1 #+TITLE: Org-ref - The best reference handling for org-mode
7 This document is an experiment at creating a literate program to provide similar features as reftex for org-mode referencing. These features include:
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
15 Some additional features include
16 1. Get minibuffer messages for the cite/ref/label link under point
18 With helm integration (default) you can:
20 1. C-c ] to insert a citation link
22 - Enter to insert or append citation(s)
23 - C-u Enter to insert an alternative cite link
24 - C-u C-u Enter to replace the citation at point
25 2. C-u C-c ] to insert a ref link with helm completion
26 3. C-u C-u C-c ] to insert a label with completion
27 4. M-x org-ref to get a helm completion buffer with link checks, utilities and export options
30 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
31 ;;; org-ref.el --- setup bibliography, cite, ref and label org-mode links.
33 ;; Copyright(C) 2014 John Kitchin
35 ;; Author: John Kitchin <jkitchin@andrew.cmu.edu>
36 ;; This file is not currently part of GNU Emacs.
38 ;; This program is free software; you can redistribute it and/or
39 ;; modify it under the terms of the GNU General Public License as
40 ;; published by the Free Software Foundation; either version 2, or (at
41 ;; your option) any later version.
43 ;; This program is distributed in the hope that it will be useful, but
44 ;; WITHOUT ANY WARRANTY; without even the implied warranty of
45 ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
46 ;; General Public License for more details.
48 ;; You should have received a copy of the GNU General Public License
49 ;; along with this program ; see the file COPYING. If not, write to
50 ;; the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
51 ;; Boston, MA 02111-1307, USA.
55 ;; Lisp code to setup bibliography cite, ref and label org-mode links. also
56 ;; sets up reftex and helm for org-mode citations. The links are clickable and
57 ;; do things that are useful. You should really read org-ref.org for details.
59 ;; Package-Requires: ((dash) (helm) (helm-bibtex))
63 The only external require is reftex-cite
65 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
66 (require 'reftex-cite)
69 (require 'helm-bibtex)
73 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.
75 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
77 "customization group for org-ref")
79 (defcustom org-ref-bibliography-notes
81 "filename to where you will put all your notes about an entry in
82 the default bibliography."
86 (defcustom org-ref-default-bibliography
88 "list of bibtex files to search for. You should use full-paths for each file."
89 :type '(repeat :tag "List of bibtex files" file)
92 (defcustom org-ref-pdf-directory
94 "directory where pdfs are stored by key. put a trailing / in"
98 (defcustom org-ref-default-citation-link
100 "The default type of citation link to use"
104 (defcustom org-ref-insert-cite-key
106 "Keyboard shortcut to insert a citation."
110 (defcustom org-ref-bibliography-entry-format
111 '(("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>.")
113 ("book" . "%a, %t, %u (%y).")
115 ("proceedings" . "%e, %t in %S, %u (%y).")
117 ("inproceedings" . "%a, %t, %p, in %b, edited by %e, %u (%y)"))
119 "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."
123 (defcustom org-ref-open-notes-function
129 ;;(org-tree-to-indirect-buffer)
130 (outline-previous-visible-heading 1)
131 (recenter-top-bottom 0))
132 "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"
137 (defcustom org-ref-open-pdf-function
138 'org-ref-open-pdf-at-point
139 "User-defined function to open a pdf from a link. The function must get the key at point, and derive a path to the pdf file, then open it. The default function is `org-ref-open-pdf-at-point'."
144 (defcustom org-ref-insert-cite-function
145 'org-ref-helm-insert-cite-link
146 "Function to call to insert citation links. The default is `org-ref-helm-insert-cite-link' which uses `helm-bibtex'. org-ref modifies helm-bibtex a little bit to give org-mode citations, and to reorder default actions. You may use `org-ref-insert-cite-link' if you like the reftex interface."
151 (defcustom org-ref-cite-onclick-function
152 'org-ref-cite-click-helm
153 "Function that runs when you click on a cite link. The function must take no arguments. You may also use `org-ref-cite-onclick-minibuffer-menu' if you do not like helm."
157 (defcustom org-ref-show-citation-on-enter t
158 "If non-nil add a hook function to show the citation summary in
159 the minibuffer just by putting the cursor in a link"
164 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.
166 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
167 (defcustom org-ref-cite-types
168 '("cite" "nocite" ;; the default latex cite commands
169 ;; natbib cite commands, http://ctan.unixbrain.com/macros/latex/contrib/natbib/natnotes.pdf
170 "citet" "citet*" "citep" "citep*"
171 "citealt" "citealt*" "citealp" "citealp*"
173 "citeauthor" "citeauthor*"
174 "citeyear" "citeyear*"
175 "Citet" "Citep" "Citealt" "Citealp" "Citeauthor"
177 ;; http://ctan.mirrorcatalogs.com/macros/latex/contrib/biblatex/doc/biblatex.pdf
179 "parencite" "Parencite"
180 "footcite" "footcitetext"
181 "textcite" "Textcite"
182 "smartcite" "Smartcite"
183 "cite*" "parencite*" "supercite"
184 "autocite" "Autocite" "autocite*" "Autocite*"
186 "citetitle" "citetitle*"
187 "citedate" "citedate*"
189 "fullcite" "footfullcite"
190 ;; "volcite" "Volcite" cannot support the syntax
191 "notecite" "Notecite"
192 "pnotecite" "Pnotecite"
194 ;; multicites. Very limited support for these.
195 "cites" "Cites" "parencites" "Parencites"
196 "footcites" "footcitetexts"
197 "smartcites" "Smartcites" "textcites" "Textcites"
198 "supercites" "autocites" "Autocites"
199 ;; for the bibentry package
202 "List of citation types known in org-ref"
203 :type '(repeat :tag "List of citation types" string)
207 We need a hook variable to store user-defined bibtex entry cleaning functions
208 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
209 (defcustom org-ref-clean-bibtex-entry-hook nil
210 "Hook that is run in org-ref-clean-bibtex-entry. The functions should take no arguments, and operate on the bibtex entry at point."
216 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
217 (defvar org-ref-bibliography-files
219 "variable to hold bibliography files to be searched")
222 ** org-mode / reftex setup
224 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.
226 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
228 (defun org-mode-reftex-setup ()
229 (and (buffer-file-name)
230 (file-exists-p (buffer-file-name))
231 (global-auto-revert-mode t)
232 ;; I do not remember why I put this next line in. It doesn't
233 ;; work for org-files. Nothing very bad happens, but it gives
234 ;; an annoying error. Commenting it out for now.
237 (make-local-variable 'reftex-cite-format)
238 (setq reftex-cite-format 'org))
240 ;; define key for inserting citations
241 (define-key org-mode-map
242 (kbd org-ref-insert-cite-key)
243 org-ref-insert-cite-function)
245 (when org-ref-show-citation-on-enter
246 (setq org-ref-message-timer
247 (run-with-idle-timer 0.5 t 'org-ref-link-message)))
249 (defun org-ref-show-link-messages ()
250 "Turn on link messages. You will see a message in the
251 minibuffer when on a cite, ref or label link."
253 (setq org-ref-message-timer
254 (run-with-idle-timer 0.5 t 'org-ref-link-message))
256 (defun org-ref-cancel-link-messages ()
257 "Stop showing messages in minibuffer when on a link."
259 (cancel-timer org-ref-message-timer))
261 ;; this approach caused the selected region to not be highlighted any more.
262 ; (add-hook 'post-command-hook 'org-ref-link-message))
263 ; (remove-hook 'post-command-hook 'org-ref-link-message))
265 (add-hook 'org-mode-hook 'org-mode-reftex-setup)
267 (eval-after-load 'reftex-vars
269 (add-to-list 'reftex-cite-format-builtin
270 '(org "Org-mode citation"
271 ((?\C-m . "cite:%l") ; default
272 (?d . ",%l") ; for appending
278 (?h . "citeauthor:%l")
279 (?H . "citeauthor*:%l")
286 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.
288 #+BEGIN_SRC emacs-lisp :tangle no
290 (setf (nth 2 (assoc 'org reftex-cite-format-builtin))
291 (append (nth 2 (assoc 'org reftex-cite-format-builtin)) '((?W . "textcite:%l")
292 (?z . "newcite:%l"))))
295 You can define a new citation link like this:
296 #+BEGIN_SRC emacs-lisp :tangle no
297 (org-ref-define-citation-link "citez" ?z)
301 Most of this library is the creation of functional links to help with references and citations.
303 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.
305 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
306 (defun org-ref-strip-string (string)
307 "strip leading and trailing whitespace from the string"
308 (replace-regexp-in-string
309 (concat search-whitespace-regexp "$" ) ""
310 (replace-regexp-in-string
311 (concat "^" search-whitespace-regexp ) "" string)))
314 It is helpful to make the previous function operate on a list of strings here.
316 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
317 (defun org-ref-split-and-strip-string (string)
318 "split key-string and strip keys. Assumes the key-string is comma delimited"
319 (mapcar 'org-ref-strip-string (split-string string ",")))
322 ** bibliography and bibliographystyle
323 *** An html bibliography
325 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.
327 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
328 (defun org-ref-reftex-get-bib-field (field entry &optional format)
329 "similar to reftex-get-bib-field, but removes enclosing braces and quotes"
331 (setq result (reftex-get-bib-field field entry format))
332 (when (and (not (string= result "")) (string= "{" (substring result 0 1)))
333 (setq result (substring result 1 -1)))
334 (when (and (not (string= result "")) (string= "\"" (substring result 0 1)))
335 (setq result (substring result 1 -1)))
338 (defun org-ref-reftex-format-citation (entry format)
339 "return a formatted string for the bibtex entry (from bibtex-parse-entry) according
340 to the format argument. The format is a string with these percent escapes.
342 In the format, the following percent escapes will be expanded.
344 %l The BibTeX label of the citation.
345 %a List of author names, see also `reftex-cite-punctuation'.
346 %2a Like %a, but abbreviate more than 2 authors like Jones et al.
347 %A First author name only.
348 %e Works like %a, but on list of editor names. (%2e and %E work a well)
350 It is also possible to access all other BibTeX database fields:
351 %b booktitle %c chapter %d edition %h howpublished
352 %i institution %j journal %k key %m month
353 %n number %o organization %p pages %P first page
354 %r address %s school %u publisher %t title
356 %B booktitle, abbreviated %T title, abbreviated
361 Usually, only %l is needed. The other stuff is mainly for the echo area
362 display, and for (setq reftex-comment-citations t).
364 %< as a special operator kills punctuation and space around it after the
365 string has been formatted.
367 A pair of square brackets indicates an optional argument, and RefTeX
368 will prompt for the values of these arguments.
370 Beware that all this only works with BibTeX database files. When
371 citations are made from the \bibitems in an explicit thebibliography
372 environment, only %l is available."
373 ;; Format a citation from the info in the BibTeX ENTRY
375 (unless (stringp format) (setq format "\\cite{%l}"))
377 (if (and reftex-comment-citations
378 (string-match "%l" reftex-cite-comment-format))
379 (error "reftex-cite-comment-format contains invalid %%l"))
382 "\\(\\`\\|[^%]\\)\\(\\(%\\([0-9]*\\)\\([a-zA-Z]\\)\\)[.,;: ]*\\)"
384 (let ((n (string-to-number (match-string 4 format)))
385 (l (string-to-char (match-string 5 format)))
391 (org-ref-reftex-get-bib-field "&key" entry)
392 (if reftex-comment-citations
393 reftex-cite-comment-format
395 ((= l ?a) (reftex-format-names
396 (reftex-get-bib-names "author" entry)
398 ((= l ?A) (car (reftex-get-bib-names "author" entry)))
399 ((= l ?b) (org-ref-reftex-get-bib-field "booktitle" entry "in: %s"))
400 ((= l ?B) (reftex-abbreviate-title
401 (org-ref-reftex-get-bib-field "booktitle" entry "in: %s")))
402 ((= l ?c) (org-ref-reftex-get-bib-field "chapter" entry))
403 ((= l ?d) (org-ref-reftex-get-bib-field "edition" entry))
404 ((= l ?D) (org-ref-reftex-get-bib-field "doi" entry))
405 ((= l ?e) (reftex-format-names
406 (reftex-get-bib-names "editor" entry)
408 ((= l ?E) (car (reftex-get-bib-names "editor" entry)))
409 ((= l ?h) (org-ref-reftex-get-bib-field "howpublished" entry))
410 ((= l ?i) (org-ref-reftex-get-bib-field "institution" entry))
411 ((= l ?j) (org-ref-reftex-get-bib-field "journal" entry))
412 ((= l ?k) (org-ref-reftex-get-bib-field "key" entry))
413 ((= l ?m) (org-ref-reftex-get-bib-field "month" entry))
414 ((= l ?n) (org-ref-reftex-get-bib-field "number" entry))
415 ((= l ?o) (org-ref-reftex-get-bib-field "organization" entry))
416 ((= l ?p) (org-ref-reftex-get-bib-field "pages" entry))
417 ((= l ?P) (car (split-string
418 (org-ref-reftex-get-bib-field "pages" entry)
420 ((= l ?s) (org-ref-reftex-get-bib-field "school" entry))
421 ((= l ?S) (org-ref-reftex-get-bib-field "series" entry))
422 ((= l ?u) (org-ref-reftex-get-bib-field "publisher" entry))
423 ((= l ?U) (org-ref-reftex-get-bib-field "url" entry))
424 ((= l ?r) (org-ref-reftex-get-bib-field "address" entry))
425 ;; strip enclosing brackets from title if they are there
426 ((= l ?t) (org-ref-reftex-get-bib-field "title" entry))
427 ((= l ?T) (reftex-abbreviate-title
428 (org-ref-reftex-get-bib-field "title" entry)))
429 ((= l ?v) (org-ref-reftex-get-bib-field "volume" entry))
430 ((= l ?y) (org-ref-reftex-get-bib-field "year" entry)))))
433 (setq b (match-beginning 2) e (match-end 2))
434 (setq b (match-beginning 3) e (match-end 3)))
435 (setq format (concat (substring format 0 b) rpl (substring format e)))))
436 (while (string-match "%%" format)
437 (setq format (replace-match "%" t t format)))
438 (while (string-match "[ ,.;:]*%<" format)
439 (setq format (replace-match "" t t format)))
440 ;; also replace carriage returns, tabs, and multiple whitespaces
441 (setq format (replace-regexp-in-string "\n\\|\t\\|\s+" " " format))
444 (defun org-ref-get-bibtex-entry-citation (key)
445 "returns a string for the bibliography entry corresponding to key, and formatted according to the type in `org-ref-bibliography-entry-format'"
447 (let ((org-ref-bibliography-files (org-ref-find-bibliography))
448 (file) (entry) (bibtex-entry) (entry-type) (format))
450 (setq file (catch 'result
451 (loop for file in org-ref-bibliography-files do
452 (if (org-ref-key-in-file-p key (file-truename file))
454 (message "%s not found in %s" key (file-truename file))))))
457 (insert-file-contents file)
458 (bibtex-search-entry key nil 0)
459 (setq bibtex-entry (bibtex-parse-entry))
460 (setq entry-type (downcase (cdr (assoc "=type=" bibtex-entry))))
461 (setq format (cdr (assoc entry-type org-ref-bibliography-entry-format)))
463 (setq entry (org-ref-reftex-format-citation bibtex-entry format))
465 (bibtex-narrow-to-entry)
466 (setq entry (buffer-string)))))
471 : org-ref-reftex-format-citation
473 Here is how to use the function. You call it with point in an entry in a bibtex file.
475 #+BEGIN_SRC emacs-lisp :tangle no
476 (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>."))
477 (org-ref-get-bibtex-entry-citation "armiento-2014-high"))
480 : 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>.
482 I am not sure why full author names are not used.
484 This code provides some functions to generate a simple sorted bibliography in html. First we get all the keys in the buffer.
486 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
487 (defun org-ref-get-bibtex-keys ()
488 "Return a list of unique keys in the buffer."
490 (org-element-map (org-element-parse-buffer) 'link
492 (let ((plist (nth 1 link)))
493 (when (-contains? org-ref-cite-types (plist-get plist ':type))
496 (org-ref-split-and-strip-string (plist-get plist ':path)))
497 (when (not (-contains? keys key))
498 (setq keys (append keys (list key))))))))
499 ;; set with-affiliated to get keys in captions
501 ;; Sort keys alphabetically
502 (setq keys (cl-sort keys 'string-lessp :key 'downcase))
506 This function gets the html for one entry.
508 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
509 (defun org-ref-get-bibtex-entry-html (key)
510 "returns an html string for the bibliography entry corresponding to key"
512 (format "<li><a id=\"%s\">[%s] %s</a></li>" key key (org-ref-get-bibtex-entry-citation key)))
515 Now, we map over the whole list of keys, and the whole bibliography, formatted as an unordered list.
517 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
518 (defun org-ref-get-html-bibliography ()
519 "Create an html bibliography when there are keys"
520 (let ((keys (org-ref-get-bibtex-keys)))
522 (concat "<h1>Bibliography</h1>
524 (mapconcat (lambda (x) (org-ref-get-bibtex-entry-html x)) keys "\n")
528 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.
530 *** An org bibliography
531 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.
533 First, we get the string for a single entry.
534 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
535 (defun org-ref-get-bibtex-entry-org (key)
536 "returns an org string for the bibliography entry corresponding to key"
537 (let ((org-ref-bibliography-files (org-ref-find-bibliography))
538 (file) (entry) (bibtex-entry) (entry-type) (format))
540 (setq file (catch 'result
541 (loop for file in org-ref-bibliography-files do
542 (if (org-ref-key-in-file-p key (file-truename file))
544 (message "%s not found in %s" key (file-truename file))))))
547 (insert-file-contents file)
548 (bibtex-search-entry key nil 0)
549 (setq entry (bibtex-parse-entry))
554 " (org-ref-reftex-get-bib-field "author" entry)
555 (org-ref-reftex-get-bib-field "title" entry)
556 (concat " :CUSTOM_ID: " (org-ref-reftex-get-bib-field "=key=" entry) "\n"
557 (mapconcat (lambda (element) (format " :%s: %s"
558 (upcase (car element))
564 Now, we loop over the keys, and combine all the entries into a bibliography.
565 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
566 (defun org-ref-get-org-bibliography ()
567 "Create an org bibliography when there are keys"
568 (let ((keys (org-ref-get-bibtex-keys)))
570 (concat "* Bibliography
572 (mapconcat (lambda (x) (org-ref-get-bibtex-entry-org x)) keys "\n")
576 *** An ascii bibliography
578 This function gets the html for one entry.
580 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
581 (defun org-ref-get-bibtex-entry-ascii (key)
582 "returns an ascii string for the bibliography entry corresponding to key"
584 (format "[%s] %s" key (org-ref-get-bibtex-entry-citation key)))
587 Now, we map over the whole list of keys, and the whole bibliography, formatted as an unordered list.
589 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
590 (defun org-ref-get-ascii-bibliography ()
591 "Create an html bibliography when there are keys"
592 (let ((keys (org-ref-get-bibtex-keys)))
598 (mapconcat (lambda (x) (org-ref-get-bibtex-entry-ascii x)) keys "\n")
604 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.
606 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
607 (org-add-link-type "bibliography"
608 ;; this code is run on clicking. The bibliography
609 ;; may contain multiple files. this code finds the
610 ;; one you clicked on and opens it.
611 (lambda (link-string)
612 ;; get link-string boundaries
613 ;; we have to go to the beginning of the line, and then search forward
616 ;; object is the link you clicked on
617 (object (org-element-context))
618 (link-string-beginning)
622 (goto-char (org-element-property :begin object))
623 (search-forward link-string nil nil 1)
624 (setq link-string-beginning (match-beginning 0))
625 (setq link-string-end (match-end 0)))
627 ;; We set the reftex-default-bibliography
628 ;; here. it should be a local variable only in
629 ;; the current buffer. We need this for using
630 ;; reftex to do citations.
631 (set (make-local-variable 'reftex-default-bibliography)
632 (split-string (org-element-property :path object) ","))
634 ;; now if we have comma separated bibliographies
635 ;; we find the one clicked on. we want to
636 ;; search forward to next comma from point
638 (if (search-forward "," link-string-end 1 1)
639 (setq key-end (- (match-end 0) 1)) ; we found a match
640 (setq key-end (point)))) ; no comma found so take the point
641 ;; and backward to previous comma from point
643 (if (search-backward "," link-string-beginning 1 1)
644 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
645 (setq key-beginning (point)))) ; no match found
646 ;; save the key we clicked on.
647 (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
648 (find-file bibfile))) ; open file on click
651 (lambda (keyword desc format)
653 ((eq format 'org) (org-ref-get-org-bibliography))
654 ((eq format 'ascii) (org-ref-get-ascii-bibliography))
655 ((eq format 'html) (org-ref-get-html-bibliography))
657 ;; write out the latex bibliography command
658 (format "\\bibliography{%s}" (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity
659 (mapcar 'expand-file-name
660 (split-string keyword ","))
665 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.
668 \input{project-description.bbl}
671 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.
673 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
674 (org-add-link-type "nobibliography"
675 ;; this code is run on clicking. The bibliography
676 ;; may contain multiple files. this code finds the
677 ;; one you clicked on and opens it.
678 (lambda (link-string)
679 ;; get link-string boundaries
680 ;; we have to go to the beginning of the line, and then search forward
683 ;; object is the link you clicked on
684 (object (org-element-context))
686 (link-string-beginning)
690 (goto-char (org-element-property :begin object))
691 (search-forward link-string nil nil 1)
692 (setq link-string-beginning (match-beginning 0))
693 (setq link-string-end (match-end 0)))
695 ;; We set the reftex-default-bibliography
696 ;; here. it should be a local variable only in
697 ;; the current buffer. We need this for using
698 ;; reftex to do citations.
699 (set (make-local-variable 'reftex-default-bibliography)
700 (split-string (org-element-property :path object) ","))
702 ;; now if we have comma separated bibliographies
703 ;; we find the one clicked on. we want to
704 ;; search forward to next comma from point
706 (if (search-forward "," link-string-end 1 1)
707 (setq key-end (- (match-end 0) 1)) ; we found a match
708 (setq key-end (point)))) ; no comma found so take the point
709 ;; and backward to previous comma from point
711 (if (search-backward "," link-string-beginning 1 1)
712 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
713 (setq key-beginning (point)))) ; no match found
714 ;; save the key we clicked on.
715 (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
716 (find-file bibfile))) ; open file on click
719 (lambda (keyword desc format)
721 ((eq format 'org) (org-ref-get-org-bibliography))
722 ((eq format 'ascii) (org-ref-get-ascii-bibliography))
723 ((eq format 'html) (org-ref-get-html-bibliography))
725 ;; write out the latex bibliography command
727 ; (format "{\\setbox0\\vbox{\\bibliography{%s}}}"
728 ; (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity
729 ; (mapcar 'expand-file-name
730 ; (split-string keyword ","))
733 (format "\\nobibliography{%s}"
734 (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity
735 (mapcar 'expand-file-name
736 (split-string keyword ","))
742 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
743 (org-add-link-type "printbibliography"
744 (lambda (arg) (message "Nothing implemented for clicking here."))
745 (lambda (keyword desc format)
747 ((eq format 'org) (org-ref-get-org-bibliography))
748 ((eq format 'html) (org-ref-get-html-bibliography))
750 ;; write out the biblatex bibliography command
751 "\\printbibliography"))
755 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, ...
757 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
758 (org-add-link-type "bibliographystyle"
759 (lambda (arg) (message "Nothing implemented for clicking here."))
760 (lambda (keyword desc format)
763 ;; write out the latex bibliography command
764 (format "\\bibliographystyle{%s}" keyword)))))
767 *** Completion for bibliography link
770 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
771 (defun org-bibliography-complete-link (&optional arg)
772 (format "bibliography:%s" (read-file-name "enter file: " nil nil t)))
774 (defun org-ref-insert-bibliography-link ()
775 "insert a bibliography with completion"
777 (insert (org-bibliography-complete-link)))
781 This is apparently used for biblatex.
782 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
783 (org-add-link-type "addbibresource"
784 ;; this code is run on clicking. The addbibresource
785 ;; may contain multiple files. this code finds the
786 ;; one you clicked on and opens it.
787 (lambda (link-string)
788 ;; get link-string boundaries
789 ;; we have to go to the beginning of the line, and then search forward
792 ;; object is the link you clicked on
793 (object (org-element-context))
795 (link-string-beginning)
799 (goto-char (org-element-property :begin object))
800 (search-forward link-string nil nil 1)
801 (setq link-string-beginning (match-beginning 0))
802 (setq link-string-end (match-end 0)))
804 ;; We set the reftex-default-addbibresource
805 ;; here. it should be a local variable only in
806 ;; the current buffer. We need this for using
807 ;; reftex to do citations.
808 (set (make-local-variable 'reftex-default-addbibresource)
809 (split-string (org-element-property :path object) ","))
811 ;; now if we have comma separated bibliographies
812 ;; we find the one clicked on. we want to
813 ;; search forward to next comma from point
815 (if (search-forward "," link-string-end 1 1)
816 (setq key-end (- (match-end 0) 1)) ; we found a match
817 (setq key-end (point)))) ; no comma found so take the point
818 ;; and backward to previous comma from point
820 (if (search-backward "," link-string-beginning 1 1)
821 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
822 (setq key-beginning (point)))) ; no match found
823 ;; save the key we clicked on.
824 (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
825 (find-file bibfile))) ; open file on click
828 (lambda (keyword desc format)
830 ((eq format 'html) (format "")); no output for html
832 ;; write out the latex addbibresource command
833 (format "\\addbibresource{%s}" keyword)))))
838 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.
840 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
841 (defun org-ref-list-of-figures (&optional arg)
842 "Generate buffer with list of figures in them"
844 (save-excursion (widen)
845 (let* ((c-b (buffer-name))
848 (org-element-map (org-element-parse-buffer) 'link
850 "create a link for to the figure"
852 (and (string= (org-element-property :type link) "file")
854 "[^.]*\\.\\(png\\|jpg\\|eps\\|pdf\\)$"
855 (org-element-property :path link)))
858 (let* ((start (org-element-property :begin link))
859 (parent (car (cdr (org-element-property :parent link))))
860 (caption (caaar (plist-get parent :caption)))
861 (name (plist-get parent :name)))
864 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][figure %s: %s]] %s\n"
865 c-b start counter (or name "") caption)
867 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][figure %s: %s]]\n"
868 c-b start counter (or name "")))))))))
869 (switch-to-buffer "*List of Figures*")
870 (setq buffer-read-only nil)
873 (insert (mapconcat 'identity list-of-figures ""))
874 (setq buffer-read-only t)
875 (use-local-map (copy-keymap org-mode-map))
876 (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))))
880 'org-ref-list-of-figures ; on click
881 (lambda (keyword desc format)
884 (format "\\listoffigures")))))
889 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
890 (defun org-ref-list-of-tables (&optional arg)
891 "Generate a buffer with a list of tables"
895 (let* ((c-b (buffer-name))
898 (org-element-map (org-element-parse-buffer 'element) 'table
900 "create a link for to the table"
902 (let ((start (org-element-property :begin table))
903 (name (org-element-property :name table))
904 (caption (caaar (org-element-property :caption table))))
907 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][table %s: %s]] %s\n"
908 c-b start counter (or name "") caption)
910 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][table %s: %s]]\n"
911 c-b start counter (or name ""))))))))
912 (switch-to-buffer "*List of Tables*")
913 (setq buffer-read-only nil)
916 (insert (mapconcat 'identity list-of-tables ""))
917 (setq buffer-read-only t)
918 (use-local-map (copy-keymap org-mode-map))
919 (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))))
923 'org-ref-list-of-tables
924 (lambda (keyword desc format)
927 (format "\\listoftables")))))
931 The label link provides a way to create labels in org-mode. We make it clickable because we want to make sure labels are unique. This code will tell you how many instances of a label are found. We search for label links, LaTeX labels, and org-mode format for labels, tblnames too.
933 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
934 (defun org-ref-count-labels (label)
935 "Counts number of matches for label in the document"
936 (+ (count-matches (format "label:%s\\b[^-:]" label) (point-min) (point-max))
937 ;; for tblname, it is not enough to get word boundary
938 ;; tab-little and tab-little-2 match then.
939 (count-matches (format "^#\\+tblname:\\s-*%s\\b[^-:]" label) (point-min) (point-max))
940 (count-matches (format "\\label{%s}" label) (point-min) (point-max))
941 ;; this is the org-format #+label:
942 (count-matches (format "^#\\+label:\\s-*%s\\b[^-:]" label) (point-min) (point-max))
943 (let ((custom-id-count 0))
946 (when (string= label (org-entry-get (point) "CUSTOM_ID"))
947 (setq custom-id-count (+ 1 custom-id-count)))))
953 "on clicking count the number of label tags used in the buffer. A number greater than one means multiple labels!"
954 (let ((count (org-ref-count-labels label)))
955 (message (format "%s occurence%s"
961 (org-ref-count-labels label))))
962 (lambda (keyword desc format)
964 ((eq format 'html) (format "(<label>%s</label>)" path))
966 (format "\\label{%s}" keyword)))))
969 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.
971 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
972 (defun org-label-store-link ()
973 "store a link to a label. The output will be a ref to that label"
974 ;; First we have to make sure we are on a label link.
975 (let* ((object (org-element-context)))
976 (when (and (equal (org-element-type object) 'link)
977 (equal (org-element-property :type object) "label"))
978 (org-store-link-props
980 :link (concat "ref:" (org-element-property :path object))))
982 ;; Store link on table
983 (when (equal (org-element-type object) 'table)
984 (org-store-link-props
986 :link (concat "ref:" (org-element-property :name object))))
988 ;; it turns out this does not work. you can already store a link to a heading with a CUSTOM_ID
989 ;; store link on heading with custom_id
990 ; (when (and (equal (org-element-type object) 'headline)
991 ; (org-entry-get (point) "CUSTOM_ID"))
992 ; (org-store-link-props
994 ; :link (concat "ref:" (org-entry-get (point) "CUSTOM_ID"))))
996 ;; and to #+label: lines
997 (when (and (equal (org-element-type object) 'paragraph)
998 (org-element-property :name object))
999 (org-store-link-props
1001 :link (concat "ref:" (org-element-property :name object))))
1004 (add-hook 'org-store-link-functions 'org-label-store-link)
1008 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.
1010 At the moment, ref links are not usable for section links. You need [[#CUSTOM_ID]] type links.
1012 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1016 "on clicking goto the label. Navigate back with C-c &"
1017 (org-mark-ring-push)
1018 ;; next search from beginning of the buffer
1020 ;; it is possible you would not find the label if narrowing is in effect
1027 (goto-char (point-min))
1028 (re-search-forward (format "label:%s\\b" label) nil t))
1032 (goto-char (point-min))
1033 (re-search-forward (format "\\label{%s}" label) nil t))
1035 ;; #+label: name org-definition
1037 (goto-char (point-min))
1038 (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
1042 (goto-char (point-min))
1043 (re-search-forward (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t))
1045 ;; Commented out because these ref links do not actually translate correctly in LaTeX.
1046 ;; you need [[#label]] links.
1049 ; (goto-char (point-min))
1050 ; (re-search-forward (format ":CUSTOM_ID:\s-*\\(%s\\)" label) nil t))
1052 ;; we did not find anything, so go back to where we came
1053 (org-mark-ring-goto)
1054 (error "%s not found" label))
1056 (message "go back with (org-mark-ring-goto) `C-c &`"))
1058 (lambda (keyword desc format)
1060 ((eq format 'html) (format "(<ref>%s</ref>)" path))
1062 (format "\\ref{%s}" keyword)))))
1065 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.
1067 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1068 (defun org-ref-get-org-labels ()
1069 "Return a list of #+LABEL: labels."
1071 (goto-char (point-min))
1072 (let ((matches '()))
1073 (while (re-search-forward "^#\\+label:\\s-+\\(.*\\)\\b" (point-max) t)
1074 (add-to-list 'matches (match-string-no-properties 1) t))
1078 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1079 (defun org-ref-get-custom-ids ()
1080 "Return a list of custom_id properties in the buffer."
1081 (let ((results '()) custom_id)
1084 (let ((custom_id (org-entry-get (point) "CUSTOM_ID")))
1085 (when (not (null custom_id))
1086 (setq results (append results (list custom_id)))))))
1090 Here we get a list of the labels defined as raw latex labels, e.g. \label{eqtre}.
1091 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1092 (defun org-ref-get-latex-labels ()
1094 (goto-char (point-min))
1095 (let ((matches '()))
1096 (while (re-search-forward "\\\\label{\\([a-zA-z0-9:-]*\\)}" (point-max) t)
1097 (add-to-list 'matches (match-string-no-properties 1) t))
1101 Finally, we get the table names.
1103 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1104 (defun org-ref-get-tblnames ()
1105 "Return list of table names in the buffer."
1106 (org-element-map (org-element-parse-buffer 'element) 'table
1108 (org-element-property :name table))))
1111 Now, we can put all the labels together which will give us a list of candidates.
1113 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1114 (defun org-ref-get-labels ()
1115 "Returns a list of labels in the buffer that you can make a ref link to.
1116 This is used to auto-complete ref links and in helm menus."
1120 (goto-char (point-min))
1121 (let ((matches '()))
1122 ;; these are the label:stuff kinds
1123 (while (re-search-forward "[^#+]label:\\([a-zA-z0-9:-]*\\)" (point-max) t)
1124 (add-to-list 'matches (match-string-no-properties 1) t))
1126 (org-ref-get-org-labels)
1127 (org-ref-get-latex-labels)
1128 (org-ref-get-tblnames)
1129 (org-ref-get-custom-ids))))))
1132 Let us make a helm function to insert a label link. This will help you enter unique labels by showing matching labels until they are all gone and you are left with a unique one. If you are on a link, it means you want to replace it.
1133 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1134 (defun org-ref-helm-insert-label-link ()
1135 "Insert a label link. helm just shows you what labels already exist.
1136 If you are on a label link, replace it."
1138 (let* ((labels (org-ref-get-labels))
1139 (cb (current-buffer)))
1140 (helm :sources `(((name . "Existing labels")
1141 (candidates . ,labels)
1142 ;; default action is to open to the label
1143 (action . (lambda (label)
1144 ;; unfortunately I do not have markers here
1145 (org-open-link-from-string (format "ref:%s" label))))
1146 ;; if you select a label, replace current one
1147 (action . (lambda (label)
1148 (switch-to-buffer ,cb)
1150 ;; no prefix or on a link
1151 ((equal helm-current-prefix-arg nil)
1152 (let* ((object (org-element-context))
1153 (last-char (save-excursion
1154 (goto-char (org-element-property :end object))
1156 (if (looking-at " ")
1159 (when (-contains? '("label")
1160 (org-element-property :type object))
1161 ;; we are on a link, so replace it.
1164 (org-element-property :begin object)
1165 (org-element-property :end object))
1167 (replace-regexp-in-string
1168 (org-element-property :path object)
1170 (org-element-property :raw-link object))
1172 ;; no prefix options defined
1174 ;; no matching selection creates a new label
1175 ((name . "Create new label")
1177 ;; default action creates a new label, or replaces old one
1178 (action . (lambda (label)
1179 (switch-to-buffer ,cb)
1180 (let* ((object (org-element-context))
1181 (last-char (save-excursion
1182 (goto-char (org-element-property :end object))
1184 (if (looking-at " ")
1187 (if (-contains? '("label")
1188 (org-element-property :type object))
1189 ;; we are on a link, so replace it.
1192 (org-element-property :begin object)
1193 (org-element-property :end object))
1195 (replace-regexp-in-string
1196 (org-element-property :path object)
1198 (org-element-property :raw-link object))
1205 helm-pattern))))))))))))
1208 Now we create a completion function. This works from the org-machinery, e.g. if you type C-c C-l to insert a link, and use completion by pressing tab.
1210 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1211 (defun org-ref-complete-link (&optional arg)
1212 "Completion function for ref links"
1214 (setq label (completing-read "label: " (org-ref-get-labels)))
1215 (format "ref:%s" label)))
1218 Alternatively, you may want to just call a function that inserts a link with completion:
1220 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1221 (defun org-ref-insert-ref-link ()
1223 (insert (org-ref-complete-link)))
1226 Another alternative ref insertion is to use helm.
1228 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1229 (defun org-ref-helm-insert-ref-link ()
1230 "Helm menu to insert ref links to labels in the document.
1231 If you are on link, replace with newly selected label.
1232 Use C-u to insert a different kind of ref link.
1233 Use C-u C-u to insert a [[#custom-id]] link
1236 (let* ((labels (org-ref-get-labels))
1237 (bs (buffer-string))
1238 (contexts (with-temp-buffer
1240 (mapcar 'org-ref-get-label-context labels)))
1241 (cb (current-buffer)))
1243 (helm :input (thing-at-point 'word)
1244 :sources `(((name . "Available labels to ref")
1245 (candidates . ,(loop for label in labels
1246 for context in contexts
1247 ;; we do some kludgy adding spaces
1248 ;; and bars to make it "easier" to
1250 collect (cons (concat
1255 (split-string context "\n")
1258 ;; default action to replace or insert ref link.
1259 (action . (lambda (label)
1260 (switch-to-buffer ,cb)
1263 ;; no prefix or on a link
1264 ((equal helm-current-prefix-arg nil)
1265 (let* ((object (org-element-context))
1266 (last-char (save-excursion
1267 (goto-char (org-element-property :end object))
1269 (if (looking-at " ")
1272 (if (-contains? '("ref" "eqref" "pageref" "nameref")
1273 (org-element-property :type object))
1274 ;; we are on a link, so replace it.
1277 (org-element-property :begin object)
1278 (org-element-property :end object))
1280 (replace-regexp-in-string
1281 (org-element-property :path object)
1283 (org-element-property :raw-link object))
1285 ;; insert a new link
1290 ;; one prefix, alternate ref link
1291 ((equal helm-current-prefix-arg '(4))
1294 (helm :sources '((name . "Ref link types")
1295 (candidates . ("ref" "eqref" "pageref" "nameref"))
1296 (action . (lambda (x) x))))
1298 ;; two prefixes, insert section custom-id link
1299 ((equal helm-current-prefix-arg '(16))
1301 (format "[[#%s]]" label)))
1307 : org-ref-helm-insert-ref-link
1311 This refers to the page of a label in LaTeX.
1313 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1317 "on clicking goto the label. Navigate back with C-c &"
1318 (org-mark-ring-push)
1319 ;; next search from beginning of the buffer
1325 (goto-char (point-min))
1326 (re-search-forward (format "label:%s\\b" label) nil t))
1330 (goto-char (point-min))
1331 (re-search-forward (format "\\label{%s}" label) nil t))
1333 ;; #+label: name org-definition
1335 (goto-char (point-min))
1336 (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
1340 (goto-char (point-min))
1341 (re-search-forward (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t))
1343 ;; Commented out because these ref links do not actually translate correctly in LaTeX.
1344 ;; you need [[#label]] links.
1347 ; (goto-char (point-min))
1348 ; (re-search-forward (format ":CUSTOM_ID:\s-*\\(%s\\)" label) nil t))
1350 ;; we did not find anything, so go back to where we came
1351 (org-mark-ring-goto)
1352 (error "%s not found" label))
1353 (message "go back with (org-mark-ring-goto) `C-c &`"))
1355 (lambda (keyword desc format)
1357 ((eq format 'html) (format "(<pageref>%s</pageref>)" path))
1359 (format "\\pageref{%s}" keyword)))))
1362 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1363 (defun org-pageref-complete-link (&optional arg)
1364 "Completion function for ref links"
1366 (setq label (completing-read "label: " (org-ref-get-labels)))
1367 (format "ref:%s" label)))
1370 Alternatively, you may want to just call a function that inserts a link with completion:
1372 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1373 (defun org-pageref-insert-ref-link ()
1375 (insert (org-pageref-complete-link)))
1380 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.
1382 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1386 "on clicking goto the label. Navigate back with C-c &"
1387 (org-mark-ring-push)
1388 ;; next search from beginning of the buffer
1394 (goto-char (point-min))
1395 (re-search-forward (format "\\label{%s}" label) nil t))
1397 ;; we did not find anything, so go back to where we came
1398 (org-mark-ring-goto)
1399 (error "%s not found" label))
1400 (message "go back with (org-mark-ring-goto) `C-c &`"))
1402 (lambda (keyword desc format)
1404 ((eq format 'html) (format "(<nameref>%s</nameref>)" path))
1406 (format "\\nameref{%s}" keyword)))))
1410 This is just the LaTeX ref for equations. On export, the reference is enclosed in parentheses.
1412 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1416 "on clicking goto the label. Navigate back with C-c &"
1417 (org-mark-ring-push)
1418 ;; next search from beginning of the buffer
1420 (goto-char (point-min))
1423 ;; search forward for the first match
1425 (re-search-forward (format "label:%s" label) nil t)
1427 (re-search-forward (format "\\label{%s}" label) nil t)
1428 ;; #+label: name org-definition
1429 (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
1430 (org-mark-ring-goto)
1431 (error "%s not found" label))
1432 (message "go back with (org-mark-ring-goto) `C-c &`"))
1434 (lambda (keyword desc format)
1436 ((eq format 'html) (format "(<eqref>%s</eqref>)" path))
1438 (format "\\eqref{%s}" keyword)))))
1442 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.
1444 *** Implementing the click actions of cite
1446 **** Getting the key we clicked on
1447 The first thing we need is to get the bibtex key we clicked on.
1449 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1450 (defun org-ref-get-bibtex-key-under-cursor ()
1451 "returns key under the bibtex cursor. We search forward from
1452 point to get a comma, or the end of the link, and then backwards
1453 to get a comma, or the beginning of the link. that delimits the
1454 keyword we clicked on. We also strip the text properties."
1456 (let* ((object (org-element-context))
1457 (link-string (org-element-property :path object)))
1458 ;; you may click on the part before the citations. here we make
1459 ;; sure to move to the beginning so you get the first citation.
1461 (goto-char (org-element-property :begin object))
1462 (search-forward link-string (org-element-property :end object))
1463 (goto-char (match-beginning 0))
1464 ;; check if we clicked before the path and move as needed.
1465 (unless (< cp (point))
1468 (if (not (org-element-property :contents-begin object))
1469 ;; this means no description in the link
1471 ;; we need the link path start and end
1473 (goto-char (org-element-property :begin object))
1474 (search-forward link-string nil nil 1)
1475 (setq link-string-beginning (match-beginning 0))
1476 (setq link-string-end (match-end 0)))
1478 ;; The key is the text between commas, or the link boundaries
1480 (if (search-forward "," link-string-end t 1)
1481 (setq key-end (- (match-end 0) 1)) ; we found a match
1482 (setq key-end link-string-end))) ; no comma found so take the end
1483 ;; and backward to previous comma from point which defines the start character
1485 (if (search-backward "," link-string-beginning 1 1)
1486 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
1487 (setq key-beginning link-string-beginning))) ; no match found
1488 ;; save the key we clicked on.
1489 (setq bibtex-key (org-ref-strip-string (buffer-substring key-beginning key-end)))
1490 (set-text-properties 0 (length bibtex-key) nil bibtex-key)
1492 ;; link with description. assume only one key
1496 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.
1498 **** Getting the bibliographies
1499 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1500 (defun org-ref-find-bibliography ()
1501 "find the bibliography in the buffer.
1502 This function sets and returns cite-bibliography-files, which is a list of files
1503 either from bibliography:f1.bib,f2.bib
1504 \bibliography{f1,f2}
1505 internal bibliographies
1507 falling back to what the user has set in org-ref-default-bibliography
1512 (goto-char (point-min))
1513 ;; look for a bibliography link
1514 (when (re-search-forward "\\<bibliography:\\([^\]\|\n]+\\)" nil t)
1515 (setq org-ref-bibliography-files
1516 (mapcar 'org-ref-strip-string (split-string (match-string 1) ",")))
1517 (throw 'result org-ref-bibliography-files))
1520 ;; we did not find a bibliography link. now look for \bibliography
1521 (goto-char (point-min))
1522 (when (re-search-forward "\\\\bibliography{\\([^}]+\\)}" nil t)
1523 ;; split, and add .bib to each file
1524 (setq org-ref-bibliography-files
1525 (mapcar (lambda (x) (concat x ".bib"))
1526 (mapcar 'org-ref-strip-string
1527 (split-string (match-string 1) ","))))
1528 (throw 'result org-ref-bibliography-files))
1530 ;; no bibliography found. maybe we need a biblatex addbibresource
1531 (goto-char (point-min))
1532 ;; look for a bibliography link
1533 (when (re-search-forward "addbibresource:\\([^\]\|\n]+\\)" nil t)
1534 (setq org-ref-bibliography-files
1535 (mapcar 'org-ref-strip-string (split-string (match-string 1) ",")))
1536 (throw 'result org-ref-bibliography-files))
1538 ;; we did not find anything. use defaults
1539 (setq org-ref-bibliography-files org-ref-default-bibliography)))
1541 ;; set reftex-default-bibliography so we can search
1542 (set (make-local-variable 'reftex-default-bibliography) org-ref-bibliography-files)
1543 org-ref-bibliography-files)
1546 **** Finding the bibliography file a key is in
1547 Now, we can see if an entry is in a file.
1549 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1550 (defun org-ref-key-in-file-p (key filename)
1551 "determine if the key is in the file"
1552 (interactive "skey: \nsFile: ")
1553 (save-current-buffer
1554 (let ((bibtex-files (list filename)))
1555 (bibtex-search-entry key t))))
1558 Finally, we want to know which file the key is in.
1560 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1561 (defun org-ref-get-bibtex-key-and-file (&optional key)
1562 "returns the bibtex key and file that it is in. If no key is provided, get one under point"
1564 (let ((org-ref-bibliography-files (org-ref-find-bibliography))
1567 (setq key (org-ref-get-bibtex-key-under-cursor)))
1568 (setq file (catch 'result
1569 (loop for file in org-ref-bibliography-files do
1570 (if (org-ref-key-in-file-p key (file-truename file))
1571 (throw 'result file)))))
1575 **** convenience functions to act on citation at point
1577 :ID: af0b2a82-a7c9-4c08-9dac-09f93abc4a92
1579 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.
1581 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1582 (defun org-ref-open-pdf-at-point ()
1583 "open the pdf for bibtex key under point if it exists"
1585 (let* ((results (org-ref-get-bibtex-key-and-file))
1587 (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key)))
1588 (if (file-exists-p pdf-file)
1589 (org-open-file pdf-file)
1590 (message "no pdf found for %s" key))))
1593 (defun org-ref-open-url-at-point ()
1594 "open the url for bibtex key under point."
1596 (let* ((results (org-ref-get-bibtex-key-and-file))
1598 (bibfile (cdr results)))
1601 (insert-file-contents bibfile)
1602 (bibtex-search-entry key)
1603 ;; I like this better than bibtex-url which does not always find
1606 (let ((url (bibtex-autokey-get-field "url")))
1611 (let ((doi (bibtex-autokey-get-field "doi")))
1613 (if (string-match "^http" doi)
1615 (browse-url (format "http://dx.doi.org/%s" doi)))
1616 (throw 'done nil))))))))
1619 (defun org-ref-open-notes-at-point ()
1620 "open the notes for bibtex key under point."
1622 (let* ((results (org-ref-get-bibtex-key-and-file))
1624 (bibfile (cdr results)))
1627 (insert-file-contents bibfile)
1628 (bibtex-search-entry key)
1629 (org-ref-open-bibtex-notes)))))
1632 (defun org-ref-citation-at-point ()
1633 "give message of current citation at point"
1635 (let* ((cb (current-buffer))
1636 (results (org-ref-get-bibtex-key-and-file))
1638 (bibfile (cdr results)))
1639 (message "%s" (progn
1641 (insert-file-contents bibfile)
1642 (bibtex-search-entry key)
1643 (org-ref-bib-citation))))))
1646 (defun org-ref-open-citation-at-point ()
1647 "open bibtex file to key at point"
1649 (let* ((cb (current-buffer))
1650 (results (org-ref-get-bibtex-key-and-file))
1652 (bibfile (cdr results)))
1654 (bibtex-search-entry key)))
1657 **** the actual minibuffer menu
1658 Now, we create the menu. This is a rewrite of the cite action. This makes the function extendable by users.
1660 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1661 (defvar org-ref-cite-menu-funcs '()
1662 "Functions to run on cite click menu. Each entry is a list of (key menu-name function).
1663 The function must take no arguments and work on the key at point. Do not modify this variable, it is set to empty in the menu click function, and functions are conditionally added to it.")
1666 (defvar org-ref-user-cite-menu-funcs
1667 '(("C" "rossref" org-ref-crossref-at-point)
1668 ("y" "Copy entry to file" org-ref-copy-entry-at-point-to-file)
1669 ("s" "Copy summary" org-ref-copy-entry-as-summary))
1670 "user-defined functions to run on bibtex key at point.")
1673 (defun org-ref-copy-entry-as-summary ()
1674 "Copy the bibtex entry for the citation at point as a summary."
1676 (save-window-excursion
1677 (org-ref-open-citation-at-point)
1678 (kill-new (org-ref-bib-citation))))
1681 (defun org-ref-copy-entry-at-point-to-file ()
1682 "Copy the bibtex entry for the citation at point to NEW-FILE.
1683 Prompt for NEW-FILE includes bib files in org-ref-default-bibliography, and bib files in current working directory. You can also specify a new file."
1685 (let ((new-file (ido-completing-read
1687 (append org-ref-default-bibliography
1688 (f-entries "." (lambda (f) (f-ext? f "bib"))))))
1689 (key (org-ref-get-bibtex-key-under-cursor)))
1690 (save-window-excursion
1691 (org-ref-open-citation-at-point)
1692 (bibtex-copy-entry-as-kill))
1694 (let ((bibtex-files (list (file-truename new-file))))
1695 (if (assoc key (bibtex-global-key-alist))
1696 (message "That key already exists in %s" new-file)
1698 (save-window-excursion
1699 (find-file new-file)
1700 (goto-char (point-max))
1701 ;; make sure we are at the beginning of a line.
1702 (unless (looking-at "^") (insert "\n\n"))
1707 (defun org-ref-get-doi-at-point ()
1708 "Get doi for key at point."
1710 (let* ((results (org-ref-get-bibtex-key-and-file))
1712 (bibfile (cdr results))
1716 (insert-file-contents bibfile)
1717 (bibtex-search-entry key)
1718 (setq doi (bibtex-autokey-get-field "doi"))
1719 ;; in case doi is a url, remove the url part.
1720 (replace-regexp-in-string "^http://dx.doi.org/" "" doi)))))
1723 ;; functions that operate on key at point for click menu
1724 (defun org-ref-wos-at-point ()
1725 "open the doi in wos for bibtex key under point."
1727 (doi-utils-wos (org-ref-get-doi-at-point)))
1730 (defun org-ref-wos-citing-at-point ()
1731 "open the doi in wos citing articles for bibtex key under point."
1733 (doi-utils-wos-citing (org-ref-get-doi-at-point)))
1736 (defun org-ref-wos-related-at-point ()
1737 "open the doi in wos related articles for bibtex key under point."
1739 (doi-utils-wos-related (org-ref-get-doi-at-point)))
1742 (defun org-ref-google-scholar-at-point ()
1743 "open the doi in google scholar for bibtex key under point."
1745 (doi-utils-google-scholar (org-ref-get-doi-at-point)))
1748 (defun org-ref-pubmed-at-point ()
1749 "open the doi in pubmed for bibtex key under point."
1751 (doi-utils-pubmed (org-ref-get-doi-at-point)))
1754 (defun org-ref-crossref-at-point ()
1755 "open the doi in crossref for bibtex key under point."
1757 (doi-utils-crossref (org-ref-get-doi-at-point)))
1760 (defun org-ref-cite-onclick-minibuffer-menu (&optional link-string)
1761 "action when a cite link is clicked on.
1762 Provides a menu of context sensitive actions. If the bibtex entry has a pdf, you get an option to open it. If there is a doi, you get a lot of options."
1764 (let* ((results (org-ref-get-bibtex-key-and-file))
1766 (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key))
1767 (bibfile (cdr results))
1768 (url (save-excursion
1770 (insert-file-contents bibfile)
1771 (bibtex-search-entry key)
1772 (bibtex-autokey-get-field "url"))))
1773 (doi (save-excursion
1775 (insert-file-contents bibfile)
1776 (bibtex-search-entry key)
1777 ;; I like this better than bibtex-url which does not always find
1779 (bibtex-autokey-get-field "doi")))))
1781 (when (string= "" doi) (setq doi nil))
1782 (when (string= "" url) (setq url nil))
1783 (setq org-ref-cite-menu-funcs '())
1789 'org-ref-cite-menu-funcs
1790 '("o" "pen" org-ref-open-citation-at-point)))
1793 (when (file-exists-p pdf-file)
1795 'org-ref-cite-menu-funcs
1796 `("p" "df" ,org-ref-open-pdf-function) t))
1800 'org-ref-cite-menu-funcs
1801 '("n" "otes" org-ref-open-notes-at-point) t)
1806 'org-ref-cite-menu-funcs
1807 '("u" "rl" org-ref-open-url-at-point) t))
1812 'org-ref-cite-menu-funcs
1813 '("w" "os" org-ref-wos-at-point) t)
1816 'org-ref-cite-menu-funcs
1817 '("c" "iting" org-ref-wos-citing-at-point) t)
1820 'org-ref-cite-menu-funcs
1821 '("r" "elated" org-ref-wos-related-at-point) t)
1824 'org-ref-cite-menu-funcs
1825 '("g" "oogle scholar" org-ref-google-scholar-at-point) t)
1828 'org-ref-cite-menu-funcs
1829 '("P" "ubmed" org-ref-pubmed-at-point) t))
1831 ;; add user functions
1832 (dolist (tup org-ref-user-cite-menu-funcs)
1834 'org-ref-cite-menu-funcs
1839 'org-ref-cite-menu-funcs
1840 '("q" "uit" (lambda ())) t)
1842 ;; now we make a menu
1843 ;; construct menu string as a message
1846 (let* ((results (org-ref-get-bibtex-key-and-file))
1848 (bibfile (cdr results)))
1851 (insert-file-contents bibfile)
1852 (bibtex-search-entry key)
1853 (org-ref-bib-citation))))
1857 (concat "[" (elt tup 0) "]"
1859 org-ref-cite-menu-funcs "")))
1861 (let* ((input (read-char-exclusive))
1863 (char-to-string input) org-ref-cite-menu-funcs)))
1864 ;; now run the function (2nd element in choice)
1873 : org-ref-cite-onclick-minibuffer-menu
1875 *** A function to format a cite link
1877 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.
1879 #+BEGIN_SRC emacs-lisp :tangle no
1880 ;(defun org-ref-cite-link-format (keyword desc format)
1882 ; ((eq format 'html) (mapconcat (lambda (key) (format "<a name=\"#%s\">%s</a>" key key) (org-ref-split-and-strip-string keyword) ",")))
1883 ; ((eq format 'latex)
1884 ; (concat "\\cite" (when desc (format "[%s]" desc)) "{"
1885 ; (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
1889 *** The actual cite link
1890 Finally, we define the cite link. This is deprecated; the links are autogenerated later. This is here for memory.
1892 #+BEGIN_SRC emacs-lisp :tangle no
1895 ; 'org-ref-cite-onclick-minibuffer-menu
1896 ; 'org-ref-cite-link-format)
1899 *** Automatic definition of the cite links
1900 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.
1902 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1903 (defmacro org-ref-make-completion-function (type)
1904 `(defun ,(intern (format "org-%s-complete-link" type)) (&optional arg)
1910 (let ((bibtex-files (org-ref-find-bibliography)))
1911 (bibtex-global-key-alist))))))
1914 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.
1916 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1917 (defmacro org-ref-make-format-function (type)
1918 `(defun ,(intern (format "org-ref-format-%s" type)) (keyword desc format)
1923 (format "[[#%s][%s]]" key key))
1924 (org-ref-split-and-strip-string keyword) ","))
1931 (org-ref-split-and-strip-string keyword) ",") "]"))
1936 (format "<a href=\"#%s\">%s</a>" key key))
1937 (org-ref-split-and-strip-string keyword) ","))
1940 (if (string= (substring type -1) "s")
1941 ;; biblatex format for multicite commands, which all end in s. These are formated as \cites{key1}{key2}...
1942 (concat "\\" ,type (mapconcat (lambda (key) (format "{%s}" key))
1943 (org-ref-split-and-strip-string keyword) ""))
1945 (concat "\\" ,type (when desc (org-ref-format-citation-description desc)) "{"
1946 (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
1952 We create the links by mapping the function onto the list of defined link types.
1954 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1955 (defun org-ref-format-citation-description (desc)
1956 "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 ::."
1959 ((string-match "::" desc)
1960 (format "[%s][%s]" (car (setq results (split-string desc "::"))) (cadr results)))
1961 (t (format "[%s]" desc))))
1963 (defun org-ref-define-citation-link (type &optional key)
1964 "add a citation link for org-ref. With optional key, set the reftex binding. For example:
1965 (org-ref-define-citation-link \"citez\" ?z) will create a new citez link, with reftex key of z,
1966 and the completion function."
1967 (interactive "sCitation Type: \ncKey: ")
1969 ;; create the formatting function
1970 (eval `(org-ref-make-format-function ,type))
1975 org-ref-cite-onclick-function
1976 (quote ,(intern (format "org-ref-format-%s" type)))))
1978 ;; create the completion function
1979 (eval `(org-ref-make-completion-function ,type))
1981 ;; store new type so it works with adding citations, which checks
1982 ;; for existence in this list
1983 (add-to-list 'org-ref-cite-types type)
1985 ;; and finally if a key is specified, we modify the reftex menu
1987 (setf (nth 2 (assoc 'org reftex-cite-format-builtin))
1988 (append (nth 2 (assoc 'org reftex-cite-format-builtin))
1989 `((,key . ,(concat type ":%l")))))))
1991 ;; create all the link types and their completion functions
1992 (mapcar 'org-ref-define-citation-link org-ref-cite-types)
1995 *** org-ref-insert-cite-link
1996 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.
1998 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1999 (defun org-ref-insert-cite-link (alternative-cite)
2000 "Insert a default citation link using reftex. If you are on a link, it
2001 appends to the end of the link, otherwise, a new link is
2002 inserted. Use a prefix arg to get a menu of citation types."
2004 (org-ref-find-bibliography)
2005 (let* ((object (org-element-context))
2006 (link-string-beginning (org-element-property :begin object))
2007 (link-string-end (org-element-property :end object))
2008 (path (org-element-property :path object)))
2010 (if (not alternative-cite)
2013 ;; case where we are in a link
2014 ((and (equal (org-element-type object) 'link)
2015 (-contains? org-ref-cite-types (org-element-property :type object)))
2016 (goto-char link-string-end)
2017 ;; sometimes there are spaces at the end of the link
2018 ;; this code moves point pack until no spaces are there
2019 (while (looking-back " ") (backward-char))
2020 (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
2022 ;; We are next to a link, and we want to append
2025 (and (equal (org-element-type (org-element-context)) 'link)
2026 (-contains? org-ref-cite-types (org-element-property :type (org-element-context)))))
2027 (while (looking-back " ") (backward-char))
2028 (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
2030 ;; insert fresh link
2033 (concat org-ref-default-citation-link
2035 (mapconcat 'identity (reftex-citation t) ",")))))
2037 ;; you pressed a C-u so we run this code
2041 cite:zhou-2004-first-lda-u,paier-2006-errat,boes-2015-estim-bulk
2045 : org-ref-insert-cite-link
2047 *** Completion in cite links
2048 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.
2050 #+BEGIN_SRC emacs-lisp :tangle no
2051 (defun org-cite-complete-link (&optional arg)
2052 "Completion function for cite links"
2054 org-ref-default-citation-link
2057 (let ((bibtex-files (org-ref-find-bibliography)))
2058 (bibtex-global-key-alist)))))
2061 Alternatively, you may shortcut the org-machinery with this command. You will be prompted for a citation type, and then offered key completion.
2063 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2064 (defun org-ref-insert-cite-with-completion (type)
2065 "Insert a cite link with completion"
2066 (interactive (list (ido-completing-read "Type: " org-ref-cite-types)))
2067 (insert (funcall (intern (format "org-%s-complete-link" type)))))
2070 ** Storing links to a bibtex entry
2071 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.
2073 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2074 (defun org-ref-store-bibtex-entry-link ()
2075 "Save a citation link to the current bibtex entry. Saves in the default link type."
2077 (let ((link (concat org-ref-default-citation-link
2080 (bibtex-beginning-of-entry)
2081 (reftex-get-bib-field "=key=" (bibtex-parse-entry))))))
2082 (message "saved %s" link)
2083 (push (list link) org-stored-links)
2084 (car org-stored-links)))
2088 org-ref minimally supports index entries. To make an index in a file, you should put in the LaTeX header these lines
2091 #+LATEX_HEADER: \usepackage{makeidx}
2092 #+LATEX_HEADER: \makeindex
2095 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.
2098 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.
2103 [[index:hello!Sam@\textsl{Sam}]]
2104 [[index:Lin@\textbf{Lin}]]
2105 [[index:Joe|textit]]
2106 [[index:Lin@\textbf{Lin}]]
2107 [[index:Peter|see {hello}]]
2108 [[index:Jen|seealso{Jenny}]]
2110 index:encodings!input!cp850
2112 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2118 (lambda (path desc format)
2121 (format "\\index{%s}" path)))))
2123 ;; this will generate a temporary index of entries in the file.
2127 (let ((*index-links* '())
2128 (*initial-letters* '()))
2131 (org-element-map (org-element-parse-buffer) 'link
2133 (let ((type (nth 0 link))
2134 (plist (nth 1 link)))
2136 (when (equal (plist-get plist ':type) "index")
2139 (cons (plist-get plist :path)
2141 "[[elisp:(progn (switch-to-buffer \"%s\") (goto-char %s))][%s]]"
2143 (plist-get plist :begin) ;; position of link
2144 ;; grab a description
2146 (goto-char (plist-get plist :begin))
2147 (if (thing-at-point 'sentence)
2149 (replace-regexp-in-string
2150 "\n" "" (thing-at-point 'sentence))
2151 ;; or call it a link
2155 (setq *index-links* (cl-sort *index-links* 'string-lessp :key 'car))
2157 ;; now first letters
2158 (dolist (link *index-links*)
2159 (add-to-list '*initial-letters* (substring (car link) 0 1) t))
2161 ;; now create the index
2162 (switch-to-buffer (get-buffer-create "*index*"))
2165 (insert "#+TITLE: Index\n\n")
2166 (dolist (letter *initial-letters*)
2167 (insert (format "* %s\n" (upcase letter)))
2168 ;; now process the links
2171 (string= letter (substring (car (car *index-links*)) 0 1)))
2172 (let ((link (pop *index-links*)))
2173 (insert (format "%s %s\n\n" (car link) (cdr link))))))
2174 (switch-to-buffer "*index*")))
2176 (lambda (path desc format)
2179 (format "\\printindex")))))
2183 | 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*)) |
2184 | lambda | (path desc format) | (cond ((eq format (quote latex)) (format \printindex))) |
2187 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.
2189 #+LATEX_HEADER: \usepackage{glossaries}
2190 #+LATEX_HEADER: \makeglossaries
2192 And at the end of the document put \makeglossaries.
2194 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2197 nil ;; no follow action
2198 (lambda (path desc format)
2201 (format "\\newglossaryentry{%s}{%s}" path desc)))))
2207 nil ;; no follow action
2208 (lambda (path desc format)
2211 (format "\\gls{%s}" path)))))
2216 nil ;; no follow action
2217 (lambda (path desc format)
2220 (format "\\glspl{%s}" path)))))
2225 nil ;; no follow action
2226 (lambda (path desc format)
2229 (format "\\Gls{%s}" path)))))
2234 nil ;; no follow action
2235 (lambda (path desc format)
2238 (format "\\Glspl{%s}" path)))))
2242 ** create simple text citation from bibtex entry
2244 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2245 (defun org-ref-bib-citation ()
2246 "From a bibtex entry, create and return a simple citation string.
2247 This assumes you are in an article."
2249 (bibtex-beginning-of-entry)
2250 (let* ((cb (current-buffer))
2251 (bibtex-expand-strings t)
2252 (entry (loop for (key . value) in (bibtex-parse-entry t)
2253 collect (cons (downcase key) value)))
2254 (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2255 (year (reftex-get-bib-field "year" entry))
2256 (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2257 (key (reftex-get-bib-field "=key=" entry))
2258 (journal (reftex-get-bib-field "journal" entry))
2259 (volume (reftex-get-bib-field "volume" entry))
2260 (pages (reftex-get-bib-field "pages" entry))
2261 (doi (reftex-get-bib-field "doi" entry))
2262 (url (reftex-get-bib-field "url" entry))
2264 ;;authors, "title", Journal, vol(iss):pages (year).
2265 (format "%s, \"%s\", %s, %s:%s (%s)"
2266 author title journal volume pages year)))
2270 : org-ref-bib-citation
2273 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2274 (defun org-ref-bib-html-citation ()
2275 "from a bibtex entry, create and return a simple citation with html links."
2277 (bibtex-beginning-of-entry)
2278 (let* ((cb (current-buffer))
2279 (bibtex-expand-strings t)
2280 (entry (loop for (key . value) in (bibtex-parse-entry t)
2281 collect (cons (downcase key) value)))
2282 (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2283 (year (reftex-get-bib-field "year" entry))
2284 (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2285 (key (reftex-get-bib-field "=key=" entry))
2286 (journal (reftex-get-bib-field "journal" entry))
2287 (volume (reftex-get-bib-field "volume" entry))
2288 (pages (reftex-get-bib-field "pages" entry))
2289 (doi (reftex-get-bib-field "doi" entry))
2290 (url (reftex-get-bib-field "url" entry))
2292 ;;authors, "title", Journal, vol(iss):pages (year).
2293 (concat (format "%s, \"%s\", %s, %s:%s (%s)."
2294 author title journal volume pages year)
2295 (when url (format " <a href=\"%s\">link</a>" url))
2296 (when doi (format " <a href=\"http://dx.doi.org/%s\">doi</a>" doi)))
2300 ** open pdf from bibtex
2301 We bind this to a key here: [[*key%20bindings%20for%20utilities][key bindings for utilities]].
2302 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2303 (defun org-ref-open-bibtex-pdf ()
2304 "open pdf for a bibtex entry, if it exists. assumes point is in
2305 the entry of interest in the bibfile. but does not check that."
2308 (bibtex-beginning-of-entry)
2309 (let* ((bibtex-expand-strings t)
2310 (entry (bibtex-parse-entry t))
2311 (key (reftex-get-bib-field "=key=" entry))
2312 (pdf (format (concat org-ref-pdf-directory "%s.pdf") key)))
2314 (if (file-exists-p pdf)
2315 (org-open-link-from-string (format "[[file:%s]]" pdf))
2319 ** open notes from bibtex
2320 We bind this to a key here [[*key%20bindings%20for%20utilities][key bindings for utilities]].
2322 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2323 (defun org-ref-open-bibtex-notes ()
2324 "from a bibtex entry, open the notes if they exist, and create a heading if they do not.
2326 I never did figure out how to use reftex to make this happen
2327 non-interactively. the reftex-format-citation function did not
2328 work perfectly; there were carriage returns in the strings, and
2329 it did not put the key where it needed to be. so, below I replace
2330 the carriage returns and extra spaces with a single space and
2331 construct the heading by hand."
2334 (bibtex-beginning-of-entry)
2335 (let* ((cb (current-buffer))
2336 (bibtex-expand-strings t)
2337 (entry (loop for (key . value) in (bibtex-parse-entry t)
2338 collect (cons (downcase key) value)))
2339 (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2340 (year (reftex-get-bib-field "year" entry))
2341 (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2342 (key (reftex-get-bib-field "=key=" entry))
2343 (journal (reftex-get-bib-field "journal" entry))
2344 (volume (reftex-get-bib-field "volume" entry))
2345 (pages (reftex-get-bib-field "pages" entry))
2346 (doi (reftex-get-bib-field "doi" entry))
2347 (url (reftex-get-bib-field "url" entry))
2350 ;; save key to clipboard to make saving pdf later easier by pasting.
2353 (kill-ring-save (point-min) (point-max)))
2355 ;; now look for entry in the notes file
2356 (if org-ref-bibliography-notes
2357 (find-file-other-window org-ref-bibliography-notes)
2358 (error "org-ref-bib-bibliography-notes is not set to anything"))
2360 (goto-char (point-min))
2361 ;; put new entry in notes if we don't find it.
2362 (if (re-search-forward (format ":Custom_ID: %s$" key) nil 'end)
2363 (funcall org-ref-open-notes-function)
2364 ;; no entry found, so add one
2365 (insert (format "\n** TODO %s - %s" year title))
2377 [[cite:%s]] [[file:%s/%s.pdf][pdf]]\n\n"
2378 key author journal year volume pages doi url key org-ref-pdf-directory key))
2382 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2383 (defun org-ref-open-notes-from-reftex ()
2384 "Call reftex, and open notes for selected entry."
2386 (let ((bibtex-key )))
2388 ;; now look for entry in the notes file
2389 (if org-ref-bibliography-notes
2390 (find-file-other-window org-ref-bibliography-notes)
2391 (error "org-ref-bib-bibliography-notes is not set to anything"))
2393 (goto-char (point-min))
2395 (re-search-forward (format
2397 (first (reftex-citation t)) nil 'end))
2398 (funcall org-ref-open-notes-function))
2401 ** open url in browser from bibtex
2403 We bind this to a key here [[*key%20bindings%20for%20utilities][key bindings for utilities]].
2405 + 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.
2407 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2408 (defun org-ref-open-in-browser ()
2409 "Open the bibtex entry at point in a browser using the url field or doi field"
2412 (bibtex-beginning-of-entry)
2414 (let ((url (bibtex-autokey-get-field "url")))
2419 (let ((doi (bibtex-autokey-get-field "doi")))
2421 (if (string-match "^http" doi)
2423 (browse-url (format "http://dx.doi.org/%s" doi)))
2425 (message "No url or doi found"))))
2429 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.
2431 *** function to upload bibtex to citeulike
2433 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2434 (defun org-ref-upload-bibtex-entry-to-citeulike ()
2435 "with point in a bibtex entry get bibtex string and submit to citeulike.
2437 Relies on the python script /upload_bibtex_citeulike.py being in the user directory."
2439 (message "uploading to citeulike")
2441 (bibtex-narrow-to-entry)
2442 (let ((startpos (point-min))
2443 (endpos (point-max))
2444 (bibtex-string (buffer-string))
2445 (script (concat "python " starter-kit-dir "/upload_bibtex_citeulike.py&")))
2446 (with-temp-buffer (insert bibtex-string)
2447 (shell-command-on-region (point-min) (point-max) script t nil nil t)))))
2450 *** The upload script
2451 Here is the python script for uploading.
2453 *************** TODO document how to get the cookies
2457 #+BEGIN_SRC python :tangle upload_bibtex_citeulike.py
2459 import pickle, requests, sys
2462 with open('c:/Users/jkitchin/Dropbox/blogofile-jkitchin.github.com/_blog/cookies.pckl', 'rb') as f:
2463 cookies = pickle.load(f)
2465 url = 'http://www.citeulike.org/profile/jkitchin/import_do'
2467 bibtex = sys.stdin.read()
2469 data = {'pasted':bibtex,
2471 'tag_parsing':'simple',
2472 'strip_brackets':'no',
2473 'update_id':'bib-key',
2474 'btn_bibtex':'Import BibTeX file ...'}
2476 headers = {'content-type': 'multipart/form-data',
2477 'User-Agent':'jkitchin/johnrkitchin@gmail.com bibtexupload'}
2479 r = requests.post(url, headers=headers, data=data, cookies=cookies, files={})
2483 ** Build a pdf from a bibtex file
2484 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.
2486 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2487 (defun org-ref-build-full-bibliography ()
2488 "build pdf of all bibtex entries, and open it."
2490 (let* ((bibfile (file-name-nondirectory (buffer-file-name)))
2491 (bib-base (file-name-sans-extension bibfile))
2492 (texfile (concat bib-base ".tex"))
2493 (pdffile (concat bib-base ".pdf")))
2496 (insert (format "\\documentclass[12pt]{article}
2497 \\usepackage[version=3]{mhchem}
2499 \\usepackage[numbers]{natbib}
2500 \\usepackage[colorlinks=true, linkcolor=blue, urlcolor=blue, pdfstartview=FitH]{hyperref}
2504 \\bibliographystyle{unsrtnat}
2506 \\end{document}" bib-base))
2508 (shell-command (concat "pdflatex " bib-base))
2509 (shell-command (concat "bibtex " bib-base))
2510 (shell-command (concat "pdflatex " bib-base))
2511 (shell-command (concat "pdflatex " bib-base))
2512 (kill-buffer texfile)
2513 (org-open-file pdffile)
2517 ** Extract bibtex entries cited in an org-file
2518 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.
2520 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2521 (defun org-ref-extract-bibtex-entries ()
2522 "extract the bibtex entries referred to by cite links in the current buffer into a src block at the bottom of the current buffer.
2524 If no bibliography is in the buffer the `reftex-default-bibliography' is used."
2526 (let* ((temporary-file-directory (file-name-directory (buffer-file-name)))
2527 (tempname (make-temp-file "extract-bib"))
2528 (contents (buffer-string))
2529 (cb (current-buffer))
2530 basename texfile bibfile results)
2532 ;; open tempfile and insert org-buffer contents
2533 (find-file tempname)
2535 (setq basename (file-name-sans-extension
2536 (file-name-nondirectory buffer-file-name))
2537 texfile (concat tempname ".tex")
2538 bibfile (concat tempname ".bib"))
2540 ;; see if we have a bibliography, and insert the default one if not.
2542 (goto-char (point-min))
2543 (unless (re-search-forward "^bibliography:" (point-max) 'end)
2544 (insert (format "\nbibliography:%s"
2545 (mapconcat 'identity reftex-default-bibliography ",")))))
2548 ;; get a latex file and extract the references
2549 (org-latex-export-to-latex)
2552 (reftex-create-bibtex-file bibfile)
2554 ;; save results of the references
2555 (setq results (buffer-string))
2557 ;; kill buffers. these are named by basename, not full path
2558 (kill-buffer (concat basename ".bib"))
2559 (kill-buffer (concat basename ".tex"))
2560 (kill-buffer basename)
2562 (delete-file bibfile)
2563 (delete-file texfile)
2564 (delete-file tempname)
2566 ;; Now back to the original org buffer and insert the results
2567 (switch-to-buffer cb)
2568 (when (not (string= "" results))
2570 (goto-char (point-max))
2572 (org-insert-heading)
2573 (insert (format " Bibtex entries
2575 ,#+BEGIN_SRC text :tangle %s
2577 ,#+END_SRC" (concat (file-name-sans-extension (file-name-nondirectory (buffer-file-name))) ".bib") results))))))
2580 ** Find bad cite links
2582 :ID: 8515E800-EDA0-4B2A-85FD-55B6FF849203
2584 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.
2586 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2589 (defun index (substring list)
2590 "return the index of string in a list of strings"
2593 (dolist (arg list i)
2594 (if (string-match (concat "^" substring "$") arg)
2599 ;; return counter if found, otherwise return nil
2603 (defun org-ref-find-bad-citations ()
2604 "Create a list of citation keys in an org-file that do not have a bibtex entry in the known bibtex files.
2606 Makes a new buffer with clickable links."
2608 ;; generate the list of bibtex-keys and cited keys
2609 (let* ((bibtex-files (org-ref-find-bibliography))
2610 (bibtex-file-path (mapconcat (lambda (x) (file-name-directory (file-truename x))) bibtex-files ":"))
2611 (bibtex-keys (mapcar (lambda (x) (car x)) (bibtex-global-key-alist)))
2612 (bad-citations '()))
2614 (org-element-map (org-element-parse-buffer) 'link
2616 (let ((plist (nth 1 link)))
2617 (when (equal (plist-get plist ':type) "cite")
2618 (dolist (key (org-ref-split-and-strip-string (plist-get plist ':path)) )
2619 (when (not (index key bibtex-keys))
2620 (setq bad-citations (append bad-citations
2621 `(,(format "%s [[elisp:(progn (switch-to-buffer-other-frame \"%s\")(goto-char %s))][not found here]]\n"
2622 key (buffer-name)(plist-get plist ':begin)))))
2627 (switch-to-buffer-other-window "*Missing citations*")
2630 (insert "* List of bad cite links\n")
2631 (insert (mapconcat 'identity bad-citations ""))
2632 ;(setq buffer-read-only t)
2633 (use-local-map (copy-keymap org-mode-map))
2634 (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))
2636 (when (get-buffer "*Missing citations*")
2637 (kill-buffer "*Missing citations*"))
2638 (message "No bad cite links found"))))
2641 ** helm interface to org-ref
2642 In [[id:8515E800-EDA0-4B2A-85FD-55B6FF849203][Find bad cite links]] we wrote a function that finds bad links and creates a buffer of links to them.
2644 Here we develop a similar idea, but instead of an org-buffer with links, we create helm sources for bad cite links, bad ref links, and multiple labels.
2646 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2647 (defun org-ref-bad-cite-candidates ()
2648 "Returns a list of conses (key . marker) where key does not exist in the known bibliography files, and marker points to the key."
2649 (let* ((cp (point)) ; save to return to later
2650 (bibtex-files (org-ref-find-bibliography))
2651 (bibtex-file-path (mapconcat
2653 (file-name-directory (file-truename x)))
2655 (bibtex-keys (mapcar (lambda (x) (car x))
2656 (bibtex-global-key-alist)))
2657 (bad-citations '()))
2659 (org-element-map (org-element-parse-buffer) 'link
2661 (let ((plist (nth 1 link)))
2662 (when (-contains? org-ref-cite-types (plist-get plist ':type))
2663 (dolist (key (org-ref-split-and-strip-string (plist-get plist ':path)) )
2664 (when (not (index key bibtex-keys))
2665 (goto-char (plist-get plist ':begin))
2666 (re-search-forward key)
2667 (push (cons key (point-marker)) bad-citations)))
2672 ;; It seems I forgot I already defined this earlier!
2673 ;; (defun org-ref-get-labels ()
2674 ;; "Returns a list of known labels in the org document. These include label links, latex labels, label tags, and table names. The list contains all labels, not just unique ones.
2676 ;; (let ((cp (point))
2678 ;; (goto-char (point-min))
2679 ;; (while (re-search-forward "[^#+]label:\\(.*\\)\\s-" nil t)
2680 ;; (push (match-string 1) labels))
2682 ;; (goto-char (point-min))
2683 ;; (while (re-search-forward "\\label{\\(.*\\)}\\s-?" nil t)
2684 ;; (push (match-string 1) labels))
2686 ;; (goto-char (point-min))
2687 ;; (while (re-search-forward "^#\\+label:\\s-*\\(.*\\)" nil t)
2688 ;; (push (match-string 1) labels))
2690 ;; (goto-char (point-min))
2691 ;; (while (re-search-forward "^#\\+tblname:\\s-*\\(.*\\)" nil t)
2692 ;; (push (match-string 1) labels))
2693 ;; ;; check for CUSTOM_ID
2696 ;; (when (org-entry-get (point) "CUSTOM_ID")
2697 ;; (push (org-entry-get (point) "CUSTOM_ID") labels))))
2698 ;; ;; return to original place
2703 (defun org-ref-bad-ref-candidates ()
2704 "Returns a list of conses (ref . marker) where ref is a ref link that does not point to anything (i.e. a label)."
2705 ;; first get a list of legitimate labels
2707 (labels (org-ref-get-labels))
2709 ;; now loop over ref links
2710 (goto-char (point-min))
2711 (org-element-map (org-element-parse-buffer) 'link
2713 (let ((plist (nth 1 link)))
2714 (when (or (equal (plist-get plist ':type) "ref")
2715 (equal (plist-get plist ':type) "eqref")
2716 (equal (plist-get plist ':type) "pageref")
2717 (equal (plist-get plist ':type) "nameref"))
2718 (unless (-contains? labels (plist-get plist :path))
2719 (goto-char (plist-get plist :begin))
2722 (cons (plist-get plist :path)
2723 (point-marker))))))))
2728 (defun org-ref-bad-label-candidates ()
2729 "Return a list of labels where label is multiply defined."
2730 (let ((labels (org-ref-get-labels))
2731 (multiple-labels '()))
2732 (when (not (= (length labels)
2733 (length (-uniq labels))))
2734 (dolist (label labels)
2735 (when (> (-count (lambda (a)
2738 ;; this is a multiply defined label.
2740 (goto-char (point-min))
2741 (while (re-search-forward
2742 (format "[^#+]label:%s\\s-" label) nil t)
2743 (push (cons label (point-marker)) multiple-labels))
2745 (goto-char (point-min))
2746 (while (re-search-forward
2747 (format "\\label{%s}\\s-?" label) nil t)
2748 (push (cons label (point-marker)) multiple-labels))
2750 (goto-char (point-min))
2751 (while (re-search-forward
2752 (format "^#\\+label:\\s-*%s" label) nil t)
2753 (push (cons label (point-marker)) multiple-labels))
2755 (goto-char (point-min))
2756 (while (re-search-forward
2757 (format "^#\\+tblname:\\s-*%s" label) nil t)
2758 (push (cons label (point-marker)) multiple-labels))
2764 : org-ref-bad-label-candidates
2766 Now, we have a functions for candidates, we can make helm sources for each one, and then run a helm command to view them.
2768 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2770 "Opens a helm interface to actions for org-ref.
2771 Shows bad citations, ref links and labels"
2773 (let ((cb (current-buffer))
2774 (bad-citations (org-ref-bad-cite-candidates))
2775 (bad-refs (org-ref-bad-ref-candidates))
2776 (bad-labels (org-ref-bad-label-candidates)))
2778 (helm :sources `(((name . "Bad citations")
2779 (candidates . ,bad-citations)
2780 (action . (lambda (marker)
2781 (switch-to-buffer (marker-buffer marker))
2782 (goto-char marker))))
2784 ((name . "Bad Labels")
2785 (candidates . ,bad-labels)
2786 (action . (lambda (marker)
2787 (switch-to-buffer (marker-buffer marker))
2788 (goto-char marker))))
2790 ((name . "Bad ref links")
2791 (candidates . ,bad-refs)
2792 (action . (lambda (marker)
2793 (switch-to-buffer (marker-buffer marker))
2794 (goto-char marker))))
2796 ((name . "Utilities")
2797 (candidates . (("Check buffer again" . org-ref)
2798 ("Insert citation" . helm-bibtex)
2799 ("Insert label link" . org-ref-helm-insert-label-link)
2800 ("Insert ref link" . org-ref-helm-insert-ref-link)
2801 ("List of figures" . org-ref-list-of-figures)
2802 ("List of tables" . org-ref-list-of-tables)
2803 ("Table of contents" . nil)
2805 (action . (lambda (x)
2806 (switch-to-buffer ,cb)
2809 ((name . "Export functions")
2810 (candidates . (("Extract cited entries" . org-ref-extract-bibtex-entries)
2811 ("Export to html and open" . (lambda () (org-open-file (org-html-export-to-html))))
2812 ("Export to pdf and open" . (lambda ()
2813 (org-open-file (org-latex-export-to-pdf))))
2814 ("Export to manuscript pdf and open" . ox-manuscript-export-and-build-and-open)
2815 ("Export submission manuscript pdf and open" . ox-manuscript-build-submission-manuscript-and-open)
2818 (action . (lambda (x)
2819 (switch-to-buffer ,cb)
2825 ** Finding non-ascii characters
2826 I like my bibtex files to be 100% ascii. This function finds the non-ascii characters so you can replace them.
2828 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2829 (defun org-ref-find-non-ascii-characters ()
2830 "finds non-ascii characters in the buffer. Useful for cleaning up bibtex files"
2832 (occur "[^[:ascii:]]"))
2835 ** Resort a bibtex entry
2836 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.
2838 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2839 (defun org-ref-sort-bibtex-entry ()
2840 "sort fields of entry in standard order and downcase them"
2842 (bibtex-beginning-of-entry)
2843 (let* ((master '("author" "title" "journal" "volume" "number" "pages" "year" "doi" "url"))
2844 (entry (bibtex-parse-entry))
2847 (type (cdr (assoc "=type=" entry)))
2848 (key (cdr (assoc "=key=" entry))))
2850 ;; these are the fields we want to order that are in this entry
2851 (setq entry-fields (mapcar (lambda (x) (car x)) entry))
2852 ;; we do not want to reenter these fields
2853 (setq entry-fields (remove "=key=" entry-fields))
2854 (setq entry-fields (remove "=type=" entry-fields))
2856 ;;these are the other fields in the entry
2857 (setq other-fields (remove-if-not (lambda(x) (not (member x master))) entry-fields))
2860 ;; right now we only resort articles
2861 ((string= (downcase type) "article")
2864 (concat "@article{" key ",\n"
2867 (when (member field entry-fields)
2868 (format "%s = %s," (downcase field) (cdr (assoc field entry))))) master "\n")
2871 (format "%s = %s," (downcase field) (cdr (assoc field entry)))) other-fields "\n")
2873 (bibtex-find-entry key)
2875 (bibtex-clean-entry)
2879 ** Clean a bibtex entry
2880 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.
2881 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.
2882 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2883 (defun org-ref-clean-bibtex-entry(&optional keep-key)
2884 "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"
2886 (bibtex-beginning-of-entry)
2888 ;; some entries do not have a key or comma in first line. We check and add it, if needed.
2889 (unless (string-match ",$" (thing-at-point 'line))
2893 ;; check for empty pages, and put eid or article id in its place
2894 (let ((entry (bibtex-parse-entry))
2895 (pages (bibtex-autokey-get-field "pages"))
2896 (year (bibtex-autokey-get-field "year"))
2897 (doi (bibtex-autokey-get-field "doi"))
2898 ;; The Journal of Chemical Physics uses eid
2899 (eid (bibtex-autokey-get-field "eid")))
2901 ;; replace http://dx.doi.org/ in doi. some journals put that in,
2902 ;; but we only want the doi.
2903 (when (string-match "^http://dx.doi.org/" doi)
2904 (bibtex-beginning-of-entry)
2905 (goto-char (car (cdr (bibtex-search-forward-field "doi" t))))
2907 (bibtex-make-field "doi")
2909 (insert (replace-regexp-in-string "^http://dx.doi.org/" "" doi)))
2911 ;; asap articles often set year to 0, which messes up key
2912 ;; generation. fix that.
2913 (when (string= "0" year)
2914 (bibtex-beginning-of-entry)
2915 (goto-char (car (cdr (bibtex-search-forward-field "year" t))))
2917 (bibtex-make-field "year")
2919 (insert (read-string "Enter year: ")))
2921 ;; fix pages if they are empty if there is an eid to put there.
2922 (when (string= "-" pages)
2924 (bibtex-beginning-of-entry)
2925 ;; this seems like a clunky way to set the pages field.But I
2926 ;; cannot find a better way.
2927 (goto-char (car (cdr (bibtex-search-forward-field "pages" t))))
2929 (bibtex-make-field "pages")
2933 ;; replace naked & with \&
2935 (bibtex-narrow-to-entry)
2936 (bibtex-beginning-of-entry)
2937 (message "checking &")
2938 (replace-regexp " & " " \\\\& ")
2941 ;; generate a key, and if it duplicates an existing key, edit it.
2943 (let ((key (bibtex-generate-autokey)))
2945 ;; first we delete the existing key
2946 (bibtex-beginning-of-entry)
2947 (re-search-forward bibtex-entry-maybe-empty-head)
2948 (if (match-beginning bibtex-key-in-head)
2949 (delete-region (match-beginning bibtex-key-in-head)
2950 (match-end bibtex-key-in-head)))
2951 ;; check if the key is in the buffer
2952 (when (save-excursion
2953 (bibtex-search-entry key))
2955 (bibtex-search-entry key)
2956 (bibtex-copy-entry-as-kill)
2957 (switch-to-buffer-other-window "*duplicate entry*")
2959 (setq key (bibtex-read-key "Duplicate Key found, edit: " key)))
2962 (kill-new key))) ;; save key for pasting
2964 ;; run hooks. each of these operates on the entry with no arguments.
2965 ;; this did not work like i thought, it gives a symbolp error.
2966 ;; (run-hooks org-ref-clean-bibtex-entry-hook)
2971 org-ref-clean-bibtex-entry-hook)
2973 ;; sort fields within entry
2974 (org-ref-sort-bibtex-entry)
2975 ;; check for non-ascii characters
2976 (occur "[^[:ascii:]]")
2981 : org-ref-clean-bibtex-entry
2983 ** Sort the entries in a citation link by year
2984 I prefer citations in chronological order within a grouping. These functions sort the link under the cursor by year.
2986 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2987 (defun org-ref-get-citation-year (key)
2988 "get the year of an entry with key. Returns year as a string."
2990 (let* ((results (org-ref-get-bibtex-key-and-file key))
2991 (bibfile (cdr results)))
2993 (insert-file-contents bibfile)
2994 (bibtex-search-entry key nil 0)
2995 (prog1 (reftex-get-bib-field "year" (bibtex-parse-entry t))
2998 (defun org-ref-sort-citation-link ()
2999 "replace link at point with sorted link by year"
3001 (let* ((object (org-element-context))
3002 (type (org-element-property :type object))
3003 (begin (org-element-property :begin object))
3004 (end (org-element-property :end object))
3005 (link-string (org-element-property :path object))
3007 (setq keys (org-ref-split-and-strip-string link-string))
3008 (setq years (mapcar 'org-ref-get-citation-year keys))
3009 (setq data (mapcar* (lambda (a b) `(,a . ,b)) years keys))
3010 (setq data (cl-sort data (lambda (x y) (< (string-to-int (car x)) (string-to-int (car y))))))
3011 ;; now get the keys separated by commas
3012 (setq keys (mapconcat (lambda (x) (cdr x)) data ","))
3013 ;; and replace the link with the sorted keys
3014 (cl--set-buffer-substring begin end (concat type ":" keys))))
3017 ** Sort entries in citation links with shift-arrow keys
3018 Sometimes it may be helpful to manually change the order of citations. These functions define shift-arrow functions.
3019 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3020 (defun org-ref-swap-keys (i j keys)
3021 "swap the keys in a list with index i and j"
3022 (let ((tempi (nth i keys)))
3023 (setf (nth i keys) (nth j keys))
3024 (setf (nth j keys) tempi))
3027 (defun org-ref-swap-citation-link (direction)
3028 "move citation at point in direction +1 is to the right, -1 to the left"
3030 (let* ((object (org-element-context))
3031 (type (org-element-property :type object))
3032 (begin (org-element-property :begin object))
3033 (end (org-element-property :end object))
3034 (link-string (org-element-property :path object))
3036 ;; We only want this to work on citation links
3037 (when (-contains? org-ref-cite-types type)
3038 (setq key (org-ref-get-bibtex-key-under-cursor))
3039 (setq keys (org-ref-split-and-strip-string link-string))
3040 (setq i (index key keys)) ;; defined in org-ref
3041 (if (> direction 0) ;; shift right
3042 (org-ref-swap-keys i (+ i 1) keys)
3043 (org-ref-swap-keys i (- i 1) keys))
3044 (setq keys (mapconcat 'identity keys ","))
3045 ;; and replace the link with the sorted keys
3046 (cl--set-buffer-substring begin end (concat type ":" keys " "))
3047 ;; now go forward to key so we can move with the key
3048 (re-search-forward key)
3049 (goto-char (match-beginning 0)))))
3051 ;; add hooks to make it work
3052 (add-hook 'org-shiftright-hook (lambda () (org-ref-swap-citation-link 1)))
3053 (add-hook 'org-shiftleft-hook (lambda () (org-ref-swap-citation-link -1)))
3056 ** Lightweight messages about links
3057 To get a lighter weight message about the label, ref and cite links, we define a function that gives us the minibuffer message, without the menu. We run this in an idle timer.
3059 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3060 (defun org-ref-get-label-context (label)
3061 "Return a string of context around a label."
3064 (goto-char (point-min))
3065 (when (re-search-forward
3066 (format "label:%s\\b" label) nil t)
3067 (throw 'result (buffer-substring
3076 (goto-char (point-min))
3077 (when (re-search-forward
3078 (format "\\label{%s}" label) nil t)
3079 (throw 'result (buffer-substring
3088 (goto-char (point-min))
3089 (when (re-search-forward
3090 (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t)
3091 (throw 'result (buffer-substring
3100 (goto-char (point-min))
3101 (when (re-search-forward
3102 (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t)
3103 (throw 'result (buffer-substring
3111 (throw 'result "!!! NO CONTEXT FOUND !!!"))))
3114 (defun org-ref-link-message ()
3115 "Print a minibuffer message about the link that point is on."
3117 (when (eq major-mode 'org-mode)
3118 (let* ((object (org-element-context))
3119 (type (org-element-property :type object)))
3123 ((-contains? org-ref-cite-types type)
3124 (message (org-ref-get-citation-string-at-point)))
3126 ;; message some context about the label we are referring to
3127 ((string= type "ref")
3128 (message "%scount: %s"
3129 (org-ref-get-label-context
3130 (org-element-property :path object))
3131 (org-ref-count-labels
3132 (org-element-property :path object))))
3134 ((string= type "eqref")
3135 (message "%scount: %s"
3136 (org-ref-get-label-context
3137 (org-element-property :path object))
3138 (org-ref-count-labels
3139 (org-element-property :path object))))
3141 ;; message the count
3142 ((string= type "label")
3143 (let ((count (org-ref-count-labels
3144 (org-element-property :path object))))
3145 ;; get plurality on occurrence correct
3147 (number-to-string count)
3149 (when (or (= count 0)
3153 ((string= type "custom-id")
3155 (org-open-link-from-string
3156 (format "[[#%s]]" (org-element-property :path object)))
3157 (message "%s" (org-get-heading))))
3159 ;; check if the bibliography files exist.
3160 ((string= type "bibliography")
3162 ;; object is the link you clicked on
3163 (object (org-element-context))
3164 (link-string (org-element-property :path object))
3165 (link-string-beginning)
3168 (goto-char (org-element-property :begin object))
3169 (search-forward link-string nil nil 1)
3170 (setq link-string-beginning (match-beginning 0))
3171 (setq link-string-end (match-end 0)))
3173 ;; make sure we are in link and not before the :
3174 (when (> link-string-beginning (point))
3175 (goto-char link-string-beginning))
3177 ;; now if we have comma separated bibliographies
3178 ;; we find the one clicked on. we want to
3179 ;; search forward to next comma from point
3181 (if (search-forward "," link-string-end 1 1)
3182 (setq key-end (- (match-end 0) 1)) ; we found a match
3183 (setq key-end (point)))) ; no comma found so take the point
3185 ;; and backward to previous comma from point
3187 (if (search-backward "," link-string-beginning 1 1)
3188 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
3189 (setq key-beginning (point)))) ; no match found
3190 ;; save the key we clicked on.
3192 (org-ref-strip-string
3193 (buffer-substring key-beginning key-end)))
3194 (if (file-exists-p bibfile)
3195 (message "%s exists." bibfile)
3196 (message "!!! %s NOT FOUND !!!" bibfile))))
3201 I like convenience. Here are some aliases for faster typing.
3203 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3204 (defalias 'oro 'org-ref-open-citation-at-point)
3205 (defalias 'orc 'org-ref-citation-at-point)
3206 (defalias 'orp 'org-ref-open-pdf-at-point)
3207 (defalias 'oru 'org-ref-open-url-at-point)
3208 (defalias 'orn 'org-ref-open-notes-at-point)
3209 (defalias 'ornr 'org-ref-open-notes-from-reftex)
3211 (defalias 'orib 'org-ref-insert-bibliography-link)
3212 (defalias 'oric 'org-ref-insert-cite-link)
3213 (defalias 'orir 'org-ref-insert-ref-link)
3214 (defalias 'orsl 'org-ref-store-bibtex-entry-link)
3216 (defalias 'orcb 'org-ref-clean-bibtex-entry)
3219 [[https://github.com/tmalsburg/helm-bibtex][helm-bibtex]] is a very cool interface to bibtex files. Out of the box though, it is not super convenient for org-ref. Here, we modify it to make it fit our workflow and extend it where needed.
3221 1. Make the default action to insert selected keys.
3222 2. Make open entry second action
3223 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3224 (setq helm-source-bibtex
3225 '((name . "BibTeX entries")
3226 (init . helm-bibtex-init)
3227 (candidates . helm-bibtex-candidates)
3228 (filtered-candidate-transformer . helm-bibtex-candidates-formatter)
3229 (action . (("Insert citation" . helm-bibtex-insert-citation)
3230 ("Show entry" . helm-bibtex-show-entry)
3231 ("Open PDF file (if present)" . helm-bibtex-open-pdf)
3232 ("Open URL or DOI in browser" . helm-bibtex-open-url-or-doi)
3233 ("Insert reference" . helm-bibtex-insert-reference)
3234 ("Insert BibTeX key" . helm-bibtex-insert-key)
3235 ("Insert BibTeX entry" . helm-bibtex-insert-bibtex)
3236 ("Attach PDF to email" . helm-bibtex-add-PDF-attachment)
3237 ("Edit notes" . helm-bibtex-edit-notes)
3241 Now, let us define a function that inserts the cite links:
3242 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3243 (defun helm-bibtex-format-org-ref (keys)
3244 "Insert selected KEYS as cite link. Append KEYS if you are on a link.
3245 Technically, this function should return a string that is inserted by helm. This function does the insertion and gives helm an empty string to insert. This lets us handle appending to a link properly.
3247 In the helm-bibtex buffer, C-u will give you a helm menu to select a new link type for the selected entries.
3249 C-u C-u will change the key at point to the selected keys.
3251 (let* ((object (org-element-context))
3252 (last-char (save-excursion
3253 (goto-char (org-element-property :end object))
3255 (if (looking-at " ")
3259 ;; case where we are in a link
3260 ((and (equal (org-element-type object) 'link)
3263 (org-element-property :type object)))
3265 ;; no prefix. append keys
3266 ((equal helm-current-prefix-arg nil)
3267 (goto-char (org-element-property :end object))
3268 (while (looking-back " ") (backward-char))
3269 (insert (concat "," (mapconcat 'identity keys ","))))
3270 ;; double prefix, replace key at point
3271 ((equal helm-current-prefix-arg '(16))
3272 (setf (buffer-substring
3273 (org-element-property :begin object)
3274 (org-element-property :end object))
3276 (replace-regexp-in-string
3277 (car (org-ref-get-bibtex-key-and-file)) ; key
3278 (mapconcat 'identity keys ",") ; new keys
3279 (org-element-property :raw-link object))
3280 ;; replace space at end to avoid collapsing into next word.
3282 ;; and we want to go to the end of the new link
3284 (org-element-property :end (org-element-context))))
3286 (message "Not found"))))
3288 ;; We are next to a link, and we want to append
3289 ;; next to a link means one character back is on a link.
3292 (and (equal (org-element-type (org-element-context)) 'link)
3295 (org-element-property :type (org-element-context)))))
3296 (while (looking-back " ") (backward-char))
3297 (insert (concat "," (mapconcat 'identity keys ","))))
3299 ;; insert fresh link
3301 ;;(message-box "fresh link")
3303 (concat (if (equal helm-current-prefix-arg '(4))
3304 (helm :sources `((name . "link types")
3305 (candidates . ,org-ref-cite-types)
3306 (action . (lambda (x) x))))
3307 org-ref-default-citation-link)
3309 (s-join "," keys))))))
3310 ;; return empty string for helm
3313 (setq helm-bibtex-format-citation-functions
3314 '((org-mode . helm-bibtex-format-org-ref)))
3316 (defun org-ref-helm-insert-cite-link (arg)
3317 "org-ref function to use helm-bibtex to insert a citation link.
3318 With one prefix arg, insert a ref link.
3319 With two prefix args, insert a label link."
3323 (let ((helm-bibtex-bibliography (org-ref-find-bibliography)))
3326 (org-ref-helm-insert-ref-link))
3328 (org-ref-helm-insert-label-link))))
3330 (require 'helm-bibtex)
3332 ;; add our own fallback entries where we want them. These appear in reverse order of adding in the menu
3333 (setq helm-bibtex-fallback-options
3334 (-insert-at 1 '("Crossref" . "http://search.crossref.org/?q=%s") helm-bibtex-fallback-options))
3336 (setq helm-bibtex-fallback-options
3339 '("Scopus" . "http://www.scopus.com/scopus/search/submit/xadvanced.url?searchfield=TITLE-ABS-KEY(%s)")
3340 helm-bibtex-fallback-options))
3342 (setq helm-bibtex-fallback-options
3343 (-insert-at 1 '("Open Web of Science" . (lambda () (browse-url "http://apps.webofknowledge.com")))
3344 helm-bibtex-fallback-options))
3347 ** A helm click menu
3348 This code provides a helm interface to things you can do when you click on a citation link. This is an alternative to the minibuffer menu.
3349 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3350 (defun org-ref-get-citation-string-at-point ()
3351 "Get a string of a formatted citation"
3353 (let* ((results (org-ref-get-bibtex-key-and-file))
3355 (bibfile (cdr results)))
3359 (insert-file-contents bibfile)
3360 (bibtex-search-entry key)
3361 (org-ref-bib-citation)))
3362 "!!! No entry found !!!" )))
3364 (defun org-ref-cite-candidates ()
3365 "Generate the list of possible candidates for click actions on a cite link.
3366 Checks for pdf and doi, and add appropriate functions."
3368 (let* ((results (org-ref-get-bibtex-key-and-file))
3370 (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key))
3371 (bibfile (cdr results))
3372 (url (save-excursion
3374 (insert-file-contents bibfile)
3375 (bibtex-search-entry key)
3376 (bibtex-autokey-get-field "url"))))
3377 (doi (save-excursion
3379 (insert-file-contents bibfile)
3380 (bibtex-search-entry key)
3381 ;; I like this better than bibtex-url which does not always find
3383 (bibtex-autokey-get-field "doi"))))
3384 (candidates `(("Quit" . org-ref-citation-at-point)
3385 ("Open bibtex entry" . org-ref-open-citation-at-point))))
3386 ;; for some reason, when there is no doi or url, they are returned as "". I
3387 ;; prefer nil so we correct this here.
3388 (when (string= doi "") (setq doi nil))
3389 (when (string= url "") (setq url nil))
3391 ;; Conditional pdf functions
3392 (if (file-exists-p pdf-file)
3395 '("Open pdf" . org-ref-open-pdf-at-point)
3399 '("Try to get pdf" . (lambda ()
3400 (save-window-excursion
3401 (org-ref-open-citation-at-point)
3402 (bibtex-beginning-of-entry)
3403 (doi-utils-get-bibtex-entry-pdf))))
3409 '("Open notes" . org-ref-open-notes-at-point)
3412 ;; conditional url and doi functions
3416 '("Open in browser" . org-ref-open-url-at-point)
3421 (add-to-list 'candidates x t))
3422 `(("WOS" . org-ref-wos-at-point)
3423 ("Related articles in WOS" . org-ref-wos-related-at-point)
3424 ("Citing articles in WOS" . org-ref-wos-citing-at-point)
3425 ("Google Scholar" . org-ref-google-scholar-at-point)
3426 ("Pubmed" . org-ref-pubmed-at-point)
3427 ("Crossref" . org-ref-crossref-at-point)
3432 '("Copy formatted citation to clipboard" . org-ref-copy-entry-as-summary)
3437 '("Copy key to clipboard" . (lambda ()
3439 (car (org-ref-get-bibtex-key-and-file)))))
3444 '("Copy bibtex entry to file" . org-ref-copy-entry-at-point-to-file)
3449 '("Email bibtex entry and pdf" . (lambda ()
3451 (org-ref-open-citation-at-point)
3452 (email-bibtex-entry))))
3454 ;; finally return a numbered list of the candidates
3456 for cell in candidates
3457 collect (cons (format "%2s. %s" i (car cell))
3461 (defvar org-ref-helm-user-candidates '()
3462 "List of user-defined candidates to act when clicking on a cite link.
3463 This is a list of cons cells '((\"description\" . action)). The action function should not take an argument, and should assume point is on the cite key of interest.
3466 ;; example of adding your own function
3468 'org-ref-helm-user-candidates
3469 '("Example" . (lambda () (message-box "You did it!")))
3472 (defun org-ref-cite-click-helm (key)
3474 1. get name and candidates before entering helm because we need the org-buffer.
3475 2. switch back to the org buffer before evaluating the action. most of them need the point and buffer."
3477 (let ((name (org-ref-get-citation-string-at-point))
3478 (candidates (org-ref-cite-candidates))
3479 (cb (current-buffer)))
3481 (helm :sources `(((name . ,name)
3482 (candidates . ,candidates)
3483 (action . (lambda (f)
3484 (switch-to-buffer cb)
3486 ((name . "User functions")
3487 (candidates . ,org-ref-helm-user-candidates)
3488 (action . (lambda (f)
3489 (switch-to-buffer cb)
3495 : org-ref-cite-click-helm
3498 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3503 This code will tangle the elisp code out to org-ref.el and load it.
3505 [[elisp:(progn (org-babel-tangle) (load-file "org-ref.el"))]]
3507 Alternatively you may use:
3509 [[elisp:(org-babel-load-file "org-ref.org")]]