pop *index-links*)))
2377 (insert (format "%s %s\n\n" (car link) (cdr link))))))
2378 (switch-to-buffer "*index*")))
2380 (lambda (path desc format)
2383 (format "\\printindex")))))
2387 | lambda | (path) | (let ((*index-links* (quote nil)) (*initial-letters* (quote nil))) (org-element-map (org-element-parse-buffer) (quote link) (lambda (link) (let ((type (nth 0 link)) (plist (nth 1 link))) (when (equal (plist-get plist (quote :type)) index) (add-to-list (quote *index-links*) (cons (plist-get plist :path) (format [[elisp:(progn (switch-to-buffer "%s") (goto-char %s))][%s]] (current-buffer) (plist-get plist :begin) (save-excursion (goto-char (plist-get plist :begin)) (if (thing-at-point (quote sentence)) (replace-regexp-in-string \n (thing-at-point (quote sentence))) link))))))))) (setq *index-links* (cl-sort *index-links* (quote string-lessp) :key (quote car))) (dolist (link *index-links*) (add-to-list (quote *initial-letters*) (substring (car link) 0 1) t)) (switch-to-buffer (get-buffer-create *index*)) (org-mode) (erase-buffer) (insert #+TITLE: Index\n\n) (dolist (letter *initial-letters*) (insert (format * %s\n (upcase letter))) (while (and *index-links* (string= letter (substring (car (car *index-links*)) 0 1))) (let ((link (pop *index-links*))) (insert (format %s %s\n\n (car link) (cdr link)))))) (switch-to-buffer *index*)) |
2388 | lambda | (path desc format) | (cond ((eq format (quote latex)) (format \printindex))) |
2391 org-ref provides some minimal support for a glossary. See http://en.wikibooks.org/wiki/LaTeX/Glossary for details. You need to put these lines in the header.
2393 #+LATEX_HEADER: \usepackage{glossaries}
2394 #+LATEX_HEADER: \makeglossaries
2396 And at the end of the document put \makeglossaries.
2398 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2401 nil ;; no follow action
2402 (lambda (path desc format)
2405 (format "\\newglossaryentry{%s}{%s}" path desc)))))
2411 nil ;; no follow action
2412 (lambda (path desc format)
2415 (format "\\gls{%s}" path)))))
2420 nil ;; no follow action
2421 (lambda (path desc format)
2424 (format "\\glspl{%s}" path)))))
2429 nil ;; no follow action
2430 (lambda (path desc format)
2433 (format "\\Gls{%s}" path)))))
2438 nil ;; no follow action
2439 (lambda (path desc format)
2442 (format "\\Glspl{%s}" path)))))
2446 ** create simple text citation from bibtex entry
2448 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2449 (defun org-ref-bib-citation ()
2450 "From a bibtex entry, create and return a simple citation string.
2451 This assumes you are in an article."
2453 (bibtex-beginning-of-entry)
2454 (let* ((cb (current-buffer))
2455 (bibtex-expand-strings t)
2456 (entry (loop for (key . value) in (bibtex-parse-entry t)
2457 collect (cons (downcase key) value)))
2458 (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2459 (year (reftex-get-bib-field "year" entry))
2460 (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2461 (key (reftex-get-bib-field "=key=" entry))
2462 (journal (reftex-get-bib-field "journal" entry))
2463 (volume (reftex-get-bib-field "volume" entry))
2464 (pages (reftex-get-bib-field "pages" entry))
2465 (doi (reftex-get-bib-field "doi" entry))
2466 (url (reftex-get-bib-field "url" entry))
2468 ;;authors, "title", Journal, vol(iss):pages (year).
2469 (format "%s, \"%s\", %s, %s:%s (%s)"
2470 author title journal volume pages year)))
2474 : org-ref-bib-citation
2477 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2478 (defun org-ref-bib-html-citation ()
2479 "from a bibtex entry, create and return a simple citation with html links."
2481 (bibtex-beginning-of-entry)
2482 (let* ((cb (current-buffer))
2483 (bibtex-expand-strings t)
2484 (entry (loop for (key . value) in (bibtex-parse-entry t)
2485 collect (cons (downcase key) value)))
2486 (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2487 (year (reftex-get-bib-field "year" entry))
2488 (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2489 (key (reftex-get-bib-field "=key=" entry))
2490 (journal (reftex-get-bib-field "journal" entry))
2491 (volume (reftex-get-bib-field "volume" entry))
2492 (pages (reftex-get-bib-field "pages" entry))
2493 (doi (reftex-get-bib-field "doi" entry))
2494 (url (reftex-get-bib-field "url" entry))
2496 ;;authors, "title", Journal, vol(iss):pages (year).
2497 (concat (format "%s, \"%s\", %s, %s:%s (%s)."
2498 author title journal volume pages year)
2499 (when url (format " <a href=\"%s\">link</a>" url))
2500 (when doi (format " <a href=\"http://dx.doi.org/%s\">doi</a>" doi)))
2504 ** open pdf from bibtex
2505 We bind this to a key here: [[*key%20bindings%20for%20utilities][key bindings for utilities]].
2506 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2507 (defun org-ref-open-bibtex-pdf ()
2508 "open pdf for a bibtex entry, if it exists. assumes point is in
2509 the entry of interest in the bibfile. but does not check that."
2512 (bibtex-beginning-of-entry)
2513 (let* ((bibtex-expand-strings t)
2514 (entry (bibtex-parse-entry t))
2515 (key (reftex-get-bib-field "=key=" entry))
2516 (pdf (format (concat org-ref-pdf-directory "%s.pdf") key)))
2518 (if (file-exists-p pdf)
2519 (org-open-link-from-string (format "[[file:%s]]" pdf))
2523 ** open notes from bibtex
2524 We bind this to a key here [[*key%20bindings%20for%20utilities][key bindings for utilities]].
2526 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2527 (defun org-ref-open-bibtex-notes ()
2528 "from a bibtex entry, open the notes if they exist, and create a heading if they do not.
2530 I never did figure out how to use reftex to make this happen
2531 non-interactively. the reftex-format-citation function did not
2532 work perfectly; there were carriage returns in the strings, and
2533 it did not put the key where it needed to be. so, below I replace
2534 the carriage returns and extra spaces with a single space and
2535 construct the heading by hand."
2538 (bibtex-beginning-of-entry)
2539 (let* ((cb (current-buffer))
2540 (bibtex-expand-strings t)
2541 (entry (loop for (key . value) in (bibtex-parse-entry t)
2542 collect (cons (downcase key) value)))
2543 (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2544 (year (reftex-get-bib-field "year" entry))
2545 (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2546 (key (reftex-get-bib-field "=key=" entry))
2547 (journal (reftex-get-bib-field "journal" entry))
2548 (volume (reftex-get-bib-field "volume" entry))
2549 (pages (reftex-get-bib-field "pages" entry))
2550 (doi (reftex-get-bib-field "doi" entry))
2551 (url (reftex-get-bib-field "url" entry))
2554 ;; save key to clipboard to make saving pdf later easier by pasting.
2557 (kill-ring-save (point-min) (point-max)))
2559 ;; now look for entry in the notes file
2560 (if org-ref-bibliography-notes
2561 (find-file-other-window org-ref-bibliography-notes)
2562 (error "org-ref-bib-bibliography-notes is not set to anything"))
2564 (goto-char (point-min))
2565 ;; put new entry in notes if we don't find it.
2566 (if (re-search-forward (format ":Custom_ID: %s$" key) nil 'end)
2567 (funcall org-ref-open-notes-function)
2568 ;; no entry found, so add one
2569 (insert (format "\n** TODO %s - %s" year title))
2581 [[cite:%s]] [[file:%s/%s.pdf][pdf]]\n\n"
2582 key author journal year volume pages doi url key org-ref-pdf-directory key))
2586 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2587 (defun org-ref-open-notes-from-reftex ()
2588 "Call reftex, and open notes for selected entry."
2590 (let ((bibtex-key )))
2592 ;; now look for entry in the notes file
2593 (if org-ref-bibliography-notes
2594 (find-file-other-window org-ref-bibliography-notes)
2595 (error "org-ref-bib-bibliography-notes is not set to anything"))
2597 (goto-char (point-min))
2599 (re-search-forward (format
2601 (first (reftex-citation t)) nil 'end))
2602 (funcall org-ref-open-notes-function))
2605 ** open url in browser from bibtex
2607 We bind this to a key here [[*key%20bindings%20for%20utilities][key bindings for utilities]].
2609 + This function may be duplicative of bibtex-url. But I think my function is better unless you do some complicated customization of bibtex-generate-url-list.
2611 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2612 (defun org-ref-open-in-browser ()
2613 "Open the bibtex entry at point in a browser using the url field or doi field"
2616 (bibtex-beginning-of-entry)
2618 (let ((url (bibtex-autokey-get-field "url")))
2623 (let ((doi (bibtex-autokey-get-field "doi")))
2625 (if (string-match "^http" doi)
2627 (browse-url (format "http://dx.doi.org/%s" doi)))
2629 (message "No url or doi found"))))
2633 I discovered you could upload a bibtex entry to citeulike using http requests. The upload is actually done by a [[*The%20upload%20script][python script]], because it was easy to write. Here is the emacs command to do this. It is not a fast operation, and do not use it frequently.
2635 *** function to upload bibtex to citeulike
2637 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2638 (defun org-ref-upload-bibtex-entry-to-citeulike ()
2639 "with point in a bibtex entry get bibtex string and submit to citeulike.
2641 Relies on the python script /upload_bibtex_citeulike.py being in the user directory."
2643 (message "uploading to citeulike")
2645 (bibtex-narrow-to-entry)
2646 (let ((startpos (point-min))
2647 (endpos (point-max))
2648 (bibtex-string (buffer-string))
2649 (script (concat "python " starter-kit-dir "/upload_bibtex_citeulike.py&")))
2650 (with-temp-buffer (insert bibtex-string)
2651 (shell-command-on-region (point-min) (point-max) script t nil nil t)))))
2654 *** The upload script
2655 Here is the python script for uploading.
2657 *************** TODO document how to get the cookies
2660 # :tangle upload_bibtex_citeulike.py
2663 import pickle, requests, sys
2666 with open('c:/Users/jkitchin/Dropbox/blogofile-jkitchin.github.com/_blog/cookies.pckl', 'rb') as f:
2667 cookies = pickle.load(f)
2669 url = 'http://www.citeulike.org/profile/jkitchin/import_do'
2671 bibtex = sys.stdin.read()
2673 data = {'pasted':bibtex,
2675 'tag_parsing':'simple',
2676 'strip_brackets':'no',
2677 'update_id':'bib-key',
2678 'btn_bibtex':'Import BibTeX file ...'}
2680 headers = {'content-type': 'multipart/form-data',
2681 'User-Agent':'jkitchin/johnrkitchin@gmail.com bibtexupload'}
2683 r = requests.post(url, headers=headers, data=data, cookies=cookies, files={})
2687 ** Build a pdf from a bibtex file
2688 It is useful to have a pdf version of an entire bibliography to check it for formatting, spelling, or to share it. This function creates a pdf from a bibtex file. I only include the packages I commonly use in my bitex files.
2690 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2691 (defun org-ref-build-full-bibliography ()
2692 "build pdf of all bibtex entries, and open it."
2694 (let* ((bibfile (file-name-nondirectory (buffer-file-name)))
2695 (bib-base (file-name-sans-extension bibfile))
2696 (texfile (concat bib-base ".tex"))
2697 (pdffile (concat bib-base ".pdf")))
2700 (insert (format "\\documentclass[12pt]{article}
2701 \\usepackage[version=3]{mhchem}
2703 \\usepackage[numbers]{natbib}
2704 \\usepackage[colorlinks=true, linkcolor=blue, urlcolor=blue, pdfstartview=FitH]{hyperref}
2708 \\bibliographystyle{unsrtnat}
2710 \\end{document}" bib-base))
2712 (shell-command (concat "pdflatex " bib-base))
2713 (shell-command (concat "bibtex " bib-base))
2714 (shell-command (concat "pdflatex " bib-base))
2715 (shell-command (concat "pdflatex " bib-base))
2716 (kill-buffer texfile)
2717 (org-open-file pdffile)
2721 ** Extract bibtex entries cited in an org-file
2722 When you use your default bibliography file, and you want to send an org-file to a collaborator, you may need to include bibtex entries so the other person can see them. This function does that and puts the entries in a section at the end of the document that can be tangled to a bib-file.
2724 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2725 (defun org-ref-extract-bibtex-entries ()
2726 "extract the bibtex entries referred to by cite links in the current buffer into a src block at the bottom of the current buffer.
2728 If no bibliography is in the buffer the `reftex-default-bibliography' is used."
2730 (let* ((temporary-file-directory (file-name-directory (buffer-file-name)))
2731 (tempname (make-temp-file "extract-bib"))
2732 (contents (buffer-string))
2733 (cb (current-buffer))
2734 basename texfile bibfile results)
2736 ;; open tempfile and insert org-buffer contents
2737 (find-file tempname)
2739 (setq basename (file-name-sans-extension
2740 (file-name-nondirectory buffer-file-name))
2741 texfile (concat tempname ".tex")
2742 bibfile (concat tempname ".bib"))
2744 ;; see if we have a bibliography, and insert the default one if not.
2746 (goto-char (point-min))
2747 (unless (re-search-forward "^bibliography:" (point-max) 'end)
2748 (insert (format "\nbibliography:%s"
2749 (mapconcat 'identity reftex-default-bibliography ",")))))
2752 ;; get a latex file and extract the references
2753 (org-latex-export-to-latex)
2756 (reftex-create-bibtex-file bibfile)
2758 ;; save results of the references
2759 (setq results (buffer-string))
2761 ;; kill buffers. these are named by basename, not full path
2762 (kill-buffer (concat basename ".bib"))
2763 (kill-buffer (concat basename ".tex"))
2764 (kill-buffer basename)
2766 (delete-file bibfile)
2767 (delete-file texfile)
2768 (delete-file tempname)
2770 ;; Now back to the original org buffer and insert the results
2771 (switch-to-buffer cb)
2772 (when (not (string= "" results))
2774 (goto-char (point-max))
2776 (org-insert-heading)
2777 (insert (format " Bibtex entries
2779 ,#+BEGIN_SRC text :tangle %s
2781 ,#+END_SRC" (concat (file-name-sans-extension (file-name-nondirectory (buffer-file-name))) ".bib") results))))))
2784 ** Find bad cite links
2786 :ID: 8515E800-EDA0-4B2A-85FD-55B6FF849203
2788 Depending on how you enter citations, you may have citations with no corresponding bibtex entry. This function finds them and gives you a clickable table to navigate to them.
2790 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2793 (defun index (substring list)
2794 "return the index of string in a list of strings"
2797 (dolist (arg list i)
2798 (if (string-match (concat "^" substring "$") arg)
2803 ;; return counter if found, otherwise return nil
2807 (defun org-ref-find-bad-citations ()
2808 "Create a list of citation keys in an org-file that do not have a bibtex entry in the known bibtex files.
2810 Makes a new buffer with clickable links."
2812 ;; generate the list of bibtex-keys and cited keys
2813 (let* ((bibtex-files (org-ref-find-bibliography))
2814 (bibtex-file-path (mapconcat (lambda (x) (file-name-directory (file-truename x))) bibtex-files ":"))
2815 (bibtex-keys (mapcar (lambda (x) (car x)) (bibtex-global-key-alist)))
2816 (bad-citations '()))
2818 (org-element-map (org-element-parse-buffer) 'link
2820 (let ((plist (nth 1 link)))
2821 (when (-contains? org-ref-cite-types (plist-get plist :type))
2822 (dolist (key (org-ref-split-and-strip-string (plist-get plist :path)))
2823 (when (not (index key bibtex-keys))
2828 `(,(format "%s [[elisp:(progn (switch-to-buffer-other-frame \"%s\")(goto-char %s))][not found here]]\n"
2831 (plist-get plist :begin)))))
2833 ;; set with-affilates to t to get citations in a caption
2838 (switch-to-buffer-other-window "*Missing citations*")
2841 (insert "* List of bad cite links\n")
2842 (insert (mapconcat 'identity bad-citations ""))
2843 ;(setq buffer-read-only t)
2844 (use-local-map (copy-keymap org-mode-map))
2845 (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))
2847 (when (get-buffer "*Missing citations*")
2848 (kill-buffer "*Missing citations*"))
2849 (message "No bad cite links found"))))
2852 ** helm interface to org-ref
2853 In [[id:8515E800-EDA0-4B2A-85FD-55B6FF849203][Find bad cite links]] we wrote a function that finds bad links and creates a buffer of links to them.
2855 Here we develop a similar idea, but instead of an org-buffer with links, we create helm sources for bad cite links, bad ref links, and multiple labels.
2857 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2858 (defun org-ref-bad-cite-candidates ()
2859 "Returns a list of conses (key . marker) where key does not exist in the known bibliography files, and marker points to the key."
2860 (let* ((cp (point)) ; save to return to later
2861 (bibtex-files (org-ref-find-bibliography))
2862 (bibtex-file-path (mapconcat
2864 (file-name-directory (file-truename x)))
2866 (bibtex-keys (mapcar (lambda (x) (car x))
2867 (bibtex-global-key-alist)))
2868 (bad-citations '()))
2870 (org-element-map (org-element-parse-buffer) 'link
2872 (let ((plist (nth 1 link)))
2873 (when (-contains? org-ref-cite-types (plist-get plist :type))
2874 (dolist (key (org-ref-split-and-strip-string (plist-get plist :path)) )
2875 (when (not (index key bibtex-keys))
2876 (goto-char (plist-get plist :begin))
2877 (re-search-forward key)
2878 (push (cons key (point-marker)) bad-citations)))
2880 ;; add with-affiliates to get cites in caption
2886 (defun org-ref-bad-ref-candidates ()
2887 "Returns a list of conses (ref . marker) where ref is a ref link that does not point to anything (i.e. a label)."
2888 ;; first get a list of legitimate labels
2890 (labels (org-ref-get-labels))
2892 ;; now loop over ref links
2893 (goto-char (point-min))
2894 (org-element-map (org-element-parse-buffer) 'link
2896 (let ((plist (nth 1 link)))
2897 (when (or (equal (plist-get plist ':type) "ref")
2898 (equal (plist-get plist ':type) "eqref")
2899 (equal (plist-get plist ':type) "pageref")
2900 (equal (plist-get plist ':type) "nameref"))
2901 (unless (-contains? labels (plist-get plist :path))
2902 (goto-char (plist-get plist :begin))
2905 (cons (plist-get plist :path)
2906 (point-marker))))))))
2911 (defun org-ref-bad-label-candidates ()
2912 "Return a list of labels where label is multiply defined."
2913 (let ((labels (org-ref-get-labels))
2914 (multiple-labels '()))
2915 (when (not (= (length labels)
2916 (length (-uniq labels))))
2917 (dolist (label labels)
2918 (when (> (-count (lambda (a)
2921 ;; this is a multiply defined label.
2923 (goto-char (point-min))
2924 (while (re-search-forward
2925 (format "[^#+]label:%s\\s-" label) nil t)
2926 (push (cons label (point-marker)) multiple-labels))
2928 (goto-char (point-min))
2929 (while (re-search-forward
2930 (format "\\label{%s}\\s-?" label) nil t)
2931 (push (cons label (point-marker)) multiple-labels))
2933 (goto-char (point-min))
2934 (while (re-search-forward
2935 (format "^#\\+label:\\s-*%s" label) nil t)
2936 (push (cons label (point-marker)) multiple-labels))
2938 (goto-char (point-min))
2939 (while (re-search-forward
2940 (format "^#\\+tblname:\\s-*%s" label) nil t)
2941 (push (cons label (point-marker)) multiple-labels))
2947 : org-ref-bad-label-candidates
2949 Now, we have a functions for candidates, we can make helm sources for each one, and then run a helm command to view them.
2951 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2954 "Opens a helm interface to actions for org-ref.
2955 Shows bad citations, ref links and labels"
2957 (let ((cb (current-buffer))
2958 (bad-citations (org-ref-bad-cite-candidates))
2959 (bad-refs (org-ref-bad-ref-candidates))
2960 (bad-labels (org-ref-bad-label-candidates)))
2962 (helm :sources `(((name . "Bad citations")
2963 (candidates . ,bad-citations)
2964 (action . (lambda (marker)
2965 (switch-to-buffer (marker-buffer marker))
2966 (goto-char marker))))
2968 ((name . "Bad Labels")
2969 (candidates . ,bad-labels)
2970 (action . (lambda (marker)
2971 (switch-to-buffer (marker-buffer marker))
2972 (goto-char marker))))
2974 ((name . "Bad ref links")
2975 (candidates . ,bad-refs)
2976 (action . (lambda (marker)
2977 (switch-to-buffer (marker-buffer marker))
2978 (goto-char marker))))
2980 ((name . "Utilities")
2981 (candidates . (("Check buffer again" . org-ref)
2982 ("Insert citation" . helm-bibtex)
2983 ("Insert label link" . org-ref-helm-insert-label-link)
2984 ("Insert ref link" . org-ref-helm-insert-ref-link)
2985 ("List of figures" . org-ref-list-of-figures)
2986 ("List of tables" . org-ref-list-of-tables)
2987 ("Table of contents" . nil)
2989 (action . (lambda (x)
2990 (switch-to-buffer ,cb)
2993 ((name . "Export functions")
2994 (candidates . (("Extract cited entries" . org-ref-extract-bibtex-entries)
2995 ("Export to html and open" . (lambda () (org-open-file (org-html-export-to-html))))
2996 ("Export to pdf and open" . (lambda ()
2997 (org-open-file (org-latex-export-to-pdf))))
2998 ("Export to manuscript pdf and open" . ox-manuscript-export-and-build-and-open)
2999 ("Export submission manuscript pdf and open" . ox-manuscript-build-submission-manuscript-and-open)
3002 (action . (lambda (x)
3003 (switch-to-buffer ,cb)
3009 ** Finding non-ascii characters
3010 I like my bibtex files to be 100% ascii. This function finds the non-ascii characters so you can replace them.
3012 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3013 (defun org-ref-find-non-ascii-characters ()
3014 "finds non-ascii characters in the buffer. Useful for cleaning up bibtex files"
3016 (occur "[^[:ascii:]]"))
3019 ** Resort a bibtex entry
3020 I like neat and orderly bibtex entries.That means the fields are in a standard order that I like. This function reorders the fields in an entry for articles, and makes sure the fields are in lowercase.
3022 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3023 (defun org-ref-sort-bibtex-entry ()
3024 "sort fields of entry in standard order and downcase them"
3026 (bibtex-beginning-of-entry)
3027 (let* ((master '("author" "title" "journal" "volume" "number" "pages" "year" "doi" "url"))
3028 (entry (bibtex-parse-entry))
3031 (type (cdr (assoc "=type=" entry)))
3032 (key (cdr (assoc "=key=" entry))))
3034 ;; these are the fields we want to order that are in this entry
3035 (setq entry-fields (mapcar (lambda (x) (car x)) entry))
3036 ;; we do not want to reenter these fields
3037 (setq entry-fields (remove "=key=" entry-fields))
3038 (setq entry-fields (remove "=type=" entry-fields))
3040 ;;these are the other fields in the entry
3041 (setq other-fields (remove-if-not (lambda(x) (not (member x master))) entry-fields))
3044 ;; right now we only resort articles
3045 ((string= (downcase type) "article")
3048 (concat "@article{" key ",\n"
3051 (when (member field entry-fields)
3052 (format "%s = %s," (downcase field) (cdr (assoc field entry))))) master "\n")
3055 (format "%s = %s," (downcase field) (cdr (assoc field entry)))) other-fields "\n")
3057 (bibtex-find-entry key)
3059 (bibtex-clean-entry)
3063 ** Clean a bibtex entry
3064 I like neat and orderly bibtex entries. This code will eventually replace the key with my style key, clean the entry, and sort the fields in the order I like them.
3065 see [[file:emacs-24.3/lisp/textmodes/bibtex.el::bibtex-autokey-before-presentation-function]] for how to set a function that checks for uniqueness of the key.
3066 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3067 (defun org-ref-clean-bibtex-entry(&optional keep-key)
3068 "clean and replace the key in a bibtex function. When keep-key is t, do not replace it. You can use a prefix to specify the key should be kept"
3070 (bibtex-beginning-of-entry)
3072 ;; some entries do not have a key or comma in first line. We check and add it, if needed.
3073 (unless (string-match ",$" (thing-at-point 'line))
3077 ;; check for empty pages, and put eid or article id in its place
3078 (let ((entry (bibtex-parse-entry))
3079 (pages (bibtex-autokey-get-field "pages"))
3080 (year (bibtex-autokey-get-field "year"))
3081 (doi (bibtex-autokey-get-field "doi"))
3082 ;; The Journal of Chemical Physics uses eid
3083 (eid (bibtex-autokey-get-field "eid")))
3085 ;; replace http://dx.doi.org/ in doi. some journals put that in,
3086 ;; but we only want the doi.
3087 (when (string-match "^http://dx.doi.org/" doi)
3088 (bibtex-beginning-of-entry)
3089 (goto-char (car (cdr (bibtex-search-forward-field "doi" t))))
3091 (bibtex-make-field "doi")
3093 (insert (replace-regexp-in-string "^http://dx.doi.org/" "" doi)))
3095 ;; asap articles often set year to 0, which messes up key
3096 ;; generation. fix that.
3097 (when (string= "0" year)
3098 (bibtex-beginning-of-entry)
3099 (goto-char (car (cdr (bibtex-search-forward-field "year" t))))
3101 (bibtex-make-field "year")
3103 (insert (read-string "Enter year: ")))
3105 ;; fix pages if they are empty if there is an eid to put there.
3106 (when (string= "-" pages)
3108 (bibtex-beginning-of-entry)
3109 ;; this seems like a clunky way to set the pages field.But I
3110 ;; cannot find a better way.
3111 (goto-char (car (cdr (bibtex-search-forward-field "pages" t))))
3113 (bibtex-make-field "pages")
3117 ;; replace naked & with \&
3119 (bibtex-narrow-to-entry)
3120 (bibtex-beginning-of-entry)
3121 (message "checking &")
3122 (replace-regexp " & " " \\\\& ")
3125 ;; generate a key, and if it duplicates an existing key, edit it.
3127 (let ((key (bibtex-generate-autokey)))
3129 ;; first we delete the existing key
3130 (bibtex-beginning-of-entry)
3131 (re-search-forward bibtex-entry-maybe-empty-head)
3132 (if (match-beginning bibtex-key-in-head)
3133 (delete-region (match-beginning bibtex-key-in-head)
3134 (match-end bibtex-key-in-head)))
3135 ;; check if the key is in the buffer
3136 (when (save-excursion
3137 (bibtex-search-entry key))
3139 (bibtex-search-entry key)
3140 (bibtex-copy-entry-as-kill)
3141 (switch-to-buffer-other-window "*duplicate entry*")
3143 (setq key (bibtex-read-key "Duplicate Key found, edit: " key)))
3146 (kill-new key))) ;; save key for pasting
3148 ;; run hooks. each of these operates on the entry with no arguments.
3149 ;; this did not work like i thought, it gives a symbolp error.
3150 ;; (run-hooks org-ref-clean-bibtex-entry-hook)
3155 org-ref-clean-bibtex-entry-hook)
3157 ;; sort fields within entry
3158 (org-ref-sort-bibtex-entry)
3159 ;; check for non-ascii characters
3160 (occur "[^[:ascii:]]")
3165 : org-ref-clean-bibtex-entry
3167 ** Sort the entries in a citation link by year
3168 I prefer citations in chronological order within a grouping. These functions sort the link under the cursor by year.
3170 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3171 (defun org-ref-get-citation-year (key)
3172 "get the year of an entry with key. Returns year as a string."
3173 (let* ((results (org-ref-get-bibtex-key-and-file key))
3174 (bibfile (cdr results)))
3176 (insert-file-contents bibfile)
3177 (bibtex-search-entry key nil 0)
3178 (prog1 (reftex-get-bib-field "year" (bibtex-parse-entry t))
3181 (defun org-ref-sort-citation-link ()
3182 "Replace link at point with sorted link by year."
3184 (let* ((object (org-element-context))
3185 (type (org-element-property :type object))
3186 (begin (org-element-property :begin object))
3187 (end (org-element-property :end object))
3188 (link-string (org-element-property :path object))
3190 (setq keys (org-ref-split-and-strip-string link-string))
3191 (setq years (mapcar 'org-ref-get-citation-year keys))
3192 (setq data (mapcar* (lambda (a b) `(,a . ,b)) years keys))
3193 (setq data (cl-sort data (lambda (x y) (< (string-to-int (car x)) (string-to-int (car y))))))
3194 ;; now get the keys separated by commas
3195 (setq keys (mapconcat (lambda (x) (cdr x)) data ","))
3196 ;; and replace the link with the sorted keys
3197 (cl--set-buffer-substring begin end (concat type ":" keys))))
3200 ** Sort entries in citation links with shift-arrow keys
3201 Sometimes it may be helpful to manually change the order of citations. These functions define shift-arrow functions.
3202 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3203 (defun org-ref-swap-keys (i j keys)
3204 "Swap the KEYS in a list with index I and J."
3205 (let ((tempi (nth i keys)))
3206 (setf (nth i keys) (nth j keys))
3207 (setf (nth j keys) tempi))
3211 (defun org-ref-swap-citation-link (direction)
3212 "move citation at point in direction +1 is to the right, -1 to the left"
3214 (let* ((object (org-element-context))
3215 (type (org-element-property :type object))
3216 (begin (org-element-property :begin object))
3217 (end (org-element-property :end object))
3218 (link-string (org-element-property :path object))
3220 ;; We only want this to work on citation links
3221 (when (-contains? org-ref-cite-types type)
3222 (setq key (org-ref-get-bibtex-key-under-cursor))
3223 (setq keys (org-ref-split-and-strip-string link-string))
3224 (setq i (index key keys)) ;; defined in org-ref
3225 (if (> direction 0) ;; shift right
3226 (org-ref-swap-keys i (+ i 1) keys)
3227 (org-ref-swap-keys i (- i 1) keys))
3228 (setq keys (mapconcat 'identity keys ","))
3229 ;; and replace the link with the sorted keys
3230 (cl--set-buffer-substring
3234 ;; It seems the space at the end can get consumed, so we see if there
3235 ;; is a space, and add it if so. Sometimes there is a comma or period,
3236 ;; then we do not want a space.
3240 (looking-back " ")) " ")))
3241 ;; now go forward to key so we can move with the key
3242 (re-search-forward key)
3243 (goto-char (match-beginning 0)))))
3245 ;; add hooks to make it work
3246 (add-hook 'org-shiftright-hook (lambda () (org-ref-swap-citation-link 1)))
3247 (add-hook 'org-shiftleft-hook (lambda () (org-ref-swap-citation-link -1)))
3250 ** Lightweight messages about links
3251 To get a lighter weight message about the label, ref and cite links, we define a function that gives us the minibuffer message, without the menu. We run this in an idle timer.
3253 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3254 (defun org-ref-get-label-context (label)
3255 "Return a string of context around a label."
3258 (goto-char (point-min))
3259 (when (re-search-forward
3260 (format "label:%s\\b" label) nil t)
3261 (throw 'result (buffer-substring
3270 (goto-char (point-min))
3271 (when (re-search-forward
3272 (format "\\label{%s}" label) nil t)
3273 (throw 'result (buffer-substring
3282 (goto-char (point-min))
3283 (when (re-search-forward
3284 (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t)
3285 (throw 'result (buffer-substring
3294 (goto-char (point-min))
3295 (when (re-search-forward
3296 (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t)
3297 (throw 'result (buffer-substring
3305 (throw 'result "!!! NO CONTEXT FOUND !!!"))))
3308 (defun org-ref-link-message ()
3309 "Print a minibuffer message about the link that point is on."
3311 (when (eq major-mode 'org-mode)
3312 (let* ((object (org-element-context))
3313 (type (org-element-property :type object)))
3317 ((-contains? org-ref-cite-types type)
3318 (message (org-ref-get-citation-string-at-point)))
3320 ;; message some context about the label we are referring to
3321 ((string= type "ref")
3322 (message "%scount: %s"
3323 (org-ref-get-label-context
3324 (org-element-property :path object))
3325 (org-ref-count-labels
3326 (org-element-property :path object))))
3328 ((string= type "eqref")
3329 (message "%scount: %s"
3330 (org-ref-get-label-context
3331 (org-element-property :path object))
3332 (org-ref-count-labels
3333 (org-element-property :path object))))
3335 ;; message the count
3336 ((string= type "label")
3337 (let ((count (org-ref-count-labels
3338 (org-element-property :path object))))
3339 ;; get plurality on occurrence correct
3341 (number-to-string count)
3343 (when (or (= count 0)
3347 ((string= type "custom-id")
3349 (org-open-link-from-string
3350 (format "[[#%s]]" (org-element-property :path object)))
3351 (message "%s" (org-get-heading))))
3353 ;; check if the bibliography files exist.
3354 ((string= type "bibliography")
3356 ;; object is the link you clicked on
3357 (object (org-element-context))
3358 (link-string (org-element-property :path object))
3359 (link-string-beginning)
3362 (goto-char (org-element-property :begin object))
3363 (search-forward link-string nil nil 1)
3364 (setq link-string-beginning (match-beginning 0))
3365 (setq link-string-end (match-end 0)))
3367 ;; make sure we are in link and not before the :
3368 (when (> link-string-beginning (point))
3369 (goto-char link-string-beginning))
3371 ;; now if we have comma separated bibliographies
3372 ;; we find the one clicked on. we want to
3373 ;; search forward to next comma from point
3375 (if (search-forward "," link-string-end 1 1)
3376 (setq key-end (- (match-end 0) 1)) ; we found a match
3377 (setq key-end (point)))) ; no comma found so take the point
3379 ;; and backward to previous comma from point
3381 (if (search-backward "," link-string-beginning 1 1)
3382 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
3383 (setq key-beginning (point)))) ; no match found
3384 ;; save the key we clicked on.
3386 (org-ref-strip-string
3387 (buffer-substring key-beginning key-end)))
3388 (if (file-exists-p bibfile)
3389 (message "%s exists." bibfile)
3390 (message "!!! %s NOT FOUND !!!" bibfile))))
3395 I like convenience. Here are some aliases for faster typing.
3397 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3398 (defalias 'oro 'org-ref-open-citation-at-point)
3399 (defalias 'orc 'org-ref-citation-at-point)
3400 (defalias 'orp 'org-ref-open-pdf-at-point)
3401 (defalias 'oru 'org-ref-open-url-at-point)
3402 (defalias 'orn 'org-ref-open-notes-at-point)
3403 (defalias 'ornr 'org-ref-open-notes-from-reftex)
3405 (defalias 'orib 'org-ref-insert-bibliography-link)
3406 (defalias 'oric 'org-ref-insert-cite-link)
3407 (defalias 'orir 'org-ref-insert-ref-link)
3408 (defalias 'orsl 'org-ref-store-bibtex-entry-link)
3410 (defalias 'orcb 'org-ref-clean-bibtex-entry)
3413 [[https://github.com/tmalsburg/helm-bibtex][helm-bibtex]] is a very cool interface to bibtex files. Out of the box though, it is not super convenient for org-ref. Here, we modify it to make it fit our workflow and extend it where needed.
3415 Let us add keywords as a searchable field.
3416 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3417 (setq helm-bibtex-additional-search-fields '(keywords))
3420 Next, we are going to add keywords to the helm interface. This modifies the helm-bibtex function to add our keywords.
3421 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3422 (defun helm-bibtex-candidates-formatter (candidates source)
3423 "Formats BibTeX entries for display in results list."
3425 with width = (with-helm-window (helm-bibtex-window-width))
3426 for entry in candidates
3427 for entry = (cdr entry)
3428 for entry-key = (helm-bibtex-get-value "=key=" entry)
3429 if (assoc-string "author" entry 'case-fold)
3430 for fields = '("author" "title" "year" "=has-pdf=" "=has-note=" "=type=")
3432 for fields = '("editor" "title" "year" "=has-pdf=" "=has-note=" "=type=")
3433 for fields = (--map (helm-bibtex-clean-string
3434 (helm-bibtex-get-value it entry " "))
3436 for fields = (-update-at 0 'helm-bibtex-shorten-authors fields)
3437 for fields = (append fields
3438 (list (or (helm-bibtex-get-value "keywords" entry)
3441 (cons (s-format "$0 $1 $2 $3 $4$5 $6" 'elt
3442 (-zip-with (lambda (f w) (truncate-string-to-width f w 0 ?\s))
3443 fields (list 36 (- width 85) 4 1 1 7 7)))
3447 Next, we add some functions to add keywords to a bibtex entry using a helm interface, and a new action to add keywords to entries from helm-bibtex.
3448 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3449 ;; adapted from bibtex-utils.el
3450 ;; these are candidates for selecting keywords/tags
3451 (defun org-ref-bibtex-keywords ()
3452 "Get keywords defined in current bibtex file.
3453 These are in the keywords field, and are comma or semicolon separated."
3455 (goto-char (point-min))
3456 (let (keywords kstring)
3457 (while (re-search-forward "^\\s-*keywords.*{\\([^}]+\\)}" nil t)
3458 ;; TWS - remove newlines/multiple spaces:
3459 (setq kstring (replace-regexp-in-string "[ \t\n]+" " " (match-string 1)))
3462 (add-to-list 'keywords v t))
3463 (split-string kstring "\\(,\\|;\\)[ \n]*\\|{\\|}" t)))
3467 (defun org-ref-set-bibtex-keywords (keywords &optional arg)
3468 "Add KEYWORDS to a bibtex entry.
3469 If KEYWORDS is a list, it is converted to a comma-separated string. The KEYWORDS are added to the beginning of the field. Otherwise KEYWORDS should be a string of comma-separate keywords."
3470 (interactive "sKeywords: \nP")
3475 (if (listp keywords)
3476 (mapconcat 'identity keywords ", ")
3478 ;; else concatentate
3480 (if (listp keywords)
3481 (mapconcat 'identity keywords ", ")
3483 (when (not (string= "" (bibtex-autokey-get-field "keywords")))
3484 (concat ", " (bibtex-autokey-get-field "keywords"))))))
3488 (defun helm-tag-bibtex-entry ()
3489 "Helm interface to add keywords to a bibtex entry.
3490 Run this with the point in a bibtex entry."
3492 (let ((keyword-source `((name . "Existing keywords")
3493 (candidates . ,(org-ref-bibtex-keywords))
3494 (action . (lambda (candidate)
3495 (org-ref-set-bibtex-keywords
3498 (helm-marked-candidates)
3500 (fallback-source `((name . "Add new keywords")
3502 (action . (lambda (candidate)
3503 (org-ref-set-bibtex-keywords helm-pattern)
3505 (helm :sources '(keyword-source fallback-source))))
3507 (defun helm-bibtex-show-entry (key)
3508 "Show the entry in the BibTeX file.
3509 The original function in helm-bibtex has a bug where it finds the
3510 first key that partially matches. This version avoids that."
3512 (dolist (bibtex-file (if (listp helm-bibtex-bibliography)
3513 helm-bibtex-bibliography
3514 (list helm-bibtex-bibliography)))
3515 (let ((buf (helm-bibtex-buffer-visiting bibtex-file))
3517 (find-file bibtex-file)
3519 (lambda (key start end)
3520 (add-to-list 'entries (cons key start))))
3521 (if (assoc key entries)
3523 (goto-char (cdr (assoc key entries)))
3528 (defun org-ref-helm-tag-entries (candidates)
3529 "Set tags on selected bibtex entries from helm-bibtex.
3530 User is prompted for tags. This function is called from `helm-bibtex'."
3532 (let ((keywords (read-input "Keywords (comma separated): ")))
3533 (loop for key in (helm-marked-candidates)
3535 (save-window-excursion
3536 (helm-bibtex-show-entry key)
3541 ", " (bibtex-autokey-get-field "keywords")))
3545 Next, adapt the helm-bibtex source with these features:
3547 1. Make the default action to insert selected keys.
3548 2. Make open entry second action
3549 3. Add some features for adding keywords to bibtex entries.
3551 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3552 (setq helm-source-bibtex
3553 '((name . "BibTeX entries")
3554 (init . helm-bibtex-init)
3555 (candidates . helm-bibtex-candidates)
3556 (filtered-candidate-transformer . helm-bibtex-candidates-formatter)
3557 (action . (("Insert citation" . helm-bibtex-insert-citation)
3558 ("Show entry" . helm-bibtex-show-entry)
3559 ("Open PDF file (if present)" . helm-bibtex-open-pdf)
3560 ("Open URL or DOI in browser" . helm-bibtex-open-url-or-doi)
3561 ("Insert formatted reference" . helm-bibtex-insert-reference)
3562 ("Insert BibTeX key" . helm-bibtex-insert-key)
3563 ("Insert BibTeX entry" . helm-bibtex-insert-bibtex)
3564 ("Attach PDF to email" . helm-bibtex-add-PDF-attachment)
3565 ("Edit notes" . helm-bibtex-edit-notes)
3566 ("Add keywords to entries" . org-ref-helm-tag-entries)
3570 Now, let us define a function that inserts the cite links:
3571 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3572 (defun helm-bibtex-format-org-ref (keys)
3573 "Insert selected KEYS as cite link. Append KEYS if you are on a link.
3574 Technically, this function should return a string that is inserted by helm. This function does the insertion and gives helm an empty string to insert. This lets us handle appending to a link properly.
3576 In the helm-bibtex buffer, C-u will give you a helm menu to select a new link type for the selected entries.
3578 C-u C-u will change the key at point to the selected keys.
3580 (let* ((object (org-element-context))
3581 (last-char (save-excursion
3582 (goto-char (org-element-property :end object))
3584 (if (looking-at " ")
3588 ;; case where we are in a link
3589 ((and (equal (org-element-type object) 'link)
3592 (org-element-property :type object)))
3594 ;; no prefix. append keys
3595 ((equal helm-current-prefix-arg nil)
3596 (goto-char (org-element-property :end object))
3597 (while (looking-back " ") (backward-char))
3598 (insert (concat "," (mapconcat 'identity keys ","))))
3599 ;; double prefix, replace key at point
3600 ((equal helm-current-prefix-arg '(16))
3601 (setf (buffer-substring
3602 (org-element-property :begin object)
3603 (org-element-property :end object))
3605 (replace-regexp-in-string
3606 (car (org-ref-get-bibtex-key-and-file)) ; key
3607 (mapconcat 'identity keys ",") ; new keys
3608 (org-element-property :raw-link object))
3609 ;; replace space at end to avoid collapsing into next word.
3611 ;; and we want to go to the end of the new link
3613 (org-element-property :end (org-element-context))))
3615 (message "Not found"))))
3617 ;; We are next to a link, and we want to append
3618 ;; next to a link means one character back is on a link.
3621 (and (equal (org-element-type (org-element-context)) 'link)
3624 (org-element-property :type (org-element-context)))))
3625 (while (looking-back " ") (backward-char))
3626 (insert (concat "," (mapconcat 'identity keys ","))))
3628 ;; insert fresh link
3630 ;;(message-box "fresh link")
3632 (concat (if (equal helm-current-prefix-arg '(4))
3633 (helm :sources `((name . "link types")
3634 (candidates . ,org-ref-cite-types)
3635 (action . (lambda (x) x))))
3636 org-ref-default-citation-link)
3638 (s-join "," keys))))))
3639 ;; return empty string for helm
3642 (setq helm-bibtex-format-citation-functions
3643 '((org-mode . helm-bibtex-format-org-ref)))
3646 (defun org-ref-helm-insert-cite-link (arg)
3647 "org-ref function to use helm-bibtex to insert a citation link.
3648 With one prefix arg, insert a ref link.
3649 With two prefix args, insert a label link."
3653 (let ((helm-bibtex-bibliography (org-ref-find-bibliography)))
3656 (org-ref-helm-insert-ref-link))
3658 (org-ref-helm-insert-label-link))))
3661 ;; add our own fallback entries where we want them. These appear in reverse order of adding in the menu
3662 (setq helm-bibtex-fallback-options
3663 (-insert-at 1 '("Crossref" . "http://search.crossref.org/?q=%s") helm-bibtex-fallback-options))
3665 (setq helm-bibtex-fallback-options
3668 '("Scopus" . "http://www.scopus.com/scopus/search/submit/xadvanced.url?searchfield=TITLE-ABS-KEY(%s)")
3669 helm-bibtex-fallback-options))
3671 (setq helm-bibtex-fallback-options
3672 (-insert-at 1 '("WOS" . "http://gateway.webofknowledge.com/gateway/Gateway.cgi?topic=%s&GWVersion=2&SrcApp=WEB&SrcAuth=HSB&DestApp=UA&DestLinkType=GeneralSearchSummary") helm-bibtex-fallback-options))
3675 ** A helm click menu
3676 This code provides a helm interface to things you can do when you click on a citation link. This is an alternative to the minibuffer menu.
3677 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3678 (defun org-ref-get-citation-string-at-point ()
3679 "Get a string of a formatted citation"
3680 (let* ((results (org-ref-get-bibtex-key-and-file))
3682 (bibfile (cdr results)))
3686 (insert-file-contents bibfile)
3687 (bibtex-search-entry key)
3688 (org-ref-bib-citation)))
3689 "!!! No entry found !!!" )))
3692 (defun org-ref-cite-candidates ()
3693 "Generate the list of possible candidates for click actions on a cite link.
3694 Checks for pdf and doi, and add appropriate functions."
3695 (let* ((results (org-ref-get-bibtex-key-and-file))
3697 (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key))
3698 (bibfile (cdr results))
3699 (url (save-excursion
3701 (insert-file-contents bibfile)
3702 (bibtex-search-entry key)
3703 (bibtex-autokey-get-field "url"))))
3704 (doi (save-excursion
3706 (insert-file-contents bibfile)
3707 (bibtex-search-entry key)
3708 ;; I like this better than bibtex-url which does not always find
3710 (bibtex-autokey-get-field "doi"))))
3711 (candidates `(("Quit" . org-ref-citation-at-point)
3712 ("Open bibtex entry" . org-ref-open-citation-at-point))))
3713 ;; for some reason, when there is no doi or url, they are returned as "". I
3714 ;; prefer nil so we correct this here.
3715 (when (string= doi "") (setq doi nil))
3716 (when (string= url "") (setq url nil))
3718 ;; Conditional pdf functions
3719 (if (file-exists-p pdf-file)
3722 '("Open pdf" . org-ref-open-pdf-at-point)
3726 '("Try to get pdf" . (lambda ()
3727 (save-window-excursion
3728 (org-ref-open-citation-at-point)
3729 (bibtex-beginning-of-entry)
3730 (doi-utils-get-bibtex-entry-pdf))))
3736 '("Open notes" . org-ref-open-notes-at-point)
3739 ;; conditional url and doi functions
3743 '("Open in browser" . org-ref-open-url-at-point)
3748 (add-to-list 'candidates x t))
3749 `(("WOS" . org-ref-wos-at-point)
3750 ("Related articles in WOS" . org-ref-wos-related-at-point)
3751 ("Citing articles in WOS" . org-ref-wos-citing-at-point)
3752 ("Google Scholar" . org-ref-google-scholar-at-point)
3753 ("Pubmed" . org-ref-pubmed-at-point)
3754 ("Crossref" . org-ref-crossref-at-point)
3759 '("Copy formatted citation to clipboard" . org-ref-copy-entry-as-summary)
3764 '("Copy key to clipboard" . (lambda ()
3766 (car (org-ref-get-bibtex-key-and-file)))))
3771 '("Copy bibtex entry to file" . org-ref-copy-entry-at-point-to-file)
3776 '("Email bibtex entry and pdf" . (lambda ()
3778 (org-ref-open-citation-at-point)
3779 (email-bibtex-entry))))
3781 ;; finally return a numbered list of the candidates
3783 for cell in candidates
3784 collect (cons (format "%2s. %s" i (car cell))
3788 (defvar org-ref-helm-user-candidates '()
3789 "List of user-defined candidates to act when clicking on a cite link.
3790 This is a list of cons cells '((\"description\" . action)). The action function should not take an argument, and should assume point is on the cite key of interest.
3793 ;; example of adding your own function
3795 'org-ref-helm-user-candidates
3796 '("Example" . (lambda () (message-box "You did it!")))
3800 (defun org-ref-cite-click-helm (key)
3801 "Open helm for actions on a cite link.
3803 1. get name and candidates before entering helm because we need the org-buffer.
3804 2. switch back to the org buffer before evaluating the action. most of them need the point and buffer."
3806 (let ((name (org-ref-get-citation-string-at-point))
3807 (candidates (org-ref-cite-candidates))
3808 (cb (current-buffer)))
3810 (helm :sources `(((name . ,name)
3811 (candidates . ,candidates)
3812 (action . (lambda (f)
3813 (switch-to-buffer cb)
3815 ((name . "User functions")
3816 (candidates . ,org-ref-helm-user-candidates)
3817 (action . (lambda (f)
3818 (switch-to-buffer cb)
3824 : org-ref-cite-click-helm
3826 ** A hydra click interface
3827 I like hydra a lot. Here we define a hydra menu you might like for the link click action.
3829 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3830 (when (featurep 'hydra)
3832 (setq hydra-is-helpful t)
3834 (defhydra org-ref-cite-hydra (:color blue)
3836 _p_: Open pdf _w_: WOS _g_: Google Scholar _K_: Copy citation to clipboard
3837 _u_: Open url _r_: WOS related _P_: Pubmed _k_: Copy key to clipboard
3838 _n_: Open notes _c_: WOS citing _C_: Crossref _f_: Copy bibtex entry to file
3839 _o_: Open entry _e_: Email entry and pdf
3841 ("o" org-ref-open-citation-at-point nil)
3842 ("p" org-ref-open-pdf-at-point nil)
3843 ("n" org-ref-open-notes-at-point nil)
3844 ("u" org-ref-open-url-at-point nil)
3845 ("w" org-ref-wos-at-point nil)
3846 ("r" org-ref-wos-related-at-point nil)
3847 ("c" org-ref-wos-citing-at-point nil)
3848 ("g" org-ref-google-scholar-at-point nil)
3849 ("P" org-ref-pubmed-at-point nil)
3850 ("C" org-ref-crossref-at-point nil)
3851 ("K" org-ref-copy-entry-as-summary nil)
3854 (car (org-ref-get-bibtex-key-and-file)))) nil)
3855 ("f" org-ref-copy-entry-at-point-to-file nil)
3857 ("e" (save-excursion
3858 (org-ref-open-citation-at-point)
3859 (email-bibtex-entry)) nil)))
3863 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3866 ;;; org-ref.el ends here
3870 This code will tangle the elisp code out to org-ref.el and load it.
3872 [[elisp:(progn (org-babel-tangle) (load-file "org-ref.el"))]]
3874 Alternatively you may use:
3876 [[elisp:(org-babel-load-file "org-ref.org")]]