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
16 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
17 ;;; org-ref.el --- setup bibliography, cite, ref and label org-mode links.
19 ;; Copyright(C) 2014 John Kitchin
21 ;; Author: John Kitchin <jkitchin@andrew.cmu.edu>
22 ;; This file is not currently part of GNU Emacs.
24 ;; This program is free software; you can redistribute it and/or
25 ;; modify it under the terms of the GNU General Public License as
26 ;; published by the Free Software Foundation; either version 2, or (at
27 ;; your option) any later version.
29 ;; This program is distributed in the hope that it will be useful, but
30 ;; WITHOUT ANY WARRANTY; without even the implied warranty of
31 ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
32 ;; General Public License for more details.
34 ;; You should have received a copy of the GNU General Public License
35 ;; along with this program ; see the file COPYING. If not, write to
36 ;; the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
37 ;; Boston, MA 02111-1307, USA.
41 ;; Lisp code to setup bibliography cite, ref and label org-mode links. also
42 ;; sets up reftex and helm for org-mode citations. The links are clickable and
43 ;; do things that are useful. You should really read org-ref.org for details.
45 ;; Package-Requires: ((dash) (helm) (helm-bibtex))
49 The only external require is reftex-cite
51 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
52 (require 'reftex-cite)
55 (require 'helm-bibtex)
59 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.
61 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
63 "customization group for org-ref")
65 (defcustom org-ref-bibliography-notes
67 "filename to where you will put all your notes about an entry in
68 the default bibliography."
72 (defcustom org-ref-default-bibliography
74 "list of bibtex files to search for. You should use full-paths for each file."
75 :type '(repeat :tag "List of bibtex files" file)
78 (defcustom org-ref-pdf-directory
80 "directory where pdfs are stored by key. put a trailing / in"
84 (defcustom org-ref-default-citation-link
86 "The default type of citation link to use"
90 (defcustom org-ref-insert-cite-key
92 "Keyboard shortcut to insert a citation."
96 (defcustom org-ref-bibliography-entry-format
97 '(("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>.")
99 ("book" . "%a, %t, %u (%y).")
101 ("proceedings" . "%e, %t in %S, %u (%y).")
103 ("inproceedings" . "%a, %t, %p, in %b, edited by %e, %u (%y)"))
105 "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."
109 (defcustom org-ref-open-notes-function
115 ;;(org-tree-to-indirect-buffer)
116 (outline-previous-visible-heading 1)
117 (recenter-top-bottom 0))
118 "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"
123 (defcustom org-ref-open-pdf-function
124 'org-ref-open-pdf-at-point
125 "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'."
130 (defcustom org-ref-insert-cite-function
131 'org-ref-helm-insert-cite-link
132 "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."
137 (defcustom org-ref-cite-onclick-function
138 'org-ref-cite-click-helm
139 "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."
143 (defcustom org-ref-show-citation-on-enter t
144 "If non-nil add a hook function to show the citation summary in
145 the minibuffer just by putting the cursor in a link"
150 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.
152 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
153 (defcustom org-ref-cite-types
154 '("cite" "nocite" ;; the default latex cite commands
155 ;; natbib cite commands, http://ctan.unixbrain.com/macros/latex/contrib/natbib/natnotes.pdf
156 "citet" "citet*" "citep" "citep*"
157 "citealt" "citealt*" "citealp" "citealp*"
159 "citeauthor" "citeauthor*"
160 "citeyear" "citeyear*"
161 "Citet" "Citep" "Citealt" "Citealp" "Citeauthor"
163 ;; http://ctan.mirrorcatalogs.com/macros/latex/contrib/biblatex/doc/biblatex.pdf
165 "parencite" "Parencite"
166 "footcite" "footcitetext"
167 "textcite" "Textcite"
168 "smartcite" "Smartcite"
169 "cite*" "parencite*" "supercite"
170 "autocite" "Autocite" "autocite*" "Autocite*"
172 "citetitle" "citetitle*"
173 "citedate" "citedate*"
175 "fullcite" "footfullcite"
176 ;; "volcite" "Volcite" cannot support the syntax
177 "notecite" "Notecite"
178 "pnotecite" "Pnotecite"
180 ;; multicites. Very limited support for these.
181 "cites" "Cites" "parencites" "Parencites"
182 "footcites" "footcitetexts"
183 "smartcites" "Smartcites" "textcites" "Textcites"
184 "supercites" "autocites" "Autocites"
185 ;; for the bibentry package
188 "List of citation types known in org-ref"
189 :type '(repeat :tag "List of citation types" string)
193 We need a hook variable to store user-defined bibtex entry cleaning functions
194 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
195 (defcustom org-ref-clean-bibtex-entry-hook nil
196 "Hook that is run in org-ref-clean-bibtex-entry. The functions should take no arguments, and operate on the bibtex entry at point."
202 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
203 (defvar org-ref-bibliography-files
205 "variable to hold bibliography files to be searched")
208 ** org-mode / reftex setup
210 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.
212 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
214 (defun org-mode-reftex-setup ()
215 (and (buffer-file-name)
216 (file-exists-p (buffer-file-name))
217 (global-auto-revert-mode t)
218 ;; I do not remember why I put this next line in. It doesn't
219 ;; work for org-files. Nothing very bad happens, but it gives
220 ;; an annoying error. Commenting it out for now.
223 (make-local-variable 'reftex-cite-format)
224 (setq reftex-cite-format 'org))
226 ;; define key for inserting citations
227 (define-key org-mode-map
228 (kbd org-ref-insert-cite-key)
229 org-ref-insert-cite-function)
231 (when org-ref-show-citation-on-enter
232 (setq org-ref-message-timer
233 (run-with-idle-timer 0.5 t 'org-ref-link-message)))
235 (defun org-ref-show-link-messages ()
236 "Turn on link messages. You will see a message in the
237 minibuffer when on a cite, ref or label link."
239 (setq org-ref-message-timer
240 (run-with-idle-timer 0.5 t 'org-ref-link-message))
242 (defun org-ref-cancel-link-messages ()
243 "Stop showing messages in minibuffer when on a link."
245 (cancel-timer org-ref-message-timer))
247 ;; this approach caused the selected region to not be highlighted any more.
248 ; (add-hook 'post-command-hook 'org-ref-link-message))
249 ; (remove-hook 'post-command-hook 'org-ref-link-message))
251 (add-hook 'org-mode-hook 'org-mode-reftex-setup)
253 (eval-after-load 'reftex-vars
255 (add-to-list 'reftex-cite-format-builtin
256 '(org "Org-mode citation"
257 ((?\C-m . "cite:%l") ; default
258 (?d . ",%l") ; for appending
264 (?h . "citeauthor:%l")
265 (?H . "citeauthor*:%l")
272 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.
274 #+BEGIN_SRC emacs-lisp :tangle no
276 (setf (nth 2 (assoc 'org reftex-cite-format-builtin))
277 (append (nth 2 (assoc 'org reftex-cite-format-builtin)) '((?W . "textcite:%l")
278 (?z . "newcite:%l"))))
281 You can define a new citation link like this:
282 #+BEGIN_SRC emacs-lisp :tangle no
283 (org-ref-define-citation-link "citez" ?z)
287 Most of this library is the creation of functional links to help with references and citations.
289 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.
291 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
292 (defun org-ref-strip-string (string)
293 "strip leading and trailing whitespace from the string"
294 (replace-regexp-in-string
295 (concat search-whitespace-regexp "$" ) ""
296 (replace-regexp-in-string
297 (concat "^" search-whitespace-regexp ) "" string)))
300 It is helpful to make the previous function operate on a list of strings here.
302 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
303 (defun org-ref-split-and-strip-string (string)
304 "split key-string and strip keys. Assumes the key-string is comma delimited"
305 (mapcar 'org-ref-strip-string (split-string string ",")))
308 ** bibliography and bibliographystyle
309 *** An html bibliography
311 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.
313 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
314 (defun org-ref-reftex-get-bib-field (field entry &optional format)
315 "similar to reftex-get-bib-field, but removes enclosing braces and quotes"
317 (setq result (reftex-get-bib-field field entry format))
318 (when (and (not (string= result "")) (string= "{" (substring result 0 1)))
319 (setq result (substring result 1 -1)))
320 (when (and (not (string= result "")) (string= "\"" (substring result 0 1)))
321 (setq result (substring result 1 -1)))
324 (defun org-ref-reftex-format-citation (entry format)
325 "return a formatted string for the bibtex entry (from bibtex-parse-entry) according
326 to the format argument. The format is a string with these percent escapes.
328 In the format, the following percent escapes will be expanded.
330 %l The BibTeX label of the citation.
331 %a List of author names, see also `reftex-cite-punctuation'.
332 %2a Like %a, but abbreviate more than 2 authors like Jones et al.
333 %A First author name only.
334 %e Works like %a, but on list of editor names. (%2e and %E work a well)
336 It is also possible to access all other BibTeX database fields:
337 %b booktitle %c chapter %d edition %h howpublished
338 %i institution %j journal %k key %m month
339 %n number %o organization %p pages %P first page
340 %r address %s school %u publisher %t title
342 %B booktitle, abbreviated %T title, abbreviated
347 Usually, only %l is needed. The other stuff is mainly for the echo area
348 display, and for (setq reftex-comment-citations t).
350 %< as a special operator kills punctuation and space around it after the
351 string has been formatted.
353 A pair of square brackets indicates an optional argument, and RefTeX
354 will prompt for the values of these arguments.
356 Beware that all this only works with BibTeX database files. When
357 citations are made from the \bibitems in an explicit thebibliography
358 environment, only %l is available."
359 ;; Format a citation from the info in the BibTeX ENTRY
361 (unless (stringp format) (setq format "\\cite{%l}"))
363 (if (and reftex-comment-citations
364 (string-match "%l" reftex-cite-comment-format))
365 (error "reftex-cite-comment-format contains invalid %%l"))
368 "\\(\\`\\|[^%]\\)\\(\\(%\\([0-9]*\\)\\([a-zA-Z]\\)\\)[.,;: ]*\\)"
370 (let ((n (string-to-number (match-string 4 format)))
371 (l (string-to-char (match-string 5 format)))
377 (org-ref-reftex-get-bib-field "&key" entry)
378 (if reftex-comment-citations
379 reftex-cite-comment-format
381 ((= l ?a) (reftex-format-names
382 (reftex-get-bib-names "author" entry)
384 ((= l ?A) (car (reftex-get-bib-names "author" entry)))
385 ((= l ?b) (org-ref-reftex-get-bib-field "booktitle" entry "in: %s"))
386 ((= l ?B) (reftex-abbreviate-title
387 (org-ref-reftex-get-bib-field "booktitle" entry "in: %s")))
388 ((= l ?c) (org-ref-reftex-get-bib-field "chapter" entry))
389 ((= l ?d) (org-ref-reftex-get-bib-field "edition" entry))
390 ((= l ?D) (org-ref-reftex-get-bib-field "doi" entry))
391 ((= l ?e) (reftex-format-names
392 (reftex-get-bib-names "editor" entry)
394 ((= l ?E) (car (reftex-get-bib-names "editor" entry)))
395 ((= l ?h) (org-ref-reftex-get-bib-field "howpublished" entry))
396 ((= l ?i) (org-ref-reftex-get-bib-field "institution" entry))
397 ((= l ?j) (org-ref-reftex-get-bib-field "journal" entry))
398 ((= l ?k) (org-ref-reftex-get-bib-field "key" entry))
399 ((= l ?m) (org-ref-reftex-get-bib-field "month" entry))
400 ((= l ?n) (org-ref-reftex-get-bib-field "number" entry))
401 ((= l ?o) (org-ref-reftex-get-bib-field "organization" entry))
402 ((= l ?p) (org-ref-reftex-get-bib-field "pages" entry))
403 ((= l ?P) (car (split-string
404 (org-ref-reftex-get-bib-field "pages" entry)
406 ((= l ?s) (org-ref-reftex-get-bib-field "school" entry))
407 ((= l ?S) (org-ref-reftex-get-bib-field "series" entry))
408 ((= l ?u) (org-ref-reftex-get-bib-field "publisher" entry))
409 ((= l ?U) (org-ref-reftex-get-bib-field "url" entry))
410 ((= l ?r) (org-ref-reftex-get-bib-field "address" entry))
411 ;; strip enclosing brackets from title if they are there
412 ((= l ?t) (org-ref-reftex-get-bib-field "title" entry))
413 ((= l ?T) (reftex-abbreviate-title
414 (org-ref-reftex-get-bib-field "title" entry)))
415 ((= l ?v) (org-ref-reftex-get-bib-field "volume" entry))
416 ((= l ?y) (org-ref-reftex-get-bib-field "year" entry)))))
419 (setq b (match-beginning 2) e (match-end 2))
420 (setq b (match-beginning 3) e (match-end 3)))
421 (setq format (concat (substring format 0 b) rpl (substring format e)))))
422 (while (string-match "%%" format)
423 (setq format (replace-match "%" t t format)))
424 (while (string-match "[ ,.;:]*%<" format)
425 (setq format (replace-match "" t t format)))
426 ;; also replace carriage returns, tabs, and multiple whitespaces
427 (setq format (replace-regexp-in-string "\n\\|\t\\|\s+" " " format))
430 (defun org-ref-get-bibtex-entry-citation (key)
431 "returns a string for the bibliography entry corresponding to key, and formatted according to the type in `org-ref-bibliography-entry-format'"
433 (let ((org-ref-bibliography-files (org-ref-find-bibliography))
434 (file) (entry) (bibtex-entry) (entry-type) (format))
436 (setq file (catch 'result
437 (loop for file in org-ref-bibliography-files do
438 (if (org-ref-key-in-file-p key (file-truename file))
440 (message "%s not found in %s" key (file-truename file))))))
443 (insert-file-contents file)
444 (bibtex-search-entry key nil 0)
445 (setq bibtex-entry (bibtex-parse-entry))
446 (setq entry-type (downcase (cdr (assoc "=type=" bibtex-entry))))
447 (setq format (cdr (assoc entry-type org-ref-bibliography-entry-format)))
449 (setq entry (org-ref-reftex-format-citation bibtex-entry format))
451 (bibtex-narrow-to-entry)
452 (setq entry (buffer-string)))))
457 : org-ref-reftex-format-citation
459 Here is how to use the function. You call it with point in an entry in a bibtex file.
461 #+BEGIN_SRC emacs-lisp :tangle no
462 (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>."))
463 (org-ref-get-bibtex-entry-citation "armiento-2014-high"))
466 : 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>.
468 I am not sure why full author names are not used.
470 This code provides some functions to generate a simple sorted bibliography in html. First we get all the keys in the buffer.
472 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
473 (defun org-ref-get-bibtex-keys ()
474 "return a list of unique keys in the buffer."
476 (org-element-map (org-element-parse-buffer) 'link
478 (let ((plist (nth 1 link)))
479 (when (-contains? org-ref-cite-types (plist-get plist ':type))
482 (org-ref-split-and-strip-string (plist-get plist ':path)))
483 (when (not (-contains? keys key))
484 (setq keys (append keys (list key)))))))))
485 ;; Sort keys alphabetically
486 (setq keys (cl-sort keys 'string-lessp :key 'downcase))
490 This function gets the html for one entry.
492 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
493 (defun org-ref-get-bibtex-entry-html (key)
494 "returns an html string for the bibliography entry corresponding to key"
496 (format "<li><a id=\"%s\">[%s] %s</a></li>" key key (org-ref-get-bibtex-entry-citation key)))
499 Now, we map over the whole list of keys, and the whole bibliography, formatted as an unordered list.
501 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
502 (defun org-ref-get-html-bibliography ()
503 "Create an html bibliography when there are keys"
504 (let ((keys (org-ref-get-bibtex-keys)))
506 (concat "<h1>Bibliography</h1>
508 (mapconcat (lambda (x) (org-ref-get-bibtex-entry-html x)) keys "\n")
512 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.
514 *** An org bibliography
515 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.
517 First, we get the string for a single entry.
518 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
519 (defun org-ref-get-bibtex-entry-org (key)
520 "returns an org string for the bibliography entry corresponding to key"
521 (let ((org-ref-bibliography-files (org-ref-find-bibliography))
522 (file) (entry) (bibtex-entry) (entry-type) (format))
524 (setq file (catch 'result
525 (loop for file in org-ref-bibliography-files do
526 (if (org-ref-key-in-file-p key (file-truename file))
528 (message "%s not found in %s" key (file-truename file))))))
531 (insert-file-contents file)
532 (bibtex-search-entry key nil 0)
533 (setq entry (bibtex-parse-entry))
538 " (org-ref-reftex-get-bib-field "author" entry)
539 (org-ref-reftex-get-bib-field "title" entry)
540 (concat " :CUSTOM_ID: " (org-ref-reftex-get-bib-field "=key=" entry) "\n"
541 (mapconcat (lambda (element) (format " :%s: %s"
542 (upcase (car element))
548 Now, we loop over the keys, and combine all the entries into a bibliography.
549 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
550 (defun org-ref-get-org-bibliography ()
551 "Create an org bibliography when there are keys"
552 (let ((keys (org-ref-get-bibtex-keys)))
554 (concat "* Bibliography
556 (mapconcat (lambda (x) (org-ref-get-bibtex-entry-org x)) keys "\n")
560 *** An ascii bibliography
562 This function gets the html for one entry.
564 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
565 (defun org-ref-get-bibtex-entry-ascii (key)
566 "returns an ascii string for the bibliography entry corresponding to key"
568 (format "[%s] %s" key (org-ref-get-bibtex-entry-citation key)))
571 Now, we map over the whole list of keys, and the whole bibliography, formatted as an unordered list.
573 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
574 (defun org-ref-get-ascii-bibliography ()
575 "Create an html bibliography when there are keys"
576 (let ((keys (org-ref-get-bibtex-keys)))
582 (mapconcat (lambda (x) (org-ref-get-bibtex-entry-ascii x)) keys "\n")
588 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.
590 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
591 (org-add-link-type "bibliography"
592 ;; this code is run on clicking. The bibliography
593 ;; may contain multiple files. this code finds the
594 ;; one you clicked on and opens it.
595 (lambda (link-string)
596 ;; get link-string boundaries
597 ;; we have to go to the beginning of the line, and then search forward
600 ;; object is the link you clicked on
601 (object (org-element-context))
602 (link-string-beginning)
606 (goto-char (org-element-property :begin object))
607 (search-forward link-string nil nil 1)
608 (setq link-string-beginning (match-beginning 0))
609 (setq link-string-end (match-end 0)))
611 ;; We set the reftex-default-bibliography
612 ;; here. it should be a local variable only in
613 ;; the current buffer. We need this for using
614 ;; reftex to do citations.
615 (set (make-local-variable 'reftex-default-bibliography)
616 (split-string (org-element-property :path object) ","))
618 ;; now if we have comma separated bibliographies
619 ;; we find the one clicked on. we want to
620 ;; search forward to next comma from point
622 (if (search-forward "," link-string-end 1 1)
623 (setq key-end (- (match-end 0) 1)) ; we found a match
624 (setq key-end (point)))) ; no comma found so take the point
625 ;; and backward to previous comma from point
627 (if (search-backward "," link-string-beginning 1 1)
628 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
629 (setq key-beginning (point)))) ; no match found
630 ;; save the key we clicked on.
631 (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
632 (find-file bibfile))) ; open file on click
635 (lambda (keyword desc format)
637 ((eq format 'org) (org-ref-get-org-bibliography))
638 ((eq format 'ascii) (org-ref-get-ascii-bibliography))
639 ((eq format 'html) (org-ref-get-html-bibliography))
641 ;; write out the latex bibliography command
642 (format "\\bibliography{%s}" (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity
643 (mapcar 'expand-file-name
644 (split-string keyword ","))
649 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.
652 \input{project-description.bbl}
655 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.
657 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
658 (org-add-link-type "nobibliography"
659 ;; this code is run on clicking. The bibliography
660 ;; may contain multiple files. this code finds the
661 ;; one you clicked on and opens it.
662 (lambda (link-string)
663 ;; get link-string boundaries
664 ;; we have to go to the beginning of the line, and then search forward
667 ;; object is the link you clicked on
668 (object (org-element-context))
670 (link-string-beginning)
674 (goto-char (org-element-property :begin object))
675 (search-forward link-string nil nil 1)
676 (setq link-string-beginning (match-beginning 0))
677 (setq link-string-end (match-end 0)))
679 ;; We set the reftex-default-bibliography
680 ;; here. it should be a local variable only in
681 ;; the current buffer. We need this for using
682 ;; reftex to do citations.
683 (set (make-local-variable 'reftex-default-bibliography)
684 (split-string (org-element-property :path object) ","))
686 ;; now if we have comma separated bibliographies
687 ;; we find the one clicked on. we want to
688 ;; search forward to next comma from point
690 (if (search-forward "," link-string-end 1 1)
691 (setq key-end (- (match-end 0) 1)) ; we found a match
692 (setq key-end (point)))) ; no comma found so take the point
693 ;; and backward to previous comma from point
695 (if (search-backward "," link-string-beginning 1 1)
696 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
697 (setq key-beginning (point)))) ; no match found
698 ;; save the key we clicked on.
699 (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
700 (find-file bibfile))) ; open file on click
703 (lambda (keyword desc format)
705 ((eq format 'org) (org-ref-get-org-bibliography))
706 ((eq format 'ascii) (org-ref-get-ascii-bibliography))
707 ((eq format 'html) (org-ref-get-html-bibliography))
709 ;; write out the latex bibliography command
711 ; (format "{\\setbox0\\vbox{\\bibliography{%s}}}"
712 ; (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity
713 ; (mapcar 'expand-file-name
714 ; (split-string keyword ","))
717 (format "\\nobibliography{%s}"
718 (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity
719 (mapcar 'expand-file-name
720 (split-string keyword ","))
726 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
727 (org-add-link-type "printbibliography"
728 (lambda (arg) (message "Nothing implemented for clicking here."))
729 (lambda (keyword desc format)
731 ((eq format 'org) (org-ref-get-org-bibliography))
732 ((eq format 'html) (org-ref-get-html-bibliography))
734 ;; write out the biblatex bibliography command
735 "\\printbibliography"))
739 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, ...
741 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
742 (org-add-link-type "bibliographystyle"
743 (lambda (arg) (message "Nothing implemented for clicking here."))
744 (lambda (keyword desc format)
747 ;; write out the latex bibliography command
748 (format "\\bibliographystyle{%s}" keyword)))))
751 *** Completion for bibliography link
754 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
755 (defun org-bibliography-complete-link (&optional arg)
756 (format "bibliography:%s" (read-file-name "enter file: " nil nil t)))
758 (defun org-ref-insert-bibliography-link ()
759 "insert a bibliography with completion"
761 (insert (org-bibliography-complete-link)))
765 This is apparently used for biblatex.
766 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
767 (org-add-link-type "addbibresource"
768 ;; this code is run on clicking. The addbibresource
769 ;; may contain multiple files. this code finds the
770 ;; one you clicked on and opens it.
771 (lambda (link-string)
772 ;; get link-string boundaries
773 ;; we have to go to the beginning of the line, and then search forward
776 ;; object is the link you clicked on
777 (object (org-element-context))
779 (link-string-beginning)
783 (goto-char (org-element-property :begin object))
784 (search-forward link-string nil nil 1)
785 (setq link-string-beginning (match-beginning 0))
786 (setq link-string-end (match-end 0)))
788 ;; We set the reftex-default-addbibresource
789 ;; here. it should be a local variable only in
790 ;; the current buffer. We need this for using
791 ;; reftex to do citations.
792 (set (make-local-variable 'reftex-default-addbibresource)
793 (split-string (org-element-property :path object) ","))
795 ;; now if we have comma separated bibliographies
796 ;; we find the one clicked on. we want to
797 ;; search forward to next comma from point
799 (if (search-forward "," link-string-end 1 1)
800 (setq key-end (- (match-end 0) 1)) ; we found a match
801 (setq key-end (point)))) ; no comma found so take the point
802 ;; and backward to previous comma from point
804 (if (search-backward "," link-string-beginning 1 1)
805 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
806 (setq key-beginning (point)))) ; no match found
807 ;; save the key we clicked on.
808 (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
809 (find-file bibfile))) ; open file on click
812 (lambda (keyword desc format)
814 ((eq format 'html) (format "")); no output for html
816 ;; write out the latex addbibresource command
817 (format "\\addbibresource{%s}" keyword)))))
822 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.
824 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
825 (defun org-ref-list-of-figures (&optional arg)
826 "Generate buffer with list of figures in them"
828 (save-excursion (widen)
829 (let* ((c-b (buffer-name))
832 (org-element-map (org-element-parse-buffer) 'link
834 "create a link for to the figure"
836 (and (string= (org-element-property :type link) "file")
838 "[^.]*\\.\\(png\\|jpg\\|eps\\|pdf\\)$"
839 (org-element-property :path link)))
842 (let* ((start (org-element-property :begin link))
843 (parent (car (cdr (org-element-property :parent link))))
844 (caption (caaar (plist-get parent :caption)))
845 (name (plist-get parent :name)))
848 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][figure %s: %s]] %s\n"
849 c-b start counter (or name "") caption)
851 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][figure %s: %s]]\n"
852 c-b start counter (or name "")))))))))
853 (switch-to-buffer "*List of Figures*")
854 (setq buffer-read-only nil)
857 (insert (mapconcat 'identity list-of-figures ""))
858 (setq buffer-read-only t)
859 (use-local-map (copy-keymap org-mode-map))
860 (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))))
864 'org-ref-list-of-figures ; on click
865 (lambda (keyword desc format)
868 (format "\\listoffigures")))))
873 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
874 (defun org-ref-list-of-tables (&optional arg)
875 "Generate a buffer with a list of tables"
879 (let* ((c-b (buffer-name))
882 (org-element-map (org-element-parse-buffer 'element) 'table
884 "create a link for to the table"
886 (let ((start (org-element-property :begin table))
887 (name (org-element-property :name table))
888 (caption (caaar (org-element-property :caption table))))
891 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][table %s: %s]] %s\n"
892 c-b start counter (or name "") caption)
894 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][table %s: %s]]\n"
895 c-b start counter (or name ""))))))))
896 (switch-to-buffer "*List of Tables*")
897 (setq buffer-read-only nil)
900 (insert (mapconcat 'identity list-of-tables ""))
901 (setq buffer-read-only t)
902 (use-local-map (copy-keymap org-mode-map))
903 (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))))
907 'org-ref-list-of-tables
908 (lambda (keyword desc format)
911 (format "\\listoftables")))))
915 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.
917 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
918 (defun org-ref-count-labels (label)
919 "Counts number of matches for label in the document"
920 (+ (count-matches (format "label:%s\\b[^-:]" label) (point-min) (point-max) t)
921 ;; for tblname, it is not enough to get word boundary
922 ;; tab-little and tab-little-2 match then.
923 (count-matches (format "^#\\+tblname:\\s-*%s\\b[^-:]" label) (point-min) (point-max) t)
924 (count-matches (format "\\label{%s}\\b" label) (point-min) (point-max) t)
925 ;; this is the org-format #+label:
926 (count-matches (format "^#\\+label:\\s-*%s\\b[^-:]" label) (point-min) (point-max) t)
927 (let ((custom-id-count 0))
930 (when (string= label (org-entry-get (point) "CUSTOM_ID"))
931 (setq custom-id-count (+ 1 custom-id-count)))))
937 "on clicking count the number of label tags used in the buffer. A number greater than one means multiple labels!"
938 (message (format "%s occurences" (org-ref-count-labels label))))
939 (lambda (keyword desc format)
941 ((eq format 'html) (format "(<label>%s</label>)" path))
943 (format "\\label{%s}" keyword)))))
946 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.
948 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
949 (defun org-label-store-link ()
950 "store a link to a label. The output will be a ref to that label"
951 ;; First we have to make sure we are on a label link.
952 (let* ((object (org-element-context)))
953 (when (and (equal (org-element-type object) 'link)
954 (equal (org-element-property :type object) "label"))
955 (org-store-link-props
957 :link (concat "ref:" (org-element-property :path object))))
959 ;; Store link on table
960 (when (equal (org-element-type object) 'table)
961 (org-store-link-props
963 :link (concat "ref:" (org-element-property :name object))))
965 ;; it turns out this does not work. you can already store a link to a heading with a CUSTOM_ID
966 ;; store link on heading with custom_id
967 ; (when (and (equal (org-element-type object) 'headline)
968 ; (org-entry-get (point) "CUSTOM_ID"))
969 ; (org-store-link-props
971 ; :link (concat "ref:" (org-entry-get (point) "CUSTOM_ID"))))
973 ;; and to #+label: lines
974 (when (and (equal (org-element-type object) 'paragraph)
975 (org-element-property :name object))
976 (org-store-link-props
978 :link (concat "ref:" (org-element-property :name object))))
981 (add-hook 'org-store-link-functions 'org-label-store-link)
985 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.
987 At the moment, ref links are not usable for section links. You need [[#CUSTOM_ID]] type links.
989 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
993 "on clicking goto the label. Navigate back with C-c &"
995 ;; next search from beginning of the buffer
997 ;; it is possible you would not find the label if narrowing is in effect
1004 (goto-char (point-min))
1005 (re-search-forward (format "label:%s\\b" label) nil t))
1009 (goto-char (point-min))
1010 (re-search-forward (format "\\label{%s}" label) nil t))
1012 ;; #+label: name org-definition
1014 (goto-char (point-min))
1015 (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
1019 (goto-char (point-min))
1020 (re-search-forward (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t))
1022 ;; Commented out because these ref links do not actually translate correctly in LaTeX.
1023 ;; you need [[#label]] links.
1026 ; (goto-char (point-min))
1027 ; (re-search-forward (format ":CUSTOM_ID:\s-*\\(%s\\)" label) nil t))
1029 ;; we did not find anything, so go back to where we came
1030 (org-mark-ring-goto)
1031 (error "%s not found" label))
1033 (message "go back with (org-mark-ring-goto) `C-c &`"))
1035 (lambda (keyword desc format)
1037 ((eq format 'html) (format "(<ref>%s</ref>)" path))
1039 (format "\\ref{%s}" keyword)))))
1042 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.
1044 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1045 (defun org-ref-get-org-labels ()
1046 "find #+LABEL: labels"
1048 (goto-char (point-min))
1049 (let ((matches '()))
1050 (while (re-search-forward "^#\\+label:\\s-+\\(.*\\)\\b" (point-max) t)
1051 (add-to-list 'matches (match-string-no-properties 1) t))
1055 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1056 (defun org-ref-get-custom-ids ()
1057 "return a list of custom_id properties in the buffer"
1058 (let ((results '()) custom_id)
1061 (let ((custom_id (org-entry-get (point) "CUSTOM_ID")))
1062 (when (not (null custom_id))
1063 (setq results (append results (list custom_id)))))))
1067 Here we get a list of the labels defined as raw latex labels, e.g. \label{eqtre}.
1068 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1069 (defun org-ref-get-latex-labels ()
1071 (goto-char (point-min))
1072 (let ((matches '()))
1073 (while (re-search-forward "\\\\label{\\([a-zA-z0-9:-]*\\)}" (point-max) t)
1074 (add-to-list 'matches (match-string-no-properties 1) t))
1078 Finally, we get the table names.
1080 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1081 (defun org-ref-get-tblnames ()
1082 (org-element-map (org-element-parse-buffer 'element) 'table
1084 (org-element-property :name table))))
1087 Now, we can put all the labels together which will give us a list of candidates.
1089 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1090 (defun org-ref-get-labels ()
1091 "returns a list of labels in the buffer that you can make a ref link to. this is used to auto-complete ref links."
1095 (goto-char (point-min))
1096 (let ((matches '()))
1097 (while (re-search-forward "label:\\([a-zA-z0-9:-]*\\)" (point-max) t)
1098 (add-to-list 'matches (match-string-no-properties 1) t))
1099 (append matches (org-ref-get-org-labels) (org-ref-get-latex-labels) (org-ref-get-tblnames) (org-ref-get-custom-ids))))))
1102 Let us make a helm function to insert a label link. This will help you enter unique labels.
1103 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1104 (defun org-ref-helm-insert-label-link ()
1105 "Insert a label link. helm just shows you what labels already exist.
1106 If you are on a label link, replace it."
1108 (let* ((labels (org-ref-get-labels))
1109 (cb (current-buffer)))
1110 (helm :sources `(((name . "Existing labels")
1111 (candidates . ,labels)
1112 ;; default action is to open to the label
1113 (action . (lambda (label)
1114 ;; unfortunately I do not have markers here
1115 (org-open-link-from-string (format "ref:%s" label))))
1116 ;; if you select a label, replace current one
1117 (action . (lambda (label)
1118 (switch-to-buffer ,cb)
1120 ;; no prefix or on a link
1121 ((equal helm-current-prefix-arg nil)
1122 (let* ((object (org-element-context))
1123 (last-char (save-excursion
1124 (goto-char (org-element-property :end object))
1126 (if (looking-at " ")
1129 (when (-contains? '("label")
1130 (org-element-property :type object))
1131 ;; we are on a link, so replace it.
1134 (org-element-property :begin object)
1135 (org-element-property :end object))
1137 (replace-regexp-in-string
1138 (org-element-property :path object)
1140 (org-element-property :raw-link object))
1142 ;; no prefix options defined
1144 ;; no matching selection creates a new label
1145 ((name . "Create new label")
1147 ;; default action creates a new label, or replaces old one
1148 (action . (lambda (label)
1149 (switch-to-buffer ,cb)
1150 (let* ((object (org-element-context))
1151 (last-char (save-excursion
1152 (goto-char (org-element-property :end object))
1154 (if (looking-at " ")
1157 (if (-contains? '("label")
1158 (org-element-property :type object))
1159 ;; we are on a link, so replace it.
1162 (org-element-property :begin object)
1163 (org-element-property :end object))
1165 (replace-regexp-in-string
1166 (org-element-property :path object)
1168 (org-element-property :raw-link object))
1175 helm-pattern))))))))))))
1178 Now we create the completion function. This works from the org-machinery, e.g. if you type C-c C-l to insert a link, and use completion by pressing tab.
1180 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1181 (defun org-ref-complete-link (&optional arg)
1182 "Completion function for ref links"
1184 (setq label (completing-read "label: " (org-ref-get-labels)))
1185 (format "ref:%s" label)))
1188 Alternatively, you may want to just call a function that inserts a link with completion:
1190 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1191 (defun org-ref-insert-ref-link ()
1193 (insert (org-ref-complete-link)))
1196 Another alternative ref insertion is to use helm.
1198 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1199 (defun org-ref-helm-insert-ref-link ()
1200 "Helm menu to insert ref links to labels in the document.
1201 If you are on link, replace with newly selected label.
1202 Use C-u to insert a different kind of ref link.
1205 (let* ((labels (org-ref-get-labels))
1206 (contexts (mapcar 'org-ref-get-label-context labels))
1207 (cb (current-buffer)))
1209 (helm :input (thing-at-point 'word)
1210 :sources `(((name . "Available labels to ref")
1211 (candidates . ,(loop for label in labels
1212 for context in contexts
1213 ;; we do some kludgy adding spaces
1214 ;; and bars to make it "easier" to
1216 collect (cons (concat
1221 (split-string context "\n")
1224 ;; default action to replace or insert ref link.
1225 (action . (lambda (label)
1226 (switch-to-buffer ,cb)
1229 ;; no prefix or on a link
1230 ((equal helm-current-prefix-arg nil)
1231 (let* ((object (org-element-context))
1232 (last-char (save-excursion
1233 (goto-char (org-element-property :end object))
1235 (if (looking-at " ")
1238 (if (-contains? '("ref" "eqref" "pageref" "nameref")
1239 (org-element-property :type object))
1240 ;; we are on a link, so replace it.
1243 (org-element-property :begin object)
1244 (org-element-property :end object))
1246 (replace-regexp-in-string
1247 (org-element-property :path object)
1249 (org-element-property :raw-link object))
1251 ;; insert a new link
1256 ;; one prefix, alternate ref link
1257 ((equal helm-current-prefix-arg '(4))
1260 (helm :sources '((name . "Ref link types")
1261 (candidates . ("ref" "eqref" "pageref" "nameref"))
1262 (action . (lambda (x) x))))
1268 : org-ref-helm-insert-ref-link
1272 This refers to the page of a label in LaTeX.
1274 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1278 "on clicking goto the label. Navigate back with C-c &"
1279 (org-mark-ring-push)
1280 ;; next search from beginning of the buffer
1286 (goto-char (point-min))
1287 (re-search-forward (format "label:%s\\b" label) nil t))
1291 (goto-char (point-min))
1292 (re-search-forward (format "\\label{%s}" label) nil t))
1294 ;; #+label: name org-definition
1296 (goto-char (point-min))
1297 (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
1301 (goto-char (point-min))
1302 (re-search-forward (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t))
1304 ;; Commented out because these ref links do not actually translate correctly in LaTeX.
1305 ;; you need [[#label]] links.
1308 ; (goto-char (point-min))
1309 ; (re-search-forward (format ":CUSTOM_ID:\s-*\\(%s\\)" label) nil t))
1311 ;; we did not find anything, so go back to where we came
1312 (org-mark-ring-goto)
1313 (error "%s not found" label))
1314 (message "go back with (org-mark-ring-goto) `C-c &`"))
1316 (lambda (keyword desc format)
1318 ((eq format 'html) (format "(<pageref>%s</pageref>)" path))
1320 (format "\\pageref{%s}" keyword)))))
1323 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1324 (defun org-pageref-complete-link (&optional arg)
1325 "Completion function for ref links"
1327 (setq label (completing-read "label: " (org-ref-get-labels)))
1328 (format "ref:%s" label)))
1331 Alternatively, you may want to just call a function that inserts a link with completion:
1333 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1334 (defun org-pageref-insert-ref-link ()
1336 (insert (org-pageref-complete-link)))
1341 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.
1343 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1347 "on clicking goto the label. Navigate back with C-c &"
1348 (org-mark-ring-push)
1349 ;; next search from beginning of the buffer
1355 (goto-char (point-min))
1356 (re-search-forward (format "\\label{%s}" label) nil t))
1358 ;; we did not find anything, so go back to where we came
1359 (org-mark-ring-goto)
1360 (error "%s not found" label))
1361 (message "go back with (org-mark-ring-goto) `C-c &`"))
1363 (lambda (keyword desc format)
1365 ((eq format 'html) (format "(<nameref>%s</nameref>)" path))
1367 (format "\\nameref{%s}" keyword)))))
1371 This is just the LaTeX ref for equations. On export, the reference is enclosed in parentheses.
1373 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1377 "on clicking goto the label. Navigate back with C-c &"
1378 (org-mark-ring-push)
1379 ;; next search from beginning of the buffer
1381 (goto-char (point-min))
1384 ;; search forward for the first match
1386 (re-search-forward (format "label:%s" label) nil t)
1388 (re-search-forward (format "\\label{%s}" label) nil t)
1389 ;; #+label: name org-definition
1390 (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
1391 (org-mark-ring-goto)
1392 (error "%s not found" label))
1393 (message "go back with (org-mark-ring-goto) `C-c &`"))
1395 (lambda (keyword desc format)
1397 ((eq format 'html) (format "(<eqref>%s</eqref>)" path))
1399 (format "\\eqref{%s}" keyword)))))
1403 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.
1405 *** Implementing the click actions of cite
1407 **** Getting the key we clicked on
1408 The first thing we need is to get the bibtex key we clicked on.
1410 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1411 (defun org-ref-get-bibtex-key-under-cursor ()
1412 "returns key under the bibtex cursor. We search forward from
1413 point to get a comma, or the end of the link, and then backwards
1414 to get a comma, or the beginning of the link. that delimits the
1415 keyword we clicked on. We also strip the text properties."
1417 (let* ((object (org-element-context))
1418 (link-string (org-element-property :path object)))
1419 ;; you may click on the part before the citations. here we make
1420 ;; sure to move to the beginning so you get the first citation.
1422 (goto-char (org-element-property :begin object))
1423 (search-forward link-string (org-element-property :end object))
1424 (goto-char (match-beginning 0))
1425 ;; check if we clicked before the path and move as needed.
1426 (unless (< cp (point))
1429 (if (not (org-element-property :contents-begin object))
1430 ;; this means no description in the link
1432 ;; we need the link path start and end
1434 (goto-char (org-element-property :begin object))
1435 (search-forward link-string nil nil 1)
1436 (setq link-string-beginning (match-beginning 0))
1437 (setq link-string-end (match-end 0)))
1439 ;; The key is the text between commas, or the link boundaries
1441 (if (search-forward "," link-string-end t 1)
1442 (setq key-end (- (match-end 0) 1)) ; we found a match
1443 (setq key-end link-string-end))) ; no comma found so take the end
1444 ;; and backward to previous comma from point which defines the start character
1446 (if (search-backward "," link-string-beginning 1 1)
1447 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
1448 (setq key-beginning link-string-beginning))) ; no match found
1449 ;; save the key we clicked on.
1450 (setq bibtex-key (org-ref-strip-string (buffer-substring key-beginning key-end)))
1451 (set-text-properties 0 (length bibtex-key) nil bibtex-key)
1453 ;; link with description. assume only one key
1457 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.
1459 **** Getting the bibliographies
1460 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1461 (defun org-ref-find-bibliography ()
1462 "find the bibliography in the buffer.
1463 This function sets and returns cite-bibliography-files, which is a list of files
1464 either from bibliography:f1.bib,f2.bib
1465 \bibliography{f1,f2}
1466 internal bibliographies
1468 falling back to what the user has set in org-ref-default-bibliography
1473 (goto-char (point-min))
1474 ;; look for a bibliography link
1475 (when (re-search-forward "\\<bibliography:\\([^\]\|\n]+\\)" nil t)
1476 (setq org-ref-bibliography-files
1477 (mapcar 'org-ref-strip-string (split-string (match-string 1) ",")))
1478 (throw 'result org-ref-bibliography-files))
1481 ;; we did not find a bibliography link. now look for \bibliography
1482 (goto-char (point-min))
1483 (when (re-search-forward "\\\\bibliography{\\([^}]+\\)}" nil t)
1484 ;; split, and add .bib to each file
1485 (setq org-ref-bibliography-files
1486 (mapcar (lambda (x) (concat x ".bib"))
1487 (mapcar 'org-ref-strip-string
1488 (split-string (match-string 1) ","))))
1489 (throw 'result org-ref-bibliography-files))
1491 ;; no bibliography found. maybe we need a biblatex addbibresource
1492 (goto-char (point-min))
1493 ;; look for a bibliography link
1494 (when (re-search-forward "addbibresource:\\([^\]\|\n]+\\)" nil t)
1495 (setq org-ref-bibliography-files
1496 (mapcar 'org-ref-strip-string (split-string (match-string 1) ",")))
1497 (throw 'result org-ref-bibliography-files))
1499 ;; we did not find anything. use defaults
1500 (setq org-ref-bibliography-files org-ref-default-bibliography)))
1502 ;; set reftex-default-bibliography so we can search
1503 (set (make-local-variable 'reftex-default-bibliography) org-ref-bibliography-files)
1504 org-ref-bibliography-files)
1507 **** Finding the bibliography file a key is in
1508 Now, we can see if an entry is in a file.
1510 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1511 (defun org-ref-key-in-file-p (key filename)
1512 "determine if the key is in the file"
1513 (interactive "skey: \nsFile: ")
1514 (save-current-buffer
1515 (let ((bibtex-files (list filename)))
1516 (bibtex-search-entry key t))))
1519 Finally, we want to know which file the key is in.
1521 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1522 (defun org-ref-get-bibtex-key-and-file (&optional key)
1523 "returns the bibtex key and file that it is in. If no key is provided, get one under point"
1525 (let ((org-ref-bibliography-files (org-ref-find-bibliography))
1528 (setq key (org-ref-get-bibtex-key-under-cursor)))
1529 (setq file (catch 'result
1530 (loop for file in org-ref-bibliography-files do
1531 (if (org-ref-key-in-file-p key (file-truename file))
1532 (throw 'result file)))))
1536 **** convenience functions to act on citation at point
1538 :ID: af0b2a82-a7c9-4c08-9dac-09f93abc4a92
1540 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.
1542 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1543 (defun org-ref-open-pdf-at-point ()
1544 "open the pdf for bibtex key under point if it exists"
1546 (let* ((results (org-ref-get-bibtex-key-and-file))
1548 (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key)))
1549 (if (file-exists-p pdf-file)
1550 (org-open-file pdf-file)
1551 (message "no pdf found for %s" key))))
1554 (defun org-ref-open-url-at-point ()
1555 "open the url for bibtex key under point."
1557 (let* ((results (org-ref-get-bibtex-key-and-file))
1559 (bibfile (cdr results)))
1562 (insert-file-contents bibfile)
1563 (bibtex-search-entry key)
1564 ;; I like this better than bibtex-url which does not always find
1567 (let ((url (bibtex-autokey-get-field "url")))
1572 (let ((doi (bibtex-autokey-get-field "doi")))
1574 (if (string-match "^http" doi)
1576 (browse-url (format "http://dx.doi.org/%s" doi)))
1577 (throw 'done nil))))))))
1580 (defun org-ref-open-notes-at-point ()
1581 "open the notes for bibtex key under point."
1583 (let* ((results (org-ref-get-bibtex-key-and-file))
1585 (bibfile (cdr results)))
1588 (insert-file-contents bibfile)
1589 (bibtex-search-entry key)
1590 (org-ref-open-bibtex-notes)))))
1593 (defun org-ref-citation-at-point ()
1594 "give message of current citation at point"
1596 (let* ((cb (current-buffer))
1597 (results (org-ref-get-bibtex-key-and-file))
1599 (bibfile (cdr results)))
1600 (message "%s" (progn
1602 (insert-file-contents bibfile)
1603 (bibtex-search-entry key)
1604 (org-ref-bib-citation))))))
1607 (defun org-ref-open-citation-at-point ()
1608 "open bibtex file to key at point"
1610 (let* ((cb (current-buffer))
1611 (results (org-ref-get-bibtex-key-and-file))
1613 (bibfile (cdr results)))
1615 (bibtex-search-entry key)))
1618 **** the actual minibuffer menu
1619 Now, we create the menu. This is a rewrite of the cite action. This makes the function extendable by users.
1621 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1622 (defvar org-ref-cite-menu-funcs '()
1623 "Functions to run on cite click menu. Each entry is a list of (key menu-name function).
1624 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.")
1627 (defvar org-ref-user-cite-menu-funcs
1628 '(("C" "rossref" org-ref-crossref-at-point)
1629 ("y" "Copy entry to file" org-ref-copy-entry-at-point-to-file)
1630 ("s" "Copy summary" org-ref-copy-entry-as-summary))
1631 "user-defined functions to run on bibtex key at point.")
1634 (defun org-ref-copy-entry-as-summary ()
1635 "Copy the bibtex entry for the citation at point as a summary."
1637 (save-window-excursion
1638 (org-ref-open-citation-at-point)
1639 (kill-new (org-ref-bib-citation))))
1642 (defun org-ref-copy-entry-at-point-to-file ()
1643 "Copy the bibtex entry for the citation at point to NEW-FILE.
1644 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."
1646 (let ((new-file (ido-completing-read
1648 (append org-ref-default-bibliography
1649 (f-entries "." (lambda (f) (f-ext? f "bib"))))))
1650 (key (org-ref-get-bibtex-key-under-cursor)))
1651 (save-window-excursion
1652 (org-ref-open-citation-at-point)
1653 (bibtex-copy-entry-as-kill))
1655 (let ((bibtex-files (list (file-truename new-file))))
1656 (if (assoc key (bibtex-global-key-alist))
1657 (message "That key already exists in %s" new-file)
1659 (save-window-excursion
1660 (find-file new-file)
1661 (goto-char (point-max))
1662 ;; make sure we are at the beginning of a line.
1663 (unless (looking-at "^") (insert "\n\n"))
1668 (defun org-ref-get-doi-at-point ()
1669 "Get doi for key at point."
1671 (let* ((results (org-ref-get-bibtex-key-and-file))
1673 (bibfile (cdr results))
1677 (insert-file-contents bibfile)
1678 (bibtex-search-entry key)
1679 (setq doi (bibtex-autokey-get-field "doi"))
1680 ;; in case doi is a url, remove the url part.
1681 (replace-regexp-in-string "^http://dx.doi.org/" "" doi)))))
1684 ;; functions that operate on key at point for click menu
1685 (defun org-ref-wos-at-point ()
1686 "open the doi in wos for bibtex key under point."
1688 (doi-utils-wos (org-ref-get-doi-at-point)))
1691 (defun org-ref-wos-citing-at-point ()
1692 "open the doi in wos citing articles for bibtex key under point."
1694 (doi-utils-wos-citing (org-ref-get-doi-at-point)))
1697 (defun org-ref-wos-related-at-point ()
1698 "open the doi in wos related articles for bibtex key under point."
1700 (doi-utils-wos-related (org-ref-get-doi-at-point)))
1703 (defun org-ref-google-scholar-at-point ()
1704 "open the doi in google scholar for bibtex key under point."
1706 (doi-utils-google-scholar (org-ref-get-doi-at-point)))
1709 (defun org-ref-pubmed-at-point ()
1710 "open the doi in pubmed for bibtex key under point."
1712 (doi-utils-pubmed (org-ref-get-doi-at-point)))
1715 (defun org-ref-crossref-at-point ()
1716 "open the doi in crossref for bibtex key under point."
1718 (doi-utils-crossref (org-ref-get-doi-at-point)))
1721 (defun org-ref-cite-onclick-minibuffer-menu (&optional link-string)
1722 "action when a cite link is clicked on.
1723 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."
1725 (let* ((results (org-ref-get-bibtex-key-and-file))
1727 (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key))
1728 (bibfile (cdr results))
1729 (url (save-excursion
1731 (insert-file-contents bibfile)
1732 (bibtex-search-entry key)
1733 (bibtex-autokey-get-field "url"))))
1734 (doi (save-excursion
1736 (insert-file-contents bibfile)
1737 (bibtex-search-entry key)
1738 ;; I like this better than bibtex-url which does not always find
1740 (bibtex-autokey-get-field "doi")))))
1742 (when (string= "" doi) (setq doi nil))
1743 (when (string= "" url) (setq url nil))
1744 (setq org-ref-cite-menu-funcs '())
1750 'org-ref-cite-menu-funcs
1751 '("o" "pen" org-ref-open-citation-at-point)))
1754 (when (file-exists-p pdf-file)
1756 'org-ref-cite-menu-funcs
1757 `("p" "df" ,org-ref-open-pdf-function) t))
1761 'org-ref-cite-menu-funcs
1762 '("n" "otes" org-ref-open-notes-at-point) t)
1767 'org-ref-cite-menu-funcs
1768 '("u" "rl" org-ref-open-url-at-point) t))
1773 'org-ref-cite-menu-funcs
1774 '("w" "os" org-ref-wos-at-point) t)
1777 'org-ref-cite-menu-funcs
1778 '("c" "iting" org-ref-wos-citing-at-point) t)
1781 'org-ref-cite-menu-funcs
1782 '("r" "elated" org-ref-wos-related-at-point) t)
1785 'org-ref-cite-menu-funcs
1786 '("g" "oogle scholar" org-ref-google-scholar-at-point) t)
1789 'org-ref-cite-menu-funcs
1790 '("P" "ubmed" org-ref-pubmed-at-point) t))
1792 ;; add user functions
1793 (dolist (tup org-ref-user-cite-menu-funcs)
1795 'org-ref-cite-menu-funcs
1800 'org-ref-cite-menu-funcs
1801 '("q" "uit" (lambda ())) t)
1803 ;; now we make a menu
1804 ;; construct menu string as a message
1807 (let* ((results (org-ref-get-bibtex-key-and-file))
1809 (bibfile (cdr results)))
1812 (insert-file-contents bibfile)
1813 (bibtex-search-entry key)
1814 (org-ref-bib-citation))))
1818 (concat "[" (elt tup 0) "]"
1820 org-ref-cite-menu-funcs "")))
1822 (let* ((input (read-char-exclusive))
1824 (char-to-string input) org-ref-cite-menu-funcs)))
1825 ;; now run the function (2nd element in choice)
1834 : org-ref-cite-onclick-minibuffer-menu
1836 *** A function to format a cite link
1838 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.
1840 #+BEGIN_SRC emacs-lisp :tangle no
1841 ;(defun org-ref-cite-link-format (keyword desc format)
1843 ; ((eq format 'html) (mapconcat (lambda (key) (format "<a name=\"#%s\">%s</a>" key key) (org-ref-split-and-strip-string keyword) ",")))
1844 ; ((eq format 'latex)
1845 ; (concat "\\cite" (when desc (format "[%s]" desc)) "{"
1846 ; (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
1850 *** The actual cite link
1851 Finally, we define the cite link. This is deprecated; the links are autogenerated later. This is here for memory.
1853 #+BEGIN_SRC emacs-lisp :tangle no
1856 ; 'org-ref-cite-onclick-minibuffer-menu
1857 ; 'org-ref-cite-link-format)
1860 *** Automatic definition of the cite links
1861 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.
1863 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1864 (defmacro org-ref-make-completion-function (type)
1865 `(defun ,(intern (format "org-%s-complete-link" type)) (&optional arg)
1871 (let ((bibtex-files (org-ref-find-bibliography)))
1872 (bibtex-global-key-alist))))))
1875 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.
1877 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1878 (defmacro org-ref-make-format-function (type)
1879 `(defun ,(intern (format "org-ref-format-%s" type)) (keyword desc format)
1884 (format "[[#%s][%s]]" key key))
1885 (org-ref-split-and-strip-string keyword) ","))
1892 (org-ref-split-and-strip-string keyword) ",") "]"))
1897 (format "<a href=\"#%s\">%s</a>" key key))
1898 (org-ref-split-and-strip-string keyword) ","))
1901 (if (string= (substring type -1) "s")
1902 ;; biblatex format for multicite commands, which all end in s. These are formated as \cites{key1}{key2}...
1903 (concat "\\" ,type (mapconcat (lambda (key) (format "{%s}" key))
1904 (org-ref-split-and-strip-string keyword) ""))
1906 (concat "\\" ,type (when desc (org-ref-format-citation-description desc)) "{"
1907 (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
1913 We create the links by mapping the function onto the list of defined link types.
1915 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1916 (defun org-ref-format-citation-description (desc)
1917 "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 ::."
1920 ((string-match "::" desc)
1921 (format "[%s][%s]" (car (setq results (split-string desc "::"))) (cadr results)))
1922 (t (format "[%s]" desc))))
1924 (defun org-ref-define-citation-link (type &optional key)
1925 "add a citation link for org-ref. With optional key, set the reftex binding. For example:
1926 (org-ref-define-citation-link \"citez\" ?z) will create a new citez link, with reftex key of z,
1927 and the completion function."
1928 (interactive "sCitation Type: \ncKey: ")
1930 ;; create the formatting function
1931 (eval `(org-ref-make-format-function ,type))
1936 org-ref-cite-onclick-function
1937 (quote ,(intern (format "org-ref-format-%s" type)))))
1939 ;; create the completion function
1940 (eval `(org-ref-make-completion-function ,type))
1942 ;; store new type so it works with adding citations, which checks
1943 ;; for existence in this list
1944 (add-to-list 'org-ref-cite-types type)
1946 ;; and finally if a key is specified, we modify the reftex menu
1948 (setf (nth 2 (assoc 'org reftex-cite-format-builtin))
1949 (append (nth 2 (assoc 'org reftex-cite-format-builtin))
1950 `((,key . ,(concat type ":%l")))))))
1952 ;; create all the link types and their completion functions
1953 (mapcar 'org-ref-define-citation-link org-ref-cite-types)
1956 *** org-ref-insert-cite-link
1957 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.
1959 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1960 (defun org-ref-insert-cite-link (alternative-cite)
1961 "Insert a default citation link using reftex. If you are on a link, it
1962 appends to the end of the link, otherwise, a new link is
1963 inserted. Use a prefix arg to get a menu of citation types."
1965 (org-ref-find-bibliography)
1966 (let* ((object (org-element-context))
1967 (link-string-beginning (org-element-property :begin object))
1968 (link-string-end (org-element-property :end object))
1969 (path (org-element-property :path object)))
1971 (if (not alternative-cite)
1974 ;; case where we are in a link
1975 ((and (equal (org-element-type object) 'link)
1976 (-contains? org-ref-cite-types (org-element-property :type object)))
1977 (goto-char link-string-end)
1978 ;; sometimes there are spaces at the end of the link
1979 ;; this code moves point pack until no spaces are there
1980 (while (looking-back " ") (backward-char))
1981 (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
1983 ;; We are next to a link, and we want to append
1986 (and (equal (org-element-type (org-element-context)) 'link)
1987 (-contains? org-ref-cite-types (org-element-property :type (org-element-context)))))
1988 (while (looking-back " ") (backward-char))
1989 (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
1991 ;; insert fresh link
1994 (concat org-ref-default-citation-link
1996 (mapconcat 'identity (reftex-citation t) ",")))))
1998 ;; you pressed a C-u so we run this code
2002 cite:zhou-2004-first-lda-u,paier-2006-errat,boes-2015-estim-bulk
2006 : org-ref-insert-cite-link
2008 *** Completion in cite links
2009 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.
2011 #+BEGIN_SRC emacs-lisp :tangle no
2012 (defun org-cite-complete-link (&optional arg)
2013 "Completion function for cite links"
2015 org-ref-default-citation-link
2018 (let ((bibtex-files (org-ref-find-bibliography)))
2019 (bibtex-global-key-alist)))))
2022 Alternatively, you may shortcut the org-machinery with this command. You will be prompted for a citation type, and then offered key completion.
2024 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2025 (defun org-ref-insert-cite-with-completion (type)
2026 "Insert a cite link with completion"
2027 (interactive (list (ido-completing-read "Type: " org-ref-cite-types)))
2028 (insert (funcall (intern (format "org-%s-complete-link" type)))))
2031 ** Storing links to a bibtex entry
2032 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.
2034 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2035 (defun org-ref-store-bibtex-entry-link ()
2036 "Save a citation link to the current bibtex entry. Saves in the default link type."
2038 (let ((link (concat org-ref-default-citation-link
2041 (bibtex-beginning-of-entry)
2042 (reftex-get-bib-field "=key=" (bibtex-parse-entry))))))
2043 (message "saved %s" link)
2044 (push (list link) org-stored-links)
2045 (car org-stored-links)))
2049 org-ref minimally supports index entries. To make an index in a file, you should put in the LaTeX header these lines
2052 #+LATEX_HEADER: \usepackage{makeidx}
2053 #+LATEX_HEADER: \makeindex
2056 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.
2059 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.
2064 [[index:hello!Sam@\textsl{Sam}]]
2065 [[index:Lin@\textbf{Lin}]]
2066 [[index:Joe|textit]]
2067 [[index:Lin@\textbf{Lin}]]
2068 [[index:Peter|see {hello}]]
2069 [[index:Jen|seealso{Jenny}]]
2071 index:encodings!input!cp850
2073 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2079 (lambda (path desc format)
2082 (format "\\index{%s}" path)))))
2084 ;; this will generate a temporary index of entries in the file.
2088 (let ((*index-links* '())
2089 (*initial-letters* '()))
2092 (org-element-map (org-element-parse-buffer) 'link
2094 (let ((type (nth 0 link))
2095 (plist (nth 1 link)))
2097 (when (equal (plist-get plist ':type) "index")
2100 (cons (plist-get plist :path)
2102 "[[elisp:(progn (switch-to-buffer \"%s\") (goto-char %s))][%s]]"
2104 (plist-get plist :begin) ;; position of link
2105 ;; grab a description
2107 (goto-char (plist-get plist :begin))
2108 (if (thing-at-point 'sentence)
2110 (replace-regexp-in-string
2111 "\n" "" (thing-at-point 'sentence))
2112 ;; or call it a link
2116 (setq *index-links* (cl-sort *index-links* 'string-lessp :key 'car))
2118 ;; now first letters
2119 (dolist (link *index-links*)
2120 (add-to-list '*initial-letters* (substring (car link) 0 1) t))
2122 ;; now create the index
2123 (switch-to-buffer (get-buffer-create "*index*"))
2126 (insert "#+TITLE: Index\n\n")
2127 (dolist (letter *initial-letters*)
2128 (insert (format "* %s\n" (upcase letter)))
2129 ;; now process the links
2132 (string= letter (substring (car (car *index-links*)) 0 1)))
2133 (let ((link (pop *index-links*)))
2134 (insert (format "%s %s\n\n" (car link) (cdr link))))))
2135 (switch-to-buffer "*index*")))
2137 (lambda (path desc format)
2140 (format "\\printindex")))))
2144 | 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*)) |
2145 | lambda | (path desc format) | (cond ((eq format (quote latex)) (format \printindex))) |
2148 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.
2150 #+LATEX_HEADER: \usepackage{glossaries}
2151 #+LATEX_HEADER: \makeglossaries
2153 And at the end of the document put \makeglossaries.
2155 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2158 nil ;; no follow action
2159 (lambda (path desc format)
2162 (format "\\newglossaryentry{%s}{%s}" path desc)))))
2168 nil ;; no follow action
2169 (lambda (path desc format)
2172 (format "\\gls{%s}" path)))))
2177 nil ;; no follow action
2178 (lambda (path desc format)
2181 (format "\\glspl{%s}" path)))))
2186 nil ;; no follow action
2187 (lambda (path desc format)
2190 (format "\\Gls{%s}" path)))))
2195 nil ;; no follow action
2196 (lambda (path desc format)
2199 (format "\\Glspl{%s}" path)))))
2203 ** create simple text citation from bibtex entry
2205 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2206 (defun org-ref-bib-citation ()
2207 "From a bibtex entry, create and return a simple citation string.
2208 This assumes you are in an article."
2210 (bibtex-beginning-of-entry)
2211 (let* ((cb (current-buffer))
2212 (bibtex-expand-strings t)
2213 (entry (loop for (key . value) in (bibtex-parse-entry t)
2214 collect (cons (downcase key) value)))
2215 (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2216 (year (reftex-get-bib-field "year" entry))
2217 (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2218 (key (reftex-get-bib-field "=key=" entry))
2219 (journal (reftex-get-bib-field "journal" entry))
2220 (volume (reftex-get-bib-field "volume" entry))
2221 (pages (reftex-get-bib-field "pages" entry))
2222 (doi (reftex-get-bib-field "doi" entry))
2223 (url (reftex-get-bib-field "url" entry))
2225 ;;authors, "title", Journal, vol(iss):pages (year).
2226 (format "%s, \"%s\", %s, %s:%s (%s)"
2227 author title journal volume pages year)))
2231 : org-ref-bib-citation
2234 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2235 (defun org-ref-bib-html-citation ()
2236 "from a bibtex entry, create and return a simple citation with html links."
2238 (bibtex-beginning-of-entry)
2239 (let* ((cb (current-buffer))
2240 (bibtex-expand-strings t)
2241 (entry (loop for (key . value) in (bibtex-parse-entry t)
2242 collect (cons (downcase key) value)))
2243 (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2244 (year (reftex-get-bib-field "year" entry))
2245 (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2246 (key (reftex-get-bib-field "=key=" entry))
2247 (journal (reftex-get-bib-field "journal" entry))
2248 (volume (reftex-get-bib-field "volume" entry))
2249 (pages (reftex-get-bib-field "pages" entry))
2250 (doi (reftex-get-bib-field "doi" entry))
2251 (url (reftex-get-bib-field "url" entry))
2253 ;;authors, "title", Journal, vol(iss):pages (year).
2254 (concat (format "%s, \"%s\", %s, %s:%s (%s)."
2255 author title journal volume pages year)
2256 (when url (format " <a href=\"%s\">link</a>" url))
2257 (when doi (format " <a href=\"http://dx.doi.org/%s\">doi</a>" doi)))
2261 ** open pdf from bibtex
2262 We bind this to a key here: [[*key%20bindings%20for%20utilities][key bindings for utilities]].
2263 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2264 (defun org-ref-open-bibtex-pdf ()
2265 "open pdf for a bibtex entry, if it exists. assumes point is in
2266 the entry of interest in the bibfile. but does not check that."
2269 (bibtex-beginning-of-entry)
2270 (let* ((bibtex-expand-strings t)
2271 (entry (bibtex-parse-entry t))
2272 (key (reftex-get-bib-field "=key=" entry))
2273 (pdf (format (concat org-ref-pdf-directory "%s.pdf") key)))
2275 (if (file-exists-p pdf)
2276 (org-open-link-from-string (format "[[file:%s]]" pdf))
2280 ** open notes from bibtex
2281 We bind this to a key here [[*key%20bindings%20for%20utilities][key bindings for utilities]].
2283 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2284 (defun org-ref-open-bibtex-notes ()
2285 "from a bibtex entry, open the notes if they exist, and create a heading if they do not.
2287 I never did figure out how to use reftex to make this happen
2288 non-interactively. the reftex-format-citation function did not
2289 work perfectly; there were carriage returns in the strings, and
2290 it did not put the key where it needed to be. so, below I replace
2291 the carriage returns and extra spaces with a single space and
2292 construct the heading by hand."
2295 (bibtex-beginning-of-entry)
2296 (let* ((cb (current-buffer))
2297 (bibtex-expand-strings t)
2298 (entry (loop for (key . value) in (bibtex-parse-entry t)
2299 collect (cons (downcase key) value)))
2300 (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2301 (year (reftex-get-bib-field "year" entry))
2302 (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2303 (key (reftex-get-bib-field "=key=" entry))
2304 (journal (reftex-get-bib-field "journal" entry))
2305 (volume (reftex-get-bib-field "volume" entry))
2306 (pages (reftex-get-bib-field "pages" entry))
2307 (doi (reftex-get-bib-field "doi" entry))
2308 (url (reftex-get-bib-field "url" entry))
2311 ;; save key to clipboard to make saving pdf later easier by pasting.
2314 (kill-ring-save (point-min) (point-max)))
2316 ;; now look for entry in the notes file
2317 (if org-ref-bibliography-notes
2318 (find-file-other-window org-ref-bibliography-notes)
2319 (error "org-ref-bib-bibliography-notes is not set to anything"))
2321 (goto-char (point-min))
2322 ;; put new entry in notes if we don't find it.
2323 (if (re-search-forward (format ":Custom_ID: %s$" key) nil 'end)
2324 (funcall org-ref-open-notes-function)
2325 ;; no entry found, so add one
2326 (insert (format "\n** TODO %s - %s" year title))
2338 [[cite:%s]] [[file:%s/%s.pdf][pdf]]\n\n"
2339 key author journal year volume pages doi url key org-ref-pdf-directory key))
2343 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2344 (defun org-ref-open-notes-from-reftex ()
2345 "Call reftex, and open notes for selected entry."
2347 (let ((bibtex-key )))
2349 ;; now look for entry in the notes file
2350 (if org-ref-bibliography-notes
2351 (find-file-other-window org-ref-bibliography-notes)
2352 (error "org-ref-bib-bibliography-notes is not set to anything"))
2354 (goto-char (point-min))
2356 (re-search-forward (format
2358 (first (reftex-citation t)) nil 'end))
2359 (funcall org-ref-open-notes-function))
2362 ** open url in browser from bibtex
2364 We bind this to a key here [[*key%20bindings%20for%20utilities][key bindings for utilities]].
2366 + 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.
2368 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2369 (defun org-ref-open-in-browser ()
2370 "Open the bibtex entry at point in a browser using the url field or doi field"
2373 (bibtex-beginning-of-entry)
2375 (let ((url (bibtex-autokey-get-field "url")))
2380 (let ((doi (bibtex-autokey-get-field "doi")))
2382 (if (string-match "^http" doi)
2384 (browse-url (format "http://dx.doi.org/%s" doi)))
2386 (message "No url or doi found"))))
2390 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.
2392 *** function to upload bibtex to citeulike
2394 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2395 (defun org-ref-upload-bibtex-entry-to-citeulike ()
2396 "with point in a bibtex entry get bibtex string and submit to citeulike.
2398 Relies on the python script /upload_bibtex_citeulike.py being in the user directory."
2400 (message "uploading to citeulike")
2402 (bibtex-narrow-to-entry)
2403 (let ((startpos (point-min))
2404 (endpos (point-max))
2405 (bibtex-string (buffer-string))
2406 (script (concat "python " starter-kit-dir "/upload_bibtex_citeulike.py&")))
2407 (with-temp-buffer (insert bibtex-string)
2408 (shell-command-on-region (point-min) (point-max) script t nil nil t)))))
2411 *** The upload script
2412 Here is the python script for uploading.
2414 *************** TODO document how to get the cookies
2418 #+BEGIN_SRC python :tangle upload_bibtex_citeulike.py
2420 import pickle, requests, sys
2423 with open('c:/Users/jkitchin/Dropbox/blogofile-jkitchin.github.com/_blog/cookies.pckl', 'rb') as f:
2424 cookies = pickle.load(f)
2426 url = 'http://www.citeulike.org/profile/jkitchin/import_do'
2428 bibtex = sys.stdin.read()
2430 data = {'pasted':bibtex,
2432 'tag_parsing':'simple',
2433 'strip_brackets':'no',
2434 'update_id':'bib-key',
2435 'btn_bibtex':'Import BibTeX file ...'}
2437 headers = {'content-type': 'multipart/form-data',
2438 'User-Agent':'jkitchin/johnrkitchin@gmail.com bibtexupload'}
2440 r = requests.post(url, headers=headers, data=data, cookies=cookies, files={})
2444 ** Build a pdf from a bibtex file
2445 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.
2447 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2448 (defun org-ref-build-full-bibliography ()
2449 "build pdf of all bibtex entries, and open it."
2451 (let* ((bibfile (file-name-nondirectory (buffer-file-name)))
2452 (bib-base (file-name-sans-extension bibfile))
2453 (texfile (concat bib-base ".tex"))
2454 (pdffile (concat bib-base ".pdf")))
2457 (insert (format "\\documentclass[12pt]{article}
2458 \\usepackage[version=3]{mhchem}
2460 \\usepackage[numbers]{natbib}
2461 \\usepackage[colorlinks=true, linkcolor=blue, urlcolor=blue, pdfstartview=FitH]{hyperref}
2465 \\bibliographystyle{unsrtnat}
2467 \\end{document}" bib-base))
2469 (shell-command (concat "pdflatex " bib-base))
2470 (shell-command (concat "bibtex " bib-base))
2471 (shell-command (concat "pdflatex " bib-base))
2472 (shell-command (concat "pdflatex " bib-base))
2473 (kill-buffer texfile)
2474 (org-open-file pdffile)
2478 ** Extract bibtex entries cited in an org-file
2479 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.
2481 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2482 (defun org-ref-extract-bibtex-entries ()
2483 "extract the bibtex entries referred to by cite links in the current buffer into a src block at the bottom of the current buffer.
2485 If no bibliography is in the buffer the `reftex-default-bibliography' is used."
2487 (let* ((temporary-file-directory (file-name-directory (buffer-file-name)))
2488 (tempname (make-temp-file "extract-bib"))
2489 (contents (buffer-string))
2490 (cb (current-buffer))
2491 basename texfile bibfile results)
2493 ;; open tempfile and insert org-buffer contents
2494 (find-file tempname)
2496 (setq basename (file-name-sans-extension
2497 (file-name-nondirectory buffer-file-name))
2498 texfile (concat tempname ".tex")
2499 bibfile (concat tempname ".bib"))
2501 ;; see if we have a bibliography, and insert the default one if not.
2503 (goto-char (point-min))
2504 (unless (re-search-forward "^bibliography:" (point-max) 'end)
2505 (insert (format "\nbibliography:%s"
2506 (mapconcat 'identity reftex-default-bibliography ",")))))
2509 ;; get a latex file and extract the references
2510 (org-latex-export-to-latex)
2513 (reftex-create-bibtex-file bibfile)
2515 ;; save results of the references
2516 (setq results (buffer-string))
2518 ;; kill buffers. these are named by basename, not full path
2519 (kill-buffer (concat basename ".bib"))
2520 (kill-buffer (concat basename ".tex"))
2521 (kill-buffer basename)
2523 (delete-file bibfile)
2524 (delete-file texfile)
2525 (delete-file tempname)
2527 ;; Now back to the original org buffer and insert the results
2528 (switch-to-buffer cb)
2529 (when (not (string= "" results))
2531 (goto-char (point-max))
2533 (org-insert-heading)
2534 (insert (format " Bibtex entries
2536 ,#+BEGIN_SRC text :tangle %s
2538 ,#+END_SRC" (concat (file-name-sans-extension (file-name-nondirectory (buffer-file-name))) ".bib") results))))))
2541 ** Find bad cite links
2543 :ID: 8515E800-EDA0-4B2A-85FD-55B6FF849203
2545 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.
2547 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2550 (defun index (substring list)
2551 "return the index of string in a list of strings"
2554 (dolist (arg list i)
2555 (if (string-match (concat "^" substring "$") arg)
2560 ;; return counter if found, otherwise return nil
2564 (defun org-ref-find-bad-citations ()
2565 "Create a list of citation keys in an org-file that do not have a bibtex entry in the known bibtex files.
2567 Makes a new buffer with clickable links."
2569 ;; generate the list of bibtex-keys and cited keys
2570 (let* ((bibtex-files (org-ref-find-bibliography))
2571 (bibtex-file-path (mapconcat (lambda (x) (file-name-directory (file-truename x))) bibtex-files ":"))
2572 (bibtex-keys (mapcar (lambda (x) (car x)) (bibtex-global-key-alist)))
2573 (bad-citations '()))
2575 (org-element-map (org-element-parse-buffer) 'link
2577 (let ((plist (nth 1 link)))
2578 (when (equal (plist-get plist ':type) "cite")
2579 (dolist (key (org-ref-split-and-strip-string (plist-get plist ':path)) )
2580 (when (not (index key bibtex-keys))
2581 (setq bad-citations (append bad-citations
2582 `(,(format "%s [[elisp:(progn (switch-to-buffer-other-frame \"%s\")(goto-char %s))][not found here]]\n"
2583 key (buffer-name)(plist-get plist ':begin)))))
2588 (switch-to-buffer-other-window "*Missing citations*")
2591 (insert "* List of bad cite links\n")
2592 (insert (mapconcat 'identity bad-citations ""))
2593 ;(setq buffer-read-only t)
2594 (use-local-map (copy-keymap org-mode-map))
2595 (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))
2597 (when (get-buffer "*Missing citations*")
2598 (kill-buffer "*Missing citations*"))
2599 (message "No bad cite links found"))))
2602 ** helm interface to org-ref
2603 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.
2605 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.
2607 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2608 (defun org-ref-bad-cite-candidates ()
2609 "Returns a list of conses (key . marker) where key does not exist in the known bibliography files, and marker points to the key."
2610 (let* ((cp (point)) ; save to return to later
2611 (bibtex-files (org-ref-find-bibliography))
2612 (bibtex-file-path (mapconcat
2614 (file-name-directory (file-truename x)))
2616 (bibtex-keys (mapcar (lambda (x) (car x))
2617 (bibtex-global-key-alist)))
2618 (bad-citations '()))
2620 (org-element-map (org-element-parse-buffer) 'link
2622 (let ((plist (nth 1 link)))
2623 (when (-contains? org-ref-cite-types (plist-get plist ':type))
2624 (dolist (key (org-ref-split-and-strip-string (plist-get plist ':path)) )
2625 (when (not (index key bibtex-keys))
2626 (goto-char (plist-get plist ':begin))
2627 (re-search-forward key)
2628 (push (cons key (point-marker)) bad-citations)))
2633 ;; It seems I forgot I already defined this earlier!
2634 ;; (defun org-ref-get-labels ()
2635 ;; "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.
2637 ;; (let ((cp (point))
2639 ;; (goto-char (point-min))
2640 ;; (while (re-search-forward "[^#+]label:\\(.*\\)\\s-" nil t)
2641 ;; (push (match-string 1) labels))
2643 ;; (goto-char (point-min))
2644 ;; (while (re-search-forward "\\label{\\(.*\\)}\\s-?" nil t)
2645 ;; (push (match-string 1) labels))
2647 ;; (goto-char (point-min))
2648 ;; (while (re-search-forward "^#\\+label:\\s-*\\(.*\\)" nil t)
2649 ;; (push (match-string 1) labels))
2651 ;; (goto-char (point-min))
2652 ;; (while (re-search-forward "^#\\+tblname:\\s-*\\(.*\\)" nil t)
2653 ;; (push (match-string 1) labels))
2654 ;; ;; check for CUSTOM_ID
2657 ;; (when (org-entry-get (point) "CUSTOM_ID")
2658 ;; (push (org-entry-get (point) "CUSTOM_ID") labels))))
2659 ;; ;; return to original place
2664 (defun org-ref-bad-ref-candidates ()
2665 "Returns a list of conses (ref . marker) where ref is a ref link that does not point to anything (i.e. a label)."
2666 ;; first get a list of legitimate labels
2668 (labels (org-ref-get-labels))
2670 ;; now loop over ref links
2671 (goto-char (point-min))
2672 (org-element-map (org-element-parse-buffer) 'link
2674 (let ((plist (nth 1 link)))
2675 (when (or (equal (plist-get plist ':type) "ref")
2676 (equal (plist-get plist ':type) "eqref")
2677 (equal (plist-get plist ':type) "pageref")
2678 (equal (plist-get plist ':type) "nameref"))
2679 (unless (-contains? labels (plist-get plist :path))
2680 (goto-char (plist-get plist :begin))
2683 (cons (plist-get plist :path)
2684 (point-marker))))))))
2689 (defun org-ref-bad-label-candidates ()
2690 "Return a list of labels where label is multiply defined."
2691 (let ((labels (org-ref-get-labels))
2692 (multiple-labels '()))
2693 (when (not (= (length labels)
2694 (length (-uniq labels))))
2695 (dolist (label labels)
2696 (when (> (-count (lambda (a)
2699 ;; this is a multiply defined label.
2701 (goto-char (point-min))
2702 (while (re-search-forward
2703 (format "[^#+]label:%s\\s-" label) nil t)
2704 (push (cons label (point-marker)) multiple-labels))
2706 (goto-char (point-min))
2707 (while (re-search-forward
2708 (format "\\label{%s}\\s-?" label) nil t)
2709 (push (cons label (point-marker)) multiple-labels))
2711 (goto-char (point-min))
2712 (while (re-search-forward
2713 (format "^#\\+label:\\s-*%s" label) nil t)
2714 (push (cons label (point-marker)) multiple-labels))
2716 (goto-char (point-min))
2717 (while (re-search-forward
2718 (format "^#\\+tblname:\\s-*%s" label) nil t)
2719 (push (cons label (point-marker)) multiple-labels))
2725 : org-ref-bad-label-candidates
2727 Now, we have a functions for candidates, we can make helm sources for each one, and then run a helm command to view them.
2729 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2731 "Opens a helm interface to actions for org-ref.
2732 Shows bad citations, ref links and labels"
2734 (let ((cb (current-buffer))
2735 (bad-citations (org-ref-bad-cite-candidates))
2736 (bad-refs (org-ref-bad-ref-candidates))
2737 (bad-labels (org-ref-bad-label-candidates)))
2739 (helm :sources `(((name . "Bad citations")
2740 (candidates . ,bad-citations)
2741 (action . (lambda (marker)
2742 (switch-to-buffer (marker-buffer marker))
2743 (goto-char marker))))
2745 ((name . "Bad Labels")
2746 (candidates . ,bad-labels)
2747 (action . (lambda (marker)
2748 (switch-to-buffer (marker-buffer marker))
2749 (goto-char marker))))
2751 ((name . "Bad ref links")
2752 (candidates . ,bad-refs)
2753 (action . (lambda (marker)
2754 (switch-to-buffer (marker-buffer marker))
2755 (goto-char marker))))
2757 ((name . "Utilities")
2758 (candidates . (("Check buffer again" . org-ref)
2759 ("Insert citation" . helm-bibtex)
2760 ("Insert label link" . org-ref-helm-insert-label-link)
2761 ("Insert ref link" . org-ref-helm-insert-ref-link)
2762 ("List of figures" . org-ref-list-of-figures)
2763 ("List of tables" . org-ref-list-of-tables)
2764 ("Table of contents" . nil)
2766 (action . (lambda (x)
2767 (switch-to-buffer ,cb)
2770 ((name . "Export functions")
2771 (candidates . (("Extract cited entries" . org-ref-extract-bibtex-entries)
2772 ("Export to html and open" . (lambda () (org-open-file (org-html-export-to-html))))
2773 ("Export to pdf and open" . (lambda ()
2774 (org-open-file (org-latex-export-to-pdf))))
2775 ("Export to manuscript pdf and open" . ox-manuscript-export-and-build-and-open)
2776 ("Export submission manuscript pdf and open" . ox-manuscript-build-submission-manuscript-and-open)
2779 (action . (lambda (x)
2780 (switch-to-buffer ,cb)
2786 ** Finding non-ascii characters
2787 I like my bibtex files to be 100% ascii. This function finds the non-ascii characters so you can replace them.
2789 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2790 (defun org-ref-find-non-ascii-characters ()
2791 "finds non-ascii characters in the buffer. Useful for cleaning up bibtex files"
2793 (occur "[^[:ascii:]]"))
2796 ** Resort a bibtex entry
2797 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.
2799 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2800 (defun org-ref-sort-bibtex-entry ()
2801 "sort fields of entry in standard order and downcase them"
2803 (bibtex-beginning-of-entry)
2804 (let* ((master '("author" "title" "journal" "volume" "number" "pages" "year" "doi" "url"))
2805 (entry (bibtex-parse-entry))
2808 (type (cdr (assoc "=type=" entry)))
2809 (key (cdr (assoc "=key=" entry))))
2811 ;; these are the fields we want to order that are in this entry
2812 (setq entry-fields (mapcar (lambda (x) (car x)) entry))
2813 ;; we do not want to reenter these fields
2814 (setq entry-fields (remove "=key=" entry-fields))
2815 (setq entry-fields (remove "=type=" entry-fields))
2817 ;;these are the other fields in the entry
2818 (setq other-fields (remove-if-not (lambda(x) (not (member x master))) entry-fields))
2821 ;; right now we only resort articles
2822 ((string= (downcase type) "article")
2825 (concat "@article{" key ",\n"
2828 (when (member field entry-fields)
2829 (format "%s = %s," (downcase field) (cdr (assoc field entry))))) master "\n")
2832 (format "%s = %s," (downcase field) (cdr (assoc field entry)))) other-fields "\n")
2834 (bibtex-find-entry key)
2836 (bibtex-clean-entry)
2840 ** Clean a bibtex entry
2841 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.
2842 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.
2843 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2844 (defun org-ref-clean-bibtex-entry(&optional keep-key)
2845 "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"
2847 (bibtex-beginning-of-entry)
2849 ;; some entries do not have a key or comma in first line. We check and add it, if needed.
2850 (unless (string-match ",$" (thing-at-point 'line))
2854 ;; check for empty pages, and put eid or article id in its place
2855 (let ((entry (bibtex-parse-entry))
2856 (pages (bibtex-autokey-get-field "pages"))
2857 (year (bibtex-autokey-get-field "year"))
2858 (doi (bibtex-autokey-get-field "doi"))
2859 ;; The Journal of Chemical Physics uses eid
2860 (eid (bibtex-autokey-get-field "eid")))
2862 ;; replace http://dx.doi.org/ in doi. some journals put that in,
2863 ;; but we only want the doi.
2864 (when (string-match "^http://dx.doi.org/" doi)
2865 (bibtex-beginning-of-entry)
2866 (goto-char (car (cdr (bibtex-search-forward-field "doi" t))))
2868 (bibtex-make-field "doi")
2870 (insert (replace-regexp-in-string "^http://dx.doi.org/" "" doi)))
2872 ;; asap articles often set year to 0, which messes up key
2873 ;; generation. fix that.
2874 (when (string= "0" year)
2875 (bibtex-beginning-of-entry)
2876 (goto-char (car (cdr (bibtex-search-forward-field "year" t))))
2878 (bibtex-make-field "year")
2880 (insert (read-string "Enter year: ")))
2882 ;; fix pages if they are empty if there is an eid to put there.
2883 (when (string= "-" pages)
2885 (bibtex-beginning-of-entry)
2886 ;; this seems like a clunky way to set the pages field.But I
2887 ;; cannot find a better way.
2888 (goto-char (car (cdr (bibtex-search-forward-field "pages" t))))
2890 (bibtex-make-field "pages")
2894 ;; replace naked & with \&
2896 (bibtex-narrow-to-entry)
2897 (bibtex-beginning-of-entry)
2898 (message "checking &")
2899 (replace-regexp " & " " \\\\& ")
2902 ;; generate a key, and if it duplicates an existing key, edit it.
2904 (let ((key (bibtex-generate-autokey)))
2906 ;; first we delete the existing key
2907 (bibtex-beginning-of-entry)
2908 (re-search-forward bibtex-entry-maybe-empty-head)
2909 (if (match-beginning bibtex-key-in-head)
2910 (delete-region (match-beginning bibtex-key-in-head)
2911 (match-end bibtex-key-in-head)))
2912 ;; check if the key is in the buffer
2913 (when (save-excursion
2914 (bibtex-search-entry key))
2916 (bibtex-search-entry key)
2917 (bibtex-copy-entry-as-kill)
2918 (switch-to-buffer-other-window "*duplicate entry*")
2920 (setq key (bibtex-read-key "Duplicate Key found, edit: " key)))
2923 (kill-new key))) ;; save key for pasting
2925 ;; run hooks. each of these operates on the entry with no arguments.
2926 ;; this did not work like i thought, it gives a symbolp error.
2927 ;; (run-hooks org-ref-clean-bibtex-entry-hook)
2932 org-ref-clean-bibtex-entry-hook)
2934 ;; sort fields within entry
2935 (org-ref-sort-bibtex-entry)
2936 ;; check for non-ascii characters
2937 (occur "[^[:ascii:]]")
2942 : org-ref-clean-bibtex-entry
2944 ** Sort the entries in a citation link by year
2945 I prefer citations in chronological order within a grouping. These functions sort the link under the cursor by year.
2947 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2948 (defun org-ref-get-citation-year (key)
2949 "get the year of an entry with key. Returns year as a string."
2951 (let* ((results (org-ref-get-bibtex-key-and-file key))
2952 (bibfile (cdr results)))
2954 (insert-file-contents bibfile)
2955 (bibtex-search-entry key nil 0)
2956 (prog1 (reftex-get-bib-field "year" (bibtex-parse-entry t))
2959 (defun org-ref-sort-citation-link ()
2960 "replace link at point with sorted link by year"
2962 (let* ((object (org-element-context))
2963 (type (org-element-property :type object))
2964 (begin (org-element-property :begin object))
2965 (end (org-element-property :end object))
2966 (link-string (org-element-property :path object))
2968 (setq keys (org-ref-split-and-strip-string link-string))
2969 (setq years (mapcar 'org-ref-get-citation-year keys))
2970 (setq data (mapcar* (lambda (a b) `(,a . ,b)) years keys))
2971 (setq data (cl-sort data (lambda (x y) (< (string-to-int (car x)) (string-to-int (car y))))))
2972 ;; now get the keys separated by commas
2973 (setq keys (mapconcat (lambda (x) (cdr x)) data ","))
2974 ;; and replace the link with the sorted keys
2975 (cl--set-buffer-substring begin end (concat type ":" keys))))
2978 ** Sort entries in citation links with shift-arrow keys
2979 Sometimes it may be helpful to manually change the order of citations. These functions define shift-arrow functions.
2980 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2981 (defun org-ref-swap-keys (i j keys)
2982 "swap the keys in a list with index i and j"
2983 (let ((tempi (nth i keys)))
2984 (setf (nth i keys) (nth j keys))
2985 (setf (nth j keys) tempi))
2988 (defun org-ref-swap-citation-link (direction)
2989 "move citation at point in direction +1 is to the right, -1 to the left"
2991 (let* ((object (org-element-context))
2992 (type (org-element-property :type object))
2993 (begin (org-element-property :begin object))
2994 (end (org-element-property :end object))
2995 (link-string (org-element-property :path object))
2997 ;; We only want this to work on citation links
2998 (when (-contains? org-ref-cite-types type)
2999 (setq key (org-ref-get-bibtex-key-under-cursor))
3000 (setq keys (org-ref-split-and-strip-string link-string))
3001 (setq i (index key keys)) ;; defined in org-ref
3002 (if (> direction 0) ;; shift right
3003 (org-ref-swap-keys i (+ i 1) keys)
3004 (org-ref-swap-keys i (- i 1) keys))
3005 (setq keys (mapconcat 'identity keys ","))
3006 ;; and replace the link with the sorted keys
3007 (cl--set-buffer-substring begin end (concat type ":" keys " "))
3008 ;; now go forward to key so we can move with the key
3009 (re-search-forward key)
3010 (goto-char (match-beginning 0)))))
3012 ;; add hooks to make it work
3013 (add-hook 'org-shiftright-hook (lambda () (org-ref-swap-citation-link 1)))
3014 (add-hook 'org-shiftleft-hook (lambda () (org-ref-swap-citation-link -1)))
3017 ** Lightweight messages about links
3018 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.
3020 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3021 (defun org-ref-get-label-context (label)
3022 "Return a string of context around a label."
3025 (goto-char (point-min))
3026 (when (re-search-forward
3027 (format "label:%s\\b" label) nil t)
3028 (throw 'result (buffer-substring
3037 (goto-char (point-min))
3038 (when (re-search-forward
3039 (format "\\label{%s}" label) nil t)
3040 (throw 'result (buffer-substring
3049 (goto-char (point-min))
3050 (when (re-search-forward
3051 (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t)
3052 (throw 'result (buffer-substring
3061 (goto-char (point-min))
3062 (when (re-search-forward
3063 (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t)
3064 (throw 'result (buffer-substring
3073 ;; maybe we have a CUSTOM-ID
3075 (lambda () (when (string=
3077 (org-entry-get (point) "CUSTOM_ID"))
3078 (throw 'result (org-get-heading)))))
3080 (throw 'result "!!! NO CONTEXT FOUND !!!"))))
3083 (defun org-ref-link-message ()
3084 "Print a minibuffer message about the link that point is on."
3086 (when (eq major-mode 'org-mode)
3087 (let* ((object (org-element-context))
3088 (type (org-element-property :type object)))
3092 ((-contains? org-ref-cite-types type)
3093 (message (org-ref-get-citation-string-at-point)))
3095 ;; message some context about the label we are referring to
3096 ((string= type "ref")
3097 (message (org-ref-get-label-context
3098 (org-element-property :path object))))
3100 ((string= type "eqref")
3101 (message (org-ref-get-label-context
3102 (org-element-property :path object))))
3104 ;; message the count
3105 ((string= type "label")
3106 (let ((count (org-ref-count-labels
3107 (org-element-property :path object))))
3108 ;; get plurality on occurrence correct
3109 (when (> count 1) (beep))
3111 (number-to-string count)
3113 (when (or (= count 0)
3117 ;; check if the bibliography files exist.
3118 ((string= type "bibliography")
3120 ;; object is the link you clicked on
3121 (object (org-element-context))
3122 (link-string (org-element-property :path object))
3123 (link-string-beginning)
3127 (goto-char (org-element-property :begin object))
3128 (search-forward link-string nil nil 1)
3129 (setq link-string-beginning (match-beginning 0))
3130 (setq link-string-end (match-end 0)))
3132 ;; now if we have comma separated bibliographies
3133 ;; we find the one clicked on. we want to
3134 ;; search forward to next comma from point
3136 (if (search-forward "," link-string-end 1 1)
3137 (setq key-end (- (match-end 0) 1)) ; we found a match
3138 (setq key-end (point)))) ; no comma found so take the point
3139 ;; and backward to previous comma from point
3141 (if (search-backward "," link-string-beginning 1 1)
3142 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
3143 (setq key-beginning (point)))) ; no match found
3144 ;; save the key we clicked on.
3146 (org-ref-strip-string
3147 (buffer-substring key-beginning key-end)))
3148 (if (file-exists-p bibfile)
3149 (message "%s exists." bibfile)
3151 (message "!!! %s NOT FOUND !!!" bibfile))))
3156 I like convenience. Here are some aliases for faster typing.
3158 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3159 (defalias 'oro 'org-ref-open-citation-at-point)
3160 (defalias 'orc 'org-ref-citation-at-point)
3161 (defalias 'orp 'org-ref-open-pdf-at-point)
3162 (defalias 'oru 'org-ref-open-url-at-point)
3163 (defalias 'orn 'org-ref-open-notes-at-point)
3164 (defalias 'ornr 'org-ref-open-notes-from-reftex)
3166 (defalias 'orib 'org-ref-insert-bibliography-link)
3167 (defalias 'oric 'org-ref-insert-cite-link)
3168 (defalias 'orir 'org-ref-insert-ref-link)
3169 (defalias 'orsl 'org-ref-store-bibtex-entry-link)
3171 (defalias 'orcb 'org-ref-clean-bibtex-entry)
3174 [[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.
3176 1. Make the default action to insert selected keys.
3177 2. Make open entry second action
3178 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3179 (setq helm-source-bibtex
3180 '((name . "BibTeX entries")
3181 (init . helm-bibtex-init)
3182 (candidates . helm-bibtex-candidates)
3183 (filtered-candidate-transformer . helm-bibtex-candidates-formatter)
3184 (action . (("Insert citation" . helm-bibtex-insert-citation)
3185 ("Show entry" . helm-bibtex-show-entry)
3186 ("Open PDF file (if present)" . helm-bibtex-open-pdf)
3187 ("Open URL or DOI in browser" . helm-bibtex-open-url-or-doi)
3188 ("Insert reference" . helm-bibtex-insert-reference)
3189 ("Insert BibTeX key" . helm-bibtex-insert-key)
3190 ("Insert BibTeX entry" . helm-bibtex-insert-bibtex)
3191 ("Attach PDF to email" . helm-bibtex-add-PDF-attachment)
3192 ("Edit notes" . helm-bibtex-edit-notes)
3196 Now, let us define a function that inserts the cite links:
3197 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3198 (defun helm-bibtex-format-org-ref (keys)
3199 "Insert selected KEYS as cite link. Append KEYS if you are on a link.
3200 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.
3202 In the helm-bibtex buffer, C-u will give you a helm menu to select a new link type for the selected entries.
3204 C-u C-u will change the key at point to the selected keys.
3206 (let* ((object (org-element-context))
3207 (last-char (save-excursion
3208 (goto-char (org-element-property :end object))
3210 (if (looking-at " ")
3214 ;; case where we are in a link
3215 ((and (equal (org-element-type object) 'link)
3218 (org-element-property :type object)))
3220 ;; no prefix. append keys
3221 ((equal helm-current-prefix-arg nil)
3222 (goto-char (org-element-property :end object))
3223 (while (looking-back " ") (backward-char))
3224 (insert (concat "," (mapconcat 'identity keys ","))))
3225 ;; double prefix, replace key at point
3226 ((equal helm-current-prefix-arg '(16))
3227 (setf (buffer-substring
3228 (org-element-property :begin object)
3229 (org-element-property :end object))
3231 (replace-regexp-in-string
3232 (car (org-ref-get-bibtex-key-and-file)) ; key
3233 (mapconcat 'identity keys ",") ; new keys
3234 (org-element-property :raw-link object)
3236 ;; replace space at end to avoid collapsing into next word.
3239 (message "Not found"))))
3241 ;; We are next to a link, and we want to append
3242 ;; next to a link means one character back is on a link.
3245 (and (equal (org-element-type (org-element-context)) 'link)
3248 (org-element-property :type (org-element-context)))))
3249 (while (looking-back " ") (backward-char))
3250 (insert (concat "," (mapconcat 'identity keys ","))))
3252 ;; insert fresh link
3254 ;;(message-box "fresh link")
3256 (concat (if (equal helm-current-prefix-arg '(4))
3257 (helm :sources `((name . "link types")
3258 (candidates . ,org-ref-cite-types)
3259 (action . (lambda (x) x))))
3260 org-ref-default-citation-link)
3262 (s-join "," keys))))))
3263 ;; return empty string for helm
3266 (setq helm-bibtex-format-citation-functions
3267 '((org-mode . helm-bibtex-format-org-ref)))
3269 (defun org-ref-helm-insert-cite-link (arg)
3270 "org-ref function to use helm-bibtex to insert a citation link.
3271 With one prefix arg, insert a ref link.
3272 With two prefix args, insert a label link."
3276 (let ((helm-bibtex-bibliography (org-ref-find-bibliography)))
3279 (org-ref-helm-insert-ref-link))
3281 (org-ref-helm-insert-label-link))))
3283 (require 'helm-bibtex)
3285 ;; add our own fallback entries where we want them. These appear in reverse order of adding in the menu
3286 (setq helm-bibtex-fallback-options
3287 (-insert-at 1 '("Crossref" . "http://search.crossref.org/?q=%s") helm-bibtex-fallback-options))
3289 (setq helm-bibtex-fallback-options
3292 '("Scopus" . "http://www.scopus.com/scopus/search/submit/xadvanced.url?searchfield=TITLE-ABS-KEY(%s)")
3293 helm-bibtex-fallback-options))
3295 (setq helm-bibtex-fallback-options
3296 (-insert-at 1 '("Open Web of Science" . (lambda () (browse-url "http://apps.webofknowledge.com")))
3297 helm-bibtex-fallback-options))
3300 ** A helm click menu
3301 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.
3302 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3303 (defun org-ref-get-citation-string-at-point ()
3304 "Get a string of a formatted citation"
3306 (let* ((results (org-ref-get-bibtex-key-and-file))
3308 (bibfile (cdr results)))
3312 (insert-file-contents bibfile)
3313 (bibtex-search-entry key)
3314 (org-ref-bib-citation)))
3316 "!!! No entry found !!!" )))
3318 (defun org-ref-cite-candidates ()
3319 "Generate the list of possible candidates for click actions on a cite link.
3320 Checks for pdf and doi, and add appropriate functions."
3322 (let* ((results (org-ref-get-bibtex-key-and-file))
3324 (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key))
3325 (bibfile (cdr results))
3326 (url (save-excursion
3328 (insert-file-contents bibfile)
3329 (bibtex-search-entry key)
3330 (bibtex-autokey-get-field "url"))))
3331 (doi (save-excursion
3333 (insert-file-contents bibfile)
3334 (bibtex-search-entry key)
3335 ;; I like this better than bibtex-url which does not always find
3337 (bibtex-autokey-get-field "doi"))))
3338 (candidates `(("Quit" . org-ref-citation-at-point)
3339 ("Open bibtex entry" . org-ref-open-citation-at-point))))
3340 ;; for some reason, when there is no doi or url, they are returned as "". I
3341 ;; prefer nil so we correct this here.
3342 (when (string= doi "") (setq doi nil))
3343 (when (string= url "") (setq url nil))
3345 ;; Conditional pdf functions
3346 (if (file-exists-p pdf-file)
3349 '("Open pdf" . org-ref-open-pdf-at-point)
3353 '("Try to get pdf" . (lambda ()
3354 (save-window-excursion
3355 (org-ref-open-citation-at-point)
3356 (bibtex-beginning-of-entry)
3357 (doi-utils-get-bibtex-entry-pdf))))
3363 '("Open notes" . org-ref-open-notes-at-point)
3366 ;; conditional url and doi functions
3370 '("Open in browser" . org-ref-open-url-at-point)
3375 (add-to-list 'candidates x t))
3376 `(("WOS" . org-ref-wos-at-point)
3377 ("Related articles in WOS" . org-ref-wos-related-at-point)
3378 ("Citing articles in WOS" . org-ref-wos-citing-at-point)
3379 ("Google Scholar" . org-ref-google-scholar-at-point)
3380 ("Pubmed" . org-ref-pubmed-at-point)
3381 ("Crossref" . org-ref-crossref-at-point)
3386 '("Copy formatted citation to clipboard" . org-ref-copy-entry-as-summary)
3391 '("Copy key to clipboard" . (lambda ()
3393 (car (org-ref-get-bibtex-key-and-file)))))
3398 '("Copy bibtex entry to file" . org-ref-copy-entry-at-point-to-file)
3403 '("Email bibtex entry and pdf" . (lambda ()
3405 (org-ref-open-citation-at-point)
3406 (email-bibtex-entry))))
3408 ;; finally return a numbered list of the candidates
3410 for cell in candidates
3411 collect (cons (format "%2s. %s" i (car cell))
3415 (defvar org-ref-helm-user-candidates '()
3416 "List of user-defined candidates to act when clicking on a cite link.
3417 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.
3420 ;; example of adding your own function
3422 'org-ref-helm-user-candidates
3423 '("Example" . (lambda () (message-box "You did it!")))
3426 (defun org-ref-cite-click-helm (key)
3428 1. get name and candidates before entering helm because we need the org-buffer.
3429 2. switch back to the org buffer before evaluating the action. most of them need the point and buffer."
3431 (let ((name (org-ref-get-citation-string-at-point))
3432 (candidates (org-ref-cite-candidates))
3433 (cb (current-buffer)))
3435 (helm :sources `(((name . ,name)
3436 (candidates . ,candidates)
3437 (action . (lambda (f)
3438 (switch-to-buffer cb)
3440 ((name . "User functions")
3441 (candidates . ,org-ref-helm-user-candidates)
3442 (action . (lambda (f)
3443 (switch-to-buffer cb)
3449 : org-ref-cite-click-helm
3452 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
3457 This code will tangle the elisp code out to org-ref.el and load it.
3459 [[elisp:(progn (org-babel-tangle) (load-file "org-ref.el"))]]
3461 Alternatively you may use:
3463 [[elisp:(org-babel-load-file "org-ref.org")]]