added docs
[org-ref.git] / org-ref.org
1 #+TITLE: Org-ref - The best reference handling for org-mode
2 #+AUTHOR: John Kitchin
3 #+DATE: April 29, 2014
4
5 * Introduction
6
7 This document is an experiment at creating a literate program to provide similar features as reftex for org-mode referencing. These features include:
8
9 1. using completion to create links
10 2. storing links to places, 
11 3. Clickable links that do useful things
12 4. Exportable links to LaTeX
13 5. Utility functions for dealing with bibtex files and org-files
14
15 ** Header
16 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
17 ;;; org-ref.el --- setup bibliography, cite, ref and label org-mode links.
18
19 ;; Copyright(C) 2014 John Kitchin
20
21 ;; Author: John Kitchin <jkitchin@andrew.cmu.edu>
22 ;; This file is not currently part of GNU Emacs.
23
24 ;; This program is free software; you can redistribute it and/or
25 ;; modify it under the terms of the GNU General Public License as
26 ;; published by the Free Software Foundation; either version 2, or (at
27 ;; your option) any later version.
28
29 ;; This program is distributed in the hope that it will be useful, but
30 ;; WITHOUT ANY WARRANTY; without even the implied warranty of
31 ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
32 ;; General Public License for more details.
33
34 ;; You should have received a copy of the GNU General Public License
35 ;; along with this program ; see the file COPYING.  If not, write to
36 ;; the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
37 ;; Boston, MA 02111-1307, USA.
38
39 ;;; Commentary:
40 ;;
41 ;; Lisp code to setup bibliography cite, ref and label org-mode links.
42 ;; also sets up reftex for org-mode. The links are clickable and do
43 ;; things that are useful. You should really read org-ref.org for details.
44 ;;
45 ;; Package-Requires: ((dash))
46 #+END_SRC
47
48 ** requires
49 The only external require is reftex-cite
50
51 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
52 (require 'reftex-cite)
53 (require 'dash)
54 #+END_SRC
55
56 ** Custom variables
57 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.
58
59 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
60 (defgroup org-ref nil
61   "customization group for org-ref")
62
63 (defcustom org-ref-bibliography-notes
64   nil
65   "filename to where you will put all your notes about an entry in
66   the default bibliography."
67   :type 'file
68   :group 'org-ref)
69
70 (defcustom org-ref-default-bibliography
71   nil
72   "list of bibtex files to search for. You should use full-paths for each file."
73   :type '(repeat :tag "List of bibtex files" file)
74   :group 'org-ref)
75
76 (defcustom org-ref-pdf-directory
77   nil
78   "directory where pdfs are stored by key. put a trailing / in"
79   :type 'directory
80   :group 'org-ref)
81
82 (defcustom org-ref-default-citation-link
83   "cite"
84   "The default type of citation link to use"
85   :type 'string
86   :group 'org-ref)
87
88 (defcustom org-ref-insert-cite-key
89   "C-c ]"
90   "Keyboard shortcut to insert a citation."
91   :type 'string
92   :group 'org-ref)
93
94 (defcustom org-ref-bibliography-entry-format
95   '(("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>.")
96
97     ("book" . "%a, %t, %u (%y).")
98
99     ("proceedings" . "%e, %t in %S, %u (%y).")
100
101     ("inproceedings" . "%a, %t, %p, in %b, edited by %e, %u (%y)"))
102
103   "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."
104   :type 'string
105   :group 'org-ref)
106
107 (defcustom org-ref-open-notes-function
108   (lambda ()
109     (org-show-entry)
110     (show-branches)
111     (show-children)
112     (org-cycle '(64))
113     ;;(org-tree-to-indirect-buffer)
114     (outline-previous-visible-heading 1)
115     (recenter-top-bottom 0))
116   "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") 
117 #+END_SRC
118
119 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.
120
121 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
122 (defcustom org-ref-cite-types
123   '("cite" "nocite" ;; the default latex cite commands
124     ;; natbib cite commands, http://ctan.unixbrain.com/macros/latex/contrib/natbib/natnotes.pdf
125     "citet" "citet*" "citep" "citep*"
126     "citealt" "citealt*" "citealp" "citealp*"
127     "citenum" "citetext"
128     "citeauthor" "citeauthor*"
129     "citeyear" "citeyear*"
130     "Citet" "Citep" "Citealt" "Citealp" "Citeauthor"
131     ;; biblatex commands
132     ;; http://ctan.mirrorcatalogs.com/macros/latex/contrib/biblatex/doc/biblatex.pdf
133     "Cite"
134     "parencite" "Parencite"
135     "footcite" "footcitetext"
136     "textcite" "Textcite"
137     "smartcite" "Smartcite"
138     "cite*" "parencite*" "supercite"
139     "autocite" "Autocite" "autocite*" "Autocite*"
140     "Citeauthor*"
141     "citetitle" "citetitle*"
142     "citedate" "citedate*"
143     "citeurl"
144     "fullcite" "footfullcite"
145     ;; "volcite" "Volcite" cannot support the syntax
146     "notecite" "Notecite"
147     "pnotecite" "Pnotecite"
148     "fnotecite"
149     ;; multicites. Very limited support for these.
150     "cites" "Cites" "parencites" "Parencites"
151     "footcites" "footcitetexts"
152     "smartcites" "Smartcites" "textcites" "Textcites"
153     "supercites" "autocites" "Autocites"
154     ;; for the bibentry package
155     "bibentry"
156     )
157   "List of citation types known in org-ref"
158   :type '(repeat :tag "List of citation types" string)
159   :group 'org-ref)
160 #+END_SRC
161
162 We need a hook variable to store user-defined bibtex entry cleaning functions
163 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
164 (defcustom org-ref-clean-bibtex-entry-hook nil
165   "Hook that is run in org-ref-clean-bibtex-entry. The functions should take no arguments, and operate on the bibtex entry at point."
166   :group 'org-ref
167   :type 'hook)
168 #+END_SRC
169
170 ** Program variables
171 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
172 (defvar org-ref-bibliography-files
173   nil
174   "variable to hold bibliography files to be searched")
175 #+END_SRC
176
177 ** org-mode / reftex setup
178
179 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.
180
181 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
182 (require 'reftex)
183 (defun org-mode-reftex-setup ()
184     (and (buffer-file-name)
185          (file-exists-p (buffer-file-name))
186          (global-auto-revert-mode t)
187          ;; I do not remember why I put this next line in. It doesn't
188          ;; work for org-files. Nothing very bad happens, but it gives
189          ;; an annoying error. Commenting it out for now.
190          ;(reftex-parse-all)
191          )
192     (make-local-variable 'reftex-cite-format)
193     (setq reftex-cite-format 'org)
194     (define-key org-mode-map (kbd org-ref-insert-cite-key) 'org-ref-insert-cite-link))
195
196 (add-hook 'org-mode-hook 'org-mode-reftex-setup)
197
198 (eval-after-load 'reftex-vars
199   '(progn
200       (add-to-list 'reftex-cite-format-builtin
201                    '(org "Org-mode citation"
202                          ((?\C-m . "cite:%l")     ; default
203                           (?d . ",%l")            ; for appending
204                           (?a . "autocite:%l")
205                           (?t . "citet:%l")
206                           (?T . "citet*:%l")
207                           (?p . "citep:%l")
208                           (?P . "citep*:%l")
209                           (?h . "citeauthor:%l")
210                           (?H . "citeauthor*:%l")
211                           (?y . "citeyear:%l")
212                           (?x . "citetext:%l")
213                           (?n . "nocite:%l")
214                           )))))
215 #+END_SRC
216
217 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. 
218
219 #+BEGIN_SRC emacs-lisp :tangle no
220 ;; add new format
221 (setf (nth 2 (assoc 'org reftex-cite-format-builtin))
222       (append (nth 2 (assoc 'org reftex-cite-format-builtin)) '((?W  . "textcite:%l")
223             (?z  . "newcite:%l"))))
224 #+END_SRC
225
226 You can define a new citation link like this:
227 #+BEGIN_SRC emacs-lisp :tangle no
228 (org-ref-define-citation-link "citez" ?z)
229 #+END_SRC
230
231 * Links
232 Most of this library is the creation of functional links to help with references and citations.
233 ** General utilities
234 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.
235
236 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
237 (defun org-ref-strip-string (string)
238   "strip leading and trailing whitespace from the string"
239   (replace-regexp-in-string
240    (concat search-whitespace-regexp "$" ) ""
241    (replace-regexp-in-string
242     (concat "^" search-whitespace-regexp ) "" string)))
243 #+END_SRC
244
245 It is helpful to make the previous function operate on a list of strings here.
246
247 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
248 (defun org-ref-split-and-strip-string (string)
249   "split key-string and strip keys. Assumes the key-string is comma delimited"
250   (mapcar 'org-ref-strip-string (split-string string ",")))
251 #+END_SRC
252
253 ** bibliography and bibliographystyle
254 *** An html bibliography
255
256 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.
257
258 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
259 (defun org-ref-reftex-get-bib-field (field entry &optional format)
260   "similar to reftex-get-bib-field, but removes enclosing braces and quotes"
261   (let ((result))
262     (setq result (reftex-get-bib-field field entry format))
263     (when (and (not (string= result "")) (string= "{" (substring result 0 1)))
264       (setq result (substring result 1 -1)))
265     (when (and (not (string= result "")) (string= "\"" (substring result 0 1)))
266       (setq result (substring result 1 -1)))    
267       result))
268
269 (defun org-ref-reftex-format-citation (entry format)
270   "return a formatted string for the bibtex entry (from bibtex-parse-entry) according
271 to the format argument. The format is a string with these percent escapes.
272
273 In the format, the following percent escapes will be expanded.
274
275 %l   The BibTeX label of the citation.
276 %a   List of author names, see also `reftex-cite-punctuation'.
277 %2a  Like %a, but abbreviate more than 2 authors like Jones et al.
278 %A   First author name only.
279 %e   Works like %a, but on list of editor names. (%2e and %E work a well)
280
281 It is also possible to access all other BibTeX database fields:
282 %b booktitle     %c chapter        %d edition    %h howpublished
283 %i institution   %j journal        %k key        %m month
284 %n number        %o organization   %p pages      %P first page
285 %r address       %s school         %u publisher  %t title
286 %v volume        %y year
287 %B booktitle, abbreviated          %T title, abbreviated
288 %U url
289 %D doi
290 %S series
291
292 Usually, only %l is needed.  The other stuff is mainly for the echo area
293 display, and for (setq reftex-comment-citations t).
294
295 %< as a special operator kills punctuation and space around it after the
296 string has been formatted.
297
298 A pair of square brackets indicates an optional argument, and RefTeX
299 will prompt for the values of these arguments.
300
301 Beware that all this only works with BibTeX database files.  When
302 citations are made from the \bibitems in an explicit thebibliography
303 environment, only %l is available."
304   ;; Format a citation from the info in the BibTeX ENTRY
305
306   (unless (stringp format) (setq format "\\cite{%l}"))
307
308   (if (and reftex-comment-citations
309            (string-match "%l" reftex-cite-comment-format))
310       (error "reftex-cite-comment-format contains invalid %%l"))
311
312   (while (string-match
313           "\\(\\`\\|[^%]\\)\\(\\(%\\([0-9]*\\)\\([a-zA-Z]\\)\\)[.,;: ]*\\)"
314           format)
315     (let ((n (string-to-number (match-string 4 format)))
316           (l (string-to-char (match-string 5 format)))
317           rpl b e)
318       (save-match-data
319         (setq rpl
320               (cond
321                ((= l ?l) (concat
322                           (org-ref-reftex-get-bib-field "&key" entry)
323                           (if reftex-comment-citations
324                               reftex-cite-comment-format
325                             "")))
326                ((= l ?a) (reftex-format-names
327                           (reftex-get-bib-names "author" entry)
328                           (or n 2)))
329                ((= l ?A) (car (reftex-get-bib-names "author" entry)))
330                ((= l ?b) (org-ref-reftex-get-bib-field "booktitle" entry "in: %s"))
331                ((= l ?B) (reftex-abbreviate-title
332                           (org-ref-reftex-get-bib-field "booktitle" entry "in: %s")))
333                ((= l ?c) (org-ref-reftex-get-bib-field "chapter" entry))
334                ((= l ?d) (org-ref-reftex-get-bib-field "edition" entry))
335                ((= l ?D) (org-ref-reftex-get-bib-field "doi" entry))
336                ((= l ?e) (reftex-format-names
337                           (reftex-get-bib-names "editor" entry)
338                           (or n 2)))
339                ((= l ?E) (car (reftex-get-bib-names "editor" entry)))
340                ((= l ?h) (org-ref-reftex-get-bib-field "howpublished" entry))
341                ((= l ?i) (org-ref-reftex-get-bib-field "institution" entry))
342                ((= l ?j) (org-ref-reftex-get-bib-field "journal" entry))
343                ((= l ?k) (org-ref-reftex-get-bib-field "key" entry))
344                ((= l ?m) (org-ref-reftex-get-bib-field "month" entry))
345                ((= l ?n) (org-ref-reftex-get-bib-field "number" entry))
346                ((= l ?o) (org-ref-reftex-get-bib-field "organization" entry))
347                ((= l ?p) (org-ref-reftex-get-bib-field "pages" entry))
348                ((= l ?P) (car (split-string
349                                (org-ref-reftex-get-bib-field "pages" entry)
350                                "[- .]+")))
351                ((= l ?s) (org-ref-reftex-get-bib-field "school" entry))
352                ((= l ?S) (org-ref-reftex-get-bib-field "series" entry))
353                ((= l ?u) (org-ref-reftex-get-bib-field "publisher" entry))
354                ((= l ?U) (org-ref-reftex-get-bib-field "url" entry))
355                ((= l ?r) (org-ref-reftex-get-bib-field "address" entry))
356                ;; strip enclosing brackets from title if they are there
357                ((= l ?t) (org-ref-reftex-get-bib-field "title" entry))
358                ((= l ?T) (reftex-abbreviate-title
359                           (org-ref-reftex-get-bib-field "title" entry)))
360                ((= l ?v) (org-ref-reftex-get-bib-field "volume" entry))
361                ((= l ?y) (org-ref-reftex-get-bib-field "year" entry)))))
362
363       (if (string= rpl "")
364           (setq b (match-beginning 2) e (match-end 2))
365         (setq b (match-beginning 3) e (match-end 3)))
366       (setq format (concat (substring format 0 b) rpl (substring format e)))))
367   (while (string-match "%%" format)
368     (setq format (replace-match "%" t t format)))
369   (while (string-match "[ ,.;:]*%<" format)
370     (setq format (replace-match "" t t format)))
371   ;; also replace carriage returns, tabs, and multiple whitespaces
372   (setq format (replace-regexp-in-string "\n\\|\t\\|\s+" " " format))
373   format)
374
375 (defun org-ref-get-bibtex-entry-citation (key)
376   "returns a string for the bibliography entry corresponding to key, and formatted according to the type in `org-ref-bibliography-entry-format'"
377
378   (let ((org-ref-bibliography-files (org-ref-find-bibliography))
379         (file) (entry) (bibtex-entry) (entry-type) (format))
380
381     (setq file (catch 'result
382                  (loop for file in org-ref-bibliography-files do
383                        (if (org-ref-key-in-file-p key (file-truename file)) 
384                            (throw 'result file)
385                          (message "%s not found in %s" key (file-truename file))))))
386
387     (with-temp-buffer
388       (insert-file-contents file)
389       (bibtex-search-entry key nil 0)
390       (setq bibtex-entry (bibtex-parse-entry))
391       (setq entry-type (downcase (cdr (assoc "=type=" bibtex-entry))))
392       (setq format (cdr (assoc entry-type org-ref-bibliography-entry-format)))
393       (if format
394           (setq entry  (org-ref-reftex-format-citation bibtex-entry format))
395         (save-restriction
396           (bibtex-narrow-to-entry)
397           (setq entry (buffer-string)))))      
398     entry))
399 #+END_SRC
400
401 #+RESULTS:
402 : org-ref-reftex-format-citation
403
404 Here is how to use the function. You call it with point in an entry in a bibtex file.
405
406 #+BEGIN_SRC emacs-lisp :tangle no
407 (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>."))
408   (org-ref-get-bibtex-entry-citation  "armiento-2014-high"))
409 #+END_SRC
410 #+RESULTS:
411 : 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>.
412
413 I am not sure why full author names are not used.
414
415 This code provides some functions to generate a simple sorted bibliography in html. First we get all the keys in the buffer.
416
417 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
418 (defun org-ref-get-bibtex-keys ()
419   "return a list of unique keys in the buffer."
420   (let ((keys '()))
421     (org-element-map (org-element-parse-buffer) 'link
422       (lambda (link)       
423         (let ((plist (nth 1 link)))                          
424           (when (-contains? org-ref-cite-types (plist-get plist ':type))
425             (dolist 
426                 (key 
427                  (org-ref-split-and-strip-string (plist-get plist ':path)))
428               (when (not (-contains? keys key))
429                 (setq keys (append keys (list key)))))))))
430     ;; Sort keys alphabetically
431     (setq keys (cl-sort keys 'string-lessp :key 'downcase))
432     keys))
433 #+END_SRC
434
435 This function gets the html for one entry.
436
437 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
438 (defun org-ref-get-bibtex-entry-html (key)
439   "returns an html string for the bibliography entry corresponding to key"
440
441   (format "<li><a id=\"%s\">[%s] %s</a></li>" key key (org-ref-get-bibtex-entry-citation key)))
442 #+END_SRC
443
444 Now, we map over the whole list of keys, and the whole bibliography, formatted as an unordered list.
445
446 #+BEGIN_SRC emacs-lisp :tangle org-ref.el 
447 (defun org-ref-get-html-bibliography ()
448   "Create an html bibliography when there are keys"
449   (let ((keys (org-ref-get-bibtex-keys)))
450     (when keys
451       (concat "<h1>Bibliography</h1>
452 <ul>"
453               (mapconcat (lambda (x) (org-ref-get-bibtex-entry-html x)) keys "\n")
454               "\n</ul>"))))
455 #+END_SRC
456
457 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.
458
459 *** An org bibliography
460 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.
461
462 First, we get the string for a single entry.
463 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
464 (defun org-ref-get-bibtex-entry-org (key)
465   "returns an org string for the bibliography entry corresponding to key"
466   (let ((org-ref-bibliography-files (org-ref-find-bibliography))
467         (file) (entry) (bibtex-entry) (entry-type) (format))
468
469     (setq file (catch 'result
470                  (loop for file in org-ref-bibliography-files do
471                        (if (org-ref-key-in-file-p key (file-truename file)) 
472                            (throw 'result file)
473                          (message "%s not found in %s" key (file-truename file))))))
474
475     (with-temp-buffer
476       (insert-file-contents file)
477       (bibtex-search-entry key nil 0)
478       (setq entry (bibtex-parse-entry))
479       (format "** %s - %s
480   :PROPERTIES:
481   %s
482   :END:
483 " (org-ref-reftex-get-bib-field "author" entry)
484 (org-ref-reftex-get-bib-field "title" entry)
485 (concat "   :CUSTOM_ID: " (org-ref-reftex-get-bib-field "=key=" entry) "\n"
486         (mapconcat (lambda (element) (format "   :%s: %s"
487                                              (upcase (car element))
488                                              (cdr element)))
489                    entry
490                    "\n"))))))
491 #+END_SRC
492
493 Now, we loop over the keys, and combine all the entries into a bibliography.
494 #+BEGIN_SRC emacs-lisp :tangle org-ref.el 
495 (defun org-ref-get-org-bibliography ()
496   "Create an org bibliography when there are keys"
497   (let ((keys (org-ref-get-bibtex-keys)))
498     (when keys
499       (concat "* Bibliography
500 "
501               (mapconcat (lambda (x) (org-ref-get-bibtex-entry-org x)) keys "\n")
502               "\n"))))
503 #+END_SRC
504
505 *** An ascii bibliography
506
507 This function gets the html for one entry.
508
509 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
510 (defun org-ref-get-bibtex-entry-ascii (key)
511   "returns an ascii string for the bibliography entry corresponding to key"
512
513   (format "[%s] %s" key (org-ref-get-bibtex-entry-citation key)))
514 #+END_SRC
515
516 Now, we map over the whole list of keys, and the whole bibliography, formatted as an unordered list.
517
518 #+BEGIN_SRC emacs-lisp :tangle org-ref.el 
519 (defun org-ref-get-ascii-bibliography ()
520   "Create an html bibliography when there are keys"
521   (let ((keys (org-ref-get-bibtex-keys)))
522     (when keys
523       (concat 
524 "Bibliography
525 =============
526 "
527               (mapconcat (lambda (x) (org-ref-get-bibtex-entry-ascii x)) keys "\n")
528               "\n"))))
529 #+END_SRC
530
531
532 *** the links
533 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.
534
535 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
536 (org-add-link-type "bibliography"
537                    ;; this code is run on clicking. The bibliography
538                    ;; may contain multiple files. this code finds the
539                    ;; one you clicked on and opens it.
540                    (lambda (link-string)        
541                        ;; get link-string boundaries
542                        ;; we have to go to the beginning of the line, and then search forward
543                        
544                      (let* ((bibfile)
545                             ;; object is the link you clicked on
546                             (object (org-element-context))
547  
548                             (link-string-beginning) 
549                             (link-string-end))
550
551                      (save-excursion
552                        (goto-char (org-element-property :begin object))
553                        (search-forward link-string nil nil 1)
554                        (setq link-string-beginning (match-beginning 0))
555                        (setq link-string-end (match-end 0)))
556
557                        ;; We set the reftex-default-bibliography
558                        ;; here. it should be a local variable only in
559                        ;; the current buffer. We need this for using
560                        ;; reftex to do citations.
561                        (set (make-local-variable 'reftex-default-bibliography) 
562                             (split-string (org-element-property :path object) ","))
563
564                        ;; now if we have comma separated bibliographies
565                        ;; we find the one clicked on. we want to
566                        ;; search forward to next comma from point
567                        (save-excursion
568                          (if (search-forward "," link-string-end 1 1)
569                              (setq key-end (- (match-end 0) 1)) ; we found a match
570                            (setq key-end (point)))) ; no comma found so take the point
571                        ;; and backward to previous comma from point
572                        (save-excursion
573                          (if (search-backward "," link-string-beginning 1 1)
574                              (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
575                            (setq key-beginning (point)))) ; no match found
576                        ;; save the key we clicked on.
577                        (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
578                        (find-file bibfile))) ; open file on click
579
580                      ;; formatting code
581                    (lambda (keyword desc format)
582                      (cond
583                       ((eq format 'org) (org-ref-get-org-bibliography))
584                       ((eq format 'ascii) (org-ref-get-ascii-bibliography))
585                       ((eq format 'html) (org-ref-get-html-bibliography))
586                       ((eq format 'latex)
587                        ;; write out the latex bibliography command                     
588                        (format "\\bibliography{%s}" (replace-regexp-in-string  "\\.bib" "" (mapconcat 'identity
589                                                                                                       (mapcar 'expand-file-name
590                                                                                                               (split-string keyword ","))
591                                                                                                       ",")))))))
592                                                                                
593 #+END_SRC
594
595 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.
596
597 #+BEGIN_LaTeX
598   \input{project-description.bbl}
599 #+END_LaTeX
600
601 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.
602
603 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
604 (org-add-link-type "nobibliography"
605                    ;; this code is run on clicking. The bibliography
606                    ;; may contain multiple files. this code finds the
607                    ;; one you clicked on and opens it.
608                    (lambda (link-string)        
609                        ;; get link-string boundaries
610                        ;; we have to go to the beginning of the line, and then search forward
611                        
612                      (let* ((bibfile)
613                             ;; object is the link you clicked on
614                             (object (org-element-context))
615  
616                             (link-string-beginning) 
617                             (link-string-end))
618
619                      (save-excursion
620                        (goto-char (org-element-property :begin object))
621                        (search-forward link-string nil nil 1)
622                        (setq link-string-beginning (match-beginning 0))
623                        (setq link-string-end (match-end 0)))
624
625                        ;; We set the reftex-default-bibliography
626                        ;; here. it should be a local variable only in
627                        ;; the current buffer. We need this for using
628                        ;; reftex to do citations.
629                        (set (make-local-variable 'reftex-default-bibliography) 
630                             (split-string (org-element-property :path object) ","))
631
632                        ;; now if we have comma separated bibliographies
633                        ;; we find the one clicked on. we want to
634                        ;; search forward to next comma from point
635                        (save-excursion
636                          (if (search-forward "," link-string-end 1 1)
637                              (setq key-end (- (match-end 0) 1)) ; we found a match
638                            (setq key-end (point)))) ; no comma found so take the point
639                        ;; and backward to previous comma from point
640                        (save-excursion
641                          (if (search-backward "," link-string-beginning 1 1)
642                              (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
643                            (setq key-beginning (point)))) ; no match found
644                        ;; save the key we clicked on.
645                        (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
646                        (find-file bibfile))) ; open file on click
647
648                      ;; formatting code
649                    (lambda (keyword desc format)
650                      (cond
651                       ((eq format 'org) (org-ref-get-org-bibliography))
652                       ((eq format 'ascii) (org-ref-get-ascii-bibliography))
653                       ((eq format 'html) (org-ref-get-html-bibliography))
654                       ((eq format 'latex)
655                        ;; write out the latex bibliography command                     
656
657 ;                      (format "{\\setbox0\\vbox{\\bibliography{%s}}}"
658 ;                              (replace-regexp-in-string  "\\.bib" "" (mapconcat 'identity
659 ;                                                                                (mapcar 'expand-file-name
660 ;                                                                                        (split-string keyword ","))
661 ;                                                                                ",")))
662
663                        (format "\\nobibliography{%s}"
664                                (replace-regexp-in-string  "\\.bib" "" (mapconcat 'identity
665                                                                                  (mapcar 'expand-file-name
666                                                                                          (split-string keyword ","))
667                                                                                  ",")))
668
669                        ))))                                                                            
670 #+END_SRC
671
672 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
673 (org-add-link-type "printbibliography"
674                    (lambda (arg) (message "Nothing implemented for clicking here."))
675                    (lambda (keyword desc format)
676                      (cond
677                       ((eq format 'org) (org-ref-get-org-bibliography))
678                       ((eq format 'html) (org-ref-get-html-bibliography))
679                       ((eq format 'latex)
680                        ;; write out the biblatex bibliography command
681                        "\\printbibliography"))
682 ))
683 #+END_SRC
684
685 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, ...
686
687 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
688 (org-add-link-type "bibliographystyle"
689                    (lambda (arg) (message "Nothing implemented for clicking here."))
690                    (lambda (keyword desc format)
691                      (cond
692                       ((eq format 'latex)
693                        ;; write out the latex bibliography command
694                        (format "\\bibliographystyle{%s}" keyword)))))
695 #+END_SRC
696
697 *** Completion for bibliography link
698 It would be nice 
699
700 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
701 (defun org-bibliography-complete-link (&optional arg)
702  (format "bibliography:%s" (read-file-name "enter file: " nil nil t)))
703
704 (defun org-ref-insert-bibliography-link ()
705   "insert a bibliography with completion"
706   (interactive)
707   (insert (org-bibliography-complete-link)))
708 #+END_SRC
709
710 ** addbibresource
711 This is apparently used for biblatex.
712 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
713 (org-add-link-type "addbibresource"
714                    ;; this code is run on clicking. The addbibresource
715                    ;; may contain multiple files. this code finds the
716                    ;; one you clicked on and opens it.
717                    (lambda (link-string)        
718                        ;; get link-string boundaries
719                        ;; we have to go to the beginning of the line, and then search forward
720                        
721                      (let* ((bibfile)
722                             ;; object is the link you clicked on
723                             (object (org-element-context))
724  
725                             (link-string-beginning) 
726                             (link-string-end))
727
728                      (save-excursion
729                        (goto-char (org-element-property :begin object))
730                        (search-forward link-string nil nil 1)
731                        (setq link-string-beginning (match-beginning 0))
732                        (setq link-string-end (match-end 0)))
733
734                        ;; We set the reftex-default-addbibresource
735                        ;; here. it should be a local variable only in
736                        ;; the current buffer. We need this for using
737                        ;; reftex to do citations.
738                        (set (make-local-variable 'reftex-default-addbibresource) 
739                             (split-string (org-element-property :path object) ","))
740
741                        ;; now if we have comma separated bibliographies
742                        ;; we find the one clicked on. we want to
743                        ;; search forward to next comma from point
744                        (save-excursion
745                          (if (search-forward "," link-string-end 1 1)
746                              (setq key-end (- (match-end 0) 1)) ; we found a match
747                            (setq key-end (point)))) ; no comma found so take the point
748                        ;; and backward to previous comma from point
749                        (save-excursion
750                          (if (search-backward "," link-string-beginning 1 1)
751                              (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
752                            (setq key-beginning (point)))) ; no match found
753                        ;; save the key we clicked on.
754                        (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
755                        (find-file bibfile))) ; open file on click
756
757                      ;; formatting code
758                    (lambda (keyword desc format)
759                      (cond
760                       ((eq format 'html) (format "")); no output for html
761                       ((eq format 'latex)
762                          ;; write out the latex addbibresource command
763                        (format "\\addbibresource{%s}" keyword)))))
764 #+END_SRC
765
766 ** List of Figures
767
768 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.
769
770 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
771 (defun org-ref-list-of-figures (&optional arg)
772   "Generate buffer with list of figures in them"
773   (interactive)
774   (save-excursion (widen)
775   (let* ((c-b (buffer-name))
776          (counter 0)
777          (list-of-figures 
778           (org-element-map (org-element-parse-buffer) 'link
779             (lambda (link) 
780               "create a link for to the figure"
781               (when 
782                   (and (string= (org-element-property :type link) "file")
783                        (string-match-p  
784                         "[^.]*\\.\\(png\\|jpg\\|eps\\|pdf\\)$"
785                         (org-element-property :path link)))                   
786                 (incf counter)
787                 
788                 (let* ((start (org-element-property :begin link))
789                        (parent (car (cdr (org-element-property :parent link))))
790                        (caption (caaar (plist-get parent :caption)))
791                        (name (plist-get parent :name)))
792                   (if caption 
793                       (format 
794                        "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][figure %s: %s]] %s\n" 
795                        c-b start counter (or name "") caption)
796                     (format 
797                      "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][figure %s: %s]]\n" 
798                      c-b start counter (or name "")))))))))
799     (switch-to-buffer "*List of Figures*")
800     (setq buffer-read-only nil)
801     (org-mode)
802     (erase-buffer)
803     (insert (mapconcat 'identity list-of-figures ""))
804     (setq buffer-read-only t)
805     (use-local-map (copy-keymap org-mode-map))
806     (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))))
807
808 (org-add-link-type 
809  "list-of-figures"
810  'org-ref-list-of-figures ; on click
811  (lambda (keyword desc format)
812    (cond
813     ((eq format 'latex)
814      (format "\\listoffigures")))))
815 #+END_SRC
816
817 ** List of Tables
818
819 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
820 (defun org-ref-list-of-tables (&optional arg)
821   "Generate a buffer with a list of tables"
822   (interactive)
823   (save-excursion
824   (widen)
825   (let* ((c-b (buffer-name))
826          (counter 0)
827          (list-of-tables 
828           (org-element-map (org-element-parse-buffer 'element) 'table
829             (lambda (table) 
830               "create a link for to the table"
831               (incf counter)
832               (let ((start (org-element-property :begin table))
833                     (name  (org-element-property :name table))
834                     (caption (caaar (org-element-property :caption table))))
835                 (if caption 
836                     (format 
837                      "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][table %s: %s]] %s\n" 
838                      c-b start counter (or name "") caption)
839                   (format 
840                    "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][table %s: %s]]\n" 
841                    c-b start counter (or name ""))))))))
842     (switch-to-buffer "*List of Tables*")
843     (setq buffer-read-only nil)
844     (org-mode)
845     (erase-buffer)
846     (insert (mapconcat 'identity list-of-tables ""))
847     (setq buffer-read-only t)
848     (use-local-map (copy-keymap org-mode-map))
849     (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))))
850
851 (org-add-link-type 
852  "list-of-tables"
853  'org-ref-list-of-tables
854  (lambda (keyword desc format)
855    (cond
856     ((eq format 'latex)
857      (format "\\listoftables")))))
858 #+END_SRC
859 ** label
860
861 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 the org-mode format for labels. We probably should search for tblnames too.
862 *************** TODO search tblnames, custom_ids and check for case sensitivity
863 *************** END
864
865 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
866 (org-add-link-type
867  "label"
868  (lambda (label)
869    "on clicking count the number of label tags used in the buffer. A number greater than one means multiple labels!"
870    (message (format "%s occurences"
871                     (+ (count-matches (format "label:%s\\b[^-:]" label) (point-min) (point-max) t)
872                        ;; for tblname, it is not enough to get word boundary
873                        ;; tab-little and tab-little-2 match then.
874                        (count-matches (format "^#\\+tblname:\\s-*%s\\b[^-:]" label) (point-min) (point-max) t)
875                        (count-matches (format "\\label{%s}\\b" label) (point-min) (point-max) t)
876                        ;; this is the org-format #+label:
877                        (count-matches (format "^#\\+label:\\s-*%s\\b[^-:]" label) (point-min) (point-max) t)))))
878  (lambda (keyword desc format)
879    (cond
880     ((eq format 'html) (format "(<label>%s</label>)" path))
881     ((eq format 'latex)
882      (format "\\label{%s}" keyword)))))
883 #+END_SRC
884
885 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.
886
887 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
888 (defun org-label-store-link ()
889   "store a link to a label. The output will be a ref to that label"
890   ;; First we have to make sure we are on a label link. 
891   (let* ((object (org-element-context)))
892     (when (and (equal (org-element-type object) 'link) 
893                (equal (org-element-property :type object) "label"))
894       (org-store-link-props
895        :type "ref"
896        :link (concat "ref:" (org-element-property :path object))))
897
898     ;; Store link on table
899     (when (equal (org-element-type object) 'table)
900       (org-store-link-props
901        :type "ref"
902        :link (concat "ref:" (org-element-property :name object))))
903
904 ;; it turns out this does not work. you can already store a link to a heading with a CUSTOM_ID
905     ;; store link on heading with custom_id
906 ;    (when (and (equal (org-element-type object) 'headline)
907 ;              (org-entry-get (point) "CUSTOM_ID"))
908 ;      (org-store-link-props
909 ;       :type "ref"
910 ;       :link (concat "ref:" (org-entry-get (point) "CUSTOM_ID"))))
911
912     ;; and to #+label: lines
913     (when (and (equal (org-element-type object) 'paragraph)
914                (org-element-property :name object))
915       (org-store-link-props
916        :type "ref"
917        :link (concat "ref:" (org-element-property :name object))))
918 ))
919
920 (add-hook 'org-store-link-functions 'org-label-store-link)
921 #+END_SRC
922 ** ref
923
924 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. 
925
926 At the moment, ref links are not usable for section links. You need [[#CUSTOM_ID]] type links.
927
928 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
929 (org-add-link-type
930  "ref"
931  (lambda (label)
932    "on clicking goto the label. Navigate back with C-c &"
933    (org-mark-ring-push)
934    ;; next search from beginning of the buffer
935
936    ;; it is possible you would not find the label if narrowing is in effect
937    (widen)
938
939    (unless
940        (or
941         ;; our label links
942         (progn 
943           (goto-char (point-min))
944           (re-search-forward (format "label:%s\\b" label) nil t))
945
946         ;; a latex label
947         (progn
948           (goto-char (point-min))
949           (re-search-forward (format "\\label{%s}" label) nil t))
950
951         ;; #+label: name  org-definition
952         (progn
953           (goto-char (point-min))
954           (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
955         
956         ;; org tblname
957         (progn
958           (goto-char (point-min))
959           (re-search-forward (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t))
960
961 ;; Commented out because these ref links do not actually translate correctly in LaTeX.
962 ;; you need [[#label]] links.
963         ;; CUSTOM_ID
964 ;       (progn
965 ;         (goto-char (point-min))
966 ;         (re-search-forward (format ":CUSTOM_ID:\s-*\\(%s\\)" label) nil t))
967         )
968      ;; we did not find anything, so go back to where we came
969      (org-mark-ring-goto)
970      (error "%s not found" label))
971    (org-show-entry)
972    (message "go back with (org-mark-ring-goto) `C-c &`"))
973  ;formatting
974  (lambda (keyword desc format)
975    (cond
976     ((eq format 'html) (format "(<ref>%s</ref>)" path))
977     ((eq format 'latex)
978      (format "\\ref{%s}" keyword)))))
979 #+END_SRC
980
981 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.
982
983 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
984 (defun org-ref-get-org-labels ()
985  "find #+LABEL: labels"
986   (save-excursion
987     (goto-char (point-min))
988     (let ((matches '()))
989       (while (re-search-forward "^#\\+label:\\s-+\\(.*\\)\\b" (point-max) t)
990         (add-to-list 'matches (match-string-no-properties 1) t))
991 matches)))
992 #+END_SRC
993
994 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
995 (defun org-ref-get-custom-ids ()
996  "return a list of custom_id properties in the buffer"
997  (let ((results '()) custom_id)
998    (org-map-entries 
999     (lambda () 
1000       (let ((custom_id (org-entry-get (point) "CUSTOM_ID")))
1001         (when (not (null custom_id))
1002           (setq results (append results (list custom_id)))))))
1003 results))
1004 #+END_SRC
1005
1006 Here we get a list of the labels defined as raw latex labels, e.g. \label{eqtre}.
1007 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1008 (defun org-ref-get-latex-labels ()
1009   (save-excursion
1010     (goto-char (point-min))
1011     (let ((matches '()))
1012       (while (re-search-forward "\\\\label{\\([a-zA-z0-9:-]*\\)}" (point-max) t)
1013         (add-to-list 'matches (match-string-no-properties 1) t))
1014 matches)))
1015 #+END_SRC
1016
1017 Finally, we get the table names.
1018
1019 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1020 (defun org-ref-get-tblnames ()
1021   (org-element-map (org-element-parse-buffer 'element) 'table
1022     (lambda (table) 
1023       (org-element-property :name table))))
1024 #+END_SRC
1025
1026 Now, we can put all the labels together which will give us a list of candidates.
1027
1028 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
1029 (defun org-ref-get-labels ()
1030   "returns a list of labels in the buffer that you can make a ref link to. this is used to auto-complete ref links."
1031   (save-excursion
1032     (save-restriction
1033       (widen)
1034       (goto-char (point-min))
1035       (let ((matches '()))
1036         (while (re-search-forward "label:\\([a-zA-z0-9:-]*\\)" (point-max) t)
1037           (add-to-list 'matches (match-string-no-properties 1) t))
1038         (append matches (org-ref-get-org-labels) (org-ref-get-latex-labels) (org-ref-get-tblnames) (org-ref-get-custom-ids))))))
1039 #+END_SRC
1040
1041 Now we create the 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.
1042
1043 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
1044 (defun org-ref-complete-link (&optional arg)
1045   "Completion function for ref links"
1046   (let ((label))
1047     (setq label (completing-read "label: " (org-ref-get-labels)))
1048     (format "ref:%s" label)))
1049 #+END_SRC
1050
1051 Alternatively, you may want to just call a function that inserts a link with completion:
1052
1053 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
1054 (defun org-ref-insert-ref-link ()
1055  (interactive)
1056  (insert (org-ref-complete-link)))
1057 #+END_SRC
1058
1059 ** pageref
1060
1061 This refers to the page of a label in LaTeX.
1062
1063 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
1064 (org-add-link-type
1065  "pageref"
1066  (lambda (label)
1067    "on clicking goto the label. Navigate back with C-c &"
1068    (org-mark-ring-push)
1069    ;; next search from beginning of the buffer
1070    (widen)
1071    (unless
1072        (or
1073         ;; our label links
1074         (progn 
1075           (goto-char (point-min))
1076           (re-search-forward (format "label:%s\\b" label) nil t))
1077
1078         ;; a latex label
1079         (progn
1080           (goto-char (point-min))
1081           (re-search-forward (format "\\label{%s}" label) nil t))
1082
1083         ;; #+label: name  org-definition
1084         (progn
1085           (goto-char (point-min))
1086           (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
1087         
1088         ;; org tblname
1089         (progn
1090           (goto-char (point-min))
1091           (re-search-forward (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t))
1092
1093 ;; Commented out because these ref links do not actually translate correctly in LaTeX.
1094 ;; you need [[#label]] links.
1095         ;; CUSTOM_ID
1096 ;       (progn
1097 ;         (goto-char (point-min))
1098 ;         (re-search-forward (format ":CUSTOM_ID:\s-*\\(%s\\)" label) nil t))
1099         )
1100      ;; we did not find anything, so go back to where we came
1101      (org-mark-ring-goto)
1102      (error "%s not found" label))
1103    (message "go back with (org-mark-ring-goto) `C-c &`"))
1104  ;formatting
1105  (lambda (keyword desc format)
1106    (cond
1107     ((eq format 'html) (format "(<pageref>%s</pageref>)" path))
1108     ((eq format 'latex)
1109      (format "\\pageref{%s}" keyword)))))
1110 #+END_SRC
1111
1112 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
1113 (defun org-pageref-complete-link (&optional arg)
1114   "Completion function for ref links"
1115   (let ((label))
1116     (setq label (completing-read "label: " (org-ref-get-labels)))
1117     (format "ref:%s" label)))
1118 #+END_SRC
1119
1120 Alternatively, you may want to just call a function that inserts a link with completion:
1121
1122 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
1123 (defun org-pageref-insert-ref-link ()
1124  (interactive)
1125  (insert (org-pageref-complete-link)))
1126 #+END_SRC
1127
1128 ** nameref
1129
1130 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.
1131
1132 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
1133 (org-add-link-type
1134  "nameref"
1135  (lambda (label)
1136    "on clicking goto the label. Navigate back with C-c &"
1137    (org-mark-ring-push)
1138    ;; next search from beginning of the buffer
1139    (widen)
1140    (unless
1141        (or
1142         ;; a latex label
1143         (progn
1144           (goto-char (point-min))
1145           (re-search-forward (format "\\label{%s}" label) nil t))
1146         )
1147      ;; we did not find anything, so go back to where we came
1148      (org-mark-ring-goto)
1149      (error "%s not found" label))
1150    (message "go back with (org-mark-ring-goto) `C-c &`"))
1151  ;formatting
1152  (lambda (keyword desc format)
1153    (cond
1154     ((eq format 'html) (format "(<nameref>%s</nameref>)" path))
1155     ((eq format 'latex)
1156      (format "\\nameref{%s}" keyword)))))
1157 #+END_SRC
1158
1159 ** eqref
1160 This is just the LaTeX ref for equations. On export, the reference is enclosed in parentheses.
1161  
1162 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
1163 (org-add-link-type
1164  "eqref"
1165  (lambda (label)
1166    "on clicking goto the label. Navigate back with C-c &"
1167    (org-mark-ring-push)
1168    ;; next search from beginning of the buffer
1169    (widen)
1170    (goto-char (point-min))
1171    (unless
1172        (or
1173         ;; search forward for the first match
1174         ;; our label links
1175         (re-search-forward (format "label:%s" label) nil t)
1176         ;; a latex label
1177         (re-search-forward (format "\\label{%s}" label) nil t)
1178         ;; #+label: name  org-definition
1179         (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
1180      (org-mark-ring-goto)
1181      (error "%s not found" label))
1182    (message "go back with (org-mark-ring-goto) `C-c &`"))
1183  ;formatting
1184  (lambda (keyword desc format)
1185    (cond
1186     ((eq format 'html) (format "(<eqref>%s</eqref>)" path))
1187     ((eq format 'latex)
1188      (format "\\eqref{%s}" keyword)))))
1189 #+END_SRC
1190
1191 ** cite
1192 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.
1193
1194 *** Implementing the click actions of cite
1195
1196 **** Getting the key we clicked on
1197 The first thing we need is to get the bibtex key we clicked on.
1198
1199 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
1200 (defun org-ref-get-bibtex-key-under-cursor ()
1201   "returns key under the bibtex cursor. We search forward from
1202 point to get a comma, or the end of the link, and then backwards
1203 to get a comma, or the beginning of the link. that delimits the
1204 keyword we clicked on. We also strip the text properties."
1205   (interactive)
1206   (let* ((object (org-element-context))  
1207          (link-string (org-element-property :path object)))
1208     ;; you may click on the part before the citations. here we make
1209     ;; sure to move to the beginning so you get the first citation.
1210     (let ((cp (point)))
1211       (goto-char (org-element-property :begin object))
1212       (search-forward link-string (org-element-property :end object))
1213       (goto-char (match-beginning 0))
1214       ;; check if we clicked before the path and move as needed.
1215       (unless (< cp (point))
1216         (goto-char cp)))
1217         
1218     (if (not (org-element-property :contents-begin object))
1219         ;; this means no description in the link
1220         (progn    
1221           ;; we need the link path start and end
1222           (save-excursion
1223             (goto-char (org-element-property :begin object))
1224             (search-forward link-string nil nil 1)
1225             (setq link-string-beginning (match-beginning 0))
1226             (setq link-string-end (match-end 0)))
1227
1228           ;; The key is the text between commas, or the link boundaries
1229           (save-excursion
1230             (if (search-forward "," link-string-end t 1)
1231                 (setq key-end (- (match-end 0) 1)) ; we found a match
1232               (setq key-end link-string-end))) ; no comma found so take the end
1233           ;; and backward to previous comma from point which defines the start character
1234           (save-excursion
1235             (if (search-backward "," link-string-beginning 1 1)
1236                 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
1237               (setq key-beginning link-string-beginning))) ; no match found
1238           ;; save the key we clicked on.
1239           (setq bibtex-key (org-ref-strip-string (buffer-substring key-beginning key-end)))
1240           (set-text-properties 0 (length bibtex-key) nil bibtex-key)
1241           bibtex-key)
1242       ;; link with description. assume only one key
1243       link-string)))
1244 #+END_SRC
1245
1246 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.
1247
1248 **** Getting the bibliographies
1249 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1250 (defun org-ref-find-bibliography ()
1251   "find the bibliography in the buffer.
1252 This function sets and returns cite-bibliography-files, which is a list of files
1253 either from bibliography:f1.bib,f2.bib
1254 \bibliography{f1,f2}
1255 internal bibliographies
1256
1257 falling back to what the user has set in org-ref-default-bibliography
1258 "
1259   (interactive)
1260   (catch 'result
1261     (save-excursion
1262       (goto-char (point-min))
1263       ;;  look for a bibliography link
1264       (when (re-search-forward "\\<bibliography:\\([^\]\|\n]+\\)" nil t)
1265         (setq org-ref-bibliography-files
1266               (mapcar 'org-ref-strip-string (split-string (match-string 1) ",")))
1267         (throw 'result org-ref-bibliography-files))
1268
1269       
1270       ;; we did not find a bibliography link. now look for \bibliography
1271       (goto-char (point-min))
1272       (when (re-search-forward "\\\\bibliography{\\([^}]+\\)}" nil t)
1273         ;; split, and add .bib to each file
1274         (setq org-ref-bibliography-files
1275               (mapcar (lambda (x) (concat x ".bib"))
1276                       (mapcar 'org-ref-strip-string 
1277                               (split-string (match-string 1) ","))))
1278         (throw 'result org-ref-bibliography-files))
1279
1280       ;; no bibliography found. maybe we need a biblatex addbibresource
1281       (goto-char (point-min))
1282       ;;  look for a bibliography link
1283       (when (re-search-forward "addbibresource:\\([^\]\|\n]+\\)" nil t)
1284         (setq org-ref-bibliography-files
1285               (mapcar 'org-ref-strip-string (split-string (match-string 1) ",")))
1286         (throw 'result org-ref-bibliography-files))
1287           
1288       ;; we did not find anything. use defaults
1289       (setq org-ref-bibliography-files org-ref-default-bibliography)))
1290
1291     ;; set reftex-default-bibliography so we can search
1292     (set (make-local-variable 'reftex-default-bibliography) org-ref-bibliography-files)
1293     org-ref-bibliography-files)
1294 #+END_SRC
1295
1296 **** Finding the bibliography file a key is in
1297 Now, we can see if an entry is in a file. 
1298
1299 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1300 (defun org-ref-key-in-file-p (key filename)
1301   "determine if the key is in the file"
1302   (interactive "skey: \nsFile: ")
1303   (save-current-buffer
1304     (let ((bibtex-files (list filename)))
1305       (bibtex-search-entry key t))))
1306 #+END_SRC
1307
1308 Finally, we want to know which file the key is in.
1309
1310 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1311 (defun org-ref-get-bibtex-key-and-file (&optional key)
1312   "returns the bibtex key and file that it is in. If no key is provided, get one under point"
1313  (interactive)
1314  (let ((org-ref-bibliography-files (org-ref-find-bibliography))
1315        (file))
1316    (unless key
1317      (setq key (org-ref-get-bibtex-key-under-cursor)))
1318    (setq file     (catch 'result
1319                     (loop for file in org-ref-bibliography-files do
1320                           (if (org-ref-key-in-file-p key (file-truename file)) 
1321                               (throw 'result file)))))
1322    (cons key file)))
1323 #+END_SRC
1324
1325 **** convenience functions to act on citation at point
1326      :PROPERTIES:
1327      :ID:       af0b2a82-a7c9-4c08-9dac-09f93abc4a92
1328      :END:
1329 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.
1330
1331 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1332 (defun org-ref-open-pdf-at-point ()
1333   "open the pdf for bibtex key under point if it exists"
1334   (interactive)
1335   (let* ((results (org-ref-get-bibtex-key-and-file))
1336          (key (car results))
1337          (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key)))
1338     (if (file-exists-p pdf-file)
1339         (org-open-file pdf-file)
1340 (message "no pdf found for %s" key))))
1341
1342
1343 (defun org-ref-open-url-at-point ()
1344   "open the url for bibtex key under point."
1345   (interactive)
1346   (let* ((results (org-ref-get-bibtex-key-and-file))
1347          (key (car results))
1348          (bibfile (cdr results)))
1349     (save-excursion
1350       (with-temp-buffer
1351         (insert-file-contents bibfile)
1352         (bibtex-search-entry key)
1353         ;; I like this better than bibtex-url which does not always find
1354         ;; the urls
1355         (catch 'done
1356           (let ((url (bibtex-autokey-get-field "url")))
1357             (when  url
1358               (browse-url url)
1359               (throw 'done nil)))
1360
1361           (let ((doi (bibtex-autokey-get-field "doi")))
1362             (when doi
1363               (if (string-match "^http" doi)
1364                   (browse-url doi)
1365                 (browse-url (format "http://dx.doi.org/%s" doi)))
1366               (throw 'done nil))))))))
1367
1368
1369 (defun org-ref-open-notes-at-point ()
1370   "open the notes for bibtex key under point."
1371   (interactive)
1372   (let* ((results (org-ref-get-bibtex-key-and-file))
1373          (key (car results))
1374          (bibfile (cdr results)))
1375     (save-excursion
1376       (with-temp-buffer
1377         (insert-file-contents bibfile)
1378         (bibtex-search-entry key)
1379         (org-ref-open-bibtex-notes)))))
1380
1381
1382 (defun org-ref-citation-at-point ()
1383   "give message of current citation at point"
1384   (interactive)
1385   (let* ((cb (current-buffer))
1386         (results (org-ref-get-bibtex-key-and-file))
1387         (key (car results))
1388         (bibfile (cdr results)))        
1389     (message "%s" (progn
1390                     (with-temp-buffer
1391                       (insert-file-contents bibfile)
1392                       (bibtex-search-entry key)
1393                       (org-ref-bib-citation))))))
1394
1395
1396 (defun org-ref-open-citation-at-point ()
1397   "open bibtex file to key at point"
1398   (interactive)
1399   (let* ((cb (current-buffer))
1400         (results (org-ref-get-bibtex-key-and-file))
1401         (key (car results))
1402         (bibfile (cdr results)))
1403     (find-file bibfile)
1404     (bibtex-search-entry key)))
1405 #+END_SRC
1406
1407 **** the actual minibuffer menu
1408 Now, we create the menu. This is a rewrite of the cite action. This makes the function extendable by users.
1409  
1410 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
1411 (defvar org-ref-cite-menu-funcs '()
1412  "Functions to run on cite click menu. Each entry is a list of (key menu-name function). 
1413 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.")
1414
1415
1416 (defvar org-ref-user-cite-menu-funcs
1417   '(("C" "rossref" org-ref-crossref-at-point))
1418   "user-defined functions to run on bibtex key at point.")
1419
1420
1421 (defun org-ref-get-doi-at-point ()
1422   "Get doi for key at point."
1423   (interactive)
1424   (let* ((results (org-ref-get-bibtex-key-and-file))
1425          (key (car results))
1426          (bibfile (cdr results)))
1427     (save-excursion
1428       (with-temp-buffer
1429         (insert-file-contents bibfile)
1430         (bibtex-search-entry key)
1431           (bibtex-autokey-get-field "doi")))))
1432   
1433
1434 ;; functions that operate on key at point for click menu
1435 (defun org-ref-wos-at-point ()
1436   "open the doi in wos for bibtex key under point."
1437   (interactive)
1438   (doi-utils-wos (org-ref-get-doi-at-point)))
1439
1440
1441 (defun org-ref-wos-citing-at-point ()
1442   "open the doi in wos citing articles for bibtex key under point."
1443   (interactive)
1444   (doi-utils-wos-citing (org-ref-get-doi-at-point)))
1445
1446
1447 (defun org-ref-wos-related-at-point ()
1448   "open the doi in wos related articles for bibtex key under point."
1449   (interactive)
1450   (doi-utils-wos-related (org-ref-get-doi-at-point)))
1451
1452
1453 (defun org-ref-google-scholar-at-point ()
1454   "open the doi in google scholar for bibtex key under point."
1455   (interactive)
1456   (doi-utils-google-scholar (org-ref-get-doi-at-point)))
1457
1458
1459 (defun org-ref-pubmed-at-point ()
1460   "open the doi in pubmed for bibtex key under point."
1461   (interactive)
1462   (doi-utils-pubmed (org-ref-get-doi-at-point)))
1463
1464
1465 (defun org-ref-crossref-at-point ()
1466   "open the doi in crossref for bibtex key under point."
1467   (interactive)
1468   (doi-utils-crossref (org-ref-get-doi-at-point)))
1469
1470
1471 (defun org-ref-cite-onclick-minibuffer-menu (&optional link-string)
1472   "action when a cite link is clicked on.
1473 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."
1474   (interactive)
1475   (let* ((results (org-ref-get-bibtex-key-and-file))
1476          (key (car results))
1477          (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key))
1478          (bibfile (cdr results))
1479          (url (save-excursion
1480                 (with-temp-buffer
1481                   (insert-file-contents bibfile)
1482                   (bibtex-search-entry key)             
1483                   (bibtex-autokey-get-field "url"))))
1484          (doi (save-excursion
1485                 (with-temp-buffer
1486                   (insert-file-contents bibfile)
1487                   (bibtex-search-entry key)
1488                   ;; I like this better than bibtex-url which does not always find
1489                   ;; the urls             
1490                   (bibtex-autokey-get-field "doi")))))
1491
1492     (when (string= "" doi) (setq doi nil))
1493     (when (string= "" url) (setq url nil))
1494     (setq org-ref-cite-menu-funcs '())
1495          
1496     ;; open action
1497     (when
1498         bibfile
1499       (add-to-list 
1500        'org-ref-cite-menu-funcs
1501        '("o" "pen" org-ref-open-citation-at-point)))
1502
1503     ;; pdf
1504     (when (file-exists-p pdf-file)
1505       (add-to-list
1506        'org-ref-cite-menu-funcs
1507        '("p" "df" org-ref-open-pdf-at-point) t))
1508
1509     ;; notes
1510     (add-to-list
1511      'org-ref-cite-menu-funcs
1512      '("n" "otes" org-ref-open-notes-at-point) t)
1513
1514     ;; url
1515     (when (or url doi)
1516       (add-to-list
1517        'org-ref-cite-menu-funcs
1518        '("u" "rl" org-ref-open-url-at-point) t))
1519
1520     ;; doi funcs
1521     (when doi
1522       (add-to-list
1523        'org-ref-cite-menu-funcs
1524        '("w" "os" org-ref-wos-at-point) t)
1525
1526       (add-to-list
1527        'org-ref-cite-menu-funcs
1528        '("c" "iting" org-ref-wos-citing-at-point) t)
1529
1530       (add-to-list
1531        'org-ref-cite-menu-funcs
1532        '("r" "elated" org-ref-wos-related-at-point) t)
1533       
1534       (add-to-list
1535        'org-ref-cite-menu-funcs
1536        '("g" "oogle scholar" org-ref-google-scholar-at-point) t)
1537
1538       (add-to-list
1539        'org-ref-cite-menu-funcs
1540        '("P" "ubmed" org-ref-pubmed-at-point) t))
1541
1542     (add-to-list
1543      'org-ref-cite-menu-funcs
1544      '("q" "uit" (lambda ())) t)
1545
1546     ;; add user functions
1547     (dolist (tup org-ref-user-cite-menu-funcs)
1548       (add-to-list
1549        'org-ref-cite-menu-funcs
1550        tup t))
1551       
1552     ;; now we make a menu
1553     ;; construct menu string as a message
1554     (message
1555      (concat
1556       (mapconcat
1557        (lambda (tup)
1558          (concat "[" (elt tup 0) "]"
1559                  (elt tup 1) " "))
1560        org-ref-cite-menu-funcs "") ": "))
1561     ;; get the input
1562     (let* ((input (read-char-exclusive))
1563            (choice (assoc
1564                     (char-to-string input) org-ref-cite-menu-funcs)))
1565       ;; now run the function (2nd element in choice)
1566       (when choice
1567         (funcall
1568          (elt 
1569           choice
1570           2))))))
1571 #+END_SRC
1572
1573 *** A function to format a cite link
1574
1575 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.
1576
1577 #+BEGIN_SRC emacs-lisp  :tangle no
1578 ;(defun org-ref-cite-link-format (keyword desc format)
1579 ;   (cond
1580 ;    ((eq format 'html) (mapconcat (lambda (key) (format "<a name=\"#%s\">%s</a>" key key) (org-ref-split-and-strip-string keyword) ",")))
1581 ;    ((eq format 'latex)
1582 ;     (concat "\\cite" (when desc (format "[%s]" desc)) "{"
1583 ;            (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
1584 ;            "}"))))
1585 #+END_SRC
1586
1587 *** The actual cite link
1588 Finally, we define the cite link. This is deprecated; the links are autogenerated later. This is here for memory.
1589
1590 #+BEGIN_SRC emacs-lisp :tangle no
1591 ;(org-add-link-type
1592 ; "cite"
1593 ; 'org-ref-cite-onclick-minibuffer-menu
1594 ; 'org-ref-cite-link-format)
1595 #+END_SRC
1596
1597 *** Automatic definition of the cite links
1598 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. 
1599
1600 #+BEGIN_SRC emacs-lisp :tangle org-ref.el 
1601 (defmacro org-ref-make-completion-function (type)
1602   `(defun ,(intern (format "org-%s-complete-link" type)) (&optional arg)
1603      (interactive)
1604      (format "%s:%s" 
1605              ,type
1606              (completing-read 
1607               "bibtex key: " 
1608               (let ((bibtex-files (org-ref-find-bibliography)))
1609                 (bibtex-global-key-alist))))))
1610 #+END_SRC
1611
1612 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.
1613
1614 #+BEGIN_SRC emacs-lisp :tangle org-ref.el 
1615 (defmacro org-ref-make-format-function (type)
1616   `(defun ,(intern (format "org-ref-format-%s" type)) (keyword desc format)
1617      (cond
1618       ((eq format 'org)
1619        (mapconcat
1620         (lambda (key)
1621           (format "[[#%s][%s]]" key key))
1622         (org-ref-split-and-strip-string keyword) ","))
1623
1624       ((eq format 'ascii)
1625        (concat "["
1626                (mapconcat
1627                 (lambda (key)
1628                   (format "%s" key))
1629                 (org-ref-split-and-strip-string keyword) ",") "]"))
1630         
1631       ((eq format 'html) 
1632        (mapconcat 
1633         (lambda (key) 
1634           (format "<a href=\"#%s\">%s</a>" key key))
1635         (org-ref-split-and-strip-string keyword) ","))
1636
1637       ((eq format 'latex)
1638        (if (string= (substring type -1) "s")
1639            ;; biblatex format for multicite commands, which all end in s. These are formated as \cites{key1}{key2}...
1640            (concat "\\" ,type (mapconcat (lambda (key) (format "{%s}"  key))
1641                                          (org-ref-split-and-strip-string keyword) ""))
1642          ;; bibtex format
1643        (concat "\\" ,type (when desc (org-ref-format-citation-description desc)) "{"
1644                (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
1645                "}"))))))
1646 #+END_SRC
1647
1648
1649
1650 We create the links by mapping the function onto the list of defined link types. 
1651
1652 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1653 (defun org-ref-format-citation-description (desc)
1654   "return formatted citation description. if the cite link has a description, it is optional text for the citation command. You can specify pre and post text by separating these with ::."
1655   (interactive)
1656   (cond
1657    ((string-match "::" desc)
1658     (format "[%s][%s]" (car (setq results (split-string desc "::"))) (cadr results)))
1659    (t (format "[%s]" desc))))
1660
1661 (defun org-ref-define-citation-link (type &optional key)
1662   "add a citation link for org-ref. With optional key, set the reftex binding. For example:
1663 (org-ref-define-citation-link \"citez\" ?z) will create a new citez link, with reftex key of z, 
1664 and the completion function."
1665   (interactive "sCitation Type: \ncKey: ")
1666
1667   ;; create the formatting function
1668   (eval `(org-ref-make-format-function ,type))
1669
1670   (eval-expression 
1671    `(org-add-link-type 
1672      ,type
1673      'org-ref-cite-onclick-minibuffer-menu
1674      (quote ,(intern (format "org-ref-format-%s" type)))))
1675
1676   ;; create the completion function
1677   (eval `(org-ref-make-completion-function ,type))
1678   
1679   ;; store new type so it works with adding citations, which checks
1680   ;; for existence in this list
1681   (add-to-list 'org-ref-cite-types type)
1682
1683   ;; and finally if a key is specified, we modify the reftex menu
1684   (when key
1685     (setf (nth 2 (assoc 'org reftex-cite-format-builtin))
1686           (append (nth 2 (assoc 'org reftex-cite-format-builtin)) 
1687                   `((,key  . ,(concat type ":%l")))))))
1688
1689 ;; create all the link types and their completion functions
1690 (mapcar 'org-ref-define-citation-link org-ref-cite-types)
1691 #+END_SRC
1692
1693 *** org-ref-insert-cite-link
1694 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.
1695
1696 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
1697 (defun org-ref-insert-cite-link (alternative-cite)
1698   "Insert a default citation link using reftex. If you are on a link, it
1699 appends to the end of the link, otherwise, a new link is
1700 inserted. Use a prefix arg to get a menu of citation types."
1701   (interactive "P")
1702   (org-ref-find-bibliography)
1703   (let* ((object (org-element-context))
1704          (link-string-beginning (org-element-property :begin object))
1705          (link-string-end (org-element-property :end object))
1706          (path (org-element-property :path object)))  
1707
1708     (if (not alternative-cite)
1709         
1710         (cond
1711          ;; case where we are in a link
1712          ((and (equal (org-element-type object) 'link) 
1713                (-contains? org-ref-cite-types (org-element-property :type object)))
1714           (goto-char link-string-end)
1715           ;; sometimes there are spaces at the end of the link
1716           ;; this code moves point pack until no spaces are there
1717           (while (looking-back " ") (backward-char))  
1718           (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
1719
1720          ;; We are next to a link, and we want to append
1721          ((save-excursion 
1722             (backward-char)
1723             (and (equal (org-element-type (org-element-context)) 'link) 
1724                  (-contains? org-ref-cite-types (org-element-property :type (org-element-context)))))
1725           (while (looking-back " ") (backward-char))  
1726           (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
1727
1728          ;; insert fresh link
1729          (t 
1730           (insert 
1731            (concat org-ref-default-citation-link 
1732                    ":" 
1733                    (mapconcat 'identity (reftex-citation t) ",")))))
1734
1735       ;; you pressed a C-u so we run this code
1736       (reftex-citation)))
1737   )
1738 #+END_SRC
1739
1740 #+RESULTS:
1741 : org-ref-insert-cite-link
1742
1743 *** Completion in cite links
1744 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.
1745
1746 #+BEGIN_SRC emacs-lisp  :tangle no
1747 (defun org-cite-complete-link (&optional arg)
1748   "Completion function for cite links"
1749   (format "%s:%s" 
1750           org-ref-default-citation-link
1751           (completing-read 
1752            "bibtex key: " 
1753            (let ((bibtex-files (org-ref-find-bibliography)))
1754              (bibtex-global-key-alist)))))
1755 #+END_SRC
1756
1757 Alternatively, you may shortcut the org-machinery with this command. You will be prompted for a citation type, and then offered key completion.
1758
1759 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1760 (defun org-ref-insert-cite-with-completion (type)
1761   "Insert a cite link with completion"
1762   (interactive (list (ido-completing-read "Type: " org-ref-cite-types)))
1763   (insert (funcall (intern (format "org-%s-complete-link" type)))))
1764 #+END_SRC
1765
1766 ** Storing links to a bibtex entry
1767 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.
1768
1769 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1770 (defun org-ref-store-bibtex-entry-link ()
1771   "Save a citation link to the current bibtex entry. Saves in the default link type."
1772   (interactive)
1773   (let ((link (concat org-ref-default-citation-link 
1774                  ":"   
1775                  (save-excursion
1776                    (bibtex-beginning-of-entry)
1777                    (reftex-get-bib-field "=key=" (bibtex-parse-entry))))))
1778     (message "saved %s" link)
1779     (push (list link) org-stored-links)
1780     (car org-stored-links)))
1781 #+END_SRC
1782
1783 ** Index entries
1784 org-ref minimally supports index entries. To make an index in a file, you should put in the LaTeX header these lines
1785
1786
1787 #+LATEX_HEADER: \usepackage{makeidx}
1788 #+LATEX_HEADER: \makeindex
1789
1790
1791 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.
1792
1793
1794 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.
1795
1796
1797 index:hello
1798 index:hello!Peter
1799 [[index:hello!Sam@\textsl{Sam}]]
1800 [[index:Lin@\textbf{Lin}]]
1801 [[index:Joe|textit]]
1802 [[index:Lin@\textbf{Lin}]]
1803 [[index:Peter|see {hello}]]
1804 [[index:Jen|seealso{Jenny}]]
1805
1806 index:encodings!input!cp850
1807
1808 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1809 (org-add-link-type
1810  "index"
1811  (lambda (path)
1812    (occur path))
1813
1814  (lambda (path desc format)
1815    (cond
1816     ((eq format 'latex)
1817       (format "\\index{%s}" path)))))
1818
1819 ;; this will generate a temporary index of entries in the file.
1820 (org-add-link-type
1821  "printindex"
1822  (lambda (path)
1823    (let ((*index-links* '())
1824          (*initial-letters* '()))
1825
1826      ;; get links
1827      (org-element-map (org-element-parse-buffer) 'link
1828        (lambda (link)       
1829          (let ((type (nth 0 link))
1830                (plist (nth 1 link)))
1831             
1832            (when (equal (plist-get plist ':type) "index")
1833              (add-to-list
1834               '*index-links* 
1835               (cons (plist-get plist :path)
1836                     (format
1837                      "[[elisp:(progn (switch-to-buffer \"%s\") (goto-char %s))][%s]]"               
1838 (current-buffer)
1839                      (plist-get plist :begin)  ;; position of link
1840                      ;; grab a description
1841                      (save-excursion
1842                        (goto-char (plist-get plist :begin))
1843                        (if (thing-at-point 'sentence)
1844                            ;; get a sentence
1845                            (replace-regexp-in-string
1846                             "\n" "" (thing-at-point 'sentence))
1847                          ;; or call it a link
1848                          "link")))))))))
1849
1850      ;; sort the links
1851      (setq *index-links*  (cl-sort *index-links* 'string-lessp :key 'car))
1852    
1853      ;; now first letters
1854      (dolist (link *index-links*)
1855        (add-to-list '*initial-letters* (substring (car link) 0 1) t))
1856
1857      ;; now create the index
1858      (switch-to-buffer (get-buffer-create "*index*"))
1859      (org-mode)
1860      (erase-buffer)
1861      (insert "#+TITLE: Index\n\n")
1862      (dolist (letter *initial-letters*)
1863        (insert (format "* %s\n" (upcase letter)))
1864        ;; now process the links
1865        (while (and
1866                ,*index-links*
1867                (string= letter (substring (car (car *index-links*)) 0 1)))
1868          (let ((link (pop *index-links*)))
1869            (insert (format "%s %s\n\n" (car link) (cdr link))))))
1870      (switch-to-buffer "*index*")))
1871  ;; formatting
1872  (lambda (path desc format)
1873    (cond
1874     ((eq format 'latex)
1875       (format "\\printindex")))))
1876 #+END_SRC
1877
1878 #+RESULTS:
1879 | 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*)) |
1880 | lambda | (path desc format) | (cond ((eq format (quote latex)) (format \printindex)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
1881
1882 ** Glossary
1883 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.
1884  
1885 #+LATEX_HEADER: \usepackage{glossaries}
1886 #+LATEX_HEADER: \makeglossaries
1887
1888 And at the end of the document put \makeglossaries.
1889
1890 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1891 (org-add-link-type
1892  "newglossaryentry"
1893  nil ;; no follow action
1894  (lambda (path desc format)
1895    (cond
1896     ((eq format 'latex)
1897      (format "\\newglossaryentry{%s}{%s}" path desc)))))
1898
1899
1900 ;; link to entry
1901 (org-add-link-type
1902  "gls"
1903   nil ;; no follow action
1904  (lambda (path desc format)
1905    (cond
1906     ((eq format 'latex)
1907      (format "\\gls{%s}" path)))))
1908
1909 ;; plural
1910 (org-add-link-type
1911  "glspl"
1912   nil ;; no follow action
1913  (lambda (path desc format)
1914    (cond
1915     ((eq format 'latex)
1916      (format "\\glspl{%s}" path)))))
1917
1918 ;; capitalized link
1919 (org-add-link-type
1920  "Gls"
1921   nil ;; no follow action
1922  (lambda (path desc format)
1923    (cond
1924     ((eq format 'latex)
1925      (format "\\Gls{%s}" path)))))
1926
1927 ;; capitalized link
1928 (org-add-link-type
1929  "Glspl"
1930   nil ;; no follow action
1931  (lambda (path desc format)
1932    (cond
1933     ((eq format 'latex)
1934      (format "\\Glspl{%s}" path)))))
1935 #+END_SRC
1936
1937 #+RESULTS:
1938 | Glspl             | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \Glspl{%s} path))))                                                                                                                                                                                                                                                                                                                     |
1939 | Gls               | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \Gls{%s} path))))                                                                                                                                                                                                                                                                                                                       |
1940 | glspl             | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \glspl{%s} path))))                                                                                                                                                                                                                                                                                                                     |
1941 | gls               | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \gls{%s} path))))                                                                                                                                                                                                                                                                                                                       |
1942 | newglossaryentry  | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \newglossaryentry{%s}{%s} path desc))))                                                                                                                                                                                                                                                                                                 |
1943 | google            | (lambda (link-string) (browse-url (format http://www.google.com/search?q=%s (url-hexify-string link-string))))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1944 | ResearcherID      | (lambda (link-string) (browse-url (format http://www.researcherid.com/rid/%s link-string)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1945 | orcid             | (lambda (link-string) (browse-url (format http://orcid.org/%s link-string)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1946 | message           | org-mac-message-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1947 | mac-outlook       | org-mac-outlook-message-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1948 | skim              | org-mac-skim-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1949 | addressbook       | org-mac-addressbook-item-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1950 | x-together-item   | org-mac-together-item-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1951 | ans               | (lambda (path) (let* ((fields (split-string path ::)) (label (nth 0 fields)) (data (nth 1 fields)) (data-file (format %s-%s.dat tq-userid label))) (let ((temp-file data-file) (temp-buffer (get-buffer-create (generate-new-buffer-name  *temp file*)))) (unwind-protect (prog1 (save-current-buffer (set-buffer temp-buffer) (insert data)) (save-current-buffer (set-buffer temp-buffer) (write-region nil nil temp-file nil 0))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer)))) (mygit (format git add %s data-file)) (mygit (format git commit -m "%s" data-file)) (mygit git push origin master)))                                                                                                                                                                                              | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1952 | mc                | (lambda (link) (org-entry-put (point) ANSWER link) (save-restriction (save-excursion (org-narrow-to-subtree) (goto-char (point-max)) (if (bolp) nil (insert \n)) (insert (format # you chose %s link)))))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1953 | exercise          | (lambda (arg) (tq-check-internet) (tq-get-assignment arg))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1954 | solution          | (lambda (label) (tq-check-internet) (let ((default-directory (file-name-as-directory (expand-file-name tq-root-directory)))) (if (file-exists-p solutions) nil (make-directory solutions)) (let ((default-directory (file-name-as-directory (expand-file-name solutions)))) (if (file-exists-p label) (progn (find-file (concat label / label .org)) (tq-update)) (mygit (format git clone %s@%s:solutions/%s tq-current-course tq-git-server label)) (find-file (concat label / label .org))))))                                                                                                                                                                                                                                                                                                                  | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1955 | assignment        | (lambda (arg) (tq-check-internet) (tq-get-assignment arg))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1956 | doi               | doi-link-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1957 | bibentry          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-bibentry                                                                                                                                                                                                                                                                                                                                                                                     |
1958 | Autocites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Autocites                                                                                                                                                                                                                                                                                                                                                                                    |
1959 | autocites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-autocites                                                                                                                                                                                                                                                                                                                                                                                    |
1960 | supercites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-supercites                                                                                                                                                                                                                                                                                                                                                                                   |
1961 | Textcites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Textcites                                                                                                                                                                                                                                                                                                                                                                                    |
1962 | textcites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-textcites                                                                                                                                                                                                                                                                                                                                                                                    |
1963 | Smartcites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Smartcites                                                                                                                                                                                                                                                                                                                                                                                   |
1964 | smartcites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-smartcites                                                                                                                                                                                                                                                                                                                                                                                   |
1965 | footcitetexts     | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footcitetexts                                                                                                                                                                                                                                                                                                                                                                                |
1966 | footcites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footcites                                                                                                                                                                                                                                                                                                                                                                                    |
1967 | Parencites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Parencites                                                                                                                                                                                                                                                                                                                                                                                   |
1968 | parencites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-parencites                                                                                                                                                                                                                                                                                                                                                                                   |
1969 | Cites             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Cites                                                                                                                                                                                                                                                                                                                                                                                        |
1970 | cites             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-cites                                                                                                                                                                                                                                                                                                                                                                                        |
1971 | fnotecite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-fnotecite                                                                                                                                                                                                                                                                                                                                                                                    |
1972 | Pnotecite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Pnotecite                                                                                                                                                                                                                                                                                                                                                                                    |
1973 | pnotecite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-pnotecite                                                                                                                                                                                                                                                                                                                                                                                    |
1974 | Notecite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Notecite                                                                                                                                                                                                                                                                                                                                                                                     |
1975 | notecite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-notecite                                                                                                                                                                                                                                                                                                                                                                                     |
1976 | footfullcite      | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footfullcite                                                                                                                                                                                                                                                                                                                                                                                 |
1977 | fullcite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-fullcite                                                                                                                                                                                                                                                                                                                                                                                     |
1978 | citeurl           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citeurl                                                                                                                                                                                                                                                                                                                                                                                      |
1979 | citedate*         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citedate*                                                                                                                                                                                                                                                                                                                                                                                    |
1980 | citedate          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citedate                                                                                                                                                                                                                                                                                                                                                                                     |
1981 | citetitle*        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citetitle*                                                                                                                                                                                                                                                                                                                                                                                   |
1982 | citetitle         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citetitle                                                                                                                                                                                                                                                                                                                                                                                    |
1983 | Citeauthor*       | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citeauthor*                                                                                                                                                                                                                                                                                                                                                                                  |
1984 | Autocite*         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Autocite*                                                                                                                                                                                                                                                                                                                                                                                    |
1985 | autocite*         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-autocite*                                                                                                                                                                                                                                                                                                                                                                                    |
1986 | Autocite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Autocite                                                                                                                                                                                                                                                                                                                                                                                     |
1987 | autocite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-autocite                                                                                                                                                                                                                                                                                                                                                                                     |
1988 | supercite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-supercite                                                                                                                                                                                                                                                                                                                                                                                    |
1989 | parencite*        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-parencite*                                                                                                                                                                                                                                                                                                                                                                                   |
1990 | cite*             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-cite*                                                                                                                                                                                                                                                                                                                                                                                        |
1991 | Smartcite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Smartcite                                                                                                                                                                                                                                                                                                                                                                                    |
1992 | smartcite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-smartcite                                                                                                                                                                                                                                                                                                                                                                                    |
1993 | Textcite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Textcite                                                                                                                                                                                                                                                                                                                                                                                     |
1994 | textcite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-textcite                                                                                                                                                                                                                                                                                                                                                                                     |
1995 | footcitetext      | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footcitetext                                                                                                                                                                                                                                                                                                                                                                                 |
1996 | footcite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footcite                                                                                                                                                                                                                                                                                                                                                                                     |
1997 | Parencite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Parencite                                                                                                                                                                                                                                                                                                                                                                                    |
1998 | parencite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-parencite                                                                                                                                                                                                                                                                                                                                                                                    |
1999 | Cite              | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Cite                                                                                                                                                                                                                                                                                                                                                                                         |
2000 | Citeauthor        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citeauthor                                                                                                                                                                                                                                                                                                                                                                                   |
2001 | Citealp           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citealp                                                                                                                                                                                                                                                                                                                                                                                      |
2002 | Citealt           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citealt                                                                                                                                                                                                                                                                                                                                                                                      |
2003 | Citep             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citep                                                                                                                                                                                                                                                                                                                                                                                        |
2004 | Citet             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citet                                                                                                                                                                                                                                                                                                                                                                                        |
2005 | citeyear*         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                        &nb