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 **** Creating the menu for when we click on a key
1326      :PROPERTIES:
1327      :ID:       d7b7530b-802f-42b1-b61e-1e77da33e278
1328      :END:
1329 When we click on a cite link, we want to get a menu in the minibuffer. We need to create a string for this. We want a citation, and some options that depend on the key. We want to know if the key is found, if there is a pdf, if etc... Here we create that string.
1330
1331 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
1332 (defun org-ref-get-menu-options ()
1333   "returns a dynamically determined string of options for the citation under point.
1334
1335 we check to see if there is pdf, and if the key actually exists in the bibliography"
1336   (interactive)
1337   (let* ((results (org-ref-get-bibtex-key-and-file))
1338          (key (car results))
1339          (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key))
1340          (bibfile (cdr results))
1341          m1 m2 m3 m4 m5 menu-string)
1342     (setq m1 (if bibfile
1343                  "(o)pen"
1344                "(No key found)"))
1345
1346     (setq m3 (if (file-exists-p pdf-file)
1347                  "(p)df"
1348                      "(No pdf found)"))
1349
1350     (setq m4 (if (not
1351                   (and bibfile
1352                        (string= (catch 'url
1353                                   (progn
1354
1355                                     (with-temp-buffer
1356                                       (insert-file-contents bibfile)
1357                                       (bibtex-search-entry key)
1358                                       (when (not
1359                                              (string= (setq url (bibtex-autokey-get-field "url")) ""))
1360                                         (throw 'url url))
1361
1362                                       (when (not
1363                                              (string= (setq url (bibtex-autokey-get-field "doi")) ""))
1364                                         (throw 'url url))))) "")))
1365                "(u)rl" "(no url found)"))
1366     (setq m5 "(n)otes")
1367     (setq m2 (if bibfile
1368                  (progn
1369                    (setq citation (progn
1370                                     (with-temp-buffer
1371                                       (insert-file-contents bibfile)
1372                                       (bibtex-search-entry key)
1373                                       (concat
1374                                        (org-ref-bib-citation)
1375                                        "\n"
1376                                        "in: " bibfile)
1377                                       )))
1378                    citation)
1379                "no key found"))
1380
1381     (setq menu-string (mapconcat 'identity (list m2 "\n" m1 m3 m4 m5 "(m)enu" "(q)uit") "  "))
1382     menu-string))
1383 #+END_SRC
1384
1385 **** convenience functions to act on citation at point
1386      :PROPERTIES:
1387      :ID:       af0b2a82-a7c9-4c08-9dac-09f93abc4a92
1388      :END:
1389 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.
1390
1391 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1392 (defun org-ref-open-pdf-at-point ()
1393   "open the pdf for bibtex key under point if it exists"
1394   (interactive)
1395   (let* ((results (org-ref-get-bibtex-key-and-file))
1396          (key (car results))
1397          (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key)))
1398     (if (file-exists-p pdf-file)
1399         (org-open-file pdf-file)
1400 (message "no pdf found for %s" key))))
1401
1402
1403 (defun org-ref-open-url-at-point ()
1404   "open the url for bibtex key under point."
1405   (interactive)
1406   (let* ((results (org-ref-get-bibtex-key-and-file))
1407          (key (car results))
1408          (bibfile (cdr results)))
1409     (save-excursion
1410       (with-temp-buffer
1411         (insert-file-contents bibfile)
1412         (bibtex-search-entry key)
1413         ;; I like this better than bibtex-url which does not always find
1414         ;; the urls
1415         (catch 'done
1416           (let ((url (bibtex-autokey-get-field "url")))
1417             (when  url
1418               (browse-url url)
1419               (throw 'done nil)))
1420
1421           (let ((doi (bibtex-autokey-get-field "doi")))
1422             (when doi
1423               (if (string-match "^http" doi)
1424                   (browse-url doi)
1425                 (browse-url (format "http://dx.doi.org/%s" doi)))
1426               (throw 'done nil))))))))
1427
1428
1429 (defun org-ref-open-notes-at-point ()
1430   "open the notes for bibtex key under point."
1431   (interactive)
1432   (let* ((results (org-ref-get-bibtex-key-and-file))
1433          (key (car results))
1434          (bibfile (cdr results)))
1435     (save-excursion
1436       (with-temp-buffer
1437         (insert-file-contents bibfile)
1438         (bibtex-search-entry key)
1439         (org-ref-open-bibtex-notes)))))
1440
1441
1442 (defun org-ref-citation-at-point ()
1443   "give message of current citation at point"
1444   (interactive)
1445   (let* ((cb (current-buffer))
1446         (results (org-ref-get-bibtex-key-and-file))
1447         (key (car results))
1448         (bibfile (cdr results)))
1449     (message "%s" (progn
1450                     (with-temp-buffer
1451                       (insert-file-contents bibfile)
1452                       (bibtex-search-entry key)
1453                       (org-ref-bib-citation))))))
1454
1455
1456 (defun org-ref-open-citation-at-point ()
1457   "open bibtex file to key at point"
1458   (interactive)
1459   (let* ((cb (current-buffer))
1460         (results (org-ref-get-bibtex-key-and-file))
1461         (key (car results))
1462         (bibfile (cdr results)))
1463     (find-file bibfile)
1464     (bibtex-search-entry key)))
1465 #+END_SRC
1466
1467 **** the actual minibuffer menu
1468 Now, we create the menu.
1469
1470 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1471 (defun org-ref-cite-onclick-minibuffer-menu (&optional link-string)
1472   "use a minibuffer to select options for the citation under point.
1473
1474 you select your option with a single key press."
1475   (interactive)
1476   (let* ((choice (read-char (org-ref-get-menu-options)))
1477          (results (org-ref-get-bibtex-key-and-file))
1478          (key (car results))
1479          (cb (current-buffer))
1480          (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key))
1481          (bibfile (cdr results)))
1482
1483     (cond
1484      ;; open
1485      ((= choice ?o)
1486       (find-file bibfile)
1487        (bibtex-search-entry key))
1488
1489      ;; cite
1490      ((= choice ?c)
1491       (org-ref-citation-at-point))
1492
1493      ;; quit
1494      ((or
1495       (= choice ?q) ; q
1496       (= choice ?\ )) ; space
1497       ;; this clears the minibuffer
1498       (message ""))
1499
1500      ;; pdf
1501      ((= choice ?p)
1502       (org-ref-open-pdf-at-point))
1503
1504      ;; notes
1505      ((= choice ?n)
1506       (org-ref-open-notes-at-point))
1507
1508      ;; url
1509      ((= choice ?u)
1510       (org-ref-open-url-at-point))
1511
1512      ;; jmax-bibtex menu
1513      ((= choice ?m)
1514       (save-window-excursion
1515         (set-buffer (find-file-noselect bibfile))
1516         ;; get to bibtex entry and use menu there
1517         (bibtex-search-entry key)
1518         (jmax-bibtex)))
1519
1520      ;; anything else we just quit.
1521      (t (message "")))))
1522 #+END_SRC
1523
1524 *** A function to format a cite link
1525
1526 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.
1527
1528 #+BEGIN_SRC emacs-lisp  :tangle no
1529 ;(defun org-ref-cite-link-format (keyword desc format)
1530 ;   (cond
1531 ;    ((eq format 'html) (mapconcat (lambda (key) (format "<a name=\"#%s\">%s</a>" key key) (org-ref-split-and-strip-string keyword) ",")))
1532 ;    ((eq format 'latex)
1533 ;     (concat "\\cite" (when desc (format "[%s]" desc)) "{"
1534 ;            (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
1535 ;            "}"))))
1536 #+END_SRC
1537
1538 *** The actual cite link
1539 Finally, we define the cite link. This is deprecated; the links are autogenerated later. This is here for memory.
1540
1541 #+BEGIN_SRC emacs-lisp :tangle no
1542 ;(org-add-link-type
1543 ; "cite"
1544 ; 'org-ref-cite-onclick-minibuffer-menu
1545 ; 'org-ref-cite-link-format)
1546 #+END_SRC
1547
1548 *** Automatic definition of the cite links
1549 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.
1550
1551 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1552 (defmacro org-ref-make-completion-function (type)
1553   `(defun ,(intern (format "org-%s-complete-link" type)) (&optional arg)
1554      (interactive)
1555      (format "%s:%s"
1556              ,type
1557              (completing-read
1558               "bibtex key: "
1559               (let ((bibtex-files (org-ref-find-bibliography)))
1560                 (bibtex-global-key-alist))))))
1561 #+END_SRC
1562
1563 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.
1564
1565 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1566 (defmacro org-ref-make-format-function (type)
1567   `(defun ,(intern (format "org-ref-format-%s" type)) (keyword desc format)
1568      (cond
1569       ((eq format 'org)
1570        (mapconcat
1571         (lambda (key)
1572           (format "[[#%s][%s]]" key key))
1573         (org-ref-split-and-strip-string keyword) ","))
1574
1575       ((eq format 'ascii)
1576        (concat "["
1577                (mapconcat
1578                 (lambda (key)
1579                   (format "%s" key))
1580                 (org-ref-split-and-strip-string keyword) ",") "]"))
1581
1582       ((eq format 'html)
1583        (mapconcat
1584         (lambda (key)
1585           (format "<a href=\"#%s\">%s</a>" key key))
1586         (org-ref-split-and-strip-string keyword) ","))
1587
1588       ((eq format 'latex)
1589        (if (string= (substring type -1) "s")
1590            ;; biblatex format for multicite commands, which all end in s. These are formated as \cites{key1}{key2}...
1591            (concat "\\" ,type (mapconcat (lambda (key) (format "{%s}"  key))
1592                                          (org-ref-split-and-strip-string keyword) ""))
1593          ;; bibtex format
1594        (concat "\\" ,type (when desc (org-ref-format-citation-description desc)) "{"
1595                (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
1596                "}"))))))
1597 #+END_SRC
1598
1599
1600
1601 We create the links by mapping the function onto the list of defined link types.
1602
1603 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1604 (defun org-ref-format-citation-description (desc)
1605   "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 ::."
1606   (interactive)
1607   (cond
1608    ((string-match "::" desc)
1609     (format "[%s][%s]" (car (setq results (split-string desc "::"))) (cadr results)))
1610    (t (format "[%s]" desc))))
1611
1612 (defun org-ref-define-citation-link (type &optional key)
1613   "add a citation link for org-ref. With optional key, set the reftex binding. For example:
1614 (org-ref-define-citation-link \"citez\" ?z) will create a new citez link, with reftex key of z,
1615 and the completion function."
1616   (interactive "sCitation Type: \ncKey: ")
1617
1618   ;; create the formatting function
1619   (eval `(org-ref-make-format-function ,type))
1620
1621   (eval-expression
1622    `(org-add-link-type
1623      ,type
1624      'org-ref-cite-onclick-minibuffer-menu
1625      (quote ,(intern (format "org-ref-format-%s" type)))))
1626
1627   ;; create the completion function
1628   (eval `(org-ref-make-completion-function ,type))
1629
1630   ;; store new type so it works with adding citations, which checks
1631   ;; for existence in this list
1632   (add-to-list 'org-ref-cite-types type)
1633
1634   ;; and finally if a key is specified, we modify the reftex menu
1635   (when key
1636     (setf (nth 2 (assoc 'org reftex-cite-format-builtin))
1637           (append (nth 2 (assoc 'org reftex-cite-format-builtin))
1638                   `((,key  . ,(concat type ":%l")))))))
1639
1640 ;; create all the link types and their completion functions
1641 (mapcar 'org-ref-define-citation-link org-ref-cite-types)
1642 #+END_SRC
1643
1644 *** org-ref-insert-cite-link
1645 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.
1646
1647 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
1648 (defun org-ref-insert-cite-link (alternative-cite)
1649   "Insert a default citation link using reftex. If you are on a link, it
1650 appends to the end of the link, otherwise, a new link is
1651 inserted. Use a prefix arg to get a menu of citation types."
1652   (interactive "P")
1653   (org-ref-find-bibliography)
1654   (let* ((object (org-element-context))
1655          (link-string-beginning (org-element-property :begin object))
1656          (link-string-end (org-element-property :end object))
1657          (path (org-element-property :path object)))
1658
1659     (if (not alternative-cite)
1660
1661         (cond
1662          ;; case where we are in a link
1663          ((and (equal (org-element-type object) 'link)
1664                (-contains? org-ref-cite-types (org-element-property :type object)))
1665           (goto-char link-string-end)
1666           ;; sometimes there are spaces at the end of the link
1667           ;; this code moves point pack until no spaces are there
1668           (while (looking-back " ") (backward-char))
1669           (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
1670
1671          ;; We are next to a link, and we want to append
1672          ((save-excursion
1673             (backward-char)
1674             (and (equal (org-element-type (org-element-context)) 'link)
1675                  (-contains? org-ref-cite-types (org-element-property :type (org-element-context)))))
1676           (while (looking-back " ") (backward-char))
1677           (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
1678
1679          ;; insert fresh link
1680          (t
1681           (insert
1682            (concat org-ref-default-citation-link
1683                    ":"
1684                    (mapconcat 'identity (reftex-citation t) ",")))))
1685
1686       ;; you pressed a C-u so we run this code
1687       (reftex-citation)))
1688   )
1689 #+END_SRC
1690
1691 #+RESULTS:
1692 : org-ref-insert-cite-link
1693
1694 *** Completion in cite links
1695 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.
1696
1697 #+BEGIN_SRC emacs-lisp  :tangle no
1698 (defun org-cite-complete-link (&optional arg)
1699   "Completion function for cite links"
1700   (format "%s:%s"
1701           org-ref-default-citation-link
1702           (completing-read
1703            "bibtex key: "
1704            (let ((bibtex-files (org-ref-find-bibliography)))
1705              (bibtex-global-key-alist)))))
1706 #+END_SRC
1707
1708 Alternatively, you may shortcut the org-machinery with this command. You will be prompted for a citation type, and then offered key completion.
1709
1710 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1711 (defun org-ref-insert-cite-with-completion (type)
1712   "Insert a cite link with completion"
1713   (interactive (list (ido-completing-read "Type: " org-ref-cite-types)))
1714   (insert (funcall (intern (format "org-%s-complete-link" type)))))
1715 #+END_SRC
1716
1717 ** Storing links to a bibtex entry
1718 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.
1719
1720 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1721 (defun org-ref-store-bibtex-entry-link ()
1722   "Save a citation link to the current bibtex entry. Saves in the default link type."
1723   (interactive)
1724   (let ((link (concat org-ref-default-citation-link
1725                  ":"
1726                  (save-excursion
1727                    (bibtex-beginning-of-entry)
1728                    (reftex-get-bib-field "=key=" (bibtex-parse-entry))))))
1729     (message "saved %s" link)
1730     (push (list link) org-stored-links)
1731     (car org-stored-links)))
1732 #+END_SRC
1733
1734 ** Index entries
1735 org-ref minimally supports index entries. To make an index in a file, you should put in the LaTeX header these lines
1736
1737
1738 #+LATEX_HEADER: \usepackage{makeidx}
1739 #+LATEX_HEADER: \makeindex
1740
1741
1742 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.
1743
1744
1745 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.
1746
1747
1748 index:hello
1749 index:hello!Peter
1750 [[index:hello!Sam@\textsl{Sam}]]
1751 [[index:Lin@\textbf{Lin}]]
1752 [[index:Joe|textit]]
1753 [[index:Lin@\textbf{Lin}]]
1754 [[index:Peter|see {hello}]]
1755 [[index:Jen|seealso{Jenny}]]
1756
1757 index:encodings!input!cp850
1758
1759 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1760 (org-add-link-type
1761  "index"
1762  (lambda (path)
1763    (occur path))
1764
1765  (lambda (path desc format)
1766    (cond
1767     ((eq format 'latex)
1768       (format "\\index{%s}" path)))))
1769
1770 ;; this will generate a temporary index of entries in the file.
1771 (org-add-link-type
1772  "printindex"
1773  (lambda (path)
1774    (let ((*index-links* '())
1775          (*initial-letters* '()))
1776
1777      ;; get links
1778      (org-element-map (org-element-parse-buffer) 'link
1779        (lambda (link)
1780          (let ((type (nth 0 link))
1781                (plist (nth 1 link)))
1782
1783            (when (equal (plist-get plist ':type) "index")
1784              (add-to-list
1785               '*index-links*
1786               (cons (plist-get plist :path)
1787                     (format
1788                      "[[elisp:(progn (switch-to-buffer \"%s\") (goto-char %s))][%s]]"
1789 (current-buffer)
1790                      (plist-get plist :begin)  ;; position of link
1791                      ;; grab a description
1792                      (save-excursion
1793                        (goto-char (plist-get plist :begin))
1794                        (if (thing-at-point 'sentence)
1795                            ;; get a sentence
1796                            (replace-regexp-in-string
1797                             "\n" "" (thing-at-point 'sentence))
1798                          ;; or call it a link
1799                          "link")))))))))
1800
1801      ;; sort the links
1802      (setq *index-links*  (cl-sort *index-links* 'string-lessp :key 'car))
1803
1804      ;; now first letters
1805      (dolist (link *index-links*)
1806        (add-to-list '*initial-letters* (substring (car link) 0 1) t))
1807
1808      ;; now create the index
1809      (switch-to-buffer (get-buffer-create "*index*"))
1810      (org-mode)
1811      (erase-buffer)
1812      (insert "#+TITLE: Index\n\n")
1813      (dolist (letter *initial-letters*)
1814        (insert (format "* %s\n" (upcase letter)))
1815        ;; now process the links
1816        (while (and
1817                ,*index-links*
1818                (string= letter (substring (car (car *index-links*)) 0 1)))
1819          (let ((link (pop *index-links*)))
1820            (insert (format "%s %s\n\n" (car link) (cdr link))))))
1821      (switch-to-buffer "*index*")))
1822  ;; formatting
1823  (lambda (path desc format)
1824    (cond
1825     ((eq format 'latex)
1826       (format "\\printindex")))))
1827 #+END_SRC
1828
1829 #+RESULTS:
1830 | 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*)) |
1831 | lambda | (path desc format) | (cond ((eq format (quote latex)) (format \printindex)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
1832
1833 ** Glossary
1834 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.
1835
1836 #+LATEX_HEADER: \usepackage{glossaries}
1837 #+LATEX_HEADER: \makeglossaries
1838
1839 And at the end of the document put \makeglossaries.
1840
1841 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1842 (org-add-link-type
1843  "newglossaryentry"
1844  nil ;; no follow action
1845  (lambda (path desc format)
1846    (cond
1847     ((eq format 'latex)
1848      (format "\\newglossaryentry{%s}{%s}" path desc)))))
1849
1850
1851 ;; link to entry
1852 (org-add-link-type
1853  "gls"
1854   nil ;; no follow action
1855  (lambda (path desc format)
1856    (cond
1857     ((eq format 'latex)
1858      (format "\\gls{%s}" path)))))
1859
1860 ;; plural
1861 (org-add-link-type
1862  "glspl"
1863   nil ;; no follow action
1864  (lambda (path desc format)
1865    (cond
1866     ((eq format 'latex)
1867      (format "\\glspl{%s}" path)))))
1868
1869 ;; capitalized link
1870 (org-add-link-type
1871  "Gls"
1872   nil ;; no follow action
1873  (lambda (path desc format)
1874    (cond
1875     ((eq format 'latex)
1876      (format "\\Gls{%s}" path)))))
1877
1878 ;; capitalized link
1879 (org-add-link-type
1880  "Glspl"
1881   nil ;; no follow action
1882  (lambda (path desc format)
1883    (cond
1884     ((eq format 'latex)
1885      (format "\\Glspl{%s}" path)))))
1886 #+END_SRC
1887
1888 #+RESULTS:
1889 | Glspl             | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \Glspl{%s} path))))                                                                                                                                                                                                                                                                                                                     |
1890 | Gls               | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \Gls{%s} path))))                                                                                                                                                                                                                                                                                                                       |
1891 | glspl             | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \glspl{%s} path))))                                                                                                                                                                                                                                                                                                                     |
1892 | gls               | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \gls{%s} path))))                                                                                                                                                                                                                                                                                                                       |
1893 | newglossaryentry  | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \newglossaryentry{%s}{%s} path desc))))                                                                                                                                                                                                                                                                                                 |
1894 | google            | (lambda (link-string) (browse-url (format http://www.google.com/search?q=%s (url-hexify-string link-string))))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1895 | ResearcherID      | (lambda (link-string) (browse-url (format http://www.researcherid.com/rid/%s link-string)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1896 | orcid             | (lambda (link-string) (browse-url (format http://orcid.org/%s link-string)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1897 | message           | org-mac-message-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1898 | mac-outlook       | org-mac-outlook-message-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1899 | skim              | org-mac-skim-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1900 | addressbook       | org-mac-addressbook-item-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1901 | x-together-item   | org-mac-together-item-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1902 | 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                                                                                                                                                                                                                                                                                                                                                                                                         |
1903 | 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                                                                                                                                                                                                                                                                                                                                                                                                         |
1904 | exercise          | (lambda (arg) (tq-check-internet) (tq-get-assignment arg))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1905 | 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                                                                                                                                                                                                                                                                                                                                                                                                         |
1906 | assignment        | (lambda (arg) (tq-check-internet) (tq-get-assignment arg))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1907 | doi               | doi-link-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1908 | bibentry          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-bibentry                                                                                                                                                                                                                                                                                                                                                                                     |
1909 | Autocites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Autocites                                                                                                                                                                                                                                                                                                                                                                                    |
1910 | autocites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-autocites                                                                                                                                                                                                                                                                                                                                                                                    |
1911 | supercites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-supercites                                                                                                                                                                                                                                                                                                                                                                                   |
1912 | Textcites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Textcites                                                                                                                                                                                                                                                                                                                                                                                    |
1913 | textcites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-textcites                                                                                                                                                                                                                                                                                                                                                                                    |
1914 | Smartcites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Smartcites                                                                                                                                                                                                                                                                                                                                                                                   |
1915 | smartcites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-smartcites                                                                                                                                                                                                                                                                                                                                                                                   |
1916 | footcitetexts     | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footcitetexts                                                                                                                                                                                                                                                                                                                                                                                |
1917 | footcites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footcites                                                                                                                                                                                                                                                                                                                                                                                    |
1918 | Parencites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Parencites                                                                                                                                                                                                                                                                                                                                                                                   |
1919 | parencites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-parencites                                                                                                                                                                                                                                                                                                                                                                                   |
1920 | Cites             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Cites                                                                                                                                                                                                                                                                                                                                                                                        |
1921 | cites             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-cites                                                                                                                                                                                                                                                                                                                                                                                        |
1922 | fnotecite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-fnotecite                                                                                                                                                                                                                                                                                                                                                                                    |
1923 | Pnotecite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Pnotecite                                                                                                                                                                                                                                                                                                                                                                                    |
1924 | pnotecite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-pnotecite                                                                                                                                                                                                                                                                                                                                                                                    |
1925 | Notecite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Notecite                                                                                                                                                                                                                                                                                                                                                                                     |
1926 | notecite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-notecite                                                                                                                                                                                                                                                                                                                                                                                     |
1927 | footfullcite      | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footfullcite                                                                                                                                                                                                                                                                                                                                                                                 |
1928 | fullcite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-fullcite                                                                                                                                                                                                                                                                                                                                                                                     |
1929 | citeurl           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citeurl                                                                                                                                                                                                                                                                                                                                                                                      |
1930 | citedate*         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citedate*                                                                                                                                                                                                                                                                                                                                                                                    |
1931 | citedate          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citedate                                                                                                                                                                                                                                                                                                                                                                                     |
1932 | citetitle*        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citetitle*                                                                                                                                                                                                                                                                                                                                                                                   |
1933 | citetitle         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citetitle                                                                                                                                                                                                                                                                                                                                                                                    |
1934 | Citeauthor*       | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citeauthor*                                                                                                                                                                                                                                                                                                                                                                                  |
1935 | Autocite*         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Autocite*                                                                                                                                                                                                                                                                                                                                                                                    |
1936 | autocite*         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-autocite*                                                                                                                                                                                                                                                                                                                                                                                    |
1937 | Autocite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Autocite                                                                                                                                                                                                                                                                                                                                                                                     |
1938 | autocite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-autocite                                                                                                                                                                                                                                                                                                                                                                                     |
1939 | supercite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-supercite                                                                                                                                                                                                                                                                                                                                                                                    |
1940 | parencite*        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-parencite*                                                                                                                                                                                                                                                                                                                                                                                   |
1941 | cite*             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-cite*                                                                                                                                                                                                                                                                                                                                                                                        |
1942 | Smartcite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Smartcite                                                                                                                                                                                                                                                                                                                                                                                    |
1943 | smartcite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-smartcite                                                                                                                                                                                                                                                                                                                                                                                    |
1944 | Textcite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Textcite                                                                                                                                                                                                                                                                                                                                                                                     |
1945 | textcite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-textcite                                                                                                                                                                                                                                                                                                                                                                                     |
1946 | footcitetext      | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footcitetext                                                                                                                                                                                                                                                                                                                                                                                 |
1947 | footcite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footcite                                                                                                                                                                                                                                                                                                                                                                                     |
1948 | Parencite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Parencite                                                                                                                                                                                                                                                                                                                                                                                    |
1949 | parencite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-parencite                                                                                                                                                                                                                                                                                                                                                                                    |
1950 | Cite              | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Cite                                                                                                                                                                                                                                                                                                                                                                                         |
1951 | Citeauthor        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citeauthor                                                                                                                                                                                                                                                                                                                                                                                   |
1952 | Citealp           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citealp                                                                                                                                                                                                                                                                                                                                                                                      |
1953 | Citealt           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citealt                                                                                                                                                                                                                                                                                                                                                                                      |
1954 | Citep             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citep                                                                                                                                                                                                                                                                                                                                                                                        |
1955 | Citet             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citet                                                                                                                                                                                                                                                                                                                                                                                        |
1956 | citeyear*         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citeyear*                                                                                                                                                                                                                                                                                                                                                                                    |
1957 | citeyear          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citeyear                                                                                                                                                                                                                                                                                                                                                                                     |
1958 | citeauthor*       | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citeauthor*                                                                                                                                                                                                                                                                                                                                                                                  |
1959 | citeauthor        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citeauthor                                                                                                                                                                                                                                                                                                                                                                                   |
1960 | citetext          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citetext                                                                                                                                                                                                                                                                                                                                                                                     |
1961 | citenum           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citenum                                                                                                                                                                                                                                                                                                                                                                                      |
1962 | citealp*          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citealp*                                                                                                                                                                                                                                                                                                                                                                                     |
1963 | citealp           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citealp                                                                                                                                                                                                                                                                                                                                                                                      |
1964 | citealt*          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citealt*                                                                                                                                                                                                                                                                                                                                                                                     |
1965 | citealt           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citealt                                                                                                                                                                                                                                                                                                                                                                                      |
1966 | citep*            | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citep*                                                                                                                                                                                                                                                                                                                                                                                       |
1967 | citep             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citep                                                                                                                                                                                                                                                                                                                                                                                        |
1968 | citet*            | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citet*                                                                                                                                                                                                                                                                                                                                                                                       |
1969 | citet             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citet                                                                                                                                                                                                                                                                                                                                                                                        |
1970 | nocite            | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-nocite                                                                                                                                                                                                                                                                                                                                                                                       |
1971 | cite              | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-cite                                                                                                                                                                                                                                                                                                                                                                                         |
1972 | 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))))                                                                                                                                                                                                                                                  |
1973 | 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))))                                                                                                                                                                                                                                            |
1974 | 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))))                                                                                                                                                                                                                                            |
1975 | 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))))                                                                                                                                                                                                                                                        |
1976 | 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))))                                                                                                                                                                                                                                                  |
1977 | list-of-tables    | org-ref-list-of-tables                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             | (lambda (keyword desc format) (cond ((eq format (quote latex)) (format \listoftables))))                                                                                                                                                                                                                                                                                                                    |
1978 | list-of-figures   | org-ref-list-of-figures                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | (lambda (keyword desc format) (cond ((eq format (quote latex)) (format \listoffigures))))                                                                                                                                                                                                                                                                                                                   |
1979 | 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))))                                                                                                                                                                                                                                                                 |
1980 | bibliographystyle | (lambda (arg) (message Nothing implemented for clicking here.))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | (lambda (keyword desc format) (cond ((eq format (quote latex)) (format \bibliographystyle{%s} keyword))))                                                                                                                                                                                                                                                                                                   |
1981 | 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)))                                                                                                                                                                                                    |
1982 | 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 ,)) ,)))))) |
1983 | 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 ,)) ,))))))   |
1984 | rmail             | org-rmail-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1985 | mhe               | org-mhe-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1986 | irc               | org-irc-visit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1987 | info              | org-info-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1988 | gnus              | org-gnus-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1989 | docview           | org-docview-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | org-docview-export                                                                                                                                                                                                                                                                                                                                                                                          |
1990 | bibtex            | org-bibtex-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1991 | bbdb              | org-bbdb-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | org-bbdb-export                                                                                                                                                                                                                                                                                                                                                                                             |
1992 | pydoc             | (lambda (link-string) (shell-command (format python -m pydoc %s link-string)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1993 | index             | (lambda (path) (tq-index) (occur path))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1994 | 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))))                                                                                                                                                                                                                                                                     |
1995 | msx               | org-msx-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1996 | id                | org-id-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1997 | file+emacs        | org-open-file-with-emacs                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1998 | file+sys          | org-open-file-with-system                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
1999
2000
2001
2002 * Utilities
2003 ** create simple text citation from bibtex entry
2004
2005 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2006 (defun org-ref-bib-citation ()
2007   "from a bibtex entry, create and return a simple citation string."
2008
2009   (bibtex-beginning-of-entry)
2010   (let* ((cb (current-buffer))
2011          (bibtex-expand-strings t)
2012          (entry (loop for (key . value) in (bibtex-parse-entry t)
2013                       collect (cons (downcase key) value)))
2014          (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2015          (year  (reftex-get-bib-field "year" entry))
2016          (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2017          (key (reftex-get-bib-field "=key=" entry))
2018          (journal (reftex-get-bib-field "journal" entry))
2019          (volume (reftex-get-bib-field "volume" entry))
2020          (pages (reftex-get-bib-field "pages" entry))
2021          (doi (reftex-get-bib-field "doi" entry))
2022          (url (reftex-get-bib-field "url" entry))
2023          )
2024     ;;authors, "title", Journal, vol(iss):pages (year).
2025     (format "%s, \"%s\", %s, %s:%s (%s)"
2026             author title journal  volume pages year)))
2027 #+END_SRC
2028
2029 #+RESULTS:
2030 : org-ref-bib-citation
2031
2032
2033 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2034 (defun org-ref-bib-html-citation ()
2035   "from a bibtex entry, create and return a simple citation with html links."
2036
2037   (bibtex-beginning-of-entry)
2038   (let* ((cb (current-buffer))
2039          (bibtex-expand-strings t)
2040          (entry (loop for (key . value) in (bibtex-parse-entry t)
2041                       collect (cons (downcase key) value)))
2042          (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2043          (year  (reftex-get-bib-field "year" entry))
2044          (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2045          (key (reftex-get-bib-field "=key=" entry))
2046          (journal (reftex-get-bib-field "journal" entry))
2047          (volume (reftex-get-bib-field "volume" entry))
2048          (pages (reftex-get-bib-field "pages" entry))
2049          (doi (reftex-get-bib-field "doi" entry))
2050          (url (reftex-get-bib-field "url" entry))
2051          )
2052     ;;authors, "title", Journal, vol(iss):pages (year).
2053     (concat (format "%s, \"%s\", %s, %s:%s (%s)."
2054                     author title journal  volume pages year)
2055             (when url (format " <a href=\"%s\">link</a>" url))
2056             (when doi (format " <a href=\"http://dx.doi.org/%s\">doi</a>" doi)))
2057     ))
2058 #+END_SRC
2059
2060 ** open pdf from bibtex
2061 We bind this to a key here: [[*key%20bindings%20for%20utilities][key bindings for utilities]].
2062 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2063 (defun org-ref-open-bibtex-pdf ()
2064   "open pdf for a bibtex entry, if it exists. assumes point is in
2065 the entry of interest in the bibfile. but does not check that."
2066   (interactive)
2067   (save-excursion
2068     (bibtex-beginning-of-entry)
2069     (let* ((bibtex-expand-strings t)
2070            (entry (bibtex-parse-entry t))
2071            (key (reftex-get-bib-field "=key=" entry))
2072            (pdf (format (concat org-ref-pdf-directory "%s.pdf") key)))
2073       (message "%s" pdf)
2074       (if (file-exists-p pdf)
2075           (org-open-link-from-string (format "[[file:%s]]" pdf))
2076         (ding)))))
2077 #+END_SRC
2078
2079 ** open notes from bibtex
2080 We bind this to a key here [[*key%20bindings%20for%20utilities][key bindings for utilities]].
2081
2082 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2083 (defun org-ref-open-bibtex-notes ()
2084   "from a bibtex entry, open the notes if they exist, and create a heading if they do not.
2085
2086 I never did figure out how to use reftex to make this happen
2087 non-interactively. the reftex-format-citation function did not
2088 work perfectly; there were carriage returns in the strings, and
2089 it did not put the key where it needed to be. so, below I replace
2090 the carriage returns and extra spaces with a single space and
2091 construct the heading by hand."
2092   (interactive)
2093
2094   (bibtex-beginning-of-entry)
2095   (let* ((cb (current-buffer))
2096          (bibtex-expand-strings t)
2097          (entry (loop for (key . value) in (bibtex-parse-entry t)
2098                       collect (cons (downcase key) value)))
2099          (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2100          (year  (reftex-get-bib-field "year" entry))
2101          (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2102          (key (reftex-get-bib-field "=key=" entry))
2103          (journal (reftex-get-bib-field "journal" entry))
2104          (volume (reftex-get-bib-field "volume" entry))
2105          (pages (reftex-get-bib-field "pages" entry))
2106          (doi (reftex-get-bib-field "doi" entry))
2107          (url (reftex-get-bib-field "url" entry))
2108          )
2109
2110     ;; save key to clipboard to make saving pdf later easier by pasting.
2111     (with-temp-buffer
2112       (insert key)
2113       (kill-ring-save (point-min) (point-max)))
2114
2115     ;; now look for entry in the notes file
2116     (if  org-ref-bibliography-notes
2117         (find-file-other-window org-ref-bibliography-notes)
2118       (error "org-ref-bib-bibliography-notes is not set to anything"))
2119
2120     (goto-char (point-min))
2121     ;; put new entry in notes if we don't find it.
2122     (if (re-search-forward (format ":Custom_ID: %s$" key) nil 'end)
2123         (funcall org-ref-open-notes-function)
2124       ;; no entry found, so add one
2125       (insert (format "\n** TODO %s - %s" year title))
2126       (insert (format"
2127  :PROPERTIES:
2128   :Custom_ID: %s
2129   :AUTHOR: %s
2130   :JOURNAL: %s
2131   :YEAR: %s
2132   :VOLUME: %s
2133   :PAGES: %s
2134   :DOI: %s
2135   :URL: %s
2136  :END:
2137 [[cite:%s]] [[file:%s/%s.pdf][pdf]]\n\n"
2138 key author journal year volume pages doi url key org-ref-pdf-directory key))
2139 (save-buffer))))
2140 #+END_SRC
2141
2142 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2143 (defun org-ref-open-notes-from-reftex ()
2144   "Call reftex, and open notes for selected entry."
2145   (interactive)
2146   (let ((bibtex-key )))
2147
2148     ;; now look for entry in the notes file
2149     (if  org-ref-bibliography-notes
2150         (find-file-other-window org-ref-bibliography-notes)
2151       (error "org-ref-bib-bibliography-notes is not set to anything"))
2152
2153     (goto-char (point-min))
2154
2155     (re-search-forward (format
2156                         ":Custom_ID: %s$"
2157                         (first (reftex-citation t)) nil 'end))
2158     (funcall org-ref-open-notes-function))
2159 #+END_SRC
2160
2161 ** open url in browser from bibtex
2162
2163 We bind this to a key here [[*key%20bindings%20for%20utilities][key bindings for utilities]].
2164
2165 + 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.
2166
2167 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2168 (defun org-ref-open-in-browser ()
2169   "Open the bibtex entry at point in a browser using the url field or doi field"
2170 (interactive)
2171 (save-excursion
2172   (bibtex-beginning-of-entry)
2173   (catch 'done
2174     (let ((url (bibtex-autokey-get-field "url")))
2175       (when  url
2176         (browse-url url)
2177         (throw 'done nil)))
2178
2179     (let ((doi (bibtex-autokey-get-field "doi")))
2180       (when doi
2181         (if (string-match "^http" doi)
2182             (browse-url doi)
2183           (browse-url (format "http://dx.doi.org/%s" doi)))
2184         (throw 'done nil)))
2185     (message "No url or doi found"))))
2186 #+END_SRC
2187
2188 ** citeulike
2189    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.
2190
2191 *** function to upload bibtex to citeulike
2192
2193 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2194 (defun org-ref-upload-bibtex-entry-to-citeulike ()
2195   "with point in  a bibtex entry get bibtex string and submit to citeulike.
2196
2197 Relies on the python script /upload_bibtex_citeulike.py being in the user directory."
2198   (interactive)
2199   (message "uploading to citeulike")
2200   (save-restriction
2201     (bibtex-narrow-to-entry)
2202     (let ((startpos (point-min))
2203           (endpos (point-max))
2204           (bibtex-string (buffer-string))
2205           (script (concat "python " starter-kit-dir "/upload_bibtex_citeulike.py&")))
2206       (with-temp-buffer (insert bibtex-string)
2207                         (shell-command-on-region (point-min) (point-max) script t nil nil t)))))
2208 #+END_SRC
2209
2210 *** The upload script
2211 Here is the python script for uploading.
2212
2213 *************** TODO document how to get the cookies
2214 *************** END
2215
2216
2217 #+BEGIN_SRC python :tangle upload_bibtex_citeulike.py
2218 #!python
2219 import pickle, requests, sys
2220
2221 # reload cookies
2222 with open('c:/Users/jkitchin/Dropbox/blogofile-jkitchin.github.com/_blog/cookies.pckl', 'rb') as f:
2223     cookies = pickle.load(f)
2224
2225 url = 'http://www.citeulike.org/profile/jkitchin/import_do'
2226
2227 bibtex = sys.stdin.read()
2228
2229 data = {'pasted':bibtex,
2230         'to_read':2,
2231         'tag_parsing':'simple',
2232         'strip_brackets':'no',
2233         'update_id':'bib-key',
2234         'btn_bibtex':'Import BibTeX file ...'}
2235
2236 headers = {'content-type': 'multipart/form-data',
2237            'User-Agent':'jkitchin/johnrkitchin@gmail.com bibtexupload'}
2238
2239 r = requests.post(url, headers=headers, data=data, cookies=cookies, files={})
2240 print r
2241 #+END_SRC
2242
2243 ** Build a pdf from a bibtex file
2244    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.
2245
2246 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2247 (defun org-ref-build-full-bibliography ()
2248   "build pdf of all bibtex entries, and open it."
2249   (interactive)
2250   (let* ((bibfile (file-name-nondirectory (buffer-file-name)))
2251         (bib-base (file-name-sans-extension bibfile))
2252         (texfile (concat bib-base ".tex"))
2253         (pdffile (concat bib-base ".pdf")))
2254     (find-file texfile)
2255     (erase-buffer)
2256     (insert (format "\\documentclass[12pt]{article}
2257 \\usepackage[version=3]{mhchem}
2258 \\usepackage{url}
2259 \\usepackage[numbers]{natbib}
2260 \\usepackage[colorlinks=true, linkcolor=blue, urlcolor=blue, pdfstartview=FitH]{hyperref}
2261 \\usepackage{doi}
2262 \\begin{document}
2263 \\nocite{*}
2264 \\bibliographystyle{unsrtnat}
2265 \\bibliography{%s}
2266 \\end{document}" bib-base))
2267     (save-buffer)
2268     (shell-command (concat "pdflatex " bib-base))
2269     (shell-command (concat "bibtex " bib-base))
2270     (shell-command (concat "pdflatex " bib-base))
2271     (shell-command (concat "pdflatex " bib-base))
2272     (kill-buffer texfile)
2273     (org-open-file pdffile)
2274     ))
2275 #+END_SRC
2276
2277 ** Extract bibtex entries cited in an org-file
2278 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.
2279
2280 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
2281 (defun org-ref-extract-bibtex-entries ()
2282   "extract the bibtex entries referred to by cite links in the current buffer into a src block at the bottom of the current buffer.
2283
2284 If no bibliography is in the buffer the `reftex-default-bibliography' is used."
2285   (interactive)
2286   (let* ((temporary-file-directory (file-name-directory (buffer-file-name)))
2287          (tempname (make-temp-file "extract-bib"))
2288          (contents (buffer-string))
2289          (cb (current-buffer))
2290          basename texfile bibfile results)
2291
2292     ;; open tempfile and insert org-buffer contents
2293     (find-file tempname)
2294     (insert contents)
2295     (setq basename (file-name-sans-extension
2296                     (file-name-nondirectory buffer-file-name))
2297           texfile (concat tempname ".tex")
2298           bibfile (concat tempname ".bib"))
2299
2300     ;; see if we have a bibliography, and insert the default one if not.
2301     (save-excursion
2302       (goto-char (point-min))
2303       (unless (re-search-forward "^bibliography:" (point-max) 'end)
2304         (insert (format "\nbibliography:%s"
2305                         (mapconcat 'identity reftex-default-bibliography ",")))))
2306     (save-buffer)
2307
2308     ;; get a latex file and extract the references
2309     (org-latex-export-to-latex)
2310     (find-file texfile)
2311     (reftex-parse-all)
2312     (reftex-create-bibtex-file bibfile)
2313     (save-buffer)
2314     ;; save results of the references
2315     (setq results (buffer-string))
2316
2317     ;; kill buffers. these are named by basename, not full path
2318     (kill-buffer (concat basename ".bib"))
2319     (kill-buffer (concat basename ".tex"))
2320     (kill-buffer basename)
2321
2322     (delete-file bibfile)
2323     (delete-file texfile)
2324     (delete-file tempname)
2325
2326     ;; Now back to the original org buffer and insert the results
2327     (switch-to-buffer cb)
2328     (when (not (string= "" results))
2329       (save-excursion
2330         (goto-char (point-max))
2331         (insert "\n\n")
2332         (org-insert-heading)
2333         (insert (format " Bibtex entries
2334
2335 ,#+BEGIN_SRC text :tangle %s
2336 %s
2337 ,#+END_SRC" (concat (file-name-sans-extension (file-name-nondirectory (buffer-file-name))) ".bib") results))))))
2338 #+END_SRC
2339
2340 ** Find bad cite links
2341 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.
2342
2343 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
2344 (require 'cl)
2345
2346 (defun index (substring list)
2347   "return the index of string in a list of strings"
2348   (let ((i 0)
2349         (found nil))
2350     (dolist (arg list i)
2351       (if (string-match (concat "^" substring "$") arg)
2352           (progn
2353             (setq found t)
2354             (return i)))
2355       (setq i (+ i 1)))
2356     ;; return counter if found, otherwise return nil
2357     (if found i nil)))
2358
2359
2360 (defun org-ref-find-bad-citations ()
2361   "Create a list of citation keys in an org-file that do not have a bibtex entry in the known bibtex files.
2362
2363 Makes a new buffer with clickable links."
2364   (interactive)
2365   ;; generate the list of bibtex-keys and cited keys
2366   (let* ((bibtex-files (org-ref-find-bibliography))
2367          (bibtex-file-path (mapconcat (lambda (x) (file-name-directory (file-truename x))) bibtex-files ":"))
2368          (bibtex-keys (mapcar (lambda (x) (car x)) (bibtex-global-key-alist)))
2369          (bad-citations '()))
2370
2371     (org-element-map (org-element-parse-buffer) 'link
2372       (lambda (link)
2373         (let ((plist (nth 1 link)))
2374           (when (equal (plist-get plist ':type) "cite")
2375             (dolist (key (org-ref-split-and-strip-string (plist-get plist ':path)) )
2376               (when (not (index key bibtex-keys))
2377                 (setq bad-citations (append bad-citations
2378                                             `(,(format "%s [[elisp:(progn (switch-to-buffer-other-frame \"%s\")(goto-char %s))][not found here]]\n"
2379                                                        key (buffer-name)(plist-get plist ':begin)))))
2380                 ))))))
2381
2382     (if bad-citations
2383       (progn
2384         (switch-to-buffer-other-window "*Missing citations*")
2385         (org-mode)
2386         (erase-buffer)
2387         (insert "* List of bad cite links\n")
2388         (insert (mapconcat 'identity bad-citations ""))
2389                                         ;(setq buffer-read-only t)
2390         (use-local-map (copy-keymap org-mode-map))
2391         (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))
2392
2393       (when (get-buffer "*Missing citations*")
2394           (kill-buffer "*Missing citations*"))
2395       (message "No bad cite links found"))))
2396 #+END_SRC
2397
2398 ** Finding non-ascii characters
2399 I like my bibtex files to be 100% ascii. This function finds the non-ascii characters so you can replace them.
2400
2401 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2402 (defun org-ref-find-non-ascii-characters ()
2403   "finds non-ascii characters in the buffer. Useful for cleaning up bibtex files"
2404   (interactive)
2405   (occur "[^[:ascii:]]"))
2406 #+END_SRC
2407
2408 ** Resort a bibtex entry
2409 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.
2410
2411 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2412 (defun org-ref-sort-bibtex-entry ()
2413   "sort fields of entry in standard order and downcase them"
2414   (interactive)
2415   (bibtex-beginning-of-entry)
2416   (let* ((master '("author" "title" "journal" "volume" "number" "pages" "year" "doi" "url"))
2417          (entry (bibtex-parse-entry))
2418          (entry-fields)
2419          (other-fields)
2420          (type (cdr (assoc "=type=" entry)))
2421          (key (cdr (assoc "=key=" entry))))
2422
2423     ;; these are the fields we want to order that are in this entry
2424     (setq entry-fields (mapcar (lambda (x) (car x)) entry))
2425     ;; we do not want to reenter these fields
2426     (setq entry-fields (remove "=key=" entry-fields))
2427     (setq entry-fields (remove "=type=" entry-fields))
2428
2429     ;;these are the other fields in the entry
2430     (setq other-fields (remove-if-not (lambda(x) (not (member x master))) entry-fields))
2431
2432     (cond
2433      ;; right now we only resort articles
2434      ((string= (downcase type) "article")
2435       (bibtex-kill-entry)
2436       (insert
2437        (concat "@article{" key ",\n"
2438                (mapconcat
2439                 (lambda (field)
2440                   (when (member field entry-fields)
2441                     (format "%s = %s," (downcase field) (cdr (assoc field entry))))) master "\n")
2442                (mapconcat
2443                 (lambda (field)
2444                   (format "%s = %s," (downcase field) (cdr (assoc field entry)))) other-fields "\n")
2445                "\n}\n\n"))
2446       (bibtex-find-entry key)
2447       (bibtex-fill-entry)
2448       (bibtex-clean-entry)
2449        ))))
2450 #+END_SRC
2451
2452 ** Clean a bibtex entry
2453    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.
2454 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.
2455 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2456 (defun org-ref-clean-bibtex-entry(&optional keep-key)
2457   "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"
2458   (interactive "P")
2459   (bibtex-beginning-of-entry)
2460 (end-of-line)
2461   ;; some entries do not have a key or comma in first line. We check and add it, if needed.
2462   (unless (string-match ",$" (thing-at-point 'line))
2463     (end-of-line)
2464     (insert ","))
2465
2466   ;; check for empty pages, and put eid or article id in its place
2467   (let ((entry (bibtex-parse-entry))
2468         (pages (bibtex-autokey-get-field "pages"))
2469         (year (bibtex-autokey-get-field "year"))
2470         (doi  (bibtex-autokey-get-field "doi"))
2471         ;; The Journal of Chemical Physics uses eid
2472         (eid (bibtex-autokey-get-field "eid")))
2473
2474     ;; replace http://dx.doi.org/ in doi. some journals put that in,
2475     ;; but we only want the doi.
2476     (when (string-match "^http://dx.doi.org/" doi)
2477       (bibtex-beginning-of-entry)
2478       (goto-char (car (cdr (bibtex-search-forward-field "doi" t))))
2479       (bibtex-kill-field)
2480       (bibtex-make-field "doi")
2481       (backward-char)
2482       (insert (replace-regexp-in-string "^http://dx.doi.org/" "" doi)))
2483
2484     ;; asap articles often set year to 0, which messes up key
2485     ;; generation. fix that.
2486     (when (string= "0" year)
2487       (bibtex-beginning-of-entry)
2488       (goto-char (car (cdr (bibtex-search-forward-field "year" t))))
2489       (bibtex-kill-field)
2490       (bibtex-make-field "year")
2491       (backward-char)
2492       (insert (read-string "Enter year: ")))
2493
2494     ;; fix pages if they are empty if there is an eid to put there.
2495     (when (string= "-" pages)
2496       (when eid
2497         (bibtex-beginning-of-entry)
2498         ;; this seems like a clunky way to set the pages field.But I
2499         ;; cannot find a better way.
2500         (goto-char (car (cdr (bibtex-search-forward-field "pages" t))))
2501         (bibtex-kill-field)
2502         (bibtex-make-field "pages")
2503         (backward-char)
2504         (insert eid)))
2505
2506     ;; replace naked & with \&
2507     (save-restriction
2508       (bibtex-narrow-to-entry)
2509       (bibtex-beginning-of-entry)
2510       (message "checking &")
2511       (replace-regexp " & " " \\\\& ")
2512       (widen))
2513
2514     ;; generate a key, and if it duplicates an existing key, edit it.
2515     (unless keep-key
2516       (let ((key (bibtex-generate-autokey)))
2517
2518         ;; first we delete the existing key
2519         (bibtex-beginning-of-entry)
2520         (re-search-forward bibtex-entry-maybe-empty-head)
2521         (if (match-beginning bibtex-key-in-head)
2522             (delete-region (match-beginning bibtex-key-in-head)
2523                            (match-end bibtex-key-in-head)))
2524         ;; check if the key is in the buffer
2525         (when (save-excursion
2526                 (bibtex-search-entry key))
2527           (save-excursion
2528             (bibtex-search-entry key)
2529             (bibtex-copy-entry-as-kill)
2530             (switch-to-buffer-other-window "*duplicate entry*")
2531             (bibtex-yank))
2532           (setq key (bibtex-read-key "Duplicate Key found, edit: " key)))
2533
2534         (insert key)
2535         (kill-new key))) ;; save key for pasting
2536
2537     ;; run hooks. each of these operates on the entry with no arguments.
2538     ;; this did not work like  i thought, it gives a symbolp error.
2539     ;; (run-hooks org-ref-clean-bibtex-entry-hook)
2540     (mapcar (lambda (x)
2541               (save-restriction
2542                 (save-excursion
2543                   (funcall x))))
2544             org-ref-clean-bibtex-entry-hook)
2545
2546     ;; sort fields within entry
2547     (org-ref-sort-bibtex-entry)
2548     ;; check for non-ascii characters
2549     (occur "[^[:ascii:]]")
2550     ))
2551 #+END_SRC
2552
2553 #+RESULTS:
2554 : org-ref-clean-bibtex-entry
2555
2556 ** Sort the entries in a citation link by year
2557 I prefer citations in chronological order within a grouping. These functions sort the link under the cursor by year.
2558
2559 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2560 (defun org-ref-get-citation-year (key)
2561   "get the year of an entry with key. Returns year as a string."
2562   (interactive)
2563   (let* ((results (org-ref-get-bibtex-key-and-file key))
2564          (bibfile (cdr results)))
2565     (with-temp-buffer
2566       (insert-file-contents bibfile)
2567       (bibtex-search-entry key nil 0)
2568       (prog1 (reftex-get-bib-field "year" (bibtex-parse-entry t))
2569         ))))
2570
2571 (defun org-ref-sort-citation-link ()
2572  "replace link at point with sorted link by year"
2573  (interactive)
2574  (let* ((object (org-element-context))
2575         (type (org-element-property :type object))
2576         (begin (org-element-property :begin object))
2577         (end (org-element-property :end object))
2578         (link-string (org-element-property :path object))
2579         keys years data)
2580   (setq keys (org-ref-split-and-strip-string link-string))
2581   (setq years (mapcar 'org-ref-get-citation-year keys))
2582   (setq data (mapcar* (lambda (a b) `(,a . ,b)) years keys))
2583   (setq data (cl-sort data (lambda (x y) (< (string-to-int (car x)) (string-to-int (car y))))))
2584   ;; now get the keys separated by commas
2585   (setq keys (mapconcat (lambda (x) (cdr x)) data ","))
2586   ;; and replace the link with the sorted keys
2587   (cl--set-buffer-substring begin end (concat type ":" keys))))
2588 #+END_SRC
2589
2590 ** Sort entries in citation links with shift-arrow keys
2591 Sometimes it may be helpful to manually change the order of citations. These functions define shift-arrow functions.
2592 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2593 (defun org-ref-swap-keys (i j keys)
2594  "swap the keys in a list with index i and j"
2595  (let ((tempi (nth i keys)))
2596    (setf (nth i keys) (nth j keys))
2597    (setf (nth j keys) tempi))
2598   keys)
2599
2600 (defun org-ref-swap-citation-link (direction)
2601  "move citation at point in direction +1 is to the right, -1 to the left"
2602  (interactive)
2603  (let* ((object (org-element-context))
2604         (type (org-element-property :type object))
2605         (begin (org-element-property :begin object))
2606         (end (org-element-property :end object))
2607         (link-string (org-element-property :path object))
2608         key keys i)
2609    ;;   We only want this to work on citation links
2610    (when (-contains? org-ref-cite-types type)
2611         (setq key (org-ref-get-bibtex-key-under-cursor))
2612         (setq keys (org-ref-split-and-strip-string link-string))
2613         (setq i (index key keys))  ;; defined in org-ref
2614         (if (> direction 0) ;; shift right
2615             (org-ref-swap-keys i (+ i 1) keys)
2616           (org-ref-swap-keys i (- i 1) keys))
2617         (setq keys (mapconcat 'identity keys ","))
2618         ;; and replace the link with the sorted keys
2619         (cl--set-buffer-substring begin end (concat type ":" keys " "))
2620         ;; now go forward to key so we can move with the key
2621         (re-search-forward key)
2622         (goto-char (match-beginning 0)))))
2623
2624 ;; add hooks to make it work
2625 (add-hook 'org-shiftright-hook (lambda () (org-ref-swap-citation-link 1)))
2626 (add-hook 'org-shiftleft-hook (lambda () (org-ref-swap-citation-link -1)))
2627 #+END_SRC
2628 * Aliases
2629 I like convenience. Here are some aliases for faster typing.
2630
2631 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2632 (defalias 'oro 'org-ref-open-citation-at-point)
2633 (defalias 'orc 'org-ref-citation-at-point)
2634 (defalias 'orp 'org-ref-open-pdf-at-point)
2635 (defalias 'oru 'org-ref-open-url-at-point)
2636 (defalias 'orn 'org-ref-open-notes-at-point)
2637 (defalias 'ornr 'org-ref-open-notes-from-reftex)
2638
2639 (defalias 'orib 'org-ref-insert-bibliography-link)
2640 (defalias 'oric 'org-ref-insert-cite-link)
2641 (defalias 'orir 'org-ref-insert-ref-link)
2642 (defalias 'orsl 'org-ref-store-bibtex-entry-link)
2643
2644 (defalias 'orcb 'org-ref-clean-bibtex-entry)
2645 #+END_SRC
2646 * End of code
2647 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2648 (provide 'org-ref)
2649 #+END_SRC
2650
2651 * Build                                                            :noexport:
2652 This code will tangle the elisp code out to org-ref.el and load it.
2653
2654 [[elisp:(progn (org-babel-tangle) (load-file "org-ref.el"))]]
2655
2656 Alternatively you may use:
2657
2658 [[elisp:(org-babel-load-file "org-ref.org")]]
2659
2660
2661