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 user functions
1543     (dolist (tup org-ref-user-cite-menu-funcs)
1544       (add-to-list
1545        'org-ref-cite-menu-funcs
1546        tup t))
1547
1548     ;; finally quit
1549     (add-to-list
1550      'org-ref-cite-menu-funcs
1551      '("q" "uit" (lambda ())) t)
1552
1553     ;; now we make a menu
1554     ;; construct menu string as a message
1555     (message
1556      (concat
1557       (mapconcat
1558        (lambda (tup)
1559          (concat "[" (elt tup 0) "]"
1560                  (elt tup 1) " "))
1561        org-ref-cite-menu-funcs "") ": "))
1562     ;; get the input
1563     (let* ((input (read-char-exclusive))
1564            (choice (assoc
1565                     (char-to-string input) org-ref-cite-menu-funcs)))
1566       ;; now run the function (2nd element in choice)
1567       (when choice
1568         (funcall
1569          (elt
1570           choice
1571           2))))))
1572 #+END_SRC
1573
1574 *** A function to format a cite link
1575
1576 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.
1577
1578 #+BEGIN_SRC emacs-lisp  :tangle no
1579 ;(defun org-ref-cite-link-format (keyword desc format)
1580 ;   (cond
1581 ;    ((eq format 'html) (mapconcat (lambda (key) (format "<a name=\"#%s\">%s</a>" key key) (org-ref-split-and-strip-string keyword) ",")))
1582 ;    ((eq format 'latex)
1583 ;     (concat "\\cite" (when desc (format "[%s]" desc)) "{"
1584 ;            (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
1585 ;            "}"))))
1586 #+END_SRC
1587
1588 *** The actual cite link
1589 Finally, we define the cite link. This is deprecated; the links are autogenerated later. This is here for memory.
1590
1591 #+BEGIN_SRC emacs-lisp :tangle no
1592 ;(org-add-link-type
1593 ; "cite"
1594 ; 'org-ref-cite-onclick-minibuffer-menu
1595 ; 'org-ref-cite-link-format)
1596 #+END_SRC
1597
1598 *** Automatic definition of the cite links
1599 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.
1600
1601 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1602 (defmacro org-ref-make-completion-function (type)
1603   `(defun ,(intern (format "org-%s-complete-link" type)) (&optional arg)
1604      (interactive)
1605      (format "%s:%s"
1606              ,type
1607              (completing-read
1608               "bibtex key: "
1609               (let ((bibtex-files (org-ref-find-bibliography)))
1610                 (bibtex-global-key-alist))))))
1611 #+END_SRC
1612
1613 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.
1614
1615 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1616 (defmacro org-ref-make-format-function (type)
1617   `(defun ,(intern (format "org-ref-format-%s" type)) (keyword desc format)
1618      (cond
1619       ((eq format 'org)
1620        (mapconcat
1621         (lambda (key)
1622           (format "[[#%s][%s]]" key key))
1623         (org-ref-split-and-strip-string keyword) ","))
1624
1625       ((eq format 'ascii)
1626        (concat "["
1627                (mapconcat
1628                 (lambda (key)
1629                   (format "%s" key))
1630                 (org-ref-split-and-strip-string keyword) ",") "]"))
1631
1632       ((eq format 'html)
1633        (mapconcat
1634         (lambda (key)
1635           (format "<a href=\"#%s\">%s</a>" key key))
1636         (org-ref-split-and-strip-string keyword) ","))
1637
1638       ((eq format 'latex)
1639        (if (string= (substring type -1) "s")
1640            ;; biblatex format for multicite commands, which all end in s. These are formated as \cites{key1}{key2}...
1641            (concat "\\" ,type (mapconcat (lambda (key) (format "{%s}"  key))
1642                                          (org-ref-split-and-strip-string keyword) ""))
1643          ;; bibtex format
1644        (concat "\\" ,type (when desc (org-ref-format-citation-description desc)) "{"
1645                (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
1646                "}"))))))
1647 #+END_SRC
1648
1649
1650
1651 We create the links by mapping the function onto the list of defined link types.
1652
1653 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1654 (defun org-ref-format-citation-description (desc)
1655   "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 ::."
1656   (interactive)
1657   (cond
1658    ((string-match "::" desc)
1659     (format "[%s][%s]" (car (setq results (split-string desc "::"))) (cadr results)))
1660    (t (format "[%s]" desc))))
1661
1662 (defun org-ref-define-citation-link (type &optional key)
1663   "add a citation link for org-ref. With optional key, set the reftex binding. For example:
1664 (org-ref-define-citation-link \"citez\" ?z) will create a new citez link, with reftex key of z,
1665 and the completion function."
1666   (interactive "sCitation Type: \ncKey: ")
1667
1668   ;; create the formatting function
1669   (eval `(org-ref-make-format-function ,type))
1670
1671   (eval-expression
1672    `(org-add-link-type
1673      ,type
1674      'org-ref-cite-onclick-minibuffer-menu
1675      (quote ,(intern (format "org-ref-format-%s" type)))))
1676
1677   ;; create the completion function
1678   (eval `(org-ref-make-completion-function ,type))
1679
1680   ;; store new type so it works with adding citations, which checks
1681   ;; for existence in this list
1682   (add-to-list 'org-ref-cite-types type)
1683
1684   ;; and finally if a key is specified, we modify the reftex menu
1685   (when key
1686     (setf (nth 2 (assoc 'org reftex-cite-format-builtin))
1687           (append (nth 2 (assoc 'org reftex-cite-format-builtin))
1688                   `((,key  . ,(concat type ":%l")))))))
1689
1690 ;; create all the link types and their completion functions
1691 (mapcar 'org-ref-define-citation-link org-ref-cite-types)
1692 #+END_SRC
1693
1694 *** org-ref-insert-cite-link
1695 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.
1696
1697 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
1698 (defun org-ref-insert-cite-link (alternative-cite)
1699   "Insert a default citation link using reftex. If you are on a link, it
1700 appends to the end of the link, otherwise, a new link is
1701 inserted. Use a prefix arg to get a menu of citation types."
1702   (interactive "P")
1703   (org-ref-find-bibliography)
1704   (let* ((object (org-element-context))
1705          (link-string-beginning (org-element-property :begin object))
1706          (link-string-end (org-element-property :end object))
1707          (path (org-element-property :path object)))
1708
1709     (if (not alternative-cite)
1710
1711         (cond
1712          ;; case where we are in a link
1713          ((and (equal (org-element-type object) 'link)
1714                (-contains? org-ref-cite-types (org-element-property :type object)))
1715           (goto-char link-string-end)
1716           ;; sometimes there are spaces at the end of the link
1717           ;; this code moves point pack until no spaces are there
1718           (while (looking-back " ") (backward-char))
1719           (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
1720
1721          ;; We are next to a link, and we want to append
1722          ((save-excursion
1723             (backward-char)
1724             (and (equal (org-element-type (org-element-context)) 'link)
1725                  (-contains? org-ref-cite-types (org-element-property :type (org-element-context)))))
1726           (while (looking-back " ") (backward-char))
1727           (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
1728
1729          ;; insert fresh link
1730          (t
1731           (insert
1732            (concat org-ref-default-citation-link
1733                    ":"
1734                    (mapconcat 'identity (reftex-citation t) ",")))))
1735
1736       ;; you pressed a C-u so we run this code
1737       (reftex-citation)))
1738   )
1739 #+END_SRC
1740
1741 #+RESULTS:
1742 : org-ref-insert-cite-link
1743
1744 *** Completion in cite links
1745 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.
1746
1747 #+BEGIN_SRC emacs-lisp  :tangle no
1748 (defun org-cite-complete-link (&optional arg)
1749   "Completion function for cite links"
1750   (format "%s:%s"
1751           org-ref-default-citation-link
1752           (completing-read
1753            "bibtex key: "
1754            (let ((bibtex-files (org-ref-find-bibliography)))
1755              (bibtex-global-key-alist)))))
1756 #+END_SRC
1757
1758 Alternatively, you may shortcut the org-machinery with this command. You will be prompted for a citation type, and then offered key completion.
1759
1760 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1761 (defun org-ref-insert-cite-with-completion (type)
1762   "Insert a cite link with completion"
1763   (interactive (list (ido-completing-read "Type: " org-ref-cite-types)))
1764   (insert (funcall (intern (format "org-%s-complete-link" type)))))
1765 #+END_SRC
1766
1767 ** Storing links to a bibtex entry
1768 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.
1769
1770 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1771 (defun org-ref-store-bibtex-entry-link ()
1772   "Save a citation link to the current bibtex entry. Saves in the default link type."
1773   (interactive)
1774   (let ((link (concat org-ref-default-citation-link
1775                  ":"
1776                  (save-excursion
1777                    (bibtex-beginning-of-entry)
1778                    (reftex-get-bib-field "=key=" (bibtex-parse-entry))))))
1779     (message "saved %s" link)
1780     (push (list link) org-stored-links)
1781     (car org-stored-links)))
1782 #+END_SRC
1783
1784 ** Index entries
1785 org-ref minimally supports index entries. To make an index in a file, you should put in the LaTeX header these lines
1786
1787
1788 #+LATEX_HEADER: \usepackage{makeidx}
1789 #+LATEX_HEADER: \makeindex
1790
1791
1792 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.
1793
1794
1795 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.
1796
1797
1798 index:hello
1799 index:hello!Peter
1800 [[index:hello!Sam@\textsl{Sam}]]
1801 [[index:Lin@\textbf{Lin}]]
1802 [[index:Joe|textit]]
1803 [[index:Lin@\textbf{Lin}]]
1804 [[index:Peter|see {hello}]]
1805 [[index:Jen|seealso{Jenny}]]
1806
1807 index:encodings!input!cp850
1808
1809 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1810 (org-add-link-type
1811  "index"
1812  (lambda (path)
1813    (occur path))
1814
1815  (lambda (path desc format)
1816    (cond
1817     ((eq format 'latex)
1818       (format "\\index{%s}" path)))))
1819
1820 ;; this will generate a temporary index of entries in the file.
1821 (org-add-link-type
1822  "printindex"
1823  (lambda (path)
1824    (let ((*index-links* '())
1825          (*initial-letters* '()))
1826
1827      ;; get links
1828      (org-element-map (org-element-parse-buffer) 'link
1829        (lambda (link)
1830          (let ((type (nth 0 link))
1831                (plist (nth 1 link)))
1832
1833            (when (equal (plist-get plist ':type) "index")
1834              (add-to-list
1835               '*index-links*
1836               (cons (plist-get plist :path)
1837                     (format
1838                      "[[elisp:(progn (switch-to-buffer \"%s\") (goto-char %s))][%s]]"
1839 (current-buffer)
1840                      (plist-get plist :begin)  ;; position of link
1841                      ;; grab a description
1842                      (save-excursion
1843                        (goto-char (plist-get plist :begin))
1844                        (if (thing-at-point 'sentence)
1845                            ;; get a sentence
1846                            (replace-regexp-in-string
1847                             "\n" "" (thing-at-point 'sentence))
1848                          ;; or call it a link
1849                          "link")))))))))
1850
1851      ;; sort the links
1852      (setq *index-links*  (cl-sort *index-links* 'string-lessp :key 'car))
1853
1854      ;; now first letters
1855      (dolist (link *index-links*)
1856        (add-to-list '*initial-letters* (substring (car link) 0 1) t))
1857
1858      ;; now create the index
1859      (switch-to-buffer (get-buffer-create "*index*"))
1860      (org-mode)
1861      (erase-buffer)
1862      (insert "#+TITLE: Index\n\n")
1863      (dolist (letter *initial-letters*)
1864        (insert (format "* %s\n" (upcase letter)))
1865        ;; now process the links
1866        (while (and
1867                ,*index-links*
1868                (string= letter (substring (car (car *index-links*)) 0 1)))
1869          (let ((link (pop *index-links*)))
1870            (insert (format "%s %s\n\n" (car link) (cdr link))))))
1871      (switch-to-buffer "*index*")))
1872  ;; formatting
1873  (lambda (path desc format)
1874    (cond
1875     ((eq format 'latex)
1876       (format "\\printindex")))))
1877 #+END_SRC
1878
1879 #+RESULTS:
1880 | 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*)) |
1881 | lambda | (path desc format) | (cond ((eq format (quote latex)) (format \printindex)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
1882
1883 ** Glossary
1884 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.
1885
1886 #+LATEX_HEADER: \usepackage{glossaries}
1887 #+LATEX_HEADER: \makeglossaries
1888
1889 And at the end of the document put \makeglossaries.
1890
1891 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1892 (org-add-link-type
1893  "newglossaryentry"
1894  nil ;; no follow action
1895  (lambda (path desc format)
1896    (cond
1897     ((eq format 'latex)
1898      (format "\\newglossaryentry{%s}{%s}" path desc)))))
1899
1900
1901 ;; link to entry
1902 (org-add-link-type
1903  "gls"
1904   nil ;; no follow action
1905  (lambda (path desc format)
1906    (cond
1907     ((eq format 'latex)
1908      (format "\\gls{%s}" path)))))
1909
1910 ;; plural
1911 (org-add-link-type
1912  "glspl"
1913   nil ;; no follow action
1914  (lambda (path desc format)
1915    (cond
1916     ((eq format 'latex)
1917      (format "\\glspl{%s}" path)))))
1918
1919 ;; capitalized link
1920 (org-add-link-type
1921  "Gls"
1922   nil ;; no follow action
1923  (lambda (path desc format)
1924    (cond
1925     ((eq format 'latex)
1926      (format "\\Gls{%s}" path)))))
1927
1928 ;; capitalized link
1929 (org-add-link-type
1930  "Glspl"
1931   nil ;; no follow action
1932  (lambda (path desc format)
1933    (cond
1934     ((eq format 'latex)
1935      (format "\\Glspl{%s}" path)))))
1936 #+END_SRC
1937
1938 #+RESULTS:
1939 | Glspl             | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \Glspl{%s} path))))                                                                                                                                                                                                                                                                                                                     |
1940 | Gls               | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \Gls{%s} path))))                                                                                                                                                                                                                                                                                                                       |
1941 | glspl             | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \glspl{%s} path))))                                                                                                                                                                                                                                                                                                                     |
1942 | gls               | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \gls{%s} path))))                                                                                                                                                                                                                                                                                                                       |
1943 | newglossaryentry  | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \newglossaryentry{%s}{%s} path desc))))                                                                                                                                                                                                                                                                                                 |
1944 | google            | (lambda (link-string) (browse-url (format http://www.google.com/search?q=%s (url-hexify-string link-string))))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1945 | ResearcherID      | (lambda (link-string) (browse-url (format http://www.researcherid.com/rid/%s link-string)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1946 | orcid             | (lambda (link-string) (browse-url (format http://orcid.org/%s link-string)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1947 | message           | org-mac-message-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1948 | mac-outlook       | org-mac-outlook-message-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1949 | skim              | org-mac-skim-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1950 | addressbook       | org-mac-addressbook-item-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1951 | x-together-item   | org-mac-together-item-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1952 | 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                                                                                                                                                                                                                                                                                                                                                                                                         |
1953 | 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                                                                                                                                                                                                                                                                                                                                                                                                         |
1954 | exercise          | (lambda (arg) (tq-check-internet) (tq-get-assignment arg))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1955 | 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                                                                                                                                                                                                                                                                                                                                                                                                         |
1956 | assignment        | (lambda (arg) (tq-check-internet) (tq-get-assignment arg))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1957 | doi               | doi-link-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1958 | bibentry          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-bibentry                                                                                                                                                                                                                                                                                                                                                                                     |
1959 | Autocites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Autocites                                                                                                                                                                                                                                                                                                                                                                                    |
1960 | autocites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-autocites                                                                                                                                                                                                                                                                                                                                                                                    |
1961 | supercites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-supercites                                                                                                                                                                                                                                                                                                                                                                                   |
1962 | Textcites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Textcites                                                                                                                                                                                                                                                                                                                                                                                    |
1963 | textcites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-textcites                                                                                                                                                                                                                                                                                                                                                                                    |
1964 | Smartcites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Smartcites                                                                                                                                                                                                                                                                                                                                                                                   |
1965 | smartcites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-smartcites                                                                                                                                                                                                                                                                                                                                                                                   |
1966 | footcitetexts     | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footcitetexts                                                                                                                                                                                                                                                                                                                                                                                |
1967 | footcites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footcites                                                                                                                                                                                                                                                                                                                                                                                    |
1968 | Parencites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Parencites                                                                                                                                                                                                                                                                                                                                                                                   |
1969 | parencites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-parencites                                                                                                                                                                                                                                                                                                                                                                                   |
1970 | Cites             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Cites                                                                                                                                                                                                                                                                                                                                                                                        |
1971 | cites             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-cites                                                                                                                                                                                                                                                                                                                                                                                        |
1972 | fnotecite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-fnotecite                                                                                                                                                                                                                                                                                                                                                                                    |
1973 | Pnotecite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Pnotecite                                                                                                                                                                                                                                                                                                                                                                                    |
1974 | pnotecite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-pnotecite                                                                                                                                                                                                                                                                                                                                                                                    |
1975 | Notecite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Notecite                                                                                                                                                                                                                                                                                                                                                                                     |
1976 | notecite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-notecite                                                                                                                                                                                                                                                                                                                                                                                     |
1977 | footfullcite      | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footfullcite                                                                                                                                                                                                                                                                                                                                                                                 |
1978 | fullcite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-fullcite                                                                                                                                                                                                                                                                                                                                                                                     |
1979 | citeurl           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citeurl                                                                                                                                                                                                                                                                                                                                                                                      |
1980 | citedate*         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citedate*                                                                                                                                                                                                                                                                                                                                                                                    |
1981 | citedate          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citedate                                                                                                                                                                                                                                                                                                                                                                                     |
1982 | citetitle*        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citetitle*                                                                                                                                                                                                                                                                                                                                                                                   |
1983 | citetitle         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citetitle                                                                                                                                                                                                                                                                                                                                                                                    |
1984 | Citeauthor*       | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citeauthor*                                                                                                                                                                                                                                                                                                                                                                                  |
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 | autocite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-autocite                                                                                                                                                                                                                                                                                                                                                                                     |
1989 | supercite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-supercite                                                                                                                                                                                                                                                                                                                                                                                    |
1990 | parencite*        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-parencite*                                                                                                                                                                                                                                                                                                                                                                                   |
1991 | cite*             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-cite*                                                                                                                                                                                                                                                                                                                                                                                        |
1992 | Smartcite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Smartcite                                                                                                                                                                                                                                                                                                                                                                                    |
1993 | smartcite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-smartcite                                                                                                                                                                                                                                                                                                                                                                                    |
1994 | Textcite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Textcite                                                                                                                                                                                                                                                                                                                                                                                     |
1995 | textcite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-textcite                                                                                                                                                                                                                                                                                                                                                                                     |
1996 | footcitetext      | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footcitetext                                                                                                                                                                                                                                                                                                                                                                                 |
1997 | footcite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footcite                                                                                                                                                                                                                                                                                                                                                                                     |
1998 | Parencite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Parencite                                                                                                                                                                                                                                                                                                                                                                                    |
1999 | parencite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-parencite                                                                                                                                                                                                                                                                                                                                                                                    |
2000 | Cite              | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Cite                                                                                                                                                                                                                                                                                                                                                                                         |
2001 | Citeauthor        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citeauthor                                                                                                                                                                                                                                                                                                                                                                                   |
2002 | Citealp           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citealp                                                                                                                                                                                                                                                                                                                                                                                      |
2003 | Citealt           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citealt                                                                                                                                                                                                                                                                                                                                                                                      |
2004 | Citep             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citep                                                                                                                                                                                                                                                                                                                                                                                        |
2005 | Citet             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citet                                                                                                                                                                                                                                                                                                                                                                                        |
2006 | citeyear*         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citeyear*                                                                                                                                                                                                                                                                                                                                                                                    |
2007 | citeyear          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citeyear                                                                                                                                                                                                                                                                                                                                                                                     |
2008 | citeauthor*       | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citeauthor*                                                                                                                                                                                                                                                                                                                                                                                  |
2009 | citeauthor        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citeauthor                                                                                                                                                                                                                                                                                                                                                                                   |
2010 | citetext          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citetext                                                                                                                                                                                                                                                                                                                                                                                     |
2011 | citenum           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citenum                                                                                                                                                                                                                                                                                                                                                                                      |
2012 | citealp*          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citealp*                                                                                                                                                                                                                                                                                                                                                                                     |
2013 | citealp           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citealp                                                                                                                                                                                                                                                                                                                                                                                      |
2014 | citealt*          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citealt*                                                                                                                                                                                                                                                                                                                                                                                     |
2015 | citealt           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citealt                                                                                                                                                                                                                                                                                                                                                                                      |
2016 | citep*            | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citep*                                                                                                                                                                                                                                                                                                                                                                                       |
2017 | citep             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citep                                                                                                                                                                                                                                                                                                                                                                                        |
2018 | citet*            | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citet*                                                                                                                                                                                                                                                                                                                                                                                       |
2019 | citet             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citet                                                                                                                                                                                                                                                                                                                                                                                        |
2020 | nocite            | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-nocite                                                                                                                                                                                                                                                                                                                                                                                       |
2021 | cite              | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-cite                                                                                                                                                                                                                                                                                                                                                                                         |
2022 | eqref             | (lambda (label) on clicking goto the label. Navigate back with C-c & (org-mark-ring-push) (widen) (goto-char (point-min)) (if (or (re-search-forward (format label:%s label) nil t) (re-search-forward (format \label{%s} label) nil t) (re-search-forward (format ^#\+label:\s-*\(%s\)\b label) nil t)) nil (org-mark-ring-goto) (error %s not found label)) (message go back with (org-mark-ring-goto) `C-c &`))                                                                                                                                                                                                                                                                                                                                                                                                 | (lambda (keyword desc format) (cond ((eq format (quote html)) (format (<eqref>%s</eqref>) path)) ((eq format (quote latex)) (format \eqref{%s} keyword))))                                                                                                                                                                                                                                                  |
2023 | nameref           | (lambda (label) on clicking goto the label. Navigate back with C-c & (org-mark-ring-push) (widen) (if (or (progn (goto-char (point-min)) (re-search-forward (format \label{%s} label) nil t))) nil (org-mark-ring-goto) (error %s not found label)) (message go back with (org-mark-ring-goto) `C-c &`))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | (lambda (keyword desc format) (cond ((eq format (quote html)) (format (<nameref>%s</nameref>) path)) ((eq format (quote latex)) (format \nameref{%s} keyword))))                                                                                                                                                                                                                                            |
2024 | pageref           | (lambda (label) on clicking goto the label. Navigate back with C-c & (org-mark-ring-push) (widen) (if (or (progn (goto-char (point-min)) (re-search-forward (format label:%s\b label) nil t)) (progn (goto-char (point-min)) (re-search-forward (format \label{%s} label) nil t)) (progn (goto-char (point-min)) (re-search-forward (format ^#\+label:\s-*\(%s\)\b label) nil t)) (progn (goto-char (point-min)) (re-search-forward (format ^#\+tblname:\s-*\(%s\)\b label) nil t))) nil (org-mark-ring-goto) (error %s not found label)) (message go back with (org-mark-ring-goto) `C-c &`))                                                                                                                                                                                                                     | (lambda (keyword desc format) (cond ((eq format (quote html)) (format (<pageref>%s</pageref>) path)) ((eq format (quote latex)) (format \pageref{%s} keyword))))                                                                                                                                                                                                                                            |
2025 | ref               | (lambda (label) on clicking goto the label. Navigate back with C-c & (org-mark-ring-push) (widen) (if (or (progn (goto-char (point-min)) (re-search-forward (format label:%s\b label) nil t)) (progn (goto-char (point-min)) (re-search-forward (format \label{%s} label) nil t)) (progn (goto-char (point-min)) (re-search-forward (format ^#\+label:\s-*\(%s\)\b label) nil t)) (progn (goto-char (point-min)) (re-search-forward (format ^#\+tblname:\s-*\(%s\)\b label) nil t))) nil (org-mark-ring-goto) (error %s not found label)) (org-show-entry) (message go back with (org-mark-ring-goto) `C-c &`))                                                                                                                                                                                                    | (lambda (keyword desc format) (cond ((eq format (quote html)) (format (<ref>%s</ref>) path)) ((eq format (quote latex)) (format \ref{%s} keyword))))                                                                                                                                                                                                                                                        |
2026 | label             | (lambda (label) on clicking count the number of label tags used in the buffer. A number greater than one means multiple labels! (message (format %s occurences (+ (count-matches (format label:%s\b[^-:] label) (point-min) (point-max) t) (count-matches (format ^#\+tblname:\s-*%s\b[^-:] label) (point-min) (point-max) t) (count-matches (format \label{%s}\b label) (point-min) (point-max) t) (count-matches (format ^#\+label:\s-*%s\b[^-:] label) (point-min) (point-max) t)))))                                                                                                                                                                                                                                                                                                                           | (lambda (keyword desc format) (cond ((eq format (quote html)) (format (<label>%s</label>) path)) ((eq format (quote latex)) (format \label{%s} keyword))))                                                                                                                                                                                                                                                  |
2027 | list-of-tables    | org-ref-list-of-tables                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             | (lambda (keyword desc format) (cond ((eq format (quote latex)) (format \listoftables))))                                                                                                                                                                                                                                                                                                                    |
2028 | list-of-figures   | org-ref-list-of-figures                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | (lambda (keyword desc format) (cond ((eq format (quote latex)) (format \listoffigures))))                                                                                                                                                                                                                                                                                                                   |
2029 | addbibresource    | (lambda (link-string) (let* ((bibfile) (object (org-element-context)) (link-string-beginning) (link-string-end)) (save-excursion (goto-char (org-element-property :begin object)) (search-forward link-string nil nil 1) (setq link-string-beginning (match-beginning 0)) (setq link-string-end (match-end 0))) (set (make-local-variable (quote reftex-default-addbibresource)) (split-string (org-element-property :path object) ,)) (save-excursion (if (search-forward , link-string-end 1 1) (setq key-end (- (match-end 0) 1)) (setq key-end (point)))) (save-excursion (if (search-backward , link-string-beginning 1 1) (setq key-beginning (+ (match-beginning 0) 1)) (setq key-beginning (point)))) (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end))) (find-file bibfile))) | (lambda (keyword desc format) (cond ((eq format (quote html)) (format )) ((eq format (quote latex)) (format \addbibresource{%s} keyword))))                                                                                                                                                                                                                                                                 |
2030 | bibliographystyle | (lambda (arg) (message Nothing implemented for clicking here.))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | (lambda (keyword desc format) (cond ((eq format (quote latex)) (format \bibliographystyle{%s} keyword))))                                                                                                                                                                                                                                                                                                   |
2031 | printbibliography | (lambda (arg) (message Nothing implemented for clicking here.))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | (lambda (keyword desc format) (cond ((eq format (quote org)) (org-ref-get-org-bibliography)) ((eq format (quote html)) (org-ref-get-html-bibliography)) ((eq format (quote latex)) \printbibliography)))                                                                                                                                                                                                    |
2032 | nobibliography    | (lambda (link-string) (let* ((bibfile) (object (org-element-context)) (link-string-beginning) (link-string-end)) (save-excursion (goto-char (org-element-property :begin object)) (search-forward link-string nil nil 1) (setq link-string-beginning (match-beginning 0)) (setq link-string-end (match-end 0))) (set (make-local-variable (quote reftex-default-bibliography)) (split-string (org-element-property :path object) ,)) (save-excursion (if (search-forward , link-string-end 1 1) (setq key-end (- (match-end 0) 1)) (setq key-end (point)))) (save-excursion (if (search-backward , link-string-beginning 1 1) (setq key-beginning (+ (match-beginning 0) 1)) (setq key-beginning (point)))) (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end))) (find-file bibfile)))   | (lambda (keyword desc format) (cond ((eq format (quote org)) (org-ref-get-org-bibliography)) ((eq format (quote ascii)) (org-ref-get-ascii-bibliography)) ((eq format (quote html)) (org-ref-get-html-bibliography)) ((eq format (quote latex)) (format \nobibliography{%s} (replace-regexp-in-string \.bib  (mapconcat (quote identity) (mapcar (quote expand-file-name) (split-string keyword ,)) ,)))))) |
2033 | bibliography      | (lambda (link-string) (let* ((bibfile) (object (org-element-context)) (link-string-beginning) (link-string-end)) (save-excursion (goto-char (org-element-property :begin object)) (search-forward link-string nil nil 1) (setq link-string-beginning (match-beginning 0)) (setq link-string-end (match-end 0))) (set (make-local-variable (quote reftex-default-bibliography)) (split-string (org-element-property :path object) ,)) (save-excursion (if (search-forward , link-string-end 1 1) (setq key-end (- (match-end 0) 1)) (setq key-end (point)))) (save-excursion (if (search-backward , link-string-beginning 1 1) (setq key-beginning (+ (match-beginning 0) 1)) (setq key-beginning (point)))) (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end))) (find-file bibfile)))   | (lambda (keyword desc format) (cond ((eq format (quote org)) (org-ref-get-org-bibliography)) ((eq format (quote ascii)) (org-ref-get-ascii-bibliography)) ((eq format (quote html)) (org-ref-get-html-bibliography)) ((eq format (quote latex)) (format \bibliography{%s} (replace-regexp-in-string \.bib  (mapconcat (quote identity) (mapcar (quote expand-file-name) (split-string keyword ,)) ,))))))   |
2034 | rmail             | org-rmail-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
2035 | mhe               | org-mhe-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
2036 | irc               | org-irc-visit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
2037 | info              | org-info-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
2038 | gnus              | org-gnus-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
2039 | docview           | org-docview-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | org-docview-export                                                                                                                                                                                                                                                                                                                                                                                          |
2040 | bibtex            | org-bibtex-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
2041 | bbdb              | org-bbdb-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | org-bbdb-export                                                                                                                                                                                                                                                                                                                                                                                             |
2042 | pydoc             | (lambda (link-string) (shell-command (format python -m pydoc %s link-string)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
2043 | index             | (lambda (path) (tq-index) (occur path))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
2044 | attachfile        | (lambda (link-string) (org-open-file link-string))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 | (lambda (keyword desc format) (cond ((eq format (quote html)) (format )) ((eq format (quote latex)) (format \attachfile{%s} keyword))))                                                                                                                                                                                                                                                                     |
2045 | msx               | org-msx-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
2046 | id                | org-id-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
2047 | file+emacs        | org-open-file-with-emacs                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
2048 | file+sys          | org-open-file-with-system                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
2049
2050
2051
2052 * Utilities
2053 ** create simple text citation from bibtex entry
2054
2055 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2056 (defun org-ref-bib-citation ()
2057   "from a bibtex entry, create and return a simple citation string."
2058
2059   (bibtex-beginning-of-entry)
2060   (let* ((cb (current-buffer))
2061          (bibtex-expand-strings t)
2062          (entry (loop for (key . value) in (bibtex-parse-entry t)
2063                       collect (cons (downcase key) value)))
2064          (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2065          (year  (reftex-get-bib-field "year" entry))
2066          (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2067          (key (reftex-get-bib-field "=key=" entry))
2068          (journal (reftex-get-bib-field "journal" entry))
2069          (volume (reftex-get-bib-field "volume" entry))
2070          (pages (reftex-get-bib-field "pages" entry))
2071          (doi (reftex-get-bib-field "doi" entry))
2072          (url (reftex-get-bib-field "url" entry))
2073          )
2074     ;;authors, "title", Journal, vol(iss):pages (year).
2075     (format "%s, \"%s\", %s, %s:%s (%s)"
2076             author title journal  volume pages year)))
2077 #+END_SRC
2078
2079 #+RESULTS:
2080 : org-ref-bib-citation
2081
2082
2083 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2084 (defun org-ref-bib-html-citation ()
2085   "from a bibtex entry, create and return a simple citation with html links."
2086
2087   (bibtex-beginning-of-entry)
2088   (let* ((cb (current-buffer))
2089          (bibtex-expand-strings t)
2090          (entry (loop for (key . value) in (bibtex-parse-entry t)
2091                       collect (cons (downcase key) value)))
2092          (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2093          (year  (reftex-get-bib-field "year" entry))
2094          (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2095          (key (reftex-get-bib-field "=key=" entry))
2096          (journal (reftex-get-bib-field "journal" entry))
2097          (volume (reftex-get-bib-field "volume" entry))
2098          (pages (reftex-get-bib-field "pages" entry))
2099          (doi (reftex-get-bib-field "doi" entry))
2100          (url (reftex-get-bib-field "url" entry))
2101          )
2102     ;;authors, "title", Journal, vol(iss):pages (year).
2103     (concat (format "%s, \"%s\", %s, %s:%s (%s)."
2104                     author title journal  volume pages year)
2105             (when url (format " <a href=\"%s\">link</a>" url))
2106             (when doi (format " <a href=\"http://dx.doi.org/%s\">doi</a>" doi)))
2107     ))
2108 #+END_SRC
2109
2110 ** open pdf from bibtex
2111 We bind this to a key here: [[*key%20bindings%20for%20utilities][key bindings for utilities]].
2112 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2113 (defun org-ref-open-bibtex-pdf ()
2114   "open pdf for a bibtex entry, if it exists. assumes point is in
2115 the entry of interest in the bibfile. but does not check that."
2116   (interactive)
2117   (save-excursion
2118     (bibtex-beginning-of-entry)
2119     (let* ((bibtex-expand-strings t)
2120            (entry (bibtex-parse-entry t))
2121            (key (reftex-get-bib-field "=key=" entry))
2122            (pdf (format (concat org-ref-pdf-directory "%s.pdf") key)))
2123       (message "%s" pdf)
2124       (if (file-exists-p pdf)
2125           (org-open-link-from-string (format "[[file:%s]]" pdf))
2126         (ding)))))
2127 #+END_SRC
2128
2129 ** open notes from bibtex
2130 We bind this to a key here [[*key%20bindings%20for%20utilities][key bindings for utilities]].
2131
2132 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2133 (defun org-ref-open-bibtex-notes ()
2134   "from a bibtex entry, open the notes if they exist, and create a heading if they do not.
2135
2136 I never did figure out how to use reftex to make this happen
2137 non-interactively. the reftex-format-citation function did not
2138 work perfectly; there were carriage returns in the strings, and
2139 it did not put the key where it needed to be. so, below I replace
2140 the carriage returns and extra spaces with a single space and
2141 construct the heading by hand."
2142   (interactive)
2143
2144   (bibtex-beginning-of-entry)
2145   (let* ((cb (current-buffer))
2146          (bibtex-expand-strings t)
2147          (entry (loop for (key . value) in (bibtex-parse-entry t)
2148                       collect (cons (downcase key) value)))
2149          (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2150          (year  (reftex-get-bib-field "year" entry))
2151          (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2152          (key (reftex-get-bib-field "=key=" entry))
2153          (journal (reftex-get-bib-field "journal" entry))
2154          (volume (reftex-get-bib-field "volume" entry))
2155          (pages (reftex-get-bib-field "pages" entry))
2156          (doi (reftex-get-bib-field "doi" entry))
2157          (url (reftex-get-bib-field "url" entry))
2158          )
2159
2160     ;; save key to clipboard to make saving pdf later easier by pasting.
2161     (with-temp-buffer
2162       (insert key)
2163       (kill-ring-save (point-min) (point-max)))
2164
2165     ;; now look for entry in the notes file
2166     (if  org-ref-bibliography-notes
2167         (find-file-other-window org-ref-bibliography-notes)
2168       (error "org-ref-bib-bibliography-notes is not set to anything"))
2169
2170     (goto-char (point-min))
2171     ;; put new entry in notes if we don't find it.
2172     (if (re-search-forward (format ":Custom_ID: %s$" key) nil 'end)
2173         (funcall org-ref-open-notes-function)
2174       ;; no entry found, so add one
2175       (insert (format "\n** TODO %s - %s" year title))
2176       (insert (format"
2177  :PROPERTIES:
2178   :Custom_ID: %s
2179   :AUTHOR: %s
2180   :JOURNAL: %s
2181   :YEAR: %s
2182   :VOLUME: %s
2183   :PAGES: %s
2184   :DOI: %s
2185   :URL: %s
2186  :END:
2187 [[cite:%s]] [[file:%s/%s.pdf][pdf]]\n\n"
2188 key author journal year volume pages doi url key org-ref-pdf-directory key))
2189 (save-buffer))))
2190 #+END_SRC
2191
2192 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2193 (defun org-ref-open-notes-from-reftex ()
2194   "Call reftex, and open notes for selected entry."
2195   (interactive)
2196   (let ((bibtex-key )))
2197
2198     ;; now look for entry in the notes file
2199     (if  org-ref-bibliography-notes
2200         (find-file-other-window org-ref-bibliography-notes)
2201       (error "org-ref-bib-bibliography-notes is not set to anything"))
2202
2203     (goto-char (point-min))
2204
2205     (re-search-forward (format
2206                         ":Custom_ID: %s$"
2207                         (first (reftex-citation t)) nil 'end))
2208     (funcall org-ref-open-notes-function))
2209 #+END_SRC
2210
2211 ** open url in browser from bibtex
2212
2213 We bind this to a key here [[*key%20bindings%20for%20utilities][key bindings for utilities]].
2214
2215 + This function may be duplicative of bibtex-url. But I think my function is better unless you do some complicated customization of bibtex-generate-url-list.
2216
2217 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2218 (defun org-ref-open-in-browser ()
2219   "Open the bibtex entry at point in a browser using the url field or doi field"
2220 (interactive)
2221 (save-excursion
2222   (bibtex-beginning-of-entry)
2223   (catch 'done
2224     (let ((url (bibtex-autokey-get-field "url")))
2225       (when  url
2226         (browse-url url)
2227         (throw 'done nil)))
2228
2229     (let ((doi (bibtex-autokey-get-field "doi")))
2230       (when doi
2231         (if (string-match "^http" doi)
2232             (browse-url doi)
2233           (browse-url (format "http://dx.doi.org/%s" doi)))
2234         (throw 'done nil)))
2235     (message "No url or doi found"))))
2236 #+END_SRC
2237
2238 ** citeulike
2239    I discovered you could upload a bibtex entry to citeulike using http requests. The upload is actually done by a [[*The%20upload%20script][python script]], because it was easy to write. Here is the emacs command to do this. It is not a fast operation, and  do not use it frequently.
2240
2241 *** function to upload bibtex to citeulike
2242
2243 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2244 (defun org-ref-upload-bibtex-entry-to-citeulike ()
2245   "with point in  a bibtex entry get bibtex string and submit to citeulike.
2246
2247 Relies on the python script /upload_bibtex_citeulike.py being in the user directory."
2248   (interactive)
2249   (message "uploading to citeulike")
2250   (save-restriction
2251     (bibtex-narrow-to-entry)
2252     (let ((startpos (point-min))
2253           (endpos (point-max))
2254           (bibtex-string (buffer-string))
2255           (script (concat "python " starter-kit-dir "/upload_bibtex_citeulike.py&")))
2256       (with-temp-buffer (insert bibtex-string)
2257                         (shell-command-on-region (point-min) (point-max) script t nil nil t)))))
2258 #+END_SRC
2259
2260 *** The upload script
2261 Here is the python script for uploading.
2262
2263 *************** TODO document how to get the cookies
2264 *************** END
2265
2266
2267 #+BEGIN_SRC python :tangle upload_bibtex_citeulike.py
2268 #!python
2269 import pickle, requests, sys
2270
2271 # reload cookies
2272 with open('c:/Users/jkitchin/Dropbox/blogofile-jkitchin.github.com/_blog/cookies.pckl', 'rb') as f:
2273     cookies = pickle.load(f)
2274
2275 url = 'http://www.citeulike.org/profile/jkitchin/import_do'
2276
2277 bibtex = sys.stdin.read()
2278
2279 data = {'pasted':bibtex,
2280         'to_read':2,
2281         'tag_parsing':'simple',
2282         'strip_brackets':'no',
2283         'update_id':'bib-key',
2284         'btn_bibtex':'Import BibTeX file ...'}
2285
2286 headers = {'content-type': 'multipart/form-data',
2287            'User-Agent':'jkitchin/johnrkitchin@gmail.com bibtexupload'}
2288
2289 r = requests.post(url, headers=headers, data=data, cookies=cookies, files={})
2290 print r
2291 #+END_SRC
2292
2293 ** Build a pdf from a bibtex file
2294    It is useful to have a pdf version of an entire bibliography to check it for formatting, spelling, or to share it. This function creates a pdf from a bibtex file. I only include the packages  I commonly use in my bitex files.
2295
2296 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2297 (defun org-ref-build-full-bibliography ()
2298   "build pdf of all bibtex entries, and open it."
2299   (interactive)
2300   (let* ((bibfile (file-name-nondirectory (buffer-file-name)))
2301         (bib-base (file-name-sans-extension bibfile))
2302         (texfile (concat bib-base ".tex"))
2303         (pdffile (concat bib-base ".pdf")))
2304     (find-file texfile)
2305     (erase-buffer)
2306     (insert (format "\\documentclass[12pt]{article}
2307 \\usepackage[version=3]{mhchem}
2308 \\usepackage{url}
2309 \\usepackage[numbers]{natbib}
2310 \\usepackage[colorlinks=true, linkcolor=blue, urlcolor=blue, pdfstartview=FitH]{hyperref}
2311 \\usepackage{doi}
2312 \\begin{document}
2313 \\nocite{*}
2314 \\bibliographystyle{unsrtnat}
2315 \\bibliography{%s}
2316 \\end{document}" bib-base))
2317     (save-buffer)
2318     (shell-command (concat "pdflatex " bib-base))
2319     (shell-command (concat "bibtex " bib-base))
2320     (shell-command (concat "pdflatex " bib-base))
2321     (shell-command (concat "pdflatex " bib-base))
2322     (kill-buffer texfile)
2323     (org-open-file pdffile)
2324     ))
2325 #+END_SRC
2326
2327 ** Extract bibtex entries cited in an org-file
2328 When you use your default bibliography file, and you want to send an org-file to a collaborator, you may need to include bibtex entries so the other person can see them. This function does that and puts the entries in a section at the end of the document that can be tangled to a bib-file.
2329
2330 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
2331 (defun org-ref-extract-bibtex-entries ()
2332   "extract the bibtex entries referred to by cite links in the current buffer into a src block at the bottom of the current buffer.
2333
2334 If no bibliography is in the buffer the `reftex-default-bibliography' is used."
2335   (interactive)
2336   (let* ((temporary-file-directory (file-name-directory (buffer-file-name)))
2337          (tempname (make-temp-file "extract-bib"))
2338          (contents (buffer-string))
2339          (cb (current-buffer))
2340          basename texfile bibfile results)
2341
2342     ;; open tempfile and insert org-buffer contents
2343     (find-file tempname)
2344     (insert contents)
2345     (setq basename (file-name-sans-extension
2346                     (file-name-nondirectory buffer-file-name))
2347           texfile (concat tempname ".tex")
2348           bibfile (concat tempname ".bib"))
2349
2350     ;; see if we have a bibliography, and insert the default one if not.
2351     (save-excursion
2352       (goto-char (point-min))
2353       (unless (re-search-forward "^bibliography:" (point-max) 'end)
2354         (insert (format "\nbibliography:%s"
2355                         (mapconcat 'identity reftex-default-bibliography ",")))))
2356     (save-buffer)
2357
2358     ;; get a latex file and extract the references
2359     (org-latex-export-to-latex)
2360     (find-file texfile)
2361     (reftex-parse-all)
2362     (reftex-create-bibtex-file bibfile)
2363     (save-buffer)
2364     ;; save results of the references
2365     (setq results (buffer-string))
2366
2367     ;; kill buffers. these are named by basename, not full path
2368     (kill-buffer (concat basename ".bib"))
2369     (kill-buffer (concat basename ".tex"))
2370     (kill-buffer basename)
2371
2372     (delete-file bibfile)
2373     (delete-file texfile)
2374     (delete-file tempname)
2375
2376     ;; Now back to the original org buffer and insert the results
2377     (switch-to-buffer cb)
2378     (when (not (string= "" results))
2379       (save-excursion
2380         (goto-char (point-max))
2381         (insert "\n\n")
2382         (org-insert-heading)
2383         (insert (format " Bibtex entries
2384
2385 ,#+BEGIN_SRC text :tangle %s
2386 %s
2387 ,#+END_SRC" (concat (file-name-sans-extension (file-name-nondirectory (buffer-file-name))) ".bib") results))))))
2388 #+END_SRC
2389
2390 ** Find bad cite links
2391 Depending on how you enter citations, you may have citations with no corresponding bibtex entry. This function finds them and gives you a clickable table to navigate to them.
2392
2393 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
2394 (require 'cl)
2395
2396 (defun index (substring list)
2397   "return the index of string in a list of strings"
2398   (let ((i 0)
2399         (found nil))
2400     (dolist (arg list i)
2401       (if (string-match (concat "^" substring "$") arg)
2402           (progn
2403             (setq found t)
2404             (return i)))
2405       (setq i (+ i 1)))
2406     ;; return counter if found, otherwise return nil
2407     (if found i nil)))
2408
2409
2410 (defun org-ref-find-bad-citations ()
2411   "Create a list of citation keys in an org-file that do not have a bibtex entry in the known bibtex files.
2412
2413 Makes a new buffer with clickable links."
2414   (interactive)
2415   ;; generate the list of bibtex-keys and cited keys
2416   (let* ((bibtex-files (org-ref-find-bibliography))
2417          (bibtex-file-path (mapconcat (lambda (x) (file-name-directory (file-truename x))) bibtex-files ":"))
2418          (bibtex-keys (mapcar (lambda (x) (car x)) (bibtex-global-key-alist)))
2419          (bad-citations '()))
2420
2421     (org-element-map (org-element-parse-buffer) 'link
2422       (lambda (link)
2423         (let ((plist (nth 1 link)))
2424           (when (equal (plist-get plist ':type) "cite")
2425             (dolist (key (org-ref-split-and-strip-string (plist-get plist ':path)) )
2426               (when (not (index key bibtex-keys))
2427                 (setq bad-citations (append bad-citations
2428                                             `(,(format "%s [[elisp:(progn (switch-to-buffer-other-frame \"%s\")(goto-char %s))][not found here]]\n"
2429                                                        key (buffer-name)(plist-get plist ':begin)))))
2430                 ))))))
2431
2432     (if bad-citations
2433       (progn
2434         (switch-to-buffer-other-window "*Missing citations*")
2435         (org-mode)
2436         (erase-buffer)
2437         (insert "* List of bad cite links\n")
2438         (insert (mapconcat 'identity bad-citations ""))
2439                                         ;(setq buffer-read-only t)
2440         (use-local-map (copy-keymap org-mode-map))
2441         (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))
2442
2443       (when (get-buffer "*Missing citations*")
2444           (kill-buffer "*Missing citations*"))
2445       (message "No bad cite links found"))))
2446 #+END_SRC
2447
2448 ** Finding non-ascii characters
2449 I like my bibtex files to be 100% ascii. This function finds the non-ascii characters so you can replace them.
2450
2451 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2452 (defun org-ref-find-non-ascii-characters ()
2453   "finds non-ascii characters in the buffer. Useful for cleaning up bibtex files"
2454   (interactive)
2455   (occur "[^[:ascii:]]"))
2456 #+END_SRC
2457
2458 ** Resort a bibtex entry
2459 I like neat and orderly bibtex entries.That means the fields are in a standard order that I like. This function reorders the fields in an entry for articles, and makes sure the fields are in lowercase.
2460
2461 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2462 (defun org-ref-sort-bibtex-entry ()
2463   "sort fields of entry in standard order and downcase them"
2464   (interactive)
2465   (bibtex-beginning-of-entry)
2466   (let* ((master '("author" "title" "journal" "volume" "number" "pages" "year" "doi" "url"))
2467          (entry (bibtex-parse-entry))
2468          (entry-fields)
2469          (other-fields)
2470          (type (cdr (assoc "=type=" entry)))
2471          (key (cdr (assoc "=key=" entry))))
2472
2473     ;; these are the fields we want to order that are in this entry
2474     (setq entry-fields (mapcar (lambda (x) (car x)) entry))
2475     ;; we do not want to reenter these fields
2476     (setq entry-fields (remove "=key=" entry-fields))
2477     (setq entry-fields (remove "=type=" entry-fields))
2478
2479     ;;these are the other fields in the entry
2480     (setq other-fields (remove-if-not (lambda(x) (not (member x master))) entry-fields))
2481
2482     (cond
2483      ;; right now we only resort articles
2484      ((string= (downcase type) "article")
2485       (bibtex-kill-entry)
2486       (insert
2487        (concat "@article{" key ",\n"
2488                (mapconcat
2489                 (lambda (field)
2490                   (when (member field entry-fields)
2491                     (format "%s = %s," (downcase field) (cdr (assoc field entry))))) master "\n")
2492                (mapconcat
2493                 (lambda (field)
2494                   (format "%s = %s," (downcase field) (cdr (assoc field entry)))) other-fields "\n")
2495                "\n}\n\n"))
2496       (bibtex-find-entry key)
2497       (bibtex-fill-entry)
2498       (bibtex-clean-entry)
2499        ))))
2500 #+END_SRC
2501
2502 ** Clean a bibtex entry
2503    I like neat and orderly bibtex entries. This code will eventually replace the key with my style key, clean the entry, and sort the fields in the order I like them.
2504 see [[file:emacs-24.3/lisp/textmodes/bibtex.el::bibtex-autokey-before-presentation-function]] for how to set a function that checks for uniqueness of the key.
2505 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2506 (defun org-ref-clean-bibtex-entry(&optional keep-key)
2507   "clean and replace the key in a bibtex function. When keep-key is t, do not replace it. You can use a prefix to specify the key should be kept"
2508   (interactive "P")
2509   (bibtex-beginning-of-entry)
2510 (end-of-line)
2511   ;; some entries do not have a key or comma in first line. We check and add it, if needed.
2512   (unless (string-match ",$" (thing-at-point 'line))
2513     (end-of-line)
2514     (insert ","))
2515
2516   ;; check for empty pages, and put eid or article id in its place
2517   (let ((entry (bibtex-parse-entry))
2518         (pages (bibtex-autokey-get-field "pages"))
2519         (year (bibtex-autokey-get-field "year"))
2520         (doi  (bibtex-autokey-get-field "doi"))
2521         ;; The Journal of Chemical Physics uses eid
2522         (eid (bibtex-autokey-get-field "eid")))
2523
2524     ;; replace http://dx.doi.org/ in doi. some journals put that in,
2525     ;; but we only want the doi.
2526     (when (string-match "^http://dx.doi.org/" doi)
2527       (bibtex-beginning-of-entry)
2528       (goto-char (car (cdr (bibtex-search-forward-field "doi" t))))
2529       (bibtex-kill-field)
2530       (bibtex-make-field "doi")
2531       (backward-char)
2532       (insert (replace-regexp-in-string "^http://dx.doi.org/" "" doi)))
2533
2534     ;; asap articles often set year to 0, which messes up key
2535     ;; generation. fix that.
2536     (when (string= "0" year)
2537       (bibtex-beginning-of-entry)
2538       (goto-char (car (cdr (bibtex-search-forward-field "year" t))))
2539       (bibtex-kill-field)
2540       (bibtex-make-field "year")
2541       (backward-char)
2542       (insert (read-string "Enter year: ")))
2543
2544     ;; fix pages if they are empty if there is an eid to put there.
2545     (when (string= "-" pages)
2546       (when eid
2547         (bibtex-beginning-of-entry)
2548         ;; this seems like a clunky way to set the pages field.But I
2549         ;; cannot find a better way.
2550         (goto-char (car (cdr (bibtex-search-forward-field "pages" t))))
2551         (bibtex-kill-field)
2552         (bibtex-make-field "pages")
2553         (backward-char)
2554         (insert eid)))
2555
2556     ;; replace naked & with \&
2557     (save-restriction
2558       (bibtex-narrow-to-entry)
2559       (bibtex-beginning-of-entry)
2560       (message "checking &")
2561       (replace-regexp " & " " \\\\& ")
2562       (widen))
2563
2564     ;; generate a key, and if it duplicates an existing key, edit it.
2565     (unless keep-key
2566       (let ((key (bibtex-generate-autokey)))
2567
2568         ;; first we delete the existing key
2569         (bibtex-beginning-of-entry)
2570         (re-search-forward bibtex-entry-maybe-empty-head)
2571         (if (match-beginning bibtex-key-in-head)
2572             (delete-region (match-beginning bibtex-key-in-head)
2573                            (match-end bibtex-key-in-head)))
2574         ;; check if the key is in the buffer
2575         (when (save-excursion
2576                 (bibtex-search-entry key))
2577           (save-excursion
2578             (bibtex-search-entry key)
2579             (bibtex-copy-entry-as-kill)
2580             (switch-to-buffer-other-window "*duplicate entry*")
2581             (bibtex-yank))
2582           (setq key (bibtex-read-key "Duplicate Key found, edit: " key)))
2583
2584         (insert key)
2585         (kill-new key))) ;; save key for pasting
2586
2587     ;; run hooks. each of these operates on the entry with no arguments.
2588     ;; this did not work like  i thought, it gives a symbolp error.
2589     ;; (run-hooks org-ref-clean-bibtex-entry-hook)
2590     (mapcar (lambda (x)
2591               (save-restriction
2592                 (save-excursion
2593                   (funcall x))))
2594             org-ref-clean-bibtex-entry-hook)
2595
2596     ;; sort fields within entry
2597     (org-ref-sort-bibtex-entry)
2598     ;; check for non-ascii characters
2599     (occur "[^[:ascii:]]")
2600     ))
2601 #+END_SRC
2602
2603 #+RESULTS:
2604 : org-ref-clean-bibtex-entry
2605
2606 ** Sort the entries in a citation link by year
2607 I prefer citations in chronological order within a grouping. These functions sort the link under the cursor by year.
2608
2609 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2610 (defun org-ref-get-citation-year (key)
2611   "get the year of an entry with key. Returns year as a string."
2612   (interactive)
2613   (let* ((results (org-ref-get-bibtex-key-and-file key))
2614          (bibfile (cdr results)))
2615     (with-temp-buffer
2616       (insert-file-contents bibfile)
2617       (bibtex-search-entry key nil 0)
2618       (prog1 (reftex-get-bib-field "year" (bibtex-parse-entry t))
2619         ))))
2620
2621 (defun org-ref-sort-citation-link ()
2622  "replace link at point with sorted link by year"
2623  (interactive)
2624  (let* ((object (org-element-context))
2625         (type (org-element-property :type object))
2626         (begin (org-element-property :begin object))
2627         (end (org-element-property :end object))
2628         (link-string (org-element-property :path object))
2629         keys years data)
2630   (setq keys (org-ref-split-and-strip-string link-string))
2631   (setq years (mapcar 'org-ref-get-citation-year keys))
2632   (setq data (mapcar* (lambda (a b) `(,a . ,b)) years keys))
2633   (setq data (cl-sort data (lambda (x y) (< (string-to-int (car x)) (string-to-int (car y))))))
2634   ;; now get the keys separated by commas
2635   (setq keys (mapconcat (lambda (x) (cdr x)) data ","))
2636   ;; and replace the link with the sorted keys
2637   (cl--set-buffer-substring begin end (concat type ":" keys))))
2638 #+END_SRC
2639
2640 ** Sort entries in citation links with shift-arrow keys
2641 Sometimes it may be helpful to manually change the order of citations. These functions define shift-arrow functions.
2642 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2643 (defun org-ref-swap-keys (i j keys)
2644  "swap the keys in a list with index i and j"
2645  (let ((tempi (nth i keys)))
2646    (setf (nth i keys) (nth j keys))
2647    (setf (nth j keys) tempi))
2648   keys)
2649
2650 (defun org-ref-swap-citation-link (direction)
2651  "move citation at point in direction +1 is to the right, -1 to the left"
2652  (interactive)
2653  (let* ((object (org-element-context))
2654         (type (org-element-property :type object))
2655         (begin (org-element-property :begin object))
2656         (end (org-element-property :end object))
2657         (link-string (org-element-property :path object))
2658         key keys i)
2659    ;;   We only want this to work on citation links
2660    (when (-contains? org-ref-cite-types type)
2661         (setq key (org-ref-get-bibtex-key-under-cursor))
2662         (setq keys (org-ref-split-and-strip-string link-string))
2663         (setq i (index key keys))  ;; defined in org-ref
2664         (if (> direction 0) ;; shift right
2665             (org-ref-swap-keys i (+ i 1) keys)
2666           (org-ref-swap-keys i (- i 1) keys))
2667         (setq keys (mapconcat 'identity keys ","))
2668         ;; and replace the link with the sorted keys
2669         (cl--set-buffer-substring begin end (concat type ":" keys " "))
2670         ;; now go forward to key so we can move with the key
2671         (re-search-forward key)
2672         (goto-char (match-beginning 0)))))
2673
2674 ;; add hooks to make it work
2675 (add-hook 'org-shiftright-hook (lambda () (org-ref-swap-citation-link 1)))
2676 (add-hook 'org-shiftleft-hook (lambda () (org-ref-swap-citation-link -1)))
2677 #+END_SRC
2678 * Aliases
2679 I like convenience. Here are some aliases for faster typing.
2680
2681 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2682 (defalias 'oro 'org-ref-open-citation-at-point)
2683 (defalias 'orc 'org-ref-citation-at-point)
2684 (defalias 'orp 'org-ref-open-pdf-at-point)
2685 (defalias 'oru 'org-ref-open-url-at-point)
2686 (defalias 'orn 'org-ref-open-notes-at-point)
2687 (defalias 'ornr 'org-ref-open-notes-from-reftex)
2688
2689 (defalias 'orib 'org-ref-insert-bibliography-link)
2690 (defalias 'oric 'org-ref-insert-cite-link)
2691 (defalias 'orir 'org-ref-insert-ref-link)
2692 (defalias 'orsl 'org-ref-store-bibtex-entry-link)
2693
2694 (defalias 'orcb 'org-ref-clean-bibtex-entry)
2695 #+END_SRC
2696 * End of code
2697 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2698 (provide 'org-ref)
2699 #+END_SRC
2700
2701 * Build                                                            :noexport:
2702 This code will tangle the elisp code out to org-ref.el and load it.
2703
2704 [[elisp:(progn (org-babel-tangle) (load-file "org-ref.el"))]]
2705
2706 Alternatively you may use:
2707
2708 [[elisp:(org-babel-load-file "org-ref.org")]]
2709
2710
2711